Human immunodeficiency virus type 1 LTR TATA and TAR region sequences required for transcriptional regulation.

PubMed Central

Garcia, J A; Harrich, D; Soultanakis, E; Wu, F; Mitsuyasu, R; Gaynor, R B

1989-01-01

The human immunodeficiency virus (HIV) type 1 LTR is regulated at the transcriptional level by both cellular and viral proteins. Using HeLa cell extracts, multiple regions of the HIV LTR were found to serve as binding sites for cellular proteins. An untranslated region binding protein UBP-1 has been purified and fractions containing this protein bind to both the TAR and TATA regions. To investigate the role of cellular proteins binding to both the TATA and TAR regions and their potential interaction with other HIV DNA binding proteins, oligonucleotide-directed mutagenesis of both these regions was performed followed by DNase I footprinting and transient expression assays. In the TATA region, two direct repeats TC/AAGC/AT/AGCTGC surround the TATA sequence. Mutagenesis of both of these direct repeats or of the TATA sequence interrupted binding over the TATA region on the coding strand, but only a mutation of the TATA sequence affected in vivo assays for tat-activation. In addition to TAR serving as the site of binding of cellular proteins, RNA transcribed from TAR is capable of forming a stable stem-loop structure. To determine the relative importance of DNA binding proteins as compared to secondary structure, oligonucleotide-directed mutations in the TAR region were studied. Local mutations that disrupted either the stem or loop structure were defective in gene expression. However, compensatory mutations which restored base pairing in the stem resulted in complete tat-activation. This indicated a significant role for the stem-loop structure in HIV gene expression. To determine the role of TAR binding proteins, mutations were constructed which extensively changed the primary structure of the TAR region, yet left stem base pairing, stem energy and the loop sequence intact. These mutations resulted in decreased protein binding to TAR DNA and defects in tat-activation, and revealed factor binding specifically to the loop DNA sequence. Further mutagenesis which inverted this stem and loop mutation relative to the HIV LTR mRNA start site resulted in even larger decreases in tat-activation. This suggests that multiple determinants, including protein binding, the loop sequence, and RNA or DNA secondary structure, are important in tat-activation and suggests that tat may interact with cellular proteins binding to DNA to increase HIV gene expression. Images PMID:2721501

Relating Alfvén Wave Heating Model to Observations of a Solar Active Region

NASA Astrophysics Data System (ADS)

Yoritomo, J. Y.; Van Ballegooijen, A. A.

2012-12-01

We compared images from the Solar Dynamics Observatory's (SDO) Atmospheric Imaging Assembly (AIA) with simulations of propagating and dissipating Alfvén waves from a three-dimensional magnetohydrodynamic (MHD) model (van Ballegooijen et. al 2011; Asgari-Targhi & van Ballegooijen 2012). The goal was to search for observational evidence of Alfvén waves in the solar corona and understand their role in coronal heating. We looked at one particular active region on the 5th of May 2012. Certain distinct loops in the SDO/AIA observations were selected and expanded. Movies were created from these selections in an attempt to discover transverse motions that may be Alfvén waves. Using a magnetogram of that day and the corresponding synoptic map, a potential field model was created for the active region. Three-dimensional MHD models for several loops in different locations in the active region were created. Each model specifies the temperature, pressure, magnetic field strength, average heating rate, and other parameters along the loop. We find that the heating is intermittent in the loops and reflection occurs at the transition region. For loops at larger and larger height, a point is reached where thermal non-equilibrium occurs. In the center this critical height is much higher than in the periphery of the active region. Lastly, we find that the average heating rate and coronal pressure decrease with increasing height in the corona. This research was supported by an NSF grant for the Smithsonian Astrophysical Observatory (SAO) Solar REU program and a SDO/AIA grant for the Smithsonian Astrophysical Observatory.

Feel the Burn, Part II: Quantifying and mapping spectral, spatial, and temporal structures of the transition region under hot and cold coronal regions

NASA Astrophysics Data System (ADS)

Atwood, Shane; Kankelborg, Charles C.

2017-08-01

The coronal volume is filled with magnetic field, yet only part of that volume has sufficient volume to exhibit hot X-ray loops. Using XRT and AIA images, we identify footpoints of hot coronal loops. We then use IRIS rasters to compare the spatial, temporal, and spectral structure of these relatively "heated" and "unheated" regions. We seek a signature of upward-propagating energy that could be associated with hot active region loops.

Computer Generated Snapshot of Our Sun's Magnetic Field

NASA Technical Reports Server (NTRS)

2003-01-01

These banana-shaped loops are part of a computer-generated snapshot of our sun's magnetic field. The solar magnetic-field lines loop through the sun's corona, break through the sun's surface, and cornect regions of magnetic activity, such as sunspots. This image --part of a magnetic-field study of the sun by NASA's Allen Gary -- shows the outer portion (skins) of interconnecting systems of hot (2 million degrees Kelvin) coronal loops within and between two active magnetic regions on opposite sides of the sun's equator. The diameter of these coronal loops at their foot points is approximately the same size as the Earth's radius (about 6,000 kilometers).

Xrt And Shinx Joint Flare Study: Ar 11024

NASA Astrophysics Data System (ADS)

Engell, Alexander; Sylwester, J.; Siarkowski, M.

2010-05-01

From 12:00 UT on July 3 through July 7, 2009 SphinX (Solar Photometer IN X-rays) observes 130 flares with active region (AR) 11024 being the only AR on disk. XRT (X-Ray Telescope) is able to observe 64 of these flare events. The combination of both instruments results in a flare study revealing (1) a relationship between flux emergence and flare rate, (2) that the presence of active region loops typically results in different flare morphologies (single and multiple loop flares) then when there is a lack of an active region loop environment where more cusp and point-like flares are observed, (3) cusp and point-like flares often originate from the same location, and (4) a distribution of flare temperatures corresponding to the different flare morphologies. The differences between the observed flare morphologies may occur as the result of the heated plasma through the flaring process being confined by the proximity of loop structures as for the single and multiple loop flares, while for cusp and point-like flares they occur in an early-phase environment that lack loop presence. The continuing flux emergence of AR 11024 likely provides different magnetic interactions and may be the source responsible for all of the flares.

Patterns of Activity in A Global Model of A Solar Active Region

NASA Technical Reports Server (NTRS)

Bradshaw, S. J.; Viall, N. M.

2016-01-01

In this work we investigate the global activity patterns predicted from a model active region heated by distributions of nanoflares that have a range of frequencies. What differs is the average frequency of the distributions. The activity patterns are manifested in time lag maps of narrow-band instrument channel pairs. We combine hydrodynamic and forward modeling codes with a magnetic field extrapolation to create a model active region and apply the time lag method to synthetic observations. Our aim is not to reproduce a particular set of observations in detail, but to recover some typical properties and patterns observed in active regions. Our key findings are the following. (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 footpoints. (4) There is strong evidence that plasma must be re-energized on a timescale comparable to the cooling timescale to reproduce the observed coronal activity, but it is likely that a relatively broad spectrum of heating frequencies are operating 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.

Imagery and spectroscopy of supernova remnants and H-2 regions

NASA Technical Reports Server (NTRS)

Dufour, R. J.

1984-01-01

Research activities relating to supernova remnants were summarized. The topics reviewed include: progenitor stars of supernova remnants, UV/optical/radio/X-ray imagery of selected regions in the Cygnus Loop, UV/optical spectroscopy of the Cygnus Loop spur, and extragalactic supernova remnant spectra.

Magnetic Field Configuration of Active Region NOAA 6555 at the Time of a Long Duration Flare on 23 March 1991: An Exception to Standard Flare Reconnection Model

NASA Technical Reports Server (NTRS)

Choudhary, Debi Prasad; Gary, Allen G.

1998-01-01

The high-resolution H(sub alpha) images observed during the decay phase of a long duration flare on 23 March 1991 are used to study the three-dimensional magnetic field configuration of the active region NOAA 6555. Whereas, all the large flares in NOAA 6555 occurred at the location of high magnetic shear and flux emergence, this long duration flare was observed in the region of low magnetic shear at the photosphere. The H(sub alpha) loop activity started soon after the maximum phase of the flare. There were few long loop at the initial phase of the activity. Some of these were sheared in the chromosphere at an angle of about 45 deg with the east-west axis. Gradually, increasing number of shorter loops, oriented along the east-west axis, started appearing. The chromospheric Dopplergrams show blue-shifts at the end points of the loops. By using different magnetic field models, we have extrapolated the photospheric magnetograms to the chromospheric heights. The magnetic field lines computed by using the potential field model correspond to most of the observed H(sub alpha) loops. The height of the H(sub alpha) loops were derived by comparing them with the computed field lines. From the temporal evolution of the H(sub alpha) loop activity, we derive the negative rate of appearance of H(sub alpha) features as a function of height. It is found that the field lines oriented along one of the neutral lines was sheared and low lying. The higher field lines were mostly potential. The paper also outlines a possible scenario for describing the post-flare stage of the observed long duration flare.

The Strength of an Ig Switch Region is Determined by its Ability to Drive R-loop Formation and its Number of WGCW Sites

PubMed Central

Zhang, Zheng Z.; Pannunzio, Nicholas R.; Han, Li; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R.

2014-01-01

SUMMARY R-loops exist at the murine IgH switch regions and possibly other locations, but their functional importance is unclear. In biochemical systems, R-loop initiation requires DNA sequence regions containing clusters of G nucleotides, but cellular studies have not been done. Here, we vary the G-clustering, total switch region length, and the number of target sites (WGCW sites for the activation-induced deaminase) at synthetic switch regions in a murine B cell line to determine the effect on class switch recombination (CSR). G-clusters increase CSR, regardless of their immediate proximity to the WGCW sites. This increase is accompanied by an increase in R-loop formation. CSR efficiency correlates better with the absolute number of WGCW sites in the switch region rather than the total switch region length or density of WGCW sites. Thus, the overall strength of the switch region depends on G-clusters, which initiate R-loop formation, and on the number of WGCW sites. PMID:25017067

Cool Transition Region Loops Observed by the Interface Region Imaging Spectrograph

NASA Astrophysics Data System (ADS)

Huang, Zhenghua; Xia, Lidong; Li, Bo; Madjarska, Maria S.

2015-09-01

We report on the first Interface Region Imaging Spectrograph (IRIS) study of cool transition region loops, a class of loops that has received little attention in the literature. A cluster of such loops was observed on the solar disk in active region NOAA11934, in the Si iv 1402.8 Å spectral raster and 1400 Å slit-jaw images. We divide the loops into three groups and study their dynamics. The first group comprises relatively stable loops, with 382-626 km cross-sections. Observed Doppler velocities are suggestive of siphon flows, gradually changing from -10 km s-1 at one end to 20 km s-1 at the other end of the loops. Nonthermal velocities of 15 ˜ 25 km s-1 were determined. Magnetic cancellation with a rate of 1015 Mx s-1 is found at the blueshifted footpoints. These physical properties suggest that these loops are impulsively heated by magnetic reconnection, and the siphon flows play an important role in the energy redistribution. The second group corresponds to two footpoints rooted in mixed-magnetic-polarity regions, where magnetic cancellation with a rate of 1015 Mx s-1 and explosive-event line profiles with enhanced wings of up to 200 km s-1 were observed. In the third group, interaction between two cool loop systems is observed. Evidence for magnetic reconnection between the two loop systems is reflected in the explosive-event line profiles and magnetic cancellation with a rate of 3× {10}15 Mx s-1 observed in the corresponding area. The IRIS has provided opportunity for in-depth investigations of cool transition region loops. Further numerical experiments are crucial for understanding their physics and their roles in the coronal heating processes.

Interactive flare sites within an active region complex

NASA Technical Reports Server (NTRS)

Poletto, G.; Gary, G. A.; Machado, M. E.

1993-01-01

We examine here a set of images of an active region complex, acquired on June 24-25, 1980, by the Hard X-ray Imaging Spectrometer on SMM, with the purpose of establishing whether there was any interplay between the frequent activity observed at different sites in the activity center and, in such a case, how the interaction was established. By analyzing both quiet and active orbits we show that, as a rule, activity originating in one region triggers the other region's activity. However, we find little unambiguous evidence for the presence of large-scale interconnecting loops. A comparison of X-ray images with magnetic field observations suggested that we interpret the active region behavior in terms of the interaction between different loop systems, in a scenario quite analogous to the interacting bipole representation of individual flares. We conclude that active region interplay provides an easily observable case to study the time-dependent topology and the mechanisms for the spreading of activity in transient events over all energy scales.

Modification of "Pressed" Atmospheres in Active Regions of Ultracool Stars

NASA Astrophysics Data System (ADS)

Zaitsev, V. V.; Kronshtadtov, P. V.; Stepanov, A. V.

2017-12-01

Ultracool stars usually have active regions, which is confirmed by their high-power radiofrequency emission modulated by the star axial rotation. The interpretation of this emission is commonly based on the electron cyclotron maser mechanism realized in the active regions. A plasma mechanism of radiofrequency emission is not considered, because ultracool star atmospheres are tightly "pressed" against the star surface, and the plasma frequency is much lower than the electron gyrofrequency ( f L ≪ f B) at the coronal levels. This paper explores active regions of ultracool stars for the possible existence of a system of coronal magnetic loops carrying electric current generated by photospheric convection. It is shown that current dissipation induces a temperature increase inside the loops to about 107 K, which causes an increase in the scale of height of the inhomogeneous atmosphere and, at the coronal levels, effectuates condition f L ≫ f B, at which the plasma mechanism of radiofrequency emission prevails over the electron cyclotron maser mechanism. The magnetic loop parameters, intensity of electric currents generated by the photospheric convection, and efficiency of plasma heating inside the magnetic loops are evaluated on the example of the brown dwarf TVLM513-46546. The scale of the height of the modified atmosphere, which appears to be comparable to the star radius, is calculated; it is shown that the soft X-ray flow created by the hot modified atmosphere inside a coronal magnetic loop is about equal to that observed for brown dwarf TVLM513-46546.

The Heating of Solar Coronal Loops by Alfvén Wave Turbulence

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

Van Ballegooijen, A. A.; Asgari-Targhi, M.; Voss, A.

2017-11-01

In this paper we further develop a model for the heating of coronal loops by Alfvén wave turbulence (AWT). The Alfvén waves are assumed to be launched from a collection of kilogauss flux tubes in the photosphere at the two ends of the loop. Using a three-dimensional magnetohydrodynamic model for an active-region loop, we investigate how the waves from neighboring flux tubes interact in the chromosphere and corona. For a particular combination of model parameters we find that AWT can produce enough heat to maintain a peak temperature of about 2.5 MK, somewhat lower than the temperatures of 3–4 MKmore » observed in the cores of active regions. The heating rates vary strongly in space and time, but the simulated heating events have durations less than 1 minute and are unlikely to reproduce the observed broad differential emission measure distributions of active regions. The simulated spectral line nonthermal widths are predicted to be about 27 km s{sup −1}, which is high compared to the observed values. Therefore, the present AWT model does not satisfy the observational constraints. An alternative “magnetic braiding” model is considered in which the coronal field lines are subject to slow random footpoint motions, but we find that such long-period motions produce much less heating than the shorter-period waves launched within the flux tubes. We discuss several possibilities for resolving the problem of producing sufficiently hot loops in active regions.« less

Combined deficiency of MSH2 and Sμ region abolishes class switch recombination.

PubMed

Leduc, Claire; Haddad, Dania; Laviolette-Malirat, Nathalie; Nguyen Huu, Ngoc-Sa; Khamlichi, Ahmed Amine

2010-10-01

Class switch recombination (CSR) is mediated by G-rich tandem repeated sequences termed switch regions. Transcription of switch regions generates single-stranded R loops that provide substrates for activation-induced cytidine deaminase. Mice deficient in MSH2 have a mild defect in CSR and analysis of their switch junctions has led to a model in which MSH2 is more critical for switch recombination events outside than within the tandem repeats. It is also known that deletion of the whole Sμ region severely impairs but does not abrogate CSR despite the lack of detectable R loops. Here, we demonstrate that deficiency of both MSH2 and the Sμ region completely abolishes CSR and that the abrogation occurs at the genomic level. This finding further supports the crucial role of MSH2 outside the tandem repeats. It also indicates that during CSR, MSH2 has access to activation-induced cytidine deaminase targets in R-loop-deficient Iμ-Cμ sequences rarely used in CSR, suggesting an MSH2-dependent DNA processing activity at the Iμ exon that may decrease with transcription elongation across the Sμ region.

Static and Impulsive Models of Solar Active Regions

NASA Technical Reports Server (NTRS)

Patsourakos, S.; Klimchuk, James A.

2008-01-01

The physical modeling of active regions (ARs) and of the global coronal is receiving increasing interest lately. Recent attempts to model ARs using static equilibrium models were quite successful in reproducing AR images of hot soft X-ray (SXR) loops. They however failed to predict the bright EUV warm loops permeating ARs: the synthetic images were dominated by intense footpoint emission. We demonstrate that this failure is due to the very weak dependence of loop temperature on loop length which cannot simultaneously account for both hot and warm loops in the same AR. We then consider time-dependent AR models based on nanoflare heating. We demonstrate that such models can simultaneously reproduce EUV and SXR loops in ARs. Moreover, they predict radial intensity variations consistent with the localized core and extended emissions in SXR and EUV AR observations respectively. We finally show how the AR morphology can be used as a gauge of the properties (duration, energy, spatial dependence, repetition time) of the impulsive heating.

On the Occurrence of Thermal Nonequilibrium in Coronal Loops

NASA Astrophysics Data System (ADS)

Froment, C.; Auchère, F.; Mikić, Z.; Aulanier, G.; Bocchialini, K.; Buchlin, E.; Solomon, J.; Soubrié, E.

2018-03-01

Long-period EUV pulsations, recently discovered to be common in active regions, are understood to be the coronal manifestation of thermal nonequilibrium (TNE). The active regions previously studied with EIT/Solar and Heliospheric Observatory and AIA/SDO indicated that long-period intensity pulsations are localized in only one or two loop bundles. The basic idea of this study is to understand why. For this purpose, we tested the response of different loop systems, using different magnetic configurations, to different stratifications and strengths of the heating. We present an extensive parameter-space study using 1D hydrodynamic simulations (1020 in total) and conclude that the occurrence of TNE requires specific combinations of parameters. Our study shows that the TNE cycles are confined to specific ranges in parameter space. This naturally explains why only some loops undergo constant periodic pulsations over several days: since the loop geometry and the heating properties generally vary from one loop to another in an active region, only the ones in which these parameters are compatible exhibit TNE cycles. Furthermore, these parameters (heating and geometry) are likely to vary significantly over the duration of a cycle, which potentially limits the possibilities of periodic behavior. This study also confirms that long-period intensity pulsations and coronal rain are two aspects of the same phenomenon: both phenomena can occur for similar heating conditions and can appear simultaneously in the simulations.

Comparison of Two Coronal Magnetic Field Models to Reconstruct a Sigmoidal Solar Active Region with Coronal Loops

NASA Astrophysics Data System (ADS)

Duan, Aiying; Jiang, Chaowei; Hu, Qiang; Zhang, Huai; Gary, G. Allen; Wu, S. T.; Cao, Jinbin

2017-06-01

Magnetic field extrapolation is an important tool to study the three-dimensional (3D) solar coronal magnetic field, which is difficult to directly measure. Various analytic models and numerical codes exist, but their results often drastically differ. Thus, a critical comparison of the modeled magnetic field lines with the observed coronal loops is strongly required to establish the credibility of the model. Here we compare two different non-potential extrapolation codes, a nonlinear force-free field code (CESE-MHD-NLFFF) and a non-force-free field (NFFF) code, in modeling a solar active region (AR) that has a sigmoidal configuration just before a major flare erupted from the region. A 2D coronal-loop tracing and fitting method is employed to study the 3D misalignment angles between the extrapolated magnetic field lines and the EUV loops as imaged by SDO/AIA. It is found that the CESE-MHD-NLFFF code with preprocessed magnetogram performs the best, outputting a field that matches the coronal loops in the AR core imaged in AIA 94 Å with a misalignment angle of ˜10°. This suggests that the CESE-MHD-NLFFF code, even without using the information of the coronal loops in constraining the magnetic field, performs as good as some coronal-loop forward-fitting models. For the loops as imaged by AIA 171 Å in the outskirts of the AR, all the codes including the potential field give comparable results of the mean misalignment angle (˜30°). Thus, further improvement of the codes is needed for a better reconstruction of the long loops enveloping the core region.

Comparison of Two Coronal Magnetic Field Models to Reconstruct a Sigmoidal Solar Active Region with Coronal Loops

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

Duan, Aiying; Zhang, Huai; Jiang, Chaowei

Magnetic field extrapolation is an important tool to study the three-dimensional (3D) solar coronal magnetic field, which is difficult to directly measure. Various analytic models and numerical codes exist, but their results often drastically differ. Thus, a critical comparison of the modeled magnetic field lines with the observed coronal loops is strongly required to establish the credibility of the model. Here we compare two different non-potential extrapolation codes, a nonlinear force-free field code (CESE–MHD–NLFFF) and a non-force-free field (NFFF) code, in modeling a solar active region (AR) that has a sigmoidal configuration just before a major flare erupted from themore » region. A 2D coronal-loop tracing and fitting method is employed to study the 3D misalignment angles between the extrapolated magnetic field lines and the EUV loops as imaged by SDO /AIA. It is found that the CESE–MHD–NLFFF code with preprocessed magnetogram performs the best, outputting a field that matches the coronal loops in the AR core imaged in AIA 94 Å with a misalignment angle of ∼10°. This suggests that the CESE–MHD–NLFFF code, even without using the information of the coronal loops in constraining the magnetic field, performs as good as some coronal-loop forward-fitting models. For the loops as imaged by AIA 171 Å in the outskirts of the AR, all the codes including the potential field give comparable results of the mean misalignment angle (∼30°). Thus, further improvement of the codes is needed for a better reconstruction of the long loops enveloping the core region.« less

Decay-less kink oscillations in coronal loops

NASA Astrophysics Data System (ADS)

Anfinogentov, S.; Nisticò, G.; Nakariakov, V. M.

2013-12-01

Context. Kink oscillations of coronal loops in an off-limb active region are detected with the Imaging Assembly Array (AIA) instruments of the Solar Dynamics Observatory (SDO) at 171 Å. Aims: We aim to measure periods and amplitudes of kink oscillations of different loops and to determinate the evolution of the oscillation phase along the oscillating loop. Methods: Oscillating coronal loops were visually identified in the field of view of SDO/AIA and STEREO/EUVI-A: the loop length was derived by three-dimensional analysis. Several slits were taken along the loops to assemble time-distance maps. We identified oscillatory patterns and retrieved periods and amplitudes of the oscillations. We applied the cross-correlation technique to estimate the phase shift between oscillations at different segments of oscillating loops. Results: We found that all analysed loops show low-amplitude undamped transverse oscillations. Oscillation periods of loops in the same active region range from 2.5 to 11 min, and are different for different loops. The displacement amplitude is lower than 1 Mm. The oscillation phase is constant along each analysed loop. The spatial structure of the phase of the oscillations corresponds to the fundamental standing kink mode. We conclude that the observed behaviour is consistent with the empirical model in terms of a damped harmonic resonator affected by a non-resonant continuously operating external force. A movie is available in electronic form at http://www.aanda.org

Identification of Human Papillomavirus Type 16 L1 Surface Loops Required for Neutralization by Human Sera†

PubMed Central

Carter, Joseph J.; Wipf, Greg C.; Madeleine, Margaret M.; Schwartz, Stephen M.; Koutsky, Laura A.; Galloway, Denise A.

2006-01-01

The variable surface loops on human papillomavirus (HPV) virions required for type-specific neutralization by human sera remain poorly defined. To determine which loops are required for neutralization, a series of hybrid virus-like particles (VLPs) were used to adsorb neutralizing activity from HPV type 16 (HPV16)-reactive human sera before being tested in an HPV16 pseudovirion neutralization assay. The hybrid VLPs used were composed of L1 sequences of either HPV16 or HPV31, on which one or two regions were replaced with homologous sequences from the other type. The regions chosen for substitution were the five known loops that form surface epitopes recognized by monoclonal antibodies and two additional variable regions between residues 400 and 450. Pretreatment of human sera, previously found to react to HPV16 VLPs in enzyme-linked immunosorbent assays, with wild-type HPV16 VLPs and hybrid VLPs that retained the neutralizing epitopes reduced or eliminated the ability of sera to inhibit pseudovirus infection in vitro. Surprisingly, substitution of a single loop often ablated the ability of VLPs to adsorb neutralizing antibodies from human sera. However, for all sera tested, multiple surface loops were found to be important for neutralizing activity. Three regions, defined by loops DE, FG, and HI, were most frequently identified as being essential for binding by neutralizing antibodies. These observations are consistent with the existence of multiple neutralizing epitopes on the HPV virion surface. PMID:16641259

Identification of human papillomavirus type 16 L1 surface loops required for neutralization by human sera.

PubMed

Carter, Joseph J; Wipf, Greg C; Madeleine, Margaret M; Schwartz, Stephen M; Koutsky, Laura A; Galloway, Denise A

2006-05-01

The variable surface loops on human papillomavirus (HPV) virions required for type-specific neutralization by human sera remain poorly defined. To determine which loops are required for neutralization, a series of hybrid virus-like particles (VLPs) were used to adsorb neutralizing activity from HPV type 16 (HPV16)-reactive human sera before being tested in an HPV16 pseudovirion neutralization assay. The hybrid VLPs used were composed of L1 sequences of either HPV16 or HPV31, on which one or two regions were replaced with homologous sequences from the other type. The regions chosen for substitution were the five known loops that form surface epitopes recognized by monoclonal antibodies and two additional variable regions between residues 400 and 450. Pretreatment of human sera, previously found to react to HPV16 VLPs in enzyme-linked immunosorbent assays, with wild-type HPV16 VLPs and hybrid VLPs that retained the neutralizing epitopes reduced or eliminated the ability of sera to inhibit pseudovirus infection in vitro. Surprisingly, substitution of a single loop often ablated the ability of VLPs to adsorb neutralizing antibodies from human sera. However, for all sera tested, multiple surface loops were found to be important for neutralizing activity. Three regions, defined by loops DE, FG, and HI, were most frequently identified as being essential for binding by neutralizing antibodies. These observations are consistent with the existence of multiple neutralizing epitopes on the HPV virion surface.

First cytoplasmic loop of glucagon-like peptide-1 receptor can function at the third cytoplasmic loop position of rhodopsin.

PubMed

Yamashita, Takahiro; Tose, Koji; Shichida, Yoshinori

2008-01-01

G protein-coupled receptors (GPCRs) are classified into several families based on their amino acid sequences. In family 1, GPCRs such as rhodopsin and adrenergic receptor, the structure-function relationship has been extensively investigated to demonstrate that exposure of the third cytoplasmic loop is essential for selective G protein activation. In contrast, much less is known about other families. Here we prepared chimeric mutants between Gt-coupled rhodopsin and Gi/Go- and Gs-coupled glucagon-like peptide-1 (GLP-1) receptor of family 2 and tried to identify the loop region that functions at the third cytoplasmic loop position of rhodopsin. We succeeded in expressing a mutant having the first cytoplasmic loop of GLP-1 receptor and found that this mutant activated Gi and Go efficiently but did not activate Gt. Moreover, the rhodopsin mutant having the first loop of Gs-coupled secretin receptor of family 2 decreased the Gi and Go activation efficiencies. Therefore, the first loop of GLP-1 receptor would share a similar role to the third loop of rhodopsin in G protein activation. This result strongly suggested that different families of GPCRs have maintained molecular architectures of their ancestral types to generate a common mechanism, namely exposure of the cytoplasmic loop, to activate peripheral G protein.

Feel the Burn: What accounts for spatial variations in coronal heating?

NASA Astrophysics Data System (ADS)

Atwood, Shane; Kankelborg, Charles C.

2016-05-01

The coronal volume is filled with magnetic field, yet only part of that volume has sufficient heating to exhibit hot x-ray loops. How does the Sun decide where the heat goes? Using XRT and AIA images and HMI magnetograms, we identify footpoints of hot coronal loops, and magnetically similar regions underlying relatively unheated corona. We then use IRIS rasters and sit-and-stare observations to compare the spatial, temporal, and spectral structure of these relatively ``heated’’ and ``unheated’’ regions. We seek a signature of upward propagating energy that could be associated with hot active region loops.

Bright Loops at 171

NASA Technical Reports Server (NTRS)

2007-01-01

STEREO was able to capture bright loops in exquisite detail as they were arcing above an active region (May 26, 2007) over an 18 hour period. What we are actually seeing are charged particles spinning along magnetic field lines that extend above the Sun's surface. Active regions are areas of intense magnetic activity and often the source of solar storms. In fact, the clip ends with a flourish in which a small coronal mass ejection (CME) blows out into space. This is from the STEREO Ahead spacecraft at the 171 Angstroms wavelength in extreme ultraviolet light.

Simultaneous Solar Maximum Mission (SMM) and Very Large Array (VLA) observations of solar active regions

NASA Technical Reports Server (NTRS)

Willson, Robert F.

1991-01-01

Very Large Array observations at 20 cm wavelength can detect the hot coronal plasma previously observed at soft x ray wavelengths. Thermal cyclotron line emission was detected at the apex of coronal loops where the magnetic field strength is relatively constant. Detailed comparison of simultaneous Solar Maximum Mission (SMM) Satellite and VLA data indicate that physical parameters such as electron temperature, electron density, and magnetic field strength can be obtained, but that some coronal loops remain invisible in either spectral domain. The unprecedent spatial resolution of the VLA at 20 cm wavelength showed that the precursor, impulsive, and post-flare components of solar bursts originate in nearby, but separate loops or systems of loops.. In some cases preburst heating and magnetic changes are observed from loops tens of minutes prior to the impulsive phase. Comparisons with soft x ray images and spectra and with hard x ray data specify the magnetic field strength and emission mechanism of flaring coronal loops. At the longer 91 cm wavelength, the VLA detected extensive emission interpreted as a hot 10(exp 5) K interface between cool, dense H alpha filaments and the surrounding hotter, rarefield corona. Observations at 91 cm also provide evidence for time-correlated bursts in active regions on opposite sides of the solar equator; they are attributed to flare triggering by relativistic particles that move along large-scale, otherwise-invisible, magnetic conduits that link active regions in opposite hemispheres of the Sun.

The fusion loops and membrane proximal region of Epstein-Barr virus glycoprotein B (gB) can function in the context of herpes simplex virus 1 gB when substituted individually but not in combination.

PubMed

Zago, Anna; Connolly, Sarah A; Spear, Patricia G; Longnecker, Richard

2013-01-01

Among the herpesvirus glycoprotein B (gB) fusion proteins, the hydrophobic content of fusion loops and membrane proximal regions (MPRs) are inversely correlated with each other. We examined the functional importance of the hydrophobicity of these regions by replacing them in herpes simplex virus type 1 gB with corresponding regions from Epstein-Barr virus gB. We show that fusion activity is dependent on the structural context in which the specific loops and MPR sequences exist, rather than a simple hydrophobic relationship. Copyright © 2012 Elsevier B.V. All rights reserved.

The Myosin IXb Motor Activity Targets the Myosin IXb RhoGAP Domain as Cargo to Sites of Actin Polymerization

PubMed Central

van den Boom, Frank; Düssmann, Heiko; Uhlenbrock, Katharina; Abouhamed, Marouan

2007-01-01

Myosin IXb (Myo9b) is a single-headed processive myosin that exhibits Rho GTPase-activating protein (RhoGAP) activity in its tail region. Using live cell imaging, we determined that Myo9b is recruited to extending lamellipodia, ruffles, and filopodia, the regions of active actin polymerization. A functional motor domain was both necessary and sufficient for targeting Myo9b to these regions. The head domains of class IX myosins comprise a large insertion in loop2. Deletion of the large Myo9b head loop 2 insertion abrogated the enrichment in extending lamellipodia and ruffles, but enhanced significantly the enrichment at the tips of filopodia and retraction fibers. The enrichment in the tips of filopodia and retraction fibers depended on four lysine residues C-terminal to the loop 2 insertion and the tail region. Fluorescence recovery after photobleaching and photoactivation experiments in lamellipodia revealed that the dynamics of Myo9b was comparable to that of actin. The exchange rates depended on the Myo9b motor region and motor activity, and they were also dependent on the turnover of F-actin. These results demonstrate that Myo9b functions as a motorized RhoGAP molecule in regions of actin polymerization and identify Myo9b head sequences important for in vivo motor properties. PMID:17314409

An interacting loop model of solar flare bursts

NASA Technical Reports Server (NTRS)

Emslie, A. G.

1981-01-01

As a result of the strong heating produced at chromospheric levels during a solar flare burst, the local gas pressure can transiently attain very large values in certain regions. The effectiveness of the surrounding magnetic field at confining this high pressure plasma is therefore reduced and the flaring loop becomes free to expand laterally. In so doing it may drive magnetic field lines into neighboring, nonflaring, loops in the same active region, causing magnetic reconnection to take place and triggering another flare burst. The features of this interacting loop model are found to be in good agreement with the energetics and time structure of flare associated solar hard X-ray bursts.

TRACE Observations of Changes in Coronal Hole Boundaries

DTIC Science & Technology

2010-02-13

predominate SXT •3 sP nngcr TRACK Observations of Changes in Coronal Hole Boundaries 145 active regions in CHs appear as anemone , characterized by a radial...array of loops formed by connections between the CH fields and the opposite polarity part of the active region. The anemone active regions are

Activation loop targeting strategy for design of receptor-interacting protein kinase 2 (RIPK2) inhibitors.

PubMed

Suebsuwong, Chalada; Pinkas, Daniel M; Ray, Soumya S; Bufton, Joshua C; Dai, Bing; Bullock, Alex N; Degterev, Alexei; Cuny, Gregory D

2018-02-15

Development of selective kinase inhibitors remains a challenge due to considerable amino acid sequence similarity among family members particularly in the ATP binding site. Targeting the activation loop might offer improved inhibitor selectivity since this region of kinases is less conserved. However, the strategy presents difficulties due to activation loop flexibility. Herein, we report the design of receptor-interacting protein kinase 2 (RIPK2) inhibitors based on pan-kinase inhibitor regorafenib that aim to engage basic activation loop residues Lys169 or Arg171. We report development of CSR35 that displayed >10-fold selective inhibition of RIPK2 versus VEGFR2, the target of regorafenib. A co-crystal structure of CSR35 with RIPK2 revealed a resolved activation loop with an ionic interaction between the carboxylic acid installed in the inhibitor and the side-chain of Lys169. Our data provides principle feasibility of developing activation loop targeting type II inhibitors as a complementary strategy for achieving improved selectivity. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Coronal Heating: Testing Models of Coronal Heating by Forward-Modeling the AIA Emission of the Ansample of Coronal Loops

NASA Astrophysics Data System (ADS)

Malanushenko, A. V.

2015-12-01

We present a systemic exploration of the properties of coronal heating, by forward-modeling the emission of the ensemble of 1D quasi-steady loops. This approximations were used in many theoretical models of the coronal heating. The latter is described in many such models in the form of power laws, relating heat flux through the photosphere or volumetric heating to the strength of the magnetic field and length of a given field line. We perform a large search in the parameter space of these power laws, amongst other variables, and compare the resulting emission of the active region to that observed by AIA. We use a recently developed magnetic field model which uses shapes of coronal loops to guide the magnetic model; the result closely resembles observed structures by design. We take advantage of this, by comparing, in individual sub-regions of the active region, the emission of the active region and its synthetic model. This study allows us to rule out many theoretical models and formulate predictions for the heating models to come.

Excitation of flare-induced waves in coronal loops and the effects of radiative cooling

NASA Astrophysics Data System (ADS)

Provornikova, Elena; Ofman, Leon; Wang, Tongjiang

2018-01-01

EUV imaging observations from several space missions (SOHO/EIT, TRACE, and SDO/AIA) have revealed a presence of propagating intensity disturbances in solar coronal loops. These disturbances are typically interpreted as slow magnetoacoustic waves. However, recent spectroscopic observations with Hinode/EIS of active region loops revealed that the propagating intensity disturbances are associated with intermittent plasma upflows (or jets) at the footpoints which are presumably generated by magnetic reconnection. For this reason, whether these disturbances are waves or periodic flows is still being studied. This study is aimed at understanding the physical properties of observed disturbances by investigating the excitation of waves by hot plasma injections from below and the evolution of flows and wave propagation along the loop. We expand our previous studies based on isothermal 3D MHD models of an active region to a more realistic model that includes full energy equation accounting for the effects of radiative losses. Computations are initialized with an equilibrium state of a model active region using potential (dipole) magnetic field, gravitationally stratified density and temperature obtained from the polytropic equation of state. We model an impulsive injection of hot plasma into the steady plasma outflow along the loops of different temperatures, warm (∼1 MK) and hot (∼6 MK). The simulations show that hot jets launched at the coronal base excite slow magnetoacoustic waves that propagate to high altitudes along the loops, while the injected hot flows decelerate rapidly with heights. Our results support that propagating disturbances observed in EUV are mainly the wave features. We also find that the effect of radiative cooling on the damping of slow-mode waves in 1-6 MK coronal loops is small, in agreement with the previous conclusion based on 1D MHD models.

Spectroscopic Study of a Dark Lane and a Cool Loop in a Solar Limb Active Region by Hinode/EIS

NASA Astrophysics Data System (ADS)

Lee, Kyoung-Sun; Imada, S.; Moon, Y.-J.; Lee, Jin-Yi

2014-01-01

We investigated a cool loop and a dark lane over a limb active region on 2007 March 14 using the Hinode/EUV Imaging Spectrometer. The cool loop is clearly seen in the spectral lines formed at the transition region temperature. The dark lane is characterized by an elongated faint structure in the coronal spectral lines and is rooted on a bright point. We examined their electron densities, Doppler velocities, and nonthermal velocities as a function of distance from the limb. We derived electron densities using the density sensitive line pairs of Mg VII, Si X, Fe XII, Fe XIII, and Fe XIV spectra. We also compared the observed density scale heights with the calculated scale heights from each peak formation temperatures of the spectral lines under the hydrostatic equilibrium. We noted that the observed density scale heights of the cool loop are consistent with the calculated heights, with the exception of one observed cooler temperature; we also found that the observed scale heights of the dark lane are much lower than their calculated scale heights. The nonthermal velocity in the cool loop slightly decreases along the loop, while nonthermal velocity in the dark lane sharply falls off with height. Such a decrease in the nonthermal velocity may be explained by wave damping near the solar surface or by turbulence due to magnetic reconnection near the bright point.

DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner.

PubMed

Wiedemann, Eva-Maria; Peycheva, Mihaela; Pavri, Rushad

2016-12-13

Class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) locus generates antibody isotypes. CSR depends on double-strand breaks (DSBs) induced by activation-induced cytidine deaminase (AID). Although DSB formation and repair machineries are active in G1 phase, efficient CSR is dependent on cell proliferation and S phase entry; however, the underlying mechanisms are obscure. Here, we show that efficient CSR requires the replicative helicase, the Mcm complex. Mcm proteins are enriched at IgH switch regions during CSR, leading to assembly of facultative replication origins that require Mcm helicase function for productive CSR. Assembly of CSR-associated origins is facilitated by R loops and promotes the physical proximity (synapsis) of recombining switch regions, which is reduced by R loop inhibition or Mcm complex depletion. Thus, R loops contribute to replication origin specification that promotes DSB resolution in CSR. This suggests a mechanism for the dependence of CSR on S phase and cell division. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Myc-induced anchorage of the rDNA IGS region to nucleolar matrix modulates growth-stimulated changes in higher-order rDNA architecture

PubMed Central

Shiue, Chiou-Nan; Nematollahi-Mahani, Amir; Wright, Anthony P.H.

2014-01-01

Chromatin domain organization and the compartmentalized distribution of chromosomal regions are essential for packaging of deoxyribonucleic acid (DNA) in the eukaryotic nucleus as well as regulated gene expression. Nucleoli are the most prominent morphological structures of cell nuclei and nucleolar organization is coupled to cell growth. It has been shown that nuclear scaffold/matrix attachment regions often define the base of looped chromosomal domains in vivo and that they are thereby critical for correct chromosome architecture and gene expression. Here, we show regulated organization of mammalian ribosomal ribonucleic acid genes into distinct chromatin loops by tethering to nucleolar matrix via the non-transcribed inter-genic spacer region of the ribosomal DNA (rDNA). The rDNA gene loop structures are induced specifically upon growth stimulation and are dependent on the activity of the c-Myc protein. Matrix-attached rDNA genes are hypomethylated at the promoter and are thus available for transcriptional activation. rDNA genes silenced by methylation are not recruited to the matrix. c-Myc, which has been shown to induce rDNA transcription directly, is physically associated with rDNA gene looping structures and the intergenic spacer sequence in growing cells. Such a role of Myc proteins in gene activation has not been reported previously. PMID:24609384

Myc-induced anchorage of the rDNA IGS region to nucleolar matrix modulates growth-stimulated changes in higher-order rDNA architecture.

PubMed

Shiue, Chiou-Nan; Nematollahi-Mahani, Amir; Wright, Anthony P H

2014-05-01

Chromatin domain organization and the compartmentalized distribution of chromosomal regions are essential for packaging of deoxyribonucleic acid (DNA) in the eukaryotic nucleus as well as regulated gene expression. Nucleoli are the most prominent morphological structures of cell nuclei and nucleolar organization is coupled to cell growth. It has been shown that nuclear scaffold/matrix attachment regions often define the base of looped chromosomal domains in vivo and that they are thereby critical for correct chromosome architecture and gene expression. Here, we show regulated organization of mammalian ribosomal ribonucleic acid genes into distinct chromatin loops by tethering to nucleolar matrix via the non-transcribed inter-genic spacer region of the ribosomal DNA (rDNA). The rDNA gene loop structures are induced specifically upon growth stimulation and are dependent on the activity of the c-Myc protein. Matrix-attached rDNA genes are hypomethylated at the promoter and are thus available for transcriptional activation. rDNA genes silenced by methylation are not recruited to the matrix. c-Myc, which has been shown to induce rDNA transcription directly, is physically associated with rDNA gene looping structures and the intergenic spacer sequence in growing cells. Such a role of Myc proteins in gene activation has not been reported previously. © 2014 The Author(s). Published by Oxford University Press [on behalf of Nucleic Acids Research].

3D-Stereoscopic Analysis of Solar Active Region Loops. 2; SoHo/EIT Observations at Temperatures of 1.5-2.5 MK

NASA Technical Reports Server (NTRS)

Aschwanden, Markus J.; Alexander, David; Hurlburt, Neal; Newmark, Jeffrey S.; Neupert, Werner M.; Klimchuk, J. A.; Gary, G. Allen

1999-01-01

In this paper we study the three-dimensional (3D) structure of hot (T(sub e) approximately equals 1.5 - 2.5 MK) loops in solar active region NOAA 7986, observed on 1996 August 30 with the Extreme-ultraviolet Imaging Telescope (EIT) onboard the Solar and Heliospheric Observatory (SoHO). This complements a first study on cooler (T(sub e) approximately equals 1.0 - 1.5 MK) loops of the same active region, using the same method of Dynamic Stereoscopy to reconstruct the 3D geometry. We reconstruct the 3D-coordinates x(s), y(s), z(s), the density n(sub e)(s), and temperature profile T(sub e)(s) of 35 individual loop segments (as function of the loop coordinate s) using EIT 195 A and 284 A images. The major findings are: (1) All loops are found to be in hydrostatic equilibrium, in the entire temperature regime of T(sub e) = 1.0 - 2.5 MK; (2) The analyzed loops have a height of 2-3 scale heights, and thus only segments extending over about one vertical scale height have sufficient emission measure contrast for detection; (3) The temperature gradient over the lowest scale height is of order dT/ds is approximately 1 - 4 K/km; (4) The radiative loss rate is found to exceed the conductive loss rate by about two orders or magnitude, making thermal conduction negligible to explain the temperature structure of the loops; (5) A steady-state can only be achieved when the heating rate E(sub H) matches the radiative loss rate in hydrostatic equilibrium, requiring a heat deposition length lambda(sub H) of the half density scale height lambda, predicting a scaling law with the loop base pressure, EH varies as p(sub 0 exp 2). This favors coronal heating mechanisms that operate near the loop footpoints; (6) We find a reciprocal correlation between the loop pressure p(sub 0) and loop length L, i.e. p(sub 0) varies as 1/L, implying a scaling law of the steady-state requirement with loop length, i.e. E(sub H ) varies as 1/L(exp 2). The heating rate shows no correlation with the loop-aligned magnetic field component B(sub z) at the footpoints, but is correlated with the azimuthal field B(sub phi) = Bz(RDelta Phi/L) of a twisted loop, and is thus consistent with heating mechanisms based on field-aligned currents.

Loop engineering reveals the importance of active-site-decorating loops and gating residue in substrate affinity modulation of arginine deiminase (an anti-tumor enzyme).

PubMed

Cheng, Feng; Yang, Jianhua; Bocola, Marco; Schwaneberg, Ulrich; Zhu, Leilei

2018-05-05

Protein engineering of enzyme loop regions is an effective strategy to improve enzymatic properties. Previous studies that aimed to boost the activity of PpADI (an arginine deiminase from Pseudomonas plecoglossicida) under physiological conditions yielded several significantly improved variants that harbor substitutions predominantly located in active-site-decorating loops. A multi-site saturation mutagenesis at four positions in loop 1 (37, 38, 42, and 43) and three positions in loop 4 (402, 403, and 404) was performed to elucidate the importance of these loops in modulating the substrate affinity of PpADI. The identified "best" variant (M6-L1-4) showed a decreased S 0.5 ('K M ') of 0.48 mM compared with the parent M6 (0.81 mM). Subsequently, a rational design to recombine beneficial substitutions within loops 1 and 4 yielded variant L6 with a substantially decreased S 0.5 value (0.17 mM). A comprehensive simulation analysis resulted in a conclusion that high loop flexibility (especially the gating residue Arg400) is beneficial for substrate affinity due to less efficient blocking of the active site. Copyright © 2018 Elsevier Inc. All rights reserved.

First Imaging Observation of Standing Slow Wave in Coronal Fan Loops

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

Pant, V.; Tiwari, A.; Banerjee, D.

2017-09-20

We observe intensity oscillations along coronal fan loops associated with the active region AR 11428. The intensity oscillations were triggered by blast waves that were generated due to X-class flares in the distant active region AR 11429. To characterize the nature of oscillations, we created time–distance maps along the fan loops and noted that the intensity oscillations at two ends of the loops were out of phase. As we move along the fan loop, the amplitude of the oscillations first decreased and then increased. The out-of-phase nature together with the amplitude variation along the loop implies that these oscillations aremore » very likely to be standing waves. The period of the oscillations is estimated to be ∼27 minutes, damping time to be ∼45 minutes, and phase velocity projected in the plane of sky to be ∼65–83 km s{sup −1}. The projected phase speeds were in the range of the acoustic speed of coronal plasma at about 0.6 MK, which further indicates that these are slow waves. To the best of our knowledge, this is the first report on the existence of the standing slow waves in non-flaring fan loops.« less

Chromatin looping and eRNA transcription precede the transcriptional activation of gene in the β-globin locus

PubMed Central

Kim, Yea Woon; Lee, Sungkung; Yun, Jangmi; Kim, AeRi

2015-01-01

Enhancers are closely positioned with actively transcribed target genes by chromatin looping. Non-coding RNAs are often transcribed on active enhancers, referred to as eRNAs (enhancer RNAs). To explore the kinetics of enhancer–promoter looping and eRNA transcription during transcriptional activation, we induced the β-globin locus by chemical treatment and analysed cross-linking frequency between the β-globin gene and locus control region (LCR) and the amount of eRNAs transcribed on the LCR in a time course manner. The cross-linking frequency was increased after chemical induction but before the transcriptional activation of gene in the β-globin locus. Transcription of eRNAs was increased in concomitant with the increase in cross-linking frequency. These results show that chromatin looping and eRNA transcription precedes the transcriptional activation of gene. Concomitant occurrence of the two events suggests functional relationship between them. PMID:25588787

Magnetic Roots and the Driving of Extended Coronal Heating

NASA Technical Reports Server (NTRS)

Porter, Jason G.; Falconer, D. A.; Moore, Ronald L.; Harvey, Karen L.; Rabin, Douglas M.; Shimizu, T.

1998-01-01

We report results from a continuation of a previous study, in which we found large bright coronal loops within active regions and extending from active regions that have one end rooted near an island of included magnetic polarity that is a site of enhanced coronal heating and microflares. This suggested that magnetic activity such as microflaring results in enhanced heating in both the compact core field around the island and in the large loops extending from it. We might expect that the intensity variations due to enhanced heating in the compact and extended structures would be correlated. However, although some ex- tended loops do respond to the largest events taking place in the core fields near their feet, they do not show a clear response to most smaller individual events nor to the overall envelope of coronal heating activity in the core fields at their feet as determined from longer-term observations. Thus, while it is clear that the extended loops' heating is being driven from their ends at the magnetic islands, much of this heating is apparently by some form of footpoint activity that is not strongly coupled to the heating in the footpoint core fields. One possibility is that the remote heating in the extended loops is driven by reconnection at the magnetic null over the island, and that this reconnection is driven mainly by core-field activity that produces little coronal heating within the core field itself, perhaps in the manner of the numerical simulations by Karpen, Antiochos, and DeVore.

Hi-C and AIA observations of transverse magnetohydrodynamic waves in active regions

NASA Astrophysics Data System (ADS)

Morton, R. J.; McLaughlin, J. A.

2013-05-01

The recent launch of the High resolution Coronal imager (Hi-C) provided a unique opportunity of studying the EUV corona with unprecedented spatial resolution. We utilize these observations to investigate the properties of low-frequency (50-200 s) active region transverse waves, whose omnipresence had been suggested previously. The five-fold improvement in spatial resolution over SDO/AIA reveals coronal loops with widths 150-310 km and that these loops support transverse waves with displacement amplitudes <50 km. However, the results suggest that wave activity in the coronal loops is of low energy, with typical velocity amplitudes <3 km s-1. An extended time-series of SDO data suggests that low-energy wave behaviour is typical of the coronal structures both before and after the Hi-C observations. Appendix A and five movies associated to Figs. A.2-A.6 are available in electronic form at http://www.aanda.org

Heating mechanisms for intermittent loops in active region cores from AIA/SDO EUV observations

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

Cadavid, A. C.; Lawrence, J. K.; Christian, D. J.

2014-11-01

We investigate intensity variations and energy deposition in five coronal loops in active region cores. These were selected for their strong variability in the AIA/SDO 94 Å intensity channel. We isolate the hot Fe XVIII and Fe XXI components of the 94 Å and 131 Å by modeling and subtracting the 'warm' contributions to the emission. HMI/SDO data allow us to focus on 'inter-moss' regions in the loops. The detailed evolution of the inter-moss intensity time series reveals loops that are impulsively heated in a mode compatible with a nanoflare storm, with a spike in the hot 131 Å signalsmore » leading and the other five EUV emission channels following in progressive cooling order. A sharp increase in electron temperature tends to follow closely after the hot 131 Å signal confirming the impulsive nature of the process. A cooler process of growing emission measure follows more slowly. The Fourier power spectra of the hot 131 Å signals, when averaged over the five loops, present three scaling regimes with break frequencies near 0.1 min{sup –1} and 0.7 min{sup –1}. The low frequency regime corresponds to 1/f noise; the intermediate indicates a persistent scaling process and the high frequencies show white noise. Very similar results are found for the energy dissipation in a 2D 'hybrid' shell model of loop magneto-turbulence, based on reduced magnetohydrodynamics, that is compatible with nanoflare statistics. We suggest that such turbulent dissipation is the energy source for our loops.« less

On Heating the Sun's Corona by Magnetic Explosions: Feasibility in Active Regions and prospects for Quiet Regions and Coronal Holes

NASA Technical Reports Server (NTRS)

Moore, Ronald L.; Falconer, D. A.; Porter, Jason G.; Suess, Steven T.

1999-01-01

We build a case for the persistent strong coronal heating in active regions and the pervasive quasi-steady heating of the corona in quiet regions and coronal holes being driven in basically the same way as the intense transient heating in solar flares: by explosions of sheared magnetic fields in the cores of initially closed bipoles. We begin by summarizing the observational case for exploding sheared core fields being the drivers of a wide variety of flare events, with and without coronal mass ejections. We conclude that the arrangement of an event's flare heating, whether there is a coronal mass ejection, and the time and place of the ejection relative to the flare heating are all largely determined by four elements of the form and action of the magnetic field: (1) the arrangement of the impacted, interacting bipoles participating in the event, (2) which of these bipoles are active (have sheared core fields that explode) and which are passive (are heated by injection from impacted active bipoles), (3) which core field explodes first, and (4) which core-field explosions are confined within the closed field of their bipoles and which ejectively open their bipoles. We then apply this magnetic-configuration framework for flare heating to the strong coronal heating observed by the Yohkoh Soft X-ray Telescope in an active region with strongly sheared core fields observed by the MSFC vector magnetograph. All of the strong coronal heating is in continually microflaring sheared core fields or in extended loops rooted against the active core fields. Thus, the strong heating occurs in field configurations consistent with the heating being driven by frequent core-field explosions that are smaller but similar to those in confined flares and flaring arches. From analysis of the thermal and magnetic energetics of two selected core-field microflares and a bright extended loop, we find that (1) it is energetically feasible for the sheared core fields to drive all of the coronal heating in the active region via a staccato of magnetic microexplosions, (2) the microflares at the feet of the extended loop behave as the flares at the feet of flaring arches in that more coronal heating is driven within the active bipole than in the extended loop, (3) the filling factor of the X-ray plasma in the core field microflares and in the extended loop is approximately 0.1, and (4) to release enough magnetic energy for a typical microflare (10^27 - 10^28 erg), a microflaring strand of sheared core field need expand and/or untwist by only a few percent at most. Finally, we point out that (1) the field configurations for strong coronal heating in our example active region (i.e., neutral-line core fields, many embedded in the feet of extended loops) are present in abundance in the magnetic network in quiet regions and coronal holes, and (2) it is known that many network bipoles do microflare and that many produce detectable coronal heating. We therefore propose that exploding sheared core fields are the drivers of most of the heating and dynamics of the solar atmosphere, ranging from the largest and most powerful coronal mass ejections and flares, to the vigorous microflaring and coronal heating in active regions, to the multitude of fine-scale explosive events in the magnetic network. The low-lysing exploding core fields in the network drive microflares, spicules, global coronal heating, and ,consequently, the solar wind.

Conformational Changes in a Hyperthermostable Glycoside Hydrolase: Enzymatic Activity Is a Consequence of the Loop Dynamics and Protonation Balance

PubMed Central

de Oliveira, Leandro C.; da Silva, Viviam M.; Colussi, Francieli; Cabral, Aline D.; de Oliveira Neto, Mario; Squina, Fabio M.; Garcia, Wanius

2015-01-01

Endo-β-1, 4-mannanase from Thermotoga petrophila (TpMan) is a modular hyperthermostable enzyme involved in the degradation of mannan-containing polysaccharides. The degradation of these polysaccharides represents a key step for several industrial applications. Here, as part of a continuing investigation of TpMan, the region corresponding to the GH5 domain (TpManGH5) was characterized as a function of pH and temperature. The results indicated that the enzymatic activity of the TpManGH5 is pH-dependent, with its optimum activity occurring at pH 6. At pH 8, the studies demonstrated that TpManGH5 is a molecule with a nearly spherical tightly packed core displaying negligible flexibility in solution, and with size and shape very similar to crystal structure. However, TpManGH5 experiences an increase in radius of gyration in acidic conditions suggesting expansion of the molecule. Furthermore, at acidic pH values, TpManGH5 showed a less globular shape, probably due to a loop region slightly more expanded and flexible in solution (residues Y88 to A105). In addition, molecular dynamics simulations indicated that conformational changes caused by pH variation did not change the core of the TpManGH5, which means that only the above mentioned loop region presents high degree of fluctuations. The results also suggested that conformational changes of the loop region may facilitate polysaccharide and enzyme interaction. Finally, at pH 6 the results indicated that TpManGH5 is slightly more flexible at 65°C when compared to the same enzyme at 20°C. The biophysical characterization presented here is well correlated with the enzymatic activity and provide new insight into the structural basis for the temperature and pH-dependent activity of the TpManGH5. Also, the data suggest a loop region that provides a starting point for a rational design of biotechnological desired features. PMID:25723179

Genome-Wide Identification of Mitogen-Activated Protein Kinase Gene Family across Fungal Lineage Shows Presence of Novel and Diverse Activation Loop Motifs

PubMed Central

Mohanta, Tapan Kumar; Mohanta, Nibedita; Parida, Pratap; Panda, Sujogya Kumar; Ponpandian, Lakshmi Narayanan; Bae, Hanhong

2016-01-01

The mitogen-activated protein kinase (MAPK) is characterized by the presence of the T-E-Y, T-D-Y, and T-G-Y motifs in its activation loop region and plays a significant role in regulating diverse cellular responses in eukaryotic organisms. Availability of large-scale genome data in the fungal kingdom encouraged us to identify and analyse the fungal MAPK gene family consisting of 173 fungal species. The analysis of the MAPK gene family resulted in the discovery of several novel activation loop motifs (T-T-Y, T-I-Y, T-N-Y, T-H-Y, T-S-Y, K-G-Y, T-Q-Y, S-E-Y and S-D-Y) in fungal MAPKs. The phylogenetic analysis suggests that fungal MAPKs are non-polymorphic, had evolved from their common ancestors around 1500 million years ago, and are distantly related to plant MAPKs. We are the first to report the presence of nine novel activation loop motifs in fungal MAPKs. The specificity of the activation loop motif plays a significant role in controlling different growth and stress related pathways in fungi. Hence, the presences of these nine novel activation loop motifs in fungi are of special interest. PMID:26918378

3D-Stereoscopic Analysis of Solar Active Region Loops: I: SoHo/EIT Observations at Temperatures of 1.0-1.5 MK

NASA Technical Reports Server (NTRS)

Aschwanden, Markus J.; Newmark, Jeff; Delaboudiniere, Jean-Pierre; Neupert, Werner M.; Portier-Fozzani, Fabrice; Gary, G. Allen; Zucker, Arik

1998-01-01

The three-dimensional (3D) structure of solar active region NOAA 7986 observed on 1996 August 30 with the Extrem-ultraviolet Imaging Telescope (EIT) onboard the Solar and Heliospheric Observatory (SoHO) is analyzed. We develop a new method of Dynamic Stereoscopy to reconstruct the 3D geometry of dynamically changing loops, which allows us to determine the orientation of the loop plane with respect to the line-of-sight, a prerequisite to correct properly for projection effects in 3D loop models. With this method and the filter-ratio technique applied to EIT 171 A and 195 A images we determine the 3D coordinates (x(s), y(s), z(s)), the loop width) w(s), the electron density n(sub e)(s), and the electron temperature T(sub e)(s) as function of the loop length s for 30 loop segments. Fitting the loop densities with an exponential density model n(sub e)(h) we find that the so inferred scale height temperatures, T(sub e)(sup lambda) = 1.22 +/- 0.23 MK, match closely the EIT filter-ratio temperatures, T(sub e)(sup FIT) = 1.21 +/- 0.06 MK. We conclude that these rather large-scale loops (with heights of h approx. equals 50 - 200 Mm) that dominate EIT 171 A images are close to thermal equilibrium. Most of the loops show no significant thickness variation w(s), but many exhibit a trend of increasing temperature (dT/ds greater than 0) above the footpoint.

Dynamical behaviour in coronal loops

NASA Technical Reports Server (NTRS)

Haisch, Bernhard M.

1986-01-01

Rapid variability has been found in two active region coronal loops observed by the X-ray Polychromator (XRP) and the Hard X-ray Imaging Spectrometer (HXIS) onboard the Solar Maximum Mission (SMM). There appear to be surprisingly few observations of the short-time scale behavior of hot loops, and the evidence presented herein lends support to the hypothesis that coronal heating may be impulsive and driven by flaring.

Dynamical behaviour in coronal loops

NASA Astrophysics Data System (ADS)

Haisch, Bernhard M.

Rapid variability has been found in two active region coronal loops observed by the X-ray Polychromator (XRP) and the Hard X-ray Imaging Spectrometer (HXIS) onboard the Solar Maximum Mission (SMM). There appear to be surprisingly few observations of the short-time scale behavior of hot loops, and the evidence presented herein lends support to the hypothesis that coronal heating may be impulsive and driven by flaring.

The Local Dinucleotide Preference of APOBEC3G Can Be Altered from 5′-CC to 5′-TC by a Single Amino Acid Substitution

PubMed Central

Rathore, Anurag; Carpenter, Michael A; Demir, Özlem; Ikeda, Terumasa; Li, Ming; Shaban, Nadine; Law, Emily K.; Anokhin, Dmitry; Brown, William L.; Amaro, Rommie E.; Harris, Reuben S.

2013-01-01

APOBEC3A and APOBEC3G are DNA cytosine deaminases with biological functions in foreign DNA and retrovirus restriction, respectively. APOBEC3A has an intrinsic preference for cytosine preceded by thymine (5′-TC) in single-stranded DNA substrates, whereas APOBEC3G prefers the target cytosine to be preceded by another cytosine (5′-CC). To determine the amino acids responsible for these strong dinucleotide preferences, we analyzed a series of chimeras in which putative DNA binding loop regions of APOBEC3G were replaced with the corresponding regions from APOBEC3A. Loop 3 replacement enhanced APOBEC3G catalytic activity but did not alter its intrinsic 5′-CC dinucleotide substrate preference. Loop 7 replacement caused APOBEC3G to become APOBEC3A-like and strongly prefer 5′-TC substrates. Simultaneous loop 3/7 replacement resulted in a hyperactive APOBEC3G variant that also preferred 5′-TC dinucleotides. Single amino acid exchanges revealed D317 as a critical determinant of dinucleotide substrate specificity. Multi-copy explicitly solvated all-atom molecular dynamics simulations suggested a model in which D317 acts as a helix-capping residue by constraining the mobility of loop 7, forming a novel binding pocket that favorably accommodates cytosine. All catalytically active APOBEC3G variants, regardless of dinucleotide preference, retained HIV-1 restriction activity. These data support a model in which the loop 7 region governs the selection of local dinucleotide substrates for deamination but is unlikely to be part of the higher level targeting mechanisms that direct these enzymes to biological substrates such as HIV-1 cDNA. PMID:23938202

Spectroscopic study of a dark lane and a cool loop in a solar limb active region by Hinode/EIS

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

Lee, Kyoung-Sun; Imada, S.; Moon, Y.-J.

2014-01-10

We investigated a cool loop and a dark lane over a limb active region on 2007 March 14 using the Hinode/EUV Imaging Spectrometer. The cool loop is clearly seen in the spectral lines formed at the transition region temperature. The dark lane is characterized by an elongated faint structure in the coronal spectral lines and is rooted on a bright point. We examined their electron densities, Doppler velocities, and nonthermal velocities as a function of distance from the limb. We derived electron densities using the density sensitive line pairs of Mg VII, Si X, Fe XII, Fe XIII, and Femore » XIV spectra. We also compared the observed density scale heights with the calculated scale heights from each peak formation temperatures of the spectral lines under the hydrostatic equilibrium. We noted that the observed density scale heights of the cool loop are consistent with the calculated heights, with the exception of one observed cooler temperature; we also found that the observed scale heights of the dark lane are much lower than their calculated scale heights. The nonthermal velocity in the cool loop slightly decreases along the loop, while nonthermal velocity in the dark lane sharply falls off with height. Such a decrease in the nonthermal velocity may be explained by wave damping near the solar surface or by turbulence due to magnetic reconnection near the bright point.« less

Slow Magnetosonic Waves and Fast Flows in Active Region Loops

NASA Technical Reports Server (NTRS)

Ofman, L.; Wang, T. J.; Davila, J. M.

2012-01-01

Recent extreme ultraviolet spectroscopic observations indicate that slow magnetosonic waves are present in active region (AR) loops. Some of the spectral data were also interpreted as evidence of fast (approx 100-300 km/s) quasiperiodic flows. We have performed three-dimensional magnetohydrodynamic (3D MHD) modeling of a bipolar AR that contains impulsively generated waves and flows in coronal loops. The model AR is initiated with a dipole magnetic field and gravitationally stratified density, with an upflow-driven steadily or periodically in localized regions at the footpoints of magnetic loops. The resulting flows along the magnetic field lines of the AR produce higher density loops compared to the surrounding plasma by injection of material into the flux tubes and the establishment of siphon flow.We find that the impulsive onset of flows with subsonic speeds result in the excitation of damped slow magnetosonic waves that propagate along the loops and coupled nonlinearly driven fast-mode waves. The phase speed of the slow magnetosonic waves is close to the coronal sound speed. When the amplitude of the driving pulses is increased we find that slow shock-like wave trains are produced. When the upflows are driven periodically, undamped oscillations are produced with periods determined by the periodicity of the upflows. Based on the results of the 3D MHD model we suggest that the observed slow magnetosonic waves and persistent upflows may be produced by the same impulsive events at the bases of ARs.

Current systems of coronal loops in 3D MHD simulations

NASA Astrophysics Data System (ADS)

Warnecke, J.; Chen, F.; Bingert, S.; Peter, H.

2017-11-01

Aims: We study the magnetic field and current structure associated with a coronal loop. Through this we investigate to what extent the assumptions of a force-free magnetic field break down and where they might be justified. Methods: We analyze a three-dimensional (3D) magnetohydrodynamic (MHD) model of the solar corona in an emerging active region with the focus on the structure of the forming coronal loops. The lower boundary of this simulation is taken from a model of an emerging active region. As a consequence of the emerging magnetic flux and the horizontal motions at the surface a coronal loop forms self-consistently. We investigate the current density along magnetic field lines inside (and outside) this loop and study the magnetic and plasma properties in and around this loop. The loop is defined as the bundle of field lines that coincides with enhanced emission in extreme UV. Results: We find that the total current along the emerging loop changes its sign from being antiparallel to parallel to the magnetic field. This is caused by the inclination of the loop together with the footpoint motion. Around the loop, the currents form a complex non-force-free helical structure. This is directly related to a bipolar current structure at the loop footpoints at the base of the corona and a local reduction of the background magnetic field (I.e., outside the loop) caused by the plasma flow into and along the loop. Furthermore, the locally reduced magnetic pressure in the loop allows the loop to sustain a higher density, which is crucial for the emission in extreme UV. The action of the flow on the magnetic field hosting the loop turns out to also be responsible for the observed squashing of the loop. Conclusions: The complex magnetic field and current system surrounding it can only be modeled in 3D MHD models where the magnetic field has to balance the plasma pressure. A one-dimensional coronal loop model or a force-free extrapolation cannot capture the current system and the complex interaction of the plasma and the magnetic field in the coronal loop, despite the fact that the loop is under low-β conditions.

Autoregulatory Characteristics of a Bacillus anthracis Serine/Threonine Kinase▿

PubMed Central

Bryant-Hudson, Katie M.; Shakir, Salika M.; Ballard, Jimmy D.

2011-01-01

BA-Stk1 is a serine/threonine kinase (STK) expressed by Bacillus anthracis. In previous studies, we found that BA-Stk1 activity is modulated through dephosphorylation by a partner phosphatase, BA-Stp1. In this study, we identified critical phosphorylation regions of BA-Stk1 and determined the contributions of these phosphodomains to autophosphorylation and substrate phosphorylation. The data indicate that BA-Stk1 undergoes trans-autophosphorylation within a regulatory domain, referred to as the activation loop, which carries eight putative regulatory serine and threonine residues. We identified activation loop mutants that impacted kinase activity in three different manners: regulation of autophosphorylation (T162), regulation of substrate phosphorylation (T159 and S169), and regulation of overall kinase activity (T163). Tandem mass spectrometry (MS/MS) analysis of the phosphorylation profile of each mutant revealed a second site of phosphorylation on the kinase that was influenced by the phosphorylation status of the activation loop. This second region of the kinase contained a single phosphorylation residue, S214. Previous work has shown S214 to be necessary for downstream substrate phosphorylation, and we have shown that this residue is subject to dephosphorylation by BA-Stp1. These findings indicate a connection between the phosphorylation status of the activation loop and phosphorylation of S214, and this suggests a previously undescribed model for how a bacterial STK shifts from a state of autophosphorylation to targeting downstream substrates. PMID:21296958

Refined molecular hinge between allosteric and catalytic domain determines allosteric regulation and stability of fungal chorismate mutase

PubMed Central

Helmstaedt, Kerstin; Heinrich, Gabriele; Lipscomb, William N.; Braus, Gerhard H.

2002-01-01

The yeast chorismate mutase is regulated by tyrosine as feedback inhibitor and tryptophan as crosspathway activator. The monomer consists of a catalytic and a regulatory domain covalently linked by the loop L220s (212–226), which functions as a molecular hinge. Two monomers form the active dimeric enzyme stabilized by hydrophobic interactions in the vicinity of loop L220s. The role of loop L220s and its environment for enzyme regulation, dimerization, and stability was analyzed. Substitution of yeast loop L220s in place of the homologous loop from the corresponding and similarly regulated Aspergillus enzyme (and the reverse substitution) changed tyrosine inhibition to activation. Yeast loop L220s substituted into the Aspergillus enzyme resulted in a tryptophan-inhibitable enzyme. Monomeric yeast chorismate mutases could be generated by substituting two hydrophobic residues in and near the hinge region. The resulting Thr-212→Asp–Phe-28→Asp enzyme was as stable as wild type, but lost allosteric regulation and showed reduced catalytic activity. These results underline the crucial role of this molecular hinge for inhibition, activation, quaternary structure, and stability of yeast chorismate mutase. PMID:11997452

Deletion of loop fragment adjacent to active site diminishes the stability and activity of exo-inulinase.

PubMed

Arjomand, Maryam Rezaei; Habibi-Rezaei, Mehran; Ahmadian, Gholamreza; Hassanzadeh, Malihe; Karkhane, Ali Asghar; Asadifar, Mandana; Amanlou, Massoud

2016-11-01

Inulinases are classified as hydrolases and widely used in the food and medical industries. Here, we report the deletion of a six-membered adjacent active site loop fragment ( 74 YGSDVT 79 sequence) from third Ω-loop of the exo-inulinase containing aspartate residue from Aspergillus niger to study its structural and functional importance. Site-directed mutagenesis was used to create the mutant of the exo-inulinase (Δ6SL). To investigate the stability of the region spanning this loop, MD simulations were performed 80ns for 20-85 residues. Molecular docking was performed to compare the interactions in the active sites of enzymes with fructose as a ligand. Accordingly, the functional thermostability of the exo-inulinase was significantly decreased upon loop fragment deletion. Evaluation of the kinetics parameters (V max , K m , k cat and, k cat /K m ) and activation energy (E a ) of the catalysis of enzymes indicated the importance of the deleted sequence on the catalytic performance of the enzyme. In conclusion, six-membered adjacent active site loop fragment not only plays a crucial role in the stability of the enzyme, but also it involves in the enzyme catalysis through lowering the activation energy of the catalysis and effective improving the catalytic performance. Copyright © 2016. Published by Elsevier B.V.

On Heating Large Bright Coronal Loops by Magnetic Microexplosions at their Feet

NASA Technical Reports Server (NTRS)

Moore, Ronald L; Falconer, D. A.; Porter, Jason G.

1999-01-01

In previous work, by registering Yohkoh SXT coronal X-ray images with MSFC vector magnetograms, we found that: (1) many of the larger bright coronal loops rooted at one or both ends in an active region are rooted around magnetic islands of included polarity, (2) the core field encasing the neutral line encircling the island is strongly sheared, and (3) this sheared core field is the seat of frequent microflares. This suggests that the coronal heating in these extended bright loops is driven by many small explosive releases of stored magnetic energy from the sheared core field at their feet, some of which magnetic microexplosions also produce the microflare heating in the core fields. In this paper, we show that this scenario is feasible in terms of the energy Abstract: required for the observed coronal heating and the magnetic energy available in the observed sheared core fields. In a representative active region, from the X-ray and vector field data, we estimate the coronal heating consumption by a selected typical large bright loop, the coronal heating consumption by a typical microflare at the foot of this loop, the frequency of microflares at the foot, and the available magnetic energy in the microflaring core field. We find that: (1) the rate of magnetic energy release to power the microflares at the foot (approx. 6 x 10(ext 25)erg/s) is enough to also power the coronal heating in the body of the extended loop (approx. 2 x l0(exp 25 erg/s), and (2) there is enough stored magnetic energy in the sheared core field to sustain the microflaring and extended loop heating for about a day, which is a typical time for buildup of neutral-line magnetic shear in an active region. This work was funded by the Solar Physics Branch of NASA's Office of Space Science through the SR&T Program and the SEC Guest Investigator Program.

Simultaneous Solar Maximum Mission and Very Large Array (VLA) observations of solar active regions

NASA Technical Reports Server (NTRS)

Lang, K. R.

1985-01-01

Simultaneous observations of solar active regions with the Solar Maximum Mission (SMM) Satellite and the Very Large Array (VLA) have been obtained and analyzed. Combined results enhance the scientific return for beyond that expeted from using either SMM or VLA alone. A total of two weeks of simultaneous SMM/VLA data were obtained. The multiple wavelength VLA observations were used to determine the temperature and magnetic structure at different heights within coronal loops. These data are compared with simultaneous SMM observations. Several papers on the subject are in progress. They include VLA observations of compact, transient sources in the transition region; simultaneous SMM/VLA observations of the coronal loops in one active region and the evolution of another one; and sampling of the coronal plasma using thermal cyclotron lines (magnetic field - VLA) and soft X ray spectral lines (electron density and electron temperaure-SMM).

Loop models of low coronal structures observed by the Normal Incidence X-Ray Telescope (NIXT)

NASA Technical Reports Server (NTRS)

Peres, G.; Reale, F.; Golub, L.

1994-01-01

The X-ray pictures obtained with the Normal Incidence X-Ray Telescope (NIXT), apart from the ubiquitous coronal loops well known from previous X-ray observations, show a new and peculiar morphology: in many active regions there are wide and apparently low-lying areas of intense emission which resemble H alpha plages. By means of hydrostatic models of coronal arches, we analyze the distribution of temperature, density, emission measure, and plasma emissivity in the spectral band to which NIXT is sensitive, and we show that the above morphology can be explained by the characteristics of high pressure loops having a thin region of high surface brightness at the base. We therefore propose that this finding might help to identify high-pressure X-ray emitting coronal regions in NIXT images, and it is in principle applicable to any imaging instrument which has high sensitivity to 10(exp 4) - 10(exp 6) K plasma within a narrow coronal-temperature passband. As a more general result of this study, we propose that the comparison of NIXT observations with models of stationary loops might provide a new diagnostic: the determination of the loop plasma pressure from measurements of brightness distribution along the loop.

Enzymatic properties of a GH19 chitinase isolated from rice lacking a major loop structure involved in chitin binding.

PubMed

Tanaka, Jun; Fukamizo, Tamo; Ohnuma, Takayuki

2017-05-01

The catalytic domains of family GH19 chitinases have been found to consist of a conserved, α-helical core-region and different numbers (1-6) of loop structures, located at both ends of the substrate-binding groove and which extend over the glycon- and aglycon-binding sites. We expressed, purified and enzymatically characterized a GH19 chitinase from rice, Oryza sativa L. cv. Nipponbare (OsChia2a), lacking a major loop structure (loop III) connected to the functionally important β-stranded region. The new enzyme thus contained the five remaining loop structures (loops I, II, IV, V and C-term). The OsChia2a recombinant protein catalyzed hydrolysis of chitin oligosaccharides, (GlcNAc)n (n = 3-6), with inversion of anomeric configuration, indicating that OsChia2a correctly folded without loop III. From thermal unfolding experiments and calorimetric titrations using the inactive OsChia2a mutant (OsChia2a-E68Q), in which the catalytic residue Glu68 was mutated to glutamine, we found that the binding affinities towards (GlcNAc)n (n = 2-6) were almost proportional to the degree of polymerization of (GlcNAc)n, but were much lower than those obtained for a moss GH19 chitinase having only loop III [Ohnuma T, Sørlie M, Fukuda T, Kawamoto N, Taira T, Fukamizo T. 2011. Chitin oligosaccharide binding to a family GH19 chitinase from the moss, Bryum coronatum. FEBS J. 278:3991-4001]. Nevertheless, OsChia2a exhibited significant antifungal activity. It appears that loop III connected to the β-stranded region is important for (GlcNAc)n binding, but is not essential for antifungal activity. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Observations of loops and prominences

NASA Technical Reports Server (NTRS)

Strong, Keith T.

1994-01-01

We review recent observations by the Yohkoh-SXT (Soft X-ray Telescope) in collaboration with other spacecraft and ground-based observatories of coronal loops and prominences. These new results point to problems that SoHO will be able to address. With a unique combination of rapid-cadence digital imaging (greater than or equal to 32 s full-disk and greater than or equal to 2 s partial-frame images), high spatial resolution (greater than or equal to 2.5 arcsec pixels), high sensitivity (EM less than or equal to 10(exp 42) cm(exp -3)), a low-scatter mirror, and large dynamic range, SXT can observe a vast range of targets on the Sun. Over the first 21 months of Yohkoh operations SXT has taken over one million images of the corona and so is building up an invaluable long-term database on the large-scale corona and loop geometry. The most striking thing about the SXT images is the range of loop sizes and shapes. The active regions are a bright tangle of magnetic field lines, surrounded by a network of large-scale quiet-Sun loops stretching over distances in excess of 105 km. The cross-section of most loops seems to be constant. Loops displaying significant Gamma's are the exception, not the rule, implying the presence of widespread currents in the corona. All magnetic structures show changes. Time scales range from seconds to months. The question of how these structures are formed, become filled with hot plasma, and are maintained is still open. While we see the propagation of brightenings along the length of active-region loops and in X-ray jets with velocities of several hundred km/s, much higher velocities are seen in the quiet Sun. In XBP flares, for example, velocities of over 1000 km/s are common. Active-region loops seem to be in constant motion, moving slowly outward, carrying plasma with them. During flares, loops often produce localized brightenings at the base and later at the apex of the loop. Quiescent filaments and prominences have been observed regularly. Their coronal manifestation seems to be an extended arcade of loops overlying the filament. Reliable alignment of the ground-based data with the X-ray images make it possible to make a detailed intercomparison of the hot and cold plasma structures over extended periods. Hence we are able to follow the long-term evolution of these structures and see how they become destabilized and erupt.

Suppression of Heating of Coronal Loops Rooted in Opposite Polarity Sunspot Umbrae

NASA Technical Reports Server (NTRS)

Tiwari, Sanjiv K.; Thalmann, Julia K.; Moore, Ronald L.; Panesar, Navdeep K.; Winebarger, Amy R.

2016-01-01

EUV observations of active region (AR) coronae reveal the presence of loops at different temperatures. To understand the mechanisms that result in hotter or cooler loops, we study a typical bipolar AR, near solar disk center, which has moderate overall magnetic twist and at least one fully developed sunspot of each polarity. From AIA 193 and 94 Å images we identify many clearly discernible coronal loops that connect plage or a sunspot of one polarity to an opposite-­polarity plage region. The AIA 94 Å images show dim regions in the umbrae of the spots. To see which coronal loops are rooted in a dim umbral area, we performed a non-linear force-free field (NLFFF) modeling using photospheric vector magnetic field measurements obtained with the Heliosesmic Magnetic Imager (HMI) onboard SDO. The NLFFF model, validated by comparison of calculated model field lines with observed loops in AIA 193 and 94 Å, specifies the photospheric roots of the model field lines. Some model coronal magnetic field lines arch from the dim umbral area of the positive-polarity sunspot to the dim umbral area of a negative-polarity sunspot. Because these coronal loops are not visible in any of the coronal EUV and X-ray images of the AR, we conclude they are the coolest loops in the AR. This result suggests that the loops connecting opposite polarity umbrae are the least heated because the field in umbrae is so strong that the convective braiding of the field is strongly suppressed.

Height Dependence of Plasma Properties of a Dark Lane and a Cool Loop in a Solar Limb Active Region Observed by Hinode/EIS

NASA Astrophysics Data System (ADS)

Lee, K.; Imada, S.; Moon, Y.; Lee, J.

2013-12-01

We investigate spectral properties of a cool loop and a dark lane over a limb active region on 2007 March 14 by the Hinode/EUV Imaging Spectrometer. The cool loop is clearly seen in the spectral lines formed at the transition region temperature. The dark lane is characterized by an elongated faint structure in coronal spectral lines and rooted on a bright point. We determine their electron densities, Doppler velocities, and non-thermal velocities with height over the limb. We derived electron densities using the density sensitive line pairs of Mg VII, Si X, Fe XII, Fe XIII and Fe XIV spectra. Under the hydrostatic equilibrium and isothermal assumption, we determine their temperatures from the density scale height. Comparing the scale height temperatures to the peak formation temperatures of the spectral lines, we note that the scale height temperature of the cool loop is consistent with a peak formation temperature of the Fe XII and the scale height temperatures of the dark lane from each spectral lines are much lower than their peak formation temperatures. The non-thermal velocity in the cool loop slightly decreases along the loop while that in the dark lane sharply falls off with height. The variation of non-thermal velocity with height in the cool loop and the dark lane is contrast to that in off-limb polar coronal holes which are considered as source of the solar wind. Such a decrease in the non-thermal velocity may be explained by wave damping near the solar surface or turbulence due to magnetic reconnection near the bright point.

Are Complex Magnetic Field Structures Responsible for the Confined X-class Flares in Super Active Region 12192?

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

Zhang, Jun; Li, Ting; Chen, Huadong, E-mail: zjun@nao.cas.cn, E-mail: hdchen@nao.cas.cn

From 2014 October 19 to 27, six X-class flares occurred in super active region (AR) 12192. They were all confined flares and were not followed by coronal mass ejections. To examine the structures of the four flares close to the solar disk center from October 22 to 26, we firstly employ composite triple-time images in each flare process to display the stratified structure of these flare loops. The loop structures of each flare in both the lower (171 Å) and higher (131 Å) temperature channels are complex, e.g., the flare loops rooting at flare ribbons are sheared or twisted (enwound)more » together, and the complex structures were not destroyed during the flares. For the first flare, although the flare loop system appears as a spindle shape, we can estimate its structures from observations, with lengths ranging from 130 to 300 Mm, heights from 65 to 150 Mm, widths at the middle part of the spindle from 40 to 100 Mm, and shear angles from 16° to 90°. Moreover, the flare ribbons display irregular movements, such as the left ribbon fragments of the flare on October 22 sweeping a small region repeatedly, and both ribbons of the flare on October 26 moved along the same direction instead of separating from each other. These irregular movements also imply that the corresponding flare loops are complex, e.g., several sets of flare loops are twisted together. Although previous studies have suggested that the background magnetic fields prevent confined flares from erupting,based on these observations, we suggest that complex flare loop structures may be responsible for these confined flares.« less

Flight Test of the F/A-18 Active Aeroelastic Wing Airplane

NASA Technical Reports Server (NTRS)

Voracek, David

2007-01-01

A viewgraph presentation of flight tests performed on the F/A active aeroelastic wing airplane is shown. The topics include: 1) F/A-18 AAW Airplane; 2) F/A-18 AAW Control Surfaces; 3) Flight Test Background; 4) Roll Control Effectiveness Regions; 5) AAW Design Test Points; 6) AAW Phase I Test Maneuvers; 7) OBES Pitch Doublets; 8) OBES Roll Doublets; 9) AAW Aileron Flexibility; 10) Phase I - Lessons Learned; 11) Control Law Development and Verification & Validation Testing; 12) AAW Phase II RFCS Envelopes; 13) AAW 1-g Phase II Flight Test; 14) Region I - Subsonic 1-g Rolls; 15) Region I - Subsonic 1-g 360 Roll; 16) Region II - Supersonic 1-g Rolls; 17) Region II - Supersonic 1-g 360 Roll; 18) Region III - Subsonic 1-g Rolls; 19) Roll Axis HOS/LOS Comparison Region II - Supersonic (open-loop); 20) Roll Axis HOS/LOS Comparison Region II - Supersonic (closed-loop); 21) AAW Phase II Elevated-g Flight Test; 22) Region I - Subsonic 4-g RPO; and 23) Phase II - Lessons Learned

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

PubMed Central

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

1989-01-01

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

NFκB- and AP-1-mediated DNA looping regulates matrix metalloproteinase-9 transcription in TNF-α-treated human leukemia U937 cells.

PubMed

Chen, Ying-Jung; Chang, Long-Sen

2015-10-01

The aim of this study is to explore the spatial association of critical genomic elements in the effect of TNF-α on matrix metalloproteinase-9 (MMP-9) expression in human leukemia U937 cells. TNF-α up-regulated MMP-9 protein expression and mRNA level in U937 cells, and Akt-mediated-NFκB/p65 activation and JNK-mediated c-Jun activation were proven to be involved in TNF-α-induced MMP-9 up-regulation. Promoter luciferase activity assay revealed that NFκB (nt-600) and AP-1 (nt-79) binding sites were crucial for TNF-α-induced transcription of MMP-9 gene. The results of a chromatin immunoprecipitation assay indicated that TNF-α reduced histone deacetylase-1 (HDAC-1) recruitment but increased p300 (a histone acetyltransferase) recruitment to MMP-9 promoter regions surrounding NFκB and AP-1 binding sites. Consistently, TNF-α increased enrichment of the acetylated histone H3 mark on MMP-9 promoter regions. DNA affinity purification assay revealed that p300 and HDAC1 could bind oligonucleotides containing AP-1/c-Jun and NFκB/p65 binding sites. Chromosome conformation capture assay showed that TNF-α stimulated chromosomal loops in the MMP-9 promoter via NFκB/p65 and AP-1/c-Jun. The p300-associated acetyltransferase activity was crucial for p65/c-Jun-mediated DNA looping, and inhibition of HDAC activity increased the level of DNA looping. Reduction in the level of DNA looping eliminated all TNF-α-stimulated MMP-9 up-regulation. Taken together, our data suggest that p65/c-Jun-mediated DNA looping is involved in TNF-α-induced MMP-9 up-regulation and that the recruitment of p300 or HDAC1 to NFκB and AP-1 binding sites modifies the level of DNA looping. Copyright © 2015 Elsevier B.V. All rights reserved.

Steady State Model for Solar Coronal Loops

NASA Astrophysics Data System (ADS)

Sugiyama, L.; Asgari-Targhi, M.

2017-12-01

Solar coronal loops on the surface of the sun provide background magnetic and plasma structures for the release of a significant amount of the sun's energy, through energetic solar flares and coronal mass ejections and more gradual processes. Understanding their steady states is the first step in understanding loop dynamics. A consistent MHD steady state model, for a curved magnetic flux rope that contains plasma, has been developed[1] for simple coronal loops with both ends anchored in the photosphere. Plasma pressure or current makes the loop unstable to expansion in major radius and must be balanced by external forces, such as the solar gravity. The MHD momentum equation has a well defined small parameter ordering in the loop inverse aspect ratio ɛ=a/Ro (minor/major radius). Different types of common coronal loops fall in different parameter regimes, determined by the relative values of the plasma beta β=po/(Bo2/2μo), the MHD gravity parameter Ĝ≡ga/vA2 (the gravitational acceleration g normalized to the minor radius a and shear Alfvén velocity vA), and ɛ. The largest possible gravity, Ĝ ɛ1β, corresponds to the largest loops because it reduces the plasma density at the top of the loop exponentially compared to its lower ends, reducing the downward gravitational force -ρĜ there. The thin loops that are ubiquitous in solar active regions have ``high'' beta, β ɛ1, for ɛ≃0.02, and fit the predicted model scalings. The thicker loops that can give rise to flares and CMEs have ``low'' beta, β ɛ2. Cool loops, such as solar filaments outside active regions, that have a central pressure lower than that of the surrounding corona would have the strongest stability against radial expansion. The model raises a number of questions about the connection of loops to the photosphere and the force-free nature of the magnetic field there. [1] L. Sugiyama, M. Asgari-Targhi, Phys. Plasmas 24, 022904 (2017).

Decayless low-amplitude kink oscillations: a common phenomenon in the solar corona?

NASA Astrophysics Data System (ADS)

Anfinogentov, S. A.; Nakariakov, V. M.; Nisticò, G.

2015-11-01

Context. We investigate the decayless regime of coronal kink oscillations recently discovered in the Solar Dynamics Observatory (SDO)/AIA data. In contrast to decaying kink oscillations that are excited by impulsive dynamical processes, this type of transverse oscillations is not connected to any external impulsive impact, such as a flare or coronal mass ejection, and does not show any significant decay. Moreover the amplitude of these decayless oscillations is typically lower than that of decaying oscillations. Aims: The aim of this research is to estimate the prevalence of this phenomenon and its characteristic signatures. Methods: We analysed 21 active regions (NOAA 11637-11657) observed in January 2013 in the 171 Å channel of SDO/AIA. For each active region we inspected six hours of observations, constructing time-distance plots for the slits positioned across pronounced bright loops. The oscillatory patterns in time-distance plots were visually identified and the oscillation periods and amplitudes were measured. We also estimated the length of each oscillating loop. Results: Low-amplitude decayless kink oscillations are found to be present in the majority of the analysed active regions. The oscillation periods lie in the range from 1.5 to 10 min. In two active regions with insufficient observation conditions we did not identify any oscillation patterns. The oscillation periods are found to increase with the length of the oscillating loop. Conclusions: The considered type of coronal oscillations is a common phenomenon in the corona. The established dependence of the oscillation period on the loop length is consistent with their interpretation in terms of standing kink waves. Appendix A is available in electronic form at http://www.aanda.org

DIRECT OBSERVATIONS OF TETHER-CUTTING RECONNECTION DURING A MAJOR SOLAR EVENT FROM 2014 FEBRUARY 24 TO 25

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

Chen, Huadong; Zhang, Jun; Yang, Shuhong

2014-12-20

Using multi-wavelength data from the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory, we investigated two successive solar flares, a C5.1 confined flare and an X4.9 ejective flare with a halo coronal mass ejection, in NOAA active region 11990 from 2014 February 24 to 25. Before the confined flare onset, EUV brightening beneath the filament was detected. As the flare began, a twisted helical flux rope (FR) wrapping around the filament moved upward and then stopped, and in the meantime an obvious X-ray source below it was observed. Prior to the ejective X4.9 flare, some pre-existing loop structures inmore » the active region interacted with each other, which produced a brightening region beneath the filament. Meanwhile, a small flaring loop appeared below the interaction region and some new helical lines connecting the far ends of the loop structures were gradually formed and continually added into the former twisted FR. Then, due to the resulting imbalance between the magnetic pressure and tension, the new FR, together with the filament, erupted outward. Our observations coincide well with a tether-cutting model, suggesting that the two flares probably have the same triggering mechanism, i.e., tether-cutting reconnection. To our knowledge, this is the first direct observation of tether-cutting reconnection occurring between pre-existing loops in an active region. In the ejective flare case, the erupting filament exhibited an Ω-like kinked structure and underwent an exponential rise after a slow-rise phase, indicating that the kink instability might be also responsible for the eruption initiation.« less

Closed-loop control of epileptiform activities in a neural population model using a proportional-derivative controller

NASA Astrophysics Data System (ADS)

Wang, Jun-Song; Wang, Mei-Li; Li, Xiao-Li; Ernst, Niebur

2015-03-01

Epilepsy is believed to be caused by a lack of balance between excitation and inhibitation in the brain. A promising strategy for the control of the disease is closed-loop brain stimulation. How to determine the stimulation control parameters for effective and safe treatment protocols remains, however, an unsolved question. To constrain the complex dynamics of the biological brain, we use a neural population model (NPM). We propose that a proportional-derivative (PD) type closed-loop control can successfully suppress epileptiform activities. First, we determine the stability of root loci, which reveals that the dynamical mechanism underlying epilepsy in the NPM is the loss of homeostatic control caused by the lack of balance between excitation and inhibition. Then, we design a PD type closed-loop controller to stabilize the unstable NPM such that the homeostatic equilibriums are maintained; we show that epileptiform activities are successfully suppressed. A graphical approach is employed to determine the stabilizing region of the PD controller in the parameter space, providing a theoretical guideline for the selection of the PD control parameters. Furthermore, we establish the relationship between the control parameters and the model parameters in the form of stabilizing regions to help understand the mechanism of suppressing epileptiform activities in the NPM. Simulations show that the PD-type closed-loop control strategy can effectively suppress epileptiform activities in the NPM. Project supported by the National Natural Science Foundation of China (Grant Nos. 61473208, 61025019, and 91132722), ONR MURI N000141010278, and NIH grant R01EY016281.

Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene.

PubMed

Tan-Wong, Sue Mei; French, Juliet D; Proudfoot, Nicholas J; Brown, Melissa A

2008-04-01

The 85-kb breast cancer-associated gene BRCA1 is an established tumor suppressor gene, but its regulation is poorly understood. We demonstrate by gene conformation analysis in both human cell lines and mouse mammary tissue that gene loops are imposed on BRCA1 between the promoter, introns, and terminator region. Significantly, association between the BRCA1 promoter and terminator regions change upon estrogen stimulation and during lactational development. Loop formation is transcription-dependent, suggesting that transcriptional elongation plays an active role in BRCA1 loop formation. We show that the BRCA1 terminator region can suppress estrogen-induced transcription and so may regulate BRCA1 expression. Significantly, BRCA1 promoter and terminator interactions vary in different breast cancer cell lines, indicating that defects in BRCA1 chromatin structure may contribute to dysregulated expression of BRCA1 seen in breast tumors.

Kinked Loop Stretching Between Two Active Regions

NASA Image and Video Library

2017-07-25

Numerous arches of magnetic field lines danced and swayed above a large active region over about a 30-hour period (July 17-18, 2017). We can also see the magnetic field lines from the large active region reached out and connected with a smaller active region. Those linked lines then strengthened (become brighter), but soon began to develop a kink in them and rather swiftly faded from view. All of this activity is driven by strong magnetic forces associated with the active regions. The images were taken in a wavelength of extreme ultraviolet light. https://photojournal.jpl.nasa.gov/catalog/PIA21838

The Role of the β5-α11 Loop in the Active-Site Dynamics of Acylated Penicillin-Binding Protein A from Mycobacterium tuberculosis

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

Fedarovich, Alena; Nicholas, Robert A.; Davies, Christopher

Penicillin-binding protein A (PBPA) is a class B penicillin-binding protein that is important for cell division in Mycobacterium tuberculosis. We have determined a second crystal structure of PBPA in apo form and compared it with an earlier structure of apoenzyme. Significant structural differences in the active site region are apparent, including increased ordering of a β-hairpin loop and a shift of the SxN active site motif such that it now occupies a position that appears catalytically competent. Using two assays, including one that uses the intrinsic fluorescence of a tryptophan residue, we have also measured the second-order acylation rate constantsmore » for the antibiotics imipenem, penicillin G, and ceftriaxone. Of these, imipenem, which has demonstrable anti-tubercular activity, shows the highest acylation efficiency. Crystal structures of PBPA in complex with the same antibiotics were also determined, and all show conformational differences in the β5–α11 loop near the active site, but these differ for each β-lactam and also for each of the two molecules in the crystallographic asymmetric unit. Overall, these data reveal the β5–α11 loop of PBPA as a flexible region that appears important for acylation and provide further evidence that penicillin-binding proteins in apo form can occupy different conformational states.« less

Velocity Measurements for a Solar Active Region Fan Loop from Hinode/EIS Observations

NASA Astrophysics Data System (ADS)

Young, P. R.; O'Dwyer, B.; Mason, H. E.

2012-01-01

The velocity pattern of a fan loop structure within a solar active region over the temperature range 0.15-1.5 MK is derived using data from the EUV Imaging Spectrometer (EIS) on board the Hinode satellite. The loop is aligned toward the observer's line of sight and shows downflows (redshifts) of around 15 km s-1 up to a temperature of 0.8 MK, but for temperatures of 1.0 MK and above the measured velocity shifts are consistent with no net flow. This velocity result applies over a projected spatial distance of 9 Mm and demonstrates that the cooler, redshifted plasma is physically disconnected from the hotter, stationary plasma. A scenario in which the fan loops consist of at least two groups of "strands"—one cooler and downflowing, the other hotter and stationary—is suggested. The cooler strands may represent a later evolutionary stage of the hotter strands. A density diagnostic of Mg VII was used to show that the electron density at around 0.8 MK falls from 3.2 × 109 cm-3 at the loop base, to 5.0 × 108 cm-3 at a projected height of 15 Mm. A filling factor of 0.2 is found at temperatures close to the formation temperature of Mg VII (0.8 MK), confirming that the cooler, downflowing plasma occupies only a fraction of the apparent loop volume. The fan loop is rooted within a so-called outflow region that displays low intensity and blueshifts of up to 25 km s-1 in Fe XII λ195.12 (formed at 1.5 MK), in contrast to the loop's redshifts of 15 km s-1 at 0.8 MK. A new technique for obtaining an absolute wavelength calibration for the EIS instrument is presented and an instrumental effect, possibly related to a distorted point-spread function, that affects velocity measurements is identified.

VELOCITY MEASUREMENTS FOR A SOLAR ACTIVE REGION FAN LOOP FROM HINODE/EIS OBSERVATIONS

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

Young, P. R.; O'Dwyer, B.; Mason, H. E.

2012-01-01

The velocity pattern of a fan loop structure within a solar active region over the temperature range 0.15-1.5 MK is derived using data from the EUV Imaging Spectrometer (EIS) on board the Hinode satellite. The loop is aligned toward the observer's line of sight and shows downflows (redshifts) of around 15 km s{sup -1} up to a temperature of 0.8 MK, but for temperatures of 1.0 MK and above the measured velocity shifts are consistent with no net flow. This velocity result applies over a projected spatial distance of 9 Mm and demonstrates that the cooler, redshifted plasma is physicallymore » disconnected from the hotter, stationary plasma. A scenario in which the fan loops consist of at least two groups of 'strands'-one cooler and downflowing, the other hotter and stationary-is suggested. The cooler strands may represent a later evolutionary stage of the hotter strands. A density diagnostic of Mg VII was used to show that the electron density at around 0.8 MK falls from 3.2 Multiplication-Sign 10{sup 9} cm{sup -3} at the loop base, to 5.0 Multiplication-Sign 10{sup 8} cm{sup -3} at a projected height of 15 Mm. A filling factor of 0.2 is found at temperatures close to the formation temperature of Mg VII (0.8 MK), confirming that the cooler, downflowing plasma occupies only a fraction of the apparent loop volume. The fan loop is rooted within a so-called outflow region that displays low intensity and blueshifts of up to 25 km s{sup -1} in Fe XII {lambda}195.12 (formed at 1.5 MK), in contrast to the loop's redshifts of 15 km s{sup -1} at 0.8 MK. A new technique for obtaining an absolute wavelength calibration for the EIS instrument is presented and an instrumental effect, possibly related to a distorted point-spread function, that affects velocity measurements is identified.« less

A novel actin binding site of myosin required for effective muscle contraction.

PubMed

Várkuti, Boglárka H; Yang, Zhenhui; Kintses, Bálint; Erdélyi, Péter; Bárdos-Nagy, Irén; Kovács, Attila L; Hári, Péter; Kellermayer, Miklós; Vellai, Tibor; Málnási-Csizmadia, András

2012-02-12

F-actin serves as a track for myosin's motor functions and activates its ATPase activity by several orders of magnitude, enabling actomyosin to produce effective force against load. Although actin activation is a ubiquitous property of all myosin isoforms, the molecular mechanism and physiological role of this activation are unclear. Here we describe a conserved actin-binding region of myosin named the 'activation loop', which interacts with the N-terminal segment of actin. We demonstrate by biochemical, biophysical and in vivo approaches using transgenic Caenorhabditis elegans strains that the interaction between the activation loop and actin accelerates the movement of the relay, stimulating myosin's ATPase activity. This interaction results in efficient force generation, but it is not essential for the unloaded motility. We conclude that the binding of actin to myosin's activation loop specifically increases the ratio of mechanically productive to futile myosin heads, leading to efficient muscle contraction.

The evolution of active region loop plasma

NASA Technical Reports Server (NTRS)

Krall, K. R.; Antiochos, S. K.

1980-01-01

The adjustment of coronal active-region loops to changes in their heating rate is investigated numerically. The one-dimensional hydrodynamic equations are solved subject to boundary conditions in which heat flux-induced mass exchange between coronal and chromospheric components is allowed. The calculated evolution of physical parameters suggests that (1) mass supplied during chromospheric evaporation is much more effective in moderating coronal temperature excursions than when downward heat flux is dissipated by a static chromosphere, and (2) the method by which the chromosphere responds to changing coronal conditions can significantly influence coronal readjustment time scales. Observations are cited which illustrate the range of possible fluctuations in the heating rates.

Magnetic activity in the Galactic Centre region - fast downflows along rising magnetic loops

NASA Astrophysics Data System (ADS)

Kakiuchi, Kensuke; Suzuki, Takeru K.; Fukui, Yasuo; Torii, Kazufumi; Enokiya, Rei; Machida, Mami; Matsumoto, Ryoji

2018-06-01

We studied roles of the magnetic field on the gas dynamics in the Galactic bulge by a three-dimensional global magnetohydrodynamical simulation data, particularly focusing on vertical flows that are ubiquitously excited by magnetic activity. In local regions where the magnetic field is stronger, it is frequently seen that fast downflows slide along inclined magnetic field lines that are associated with buoyantly rising magnetic loops. The vertical velocity of these downflows reaches ˜100 km s-1 near the footpoint of the loops by the gravitational acceleration towards the Galactic plane. The two footpoints of rising magnetic loops are generally located at different radial locations and the field lines are deformed by the differential rotation. The angular momentum is transported along the field lines, and the radial force balance breaks down. As a result, a fast downflow is often observed only at the one footpoint located at the inner radial position. The fast downflow compresses the gas to form a dense region near the footpoint, which will be important in star formation afterwards. Furthermore, the horizontal components of the velocity are also fast near the footpoint because the downflow is accelerated along the magnetic sliding slope. As a result, the high-velocity flow creates various characteristic features in a simulated position-velocity diagram, depending on the viewing angle.

Structural basis of arrestin-3 activation and signaling

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

Chen, Qiuyan; Perry, Nicole A.; Vishnivetskiy, Sergey A.

A unique aspect of arrestin-3 is its ability to support both receptor-dependent and receptor-independent signaling. Here, we show that inositol hexakisphosphate (IP6) is a non-receptor activator of arrestin-3 and report the structure of IP6-activated arrestin-3 at 2.4-Å resolution. IP6-activated arrestin-3 exhibits an inter-domain twist and a displaced C-tail, hallmarks of active arrestin. IP6 binds to the arrestin phosphate sensor, and is stabilized by trimerization. Analysis of the trimerization surface, which is also the receptor-binding surface, suggests a feature called the finger loop as a key region of the activation sensor. We show that finger loop helicity and flexibility may underliemore » coupling to hundreds of diverse receptors and also promote arrestin-3 activation by IP6. Importantly, we show that effector-binding sites on arrestins have distinct conformations in the basal and activated states, acting as switch regions. These switch regions may work with the inter-domain twist to initiate and direct arrestin-mediated signaling.« less

SDO/AIA AND HINODE/EIS OBSERVATIONS OF INTERACTION BETWEEN AN EUV WAVE AND ACTIVE REGION LOOPS

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

Yang, Liheng; Zhang, Jun; Li, Ting

2013-09-20

We present detailed analysis of an extreme-ultraviolet (EUV) wave and its interaction with active region (AR) loops observed by the Solar Dynamics Observatory/Atmospheric Imaging Assembly and the Hinode EUV Imaging Spectrometer (EIS). This wave was initiated from AR 11261 on 2011 August 4 and propagated at velocities of 430-910 km s{sup –1}. It was observed to traverse another AR and cross over a filament channel on its path. The EUV wave perturbed neighboring AR loops and excited a disturbance that propagated toward the footpoints of these loops. EIS observations of AR loops revealed that at the time of the wavemore » transit, the original redshift increased by about 3 km s{sup –1}, while the original blueshift decreased slightly. After the wave transit, these changes were reversed. When the EUV wave arrived at the boundary of a polar coronal hole, two reflected waves were successively produced and part of them propagated above the solar limb. The first reflected wave above the solar limb encountered a large-scale loop system on its path, and a secondary wave rapidly emerged 144 Mm ahead of it at a higher speed. These findings can be explained in the framework of a fast-mode magnetosonic wave interpretation for EUV waves, in which observed EUV waves are generated by expanding coronal mass ejections.« less

Changes in regional and temporal patterns of activity associated with aging during the performance of a lexical set-shifting task.

PubMed

Martins, Ruben; Simard, France; Provost, Jean-Sebastien; Monchi, Oury

2012-06-01

Some older individuals seem to use compensatory mechanisms to maintain high-level performance when submitted to cognitive tasks. However, whether and how these mechanisms affect fronto-striatal activity has never been explored. The purpose of this study was to investigate how aging affects brain patterns during the performance of a lexical analog of the Wisconsin Card Sorting Task, which has been shown to strongly depend on fronto-striatal activity. In the present study, both younger and older individuals revealed significant fronto-striatal loop activity associated with planning and execution of set-shifts, though age-related striatal activity reduction was observed. Most importantly, while the younger group showed the involvement of a "cognitive loop" during the receiving negative feedback period (which indicates that a set-shift will be required to perform the following trial) and the involvement of a "motor loop" during the matching after negative feedback period (when the set-shift must be performed), older participants showed significant activation of both loops during the matching after negative feedback period only. These findings are in agreement with the "load-shift" model postulated by Velanova et al. (Velanova K, Lustig C, Jacoby LL, Buckner RL. 2007. Evidence for frontally mediated controlled processing differences in older adults. Cereb Cortex. 17:1033-1046.) and indicate that the model is not limited to memory retrieval but also applies to executive processes relying on fronto-striatal regions.

The origin of morphological asymmetries in bipolar active regions. [magnetic field in solar convective envelope

NASA Technical Reports Server (NTRS)

Fan, Y.; Fisher, G. H.; Deluca, E. E.

1993-01-01

A series of 3D numerical simulations was carried out to examine the dynamical evolution of emerging flux loops in the solar convective envelope. The innermost portions of the loops are anchored beneath the base of the convective zone by the subadiabatic temperature gradient of the underlying overshoot region. It is found that, as the emerging loops approach the photosphere, the magnetic field strength of the leading side of each rising loop is about twice as large as that of the following side at the same depth. The evacuation of plasma out of the leading side of the rising loop results in an enhanced magnetic field strength there compared with the following side. It is argued that this result provides a natural explanation for the fact that the preceding (leading) polarity tends to have a less organized and more fragmented appearance, and that the preceding spots tend to be larger in area and fewer in number, and have a longer lifetime than the following spots.

Replication stress induces accumulation of FANCD2 at central region of large fragile genes

PubMed Central

Okamoto, Yusuke; Iwasaki, Watal M; Kugou, Kazuto; Takahashi, Kazuki K; Oda, Arisa; Sato, Koichi; Kobayashi, Wataru; Kawai, Hidehiko; Sakasai, Ryo; Takaori-Kondo, Akifumi; Yamamoto, Takashi; Kanemaki, Masato T; Taoka, Masato; Isobe, Toshiaki; Kurumizaka, Hitoshi; Innan, Hideki; Ohta, Kunihiro; Ishiai, Masamichi; Takata, Minoru

2018-01-01

Abstract During mild replication stress provoked by low dose aphidicolin (APH) treatment, the key Fanconi anemia protein FANCD2 accumulates on common fragile sites, observed as sister foci, and protects genome stability. To gain further insights into FANCD2 function and its regulatory mechanisms, we examined the genome-wide chromatin localization of FANCD2 in this setting by ChIP-seq analysis. We found that FANCD2 mostly accumulates in the central regions of a set of large transcribed genes that were extensively overlapped with known CFS. Consistent with previous studies, we found that this FANCD2 retention is R-loop-dependent. However, FANCD2 monoubiquitination and RPA foci formation were still induced in cells depleted of R-loops. Interestingly, we detected increased Proximal Ligation Assay dots between FANCD2 and R-loops following APH treatment, which was suppressed by transcriptional inhibition. Collectively, our data suggested that R-loops are required to retain FANCD2 in chromatin at the middle intronic region of large genes, while the replication stress-induced upstream events leading to the FA pathway activation are not triggered by R-loops. PMID:29394375

LARGE-SCALE CONTRACTION AND SUBSEQUENT DISRUPTION OF CORONAL LOOPS DURING VARIOUS PHASES OF THE M6.2 FLARE ASSOCIATED WITH THE CONFINED FLUX ROPE ERUPTION

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

Kushwaha, Upendra; Joshi, Bhuwan; Moon, Yong-Jae

We investigate evolutionary phases of an M6.2 flare and the associated confined eruption of a prominence. The pre-flare phase exhibits spectacular large-scale contraction of overlying extreme ultraviolet (EUV) coronal loops during which the loop system was subjected to an altitude decrease of ∼20 Mm (40% of the initial height) for an extended span of ∼30 minutes. This contraction phase is accompanied by sequential EUV brightenings associated with hard X-ray (HXR; up to 25 keV) and microwave (MW) sources from low-lying loops in the core region which together with X-ray spectra indicate strong localized heating in the source region before themore » filament activation. With the onset of the flare’s impulsive phase, we detect HXR and MW sources that exhibit intricate temporal and spatial evolution in relation to the fast rise of the prominence. Following the flare maximum, the filament eruption slowed down and subsequently became confined within the large overlying active region loops. During the confinement process of the erupting prominence, we detect MW emission from the extended coronal region with multiple emission centroids, which likely represent emission from hot blobs of plasma formed after the collapse of the expanding flux rope and entailing prominence material. RHESSI spectroscopy reveals high plasma temperature (∼30 MK) and substantial non-thermal characteristics (δ ∼ 5) during the impulsive phase of the flare. The time evolution of thermal energy exhibits a good correspondence with the variations in cumulative non-thermal energy, which suggests that the energy of accelerated particles is efficiently converted to hot flare plasma, implying an effective validation of the Neupert effect.« less

Observation and Modeling of Chromospheric Evaporation in a Coronal Loop Related to Active Region Transient Brightening

NASA Astrophysics Data System (ADS)

Gupta, G. R.; Sarkar, Aveek; Tripathi, Durgesh

2018-04-01

Using the observations recorded by the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory and the Interface Region Imaging Spectrograph (IRIS) and the Extreme-ultraviolet Imaging Spectrometer and X-Ray Telescope both on board Hinode, we present evidence of chromospheric evaporation in a coronal loop after the occurrence of two active region transient brightenings (ARTBs) at the two footpoints. The chromospheric evaporation started nearly simultaneously in all of the three hot channels of AIA 131, 94, and 335 Å and was observed to be temperature dependent, being fastest in the highest temperature channel. The whole loop became fully brightened following the ARTBs after ≈25 s in 131 Å, ≈40 s in 94 Å, and ≈6.5 minutes in 335 Å. The differential emission measurements at the two footpoints (i.e., of two ARTBs) and at the loop top suggest that the plasma attained a maximum temperature of ∼10 MK at all these locations. The spectroscopic observations from IRIS revealed the presence of redshifted emission of ∼20 km s‑1 in cooler lines like C II and Si IV during the ARTBs that was cotemporal with the evaporation flow at the footpoint of the loop. During the ARTBs, the line width of C II and Si IV increased nearly by a factor of two during the peak emission. Moreover, enhancement in the line width preceded that in the Doppler shift, which again preceded enhancement in the intensity. The observed results were qualitatively reproduced by 1D hydrodynamic simulations, where energy was deposited at both of the footpoints of a monolithic coronal loop that mimicked the ARTBs identified in the observations.

Characteristics, location and origin of flare activity in a complex active region

NASA Technical Reports Server (NTRS)

Machado, M. E.; Gary, G. A.; Hagyard, M. J.; Hernandez, A. M.; Rovira, M. G.

1986-01-01

The observational characteristics of series of multiple-loop flares from a complex active region are summarized. The location of the highest observed photospheric magnetic shear is found to be the commonly observed site of flare onset, but not, in many cases, the magnetic region where the largest time-integrated energy release is observed. The observations thus reveal a consistent pattern of energy-release processes related to the magnetic-field topology.

Spectroscopic Study of a Dark Lane and a Cool Loop in a Solar Limb Active Region by Hinode/EIS

NASA Astrophysics Data System (ADS)

Lee, K.; Imada, S.; Moon, Y.; Lee, J.

2012-12-01

We investigate a cool loop and a dark lane over a limb active region on 2007 March 14 by the Hinode/EUV Imaging Spectrometer (EIS). The cool loop is clearly seen in the EIS spectral lines formed at the transition region temperature (log T = 5.8). The dark lane is characterized by an elongated faint structure in coronal spectral lines (log T = 5.8 - 6.1) and rooted on a bright point. We examine their electron densities, Doppler velocities, and non-thermal velocities as a function of distance from the limb using the spectral lines formed at different temperatures (log T = 5.4 - 6.4). The electron densities of the cool loop and the dark lane are derived from the density sensitive line pairs of Mg VII, Fe XII, and Fe XIV spectra. Under the hydrostatic equilibrium and isothermal assumption, we determine their temperatures from the density scale height. Comparing the scale height temperatures to the peak formation temperatures of the spectral lines, we note that the scale height temperature of the cool loop is consistent with a peak formation temperature of the Mg VII (log T = 5.8) and the scale height temperature of the dark lane is close to a peak formation temperature of the Fe XII and Fe XIII (log T = 6.1 - 6.2). It is interesting to note that the structures of the cool loop and the dark lane are most visible in these temperature lines. While the non-thermal velocity in the cool loop slightly decreases (less than 7 km {s-1}) along the loop, that in the dark lane sharply falls off with height. The variation of non-thermal velocity with height in the cool loop and the dark lane is contrast to that in off-limb polar coronal holes which are considered as source of the fast solar wind. Such a decrease in the non-thermal velocity may be explained by wave damping near the solar surface or turbulence due to magnetic reconnection near the bright point.

The elusive role of the SPRY2 domain in RyR1

PubMed Central

Willemse, Hermia; Mirza, Shamaruh; Gallant, Esther M; Board, Philip G

2011-01-01

The second of three SPRY domains (SPRY2, S1085-V1208) located in the skeletal muscle ryanodine receptor (RyR1) is contained within regions of RyR1 that influence EC coupling and bind to imperatoxin A, a toxin probe of RyR1 channel gating. We examined the binding of the F loop (P1107-A1121) in SPRY2 to the ASI/basic region in RyR1 (T3471-G3500, containing both alternatively spliced (ASI) residues and neighboring basic amino acids). We then investigated the possible influence of this interaction on excitation contraction (EC) coupling. A peptide with the F loop sequence and an antibody to the SPRY2 domain each enhanced RyR1 activity at low concentrations and inhibited at higher concentrations. A peptide containing the ASI/basic sequence bound to SPRY2 and binding decreased ∼10-fold following mutation or structural disruption of the basic residues. Binding was abolished by mutation of three critical acidic F loop residues. Together these results suggest that the ASI/basic and SPRY2 domains interact in an F loop regulatory module. Although a region that includes the SPRY2 domain influences EC coupling, as does the ASI/basic region, Ca2+ release during ligand- and depolarization-induced RyR1 activation were not altered by mutation of the three critical F loop residues following expression of mutant RyR1 in RyR1-null myotubes. Therefore the electrostatic regulatory interaction between the SPRY2 F loop residues (that bind to imperatoxin A) and the ASI/basic residues of RyR1 does not influence bi-directional DHPR-RyR1 signaling during skeletal EC coupling, possibly because the interaction is interrupted by the influence of factors present in intact muscle cells. PMID:21239886

Ballet of Loops

NASA Image and Video Library

2018-06-11

Giant, bright coronal loops trace out the magnetic field lines above an active region from June 4-6, 2018. The wavelength of extreme ultraviolet light shown here is emitted by ionized iron travelling along the field lines, super-heated to approximately 1 million degrees K. Coronal loops were not seen in this level of detail until the Solar Dynamics Observatory was launched in 2010 and came online, giving solar scientists new data with which to study the Sun and its processes. https://photojournal.jpl.nasa.gov/catalog/PIA22508

Suppression of heating of coronal loops rooted in opposite polarity sunspot umbrae

NASA Astrophysics Data System (ADS)

Tiwari, Sanjiv K.; Thalmann, Julia K.; Moore, Ronald L.; Panesar, Navdeep; Winebarger, Amy R.

2016-05-01

EUV observations of active region (AR) coronae reveal the presence of loops at different temperatures. To understand the mechanisms that result in hotter or cooler loops, we study a typical bipolar AR, near solar disk center, which has moderate overall magnetic twist and at least one fully developed sunspot of each polarity. From AIA 193 and 94 A images we identify many clearly discernible coronal loops that connect plage or a sunspot of one polarity to an opposite-polarity plage region. The AIA 94 A images show dim regions in the umbrae of the spots. To see which coronal loops are rooted in a dim umbral area, we performed a non-linear force-free field (NLFFF) modeling using photospheric vector magnetic field measurements obtained with the HMI onboard SDO. After validation of the NLFFF model by comparison of calculated model field lines and observed loops in AIA 193 and 94, we specify the photospheric roots of the model field lines. The model field then shows the coronal magnetic loops that arch from the dim umbral areas of the opposite polarity sunspots. Because these coronal loops are not visible in any of the coronal EUV and X-ray images of the AR, we conclude they are the coolest loops in the AR. This result suggests that the loops connecting opposite polarity umbrae are the least heated because the field in umbrae is so strong that the convective braiding of the field is strongly suppressed.We hypothesize that the convective freedom at the feet of a coronal loop, together with the strength of the field in the body of the loop, determines the strength of the heating. In particular, we expect the hottest coronal loops to have one foot in an umbra and the other foot in opposite-polarity penumbra or plage (coronal moss), the areas of strong field in which convection is not as strongly suppressed as in umbra. Many transient, outstandingly bright, loops in the AIA 94 movie of the AR do have this expected rooting pattern. We will also present another example of AR in which we find a similar rooting pattern of coronal loops.

Activation of Latent Dihydroorotase from Aquifex aeolicus by Pressure*

PubMed Central

Hervé, Guy; Evans, Hedeel Guy; Fernado, Roshini; Patel, Chandni; Hachem, Fatme; Evans, David R.

2017-01-01

Elevated hydrostatic pressure was used to probe conformational changes of Aquifex aeolicus dihydroorotase (DHO), which catalyzes the third step in de novo pyrimidine biosynthesis. The isolated protein, a 45-kDa monomer, lacks catalytic activity but becomes active upon formation of a dodecameric complex with aspartate transcarbamoylase (ATC). X-ray crystallographic studies of the isolated DHO and of the complex showed that association induces several major conformational changes in the DHO structure. In the isolated DHO, a flexible loop occludes the active site blocking the access of substrates. The loop is mostly disordered but is tethered to the active site region by several electrostatic and hydrogen bonds. This loop becomes ordered and is displaced from the active site upon formation of DHO-ATC complex. The application of pressure to the complex causes its time-dependent dissociation and the loss of both DHO and ATC activities. Pressure induced irreversible dissociation of the obligate ATC trimer, and as a consequence the DHO is also inactivated. However, moderate hydrostatic pressure applied to the isolated DHO subunit mimics the complex formation and reversibly activates the isolated subunit in the absence of ATC, suggesting that the loop has been displaced from the active site. This effect of pressure is explained by the negative volume change associated with the disruption of ionic interactions and exposure of ionized amino acids to the solvent (electrostriction). The interpretation that the loop is relocated by pressure was validated by site-directed mutagenesis and by inhibition by small peptides that mimic the loop residues. PMID:27746403

STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF CIRCULAR PERMUTATION ON THE ACTIVE SITE OF OLD YELLOW ENZYME.

PubMed

Daugherty, Ashley B; Horton, John R; Cheng, Xiaodong; Lutz, Stefan

2015-02-06

Circular permutation of the NADPH-dependent oxidoreductase Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme's catalytic performance. Termini relocation into four regions of the protein (sectors I-IV) near the active site has proven effective in altering enzyme function. To better understand the structural consequences and rationalize the observed functional gains in these OYE1 variants, we selected representatives from sectors I-III for further characterization by biophysical methods and X-ray crystallography. These investigations not only show trends in enzyme stability and quaternary structure as a function of termini location, but also provide a possible explanation for the catalytic gains in our top-performing OYE variant (new N-terminus at residue 303; sector III). Crystallographic analysis indicates that termini relocation into sector III affects the loop β6 region (amino acid positions: 290-310) of OYE1 which forms a lid over the active site. Peptide backbone cleavage greatly enhances local flexibility, effectively converting the loop into a tether and consequently increasing the environmental exposure of the active site. Interestingly, such active site remodeling does not negatively impact the enzyme's activity and stereoselectivity, nor does it perturb the conformation of other key active site residues with the exception of Y375. These observations were confirmed in truncation experiments, deleting all residues of the loop β6 region in our OYE variant. Intrigued by the finding that circular permutation leaves most of the key catalytic residues unchanged, we also tested OYE permutants for possible additive or synergistic effects of amino acid substitutions. Distinct functional changes in these OYE variants were detected upon mutations at W116, known in native OYE1 to cause inversion of diastereo-selectivity for ( S )-carvone reduction. Our findings demonstrate the contribution of loop β6 toward determining the stereoselectivity of OYE1, an important insight for future OYE engineering efforts.

Structural and Functional Consequences of Circular Permutation on the Active Site of Old Yellow Enzyme

DOE PAGES

Daugherty, Ashley B.; Horton, John R.; Cheng, Xiaodong; ...

2014-12-09

Circular permutation of the NADPH-dependent oxidoreductase Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme’s catalytic performance. Termini relocation into four regions of the protein (sectors I–IV) near the active site has proven effective in altering enzyme function. To better understand the structural consequences and rationalize the observed functional gains in these OYE1 variants, we selected representatives from sectors I–III for further characterization by biophysical methods and X-ray crystallography. These investigations not only show trends in enzyme stability and quaternary structure as a function of termini location but also provide a possible explanation for the catalytic gainsmore » in our top-performing OYE variant (new N-terminus at residue 303; sector III). Crystallographic analysis indicates that termini relocation into sector III affects the loop β6 region (amino acid positions: 290–310) of OYE1, which forms a lid over the active site. Peptide backbone cleavage greatly enhances local flexibility, effectively converting the loop into a tether and consequently increasing the environmental exposure of the active site. Interestingly, such an active site remodeling does not negatively impact the enzyme’s activity and stereoselectivity; neither does it perturb the conformation of other key active site residues with the exception of Y375. These observations were confirmed in truncation experiments, deleting all residues of the loop β6 region in our OYE variant. Intrigued by the finding that circular permutation leaves most of the key catalytic residues unchanged, we also tested OYE permutants for possible additive or synergistic effects of amino acid substitutions. Distinct functional changes in these OYE variants were detected upon mutations at W116, known in native OYE1 to cause inversion of diastereoselectivity for (S)-carvone reduction. In conclusion, our findings demonstrate the contribution of loop β6 toward determining the stereoselectivity of OYE1, an important insight for future OYE engineering efforts.« less

Spatial structure and temporal development of a solar X-ray flare observed from Skylab on June 15, 1973

NASA Technical Reports Server (NTRS)

Pallavicini, R.; Vaiana, G. S.; Kahler, S. W.; Krieger, A. S.

1975-01-01

Morphological and quantitative analyses are presented of a 1B solar flare that was observed with high spatial and temporal resolution by the S-054 grazing-incidence X-ray telescope aboard Skylab. It is found that the flare had the configuration of a compact region with a characteristic size of the order of 30 arcsec at the intensity peak, the interior of the region appeared to be highly structured and to consist of temporally changing complex loop systems, brightening over an extended part of the active region preceded the flare onset, and the impulsive phase was marked by rapid brightening in the loop structures. The X-ray photographs also indicate that the X-ray emission was centered over the neutral line of the longitudinal magnetic field, loop systems formed at successively increasing heights during the decay phase, and different regions of the flare had distinctly different light curves. The flux profiles for the different regions are shown to suggest continued heating during the decay phase. It is concluded that flare models should be based on a multiplicity of volumes ordered in loops of successively larger scale lengths and heights rather than on a single point of energy release and deposition.

Simulations of Solar Jets Confined by Coronal Loops

NASA Technical Reports Server (NTRS)

Wyper, P. F.; De Vore, C. R.

2016-01-01

Coronal jets are collimated, dynamic events that occur over a broad range of spatial scales in the solar corona. In the open magnetic field of coronal holes, jets form quasi-radial spires that can extend far out into the heliosphere, while in closed-field regions the jet outflows are confined to the corona. We explore the application of the embedded-bipole model to jets occurring in closed coronal loops. In this model, magnetic free energy is injected slowly by footpoint motions that introduce twist within the closed dome of the jet source region, and is released rapidly by the onset of an ideal kink-like instability. Two length scales characterize the system: the width (N) of the jet source region and the footpoint separation (L) of the coronal loop that envelops the jet source. We find that both the conditions for initiation and the subsequent dynamics are highly sensitive to the ratio L/N. The longest-lasting and most energetic jets occur along long coronal loops with large L/N ratios, and share many of the features of open-field jets, while smaller L/N ratios produce shorter-duration, less energetic jets that are affected by reflections from the far-loop footpoint. We quantify the transition between these behaviors and show that our model replicates key qualitative and quantitative aspects of both quiet Sun and active-region loop jets. We also find that there connection between the closed dome and surrounding coronal loop is very extensive: the cumulative reconnected flux at least matches the total flux beneath the dome for small L/N, and is more than double that value for large L/N.

SIMULATIONS OF SOLAR JETS CONFINED BY CORONAL LOOPS

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

Wyper, P. F.; DeVore, C. R., E-mail: peter.f.wyper@nasa.gov, E-mail: c.richard.devore@nasa.gov

Coronal jets are collimated, dynamic events that occur over a broad range of spatial scales in the solar corona. In the open magnetic field of coronal holes, jets form quasi-radial spires that can extend far out into the heliosphere, while in closed-field regions the jet outflows are confined to the corona. We explore the application of the embedded-bipole model to jets occurring in closed coronal loops. In this model, magnetic free energy is injected slowly by footpoint motions that introduce twist within the closed dome of the jet source region, and is released rapidly by the onset of an idealmore » kink-like instability. Two length scales characterize the system: the width (N) of the jet source region and the footpoint separation (L) of the coronal loop that envelops the jet source. We find that both the conditions for initiation and the subsequent dynamics are highly sensitive to the ratio L/N. The longest-lasting and most energetic jets occur along long coronal loops with large L/N ratios, and share many of the features of open-field jets, while smaller L/N ratios produce shorter-duration, less energetic jets that are affected by reflections from the far-loop footpoint. We quantify the transition between these behaviors and show that our model replicates key qualitative and quantitative aspects of both quiet Sun and active-region loop jets. We also find that the reconnection between the closed dome and surrounding coronal loop is very extensive: the cumulative reconnected flux at least matches the total flux beneath the dome for small L/N, and is more than double that value for large L/N.« less

Evidence for magnetic energy storage in coronal active regions

NASA Technical Reports Server (NTRS)

Krieger, A. S.; De Feiter, L. D.; Vaiana, G. S.

1976-01-01

Examination of X-ray images obtained by the S-054 X-ray spectrographic telescope on Skylab shows the presence of some atypical X-ray-emitting coronal structures in active regions which are not consistent with potential extrapolations of photospheric magnetic fields. Analysis of the observed temporal changes in the X-ray-emitting active-region structures demonstrates that the majority of these consist of brightness changes representing temperature (and perhaps density) variations of the material in the loops.

Active Regions' Magnetic Connection

NASA Image and Video Library

2017-05-22

Several bright bands of plasma connect from one active region to another, even though they are tens of thousands of miles away from each other (May 17-18, 2017). Active regions are, by their nature, strong magnetic areas with north and south poles. The plasma consists of charged particles that stream along the magnetic field lines between these two regions. These connecting lines are clearly visible in this wavelength of extreme ultraviolet light. Other loops and strands of bright plasma can be seen rising up and out of smaller active regions as well. The video covers about one day's worth of activity. Movies are available at https://photojournal.jpl.nasa.gov/catalog/PIA21638

Effect of T- and C-loop mutations on the Herbaspirillum seropedicae GlnB protein in nitrogen signalling.

PubMed

Bonatto, Ana C; Souza, Emanuel M; Pedrosa, Fábio O; Yates, M Geoffrey; Benelli, Elaine M

2005-01-01

Proteins of the PII family are found in species of all kingdoms. Although these proteins usually share high identity, their functions are specific to the different organisms. Comparison of structural data from Escherichia coli GlnB and GlnK and Herbaspirillum seropedicae GlnB showed that the T-loop and C-terminus were variable regions. To evaluate the role of these regions in signal transduction by the H. seropedicae GlnB protein, four mutants were constructed: Y51F, G108A/P109a, G108W and Q3R/T5A. The activities of the native and mutated proteins were assayed in an E. coli background constitutively expressing the Klebsiella pneumoniae nifLA operon. The results suggested that the T-loop and C-terminus regions of H. seropedicae GlnB are involved in nitrogen signal transduction.

Evidence of suppressed heating of coronal loops rooted in opposite polarity sunspot umbrae

NASA Astrophysics Data System (ADS)

Tiwari, Sanjiv K.; Thalmann, Julia K.; Winebarger, Amy R.; Panesar, Navdeep K.; Moore, Ronald

2015-04-01

Observations of active region (AR) coronae in different EUV wavelengths reveal the presence of various loops at different temperatures. To understand the mechanisms that result in hotter or cooler loops, we study a typical bipolar AR, near solar disk center, which has moderate overall magnetic twist and at least one fully developed sunspot of each polarity. From AIA 193 and 94 A images we identify many clearly discernible coronal loops that connect opposite-polarity plage or a sunspot to a opposite-polarity plage region. The AIA 94 A images show dim regions in the umbrae of the spots. To see which coronal loops are rooted in a dim umbral area, we performed a non-linear force-free field (NLFFF) modeling using photospheric vector magnetic field measurements obtained with the Heliosesmic Magnetic Imager (HMI) onboard SDO. After validation of the NLFFF model by comparison of calculated model field lines and observed loops in AIA 193 and 94 A, we specify the photospheric roots of the model field lines. The model field then shows the coronal magnetic loops that arch from the dim umbral area of the positive-polarity sunspot to the dim umbral area of a negative-polarity sunspot. Because these coronal loops are not visible in any of the coronal EUV and X-ray images of the AR, we conclude they are the coolest loops in the AR. This result suggests that the loops connecting opposite polarity umbrae are the least heated because the field in umbrae is so strong that the convective braiding of the field is strongly suppressed.From this result, we further hypothesize that the convective freedom at the feet of a coronal loop, together with the strength of the field in the body of the loop, determines the strength of the heating. In particular, we expect the hottest coronal loops to have one foot in an umbra and the other foot in opposite-polarity penumbra or plage (coronal moss), the areas of strong field in which convection is not as strongly suppressed as in umbrae. Many transient, outstandingly bright, loops in the AIA 94 A movie of the AR do have this expected rooting pattern.

Conformation-selective inhibitors reveal differences in the activation and phosphate-binding loops of the tyrosine kinases Abl and Src

PubMed Central

Hari, Sanjay B.; Perera, B. Gayani K.; Ranjitkar, Pratistha; Seeliger, Markus A.; Maly, Dustin J.

2013-01-01

Over the last decade, an increasingly diverse array of potent and selective inhibitors that target the ATP-binding sites of protein kinases have been developed. Many of these inhibitors, like the clinically approved drug imatinib (Gleevec), stabilize a specific catalytically inactive ATP-binding site conformation of their kinases targets. Imatinib is notable in that it is highly selective for its kinase target, Abl, over other closely-related tyrosine kinases, like Src. In addition, imatinib is highly sensitive to the phosphorylation state of Abl's activation loop, which is believed to be a general characteristic of all inhibitors that stabilize a similar inactive ATP-binding site conformation. In this report, we perform a systematic analysis of a diverse series of ATP-competitive inhibitors that stabilize a similar inactive ATP-binding site conformation as imatinib with the tyrosine kinases Src and Abl. In contrast to imatinib, many of these inhibitors have very similar potencies against Src and Abl. Furthermore, only a subset of this class of inhibitors is sensitive to the phosphorylation state of the activation loop of these kinases. In attempting to explain this observation, we have uncovered an unexpected correlation between Abl's activation loop and another flexible active site feature, called the phosphate-binding loop (p-loop). These studies shed light on how imatinib is able to obtain its high target selectivity and reveal how the conformational preference of flexible active site regions can vary between closely related kinases. PMID:24106839

TRACE Images of the Solar Chromosphere, Transition Region, and Low Corona at High Cadence and High Spatial Resolution

NASA Astrophysics Data System (ADS)

Tarbell, T. D.; Handy, B. N.; Judge, P. G.

1999-05-01

We present TRACE images and movies showing C IV emission (transition region at 80,000 degrees) and UV continuum (temperature minimum region) of quiet and active regions. TRACE images using the 1550, 1600, and 1700 Angstroms filters can be combined to estimate the total emission in the C IV 1548 and 1550 lines and the UV continuum. These are supplemented in different observations with MDI magnetograms, TRACE 171 Angstroms images (Fe IX/X and perhaps O VI), and SUMER spectra of chromospheric and transition region lines from SOHO JOP 72. In quiet sun, bright C IV transients are seen in the vicinity of flux emergence, flux cancellation, and less dramatic interactions of small magnetic structures. Some of these are accompanied by high-velocity explosive events seen in SUMER spectra. The C IV emission can be well-separated from the photospheric magnetic footpoints, suggesting that it takes place on current sheets higher in the atmosphere separating different flux systems. In active regions, both bright and dark fibrils or loops are seen in C IV. Many nano/micro/sub flares are seen, some but not all of which are associated with emerging flux. The C IV emission of "moss" regions, footpoints of hot coronal loops, is contrasted with that of similar plage which does not have hot loops above it. This work was supported by the NASA contracts and grants for TRACE, MDI, and SOHO.

MacA is a second cytochrome c peroxidase of Geobacter sulfurreducens.

PubMed

Seidel, Julian; Hoffmann, Maren; Ellis, Katie E; Seidel, Antonia; Spatzal, Thomas; Gerhardt, Stefan; Elliott, Sean J; Einsle, Oliver

2012-04-03

The metal-reducing δ-proteobacterium Geobacter sulfurreducens produces a large number of c-type cytochromes, many of which have been implicated in the transfer of electrons to insoluble metal oxides. Among these, the dihemic MacA was assigned a central role. Here we have produced G. sulfurreducens MacA by recombinant expression in Escherichia coli and have solved its three-dimensional structure in three different oxidation states. Sequence comparisons group MacA into the family of diheme cytochrome c peroxidases, and the protein indeed showed hydrogen peroxide reductase activity with ABTS(-2) as an electron donor. The observed K(M) was 38.5 ± 3.7 μM H(2)O(2) and v(max) was 0.78 ± 0.03 μmol of H(2)O(2)·min(-1)·mg(-1), resulting in a turnover number k(cat) = 0.46 · s(-1). In contrast, no Fe(III) reductase activity was observed. MacA was found to display electrochemical properties similar to other bacterial diheme peroxidases, in addition to the ability to electrochemically mediate electron transfer to the soluble cytochrome PpcA. Differences in activity between CcpA and MacA can be rationalized with structural variations in one of the three loop regions, loop 2, that undergoes conformational changes during reductive activation of the enzyme. This loop is adjacent to the active site heme and forms an open loop structure rather than a more rigid helix as in CcpA. For the activation of the protein, the loop has to displace the distal ligand to the active site heme, H93, in loop 1. A H93G variant showed an unexpected formation of a helix in loop 2 and disorder in loop 1, while a M297H variant that altered the properties of the electron transfer heme abolished reductive activation.

MacA is a Second Cytochrome c Peroxidase of Geobacter sulfurreducens

PubMed Central

Seidel, Julian; Hoffmann, Maren; Ellis, Katie E.; Seidel, Antonia; Spatzal, Thomas; Gerhardt, Stefan; Elliott, Sean J.

2012-01-01

The metal-reducing δ-proteobacterium Geobacter sulfurreducens produces a large number of c-type cytochromes, many of which have been implicated in the transfer of electrons to insoluble metal oxides. Among these, the dihemic MacA was assigned a central role. Here we have produced G. sulfurreducens MacA by recombinant expression in Escherichia coli and have solved its three-dimensional structure in three different oxidation states. Sequence comparisons group MacA into the family of diheme cytochrome c peroxidases, and the protein indeed showed hydrogen peroxide reductase activity with ABTS2– as an electron donor. The observed KM was 38.5 ± 3.7 μM H2O2 and vmax was 0.78 ± 0.03 μmol H2O2·min–1·mg–1, resulting in a turnover number kcat = 0.46 · s–1. In contrast, no Fe(III) reductase activity was observed. MacA was found to display similar electrochemical properties to other bacterial diheme peroxidases, in additional to the ability to electrochemically mediate electron transfer to the soluble cytochrome PpcA. Differences in activity between CcpA and MacA can be rationalized with structural variations in one of the three loop regions, loop 2, that undergo conformational changes during reductive activation of the enzyme. This loop is adjacent to the active site heme and forms an open loop structure rather than a more rigid helix as in CcpA. For the activation of the protein the loop has to displace the distal ligand to the active site heme, H93, in loop 1. A H93G variant showed an unexpected formation of a helix in loop 2 and disorder in loop 1, while a M297H variant that altered the properties of the electron transfer heme abolished reductive activation. PMID:22417533

Synthesis of single- and double-chain fluorocarbon and hydrocarbon galactosyl amphiphiles and their anti-HIV-1 activity.

PubMed

Faroux-Corlay, B; Clary, L; Gadras, C; Hammache, D; Greiner, J; Santaella, C; Aubertin, A M; Vierling, P; Fantini, J

2000-07-24

Galactosylceramide (GalCer) is an alternative receptor allowing HIV-1 entry into CD4(-)/GalCer(+) cells. This glycosphingolipid recognizes the V3 loop of HIV gp120, which plays a key role in the fusion of the HIV envelope and cellular membrane. To inhibit HIV uptake and infection, we designed and synthesized analogs of GalCer. These amphiphiles and bolaamphiphiles consist of single and double hydrocarbon and/or fluorocarbon chain beta-linked to galactose and galactosamine. They derive from serine (GalSer), cysteine (GalCys), and ethanolamine (GalAE). The anti-HIV activity and cytotoxicity of these galactolipids were evaluated in vitro on CEM-SS (a CD4(+) cell line), HT-29, a CD4(-) cell line expressing high levels of GalCer receptor, and/or HT29 genetically modified to express CD4. GalSer and GalAE derivatives, tested in aqueous medium or as part of liposome preparation, showed moderate anti-HIV-1 activities (IC50 in the 20-220 microM range), whereas none of the GalCys derivatives was found to be active. Moreover, only some of these anti-HIV active analogs inhibited the binding of [3H]suramin (a polysulfonyl compound which displays a high affinity for the V3 loop) to SPC3, a synthetic peptide which contains the conserved GPGRAF region of the V3 loop. Our results most likely indicate that the neutralization of the virion through masking of this conserved V3 loop region is not the only mechanism involved in the HIV-1 antiviral activity of our GalCer analogs.

Radio-derived three-dimensional structure of a solar active region

NASA Astrophysics Data System (ADS)

Tun, Samuel D.

Solar active regions are the source of the most violent events observed on the Sun, some of which have a direct impact to modern civilization. Efforts to understand and predict such events require determination of the three-dimensional distributions of density, temperature, and magnetic fields above such active regions. This thesis presents the structure of the solar atmosphere above active region AR 10923, observed on 2006 Nov 10, as deduced from multi-wavelength studies including combined microwave observations from the Very Large Array (VLA) and the Owens Valley Solar Array (OVSA). The VLA observations provide excellent image quality at a few widely spaced frequencies while the OVSA data provide information at many intermediate frequencies to fill in the spectral coverage. In order to optimize the OVSA data for spectroscopic studies, the L1 method of self-calibration was implemented at this observatory, producing the best single frequency maps produced to date. Images at the 25 distinct, available frequencies are used to provide spatially resolved spectra along many lines of sight in the active region, from which microwave spectral diagnostics are obtained for deducing two-dimensional maps of temperature, magnetic field strength, and column density. The derived quantities are compared with multi-wavelength observations from SoHO and Hinode spacecraft, and with a standard potential magnetic field extrapolation. It is found that a two component temperature model is required to fit the data, in which a hot (> 2 MK) lower corona above the strong-field plage and sunspot regions (emitting via the gyroresonance process) is overlaid with somewhat cooler (˜ 1 MK) coronal loops that partially absorb the gyroresonance emission through the free-free (Bremsstrahlung) process. It is also found that the potential magnetic field extrapolation model can quantitatively account for the observed gyroresonance emission over most of the active region, but in a few areas a higher field strength is required. These areas of discrepancy are found to coincide with the foot points of hot X-ray loops over the sunspot's penumbra. The results and the extrapolation are used to explore the coronal configuration needed to explain the observations, from which it is found that the bulk of radio and X-ray free-free emission emanates from two loop systems, distinguished by the location of their loop foot points. The proposed stratification may explain the observed distribution of column emission measure and the differences in this quantity as obtained from X-rays or radio emission.

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

Daugherty, Ashley B.; Horton, John R.; Cheng, Xiaodong

Circular permutation of the NADPH-dependent oxidoreductase Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme’s catalytic performance. Termini relocation into four regions of the protein (sectors I–IV) near the active site has proven effective in altering enzyme function. To better understand the structural consequences and rationalize the observed functional gains in these OYE1 variants, we selected representatives from sectors I–III for further characterization by biophysical methods and X-ray crystallography. These investigations not only show trends in enzyme stability and quaternary structure as a function of termini location but also provide a possible explanation for the catalytic gainsmore » in our top-performing OYE variant (new N-terminus at residue 303; sector III). Crystallographic analysis indicates that termini relocation into sector III affects the loop β6 region (amino acid positions: 290–310) of OYE1, which forms a lid over the active site. Peptide backbone cleavage greatly enhances local flexibility, effectively converting the loop into a tether and consequently increasing the environmental exposure of the active site. Interestingly, such an active site remodeling does not negatively impact the enzyme’s activity and stereoselectivity; neither does it perturb the conformation of other key active site residues with the exception of Y375. These observations were confirmed in truncation experiments, deleting all residues of the loop β6 region in our OYE variant. Intrigued by the finding that circular permutation leaves most of the key catalytic residues unchanged, we also tested OYE permutants for possible additive or synergistic effects of amino acid substitutions. Distinct functional changes in these OYE variants were detected upon mutations at W116, known in native OYE1 to cause inversion of diastereoselectivity for (S)-carvone reduction. In conclusion, our findings demonstrate the contribution of loop β6 toward determining the stereoselectivity of OYE1, an important insight for future OYE engineering efforts.« less

Energized Active Regions

NASA Image and Video Library

2017-06-02

A pair of relatively small (but frenetic) active regions rotated into view, spouting off numerous small flares and sweeping loops of plasma (May 31-June 2, 2017). At first, only the one active region was observed, but mid-way though the video clip a second one behind the first can be picked out. The dynamic regions were easily the most remarkable areas on the sun during this 42-hour period. The images were taken in a wavelength of extreme ultraviolet light. Movies are available at https://photojournal.jpl.nasa.gov/catalog/PIA21756

Plasma Composition in a Sigmoidal Anemone Active Region

NASA Astrophysics Data System (ADS)

Baker, D.; Brooks, D. H.; Démoulin, P.; van Driel-Gesztelyi, L.; Green, L. M.; Steed, K.; Carlyle, J.

2013-11-01

Using spectra obtained by the EUV Imaging Spectrometer (EIS) instrument onboard Hinode, we present a detailed spatially resolved abundance map of an active region (AR)-coronal hole (CH) complex that covers an area of 359'' × 485''. The abundance map provides first ionization potential (FIP) bias levels in various coronal structures within the large EIS field of view. Overall, FIP bias in the small, relatively young AR is 2-3. This modest FIP bias is a consequence of the age of the AR, its weak heating, and its partial reconnection with the surrounding CH. Plasma with a coronal composition is concentrated at AR loop footpoints, close to where fractionation is believed to take place in the chromosphere. In the AR, we found a moderate positive correlation of FIP bias with nonthermal velocity and magnetic flux density, both of which are also strongest at the AR loop footpoints. Pathways of slightly enhanced FIP bias are traced along some of the loops connecting opposite polarities within the AR. We interpret the traces of enhanced FIP bias along these loops to be the beginning of fractionated plasma mixing in the loops. Low FIP bias in a sigmoidal channel above the AR's main polarity inversion line, where ongoing flux cancellation is taking place, provides new evidence of a bald patch magnetic topology of a sigmoid/flux rope configuration.

A loop-based neural architecture for structured behavior encoding and decoding.

PubMed

Gisiger, Thomas; Boukadoum, Mounir

2018-02-01

We present a new type of artificial neural network that generalizes on anatomical and dynamical aspects of the mammal brain. Its main novelty lies in its topological structure which is built as an array of interacting elementary motifs shaped like loops. These loops come in various types and can implement functions such as gating, inhibitory or executive control, or encoding of task elements to name a few. Each loop features two sets of neurons and a control region, linked together by non-recurrent projections. The two neural sets do the bulk of the loop's computations while the control unit specifies the timing and the conditions under which the computations implemented by the loop are to be performed. By functionally linking many such loops together, a neural network is obtained that may perform complex cognitive computations. To demonstrate the potential offered by such a system, we present two neural network simulations. The first illustrates the structure and dynamics of a single loop implementing a simple gating mechanism. The second simulation shows how connecting four loops in series can produce neural activity patterns that are sufficient to pass a simplified delayed-response task. We also show that this network reproduces electrophysiological measurements gathered in various regions of the brain of monkeys performing similar tasks. We also demonstrate connections between this type of neural network and recurrent or long short-term memory network models, and suggest ways to generalize them for future artificial intelligence research. Copyright © 2017 Elsevier Ltd. All rights reserved.

Simultaneous Solar Maximum Mission (SMM) and very large array observations of solar active regions

NASA Technical Reports Server (NTRS)

Lang, K. R.

1986-01-01

The research deals mainly with Very Large Array and Solar Maximum Mission observations of the ubiquitous coronal loops that dominate the structure of the low corona. As illustrated, the observations of thermal cyclotron lines at microwave wavelengths provide a powerful new method of accurately specifying the coronal magnetic field strength. Processes are delineated that trigger solar eruptions from coronal loops, including preburst heating and the magnetic interaction of coronal loops. Evidence for coherent burst mechanisms is provided for both the Sun and nearby stars, while other observations suggest the presence of currents that may amplify the coronal magnetic field to unexpectedly high levels. The existence is reported of a new class of compact, variable moving sources in regions of apparently weak photospheric field.

Semirational Directed Evolution of Loop Regions in Aspergillus japonicus β-Fructofuranosidase for Improved Fructooligosaccharide Production

PubMed Central

Trollope, K. M.; Görgens, J. F.

2015-01-01

The Aspergillus japonicus β-fructofuranosidase catalyzes the industrially important biotransformation of sucrose to fructooligosaccharides. Operating at high substrate loading and temperatures between 50 and 60°C, the enzyme activity is negatively influenced by glucose product inhibition and thermal instability. To address these limitations, the solvent-exposed loop regions of the β-fructofuranosidase were engineered using a combined crystal structure- and evolutionary-guided approach. This semirational approach yielded a functionally enriched first-round library of 36 single-amino-acid-substitution variants with 58% retaining activity, and of these, 71% displayed improved activities compared to the parent. The substitutions yielding the five most improved variants subsequently were exhaustively combined and evaluated. A four-substitution combination variant was identified as the most improved and reduced the time to completion of an efficient industrial-like reaction by 22%. Characterization of the top five combination variants by isothermal denaturation assays indicated that these variants displayed improved thermostability, with the most thermostable variant displaying a 5.7°C increased melting temperature. The variants displayed uniquely altered, concentration-dependent substrate and product binding as determined by differential scanning fluorimetry. The altered catalytic activity was evidenced by increased specific activities of all five variants, with the most improved variant doubling that of the parent. Variant homology modeling and computational analyses were used to rationalize the effects of amino acid changes lacking direct interaction with substrates. Data indicated that targeting substitutions to loop regions resulted in improved enzyme thermostability, specific activity, and relief from product inhibition. PMID:26253664

Heat Shock Protein Genes Undergo Dynamic Alteration in Their Three-Dimensional Structure and Genome Organization in Response to Thermal Stress

PubMed Central

Chowdhary, Surabhi; Kainth, Amoldeep S.

2017-01-01

ABSTRACT Three-dimensional (3D) chromatin organization is important for proper gene regulation, yet how the genome is remodeled in response to stress is largely unknown. Here, we use a highly sensitive version of chromosome conformation capture in combination with fluorescence microscopy to investigate Heat Shock Protein (HSP) gene conformation and 3D nuclear organization in budding yeast. In response to acute thermal stress, HSP genes undergo intense intragenic folding interactions that go well beyond 5′-3′ gene looping previously described for RNA polymerase II genes. These interactions include looping between upstream activation sequence (UAS) and promoter elements, promoter and terminator regions, and regulatory and coding regions (gene “crumpling”). They are also dynamic, being prominent within 60 s, peaking within 2.5 min, and attenuating within 30 min, and correlate with HSP gene transcriptional activity. With similarly striking kinetics, activated HSP genes, both chromosomally linked and unlinked, coalesce into discrete intranuclear foci. Constitutively transcribed genes also loop and crumple yet fail to coalesce. Notably, a missense mutation in transcription factor TFIIB suppresses gene looping, yet neither crumpling nor HSP gene coalescence is affected. An inactivating promoter mutation, in contrast, obviates all three. Our results provide evidence for widespread, transcription-associated gene crumpling and demonstrate the de novo assembly and disassembly of HSP gene foci. PMID:28970326

Heat Shock Protein Genes Undergo Dynamic Alteration in Their Three-Dimensional Structure and Genome Organization in Response to Thermal Stress.

PubMed

Chowdhary, Surabhi; Kainth, Amoldeep S; Gross, David S

2017-12-15

Three-dimensional (3D) chromatin organization is important for proper gene regulation, yet how the genome is remodeled in response to stress is largely unknown. Here, we use a highly sensitive version of chromosome conformation capture in combination with fluorescence microscopy to investigate Heat Shock Protein ( HSP ) gene conformation and 3D nuclear organization in budding yeast. In response to acute thermal stress, HSP genes undergo intense intragenic folding interactions that go well beyond 5'-3' gene looping previously described for RNA polymerase II genes. These interactions include looping between upstream activation sequence (UAS) and promoter elements, promoter and terminator regions, and regulatory and coding regions (gene "crumpling"). They are also dynamic, being prominent within 60 s, peaking within 2.5 min, and attenuating within 30 min, and correlate with HSP gene transcriptional activity. With similarly striking kinetics, activated HSP genes, both chromosomally linked and unlinked, coalesce into discrete intranuclear foci. Constitutively transcribed genes also loop and crumple yet fail to coalesce. Notably, a missense mutation in transcription factor TFIIB suppresses gene looping, yet neither crumpling nor HSP gene coalescence is affected. An inactivating promoter mutation, in contrast, obviates all three. Our results provide evidence for widespread, transcription-associated gene crumpling and demonstrate the de novo assembly and disassembly of HSP gene foci. Copyright © 2017 American Society for Microbiology.

Coalescence of two current loops with a kink instability simulated by a three-dimensional electromagnetic particle code

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Sakai, J.-I.; Zhao, Jie; Neubert, T.; Buneman, Oscar

1994-01-01

We have studied the dynamics of a coalescence of current loops using three-dimensional electromagnetic (EM) particle simulation code. Our focus is the investigation of such kinetic processes as energy trasnfer, heating particles, and electromagnetic emissions associated with a current loop coalescence which cannot be studied by MHD simulations. First, the two loops undergo a pinching oscillation due to a pressure imbalance between the inside and outside of the current loop. During the pinching oscillation, a kinetic kink instability is excited and electrons in the loops are heated perpendicularly to an ambient magnetic field. Next, the two current loops collide and coalesce, while at the same time a helical structure grows further. Subsequently, the perturbed current, which is due to these helically bunched electrons, can drive a whistler instability. It should be noted in this case that the whistler wave is excited by the kinetic kink instability and not a beam instability. After the coalescence of two helical loops, tilting motions can be observed in the direction of left-hand rotation, and the helical structure will relax resulting in strong plasma heating mostly in the direction perpendicular to the ambient magnetic field. It is also shown that high-frequency electromagnetic waves can be emitted from the region where the two loops coalesce and propagate strongly in the direction of the electron drift velocity. These processes may be important in understanding heating mechansims for coronal loops as well as radio wave emission mechanisms from active regions of solar plasmas.

Analysis of the Functions of Recombination-Related Genes in the Generation of Large Chromosomal Deletions by Loop-Out Recombination in Aspergillus oryzae

PubMed Central

Ogawa, Masahiro; Koyama, Yasuji

2012-01-01

Loop-out-type recombination is a type of intrachromosomal recombination followed by the excision of a chromosomal region. The detailed mechanism underlying this recombination and the genes involved in loop-out recombination remain unknown. In the present study, we investigated the functions of ku70, ligD, rad52, rad54, and rdh54 in the construction of large chromosomal deletions via loop-out recombination and the effect of the position of the targeted chromosomal region on the efficiency of loop-out recombination in Aspergillus oryzae. The efficiency of generation of large chromosomal deletions in the near-telomeric region of chromosome 3, including the aflatoxin gene cluster, was compared with that in the near-centromeric region of chromosome 8, including the tannase gene. In the Δku70 and Δku70-rdh54 strains, only precise loop-out recombination occurred in the near-telomeric region. In contrast, in the ΔligD, Δku70-rad52, and Δku70-rad54 strains, unintended chromosomal deletions by illegitimate loop-out recombination occurred in the near-telomeric region. In addition, large chromosomal deletions via loop-out recombination were efficiently achieved in the near-telomeric region, but barely achieved in the near-centromeric region, in the Δku70 strain. Induction of DNA double-strand breaks by I-SceI endonuclease facilitated large chromosomal deletions in the near-centromeric region. These results indicate that ligD, rad52, and rad54 play a role in the generation of large chromosomal deletions via precise loop-out-type recombination in the near-telomeric region and that loop-out recombination between distant sites is restricted in the near-centromeric region by chromosomal structure. PMID:22286092

A numerical study of the thermal stability of low-lying coronal loops

NASA Technical Reports Server (NTRS)

Klimchuk, J. A.; Antiochos, S. K.; Mariska, J. T.

1986-01-01

The nonlinear evolution of loops that are subjected to a variety of small but finite perturbations was studied. Only the low-lying loops are considered. The analysis was performed numerically using a one-dimensional hydrodynamical model developed at the Naval Research Laboratory. The computer codes solve the time-dependent equations for mass, momentum, and energy transport. The primary interest is the active region filaments, hence a geometry appropriate to those structures was considered. The static solutions were subjected to a moderate sized perturbation and allowed to evolve. The results suggest that both hot and cool loops of the geometry considered are thermally stable against amplitude perturbations of all kinds.

Small but Dynamic Active Region

NASA Image and Video Library

2018-04-20

The sun featured just one, rather small active region over the past few days, but it developed rapidly and sported a lot of magnetic activity in just one day (Apr. 11-12, 2018). The activity was observed in a wavelength of extreme ultraviolet light. The loops and twisting arches above it are evidence of magnetic forces tangling with each other. The video clip was produced using Helioviewer software. Movies are available at https://photojournal.jpl.nasa.gov/catalog/PIA06676

Clasp/SJ Observation of Time Variations of Lyman-Alpha Emissions in a Solar Active Region

NASA Technical Reports Server (NTRS)

Ishikawa, S.; Kubo, M.; Katsukawa, Y.; Kano, R.; Narukage, N.; Ishikawa, R.; Bando, T.; Winebarger, A.; Kobayashi, K.; Trujillo Bueno, J.;

Damped transverse oscillations of interacting coronal loops

NASA Astrophysics Data System (ADS)

Soler, Roberto; Luna, Manuel

2015-10-01

Damped transverse oscillations of magnetic loops are routinely observed in the solar corona. This phenomenon is interpreted as standing kink magnetohydrodynamic waves, which are damped by resonant absorption owing to plasma inhomogeneity across the magnetic field. The periods and damping times of these oscillations can be used to probe the physical conditions of the coronal medium. Some observations suggest that interaction between neighboring oscillating loops in an active region may be important and can modify the properties of the oscillations. Here we theoretically investigate resonantly damped transverse oscillations of interacting nonuniform coronal loops. We provide a semi-analytic method, based on the T-matrix theory of scattering, to compute the frequencies and damping rates of collective oscillations of an arbitrary configuration of parallel cylindrical loops. The effect of resonant damping is included in the T-matrix scheme in the thin boundary approximation. Analytic and numerical results in the specific case of two interacting loops are given as an application.

3D MHD MODELING OF TWISTED CORONAL LOOPS

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

Reale, F.; Peres, G.; Orlando, S.

We perform MHD modeling of a single bright coronal loop to include the interaction with a non-uniform magnetic field. The field is stressed by random footpoint rotation in the central region and its energy is dissipated into heating by growing currents through anomalous magnetic diffusivity that switches on in the corona above a current density threshold. We model an entire single magnetic flux tube in the solar atmosphere extending from the high- β chromosphere to the low- β corona through the steep transition region. The magnetic field expands from the chromosphere to the corona. The maximum resolution is ∼30 km.more » We obtain an overall evolution typical of loop models and realistic loop emission in the EUV and X-ray bands. The plasma confined in the flux tube is heated to active region temperatures (∼3 MK) after ∼2/3 hr. Upflows from the chromosphere up to ∼100 km s{sup −1} fill the core of the flux tube to densities above 10{sup 9} cm{sup −3}. More heating is released in the low corona than the high corona and is finely structured both in space and time.« less

Time-resolved Emission from Bright Hot Pixels of an Active Region Observed in the EUV Band with SDO/AIA and Multi-stranded Loop Modeling

NASA Astrophysics Data System (ADS)

Tajfirouze, E.; Reale, F.; Petralia, A.; Testa, P.

2016-01-01

Evidence of small amounts of very hot plasma has been found in active regions and might be an indication of impulsive heating released at spatial scales smaller than the cross-section of a single loop. We investigate the heating and substructure of coronal loops in the core of one such active region by analyzing the light curves in the smallest resolution elements of solar observations in two EUV channels (94 and 335 Å) from the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory. We model the evolution of a bundle of strands heated by a storm of nanoflares by means of a hydrodynamic 0D loop model (EBTEL). The light curves obtained from a random combination of those of single strands are compared to the observed light curves either in a single pixel or in a row of pixels, simultaneously in the two channels, and using two independent methods: an artificial intelligent system (Probabilistic Neural Network) and a simple cross-correlation technique. We explore the space of the parameters to constrain the distribution of the heat pulses, their duration, their spatial size, and, as a feedback on the data, their signatures on the light curves. From both methods the best agreement is obtained for a relatively large population of events (1000) with a short duration (less than 1 minute) and a relatively shallow distribution (power law with index 1.5) in a limited energy range (1.5 decades). The feedback on the data indicates that bumps in the light curves, especially in the 94 Å channel, are signatures of a heating excess that occurred a few minutes before.

NEW ASPECTS OF A LID-REMOVAL MECHANISM IN THE ONSET OF AN ERUPTION SEQUENCE THAT PRODUCED A LARGE SOLAR ENERGETIC PARTICLE (SEP) EVENT

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

Sterling, Alphonse C.; Moore, Ronald L.; Falconer, David A.

We examine a sequence of two ejective eruptions from a single active region on 2012 January 23, using magnetograms and EUV images from the Solar Dynamics Observatory's (SDO) Helioseismic and Magnetic Imager (HMI) and Atmospheric and Imaging Assembly (AIA), and EUV images from STEREO/EUVI. This sequence produced two coronal mass ejections (CMEs) and a strong solar energetic particle event (SEP); here we focus on the magnetic onset of this important space weather episode. Cheng et al. showed that the first eruption's ({sup E}ruption 1{sup )} flux rope was apparent only in ''hotter'' AIA channels, and that it removed overlying field thatmore » allowed the second eruption ({sup E}ruption 2{sup )} to begin via ideal MHD instability; here we say that Eruption 2 began via a ''lid removal'' mechanism. We show that during Eruption 1's onset, its flux rope underwent a ''tether weakening'' (TW) reconnection with field that arched from the eruption-source active region to an adjacent active region. Standard flare loops from Eruption 1 developed over Eruption 2's flux rope and enclosed filament, but these overarching new loops were unable to confine that flux rope/filament. Eruption 1's flare loops, from both TW reconnection and standard-flare-model internal reconnection, were much cooler than Eruption 2's flare loops (GOES thermal temperatures of ∼7.5 MK and 9 MK, compared to ∼14 MK). The corresponding three sequential GOES flares were, respectively, due to TW reconnection plus earlier phase Eruption 1 tether-cutting reconnection, Eruption 1 later-phase tether-cutting reconnection, and Eruption 2 tether-cutting reconnection.« less

FLARE ENERGY BUILD-UP IN A DECAYING ACTIVE REGION NEAR A CORONAL HOLE

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

Su Yingna; Van Ballegooijen, Adriaan; Golub, Leon

2009-10-10

A B1.7 two-ribbon flare occurred in a highly non-potential decaying active region near a coronal hole at 10:00 UT on 2008 May 17. This flare is 'large' in the sense that it involves the entire region, and it is associated with both a filament eruption and a coronal mass ejection. We present multi-wavelength observations from EUV (TRACE, STEREO/EUVI), X-rays (Hinode/XRT), and Halpha (THEMIS, BBSO) prior to, during and after the flare. Prior to the flare, the region contained two filaments. The long J-shaped sheared loops corresponding to the southern filament were evolved from two short loop systems, which happened aroundmore » 22:00 UT after a filament eruption on May 16. Formation of highly sheared loops in the southeastern part of the region was observed by STEREO 8 hr before the flare. We also perform nonlinear force-free field (NLFFF) modeling for the region at two times prior to the flare, using the flux rope insertion method. The models include the non-force-free effect of magnetic buoyancy in the photosphere. The best-fit NLFFF models show good fit to observations both in the corona (X-ray and EUV loops) and chromosphere (Halpha filament). We find that the horizontal fields in the photosphere are relatively insensitive to the present of flux ropes in the corona. The axial flux of the flux rope in the NLFFF model on May 17 is twice that on May 16, and the model on May 17 is only marginally stable. We also find that the quasi-circular flare ribbons are associated with the separatrix between open and closed fields. This observation and NLFFF modeling suggest that this flare may be triggered by the reconnection at the null point on the separatrix surface.« less

The Ndc80 internal loop is required for recruitment of the Ska complex to establish end-on microtubule attachment to kinetochores.

PubMed

Zhang, Gang; Kelstrup, Christian D; Hu, Xiao-Wen; Kaas Hansen, Mathilde J; Singleton, Martin R; Olsen, Jesper V; Nilsson, Jakob

2012-07-01

The Ndc80 complex establishes end-on attachment of kinetochores to microtubules, which is essential for chromosome segregation. The Ndc80 subunit is characterized by an N-terminal region that binds directly to microtubules, and a long coiled-coil region that interacts with Nuf2. A loop region in Ndc80 that generates a kink in the structure disrupts the long coiled-coil region but the exact function of this loop, has until now, not been clear. Here we show that this loop region is essential for end-on attachment of kinetochores to microtubules in human cells. Cells expressing loop mutants of Ndc80 are unable to align the chromosomes, and stable kinetochore fibers are absent. Through quantitative mass spectrometry and immunofluorescence we found that the binding of the spindle and kinetochore associated (Ska) complex depends on the loop region, explaining why end-on attachment is defective. This underscores the importance of the Ndc80 loop region in coordinating chromosome segregation through the recruitment of specific proteins to the kinetochore.

Conversion from mutual helicity to self-helicity observed with IRIS

NASA Astrophysics Data System (ADS)

Li, L. P.; Peter, H.; Chen, F.; Zhang, J.

2014-10-01

Context. In the upper atmosphere of the Sun observations show convincing evidence for crossing and twisted structures, which are interpreted as mutual helicity and self-helicity. Aims: We use observations with the new Interface Region Imaging Spectrograph (IRIS) to show the conversion of mutual helicity into self-helicity in coronal structures on the Sun. Methods: Using far UV spectra and slit-jaw images from IRIS and coronal images and magnetograms from SDO, we investigated the evolution of two crossing loops in an active region, in particular, the properties of the Si IV line profile in cool loops. Results: In the early stage two cool loops cross each other and accordingly have mutual helicity. The Doppler shifts in the loops indicate that they wind around each other. As a consequence, near the crossing point of the loops (interchange) reconnection sets in, which heats the plasma. This is consistent with the observed increase of the line width and of the appearance of the loops at higher temperatures. After this interaction, the two new loops run in parallel, and in one of them shows a clear spectral tilt of the Si IV line profile. This is indicative of a helical (twisting) motion, which is the same as to say that the loop has self-helicity. Conclusions: The high spatial and spectral resolution of IRIS allowed us to see the conversion of mutual helicity to self-helicity in the (interchange) reconnection of two loops. This is observational evidence for earlier theoretical speculations. Movie associated with Fig. 1 and Appendix A are available in electronic form at http://www.aanda.org

Well-observed dynamics of flaring and peripheral coronal magnetic loops during an M-class limb flare

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

Shen, Jinhua; Zhou, Tuanhui; Ji, Haisheng

2014-08-20

In this paper, we present a variety of well-observed dynamic behaviors for the flaring and peripheral magnetic loops of the M6.6 class extreme limb flare that occurred on 2011 February 24 (SOL2011-02-24T07:20) from EUV observations by the Atmospheric Imaging Assembly on the Solar Dynamics Observatory and X-ray observations by RHESSI. The flaring loop motion confirms the earlier contraction-expansion picture. We find that the U-shaped trajectory delineated by the X-ray corona source of the flare roughly follows the direction of a filament eruption associated with the flare. Different temperature structures of the coronal source during the contraction and expansion phases stronglymore » suggest different kinds of magnetic reconnection processes. For some peripheral loops, we discover that their dynamics are closely correlated with the filament eruption. During the slow rising to abrupt, fast rising of the filament, overlying peripheral magnetic loops display different responses. Two magnetic loops on the elbow of the active region had a slow descending motion followed by an abrupt successive fast contraction, while magnetic loops on the top of the filament were pushed outward, slowly being inflated for a while and then erupting as a moving front. We show that the filament activation and eruption play a dominant role in determining the dynamics of the overlying peripheral coronal magnetic loops.« less

An RNA internal loop acts as a hinge to facilitate ribozyme folding and catalysis.

PubMed Central

Szewczak, A A; Cech, T R

1997-01-01

RNA molecules commonly consist of helical regions separated by internal loops, and in many cases these internal loops have been found to assume stable structures. We have examined the function and dynamics of an internal loop, J5/5a, that joins the two halves of the P4-P6 domain of the Tetrahymena self-splicing group I intron. P4-P6 RNAs with mutations in the J5/5a region showed nondenaturing gel electrophoretic mobilities and levels of Fe(II)-EDTA cleavage protection intermediate between those of wild-type RNA and a mutant incapable of folding into the native P4-P6 tertiary structure. Mutants with the least structured J5/5a loops behaved the most like wild-type P4-P6, and required smaller amounts of Mg2+ to rescue folding. The activity of reconstituted introns containing mutant P4-P6 RNAs correlated similarly with the nature of the J5/5a mutation. Our results suggest that, in solution, the P4-P6 RNA is in a two-state equilibrium between folded and unfolded states. We conclude that this internal loop mainly acts as a flexible hinge, allowing the coaxially stacked helical regions on either side of it to interact via specific tertiary contacts. To a lesser extent, the specific bases within the loop contribute to folding. Furthermore, it is crucial that the junction remain unstructured in the unfolded state. These conclusions cannot be derived from a simple examination of the P4-P6 crystal structure (Cate JH et al., 1996, Science 273:1678-1685), showing once again that structure determination must be supplemented with mutational and thermodynamic analysis to provide a complete picture of a folded macromolecule. PMID:9257643

Interstitial loop transformations in FeCr

DOE PAGES

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

2015-03-27

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

CLASP/SJ Observations of Rapid Time Variations in the Ly α Emission in a Solar Active Region

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

Ishikawa, Shin-nosuke; Kubo, Masahito; Katsukawa, Yukio

The Chromospheric Ly α SpectroPolarimeter (CLASP) is a sounding rocket experiment launched on 2015 September 3 to investigate the solar chromosphere and transition region. The slit-jaw (SJ) optical system captured Ly α images with a high time cadence of 0.6 s. From the CLASP/SJ observations, many variations in the solar chromosphere and transition region emission with a timescale of <1 minute were discovered. In this paper, we focus on the active region within the SJ field of view and investigate the relationship between short (<30 s) temporal variations in the Ly α emission and the coronal structures observed by Solarmore » Dynamics Observatory/Atmospheric Imaging Assembly (AIA). We compare the Ly α temporal variations at the coronal loop footpoints observed in the AIA 211 Å (≈2 MK) and AIA 171 Å (≈0.6 MK) channels with those in the regions with bright Ly α features without a clear association with the coronal loop footpoints. We find more short (<30 s) temporal variations in the Ly α intensity in the footpoint regions. Those variations did not depend on the temperature of the coronal loops. Therefore, the temporal variations in the Ly α intensity at this timescale range could be related to the heating of the coronal structures up to temperatures around the sensitivity peak of 171 Å. No signature was found to support the scenario that these Ly α intensity variations were related to the nanoflares. Waves or jets from the lower layers (lower chromosphere or photosphere) are possible causes for this phenomenon.« less

Contagious Coronal Heating from Recurring Emergence of Magnetic Flux

NASA Astrophysics Data System (ADS)

Moore, R. L.; Falconer, D. A.; Sterling, A. C.

2002-01-01

For each of six old bipolar active regions, we present and interpret Yohkoh/SXT and SOHO/MDI observations of the development, over several days, of enhanced coronal heating in and around the old bipole in response to new magnetic flux emergence within the old bipole. The observations show: 1. In each active region, new flux emerges in the equatorward side of the old bipole, around a lone remaining leading sunspot and/or on the equatorward end of the neutral line of the old bipole. 2. The emerging field is marked by intense internal coronal heating, and enhanced coronal heating occurs in extended loops stemming from the emergence site. 3. In five of the six cases, a "rooster tail" of coronal loops in the poleward extent of the old bipole also brightens in response to the flux emergence. 4. There are episodes of enhanced coronal heating in surrounding magnetic fields that are contiguous with the old bipole but are not directly connected to the emerging field. From these observations, we suggest that the accommodation of localized newly emerged flux within an old active region entails far reaching adjustments in the 3D magnetic field throughout the active region and in surrounding fields in which the active region is embedded, and that these adjustments produce the extensive enhanced coronal heating. We Also Note That The Reason For The recurrence of flux emergence in old active regions may be that active-region flux tends to emerge in giant-cell convection downflows. If so, the poleward "rooster tail" is a coronal flag of a long-lasting downflow in the convection zone. This work was funded by NASA's Office of Space Science through the Solar Physics Supporting Research and Technology Program and the Sun-Earth Connection Guest Investigator Program.

Contagious Coronal Heating from Recurring Emergence of Magnetic Flux

NASA Technical Reports Server (NTRS)

Moore, Ronald L.; Falconer, David; Sterling, Alphonse; Whitaker, Ann F. (Technical Monitor)

2001-01-01

For each of six old bipolar active regions, we present and interpret Yohkoh/SXT and SOHO/MDI observations of the development, over several days, of enhanced coronal heating in and around the old bipole in response to new magnetic flux emerge= within the old bipole. The observations show: 1. In each active region, new flux emerges in the equatorward side of the old bipole, around a lone remaining leading sunspot and/or on the equatorward end of the neutral line of the old bipole. 2. The emerging field is marked by intense internal coronal heating, and enhanced coronal heating occurs in extended loops stemming from the emergence site. 3. In five of the six cases, a "rooster tail" of coronal loops in the poleward extent of the old bipole also brightens in response to the flux emergence. 4. There are episodes of enhanced coronal heating in surrounding magnetic fields that are contiguous with the old bipole but are not directly connected to the emerging field. From these observations, we suggest that the accommodation of localized newly emerged flux within an old active region entails far reaching adjustments in the 3D magnetic field throughout the active region and in surrounding fields in which the active region is embedded, and that these adjustments produce the extensive enhanced coronal heating. We also note that the reason for the recurrence of flux emergence in old active regions may be that active region flux tends to emerge in giant-cell convection downflows. If so, the poleward "rooster tail" is a coronal flag of a long-lasting downflow in the convection zone. This work was funded by NASA's Office of Space Science through the Solar Physics Supporting Research and Technology Program and the Sun-Earth Connection Guest Investigator Program.

TRIGGER MECHANISM OF SOLAR SUBFLARES IN A BRAIDED CORONAL MAGNETIC STRUCTURE

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

Tiwari, Sanjiv K.; Alexander, Caroline E.; Winebarger, Amy R.

Fine-scale braiding of coronal magnetic loops by continuous footpoint motions may power coronal heating via nanoflares, which are spontaneous fine-scale bursts of internal reconnection. An initial nanoflare may trigger an avalanche of reconnection of the braids, making a microflare or larger subflare. In contrast to this internal triggering of subflares, we observe external triggering of subflares in a braided coronal magnetic field observed by the High-resolution Coronal Imager (Hi-C). We track the development of these subflares using 12 s cadence images acquired by SDO/AIA in 1600, 193, 94 Å, and registered magnetograms of SDO/HMI, over four hours centered on the Hi-Cmore » observing time. These data show numerous recurring small-scale brightenings in transition-region emission happening on polarity inversion lines where flux cancellation is occurring. We present in detail an example of an apparent burst of reconnection of two loops in the transition region under the braided coronal field which is appropriate for releasing a short reconnected loop downward and a longer reconnected loop upward. The short loop presumably submerges into the photosphere, participating in observed flux cancellation. A subflare in the overlying braided magnetic field is apparently triggered by the disturbance of the braided field by the reconnection-released upward loop. At least 10 subflares observed in this braided structure appear to be triggered this way. How common this external trigger mechanism for coronal subflares is in other active regions, and how important it is for coronal heating in general, remain to be seen.« less

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

PubMed Central

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

2009-01-01

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

DIFFRACTION, REFRACTION, AND REFLECTION OF AN EXTREME-ULTRAVIOLET WAVE OBSERVED DURING ITS INTERACTIONS WITH REMOTE ACTIVE REGIONS

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

Shen Yuandeng; Liu Yu; Zhao Ruijuan

2013-08-20

We present observations of the diffraction, refraction, and reflection of a global extreme-ultraviolet (EUV) wave propagating in the solar corona. These intriguing phenomena are observed when the wave interacts with two remote active regions, and together they exhibit properties of an EUV wave. When the wave approached AR11465, it became weaker and finally disappeared in the active region, but a few minutes later a new wavefront appeared behind the active region, and it was not concentric with the incoming wave. In addition, a reflected wave was also simultaneously observed on the wave incoming side. When the wave approached AR11459, itmore » transmitted through the active region directly and without reflection. The formation of the new wavefront and the transmission could be explained with diffraction and refraction effects, respectively. We propose that the different behaviors observed during the interactions may be caused by different speed gradients at the boundaries of the two active regions. We find that the EUV wave formed ahead of a group of expanding loops a few minutes after the start of the loops' expansion, which represents the initiation of the associated coronal mass ejection (CME). Based on these results, we conclude that the EUV wave should be a nonlinear magnetosonic wave or shock driven by the associated CME, which propagated faster than the ambient fast mode speed and gradually slowed down to an ordinary linear wave. Our observations support the hybrid model that includes both fast wave and slow non-wave components.« less

Structural Insights into the Role of the Cyclic Backbone in a Squash Trypsin Inhibitor*

PubMed Central

Daly, Norelle L.; Thorstholm, Louise; Greenwood, Kathryn P.; King, Gordon J.; Rosengren, K. Johan; Heras, Begoña; Martin, Jennifer L.; Craik, David J.

2013-01-01

MCoTI-II is a head-to-tail cyclic peptide with potent trypsin inhibitory activity and, on the basis of its exceptional proteolytic stability, is a valuable template for the design of novel drug leads. Insights into inhibitor dynamics and interactions with biological targets are critical for drug design studies, particularly for protease targets. Here, we show that the cyclization and active site loops of MCoTI-II are flexible in solution, but when bound to trypsin, the active site loop converges to a single well defined conformation. This finding of reduced flexibility on binding is in contrast to a recent study on the homologous peptide MCoTI-I, which suggested that regions of the peptide are more flexible upon binding to trypsin. We provide a possible explanation for this discrepancy based on degradation of the complex over time. Our study also unexpectedly shows that the cyclization loop, not present in acyclic homologues, facilitates potent trypsin inhibitory activity by engaging in direct binding interactions with trypsin. PMID:24169696

Magnetic location of C IV events in the quiet network

NASA Technical Reports Server (NTRS)

Porter, Jason G.; Reichmann, Ed J.; Moore, Ronald L.; Harvey, Karen L.

1986-01-01

Ultraviolet Spectrograph and Polarimeter (UVSP) observations of C IV intensity in the quiet sun were examined and compared to magnetograms and He I 10830 A spectroheliograms from Kitt Peak National Laboratory. The observations were made between 3 and 9 April, 1985. Spatially rastered UVSP intensity measurements were obtained at 11 wavelength positions in the 1548 A line of C IV. It was concluded that the stochastic process whereby convective shuffling of loop footprints leads to many topically dissipative events in active regions and the larger bipoles treated here continues to operate in regions of fewer, weaker flux loops, but the resulting events above threshold are less frequent.

The Evolution of Transition Region Loops Using IRIS and AIA

NASA Technical Reports Server (NTRS)

Winebarger, Amy R.; DePontieu, Bart

2014-01-01

Over the past 50 years, the model for the structure of the solar transition region has evolved from a simple transition layer between the cooler chromosphere to the hotter corona to a complex and diverse region that is dominated by complete loops that never reach coronal temperatures. The IRIS slitjaw images show many complete transition region loops. Several of the "coronal" channels in the SDO AIA instrument include contributions from weak transition region lines. In this work, we combine slitjaw images from IRIS with these channels to determine the evolution of the loops. We develop a simple model for the temperature and density evolution of the loops that can explain the simultaneous observations. Finally, we estimate the percentage of AIA emission that originates in the transition region.

Structure and Function of the Intracellular Region of the Plexin-B1 Transmembrane Receptor*

PubMed Central

Tong, Yufeng; Hota, Prasanta K.; Penachioni, Junia Y.; Hamaneh, Mehdi B.; Kim, SoonJeung; Alviani, Rebecca S.; Shen, Limin; He, Hao; Tempel, Wolfram; Tamagnone, Luca; Park, Hee-Won; Buck, Matthias

2009-01-01

Members of the plexin family are unique transmembrane receptors in that they interact directly with Rho family small GTPases; moreover, they contain a GTPase-activating protein (GAP) domain for R-Ras, which is crucial for plexin-mediated regulation of cell motility. However, the functional role and structural basis of the interactions between the different intracellular domains of plexins remained unclear. Here we present the 2.4 Å crystal structure of the complete intracellular region of human plexin-B1. The structure is monomeric and reveals that the GAP domain is folded into one structure from two segments, separated by the Rho GTPase binding domain (RBD). The RBD is not dimerized, as observed previously. Instead, binding of a conserved loop region appears to compete with dimerization and anchors the RBD to the GAP domain. Cell-based assays on mutant proteins confirm the functional importance of this coupling loop. Molecular modeling based on structural homology to p120GAP·H-Ras suggests that Ras GTPases can bind to the plexin GAP region. Experimentally, we show that the monomeric intracellular plexin-B1 binds R-Ras but not H-Ras. These findings suggest that the monomeric form of the intracellular region is primed for GAP activity and extend a model for plexin activation. PMID:19843518

Microflaring in Low-Lying Core Fields and Extended Coronal Heating in the Quiet Sun

NASA Technical Reports Server (NTRS)

Porter, Jason G.; Falconer, D. A.; Moore, Ronald L.

1999-01-01

We have previously reported analyses of Yohkoh SXT data examining the relationship between the heating of extended coronal loops (both within and stemming from active regions) and microflaring in core fields lying along neutral lines near their footpoints (J. G. Porter, D. A. Falconer, and R. L. Moore 1998, in Solar Jets and Coronal Plumes, ed. T. Guyenne, ESA SP-421, and references therein). We found a surprisingly poor correlation of intensity variations in the extended loops with individual microflares in the compact heated areas at their feet, despite considerable circumstancial evidence linking the heating processes in these regions. Now, a study of Fe XII image sequences from SOHO EIT show that similar associations of core field structures with the footpoints of very extended coronal features can be found in the quiet Sun. The morphology is consistent with the finding of Wang et al. (1997, ApJ 484, L75) that polar plumes are rooted at sites of mixed polarity in the magnetic network. We find that the upstairs/downstairs intensity variations often follow the trend, identified in the active region observations, of a weak correspondence. Apparently much of the coronal heating in the extended loops is driven by a type of core field magnetic activity that is "cooler" than the events having the coronal signature of microflares, i.e., activity that results in little heating within the core fields themselves. This work was funded by the Solar Physics Branch of NASA's Office of Space Science through the SR&T Program and the SEC Guest Investigator Program.

Long-period intensity pulsations in the solar corona during activity cycle 23

NASA Astrophysics Data System (ADS)

Auchère, F.; Bocchialini, K.; Solomon, J.; Tison, E.

2014-03-01

We report on the detection (10σ) of 917 events of long-period (3 to 16 h) intensity pulsations in the 19.5 nm passband of the SOHO Extreme ultraviolet Imaging Telescope. The data set spans from January 1997 to July 2010, i.e. the entire solar cycle 23 and the beginning of cycle 24. The events can last for up to six days and have relative amplitudes up to 100%. About half of the events (54%) are found to happen in active regions, and 50% of these have been visually associated with coronal loops. The remaining 46% are localized in the quiet Sun. We performed a comprehensive analysis of the possible instrumental artefacts and we conclude that the observed signal is of solar origin. We discuss several scenarios that could explain the main characteristics of the active region events. The long periods and the amplitudes observed rule out any explanation in terms of magnetohydrodynamic waves. Thermal non-equilibrium could produce the right periods, but it fails to explain all the observed properties of coronal loops and the spatial coherence of the events. We propose that moderate temporal variations of the heating term in the energy equation, so as to avoid a thermal non-equilibrium state, could be sufficient to explain those long-period intensity pulsations. The large number of detections suggests that these pulsations are common in active regions. This would imply that the measurement of their properties could provide new constraints on the heating mechanisms of coronal loops. Movies are available in electronic form at http://www.aanda.org

Solar Coronal Loop Dynamics Near the Null Point Above Active Region NOAA 2666

NASA Astrophysics Data System (ADS)

Filippov, B.

2018-06-01

We analyse observations of a saddle-like structure in the corona above the western limb of the Sun on 2017 July 18. The structure was clearly outlined by coronal loops with typical coronal temperature no more than 1 MK. The dynamics of loops showed convergence towards the centre of the saddle in the vertical direction and divergence in the horizontal direction. The event is a clear example of smooth coronal magnetic field reconnection. No heating manifestations in the reconnection region or magnetically connected areas were observed. Potential magnetic field calculations, which use as the boundary condition the SDO/HMI magnetogram taken on July 14, showed the presence of a null point at the height of 122 arcsec above the photosphere just at the centre of the saddle structure. The shape of field lines fits the fan-spine magnetic configuration above NOAA 2666.

Coronal magnetic structures observing campaign. I - Simultaneous microwave and soft X-ray observations of active regions at the solar limb

NASA Astrophysics Data System (ADS)

Nitta, N.; White, S. M.; Kundu, M. R.; Gopalswamy, N.; Holman, G. D.; Brosius, J. W.; Schmelz, J. T.; Saba, J. L. R.; Strong, K. T.

1991-06-01

Using simultaneous microwave and soft X-ray measurements made with the Very Large Array (VLA) at 6 and 20 cm and the X-ray Polychromator (XRP) aboard the Solar Maximum Mission (SMM), we have studied two active regions near the solar limb. These observations were taken as part of the Coronal Magnetic Structures Observing Campaign (CoMStOC), a collaboration designed to study the magnetic field in the solar corona. The images in soft X-rays and at 20 cm wavelength are similar: both show peaks above the active regions and extended bridge of emission 200,000 km long connecting the two regions. The brightness temperature of the 20 cm emission is lower than that predicted from the X-ray emitting material, however; it can be attributed to free-free emission in cooler (<106 K) plasma not visible to XRP, with an optical depth ˜1. The 6 cm emission is concentrated at lower altitudes and in a ˜160,000 km long bundle of loops in the northern active region. Comparison of the 6 cm map with the potential magnetic field lines computed from photospheric magnetic fields (measured 2 days earlier) indicates that the 6 cm emission is associated with fields of less than ˜200 G. Such fields would be too weak to attribute the observed 6 cm emission to gyroresonance radiation. Analysis of the 6 cm loop bundle indicates that it is strongly asymmetric, with the magnetic field in the northern leg ˜2 times stronger than in the southern leg; the 6 cm emission most likely arises from a combination of hot ( ≥ 2 × 106 K) and cool plasmas, while the 20 cm emission becomes optically thick in the cooler (˜9 × 103 K) plasma. We estimate an Alfvén speed ˜7000 km s-1 and ratio of electron gyrofrequency to plasma frequency ˜1.0 in the northern leg of the 6 cm loop.

RNA Polymerase Activity and Specific RNA Structure Are Required for Efficient HCV Replication in Cultured Cells

PubMed Central

Date, Tomoko; Akazawa, Daisuke; Tian, Xiao; Suzuki, Tetsuro; Kato, Takanobu; Tanaka, Yasuhito; Mizokami, Masashi; Wakita, Takaji; Toyoda, Tetsuya

2010-01-01

We have previously reported that the NS3 helicase (N3H) and NS5B-to-3′X (N5BX) regions are important for the efficient replication of hepatitis C virus (HCV) strain JFH-1 and viral production in HuH-7 cells. In the current study, we investigated the relationships between HCV genome replication, virus production, and the structure of N5BX. We found that the Q377R, A450S, S455N, R517K, and Y561F mutations in the NS5B region resulted in up-regulation of J6CF NS5B polymerase activity in vitro. However, the activation effects of these mutations on viral RNA replication and virus production with JFH-1 N3H appeared to differ. In the presence of the N3H region and 3′ untranslated region (UTR) of JFH-1, A450S, R517K, and Y561F together were sufficient to confer HCV genome replication activity and virus production ability to J6CF in cultured cells. Y561F was also involved in the kissing-loop interaction between SL3.2 in the NS5B region and SL2 in the 3′X region. We next analyzed the 3′ structure of HCV genome RNA. The shorter polyU/UC tracts of JFH-1 resulted in more efficient RNA replication than J6CF. Furthermore, 9458G in the JFH-1 variable region (VR) was responsible for RNA replication activity because of its RNA structures. In conclusion, N3H, high polymerase activity, enhanced kissing-loop interactions, and optimal viral RNA structure in the 3′UTR were required for J6CF replication in cultured cells. PMID:20442786

The association of transequatorial loops in the solar corona with coronal mass ejection onset

NASA Astrophysics Data System (ADS)

Glover, A.; Harra, L. K.; Matthews, S. A.; Foley, C. A.

2003-03-01

It has been shown that transequatorial loops can disappear in association with the onset of a coronal mass ejection (CME) (Khan & Hudson \\cite{khan}). We extend this result by considering a larger sample of transequatorial loop systems (TLS) to investigate their associated flaring and CME activity. We find 10 of a total 18 TLS considered here to be associated with flaring and CME onset originating from a connected active region. A total 33 cases of flaring and associated CME onset are observed from these 10 systems during their lifetime. We observe the influence of this activity on the TLS in each case. In contrast to the Khan & Hudson result, we find evidence that transequatorial loop eruption leading to soft X-ray brightening equivalent in temperature to a B-class flare is equally as common as dimming in the corona. Consequently we conclude that the scenario observed by Khan & Hudson is not universal and that other types of CME-TLS association occur. It was found that for transequatorial loops that were associated with CMEs the asymmetry in longitude was larger than for those that were not associated to a CME by 10o. In addition, the extent in latitude (as a measure of the loop length) was nearly twice as large for those TLS associated with CMEs than those that were not. The asymmetry in latitude was actually on average larger for those TLS not associated with CMEs, than for those that were. This suggests that differential rotation is not a major contributor to the production of CMEs from transequatorial loops. Instead it is more likely for a CME to be produced if the loop is long, and if there is a large asymmetry in longitude. The implications of these results for CME onset prediction are discussed.

Analysing spectroscopically the propagation of a CME from its source on the disk to its impact as it propagates outwards

NASA Astrophysics Data System (ADS)

Harra, Louise K.; Doschek, G. A.; Matthews, Sarah A.; De Pontieu, Bart; Long, David

We analyse a complex coronal mass ejection observed by Hinode, SDO and IRIS. SDO AIA shows that the eruption occurs between several active regions with flaring occurring in all of them. Hinode EIS observed one of the flaring active regions that shows a fast outwards propagation which is related to the CME lifting off. The eruption is then observed as it propagates away from the Sun, pushing the existing post-flare loops downwards as it goes. Spectroscopic observations are made during this time with IRIS measuring the impact that this CME front has as it pushes the loops downwards. Strong enhancements in the cool Mg II emission at these locations that show complex dynamics. We discuss these new observations in context of CME models.

Early evolution of an energetic coronal mass ejection and its relation to EUV waves

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

Liu, Rui; Wang, Yuming; Shen, Chenglong, E-mail: rliu@ustc.edu.cn

2014-12-10

We study a coronal mass ejection (CME) associated with an X-class flare whose initiation is clearly observed in the low corona with high-cadence, high-resolution EUV images, providing us a rare opportunity to witness the early evolution of an energetic CME in detail. The eruption starts with a slow expansion of cool overlying loops (∼1 MK) following a jet-like event in the periphery of the active region. Underneath the expanding loop system, a reverse S-shaped dimming is seen immediately above the brightening active region in hot EUV passbands. The dimming is associated with a rising diffuse arch (∼6 MK), which wemore » interpret as a preexistent, high-lying flux rope. This is followed by the arising of a double hot channel (∼10 MK) from the core of the active region. The higher structures rise earlier and faster than lower ones, with the leading front undergoing extremely rapid acceleration up to 35 km s{sup –2}. This suggests that the torus instability is the major eruption mechanism and that it is the high-lying flux rope rather than the hot channels that drives the eruption. The compression of coronal plasmas skirting and overlying the expanding loop system, whose aspect ratio h/r increases with time as a result of the rapid upward acceleration, plays a significant role in driving an outward-propagating global EUV wave and a sunward-propagating local EUV wave, respectively.« less

Loop heating by D.C. electric current and electromagnetic wave emissions simulated by 3-D EM particle zone

NASA Technical Reports Server (NTRS)

Sakai, J. I.; Zhao, J.; Nishikawa, K.-I.

1994-01-01

We have shown that a current-carrying plasma loop can be heated by magnetic pinch driven by the pressure imbalance between inside and outside the loop, using a 3-dimensional electromagnetic (EM) particle code. Both electrons and ions in the loop can be heated in the direction perpendicular to the ambient magnetic field, therefore the perpendicular temperature can be increased about 10 times compared with the parallel temperature. This temperature anisotropy produced by the magnetic pinch heating can induce a plasma instability, by which high-frequency electromagnetic waves can be excited. The plasma current which is enhanced by the magnetic pinch can also excite a kinetic kink instability, which can heat ions perpendicular to the magnetic field. The heating mechanism of ions as well as the electromagnetic emission could be important for an understanding of the coronal loop heating and the electromagnetic wave emissions from active coronal regions.

CAN LARGE TIME DELAYS OBSERVED IN LIGHT CURVES OF CORONAL LOOPS BE EXPLAINED IN IMPULSIVE HEATING?

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

Lionello, Roberto; Linker, Jon A.; Mikić, Zoran

The light curves of solar coronal loops often peak first in channels associated with higher temperatures and then in those associated with lower temperatures. The delay times between the different narrowband EUV channels have been measured for many individual loops and recently for every pixel of an active region observation. The time delays between channels for an active region exhibit a wide range of values. The maximum time delay in each channel pair can be quite large, i.e., >5000 s. These large time delays make-up 3%–26% (depending on the channel pair) of the pixels where a trustworthy, positive time delaymore » is measured. It has been suggested that these time delays can be explained by simple impulsive heating, i.e., a short burst of energy that heats the plasma to a high temperature, after which the plasma is allowed to cool through radiation and conduction back to its original state. In this paper, we investigate whether the largest observed time delays can be explained by this hypothesis by simulating a series of coronal loops with different heating rates, loop lengths, abundances, and geometries to determine the range of expected time delays between a set of four EUV channels. We find that impulsive heating cannot address the largest time delays observed in two of the channel pairs and that the majority of the large time delays can only be explained by long, expanding loops with photospheric abundances. Additional observations may rule out these simulations as an explanation for the long time delays. We suggest that either the time delays found in this manner may not be representative of real loop evolution, or that the impulsive heating and cooling scenario may be too simple to explain the observations, and other potential heating scenarios must be explored.« less

Alfven-wave dissipation: A support mechanism for quiescent prominences

NASA Technical Reports Server (NTRS)

Jensen, Eberhart

1986-01-01

High resolution filtergrams or spectrograms of the main body of quiescent prominences often show a very vivid dynamical picture that cannot be reconciled with static models. Even if large differences exist between individual prominences in this respect, at least parts of the prominence are usually found to be in a 'choppy', turbulent state. Evidence for systematic flows are found in local regions in the prominence and also in the transition zone in the surroundings. These two regions are probably decoupled magnetically. Alfven waves are generally believed to be responsible for the heating in the upper chromosphere and corona (Hollweg 1986). Since evidence for the presence of Alfven-waves has also been found in the solar wind field, it is highly probable that such waves are generated in the convection zone of the sun and propagated outwards in the solar atmosphere wherever a proper magnetic field is present to carry the waves. The most basic magnetic formations in the solar atmosphere are simple loops. They occur all over the solar surface and cover a large range of magnetic field strengths. Loops with the strongest magnetic fields are found in active regions. It is to be expected that the Alfven-wave flux which is channelled into the loops from below, could show considerable variation both with heliocentric latitude, with time and locally between neighbouring loops. What happens when a magnetic loop is exposed to the appropriate Alfven-wave flux required to heat the upper solar atmosphere is examined.

Non-active site mutations disturb the loop dynamics, dimerization, viral budding and egress of VP40 of the Ebola virus.

PubMed

Balmith, Marissa; Soliman, Mahmoud E S

2017-02-28

The first account of the dynamic features of the loop region of VP40 of the Ebola virus (EboV) using accelerated molecular dynamics (aMD) simulations is reported herein. Due to its major role in the Ebola life cycle, VP40 is considered a promising therapeutic target. The available experimental data on the N-terminal domain (NTD) loop indicates that mutations K127A, T129A and N130A demonstrate an unrecognized role for NTD-plasma membrane (PM) interaction for efficient VP40-PM localization, oligomerization, matrix assembly and egress. Despite experimental results, the molecular description of VP40 and the information it can provide still remain vague. Therefore, to gain further molecular insight into the effect of mutations on the loop region of VP40 and its effects on the overall protein conformation and VP40 dimerization, aMD simulations and post-dynamic analyses were employed for wildtype (WT) and mutant systems. The results showed significant variations in the presence of mutations as per RMSF, RMSD, R g , PCA and distance calculations in comparison to the WT. These results could provide researchers with insight with regards to the conformational aspects concerning VP40 and its close relation to the experimental data. We believe that the results presented in this study will ultimately provide a useful understanding of the structural landscape of the loop region of VP40, which would contribute towards the discovery of novel EboV inhibitors.

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

Ren, Jinqi; Cook, Aaron A.; Bergmeier, Wolfgang

The dynamic regulation of ERK1 and -2 (ERK1/2) is required for precise signal transduction controlling cell proliferation, differentiation, and survival. However, the underlying mechanisms regulating the activation of ERK1/2 are not completely understood. In this study, we show that phosphorylation of RasGRP2, a guanine nucleotide exchange factor (GEF), inhibits its ability to activate the small GTPase Rap1 that ultimately leads to decreased activation of ERK1/2 in cells. ERK2 phosphorylates RasGRP2 at Ser394 located in the linker region implicated in its autoinhibition. These studies identify RasGRP2 as a novel substrate of ERK1/2 and define a negative-feedback loop that regulates the BRaf–MEK–ERKmore » signaling cascade. This negative-feedback loop determines the amplitude and duration of active ERK1/2. -- Highlights: •ERK2 phosphorylates the guanine nucleotide exchange factor RasGRP2 at Ser394. •Phosphorylated RasGRP2 has decreased capacity to active Rap1b in vitro and in cells. •Phosphorylation of RasGRP2 by ERK1/2 introduces a negative-feedback loop into the BRaf-MEK-ERK pathway.« less

Fine flow structures in the transition region small-scale loops

NASA Astrophysics Data System (ADS)

Yan, L.; Peter, H.; He, J.; Wei, Y.

2016-12-01

The observation and model have suggested that the transition region EUV emission from the quiet sun region is contributed by very small scale loops which have not been resolved. Recently, the observation from IRIS has revealed that this kind of small scale loops. Based on the high resolution spectral and imaging observation from IRIS, much more detail work needs to be done to reveal the fine flow features in this kind of loop to help us understand the loop heating. Here, we present a detail statistical study of the spatial and temporal evolution of Si IV line profiles of small scale loops and report the spectral features: there is a transition from blue (red) wing enhancement dominant to red (blue) wing enhancement dominant along the cross-section of the loop, which is independent of time. This feature appears as the loop appear and disappear as the loop un-visible. This is probably the signature of helical flow along the loop. The result suggests that the brightening of this kind of loop is probably due to the current dissipation heating in the twisted magnetic field flux tube.

Genetic instability associated with loop or stem–loop structures within transcription units can be independent of nucleotide excision repair

PubMed Central

Burns, John A; Chowdhury, Moinuddin A; Cartularo, Laura; Berens, Christian; Scicchitano, David A

2018-01-01

Abstract Simple sequence repeats (SSRs) are found throughout the genome, and under some conditions can change in length over time. Germline and somatic expansions of trinucleotide repeats are associated with a series of severely disabling illnesses, including Huntington's disease. The underlying mechanisms that effect SSR expansions and contractions have been experimentally elusive, but models suggesting a role for DNA repair have been proposed, in particular the involvement of transcription-coupled nucleotide excision repair (TCNER) that removes transcription-blocking DNA damage from the transcribed strand of actively expressed genes. If the formation of secondary DNA structures that are associated with SSRs were to block RNA polymerase progression, TCNER could be activated, resulting in the removal of the aberrant structure and a concomitant change in the region's length. To test this, TCNER activity in primary human fibroblasts was assessed on defined DNA substrates containing extrahelical DNA loops that lack discernible internal base pairs or DNA stem–loops that contain base pairs within the stem. The results show that both structures impede transcription elongation, but there is no corresponding evidence that nucleotide excision repair (NER) or TCNER operates to remove them. PMID:29474673

Differential contributions of the superior and inferior parietal cortex to feedback versus feedforward control of tools.

PubMed

Macuga, Kristen L; Frey, Scott H

2014-05-15

Damage to the superior and/or inferior parietal lobules (SPL, IPL) (Sirigu et al., 1996) or cerebellum (Grealy and Lee, 2011) can selectively disrupt motor imagery, motivating the hypothesis that these regions participate in predictive (i.e., feedforward) control. If so, then the SPL, IPL, and cerebellum should show greater activity as the demands on feedforward control increase from visually-guided execution (closed-loop) to execution without visual feedback (open-loop) to motor imagery. Using fMRI and a Fitts' reciprocal aiming task with tools directed at targets in far space, we found that the SPL and cerebellum exhibited greater activity during closed-loop control. Conversely, open-loop and imagery conditions were associated with increased activity within the IPL and prefrontal areas. These results are consistent with a superior-to-inferior gradient in the representation of feedback-to-feedforward control within the posterior parietal cortex. Additionally, the anterior SPL displayed greater activity when aiming movements were performed with a stick vs. laser pointer. This may suggest that it is involved in the remapping of far into near (reachable) space (Maravita and Iriki, 2004), or in distalization of the end-effector from hand to stick (Arbib et al., 2009). Copyright © 2014 Elsevier Inc. All rights reserved.

Engineering Ascorbate Peroxidase Activity Into Cytochrome C Peroxidase

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

Meharenna, Y.T.; Oertel, P.; Bhaskar, B.

2009-05-26

Cytochrome c peroxidase (CCP) and ascorbate peroxidase (APX) have very similar structures, and yet neither CCP nor APX exhibits each others activities with respect to reducing substrates. APX has a unique substrate binding site near the heme propionates where ascorbate H-bonds with a surface Arg and one heme propionate (Sharp et al. (2003) Nat. Struct. Biol. 10, 303--307). The corresponding region in CCP has a much longer surface loop, and the critical Arg residue that is required for ascorbate binding in APX is Asn in CCP. In order to convert CCP into an APX, the ascorbate-binding loop and critical argininemore » were engineered into CCP to give the CCP2APX mutant. The mutant crystal structure shows that the engineered site is nearly identical to that found in APX. While wild-type CCP shows no APX activity, CCP2APX catalyzes the peroxidation of ascorbate at a rate of {approx}12 min{sup -1}, indicating that the engineered ascorbate-binding loop can bind ascorbate.« less

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

PubMed Central

Brackley, Chris A.; Johnson, James; Kelly, Steven; Cook, Peter R.; Marenduzzo, Davide

2016-01-01

Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a fitting-free, minimal model: bivalent or multivalent red and green ‘transcription factors’ bind to cognate sites in strings of beads (‘chromatin’) to form molecular bridges stabilizing loops. In the absence of additional explicit forces, molecular dynamic simulations reveal that bound factors spontaneously cluster—red with red, green with green, but rarely red with green—to give structures reminiscent of transcription factories. Binding of just two transcription factors (or proteins) to active and inactive regions of human chromosomes yields rosettes, topological domains and contact maps much like those seen experimentally. This emergent ‘bridging-induced attraction’ proves to be a robust, simple and generic force able to organize interphase chromosomes at all scales. PMID:27060145

FAST CONTRACTION OF CORONAL LOOPS AT THE FLARE PEAK

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

Liu Rui; Wang Haimin

On 2005 September 8, a coronal loop overlying the active region NOAA 10808 was observed in TRACE 171 A to contract at {approx}100 km s{sup -1} at the peak of an X5.4-2B flare at 21:05 UT. Prior to the fast contraction, the loop underwent a much slower contraction at {approx}6 km s{sup -1} for about 8 minutes, initiating during the flare preheating phase. The sudden switch to fast contraction is presumably corresponding to the onset of the impulsive phase. The contraction resulted in the oscillation of a group of loops located below, with the period of about 10 minutes. Meanwhile,more » the contracting loop exhibited a similar oscillatory pattern superimposed on the dominant downward motion. We suggest that the fast contraction reflects a suddenly reduced magnetic pressure underneath due either to (1) the eruption of magnetic structures located at lower altitudes or to (2) the rapid conversion of magnetic free energy in the flare core region. Electrons accelerated in the shrinking trap formed by the contracting loop can theoretically contribute to a late-phase hard X-ray burst, which is associated with Type IV radio emission. To complement the X5.4 flare which was probably confined, a similar event observed in SOHO/EIT 195 A on 2004 July 20 in an eruptive, M8.6 flare is briefly described, in which the contraction was followed by the expansion of the same loop leading up to a halo coronal mass ejection. These observations further substantiate the conjecture of coronal implosion and suggest coronal implosion as a new exciter mechanism for coronal loop oscillations.« less

High-resolution imaging spectroscopy of two micro-pores and an arch filament system in a small emerging-flux region

NASA Astrophysics Data System (ADS)

González Manrique, S. J.; Bello González, N.; Denker, C.

2017-04-01

Context. Emerging flux regions mark the first stage in the accumulation of magnetic flux eventually leading to pores, sunspots, and (complex) active regions. These flux regions are highly dynamic, show a variety of fine structure, and in many cases live only for a short time (less than a day) before dissolving quickly into the ubiquitous quiet-Sun magnetic field. Aims: The purpose of this investigation is to characterize the temporal evolution of a minute emerging flux region, the associated photospheric and chromospheric flow fields, and the properties of the accompanying arch filament system. We aim to explore flux emergence and decay processes and investigate if they scale with structure size and magnetic flux contents. Methods: This study is based on imaging spectroscopy with the Göttingen Fabry-Pérot Interferometer at the Vacuum Tower Telescope, Observatorio del Teide, Tenerife, Spain on 2008 August 7. Photospheric horizontal proper motions were measured with Local correlation tracking using broadband images restored with multi-object multi-frame blind deconvolution. Cloud model (CM) inversions of line scans in the strong chromospheric absorption Hαλ656.28 nm line yielded CM parameters (Doppler velocity, Doppler width, optical thickness, and source function), which describe the cool plasma contained in the arch filament system. Results: The high-resolution observations cover the decay and convergence of two micro-pores with diameters of less than one arcsecond and provide decay rates for intensity and area. The photospheric horizontal flow speed is suppressed near the two micro-pores indicating that the magnetic field is already sufficiently strong to affect the convective energy transport. The micro-pores are accompanied by a small arch filament system as seen in Hα, where small-scale loops connect two regions with Hα line-core brightenings containing an emerging flux region with opposite polarities. The Doppler width, optical thickness, and source function reach the largest values near the Hα line-core brightenings. The chromospheric velocity of the cloud material is predominantly directed downwards near the footpoints of the loops with velocities of up to 12 km s-1, whereas loop tops show upward motions of about 3 km s-1. Some of the loops exhibit signs of twisting motions along the loop axis. Conclusions: Micro-pores are the smallest magnetic field concentrations leaving a photometric signature in the photosphere. In the observed case, they are accompanied by a miniature arch filament system indicative of newly emerging flux in the form of Ω-loops. Flux emergence and decay take place on a time-scale of about two days, whereas the photometric decay of the micro-pores is much more rapid (a few hours), which is consistent with the incipient submergence of Ω-loops. Considering lifetime and evolution timescales, impact on the surrounding photospheric proper motions, and flow speed of the chromospheric plasma at the loop tops and footpoints, the results are representative for the smallest emerging flux regions still recognizable as such.

Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions.

PubMed

Tran, Tran T; Kulis, Christina; Long, Steven M; Bryant, Darryn; Adams, Peter; Smythe, Mark L

2010-11-01

Medicinal chemists synthesize arrays of molecules by attaching functional groups to scaffolds. There is evidence suggesting that some scaffolds yield biologically active molecules more than others, these are termed privileged substructures. One role of the scaffold is to present its side-chains for molecular recognition, and biologically relevant scaffolds may present side-chains in biologically relevant geometries or shapes. Since drug discovery is primarily focused on the discovery of compounds that bind to proteinaceous targets, we have been deciphering the scaffold shapes that are used for binding proteins as they reflect biologically relevant shapes. To decipher the scaffold architecture that is important for binding protein surfaces, we have analyzed the scaffold architecture of protein loops, which are defined in this context as continuous four residue segments of a protein chain that are not part of an α-helix or β-strand secondary structure. Loops are an important molecular recognition motif of proteins. We have found that 39 clusters reflect the scaffold architecture of 89% of the 23,331 loops in the dataset, with average intra-cluster and inter-cluster RMSD of 0.47 and 1.91, respectively. These protein loop scaffolds all have distinct shapes. We have used these 39 clusters that reflect the scaffold architecture of protein loops as biological descriptors. This involved generation of a small dataset of scaffold-based peptidomimetics. We found that peptidomimetic scaffolds with reported biological activities matched loop scaffold geometries and those peptidomimetic scaffolds with no reported biologically activities did not. This preliminary evidence suggests that organic scaffolds with tight matches to the preferred loop scaffolds of proteins, implies the likelihood of the scaffold to be biologically relevant.

Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions

NASA Astrophysics Data System (ADS)

Tran, Tran T.; Kulis, Christina; Long, Steven M.; Bryant, Darryn; Adams, Peter; Smythe, Mark L.

2010-11-01

Medicinal chemists synthesize arrays of molecules by attaching functional groups to scaffolds. There is evidence suggesting that some scaffolds yield biologically active molecules more than others, these are termed privileged substructures. One role of the scaffold is to present its side-chains for molecular recognition, and biologically relevant scaffolds may present side-chains in biologically relevant geometries or shapes. Since drug discovery is primarily focused on the discovery of compounds that bind to proteinaceous targets, we have been deciphering the scaffold shapes that are used for binding proteins as they reflect biologically relevant shapes. To decipher the scaffold architecture that is important for binding protein surfaces, we have analyzed the scaffold architecture of protein loops, which are defined in this context as continuous four residue segments of a protein chain that are not part of an α-helix or β-strand secondary structure. Loops are an important molecular recognition motif of proteins. We have found that 39 clusters reflect the scaffold architecture of 89% of the 23,331 loops in the dataset, with average intra-cluster and inter-cluster RMSD of 0.47 and 1.91, respectively. These protein loop scaffolds all have distinct shapes. We have used these 39 clusters that reflect the scaffold architecture of protein loops as biological descriptors. This involved generation of a small dataset of scaffold-based peptidomimetics. We found that peptidomimetic scaffolds with reported biological activities matched loop scaffold geometries and those peptidomimetic scaffolds with no reported biologically activities did not. This preliminary evidence suggests that organic scaffolds with tight matches to the preferred loop scaffolds of proteins, implies the likelihood of the scaffold to be biologically relevant.

Insulators form gene loops by interacting with promoters in Drosophila.

PubMed

Erokhin, Maksim; Davydova, Anna; Kyrchanova, Olga; Parshikov, Alexander; Georgiev, Pavel; Chetverina, Darya

2011-09-01

Chromatin insulators are regulatory elements involved in the modulation of enhancer-promoter communication. The 1A2 and Wari insulators are located immediately downstream of the Drosophila yellow and white genes, respectively. Using an assay based on the yeast GAL4 activator, we have found that both insulators are able to interact with their target promoters in transgenic lines, forming gene loops. The existence of an insulator-promoter loop is confirmed by the fact that insulator proteins could be detected on the promoter only in the presence of an insulator in the transgene. The upstream promoter regions, which are required for long-distance stimulation by enhancers, are not essential for promoter-insulator interactions. Both insulators support basal activity of the yellow and white promoters in eyes. Thus, the ability of insulators to interact with promoters might play an important role in the regulation of basal gene transcription.

Importance of nuclear localization for the apoptosis-induced activity of a fungal galectin AAL (Agrocybe aegerita lectin)

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

Liang, Yi; Feng, Lei; Tong, Xin

2009-08-28

Agrocybe aegerita lectin (AAL) was identified previously in our group as a novel galectin from medicinal fungi Agrocybe aegerita, and has been shown to effectively induce cancer cell cycle arrest and apoptosis in vitro and tumor regression in vivo. Here, AAL was observed to translocate into the HeLa cell nucleus and induce cell apoptosis when it was predominantly in the nucleus. The N-terminus and C-terminus of AAL were required for nuclear localization. Site mutated proteins were generated based on AAL structure. Dimer interface mutant I25G, carbohydrate recognition domain (CRD) mutant R63H, and loop region mutant L33A could not enter themore » nucleus and lost the ability to induce apoptosis. CRD mutant H59Q and loop region mutant I144G maintained nuclear localization activity, and H59Q retained residual bioability but I144G had no activity, indicating that nuclear localization is important but not sufficient for AAL to become apoptotically active. Our findings provide a novel antitumor mechanism of fungal galectin.« less

Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis

PubMed Central

El Hage, Aziz; French, Sarah L.; Beyer, Ann L.; Tollervey, David

2010-01-01

Pre-rRNA transcription by RNA Polymerase I (Pol I) is very robust on active rDNA repeats. Loss of yeast Topoisomerase I (Top1) generated truncated pre-rRNA fragments, which were stabilized in strains lacking TRAMP (Trf4/Trf5–Air1/Air2–Mtr4 polyadenylation complexes) or exosome degradation activities. Loss of both Top1 and Top2 blocked pre-rRNA synthesis, with pre-rRNAs truncated predominately in the 18S 5′ region. Positive supercoils in front of Pol I are predicted to slow elongation, while rDNA opening in its wake might cause R-loop formation. Chromatin immunoprecipitation analysis showed substantial levels of RNA/DNA hybrids in the wild type, particularly over the 18S 5′ region. The absence of RNase H1 and H2 in cells depleted of Top1 increased the accumulation of RNA/DNA hybrids and reduced pre-rRNA truncation and pre-rRNA synthesis. Hybrid accumulation over the rDNA was greatly exacerbated when Top1, Top2, and RNase H were all absent. Electron microscopy (EM) analysis revealed Pol I pileups in the wild type, particularly over the 18S. Pileups were longer and more frequent in the absence of Top1, and their frequency was exacerbated when RNase H activity was also lacking. We conclude that the loss of Top1 enhances inherent R-loop formation, particularly over the 5′ region of the rDNA, imposing persistent transcription blocks when RNase H is limiting. PMID:20634320

Mechanism of APC/CCDC20 activation by mitotic phosphorylation.

PubMed

Qiao, Renping; Weissmann, Florian; Yamaguchi, Masaya; Brown, Nicholas G; VanderLinden, Ryan; Imre, Richard; Jarvis, Marc A; Brunner, Michael R; Davidson, Iain F; Litos, Gabriele; Haselbach, David; Mechtler, Karl; Stark, Holger; Schulman, Brenda A; Peters, Jan-Michael

2016-05-10

Chromosome segregation and mitotic exit are initiated by the 1.2-MDa ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome) and its coactivator CDC20 (cell division cycle 20). To avoid chromosome missegregation, APC/C(CDC20) activation is tightly controlled. CDC20 only associates with APC/C in mitosis when APC/C has become phosphorylated and is further inhibited by a mitotic checkpoint complex until all chromosomes are bioriented on the spindle. APC/C contains 14 different types of subunits, most of which are phosphorylated in mitosis on multiple sites. However, it is unknown which of these phospho-sites enable APC/C(CDC20) activation and by which mechanism. Here we have identified 68 evolutionarily conserved mitotic phospho-sites on human APC/C bound to CDC20 and have used the biGBac technique to generate 47 APC/C mutants in which either all 68 sites or subsets of them were replaced by nonphosphorylatable or phospho-mimicking residues. The characterization of these complexes in substrate ubiquitination and degradation assays indicates that phosphorylation of an N-terminal loop region in APC1 is sufficient for binding and activation of APC/C by CDC20. Deletion of the N-terminal APC1 loop enables APC/C(CDC20) activation in the absence of mitotic phosphorylation or phospho-mimicking mutations. These results indicate that binding of CDC20 to APC/C is normally prevented by an autoinhibitory loop in APC1 and that its mitotic phosphorylation relieves this inhibition. The predicted location of the N-terminal APC1 loop implies that this loop controls interactions between the N-terminal domain of CDC20 and APC1 and APC8. These results reveal how APC/C phosphorylation enables CDC20 to bind and activate the APC/C in mitosis.

Mechanism of APC/CCDC20 activation by mitotic phosphorylation

PubMed Central

Qiao, Renping; Weissmann, Florian; Yamaguchi, Masaya; Brown, Nicholas G.; VanderLinden, Ryan; Imre, Richard; Jarvis, Marc A.; Brunner, Michael R.; Davidson, Iain F.; Litos, Gabriele; Haselbach, David; Mechtler, Karl; Stark, Holger; Schulman, Brenda A.; Peters, Jan-Michael

2016-01-01

Chromosome segregation and mitotic exit are initiated by the 1.2-MDa ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome) and its coactivator CDC20 (cell division cycle 20). To avoid chromosome missegregation, APC/CCDC20 activation is tightly controlled. CDC20 only associates with APC/C in mitosis when APC/C has become phosphorylated and is further inhibited by a mitotic checkpoint complex until all chromosomes are bioriented on the spindle. APC/C contains 14 different types of subunits, most of which are phosphorylated in mitosis on multiple sites. However, it is unknown which of these phospho-sites enable APC/CCDC20 activation and by which mechanism. Here we have identified 68 evolutionarily conserved mitotic phospho-sites on human APC/C bound to CDC20 and have used the biGBac technique to generate 47 APC/C mutants in which either all 68 sites or subsets of them were replaced by nonphosphorylatable or phospho-mimicking residues. The characterization of these complexes in substrate ubiquitination and degradation assays indicates that phosphorylation of an N-terminal loop region in APC1 is sufficient for binding and activation of APC/C by CDC20. Deletion of the N-terminal APC1 loop enables APC/CCDC20 activation in the absence of mitotic phosphorylation or phospho-mimicking mutations. These results indicate that binding of CDC20 to APC/C is normally prevented by an autoinhibitory loop in APC1 and that its mitotic phosphorylation relieves this inhibition. The predicted location of the N-terminal APC1 loop implies that this loop controls interactions between the N-terminal domain of CDC20 and APC1 and APC8. These results reveal how APC/C phosphorylation enables CDC20 to bind and activate the APC/C in mitosis. PMID:27114510

A gigantic coronal jet ejected from a compact active region in a coronal hole

NASA Technical Reports Server (NTRS)

Shibata, K.; Nitta, N.; Strong, K. T.; Matsumoto, R.; Yokoyama, T.; Hirayama, T.; Hudson, H.; Ogawara, Y.

1994-01-01

A gigantic coronal jet greater than 3 x 10(exp 5) km long (nearly half the solar radius) has been found with the soft X-ray telescope (SXT) on board the solar X-ray satellite, Yohkoh. The jet was ejected on 1992 January 11 from an 'anemone-type' active region (AR) appearing in a coronal hole and is one of the largest coronal X-ray jets observed so far by SXT. This gigantic jet is the best observed example of many other smaller X-ray jets, because the spatial structures of both the jet and the AR located at its base are more easily resolved. The range of apparent translational velocities of the bulk of the jet was between 90 and 240 km s(exp -1), with the corresponding kinetic energy estimated to be of order of 10(exp 28) ergs. A detailed analysis reveals that the jet was associated with a loop brightening (a small flare) that occurred in the active region. Several features of this observation suggest and are consistent with a magnetic reconnection mechanism for the production of such a 'jet-loop-brightening' event.

Electron acceleration in connection with radio noise storm onsets or enhancements

NASA Astrophysics Data System (ADS)

Vilmer, N.; Trottet, G.

2008-11-01

Radio noise storms are generated by suprathermal (≃ 10 keV) electrons accelerated continuously over time scales of hours or days in active region magnetic fields. They are related to emerging magnetic loops interacting with overlying loops and leading to magnetic coronal reconfiguration (e.g. Bentley et al. 2000). Noise storm onsets or enhancements have been sometimes observed in association with a flare-like sudden energy release in the active region producing a localized microwave (Raulin et al. 1991) or soft X-ray brightening (Raulin & Klein 1994). A few cases have also been reported in which 10-30 keV emission from a superhot plasma or from non-thermal electrons have been observed at the onset of noise storms (Crosby et al. 1996) confirming that a flare-like energy release in the lower corona could be a necessary condition for noise storms to start. No spatially resolved hard X-ray observations were however available in the case of the latter analysis, allowing to check that the flare-like emission and the noise storm were originating from the same active region. We present here an event for which both radio and hard X-ray (HXR) spatially resolved observations are available.

Joint NuSTAR and IRIS observation of a microflaring active region

NASA Astrophysics Data System (ADS)

Hannah, I. G.; Kleint, L.; Krucker, S.; Glesener, L.; Grefenstette, B.

2017-12-01

We present observations of a weakly microflaring active region observed in X-rays with NuSTAR, UV with IRIS and EUV with SDO/AIA. NuSTAR was pointed at this unnamed active region near the East limb between 23:27UT and 23:37UT 26-July-2016, finding mostly quiescent emission except for a small microflare about 23:35UT. The NuSTAR spectrum for the pre-microflare time (23:27UT to 23:34UT) is well fitted by a single thermal component of about 3MK and combined with SDO/AIA we can determine the differential emission measure (DEM), finding it, as expected, drops very sharply to higher temperatures. During the subsequent microflare, the increase in NuSTAR counts matches a little brightening loop observed with IRIS SJI 1400Å and SDO/AIA. Fortuitously the IRIS slit crosses this microflaring loop and we find an increased emission in Si IV 1394Å, Si IV 1403Å and O IV 1402Å but only average line widths and velocities. The NuSTAR microflare spectrum shows heating to higher temperatures and also allows us to investigate the energetics of this event.

Crystal structure of the cytoplasmic phosphatase and tensin homolog (PTEN)-like region of Ciona intestinalis voltage-sensing phosphatase provides insight into substrate specificity and redox regulation of the phosphoinositide phosphatase activity.

PubMed

Matsuda, Makoto; Takeshita, Kohei; Kurokawa, Tatsuki; Sakata, Souhei; Suzuki, Mamoru; Yamashita, Eiki; Okamura, Yasushi; Nakagawa, Atsushi

2011-07-01

Ciona intestinalis voltage-sensing phosphatase (Ci-VSP) has a transmembrane voltage sensor domain and a cytoplasmic region sharing similarity to the phosphatase and tensin homolog (PTEN). It dephosphorylates phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate upon membrane depolarization. The cytoplasmic region is composed of a phosphatase domain and a putative membrane interaction domain, C2. Here we determined the crystal structures of the Ci-VSP cytoplasmic region in three distinct constructs, wild-type (248-576), wild-type (236-576), and G365A mutant (248-576). The crystal structure of WT-236 and G365A-248 had the disulfide bond between the catalytic residue Cys-363 and the adjacent residue Cys-310. On the other hand, the disulfide bond was not present in the crystal structure of WT-248. These suggest the possibility that Ci-VSP is regulated by reactive oxygen species as found in PTEN. These structures also revealed that the conformation of the TI loop in the active site of the Ci-VSP cytoplasmic region was distinct from the corresponding region of PTEN; Ci-VSP has glutamic acid (Glu-411) in the TI loop, orienting toward the center of active site pocket. Mutation of Glu-411 led to acquirement of increased activity toward phosphatidylinositol 3,5-bisphosphate, suggesting that this site is required for determining substrate specificity. Our results provide the basic information of the enzymatic mechanism of Ci-VSP.

E2-mediated cathepsin D (CTSD) activation involves looping of distal enhancer elements.

PubMed

Bretschneider, Nancy; Kangaspeska, Sara; Seifert, Martin; Reid, George; Gannon, Frank; Denger, Stefanie

2008-08-01

Estrogen receptor alpha (ERalpha) is a ligand dependent transcription factor that regulates the expression of target genes through interacting with cis-acting estrogen response elements (EREs). However, only a minority of ERalpha binding sites are located within the proximal promoter regions of responsive genes. Here we report the characterization of an ERE located 9kbp upstream of the TSS of the cathepsin D gene (CTSD) that up-regulates CTSD expression upon estrogen stimulation in MCF-7 cells. Using ChIP, we show recruitment of ERalpha and phosphorylated PolII at the CTSD distal enhancer region. Moreover, we determine the kinetics of transient CpG methylation on the promoter region of CTSD and for the first time, at a distal enhancer element. We show that ERalpha is crucial for long-distance regulation of CTSD expression involving a looping mechanism.

Conserved water mediated recognition and the dynamics of active site Cys 331 and Tyr 411 in hydrated structure of human IMPDH-II.

PubMed

Bairagya, Hridoy R; Mukhopadhyay, Bishnu P; Bera, Asim K

2011-01-01

Inosine monophosphate dehydrogenase (IMPDH) of human is involved in GMP biosynthesis pathway, increased level of IMPDH-II (an isoform of enzyme) activity have found in leukemic and sarcoma cells. Modeling and extensive molecular dynamics simulation (15 ns) studies of IMPDH-II (1B3O PDB structure) have indicated the intricate involvement of four conserved water molecules (W 1, W 2, W 3, and W 4) in the conformational transition or the mobilities of "flap" (residues 400-450) and "loop" (residues 325-342) regions in enzyme. The stabilization of active site residues Asn 303, Gly 324, Ser 329, Cys 331, Asp 364, and Tyr 411 through variable H-bonding coordination from the conserved water molecular center seems interesting in the uninhibited hydrated form of human IMPDH-II structures. This conformational transition or the flexibility of mobile regions, water molecular recognition to active site residues Cys 331 and Tyr 411, and the presence of a hydrophilic cavity approximately 540 Å(3) (enclaved by the loop and flap region) near the C-terminal surface of this enzyme may explore a rational hope toward the water mimic inhibitor or anticancer agent design for human. 2010 John Wiley & Sons, Ltd.

Reduced functional connectivity within the limbic cortico-striato-thalamo-cortical loop in unmedicated adults with obsessive-compulsive disorder.

PubMed

Posner, Jonathan; Marsh, Rachel; Maia, Tiago V; Peterson, Bradley S; Gruber, Allison; Simpson, H Blair

2014-06-01

Cortico-striato-thalamo-cortical (CSTC) loops project from the cortex to the striatum, then from the striatum to the thalamus via the globus pallidus, and finally from the thalamus back to the cortex again. These loops have been implicated in Obsessive-Compulsive Disorder (OCD) with particular focus on the limbic CSTC loop, which encompasses the orbitofrontal and anterior cingulate cortices, as well as the ventral striatum. Resting state functional-connectivity MRI (rs-fcMRI) studies, which examine temporal correlations in neural activity across brain regions at rest, have examined CSTC loop connectivity in patients with OCD and suggest hyperconnectivity within these loops in medicated adults with OCD. We used rs-fcMRI to examine functional connectivity within CSTC loops in unmedicated adults with OCD (n = 23) versus healthy controls (HCs) (n = 20). Contrary to prior rs-fcMRI studies in OCD patients on medications that report hyperconnectivity in the limbic CSTC loop, we found that compared with HCs, unmedicated OCD participants had reduced connectivity within the limbic CSTC loop. Exploratory analyses revealed that reduced connectivity within the limbic CSTC loop correlated with OCD symptom severity in the OCD group. Our finding of limbic loop hypoconnectivity in unmedicted OCD patients highlights the potential confounding effects of antidepressants on connectivity measures and the value of future examinations of the effects of pharmacological and/or behavioral treatments on limbic CSTC loop connectivity. Copyright © 2013 Wiley Periodicals, Inc.

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

Xie, Haixia; Li, Bo; Huang, Zhenghua

How the solar corona is heated to high temperatures remains an unsolved mystery in solar physics. In the present study we analyze observations of 50 whole active region loops taken with the Extreme-ultraviolet Imaging Spectrometer on board the Hinode satellite. Eleven loops were classified as cool loops (<1 MK) and 39 as warm loops (1–2 MK). We study their plasma parameters, such as densities, temperatures, filling factors, nonthermal velocities, and Doppler velocities. We combine spectroscopic analysis with linear force-free magnetic field extrapolation to derive the 3D structure and positioning of the loops, their lengths and heights, and the magnetic fieldmore » strength along the loops. We use density-sensitive line pairs from Fe xii, Fe xiii, Si x, and Mg vii ions to obtain electron densities by taking special care of intensity background subtraction. The emission measure loci method is used to obtain the loop temperatures. We find that the loops are nearly isothermal along the line of sight. Their filling factors are between 8% and 89%. We also compare the observed parameters with the theoretical Rosner–Tucker–Vaiana (RTV) scaling law. We find that most of the loops are in an overpressure state relative to the RTV predictions. In a follow-up study, we will report a heating model of a parallel-cascade-based mechanism and will compare the model parameters with the loop plasma and structural parameters derived here.« less

Structural maintenance of chromosome complexes differentially compact mitotic chromosomes according to genomic context

PubMed Central

Schalbetter, S. A.; Goloborodko, A.; Fudenberg, G.; Belton, J.-M.; Miles, C.; Yu, M.; Dekker, J.; Mirny, L.; Baxter, J.

2017-01-01

Structural Maintenance of Chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modeling, we study how cohesin and condensin, two deeply conserved SMC complexes, organize chromosomes in the budding yeast Saccharomyces cerevisiae. The canonical role of cohesin is to co-align sister chromatids whilst condensin generally compacts mitotic chromosomes. We find strikingly different roles for the two complexes in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosome arms, independently of sister chromatid cohesion. Polymer simulations demonstrate this role can be fully accounted for through cis-looping of chromatin. Second, condensin is generally dispensable for compaction along chromosome arms. Instead it plays a targeted role compacting the rDNA proximal regions and promoting resolution of peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that distinct SMC-dependent looping activities are selectively deployed to appropriately compact chromosomes. PMID:28825700

New Evidence that Magnetoconvection Drives Solar–Stellar Coronal Heating

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

Tiwari, Sanjiv K.; Panesar, Navdeep K.; Moore, Ronald L.

2017-07-10

How magnetic energy is injected and released in the solar corona, keeping it heated to several million degrees, remains elusive. Coronal heating generally increases with increasing magnetic field strength. From a comparison of a nonlinear force-free model of the three-dimensional active region coronal field to observed extreme-ultraviolet loops, we find that (1) umbra-to-umbra coronal loops, despite being rooted in the strongest magnetic flux, are invisible, and (2) the brightest loops have one foot in an umbra or penumbra and the other foot in another sunspot’s penumbra or in unipolar or mixed-polarity plage. The invisibility of umbra-to-umbra loops is new evidencemore » that magnetoconvection drives solar-stellar coronal heating: evidently, the strong umbral field at both ends quenches the magnetoconvection and hence the heating. Broadly, our results indicate that depending on the field strength in both feet, the photospheric feet of a coronal loop on any convective star can either engender or quench coronal heating in the loop’s body.« less

The Formation of Coronal Loops by Thermal Instability in Three Dimensions

NASA Technical Reports Server (NTRS)

Mok, Yung; Mikic, Zoran; Lionello, Roberto; Linker, Jon A.

2008-01-01

Plasma loops in solar active regions have been observed in EUV and soft X-rays for decades. Their formation mechanism and properties, however, are still not fully understood. Predictions by early models, based on 1D hydrostatic equilibria with uniform plasma heating, are not consistent with high-resolution measurements. In this Letter, we demonstrate, via 3D simulations, that a class of heating models can lead to the dynamic formation of plasma loops provided the plasma is heated sufficiently to match SXT soft X-ray measurements. We show that individual flux tubes in a 3D magnetic structure tend to stand out against their neighbors. The loops have large aspect ratios and nearly uniform cross sections in the corona, similar to those observed by EIT and TRACE. The coronal EUV emission from these thermally unstable solutions is roughly consistent with EIT measurements. The solution oscillates in time through a large-amplitude, nonlinear cycle, leading to repeated brightening and fading of the loops.

OBSERVING CORONAL NANOFLARES IN ACTIVE REGION MOSS

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

Testa, Paola; DeLuca, Ed; Golub, Leon

2013-06-10

The High-resolution Coronal Imager (Hi-C) has provided Fe XII 193A images of the upper transition region moss at an unprecedented spatial ({approx}0.''3-0.''4) and temporal (5.5 s) resolution. The Hi-C observations show in some moss regions variability on timescales down to {approx}15 s, significantly shorter than the minute-scale variability typically found in previous observations of moss, therefore challenging the conclusion of moss being heated in a mostly steady manner. These rapid variability moss regions are located at the footpoints of bright hot coronal loops observed by the Solar Dynamics Observatory/Atmospheric Imaging Assembly in the 94 A channel, and by the Hinode/X-Raymore » Telescope. The configuration of these loops is highly dynamic, and suggestive of slipping reconnection. We interpret these events as signatures of heating events associated with reconnection occurring in the overlying hot coronal loops, i.e., coronal nanoflares. We estimate the order of magnitude of the energy in these events to be of at least a few 10{sup 23} erg, also supporting the nanoflare scenario. These Hi-C observations suggest that future observations at comparable high spatial and temporal resolution, with more extensive temperature coverage, are required to determine the exact characteristics of the heating mechanism(s).« less

Conformational Flexibility of Human Casein Kinase Catalytic Subunit Explored by Metadynamics

PubMed Central

Gouron, Aurélie; Milet, Anne; Jamet, Helene

2014-01-01

Casein kinase CK2 is an essential enzyme in higher organisms, catalyzing the transfer of the γ phosphate from ATP to serine and threonine residues on protein substrates. In a number of animal tumors, CK2 activity has been shown to escape normal cellular control, making it a potential target for cancer therapy. Several crystal structures of human CK2 have been published with different conformations for the CK2α catalytic subunit. This variability reflects a high flexibility for two regions of CK2α: the interdomain hinge region, and the glycine-rich loop (p-loop). Here, we present a computational study simulating the equilibrium between three conformations involving these regions. Simulations were performed using well-tempered metadynamics combined with a path collective variables approach. This provides a reference pathway describing the conformational changes being studied, based on analysis of free energy surfaces. The free energies of the three conformations were found to be close and the paths proposed had low activation barriers. Our results indicate that these conformations can exist in water. This information should be useful when designing inhibitors specific to one conformation. PMID:24606937

Structure and Dynamics of Coronal Plasma

NASA Technical Reports Server (NTRS)

Golub, Leon

1998-01-01

Brief summaries of the four published papers produced within the present performance period of NASA Grant NAGW-4081 are presented. The full text of the papers are appended to the report. The first paper titled "Coronal Structures Observed in X-rays and H-alpa Structures" was published in the Kofu Symposium proceedings. The study analyzes cool and hot behavior of two x-ray events, a small flare and a surge. It was found that a large H-alpha surge appears in x-rays as a very weak event, while a weak H-alpha feature corresponds to the brightest x-ray emission on the disk at the time of the observation. Calculations of the heating necessary to produce these signatures, and implications for the driving and heating mechanisms of flares vs. surges are presented. The second paper "Differential Magnetic Field Shear in an Active Region" has been published in The Astrophysical Journal. The study compared the three dimensional extrapolation of magnetic fields with the observed coronal structure in an active region. Based on the fit between observed coronal structure throughout the volume of the region and the calculated magnetic field configurations, the authors propose a differential magnetic field shear model for this active region. The decreasing field shear in the outer portions of the AR may indicate a continual relaxation of the magnetic field with time, corresponding to a net transport of helicity outward. The third paper "Difficulties in Observing Coronal Structure" has been published in the journal Solar Physics. This paper discusses the evidence that the temperature and density structure of the corona are far more complicated than had previously been thought. The discussion is based on five studies carried out by the group on coronal plasma properties, showing that any one x-ray instrument does see all of the plasma present in the corona, that hot and cool material may appear to be co-spatial at a given location in the corona, and that simple magnetic field extrapolations provide only a poor fit to the observed structure. The fourth paper "Analysis and Comparison of Loop Structures Imaged with NIXT and Yohkoh/SXT" has been published in Astronomy and Astrophysics. This paper analyzes and compares a variety of coronal loops, deriving loop pressure and emission measure from loop models. They are able to determine the volume filling factor in the corona, which is found to be in the range 0.001 to 0.01 for compact loops, and of order 1 for large structures. The small values suggest highly filamented structures, especially at lower temperatures.

Mechanism of retinoic acid-induced transcription: histone code, DNA oxidation and formation of chromatin loops.

PubMed

Zuchegna, Candida; Aceto, Fabiana; Bertoni, Alessandra; Romano, Antonella; Perillo, Bruno; Laccetti, Paolo; Gottesman, Max E; Avvedimento, Enrico V; Porcellini, Antonio

2014-01-01

Histone methylation changes and formation of chromatin loops involving enhancers, promoters and 3' end regions of genes have been variously associated with active transcription in eukaryotes. We have studied the effect of activation of the retinoic A receptor, at the RARE-promoter chromatin of CASP9 and CYP26A1 genes, 15 and 45 min following RA exposure, and we found that histone H3 lysines 4 and 9 are demethylated by the lysine-specific demethylase, LSD1 and by the JMJ-domain containing demethylase, D2A. The action of the oxidase (LSD1) and a dioxygenase (JMJD2A) in the presence of Fe++ elicits an oxidation wave that locally modifies the DNA and recruits the enzymes involved in base and nucleotide excision repair (BER and NER). These events are essential for the formation of chromatin loop(s) that juxtapose the RARE element with the 5' transcription start site and the 3' end of the genes. The RARE bound-receptor governs the 5' and 3' end selection and directs the productive transcription cycle of RNA polymerase. These data mechanistically link chromatin loops, histone methylation changes and localized DNA repair with transcription. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Endo-β-D-1,4-mannanase from Chrysonilia sitophila displays a novel loop arrangement for substrate selectivity.

PubMed

Gonçalves, Ana Maria D; Silva, Catarina S; Madeira, Tânia I; Coelho, Ricardo; de Sanctis, Daniele; San Romão, Maria Vitória; Bento, Isabel

2012-11-01

The crystal structure of wild-type endo-β-D-1,4-mannanase (EC 3.2.1.78) from the ascomycete Chrysonilia sitophila (CsMan5) has been solved at 1.40 Å resolution. The enzyme isolated directly from the source shows mixed activity as both an endo-glucanase and an endo-mannanase. CsMan5 adopts the (β/α)(8)-barrel fold that is well conserved within the GH5 family and has highest sequence and structural homology to the GH5 endo-mannanases. Superimposition with proteins of this family shows a unique structural arrangement of three surface loops of CsMan5 that stretch over the active centre, promoting an altered topography of the binding cleft. The most relevant feature results from the repositioning of a long loop at the extremity of the binding cleft, resulting in a shortened glycone-binding region with two subsites. The other two extended loops flanking the binding groove produce a narrower cleft compared with the wide architecture observed in GH5 homologues. Two aglycone subsites (+1 and +2) are identified and a nonconserved tryptophan (Trp271) at the +1 subsite may offer steric hindrance. Taken together, these findings suggest that the discrimination of mannan substrates is achieved through modified loop length and structure.

Functional characteristics of a double positive feedback loop coupled with autorepression

NASA Astrophysics Data System (ADS)

Banerjee, Subhasis; Bose, Indrani

2008-12-01

We study the functional characteristics of a two-gene motif consisting of a double positive feedback loop and an autoregulatory negative feedback loop. The motif appears in the gene regulatory network controlling the functional activity of pancreatic β-cells. The model exhibits bistability and hysteresis in appropriate parameter regions. The two stable steady states correspond to low (OFF state) and high (ON state) protein levels, respectively. Using a deterministic approach, we show that the region of bistability increases in extent when the copy number of one of the genes is reduced from 2 to 1. The negative feedback loop has the effect of reducing the size of the bistable region. Loss of a gene copy, brought about by mutations, hampers the normal functioning of the β-cells giving rise to the genetic disorder, maturity-onset diabetes of the young (MODY). The diabetic phenotype makes its appearance when a sizable fraction of the β-cells is in the OFF state. Using stochastic simulation techniques we show that, on reduction of the gene copy number, there is a transition from the monostable ON to the ON state in the bistable region of the parameter space. Fluctuations in the protein levels, arising due to the stochastic nature of gene expression, can give rise to transitions between the ON and OFF states. We show that as the strength of autorepression increases, the ON → OFF state transitions become less probable whereas the reverse transitions are more probable. The implications of the results in the context of the occurrence of MODY are pointed out.

Cerebro-cerebellar circuits in autism spectrum disorder.

PubMed

D'Mello, Anila M; Stoodley, Catherine J

2015-01-01

The cerebellum is one of the most consistent sites of abnormality in autism spectrum disorder (ASD) and cerebellar damage is associated with an increased risk of ASD symptoms, suggesting that cerebellar dysfunction may play a crucial role in the etiology of ASD. The cerebellum forms multiple closed-loop circuits with cerebral cortical regions that underpin movement, language, and social processing. Through these circuits, cerebellar dysfunction could impact the core ASD symptoms of social and communication deficits and repetitive and stereotyped behaviors. The emerging topography of sensorimotor, cognitive, and affective subregions in the cerebellum provides a new framework for interpreting the significance of regional cerebellar findings in ASD and their relationship to broader cerebro-cerebellar circuits. Further, recent research supports the idea that the integrity of cerebro-cerebellar loops might be important for early cortical development; disruptions in specific cerebro-cerebellar loops in ASD might impede the specialization of cortical regions involved in motor control, language, and social interaction, leading to impairments in these domains. Consistent with this concept, structural, and functional differences in sensorimotor regions of the cerebellum and sensorimotor cerebro-cerebellar circuits are associated with deficits in motor control and increased repetitive and stereotyped behaviors in ASD. Further, communication and social impairments are associated with atypical activation and structure in cerebro-cerebellar loops underpinning language and social cognition. Finally, there is converging evidence from structural, functional, and connectivity neuroimaging studies that cerebellar right Crus I/II abnormalities are related to more severe ASD impairments in all domains. We propose that cerebellar abnormalities may disrupt optimization of both structure and function in specific cerebro-cerebellar circuits in ASD.

Cerebro-cerebellar circuits in autism spectrum disorder

PubMed Central

D'Mello, Anila M.; Stoodley, Catherine J.

2015-01-01

The cerebellum is one of the most consistent sites of abnormality in autism spectrum disorder (ASD) and cerebellar damage is associated with an increased risk of ASD symptoms, suggesting that cerebellar dysfunction may play a crucial role in the etiology of ASD. The cerebellum forms multiple closed-loop circuits with cerebral cortical regions that underpin movement, language, and social processing. Through these circuits, cerebellar dysfunction could impact the core ASD symptoms of social and communication deficits and repetitive and stereotyped behaviors. The emerging topography of sensorimotor, cognitive, and affective subregions in the cerebellum provides a new framework for interpreting the significance of regional cerebellar findings in ASD and their relationship to broader cerebro-cerebellar circuits. Further, recent research supports the idea that the integrity of cerebro-cerebellar loops might be important for early cortical development; disruptions in specific cerebro-cerebellar loops in ASD might impede the specialization of cortical regions involved in motor control, language, and social interaction, leading to impairments in these domains. Consistent with this concept, structural, and functional differences in sensorimotor regions of the cerebellum and sensorimotor cerebro-cerebellar circuits are associated with deficits in motor control and increased repetitive and stereotyped behaviors in ASD. Further, communication and social impairments are associated with atypical activation and structure in cerebro-cerebellar loops underpinning language and social cognition. Finally, there is converging evidence from structural, functional, and connectivity neuroimaging studies that cerebellar right Crus I/II abnormalities are related to more severe ASD impairments in all domains. We propose that cerebellar abnormalities may disrupt optimization of both structure and function in specific cerebro-cerebellar circuits in ASD. PMID:26594140

LDB1-mediated enhancer looping can be established independent of mediator and cohesin.

PubMed

Krivega, Ivan; Dean, Ann

2017-08-21

Mechanistic studies in erythroid cells indicate that LDB1, as part of a GATA1/TAL1/LMO2 complex, brings erythroid-expressed genes into proximity with enhancers for transcription activation. The role of co-activators in establishing this long-range interaction is poorly understood. Here we tested the contributions of the RNA Pol II pre-initiation complex (PIC), mediator and cohesin to establishment of locus control region (LCR)/β-globin proximity. CRISPR/Cas9 editing of the β-globin promoter to eliminate the RNA Pol II PIC by deleting the TATA-box resulted in loss of transcription, but enhancer-promoter interaction was unaffected. Additional deletion of the promoter GATA1 site eliminated LDB1 complex and mediator occupancy and resulted in loss of LCR/β-globin proximity. To separate the roles of LDB1 and mediator in LCR looping, we expressed a looping-competent but transcription-activation deficient form of LDB1 in LDB1 knock down cells: LCR/β-globin proximity was restored without mediator core occupancy. Further, Cas9-directed tethering of mutant LDB1 to the β-globin promoter forced LCR loop formation in the absence of mediator or cohesin occupancy. Moreover, ENCODE data and our chromatin immunoprecipitation results indicate that cohesin is almost completely absent from validated and predicted LDB1-regulated erythroid enhancer-gene pairs. Thus, lineage specific factors largely mediate enhancer-promoter looping in erythroid cells independent of mediator and cohesin. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

Long-range looping of a locus control region drives tissue-specific chromatin packing within a multigene cluster

PubMed Central

Tsai, Yu-Cheng; Cooke, Nancy E.; Liebhaber, Stephen A.

2016-01-01

Abstract The relationships of higher order chromatin organization to mammalian gene expression remain incompletely defined. The human Growth Hormone (hGH) multigene cluster contains five gene paralogs. These genes are selectively activated in either the pituitary or the placenta by distinct components of a remote locus control region (LCR). Prior studies have revealed that appropriate activation of the placental genes is dependent not only on the actions of the LCR, but also on the multigene composition of the cluster itself. Here, we demonstrate that the hGH LCR ‘loops’ over a distance of 28 kb in primary placental nuclei to make specific contacts with the promoters of the two GH genes in the cluster. This long-range interaction sequesters the GH genes from the three hCS genes which co-assemble into a tightly packed ‘hCS chromatin hub’. Elimination of the long-range looping, via specific deletion of the placental LCR components, triggers a dramatic disruption of the hCS chromatin hub. These data reveal a higher-order structural pathway by which long-range looping from an LCR impacts on local chromatin architecture that is linked to tissue-specific gene regulation within a multigene cluster. PMID:26893355

Active Region Formation and Subsurface Structure

NASA Astrophysics Data System (ADS)

Stein, F.; Nordlund, Robert A.

2016-10-01

We present results from emerging magnetic flux simulations showing how several different active regions form and their very different subsurface structures. The simulations assumed an infinite sheet of uniform, untwisted, horizontal field advected into the computational domain by inflows at a depth of 20 Mm. Results from two different horizontal field strengths, 1 and 5 kG, will be presented. Convective up and down flows buckle the horizontal field into Omega and U loops. Upflows and magnetic buoyancy carry the field toward the surface, while fast downflows pin down the field. Small (granular) convective motions, near the surface, shred the emerging field into fine filaments that emerge as the observed "pepper and salt" pattern. The large (supergranular) motions, at depth, keep the overall loop structure intact, so that as the overall omega-loop emerges through the surface the opposite polarity fields counter-stream into large unipolar flux concentrations producing first pores which then coalesce into spots. These tend to be located over the supergranular downflow lanes near the bottom of the domain. The pores and spots exhibit a great variety of subsurface field structures - from monolithic but twisted bundles to intertwined separate spaghetti sturctures. We will show movies of the surface evolution of the field and emergent continuum intensity and of the subsurface evolution of the magnetic field lines.

Crystal Structure of Arginase from Plasmodium falciparum and Implications for l-Arginine Depletion in Malarial Infection

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

Dowling, Daniel P.; Ilies, Monica; Olszewski, Kellen L.

The 2.15 {angstrom} resolution crystal structure of arginase from Plasmodium falciparum, the parasite that causes cerebral malaria, is reported in complex with the boronic acid inhibitor 2(S)-amino-6-boronohexanoic acid (ABH) (K{sub d} = 11 {micro}M). This is the first crystal structure of a parasitic arginase. Various protein constructs were explored to identify an optimally active enzyme form for inhibition and structural studies and to probe the structure and function of two polypeptide insertions unique to malarial arginase: a 74-residue low-complexity region contained in loop L2 and an 11-residue segment contained in loop L8. Structural studies indicate that the low-complexity region ismore » largely disordered and is oriented away from the trimer interface; its deletion does not significantly compromise enzyme activity. The loop L8 insertion is located at the trimer interface and makes several intra- and intermolecular interactions important for enzyme function. In addition, we also demonstrate that arg- Plasmodium berghei sporozoites show significantly decreased liver infectivity in vivo. Therefore, inhibition of malarial arginase may serve as a possible candidate for antimalarial therapy against liver-stage infection, and ABH may serve as a lead for the development of inhibitors.« less

Manipulating Protein-Protein Interactions in Nonribosomal Peptide Synthetase Type II Peptidyl Carrier Proteins.

PubMed

Jaremko, Matt J; Lee, D John; Patel, Ashay; Winslow, Victoria; Opella, Stanley J; McCammon, J Andrew; Burkart, Michael D

2017-10-10

In an effort to elucidate and engineer interactions in type II nonribosomal peptide synthetases, we analyzed biomolecular recognition between the essential peptidyl carrier proteins and adenylation domains using nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics, and mutational studies. Three peptidyl carrier proteins, PigG, PltL, and RedO, in addition to their cognate adenylation domains, PigI, PltF, and RedM, were investigated for their cross-species activity. Of the three peptidyl carrier proteins, only PigG showed substantial cross-pathway activity. Characterization of the novel NMR solution structure of holo-PigG and molecular dynamics simulations of holo-PltL and holo-PigG revealed differences in structures and dynamics of these carrier proteins. NMR titration experiments revealed perturbations of the chemical shifts of the loop 1 residues of these peptidyl carrier proteins upon their interaction with the adenylation domain. These experiments revealed a key region for the protein-protein interaction. Mutational studies supported the role of loop 1 in molecular recognition, as mutations to this region of the peptidyl carrier proteins significantly modulated their activities.

Hi-C Observations of an Active Region Corona, and Investigation of the Underlying Magnetic Structure

NASA Technical Reports Server (NTRS)

Tiwari, S. K.; Alexander, C. E.; Winebarger, A.; Moore, R. L.

2014-01-01

The solar corona is much hotter (>=10(exp 6) K) than its surface (approx 6000 K), puzzling astrophysicists for several decades. Active region (AR) corona is again hotter than the quiet Sun (QS) corona by a factor of 4-10. The most widely accepted mechanism that could heat the active region corona is the energy release by current dissipation via reconnection of braided magnetic field structure, first proposed by E. N. Parker three decades ago. The first observational evidence for this mechanism has only recently been presented by Cirtain et al. by using High-resolution Coronal Imager (Hi-C) observations of an AR corona at a spatial resolution of 0.2 arcsec, which is required to resolve the coronal loops, and was not available before the rocket flight of Hi-C in July 2012. The Hi-C project is led by NASA/MSFC. In the case of the QS, work done by convection/granulation on the inter-granular feet of the coronal field lines translates into the heat observed in the corona. In the case of the AR, as here, there could be flux emergence, cancellation/submergence, or shear flows generating large stress and tension in coronal field loops which is released as heat in the corona. We are currently investigating the changes taking place in photospheric feet of the magnetic field involved with brightenings in the Hi-C AR corona. For this purpose, we are also using SDO/AIA data of +/- 2 hours around the 5 minutes Hi-C flight. In the present talk, I will first summarize some of the results of the Hi-C observations and then present some results from our recent analysis on what photospheric processes feed the magnetic energy that dissipates into heat in coronal loops.

ANALYSIS OF CORONAL RAIN OBSERVED BY IRIS , HINODE /SOT, AND SDO /AIA: TRANSVERSE OSCILLATIONS, KINEMATICS, AND THERMAL EVOLUTION

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

Kohutova, P.; Verwichte, E., E-mail: p.kohutova@warwick.ac.uk

Coronal rain composed of cool plasma condensations falling from coronal heights along magnetic field lines is a phenomenon occurring mainly in active region coronal loops. Recent high-resolution observations have shown that coronal rain is much more common than previously thought, suggesting its important role in the chromosphere-corona mass cycle. We present the analysis of MHD oscillations and kinematics of the coronal rain observed in chromospheric and transition region lines by the Interface Region Imaging Spectrograph (IRIS) , the Hinode Solar Optical Telescope (SOT), and the Solar Dynamics Observatory ( SDO) Atmospheric Imaging Assembly (AIA). Two different regimes of transverse oscillationsmore » traced by the rain are detected: small-scale persistent oscillations driven by a continuously operating process and localized large-scale oscillations excited by a transient mechanism. The plasma condensations are found to move with speeds ranging from few km s{sup −1} up to 180 km s{sup −1} and with accelerations largely below the free-fall rate, likely explained by pressure effects and the ponderomotive force resulting from the loop oscillations. The observed evolution of the emission in individual SDO /AIA bandpasses is found to exhibit clear signatures of a gradual cooling of the plasma at the loop top. We determine the temperature evolution of the coronal loop plasma using regularized inversion to recover the differential emission measure (DEM) and by forward modeling the emission intensities in the SDO /AIA bandpasses using a two-component synthetic DEM model. The inferred evolution of the temperature and density of the plasma near the apex is consistent with the limit cycle model and suggests the loop is going through a sequence of periodically repeating heating-condensation cycles.« less

Submembranous recruitment of creatine kinase B supports formation of dynamic actin-based protrusions of macrophages and relies on its C-terminal flexible loop.

PubMed

Venter, Gerda; Polling, Saskia; Pluk, Helma; Venselaar, Hanka; Wijers, Mietske; Willemse, Marieke; Fransen, Jack A M; Wieringa, Bé

2015-02-01

Subcellular partitioning of creatine kinase contributes to the formation of patterns in intracellular ATP distribution and the fuelling of cellular processes with a high and sudden energy demand. We have previously shown that brain-type creatine kinase (CK-B) accumulates at the phagocytic cup in macrophages where it is involved in the compartmentalized generation of ATP for actin remodeling. Here, we report that CK-B catalytic activity also helps in the formation of protrusive ruffle structures which are actin-dependent and abundant on the surface of both unstimulated and LPS-activated macrophages. Recruitment of CK-B to these structures occurred transiently and inhibition of the enzyme's catalytic activity with cyclocreatine led to a general smoothening of surface morphology as visualized by scanning electron microscopy. Comparison of the dynamics of distribution of YFP-tagged CK-mutants and isoforms by live imaging revealed that amino acid residues in the C-terminal segment (aa positions 323-330) that forms one of the protein's two mobile loops are involved in partitioning over inner regions of the cytosol and nearby sites where membrane protrusions occur during induction of phagocytic cup formation. Although wt CK-B, muscle-type CK (CK-M), and a catalytically dead CK-B-E232Q mutant with intact loop region were normally recruited from the cytosolic pool, no dynamic transition to the phagocytic cup area was seen for the CK-homologue arginine kinase and a CK-B-D326A mutant protein. Bioinformatics analysis helped us to predict that conformational flexibility of the C-terminal loop, independent of conformational changes induced by substrate binding or catalytic activity, is likely involved in exposing the enzyme for binding at or near the sites of membrane protrusion formation. Copyright © 2014 Elsevier GmbH. All rights reserved.

LINE-OF-SIGHT SHELL STRUCTURE OF THE CYGNUS LOOP

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

Uchida, Hiroyuki; Tsunemi, Hiroshi; Katsuda, Satoru

We conducted a comprehensive study on the shell structure of the Cygnus Loop using 41 observation data obtained by the Suzaku and the XMM-Newton satellites. To investigate the detailed plasma structure of the Cygnus Loop, we divided our fields of view into 1042 box regions. From the spectral analysis, the spectra obtained from the limb of the Loop are well fitted by the single-component non-equilibrium ionization plasma model. On the other hand, the spectra obtained from the inner regions are well fitted by the two-component model. As a result, we confirmed that the low-temperature and high-temperature components originated from themore » surrounding interstellar matter (ISM) and the ejecta of the Loop, respectively. From the best-fit results, we showed a flux distribution of the ISM component. The distribution clearly shows the limb-brightening structure, and we found out some low-flux regions. Among them, the south blowout region has the lowest flux. We also found other large low-flux regions at slightly west and northeast from the center. We estimated the former thin shell region to be approx1.{sup 0}3 in diameter and concluded that there exists a blowout along the line of sight in addition to the south blowout. We also calculated the emission measure distribution of the ISM component and showed that the Cygnus Loop is far from the result obtained by a simple Sedov evolution model. From the results, we support that the Cygnus Loop originated from a cavity explosion. The emission measure distribution also suggests that the cavity-wall density is higher in the northeast than that in the southwest. These results suggest that the thickness of the cavity wall surrounding the Cygnus Loop is not uniform.« less

Cap-independent translation of human SP-A 5′-UTR variants: a double-loop structure and cis-element contribution

PubMed Central

Wang, Guirong; Guo, Xiaoxuan; Silveyra, Patricia; Kimball, Scot R.; Floros, Joanna

2009-01-01

Human surfactant protein A (hSP-A), a molecule of innate immunity and surfactant-related functions, consists of two functional genes, SP-A1 and SP-A2. SP-A expression is regulated by several factors including environmental stressors. SP-A1 and SP-A2 5′-untranslated region (5′-UTR) splice variants have a differential impact on translation efficiency and mRNA stability. To study whether these variants mediate internal ribosome entry site (IRES) activity (i.e., cap-independent translation), we performed transient transfection experiments in H441 cells with constructs containing one SP-A1 (A′D′, AB′D′, or A′CD′) or SP-A2 (ABD) 5′-UTR splice variant between the Renilla and firefly luciferase genes of a bicistronic reporter vector. We found that 1) variants A′D′, ABD, and AB′D′ exhibit significantly higher IRES activities than negative control (no SP-A 5′-UTR) and A′CD′ has no activity; the order of highest IRES activity was ABD > A′D′ > AB′D; 2) IRES activity of ABD significantly increased in response to diesel particulate matter (20 μg/ml) but not in response to ozone (1 ppm for 1 h); 3) deletion mutants of ABD revealed regulatory elements associated with IRES activity; one at the end of exon A attenuated activity, whereas a region containing a short adenosine-rich motif in the second half of exon B and the start of exon D enhanced activity; 4) elimination of a predicted double-loop structure or increase in free energy significantly reduced IRES activity; 5) elimination of one or both double-loop structures in A′D′ did not affect cap-dependent translation activity. Thus several factors, including cis-elements and secondary structure type and stability, are required for hSP-A 5′-UTR variant-mediated cap-independent translation. PMID:19181744

On the nature of fast sausage waves in coronal loops

NASA Astrophysics Data System (ADS)

Bahari, Karam

2018-05-01

The effect of the parameters of coronal loops on the nature of fast sausage waves are investigated. To do this three models of the coronal loop considered, a simple loop model, a current-carrying loop model and a model with radially structured density called "Inner μ" profile. For all the models the Magnetohydrodynamic (MHD) equations solved analytically in the linear approximation and the restoring forces of oscillations obtained. The ratio of the magnetic tension force to the pressure gradient force obtained as a function of the distance from the axis of the loop. In the simple loop model for all values of the loop parameters the fast sausages wave have a mixed nature of Alfvénic and fast MHD waves, in the current-carrying loop model with thick annulus and low density contrast the fast sausage waves can be considered as purely Alfvénic wave in the core region of the loop, and in the "Inner μ" profile for each set of the parameters of the loop the wave can be considered as a purely Alfvénic wave in some regions of the loop.

Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid

PubMed Central

Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi

2016-01-01

The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane. PMID:27330112

Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid.

PubMed

Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi

2016-07-05

The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane.

The NST observation of a small loop eruption in He I D3 line on 2016 May 30

NASA Astrophysics Data System (ADS)

Kim, Yeon-Han; Xu, Yan; Bong, Su-Chan; Lim, Eunkyung; Yang, Heesu; Park, Young-Deuk; Yurchyshyn, Vasyl B.; Ahn, Kwangsu; Goode, Philip R.

2017-08-01

Since the He I D3 line has a unique response to a flare impact on the low solar atmosphere, it can be a powerful diagnostic tool for energy transport processes. In order to obtain comprehensive data sets for studying solar flare activities in D3 spectral line, we performed observations for several days using the 1.6m New Solar Telescope of Big Bear Solar Observatory (BBSO) in 2015 and 2016, equipped with the He I D3 filter, the photospheric broadband filter, and Near IR imaging spectrograph (NIRIS). On 2016 May 30, we observed a small loop eruption in He I D3 images associated with a B class brightening, which is occurred around 17:10 UT in a small active region, and dynamic variations of photospheric features in G-band images. Accordingly, the cause of the loop eruption can be magnetic reconnection driven by photospheric plasma motions. In this presentation, we will give the observation results and the interpretation.

Tight Loops Close-Up [video

NASA Image and Video Library

2014-05-19

NASA's Solar Dynamics Observatory (SDO) zoomed in almost to its maximum level to watch tight, bright loops and much longer, softer loops shift and sway above an active region on the sun, while a darker blob of plasma in their midst was pulled about every which way (May 13-14, 2014). The video clip covers just over a day beginning at 14:19 UT on May 13. The frames were taken in the 171-angstroms wavelength of extreme ultraviolet light, but colorized red, instead of its usual bronze tone. This type of dynamic activity continues almost non-stop on the sun as opposing magnetic forces tangle with each other. Credit: NASA/Solar Dynamics Observatory NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Automatic Event Detection in Search for Inter-Moss Loops in IRIS Si IV Slit-Jaw Images

NASA Technical Reports Server (NTRS)

Fayock, Brian; Winebarger, Amy R.; De Pontieu, Bart

2015-01-01

The high-resolution capabilities of the Interface Region Imaging Spectrometer (IRIS) mission have allowed the exploration of the finer details of the solar magnetic structure from the chromosphere to the lower corona that have previously been unresolved. Of particular interest to us are the relatively short-lived, low-lying magnetic loops that have foot points in neighboring moss regions. These inter-moss loops have also appeared in several AIA pass bands, which are generally associated with temperatures that are at least an order of magnitude higher than that of the Si IV emission seen in the 1400 angstrom pass band of IRIS. While the emission lines seen in these pass bands can be associated with a range of temperatures, the simultaneous appearance of these loops in IRIS 1400 and AIA 171, 193, and 211 suggest that they are not in ionization equilibrium. To study these structures in detail, we have developed a series of algorithms to automatically detect signal brightening or events on a pixel-by-pixel basis and group them together as structures for each of the above data sets. These algorithms have successfully picked out all activity fitting certain adjustable criteria. The resulting groups of events are then statistically analyzed to determine which characteristics can be used to distinguish the inter-moss loops from all other structures. While a few characteristic histograms reveal that manually selected inter-moss loops lie outside the norm, a combination of several characteristics will need to be used to determine the statistical likelihood that a group of events be categorized automatically as a loop of interest. The goal of this project is to be able to automatically pick out inter-moss loops from an entire data set and calculate the characteristics that have previously been determined manually, such as length, intensity, and lifetime. We will discuss the algorithms, preliminary results, and current progress of automatic characterization.

The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription

PubMed Central

Yun, Won Ju; Kim, Yea Woon; Kang, Yujin; Lee, Jungbae; Dean, Ann; Kim, AeRi

2014-01-01

TAL1 is a key hematopoietic transcription factor that binds to regulatory regions of a large cohort of erythroid genes as part of a complex with GATA-1, LMO2 and Ldb1. The complex mediates long-range interaction between the β-globin locus control region (LCR) and active globin genes, and although TAL1 is one of the two DNA-binding complex members, its role is unclear. To explore the role of TAL1 in transcription activation of the human γ-globin genes, we reduced the expression of TAL1 in erythroid K562 cells using lentiviral short hairpin RNA, compromising its association in the β-globin locus. In the TAL1 knockdown cells, the γ-globin transcription was reduced to 35% and chromatin looping of the Gγ-globin gene with the LCR was disrupted with decreased occupancy of the complex member Ldb1 and LMO2 in the locus. However, GATA-1 binding, DNase I hypersensitive site formation and several histone modifications were largely maintained across the β-globin locus. In addition, overexpression of TAL1 increased the γ-globin transcription and increased interaction frequency between the Gγ-globin gene and LCR. These results indicate that TAL1 plays a critical role in chromatin loop formation between the γ-globin genes and LCR, which is a critical step for the transcription of the γ-globin genes. PMID:24470145

The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription.

PubMed

Yun, Won Ju; Kim, Yea Woon; Kang, Yujin; Lee, Jungbae; Dean, Ann; Kim, AeRi

2014-04-01

TAL1 is a key hematopoietic transcription factor that binds to regulatory regions of a large cohort of erythroid genes as part of a complex with GATA-1, LMO2 and Ldb1. The complex mediates long-range interaction between the β-globin locus control region (LCR) and active globin genes, and although TAL1 is one of the two DNA-binding complex members, its role is unclear. To explore the role of TAL1 in transcription activation of the human γ-globin genes, we reduced the expression of TAL1 in erythroid K562 cells using lentiviral short hairpin RNA, compromising its association in the β-globin locus. In the TAL1 knockdown cells, the γ-globin transcription was reduced to 35% and chromatin looping of the (G)γ-globin gene with the LCR was disrupted with decreased occupancy of the complex member Ldb1 and LMO2 in the locus. However, GATA-1 binding, DNase I hypersensitive site formation and several histone modifications were largely maintained across the β-globin locus. In addition, overexpression of TAL1 increased the γ-globin transcription and increased interaction frequency between the (G)γ-globin gene and LCR. These results indicate that TAL1 plays a critical role in chromatin loop formation between the γ-globin genes and LCR, which is a critical step for the transcription of the γ-globin genes.

CLOSED-FIELD CORONAL HEATING DRIVEN BY WAVE TURBULENCE

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

Downs, Cooper; Lionello, Roberto; Mikić, Zoran

To simulate the energy balance of coronal plasmas on macroscopic scales, we often require the specification of the coronal heating mechanism in some functional form. To go beyond empirical formulations and to build a more physically motivated heating function, we investigate the wave-turbulence-driven (WTD) phenomenology for the heating of closed coronal loops. Our implementation is designed to capture the large-scale propagation, reflection, and dissipation of wave turbulence along a loop. The parameter space of this model is explored by solving the coupled WTD and hydrodynamic evolution in 1D for an idealized loop. The relevance to a range of solar conditionsmore » is also established by computing solutions for over one hundred loops extracted from a realistic 3D coronal field. Due to the implicit dependence of the WTD heating model on loop geometry and plasma properties along the loop and at the footpoints, we find that this model can significantly reduce the number of free parameters when compared to traditional empirical heating models, and still robustly describe a broad range of quiet-Sun and active region conditions. The importance of the self-reflection term in producing relatively short heating scale heights and thermal nonequilibrium cycles is also discussed.« less

Toward a Quantitative Comparison of Magnetic Field Extrapolations and Observed Coronal Loops

NASA Astrophysics Data System (ADS)

Warren, Harry P.; Crump, Nicholas A.; Ugarte-Urra, Ignacio; Sun, Xudong; Aschwanden, Markus J.; Wiegelmann, Thomas

2018-06-01

It is widely believed that loops observed in the solar atmosphere trace out magnetic field lines. However, the degree to which magnetic field extrapolations yield field lines that actually do follow loops has yet to be studied systematically. In this paper, we apply three different extrapolation techniques—a simple potential model, a nonlinear force-free (NLFF) model based on photospheric vector data, and an NLFF model based on forward fitting magnetic sources with vertical currents—to 15 active regions that span a wide range of magnetic conditions. We use a distance metric to assess how well each of these models is able to match field lines to the 12202 loops traced in coronal images. These distances are typically 1″–2″. We also compute the misalignment angle between each traced loop and the local magnetic field vector, and find values of 5°–12°. We find that the NLFF models generally outperform the potential extrapolation on these metrics, although the differences between the different extrapolations are relatively small. The methodology that we employ for this study suggests a number of ways that both the extrapolations and loop identification can be improved.

Conformation of receptor-bound visual arrestin.

PubMed

Kim, Miyeon; Vishnivetskiy, Sergey A; Van Eps, Ned; Alexander, Nathan S; Cleghorn, Whitney M; Zhan, Xuanzhi; Hanson, Susan M; Morizumi, Takefumi; Ernst, Oliver P; Meiler, Jens; Gurevich, Vsevolod V; Hubbell, Wayne L

2012-11-06

Arrestin-1 (visual arrestin) binds to light-activated phosphorylated rhodopsin (P-Rh*) to terminate G-protein signaling. To map conformational changes upon binding to the receptor, pairs of spin labels were introduced in arrestin-1 and double electron-electron resonance was used to monitor interspin distance changes upon P-Rh* binding. The results indicate that the relative position of the N and C domains remains largely unchanged, contrary to expectations of a "clam-shell" model. A loop implicated in P-Rh* binding that connects β-strands V and VI (the "finger loop," residues 67-79) moves toward the expected location of P-Rh* in the complex, but does not assume a fully extended conformation. A striking and unexpected movement of a loop containing residue 139 away from the adjacent finger loop is observed, which appears to facilitate P-Rh* binding. This change is accompanied by smaller movements of distal loops containing residues 157 and 344 at the tips of the N and C domains, which correspond to "plastic" regions of arrestin-1 that have distinct conformations in monomers of the crystal tetramer. Remarkably, the loops containing residues 139, 157, and 344 appear to have high flexibility in both free arrestin-1 and the P-Rh*complex.

Closed-field Coronal Heating Driven by Wave Turbulence

NASA Astrophysics Data System (ADS)

Downs, Cooper; Lionello, Roberto; Mikić, Zoran; Linker, Jon A.; Velli, Marco

2016-12-01

To simulate the energy balance of coronal plasmas on macroscopic scales, we often require the specification of the coronal heating mechanism in some functional form. To go beyond empirical formulations and to build a more physically motivated heating function, we investigate the wave-turbulence-driven (WTD) phenomenology for the heating of closed coronal loops. Our implementation is designed to capture the large-scale propagation, reflection, and dissipation of wave turbulence along a loop. The parameter space of this model is explored by solving the coupled WTD and hydrodynamic evolution in 1D for an idealized loop. The relevance to a range of solar conditions is also established by computing solutions for over one hundred loops extracted from a realistic 3D coronal field. Due to the implicit dependence of the WTD heating model on loop geometry and plasma properties along the loop and at the footpoints, we find that this model can significantly reduce the number of free parameters when compared to traditional empirical heating models, and still robustly describe a broad range of quiet-Sun and active region conditions. The importance of the self-reflection term in producing relatively short heating scale heights and thermal nonequilibrium cycles is also discussed.

Expanding and Contracting Coronal Loops as Evidence of Vortex Flows Induced by Solar Eruptions

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

Dudík, J.; Zuccarello, F. P.; Aulanier, G.

Eruptive solar flares were predicted to generate large-scale vortex flows at both sides of the erupting magnetic flux rope. This process is analogous to a well-known hydrodynamic process creating vortex rings. The vortices lead to advection of closed coronal loops located at the peripheries of the flaring active region. Outward flows are expected in the upper part and returning flows in the lower part of the vortex. Here, we examine two eruptive solar flares, the X1.1-class flare SOL2012-03-05T03:20 and the C3.5-class SOL2013-06-19T07:29. In both flares, we find that the coronal loops observed by the Atmospheric Imaging Assembly in its 171more » Å, 193 Å, or 211 Å passbands show coexistence of expanding and contracting motions, in accordance with the model prediction. In the X-class flare, multiple expanding and contracting loops coexist for more than 35 minutes, while in the C-class flare, an expanding loop in 193 Å appears to be close by and cotemporal with an apparently imploding loop arcade seen in 171 Å. Later, the 193 Å loop also switches to contraction. These observations are naturally explained by vortex flows present in a model of eruptive solar flares.« less

Loop III region of platelet-derived growth factor (PDGF) B-chain mediates binding to PDGF receptors and heparin.

PubMed Central

Schilling, D; Reid IV, J D; Hujer, A; Morgan, D; Demoll, E; Bummer, P; Fenstermaker, R A; Kaetzel, D M

1998-01-01

Site-directed mutagenesis of the platelet-derived growth factor (PDGF) B-chain was conducted to determine the importance of cationic amino acid residues (Arg160-Lys161-Lys162; RKK) located within the loop III region in mediating the biological and cell-association properties of the molecule. Binding to both PDGF alpha-and beta-receptors was inhibited by the conversion of all three cationic residues into anionic glutamates (RKK-->EEE), whereas an RKK-->SSS mutant also exhibited a modest loss in affinity for beta-receptors. Replacements with serine at either Arg160 (RKK-->SKK) or at all three positions (RKK-->SSS) had little effect on binding to alpha-receptors. Replacements with either glutamic or serine residues at any of the three positions also resulted in significant inhibition of heparin-binding activity. Furthermore, the RKK-->EEE mutant exhibited decreased association with the cell surface and accumulated in the culture medium as 29-32 kDa forms. Stable transfection of U87 astrocytoma cells with RKK-->EEE mutants of either the A-chain or the B-chain inhibited malignant growth in athymic nude mice. Despite altered receptor-binding activities, each of the loop III mutants retained full mitogenic activity when applied to cultured Swiss 3T3 cells. CD spectrophotometric analysis of the RKK-->EEE mutant revealed a secondary structure indistinguishable from the wild type, with a high degree of beta-sheet structure and random coil content (50% and 43% respectively). These findings indicate an important role of the Arg160-Lys161-Lys162 sequence in mediating the biological and cell-associative activities of the PDGF-BB homodimer, and reveal that the mitogenic activity of PDGF-BB is insufficient to mediate its full oncogenic properties. PMID:9677323

Evidence for Nonuniform Heating of Coronal Loops Inferred from Multithread Modeling of TRACE Data

NASA Astrophysics Data System (ADS)

Aschwanden, Markus J.; Nightingale, Richard W.; Alexander, David

2000-10-01

The temperature Te(s) and density structure ne(s) of active region loops in EUV observed with TRACE is modeled with a multithread model, synthesized from the summed emission of many loop threads that have a distribution of maximum temperatures and that satisfy the steady state Rosner-Tucker-Vaiana (RTV) scaling law, modified by Serio et al. for gravitational stratification (called RTVSp in the following). In a recent Letter, Reale & Peres demonstrated that this method can explain the almost isothermal appearance of TRACE loops (observed by Lenz et al.) as derived from the filter-ratio method. From model-fitting of the 171 and 195 Å fluxes of 41 loops, which have loop half-lengths in the range of L=4-320 Mm, we find that (1) the EUV loops consist of near-isothermal loop threads with substantially smaller temperature gradients than are predicted by the RTVSp model; (2) the loop base pressure, p0~0.3+/-0.1 dynes cm-2, is independent of the loop length L, and it agrees with the RTVSp model for the shortest loops but exceeds the RTVSp model up to a factor of 35 for the largest loops; and (3) the pressure scale height is consistent with hydrostatic equilibrium for the shortest loops but exceeds the temperature scale height up to a factor of ~3 for the largest loops. The data indicate that cool EUV loops in the temperature range of Te~0.8-1.6 MK cannot be explained with the static steady state RTVSp model in terms of uniform heating but are fully consistent with Serio's model in the case of nonuniform heating (RTVSph), with heating scale heights in the range of sH=17+/-6 Mm. This heating function provides almost uniform heating for small loops (L<~20 Mm), but restricts heating to the footpoints of large loops (L~50-300 Mm).

Proteins with Novel Structure, Function and Dynamics

NASA Technical Reports Server (NTRS)

Pohorille, Andrew

2014-01-01

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Three-dimensional geometry of coronal loops inferred by the Principal Component Analysis

NASA Astrophysics Data System (ADS)

Nisticò, Giuseppe; Nakariakov, Valery

We propose a new method for the determination of the three dimensional (3D) shape of coronal loops from stereoscopy. The common approach requires to find a 1D geometric curve, as circumference or ellipse, that best-fits the 3D tie-points which sample the loop shape in a given coordinate system. This can be easily achieved by the Principal Component (PC) analysis. It mainly consists in calculating the eigenvalues and eigenvectors of the covariance matrix of the 3D tie-points: the eigenvalues give a measure of the variability of the distribution of the tie-points, and the corresponding eigenvectors define a new cartesian reference frame directly related to the loop. The eigenvector associated with the smallest eigenvalues defines the normal to the loop plane, while the other two determine the directions of the loop axes: the major axis is related to the largest eigenvalue, and the minor axis with the second one. The magnitude of the axes is directly proportional to the square roots of these eigenvalues. The technique is fast and easily implemented in some examples, returning best-fitting estimations of the loop parameters and 3D reconstruction with a reasonable small number of tie-points. The method is suitable for serial reconstruction of coronal loops in active regions, providing a useful tool for comparison between observations and theoretical magnetic field extrapolations from potential or force-free fields.

Anatomical Modularity of Verbal Working Memory? Functional Anatomical Evidence from a Famous Patient with Short-Term Memory Deficits.

PubMed

Paulesu, Eraldo; Shallice, Tim; Danelli, Laura; Sberna, Maurizio; Frackowiak, Richard S J; Frith, Chris D

2017-01-01

Cognitive skills are the emergent property of distributed neural networks. The distributed nature of these networks does not necessarily imply a lack of specialization of the individual brain structures involved. However, it remains questionable whether discrete aspects of high-level behavior might be the result of localized brain activity of individual nodes within such networks. The phonological loop of working memory, with its simplicity, seems ideally suited for testing this possibility. Central to the development of the phonological loop model has been the description of patients with focal lesions and specific deficits. As much as the detailed description of their behavior has served to refine the phonological loop model, a classical anatomoclinical correlation approach with such cases falls short in telling whether the observed behavior is based on the functions of a neural system resembling that seen in normal subjects challenged with phonological loop tasks or whether different systems have taken over. This is a crucial issue for the cross correlation of normal cognition, normal physiology, and cognitive neuropsychology. Here we describe the functional anatomical patterns of JB, a historical patient originally described by Warrington et al. (1971), a patient with a left temporo-parietal lesion and selective short phonological store deficit. JB was studied with the H 2 15 O PET activation technique during a rhyming task, which primarily depends on the rehearsal system of the phonological loop. No residual function was observed in the left temporo-parietal junction, a region previously associated with the phonological buffer of working memory. However, Broca's area, the major counterpart of the rehearsal system, was the major site of activation during the rhyming task. Specific and autonomous activation of Broca's area in the absence of afferent inputs from the other major anatomical component of the phonological loop shows that a certain degree of functional independence or modularity exists in this distributed anatomical-cognitive system.

Anatomical Modularity of Verbal Working Memory? Functional Anatomical Evidence from a Famous Patient with Short-Term Memory Deficits

PubMed Central

Paulesu, Eraldo; Shallice, Tim; Danelli, Laura; Sberna, Maurizio; Frackowiak, Richard S. J.; Frith, Chris D.

2017-01-01

Cognitive skills are the emergent property of distributed neural networks. The distributed nature of these networks does not necessarily imply a lack of specialization of the individual brain structures involved. However, it remains questionable whether discrete aspects of high-level behavior might be the result of localized brain activity of individual nodes within such networks. The phonological loop of working memory, with its simplicity, seems ideally suited for testing this possibility. Central to the development of the phonological loop model has been the description of patients with focal lesions and specific deficits. As much as the detailed description of their behavior has served to refine the phonological loop model, a classical anatomoclinical correlation approach with such cases falls short in telling whether the observed behavior is based on the functions of a neural system resembling that seen in normal subjects challenged with phonological loop tasks or whether different systems have taken over. This is a crucial issue for the cross correlation of normal cognition, normal physiology, and cognitive neuropsychology. Here we describe the functional anatomical patterns of JB, a historical patient originally described by Warrington et al. (1971), a patient with a left temporo-parietal lesion and selective short phonological store deficit. JB was studied with the H215O PET activation technique during a rhyming task, which primarily depends on the rehearsal system of the phonological loop. No residual function was observed in the left temporo-parietal junction, a region previously associated with the phonological buffer of working memory. However, Broca's area, the major counterpart of the rehearsal system, was the major site of activation during the rhyming task. Specific and autonomous activation of Broca's area in the absence of afferent inputs from the other major anatomical component of the phonological loop shows that a certain degree of functional independence or modularity exists in this distributed anatomical-cognitive system. PMID:28567009

Decaying and decayless transverse oscillations of a coronal loop

NASA Astrophysics Data System (ADS)

Nisticò, G.; Nakariakov, V. M.; Verwichte, E.

2013-04-01

Aims: We investigate kink oscillations of loops observed in an active region with the Atmospheric Imaging Assembly (AIA) instrument on board the Solar Dynamics Observatory (SDO) spacecraft before and after a flare. Methods: The oscillations were depicted and analysed with time-distance maps, extracted from the cuts taken parallel or perpendicular to the loop axis. Moving loops were followed in time with steadily moving slits. The period of oscillations and its time variation were determined by best-fitting harmonic functions. Results: We show that before and well after the occurrence of the flare, the loops experience low-amplitude decayless oscillations. The flare and the coronal mass ejection associated to it trigger large-amplitude oscillations that decay exponentially in time. The periods of the kink oscillations in both regimes (about 240 s) are similar. An empirical model of the phenomenon in terms of a damped linear oscillator excited by a continuous low-amplitude harmonic driver and by an impulsive high-amplitude driver is found to be consistent with the observations. Two movies are available in electronic form at http://www.aanda.org

Measuring Temperature-Dependent Propagating Disturbances in Coronal Fan Loops Using Multiple SDO-AIA Channels and Surfing Transform Technique

NASA Technical Reports Server (NTRS)

Uritskiy, Vadim M.; Davila, Joseph M.; Viall, Nicholeen M.; Ofman, Leon

2013-01-01

A set of co-aligned high resolution images from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO) is used to investigate propagating disturbances (PDs) in warm fan loops at the periphery of a non-flaring active region NOAA AR 11082. To measure PD speeds at multiple coronal temperatures, a new data analysis methodology is proposed enabling quantitative description of sub visual coronal motions with low signal-to-noise ratios of the order of 0.1. The technique operates with a set of one-dimensional surfing signals extracted from position-timeplots of several AIA channels through a modified version of Radon transform. The signals are used to evaluate a two-dimensional power spectral density distribution in the frequency - velocity space which exhibits a resonance in the presence of quasi-periodic PDs. By applying this analysis to the same fan loop structures observed in several AIA channels, we found that the traveling velocity of PDs increases with the temperature of the coronal plasma following the square root dependence predicted for the slow mode magneto-acoustic wave which seems to be the dominating wave mode in the studied loop structures. This result extends recent observations by Kiddie et al. (2012) to a more general class of fan loop systems not associated with sunspots and demonstrating consistent slow mode activity in up to four AIA channels.

RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination.

PubMed

Ribeiro de Almeida, Claudia; Dhir, Somdutta; Dhir, Ashish; Moghaddam, Amin E; Sattentau, Quentin; Meinhart, Anton; Proudfoot, Nicholas J

2018-05-17

Class switch recombination (CSR) at the immunoglobulin heavy-chain (IgH) locus is associated with the formation of R-loop structures over switch (S) regions. While these often occur co-transcriptionally between nascent RNA and template DNA, we now show that they also form as part of a post-transcriptional mechanism targeting AID to IgH S-regions. This depends on the RNA helicase DDX1 that is also required for CSR in vivo. DDX1 binds to G-quadruplex (G4) structures present in intronic switch transcripts and converts them into S-region R-loops. This in turn targets the cytidine deaminase enzyme AID to S-regions so promoting CSR. Notably R-loop levels over S-regions are diminished by chemical stabilization of G4 RNA or by the expression of a DDX1 ATPase-deficient mutant that acts as a dominant-negative protein to reduce CSR efficiency. In effect, we provide evidence for how S-region transcripts interconvert between G4 and R-loop structures to promote CSR in the IgH locus. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Molecular Dynamics Analysis Reveals Structural Insights into Mechanism of Nicotine N-Demethylation Catalyzed by Tobacco Cytochrome P450 Mono-Oxygenase

PubMed Central

Wang, Shan; Yang, Shuo; An, Baiyi; Wang, Shichen; Yin, Yuejia; Lu, Yang; Xu, Ying; Hao, Dongyun

2011-01-01

CYP82E4, a cytochrome P450 monooxygenase, has nicotine N-demethylase (NND) activity, which mediates the bioconversion of nicotine into nornicotine in senescing tobacco leaves. Nornicotine is a precursor of the carcinogen, tobacco-specific nitrosamine. CYP82E3 is an ortholog of CYP82E4 with 95% sequence identity, but it lacks NND activity. A recent site-directed mutagenesis study revealed that a single amino acid substitution, i.e., cysteine to tryptophan at the 330 position in the middle of protein, restores the NND activity of CYP82E3 entirely. However, the same amino acid change caused the loss of the NND activity of CYP82E4. To determine the mechanism of the functional turnover of the two molecules, four 3D structures, i.e., the two molecules and their corresponding cys–trp mutants were modeled. The resulting structures exhibited that the mutation site is far from the active site, which suggests that no direct interaction occurs between the two sites. Simulation studies in different biological scenarios revealed that the mutation introduces a conformation drift with the largest change at the F-G loop. The dynamics trajectories analysis using principal component analysis and covariance analysis suggests that the single amino acid change causes the opening and closing of the transfer channels of the substrates, products, and water by altering the motion of the F-G and B-C loops. The motion of helix I is also correlated with the motion of both the F-G loop and the B-C loop and; the single amino acid mutation resulted in the curvature of helix I. These results suggest that the single amino acid mutation outside the active site region may have indirectly mediated the flexibility of the F-G and B-C loops through helix I, causing a functional turnover of the P450 monooxygenase. PMID:21858078

The solution structure of the prototype foamy virus RNase H domain indicates an important role of the basic loop in substrate binding.

PubMed

Leo, Berit; Schweimer, Kristian; Rösch, Paul; Hartl, Maximilian J; Wöhrl, Birgitta M

2012-09-10

The ribonuclease H (RNase H) domains of retroviral reverse transcriptases play an essential role in the replication cycle of retroviruses. During reverse transcription of the viral genomic RNA, an RNA/DNA hybrid is created whose RNA strand needs to be hydrolyzed by the RNase H to enable synthesis of the second DNA strand by the DNA polymerase function of the reverse transcriptase. Here, we report the solution structure of the separately purified RNase H domain from prototype foamy virus (PFV) revealing the so-called C-helix and the adjacent basic loop, which both were suggested to be important in substrate binding and activity. The solution structure of PFV RNase H shows that it contains a mixed five-stranded β-sheet, which is sandwiched by four α-helices (A-D), including the C-helix, on one side and one α-helix (helix E) on the opposite side. NMR titration experiments demonstrate that upon substrate addition signal changes can be detected predominantly in the basic loop as well as in the C-helix. All these regions are oriented towards the bound substrate. In addition, signal intensities corresponding to residues in the B-helix and the active site decrease, while only minor or no changes of the overall structure of the RNase H are detectable upon substrate binding. Dynamic studies confirm the monomeric state of the RNase H domain. Structure comparisons with HIV-1 RNase H, which lacks the basic protrusion, indicate that the basic loop is relevant for substrate interaction, while the C-helix appears to fulfill mainly structural functions, i.e. positioning the basic loop in the correct orientation for substrate binding. The structural data of PFV RNase H demonstrate the importance of the basic loop, which contains four positively charged lysines, in substrate binding and the function of the C-helix in positioning of the loop. In the dimeric full length HIV-1 RT, the function of the basic loop is carried out by a different loop, which also harbors basic residues, derived from the connection domain of the p66 subunit. Our results suggest that RNases H which are also active as separate domains might need a functional basic loop for proper substrate binding.

Coronal Jets in Closed Magnetic Regions on the Sun

NASA Astrophysics Data System (ADS)

Wyper, Peter Fraser; DeVore, C. R.

2015-04-01

Coronal jets are dynamic, collimated structures observed in solar EUV and X-ray emission. They appear predominantly in the open field of coronal holes, but are also observed in areas of closed field, especially active regions. A common feature of coronal jets is that they originate from the field above a parasitic polarity of opposite sign to the surrounding field. Some process - such as instability onset or flux emergence - induces explosive reconnection between the closed “anemone” field and the surrounding open field that generates the jet. The lesser number of coronal jets in closed-field regions suggests a possible stabilizing effect of the closed configuration with respect to coronal jet formation. If the scale of the jet region is small compared with the background loop length, as in for example type II spicules, the nearby magnetic field may be treated as locally open. As such, one would expect that if a stabilizing effect exists it becomes most apparent as the scale of the anemone region approaches that of the background coronal loops.To investigate if coronal jets are indeed suppressed along shorter coronal loops, we performed a number of simulations of jets driven by a rotation of the parasitic polarity (as in the previous open-jet calculations by Pariat et. al 2009, 2010, 2015) embedded in a large-scale closed bipolar field. The simulations were performed with the state of the art Adaptively Refined Magnetohydrodynamics Solver. We will report here how the magnetic configuration above the anemone region determines the nature of the jet, when it is triggered, and how much of the stored magnetic energy is released. We show that regions in which the background field and the parasitic polarity region are of comparable scale naturally suppress explosive energy release. We will also show how in the post-jet relaxation phase a combination of confined MHD waves and weak current layers are generated by the jet along the background coronal loops, both of which may have implications for coronal heating.This work was supported by an appointment to the NASA Postdoctoral Program (P.F.W.) and by NASA’s Living With a Star Targeted Research and Technology program (C.R.D.).

Stability of multiloop LQ regulators with nonlinearities. I - Regions of attraction. II - Regions of ultimate boundedness

NASA Technical Reports Server (NTRS)

Joshi, S. M.

1986-01-01

An investigation is conducted for the closed loop stability of linear time-invariant systems controlled by linear quadratic (LQ) regulators, in cases where nonlinearities exist in the control channels lying outside the stability sector in regions away from the origin. The estimate of the region of attraction thus obtained furnishes methods for the selection of performance function weights for more robust LQ designs. Attention is then given to the closed loop stability of linear time-invariant systems controlled by the LQ regulators when the nonlinearities in the loops escape the stability sector in a bounded region containing the origin.

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

Khlystova, Anna; Toriumi, Shin, E-mail: hlystova@iszf.irk.ru, E-mail: shin.toriumi@nao.ac.jp

We study the plasma flows in the solar photosphere during the emergence of two small active regions, NOAA 9021 and 10768. Using Solar and Heliospheric Observatory /Michelson Doppler Imager data, we find that the strong plasma upflows appear at the initial stage of active region formation, with maximum upflow velocities of −1650 and −1320 m s{sup −1}. The structures with enhanced upflows have size ∼8 Mm in diameter, and they exist for 1–2 hr. The parameters of the enhanced upflows are consistent with those of the large active region NOAA 10488, which may suggest the possibility that the elementary emergingmore » magnetic loops that appear at the earliest phase of active region formation have similar properties, irrespective of scales of active regions. Comparison between the observations and a numerical simulation of magnetic flux emergence shows a striking consistency. We find that the driving force of the plasma upflow is at first the gas pressure gradient and later the magnetic pressure gradient.« less

Conformational flexibility of human casein kinase catalytic subunit explored by metadynamics.

PubMed

Gouron, Aurélie; Milet, Anne; Jamet, Helene

2014-03-04

Casein kinase CK2 is an essential enzyme in higher organisms, catalyzing the transfer of the γ phosphate from ATP to serine and threonine residues on protein substrates. In a number of animal tumors, CK2 activity has been shown to escape normal cellular control, making it a potential target for cancer therapy. Several crystal structures of human CK2 have been published with different conformations for the CK2α catalytic subunit. This variability reflects a high flexibility for two regions of CK2α: the interdomain hinge region, and the glycine-rich loop (p-loop). Here, we present a computational study simulating the equilibrium between three conformations involving these regions. Simulations were performed using well-tempered metadynamics combined with a path collective variables approach. This provides a reference pathway describing the conformational changes being studied, based on analysis of free energy surfaces. The free energies of the three conformations were found to be close and the paths proposed had low activation barriers. Our results indicate that these conformations can exist in water. This information should be useful when designing inhibitors specific to one conformation. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Feedback Synthesizes Neural Codes for Motion.

PubMed

Clarke, Stephen E; Maler, Leonard

2017-05-08

In senses as diverse as vision, hearing, touch, and the electrosense, sensory neurons receive bottom-up input from the environment, as well as top-down input from feedback loops involving higher brain regions [1-4]. Through connectivity with local inhibitory interneurons, these feedback loops can exert both positive and negative control over fundamental aspects of neural coding, including bursting [5, 6] and synchronous population activity [7, 8]. Here we show that a prominent midbrain feedback loop synthesizes a neural code for motion reversal in the hindbrain electrosensory ON- and OFF-type pyramidal cells. This top-down mechanism generates an accurate bidirectional encoding of object position, despite the inability of the electrosensory afferents to generate a consistent bottom-up representation [9, 10]. The net positive activity of this midbrain feedback is additionally regulated through a hindbrain feedback loop, which reduces stimulus-induced bursting and also dampens the ON and OFF cell responses to interfering sensory input [11]. We demonstrate that synthesis of motion representations and cancellation of distracting signals are mediated simultaneously by feedback, satisfying an accepted definition of spatial attention [12]. The balance of excitatory and inhibitory feedback establishes a "focal" distance for optimized neural coding, whose connection to a classic motion-tracking behavior provides new insight into the computational roles of feedback and active dendrites in spatial localization [13, 14]. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Hardware-in-the-Loop Simulator for Software Development for a Mars Airplane

NASA Technical Reports Server (NTRS)

Slagowski, Stefan E.; Vican, Justin E.; Kenney, P. Sean

2007-01-01

Draper Laboratory recently developed a Hardware-In-The-Loop Simulator (HILSIM) to provide a simulation of the Aerial Regional-scale Environmental Survey (ARES) airplane executing a mission in the Martian environment. The HILSIM was used to support risk mitigation activities under the Planetary Airplane Risk Reduction (PARR) program. PARR supported NASA Langley Research Center's (LaRC) ARES proposal efforts for the Mars Scout 2011 opportunity. The HILSIM software was a successful integration of two simulation frameworks, Draper's CSIM and NASA LaRC's Langley Standard Real-Time Simulation in C++ (LaSRS++).

Small Coronal Holes Near Active Regions as Sources of Slow Solar Wind

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

Wang, Y.-M., E-mail: yi.wang@nrl.navy.mil

We discuss the nature of the small areas of rapidly diverging, open magnetic flux that form in the strong unipolar fields at the peripheries of active regions (ARs), according to coronal extrapolations of photospheric field measurements. Because such regions usually have dark counterparts in extreme-ultraviolet (EUV) images, we refer to them as coronal holes, even when they appear as narrow lanes or contain sunspots. Revisiting previously identified “AR sources” of slow solar wind from 1998 and 1999, we find that they are all associated with EUV coronal holes; the absence of well-defined He i 1083.0 nm counterparts to some ofmore » these holes is attributed to the large flux of photoionizing radiation from neighboring AR loops. Examining a number of AR-associated EUV holes during the 2014 activity maximum, we confirm that they are characterized by wind speeds of ∼300–450 km s{sup −1}, O{sup 7+}/O{sup 6+} ratios of ∼0.05–0.4, and footpoint field strengths typically of order 30 G. The close spacing between ARs at sunspot maximum limits the widths of unipolar regions and their embedded holes, while the continual emergence of new flux leads to rapid changes in the hole boundaries. Because of the highly nonradial nature of AR fields, the smaller EUV holes are often masked by the overlying canopy of loops, and may be more visible toward one solar limb than at central meridian. As sunspot activity declines, the AR remnants merge to form much larger, weaker, and longer-lived unipolar regions, which harbor the “classical” coronal holes that produce recurrent high-speed streams.« less

Creating stable stem regions for loop elongation in Fcabs — Insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations

PubMed Central

Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W.; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

2014-01-01

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. PMID:24792385

Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations.

PubMed

Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

2014-09-01

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. Copyright © 2014. Published by Elsevier B.V.

EMC MODEL FORECAST VERIFICATION STATS

Science.gov Websites

48-H FCST 54-H FCST 60-H FCST 72-H FCST 84-H FCST Loop 500 mb Height BIAS and RMSE CONUS VALID 00Z sub-regions) Surface Wind Vector BIAS and RMSE REGION VALID 00Z VALID 12Z VALID 00Z (loop) VALID 12Z (loop) GMC (Gulf of Mexico Coast) * * * * SEC (Southeast Coast) * * * * NEC (Northeast Coast

A Series of Jets that Drove Streamer-Puff CMEs from Giant Active Region of 2014

NASA Technical Reports Server (NTRS)

Panesar, Navdeep K.; Sterling, Alphonse C.; Moore, Ronald L.

2016-01-01

We investigate characteristics of solar coronal jets that originated from active region NOAA 12192 and produced coronal mass ejections (CMEs). This active region produced many non­-jet major flare eruptions (X and M class) that made no CME. A multitude of jets occurred from the southeast edge of the active region, and in contrast to the major-­flare eruptions in the core, six of these jets resulted in CMEs. Our jet observations are from SDO/AIA EUV channels and from Hinode/XRT, and CME observations are from the SOHO/LASCO C2 coronograph. Each jet-­driven CME was relatively slow-­moving (approx. 200 - 300 km/s) compared to most CMEs; had angular width (20deg - 50deg) comparable to that of the streamer base; and was of the "streamer­-puff" variety, whereby a pre-existing streamer was transiently inflated but not removed (blown out) by the passage of the CME. Much of the chromospheric-­temperature plasma of the jets producing the CMEs escaped from the Sun, whereas relatively more of the chromospheric plasma in the non-CME-producing jets fell back to the solar surface. We also found that the CME-producing jets tended to be faster in speed and longer in duration than the non-CME-­producing jets. We expect that the jets result from eruptions of mini-filaments. We further propose that the CMEs are driven by magnetic twist injected into streamer-­base coronal loops when erupting twisted mini-filament field reconnects with the ambient field at the foot of those loops.

A Series of Jets that Drove Streamer-Puff CMEs from Giant Active Region of 2014

NASA Technical Reports Server (NTRS)

Panesar, Navdeep K.; Sterling, Alphonse C.; Moore, Ronald L.

2016-01-01

We investigate characteristics of solar coronal jets that originated from active region NOAA 12192 and produced coronal mass ejections (CMEs). This active region produced many non-jet major flare eruptions (X and M class) that made no CME. A multiitude of jets occurred from the southeast edge of the active region, and in contrast to the major-flare eruptions in the core, six of these jets resulted in CMEs. Our jet observations are from multiple SDO/AIA EUV channels, including 304, 171 and 193 Angstrom, and CME observations are taken from SOHO/LASCO C2 coronograph. Each jet-driven CME was relatively slow-moving (approximately 200 - 300 km s(sup-1) compared to most CMEs; had angular width (20deg - 50deg) comparable to that of the streamer base; and was of the "streamer-puff" variety, whereby a preexisting streamer was transiently inflated but not removed (blown out) by the passage of the CME. Much of the chromospheric-temperature plasma of the jets producing the CMEs escaped from the Sun, whereas relatively more of the chromospheric plasma in the non-CME-producing jets fell back to the solar surface. We also found that the CME-producing jets tended to be faster in speed and longer in duration than the non-CME-producing jets. We expect that the jets result from eruptions of mini-filaments. We further propose that the CMEs are driven by magnetic twist injected into streamer-base coronal loops when erupting twisted mini-filament field reconnects with the ambient field at the foot of those loops.

High-resolution observations of active region moss and its dynamics

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

Morton, R. J.; McLaughlin, J. A., E-mail: richard.morton@northumbria.ac.uk

2014-07-10

The High Resolution Coronal Imager has provided the sharpest view of the EUV corona to date. In this paper, we exploit its impressive resolving power to provide the first analysis of the fine-scale structure of moss in an active region. The data reveal that the moss is made up of a collection of fine threads that have widths with a mean and standard deviation of 440 ± 190 km (FWHM). The brightest moss emission is located at the visible head of the fine-scale structure and the fine structure appears to extend into the lower solar atmosphere. The emission decreases alongmore » the features, implying that the lower sections are most likely dominated by cooler transition region plasma. These threads appear to be the cool, lower legs of the hot loops. In addition, the increased resolution allows for the first direct observation of physical displacements of the moss fine structure in a direction transverse to its central axis. Some of these transverse displacements demonstrate periodic behavior, which we interpret as a signature of kink (Alfvénic) waves. Measurements of the properties of the transverse motions are made and the wave motions have means and standard deviations of 55 ± 37 km for the transverse displacement amplitude, 77 ± 33 s for the period, and 4.7 ± 2.5 km s{sup –1} for the velocity amplitude. The presence of waves in the transition region of hot loops could have important implications for the heating of active regions.« less

Functional sub-division of the Drosophila genome via chromatin looping: the emerging importance of CP190.

PubMed

Ahanger, Sajad H; Shouche, Yogesh S; Mishra, Rakesh K

2013-01-01

Insulators help in organizing the eukaryotic genomes into physically and functionally autonomous regions through the formation of chromatin loops. Recent findings in Drosophila and vertebrates suggest that insulators anchor multiple loci through long-distance interactions which may be mechanistically linked to insulator function. Important to such processes in Drosophila is CP190, a common co-factor of insulator complexes. CP190 is also known to associate with the nuclear matrix, components of the RNAi machinery, active promoters and borders of the repressive chromatin domains. Although CP190 plays a pivotal role in insulator function in Drosophila, vertebrates lack a probable functional equivalent of CP190 and employ CTCF as the major factor to carry out insulator function/chromatin looping. In this review, we discuss the emerging role of CP190 in tethering genome, specifically in the perspective of insulator function in Drosophila. Future studies aiming genome-wide role of CP190 in chromatin looping is likely to give important insights into the mechanism of genome organization.

Functional sub-division of the Drosophila genome via chromatin looping

PubMed Central

Ahanger, Sajad H.; Shouche, Yogesh S.; Mishra, Rakesh K.

2013-01-01

Insulators help in organizing the eukaryotic genomes into physically and functionally autonomous regions through the formation of chromatin loops. Recent findings in Drosophila and vertebrates suggest that insulators anchor multiple loci through long-distance interactions which may be mechanistically linked to insulator function. Important to such processes in Drosophila is CP190, a common co-factor of insulator complexes. CP190 is also known to associate with the nuclear matrix, components of the RNAi machinery, active promoters and borders of the repressive chromatin domains. Although CP190 plays a pivotal role in insulator function in Drosophila, vertebrates lack a probable functional equivalent of CP190 and employ CTCF as the major factor to carry out insulator function/chromatin looping. In this review, we discuss the emerging role of CP190 in tethering genome, specifically in the perspective of insulator function in Drosophila. Future studies aiming genome-wide role of CP190 in chromatin looping is likely to give important insights into the mechanism of genome organization. PMID:23333867

Identification of functional domains in Arabidopsis thaliana mRNA decapping enzyme (AtDcp2)

PubMed Central

Gunawardana, Dilantha; Cheng, Heung-Chin; Gayler, Kenwyn R.

2008-01-01

The Arabidopsis thaliana decapping enzyme (AtDcp2) was characterized by bioinformatics analysis and by biochemical studies of the enzyme and mutants produced by recombinant expression. Three functionally significant regions were detected: (i) a highly disordered C-terminal region with a putative PSD-95, Discs-large, ZO-1 (PDZ) domain-binding motif, (ii) a conserved Nudix box constituting the putative active site and (iii) a putative RNA binding domain consisting of the conserved Box B and a preceding loop region. Mutation of the putative PDZ domain-binding motif improved the stability of recombinant AtDcp2 and secondary mutants expressed in Escherichia coli. Such recombinant AtDcp2 specifically hydrolysed capped mRNA to produce 7-methyl GDP and decapped RNA. AtDcp2 activity was Mn2+- or Mg2+-dependent and was inhibited by the product 7-methyl GDP. Mutation of the conserved glutamate-154 and glutamate-158 in the Nudix box reduced AtDcp2 activity up to 400-fold and showed that AtDcp2 employs the catalytic mechanism conserved amongst Nudix hydrolases. Unlike many Nudix hydrolases, AtDcp2 is refractory to inhibition by fluoride ions. Decapping was dependent on binding to the mRNA moiety rather than to the 7-methyl diguanosine triphosphate cap of the substrate. Mutational analysis of the putative RNA-binding domain confirmed the functional significance of an 11-residue loop region and the conserved Box B. PMID:18025047

Formation of Large-scale Coronal Loops Interconnecting Two Active Regions through Gradual Magnetic Reconnection and an Associated Heating Process

NASA Astrophysics Data System (ADS)

Du, Guohui; Chen, Yao; Zhu, Chunming; Liu, Chang; Ge, Lili; Wang, Bing; Li, Chuanyang; Wang, Haimin

2018-06-01

Coronal loops interconnecting two active regions (ARs), called interconnecting loops (ILs), are prominent large-scale structures in the solar atmosphere. They carry a significant amount of magnetic flux and therefore are considered to be an important element of the solar dynamo process. Earlier observations showed that eruptions of ILs are an important source of CMEs. It is generally believed that ILs are formed through magnetic reconnection in the high corona (>150″–200″), and several scenarios have been proposed to explain their brightening in soft X-rays (SXRs). However, the detailed IL formation process has not been fully explored, and the associated energy release in the corona still remains unresolved. Here, we report the complete formation process of a set of ILs connecting two nearby ARs, with successive observations by STEREO-A on the far side of the Sun and by SDO and Hinode on the Earth side. We conclude that ILs are formed by gradual reconnection high in the corona, in line with earlier postulations. In addition, we show evidence that ILs brighten in SXRs and EUVs through heating at or close to the reconnection site in the corona (i.e., through the direct heating process of reconnection), a process that has been largely overlooked in earlier studies of ILs.

Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

PubMed

Nandy, Suman Kumar; Seal, Alpana

2016-01-01

Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

Structure and Dynamics of Cool Flare Loops Observed by the Interface Region Imaging Spectrograph

NASA Astrophysics Data System (ADS)

Mikuła, K.; Heinzel, P.; Liu, W.; Berlicki, A.

2017-08-01

Flare loops were well observed with the Interface Region Imaging Spectrograph (IRIS) during the gradual phase of two solar flares on 2014 March 29 and 2015 June 22. Cool flare loops are visible in various spectral lines formed at chromospheric and transition-region temperatures and exhibit large downflows which correspond to the standard scenario. The principal aim of this work is to analyze the structure and dynamics of cool flare loops observed in Mg II lines. Synthetic profiles of the Mg II h line are computed using the classical cloud model and assuming a uniform background intensity. In this paper, we study novel IRIS NUV observations of such loops in Mg II h and k lines and also show the behavior of hotter lines detected in the FUV channel. We obtained the spatial evolution of the velocities: near the loop top, the flow velocities are small and they are increasing toward the loop legs. Moreover, from slit-jaw image (SJI) movies, we observe some plasma upflows into the loops, which are also detectable in Mg II spectra. The brightness of the loops systematically decreases with increasing flow velocity, and we ascribe this to the effect of Doppler dimming, which works for Mg II lines. Emission profiles of Mg II were found to be extremely broad, and we explain this through the large unresolved non-thermal motions.

Structure and Dynamics of Cool Flare Loops Observed by the Interface Region Imaging Spectrograph

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

Mikuła, K.; Berlicki, A.; Heinzel, P.

Flare loops were well observed with the Interface Region Imaging Spectrograph ( IRIS ) during the gradual phase of two solar flares on 2014 March 29 and 2015 June 22. Cool flare loops are visible in various spectral lines formed at chromospheric and transition-region temperatures and exhibit large downflows which correspond to the standard scenario. The principal aim of this work is to analyze the structure and dynamics of cool flare loops observed in Mg ii lines. Synthetic profiles of the Mg ii h line are computed using the classical cloud model and assuming a uniform background intensity. In thismore » paper, we study novel IRIS NUV observations of such loops in Mg ii h and k lines and also show the behavior of hotter lines detected in the FUV channel. We obtained the spatial evolution of the velocities: near the loop top, the flow velocities are small and they are increasing toward the loop legs. Moreover, from slit-jaw image (SJI) movies, we observe some plasma upflows into the loops, which are also detectable in Mg ii spectra. The brightness of the loops systematically decreases with increasing flow velocity, and we ascribe this to the effect of Doppler dimming, which works for Mg ii lines. Emission profiles of Mg ii were found to be extremely broad, and we explain this through the large unresolved non-thermal motions.« less

Dynamics of quiescent prominences; Proceedings of the 117th Colloquium of IAU, Hvar, Yugoslavia, Sept. 25-29, 1989

NASA Technical Reports Server (NTRS)

Ruzdjak, Vladimir (Editor); Tandberg-Hanssen, Einar (Editor)

1990-01-01

Topics discussed include formation of a filament around a magnetic region, evolution of fine structures in a filament, the spatial distribution of prominence threads, high resolution analysis of quiescent prominences at NSO/Sacramento Peak Observatory, small-scale Doppler velocities in a quiescent prominence, Doppler velocity oscillations in quiescent prominences, oscillatory relaxation of an eruptive prominence, and matter flow velocities in an active region emission loop observed in H-alpha. Attention is also given to an automated procedure for measurement of prominence transverse velocities, the nonlinear evolution of magnetized filaments, thermal equilibrium of coronal loops and prominence formation, thermal instability in planar coronal strucutres, radiative transfer in cylindrical prominence threads, numerical simulation of a catastrophe model for prominence eruptions, and the law of evolution and destruction of solar prominences.

Far-ultraviolet imagery of the Barnard Loop Nebula

NASA Technical Reports Server (NTRS)

Carruthers, G. R.; Opal, C. B.

1977-01-01

An electrographic Schmidt camera carried on a sounding rocket has yielded far-ultraviolet (1050-2000 A and 1230-2000 A) images of the Barnard Loop Nebula and of the general background in the Orion region due to scattering of ultraviolet starlight by interstellar dust particles. The total intensity in the Barnard Loop region agrees well with OAO-2 measurements, but the discrete Loop structure contributes only some 15% of the total. The measurements are consistent with a relatively high albedo for the dust grains in the far-ultraviolet.

On the performance of digital phase locked loops in the threshold region

NASA Technical Reports Server (NTRS)

Hurst, G. T.; Gupta, S. C.

1974-01-01

Extended Kalman filter algorithms are used to obtain a digital phase lock loop structure for demodulation of angle modulated signals. It is shown that the error variance equations obtained directly from this structure enable one to predict threshold if one retains higher frequency terms. This is in sharp contrast to the similar analysis of the analog phase lock loop, where the higher frequency terms are filtered out because of the low pass filter in the loop. Results are compared to actual simulation results and threshold region results obtained previously.

Identification of outer membrane proteins with emulsifying activity by prediction of beta-barrel regions.

PubMed

Walzer, Gil; Rosenberg, Eugene; Ron, Eliora Z

2009-01-01

Microbial bioemulsifiers are secreted by many bacteria and are important for bacterial interactions with hydrophobic substrates or nutrients and for a variety of biotechnological applications. We have recently shown that the OmpA protein in several members of the Acinetobacter family has emulsifying properties. These properties of OmpA depend on the amino acid composition of four putative extra-membrane loops, which in various strains of Acinetobacter, but not in E. coli, are highly hydrophobic. As many Acinetobacter strains can utilize hydrophobic carbon sources, such as oil, the emulsifying activity of their OmpA may be important for the utilization and uptake of hydrocarbons. We assumed that if outer membrane proteins with emulsifying activity are physiologically important, they may exist in additional oil degrading bacteria. In order to identify such proteins, it was necessary to obtain bioinformatics-based predictions for hydrophobic extra-membrane loops. Here we describe a method for using protein sequence data for predicting the hydrophobic properties of the extra-membrane loops of outer membrane proteins. The feasibility of this method is demonstrated by its use to identify a new microbial bioemulsifier - OprG - an outer membrane protein of the oil degrading Pseudomonas putida KT2440.

3D Structures & dynamic of the solar corona: inputs from stereovision technics and joined Ground Based and Space Observations for the development of Space Weather

NASA Astrophysics Data System (ADS)

Portier-Fozzani, F.; Noens, J.-C.

In this presentation, I will present different techniques for 3D coronal structures reconstructions. Multiscale vision model (MVM, collaboration with A. Bijaoui) based on wavelet decomposition were used to prepare data. With SOHO/EIT, geometrical constraints were added to be able to measure by stereovision loop size parameters. Thus from these parameters, while including information of several observation wavelenghts, it has been possible by using the CHIANTI code to derive temperature and density along and across the loops, and thus to determine loops physical properties. During the emergence of a new active region, a more sophisticated method, was made to measure the twist degree variations. Loops appear twisted and detwist as expand. The magnetic helicity conservation gives thus important criteria to derive the limit of the stability for a non forced phenomena. Sigmoids, twisted ARLs, sheared filament are related with flares and CMEs. In that case 3D measurement can say upon which level of twist the structure will become unstable. With basic geometrical measures, it has been seen that a new active region reconnected a sigmoide leading to a flare. Also, for CMEs, the measure of the filament ejection angle from stereo EUV images, and the following of temporal evolution from coronagraphic measurement such as done by HACO at the Pic Du Midi Observatory, gives possibility to determine if the CME is coming toward the Earth, and when eventually would be the impact with the magnetosphere. The input of new missions such as STEREO/SECCHI would allow us to better understood the coronal dynamic. Such joined observations GBO-space, used simultaneously together with 3D methods, will allow to develop efficiently forecasting for Space Weather.

Coronal Heating and the Magnetic Field in Solar Active Regions

NASA Astrophysics Data System (ADS)

Falconer, D. A.; Tiwari, S. K.; Winebarger, A. R.; Moore, R. L.

2017-12-01

A strong dependence of active-region (AR) coronal heating on the magnetic field is demonstrated by the strong correlation of AR X-ray luminosity with AR total magnetic flux (Fisher et al 1998 ApJ). AR X-ray luminosity is also correlated with AR length of strong-shear neutral line in the photospheric magnetic field (Falconer 1997). These two whole-AR magnetic parameters are also correlated with each other. From 150 ARs observed within 30 heliocentric degrees from disk center by AIA and HMI on SDO, using AR luminosity measured from the hot component of the AIA 94 Å band (Warren et al 2012, ApJ) near the time of each of 3600 measured HMI vector magnetograms of these ARs and a wide selection of whole-AR magnetic parameters from each vector magnetogram after it was deprojected to disk center, we find: (1) The single magnetic parameter having the strongest correlation with AR 94-hot luminosity is the length of strong-field neutral line. (2) The two-parameter combination having the strongest still-stronger correlation with AR 94-hot luminosity is a combination of AR total magnetic flux and AR neutral-line length weighted by the vertical-field gradient across the neutral line. We interpret these results to be consistent with the results of both Fisher et al (1998) and Falconer (1997), and with the correlation of AR coronal loop heating with loop field strength recently found by Tiwari et al (2017, ApJ Letters). Our interpretation is that, in addition to depending strongly on coronal loop field strength, AR coronal heating has a strong secondary positive dependence on the rate of flux cancelation at neutral lines at coronal loop feet. This work was funded by the Living With a Star Science and Heliophysics Guest Investigators programs of NASA's Heliophysics Division.

New Aspects of a Lid-Removal Mechanism in the Onset of a SEP-Producing Eruption Sequence

NASA Technical Reports Server (NTRS)

Sterling, Alphonse C.; Moore, Ronald L.; Falconer, David A.; Knox, Javon M.

2014-01-01

We examine a sequence of two ejective eruptions from a single active region on 2012 January 23, using magnetograms and EUV images from SDO/HMI and SDO/AIA, and EUV images from STEREO. Cheng et al. (2013) showed that the first eruption's ("Eruption 1'') flux rope was apparent only in "hotter'' AIA channels, and that it removed overlying field that allowed the second eruption (``Eruption 2'') to begin via ideal MHD instability; here we say Eruption 2 began via a ``lid removal'' mechanism. We show that during Eruption-1's onset, its flux rope underwent ``tether weakening'' (TW) reconnection with the field of an adjacent active region. Standard flare loops from Eruption 1 developed over Eruption-2's flux rope and enclosed filament, but these overarching new loops were unable to confine that flux rope/filament. Eruption-1's flare loops, from both TW reconnection and standard-flare-model internal reconnection, were much cooler than Eruption-2's flare loops (GOES thermal temperatures of approx. 9 MK compared to approx. 14 MK). This eruption sequence produced a strong solar energetic particle (SEP) event (10 MeV protons, >10(exp 3) pfu for 43 hrs), apparently starting when Eruption-2's CME blasted through Eruption-1's CME at 5-10 R_s. This occurred because the two CMEs originated in close proximity and in close time sequence: Eruption-1's fast rise started soon after the TW reconnection; the lid removal by Eruption-1's ejection triggered the slow onset of Eruption 2; and Eruption-2's CME, which started approx. 1 hr later, was three times faster than Eruption-1's CME.

Evidence of Significant Energy Input in the Late Phase of A Solar Flare from NuSTAR X-Ray Observations

NASA Technical Reports Server (NTRS)

Kuhar, Matej; Krucker, Sam; Hannah, Iain G.; Glesener, Lindsay; Saint-Hilaire, Pascal; Grefenstette, Brian W.; Hudson, Hugh S.; White, Stephen M.; Smith, David M.; Marsh, Andrew J.;

Modeling of energy buildup for a flare-productive region

NASA Technical Reports Server (NTRS)

Wu, S. T.; Krall, K. R.; Hu, Y. Q.; Hagyard, M. J.; Smith, J. B., Jr.

1984-01-01

A self-consistent MHD model of shearing magnetic loops is used to investigate magnetic energy buildup in active region AR 2372 (Boulder number), in the period of April 5-7, 1980. The magnetic field and sunspot motions in this region, derived using observational data obtained by the Marshall Space Flight Center Solar Observatory, suggest the initial boundary conditions for the model. It is found that the plasma parameters (i.e., density, temperature, and plasma flow velocity) do not change appreciably during the process of energy buildup as the magnetic loops are sheared. Thus, almost all of the added energy is stored in the magnetic field. Furthermore, it is shown that dynamical processes are not important during a slow buildup (i.e., for a shearing velocity less than 1 km/s). Finally, it is concluded that the amount of magnetic energy stored and the location of this stored magnetic energy depend on the initial magnetic field (whether potential or sheared) and the magnitude of the shearing motion.

Structure of the PTEN-like region of auxilin, a detector of clathrin-coated vesicle budding

PubMed Central

Guan, Rong; Han, Dai; Harrison, Stephen C.; Kirchhausen, Tomas

2010-01-01

Auxilin, a J-domain containing protein, recruits the Hsc70 uncoating ATPase to newly budded clathrin-coated vesicles. The timing of auxilin arrival determines that uncoating will commence only after the clathrin lattice has fully assembled and after membrane fission is complete. Auxilin has a region resembling PTEN, a PI3P phosphatase. We have determined the crystal structure of this region of bovine auxilin 1; it indeed resembles PTEN closely. A change in the structure of the P-loop accounts for the lack of phosphatase activity. Inclusion of phosphatidylinositol phosphates substantially enhances liposome binding by wild-type auxilin, but not by various mutants bearing changes in loops of the C2 domain. Nearly all these mutations also prevent recruitment of auxilin to newly budded coated vesicles. We propose a specific geometry for auxilin association with a membrane bilayer and discuss implications of this model for the mechanism by which auxilin detects separation of a vesicle from its parent membrane. PMID:20826345

A dihydropyridine receptor alpha1s loop region critical for skeletal muscle contraction is intrinsically unstructured and binds to a SPRY domain of the type 1 ryanodine receptor.

PubMed

Cui, Yanfang; Tae, Han-Shen; Norris, Nicole C; Karunasekara, Yamuna; Pouliquin, Pierre; Board, Philip G; Dulhunty, Angela F; Casarotto, Marco G

2009-03-01

The II-III loop of the dihydropyridine receptor (DHPR) alpha(1s) subunit is a modulator of the ryanodine receptor (RyR1) Ca(2+) release channel in vitro and is essential for skeletal muscle contraction in vivo. Despite its importance, the structure of this loop has not been reported. We have investigated its structure using a suite of NMR techniques which revealed that the DHPR II-III loop is an intrinsically unstructured protein (IUP) and as such belongs to a burgeoning structural class of functionally important proteins. The loop does not possess a stable tertiary fold: it is highly flexible, with a strong N-terminal helix followed by nascent helical/turn elements and unstructured segments. Its residual structure is loosely globular with the N and C termini in close proximity. The unstructured nature of the II-III loop may allow it to easily modify its interaction with RyR1 following a surface action potential and thus initiate rapid Ca(2+) release and contraction. The in vitro binding partner for the II-III was investigated. The II-III loop interacts with the second of three structurally distinct SPRY domains in RyR1, whose function is unknown. This interaction occurs through two preformed N-terminal alpha-helical regions and a C-terminal hydrophobic element. The A peptide corresponding to the helical N-terminal region is a common probe of RyR function and binds to the same SPRY domain as the full II-III loop. Thus the second SPRY domain is an in vitro binding site for the II-III loop. The possible in vivo role of this region is discussed.

A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior*

PubMed Central

Kromann-Hansen, Tobias; Oldenburg, Emil; Yung, Kristen Wing Yu; Ghassabeh, Gholamreza H.; Muyldermans, Serge; Declerck, Paul J.; Huang, Mingdong; Andreasen, Peter A.; Ngo, Jacky Chi Ki

2016-01-01

A peptide segment that binds the active site of a serine protease in a substrate-like manner may behave like an inhibitor or a substrate. However, there is sparse information on which factors determine the behavior a particular peptide segment will exhibit. Here, we describe the first x-ray crystal structure of a nanobody in complex with a serine protease. The nanobody displays a new type of interaction between an antibody and a serine protease as it inserts its complementary determining region-H3 loop into the active site of the protease in a substrate-like manner. The unique binding mechanism causes the nanobody to behave as a strong inhibitor as well as a poor substrate. Intriguingly, its substrate behavior is incomplete, as 30–40% of the nanobody remained intact and inhibitory after prolonged incubation with the protease. Biochemical analysis reveals that an intra-loop interaction network within the complementary determining region-H3 of the nanobody balances its inhibitor versus substrate behavior. Collectively, our results unveil molecular factors, which may be a general mechanism to determine the substrate versus inhibitor behavior of other protease inhibitors. PMID:27226628

Big words, halved brains and small worlds: complex brain networks of figurative language comprehension.

PubMed

Arzouan, Yossi; Solomon, Sorin; Faust, Miriam; Goldstein, Abraham

2011-04-27

Language comprehension is a complex task that involves a wide network of brain regions. We used topological measures to qualify and quantify the functional connectivity of the networks used under various comprehension conditions. To that aim we developed a technique to represent functional networks based on EEG recordings, taking advantage of their excellent time resolution in order to capture the fast processes that occur during language comprehension. Networks were created by searching for a specific causal relation between areas, the negative feedback loop, which is ubiquitous in many systems. This method is a simple way to construct directed graphs using event-related activity, which can then be analyzed topologically. Brain activity was recorded while subjects read expressions of various types and indicated whether they found them meaningful. Slightly different functional networks were obtained for event-related activity evoked by each expression type. The differences reflect the special contribution of specific regions in each condition and the balance of hemispheric activity involved in comprehending different types of expressions and are consistent with the literature in the field. Our results indicate that representing event-related brain activity as a network using a simple temporal relation, such as the negative feedback loop, to indicate directional connectivity is a viable option for investigation which also derives new information about aspects not reflected in the classical methods for investigating brain activity.

Flares observed by the normal incidence X-ray telescope on 1989 September 11

NASA Technical Reports Server (NTRS)

Herant, M.; Pardo, F.; Spiller, E.; Golub, L.

1991-01-01

Two solar flare events have been observed in soft X-rays during a sounding-rocket flight of the Normal-Incidence X-ray Telescope payload on September 11, 1989. The flare in X-rays involves a single bright loop crossing the neutral line, and having its footpoints at the southern ends of the ribbons; this loop accounts for more than 66 percent of the emission. Within the remainder of each of the flare ribbons, a complex coronal structure is also observed to be interacting with the main flare loop. A second event, in an active region at the limb, has a strong correlation with H-alpha images obtained at the same time. This indicates the coexistence, and indeed the close proximity, of coronal and chromospheric temperature material. Interpretations of this phenomenon are discussed.

Helicity charging and eruption of magnetic flux from the Sun

NASA Technical Reports Server (NTRS)

Rust, David M.; Kumar, A.

1994-01-01

The ejection of helical toroidal fields from the solar atmosphere and their detection in interplanetary space are described. The discovery that solar magnetic fields are twisted and that they are segregated by hemisphere according to their chirality has important implications for the escape process. The roles played by erupting prominences, coronal mass ejections (CME's) and active region (AR) loops in expressing the escape of magnetic flux and helicity are discussed. Sporadic flux escape associated with filament eruptions accounts for less than one-tenth the flux loss. Azimuthal flux loss by CME's could account for more, but the major contributor to flux escape may be AR loop expansion. It is shown how the transfer of magnetic helicity from the sun's interior into emerged loops ('helicity charging') could be the effective driver of solar eruptions and of flux loss from the sun.

The biological activity of botulinum neurotoxin type C is dependent upon novel types of ganglioside binding sites.

PubMed

Strotmeier, Jasmin; Gu, Shenyan; Jutzi, Stephan; Mahrhold, Stefan; Zhou, Jie; Pich, Andreas; Eichner, Timo; Bigalke, Hans; Rummel, Andreas; Jin, Rongsheng; Binz, Thomas

2011-07-01

The seven botulinum neurotoxins (BoNT) cause muscle paralysis by selectively cleaving core components of the vesicular fusion machinery. Their extraordinary activity primarily relies on highly specific entry into neurons. Data on BoNT/A, B, E, F and G suggest that entry follows a dual receptor interaction with complex gangliosides via an established ganglioside binding region and a synaptic vesicle protein. Here, we report high resolution crystal structures of the BoNT/C cell binding fragment alone and in complex with sialic acid. The WY-motif characteristic of the established ganglioside binding region was located on an exposed loop. Sialic acid was co-ordinated at a novel position neighbouring the binding pocket for synaptotagmin in BoNT/B and G and the sialic acid binding site in BoNT/D and TeNT respectively. Employing synaptosomes and immobilized gangliosides binding studies with BoNT/C mutants showed that the ganglioside binding WY-loop, the newly identified sialic acid-co-ordinating pocket and the area corresponding to the established ganglioside binding region of other BoNTs are involved in ganglioside interaction. Phrenic nerve hemidiaphragm activity tests employing ganglioside deficient mice furthermore evidenced that the biological activity of BoNT/C depends on ganglioside interaction with at least two binding sites. These data suggest a unique cell binding and entry mechanism for BoNT/C among clostridial neurotoxins. © 2011 Blackwell Publishing Ltd.

Conformation of receptor-bound visual arrestin

PubMed Central

Kim, Miyeon; Vishnivetskiy, Sergey A.; Van Eps, Ned; Alexander, Nathan S.; Cleghorn, Whitney M.; Zhan, Xuanzhi; Hanson, Susan M.; Morizumi, Takefumi; Ernst, Oliver P.; Meiler, Jens; Gurevich, Vsevolod V.; Hubbell, Wayne L.

2012-01-01

Arrestin-1 (visual arrestin) binds to light-activated phosphorylated rhodopsin (P-Rh*) to terminate G-protein signaling. To map conformational changes upon binding to the receptor, pairs of spin labels were introduced in arrestin-1 and double electron–electron resonance was used to monitor interspin distance changes upon P-Rh* binding. The results indicate that the relative position of the N and C domains remains largely unchanged, contrary to expectations of a “clam-shell” model. A loop implicated in P-Rh* binding that connects β-strands V and VI (the “finger loop,” residues 67–79) moves toward the expected location of P-Rh* in the complex, but does not assume a fully extended conformation. A striking and unexpected movement of a loop containing residue 139 away from the adjacent finger loop is observed, which appears to facilitate P-Rh* binding. This change is accompanied by smaller movements of distal loops containing residues 157 and 344 at the tips of the N and C domains, which correspond to “plastic” regions of arrestin-1 that have distinct conformations in monomers of the crystal tetramer. Remarkably, the loops containing residues 139, 157, and 344 appear to have high flexibility in both free arrestin-1 and the P-Rh*complex. PMID:23091036

Active region upflows. I. Multi-instrument observations

NASA Astrophysics Data System (ADS)

Vanninathan, K.; Madjarska, M. S.; Galsgaard, K.; Huang, Z.; Doyle, J. G.

2015-12-01

Context. We study upflows at the edges of active regions, called AR outflows, using multi-instrument observations. Aims: This study intends to provide the first direct observational evidence of whether chromospheric jets play an important role in furnishing mass that could sustain coronal upflows. The evolution of the photospheric magnetic field, associated with the footpoints of the upflow region and the plasma properties of active region upflows is investigated with the aim of providing information for benchmarking data-driven modelling of this solar feature. Methods: We spatially and temporally combine multi-instrument observations obtained with the Extreme-ultraviolet Imaging Spectrometer on board the Hinode, the Atmospheric Imaging Assembly and the Helioseismic Magnetic Imager instruments on board the Solar Dynamics Observatory and the Interferometric BI-dimensional Spectro-polarimeter installed at the National Solar Observatory, Sac Peak, to study the plasma parameters of the upflows and the impact of the chromosphere on active region upflows. Results: Our analysis shows that the studied active region upflow presents similarly to those studied previously, i.e. it displays blueshifted emission of 5-20 kms-1 in Fe xii and Fe xiii and its average electron density is 1.8 × 109 cm-3 at 1 MK. The time variation of the density is obtained showing no significant change (in a 3σ error). The plasma density along a single loop is calculated revealing a drop of 50% over a distance of ~20 000 km along the loop. We find a second velocity component in the blue wing of the Fe xii and Fe xiii lines at 105 kms-1 reported only once before. For the first time we study the time evolution of this component at high cadence and find that it is persistent during the whole observing period of 3.5 h with variations of only ±15 kms-1. We also, for the first time, study the evolution of the photospheric magnetic field at high cadence and find that magnetic flux diffusion is responsible for the formation of the upflow region. High cadence Hα observations are used to study the chromosphere at the footpoints of the upflow region. We find no significant jet-like (spicule/rapid blue excursion) activity to account for several hours/days of plasma upflow. The jet-like activity in this region is not continuous and blueward asymmetries are a bare minimum. Using an image enhancement technique for imaging and spectral data, we show that the coronal structures seen in the AIA 193 Å channel are comparable to the EIS Fe xii images, while images in the AIA 171 Å channel reveal additional loops that are a result of contribution from cooler emission to this channel. Conclusions: Our results suggest that at chromospheric heights there are no signatures that support the possible contribution of spicules to active region upflows. We suggest that magnetic flux diffusion is responsible for the formation of the coronal upflows. The existence of two velocity components possibly indicates the presence of two different flows, which are produced by two different physical mechanisms, e.g. magnetic reconnection and pressure-driven jets. Movies associated to Figs. A.1-A.3 are available in electronic form at http://www.aanda.org

Interactions of Twisted Ω-loops in a Model Solar Convection Zone

NASA Astrophysics Data System (ADS)

Jouve, L.; Brun, A. S.; Aulanier, G.

2018-04-01

This study aims at investigating the ability of strong interactions between magnetic field concentrations during their rise through the convection zone to produce complex active regions at the solar surface. To do so, we perform numerical simulations of buoyant magnetic structures evolving and interacting in a model solar convection zone. We first produce a 3D model of rotating convection and then introduce idealized magnetic structures close to the bottom of the computational domain. These structures possess a certain degree of field line twist and they are made buoyant on a particular extension in longitude. The resulting twisted Ω-loops will thus evolve inside a spherical convective shell possessing large-scale mean flows. We present results on the interaction between two such loops with various initial parameters (mainly buoyancy and twist) and on the complexity of the emerging magnetic field. In agreement with analytical predictions, we find that if the loops are introduced with opposite handedness and same axial field direction or the same handedness but opposite axial field, they bounce against each other. The emerging region is then constituted of two separated bipolar structures. On the contrary, if the loops are introduced with the same direction of axial and peripheral magnetic fields and are sufficiently close, they merge while rising. This more interesting case produces complex magnetic structures with a high degree of non-neutralized currents, especially when the convective motions act significantly on the magnetic field. This indicates that those interactions could be good candidates to produce eruptive events like flares or CMEs.

Semi-active control of helicopter vibration using controllable stiffness and damping devices

NASA Astrophysics Data System (ADS)

Anusonti-Inthra, Phuriwat

Semi-active concepts for helicopter vibration reduction are developed and evaluated in this dissertation. Semi-active devices, controllable stiffness devices or controllable orifice dampers, are introduced; (i) in the blade root region (rotor-based concept) and (ii) between the rotor and the fuselage as semi-active isolators (in the non-rotating frame). Corresponding semi-active controllers for helicopter vibration reduction are also developed. The effectiveness of the rotor-based semi-active vibration reduction concept (using stiffness and damping variation) is demonstrated for a 4-bladed hingeless rotor helicopter in moderate- to high-speed forward flight. A sensitivity study shows that the stiffness variation of root element can reduce hub vibrations when proper amplitude and phase are used. Furthermore, the optimal semi-active control scheme can determine the combination of stiffness variations that produce significant vibration reduction in all components of vibratory hub loads simultaneously. It is demonstrated that desired cyclic variations in properties of the blade root region can be practically achieved using discrete controllable stiffness devices and controllable dampers, especially in the flap and lag directions. These discrete controllable devices can produce 35--50% reduction in a composite vibration index representing all components of vibratory hub loads. No detrimental increases are observed in the lower harmonics of blade loads and blade response (which contribute to the dynamic stresses) and controllable device internal loads, when the optimal stiffness and damping variations are introduced. The effectiveness of optimal stiffness and damping variations in reducing hub vibration is retained over a range of cruise speeds and for variations in fundamental rotor properties. The effectiveness of the semi-active isolator is demonstrated for a simplified single degree of freedom system representing the semi-active isolation system. The rotor, represented by a lumped mass under harmonic force excitation, is supported by a spring and a parallel damper on the fuselage (assumed to have infinite mass). Properties of the spring or damper can then be controlled to reduce transmission of the force into the fuselage or the support structure. This semi-active isolation concept can produce additional 30% vibration reduction beyond the level achieved by a passive isolator. Different control schemes (i.e. open-loop, closed-loop, and closed-loop adaptive schemes) are developed and evaluated to control transmission of vibratory loads to the support structure (fuselage), and it is seen that a closed-loop adaptive controller is required to retain vibration reduction effectiveness when there is a change in operating condition. (Abstract shortened by UMI.)

Chromospheric counterparts of solar transition region unresolved fine structure loops

NASA Astrophysics Data System (ADS)

Pereira, Tiago M. D.; Rouppe van der Voort, Luc; Hansteen, Viggo H.; De Pontieu, Bart

2018-04-01

Low-lying loops have been discovered at the solar limb in transition region temperatures by the Interface Region Imaging Spectrograph (IRIS). They do not appear to reach coronal temperatures, and it has been suggested that they are the long-predicted unresolved fine structures (UFS). These loops are dynamic and believed to be visible during both heating and cooling phases. Making use of coordinated observations between IRIS and the Swedish 1-m Solar Telescope, we study how these loops impact the solar chromosphere. We show for the first time that there is indeed a chromospheric signal of these loops, seen mostly in the form of strong Doppler shifts and a conspicuous lack of chromospheric heating. In addition, we find that several instances have a inverse Y-shaped jet just above the loop, suggesting that magnetic reconnection is driving these events. Our observations add several puzzling details to the current knowledge of these newly discovered structures; this new information must be considered in theoretical models. Two movies associated to Fig. 1 are available at http://https://www.aanda.org

Active site and loop 4 movements within human glycolate oxidase: implications for substrate specificity and drug design.

PubMed

Murray, Michael S; Holmes, Ross P; Lowther, W Todd

2008-02-26

Human glycolate oxidase (GO) catalyzes the FMN-dependent oxidation of glycolate to glyoxylate and glyoxylate to oxalate, a key metabolite in kidney stone formation. We report herein the structures of recombinant GO complexed with sulfate, glyoxylate, and an inhibitor, 4-carboxy-5-dodecylsulfanyl-1,2,3-triazole (CDST), determined by X-ray crystallography. In contrast to most alpha-hydroxy acid oxidases including spinach glycolate oxidase, a loop region, known as loop 4, is completely visible when the GO active site contains a small ligand. The lack of electron density for this loop in the GO-CDST complex, which mimics a large substrate, suggests that a disordered to ordered transition may occur with the binding of substrates. The conformational flexibility of Trp110 appears to be responsible for enabling GO to react with alpha-hydroxy acids of various chain lengths. Moreover, the movement of Trp110 disrupts a hydrogen-bonding network between Trp110, Leu191, Tyr134, and Tyr208. This loss of interactions is the first indication that active site movements are directly linked to changes in the conformation of loop 4. The kinetic parameters for the oxidation of glycolate, glyoxylate, and 2-hydroxy octanoate indicate that the oxidation of glycolate to glyoxylate is the primary reaction catalyzed by GO, while the oxidation of glyoxylate to oxalate is most likely not relevant under normal conditions. However, drugs that exploit the unique structural features of GO may ultimately prove to be useful for decreasing glycolate and glyoxylate levels in primary hyperoxaluria type 1 patients who have the inability to convert peroxisomal glyoxylate to glycine.

Heating the sun's lower transition region with fine-scale electric currents

NASA Technical Reports Server (NTRS)

Rabin, D.; Moore, R.

1984-01-01

Analytical and observational data are presented to show that the lower transition zone, a 100 km thick region at 10,000-200,000 K between the solar chromosphere and corona, is heated by local electric currents. The study was spurred by correlations between the enhanced atmospheric heating and magnetospheric flux in the chromospheric network and active regions. Field aligned current heated flux loops are asserted to mainly reside in and make up most of the transition region. It is shown that thermal conduction from the sides of hot gas columns generated by the current dissipation is the source of the observed temperature distribution in the transition regions.

Active region flows

NASA Technical Reports Server (NTRS)

Foukal, Peter

1987-01-01

A wide range of observations has shown that active region phenomena in the photospheric, chromospheric and coronal temperature regimes are dynamical in nature. At the photosphere, recent observations of full line profiles place an upper limit of about + or - 20/msec on any downflows at supergranule cell edges. Observations of the full Stokes 5 profiles in the network show no evidence for downflows in magnetic flux tubes. In the area of chromospheric dynamics, several models were put forward recently to reproduce the observed behavior of spicules. However, it is pointed out that these adiabatic models do not include the powerful radiative dissipation which tend to damp out the large amplitude disturbances that produce the spicular acceleration in the models. In the corona, loop flows along field lines clearly transport mass and energy at rates important for the dynamics of these structures. However, advances in understanding the heating and mass balance of the loop structures seem to require new kinds of observations. Some results are presented using a remote sensing diagnostic of the intensity and orientation of macroscopic plasma electric fields predicted by models of reconnective heating and also wave heating.

EVIDENCE FOR COLLAPSING FIELDS IN THE CORONA AND PHOTOSPHERE DURING THE 2011 FEBRUARY 15 X2.2 FLARE: SDO/AIA AND HMI OBSERVATIONS

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

Gosain, S., E-mail: sgosain@nso.edu; Udaipur Solar Observatory, P.O. Box 198, Dewali, Udaipur, Rajasthan 313001

2012-04-10

We use high-resolution Solar Dynamics Observatory (SDO)/Atmospheric Imaging Assembly observations to study the evolution of the coronal loops in a flaring solar active region, NOAA 11158. We identify three distinct phases of the coronal loop dynamics during this event: (1) slow-rise phase: slow rising motion of the loop-tops prior to the flare in response to the slow rise of the underlying flux rope; (2) collapse phase: sudden contraction of the loop-tops, with the lower loops collapsing earlier than the higher loops; and (3) oscillation phase: the loops exhibit global kink oscillations after the collapse phase at different periods, with themore » period decreasing with the decreasing height of the loops. The period of these loop oscillations is used to estimate the field strength in the coronal loops. Furthermore, we also use SDO/Helioseismic and Magnetic Imager (HMI) observations to study the photospheric changes close to the polarity inversion line (PIL). The longitudinal magnetograms show a stepwise permanent decrease in the magnetic flux after the flare over a coherent patch along the PIL. Furthermore, we examine the HMI Stokes I, Q, U, V profiles over this patch and find that the Stokes-V signal systematically decreases while the Stokes-Q and U signals increase after the flare. These observations suggest that close to the PIL the field configuration became more horizontal after the flare. We also use HMI vector magnetic field observations to quantify the changes in the field inclination angle and find an inward collapse of the field lines toward the PIL by {approx}10 Degree-Sign . These observations are consistent with the 'coronal implosion' scenario and its predictions about flare-related photospheric field changes.« less

FLARE-GENERATED SHOCK WAVE PROPAGATION THROUGH SOLAR CORONAL ARCADE LOOPS AND AN ASSOCIATED TYPE II RADIO BURST

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

Kumar, Pankaj; Cho, Kyung-Suk; Innes, D. E., E-mail: pankaj@kasi.re.kr

2016-09-01

This paper presents multiwavelength observations of a flare-generated type II radio burst. The kinematics of the shock derived from the type II burst closely match a fast extreme ultraviolet (EUV) wave seen propagating through coronal arcade loops. The EUV wave was closely associated with an impulsive M1.0 flare without a related coronal mass ejection, and was triggered at one of the footpoints of the arcade loops in active region NOAA 12035. It was initially observed in the 335 Å images from the Atmospheric Image Assembly with a speed of ∼800 km s{sup −1} and it accelerated to ∼1490 km s{supmore » −1} after passing through the arcade loops. A fan–spine magnetic topology was revealed at the flare site. A small, confined filament eruption (∼340 km s{sup −1}) was also observed moving in the opposite direction to the EUV wave. We suggest that breakout reconnection in the fan–spine topology triggered the flare and associated EUV wave that propagated as a fast shock through the arcade loops.« less

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

Chitta, L. P.; Peter, H.; Solanki, S. K.

How and where are coronal loops rooted in the solar lower atmosphere? The details of the magnetic environment and its evolution at the footpoints of coronal loops are crucial to understanding the processes of mass and energy supply to the solar corona. To address the above question, we use high-resolution line-of-sight magnetic field data from the Imaging Magnetograph eXperiment instrument on the Sunrise balloon-borne observatory and coronal observations from the Atmospheric Imaging Assembly onboard the Solar Dynamics Observatory of an emerging active region. We find that the coronal loops are often rooted at the locations with minor small-scale but persistentmore » opposite-polarity magnetic elements very close to the larger dominant polarity. These opposite-polarity small-scale elements continually interact with the dominant polarity underlying the coronal loop through flux cancellation. At these locations we detect small inverse Y-shaped jets in chromospheric Ca ii H images obtained from the Sunrise Filter Imager during the flux cancellation. Our results indicate that magnetic flux cancellation and reconnection at the base of coronal loops due to mixed polarity fields might be a crucial feature for the supply of mass and energy into the corona.« less

Coronal Heating, Weak MHD Turbulence, and Scaling Laws

NASA Technical Reports Server (NTRS)

Rappazzo, A. F.; Velli, M.; Einaudi, G.; Dahlburg, R. B.

2007-01-01

Long-time high-resolution simulations of the dynamics of a coronal loop in Cartesian geometry are carried out, within the framework of reduced magnetohydrodynamics (RMHD), to understand coronal heating driven by the motion of field lines anchored in the photosphere. We unambiguously identify MHD anisotropic turbulence as the physical mechanism responsible for the transport of energy from the large scales, where energy is injected by photospheric motions, to the small scales, where it is dissipated. As the loop parameters vary, different regimes of turbulence develop: strong turbulence is found for weak axial magnetic fields and long loops, leading to Kolmogorov-like spectra in the perpendicular direction, while weaker and weaker regimes (steeper spectral slopes of total energy) are found for strong axial magnetic fields and short loops. As a consequence we predict that the scaling of the heating rate with axial magnetic field intensity B, which depends on the spectral index of total energy for given loop parameters, must vary from B3/2 for weak fields to B2 for strong fields at a given aspect ratio. The predicted heating rate is within the lower range of observed active region and quiet-Sun coronal energy losses.

Blowout Surge due to Interaction between a Solar Filament and Coronal Loops

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

Li, Haidong; Jiang, Yunchun; Yang, Jiayan

2017-06-20

We present an observation of the interaction between a filament and the outer spine-like loops that produces a blowout surge within one footpoint of large-scale coronal loops on 2015 February 6. Based the observation of the AIA 304 and 94 Å, the activated filament is initially embedded below a dome of a fan-spine configuration. Due to the ascending motion, the erupting filament reconnects with the outer spine-like field. We note that the material in the filament blows out along the outer spine-like field to form the surge with a wider spire, and a two-ribbon flare appears at the site ofmore » the filament eruption. In this process, small bright blobs appear at the interaction region and stream up along the outer spine-like field and down along the eastern fan-like field. As a result, a leg of the filament becomes radial and the material in it erupts, while another leg forms the new closed loops. Our results confirm that the successive reconnection occurring between the erupting filament and the coronal loops may lead to a strong thermal/magnetic pressure imbalance, resulting in a blowout surge.« less

Design strategies for dynamic closed-loop optogenetic neurocontrol in vivo

NASA Astrophysics Data System (ADS)

Bolus, M. F.; Willats, A. A.; Whitmire, C. J.; Rozell, C. J.; Stanley, G. B.

2018-04-01

Objective. Controlling neural activity enables the possibility of manipulating sensory perception, cognitive processes, and body movement, in addition to providing a powerful framework for functionally disentangling the neural circuits that underlie these complex phenomena. Over the last decade, optogenetic stimulation has become an increasingly important and powerful tool for understanding neural circuit function, owing to the ability to target specific cell types and bidirectionally modulate neural activity. To date, most stimulation has been provided in open-loop or in an on/off closed-loop fashion, where previously-determined stimulation is triggered by an event. Here, we describe and demonstrate a design approach for precise optogenetic control of neuronal firing rate modulation using feedback to guide stimulation continuously. Approach. Using the rodent somatosensory thalamus as an experimental testbed for realizing desired time-varying patterns of firing rate modulation, we utilized a moving average exponential filter to estimate firing rate online from single-unit spiking measured extracellularly. This estimate of instantaneous rate served as feedback for a proportional integral (PI) controller, which was designed during the experiment based on a linear-nonlinear Poisson (LNP) model of the neuronal response to light. Main results. The LNP model fit during the experiment enabled robust closed-loop control, resulting in good tracking of sinusoidal and non-sinusoidal targets, and rejection of unmeasured disturbances. Closed-loop control also enabled manipulation of trial-to-trial variability. Significance. Because neuroscientists are faced with the challenge of dissecting the functions of circuit components, the ability to maintain control of a region of interest in spite of changes in ongoing neural activity will be important for disambiguating function within networks. Closed-loop stimulation strategies are ideal for control that is robust to such changes, and the employment of continuous feedback to adjust stimulation in real-time can improve the quality of data collected using optogenetic manipulation.

Evidence for siphon flows with shocks in solar magnetic flux tubes

NASA Technical Reports Server (NTRS)

Degenhardt, D.; Solanki, S. K.; Montesinos, B.; Thomas, J. H.

1993-01-01

We synthesize profiles of the infrared line Fe I 15648.5 A (g = 3) for a recently developed theoretical model of siphon flows along photospheric magnetic loops. The synthesized line profiles are compared with the observations from which Rueedi et al. (1992) deduced the presence of such flows across the neutral line of an active region plage. This comparison supports the interpretation of Rueedi et al. (1992). It also suggests that the average footpoint separation of the observed loops carrying the siphon flow is 8-15 sec and that the siphon flow experiences a standing tube shock in the downstream leg near the top of the arch.

Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure.

PubMed

Takahashi, Shuntaro; Sugimoto, Naoki

2017-12-01

DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and topology of G-quadruplexes. Here, we investigated volumetric changes induced by pressure in the folding of the G-quadruplex formed by the thrombin binding aptamer (TBA) with mutations within the loop regions. The change of partial molar volume in the transition from coil to G-quadruplex, ∆V tr , of TBA with a mutation from T to A in the 5' most loop (TBA T3A) was 75.5cm 3 mol -1 , which was larger than that of TBA (54.6cm 3 mol -1 ). TBA with a G to T mutation in the central loop (TBA G8T) had thermal stability similar to TBA T3A but a smaller ∆V tr of 41.1cm 3 mol -1 . In the presence of poly(ethylene)glycol 200 (PEG200), ∆V tr values were 14.7cm 3 mol -1 for TBA T3A and 13.2cm 3 mol -1 for TBA G8T. These results suggest that the two mutations destabilize the G-quadruplex structure differently. Thus, volumetric data obtained using pressure-based thermodynamic analyses provides information about the dynamics of the loop regions and the roles of loops in the stabilities and folding of G-quadruplex structures. Copyright © 2017 Elsevier B.V. All rights reserved.

Successive Two-sided Loop Jets Caused by Magnetic Reconnection between Two Adjacent Filamentary Threads

NASA Astrophysics Data System (ADS)

Tian, Zhanjun; Liu, Yu; Shen, Yuandeng; Elmhamdi, Abouazza; Su, Jiangtao; Liu, Ying D.; Kordi, Ayman. S.

2017-08-01

We present observational analysis of two successive two-sided loop jets observed by the ground-based New Vacuum Solar Telescope and the space-borne Solar Dynamics Observatory. The two successive two-sided loop jets manifested similar evolution processes and both were associated with the interaction of two small-scale adjacent filamentary threads, magnetic emerging, and cancellation processes at the jet’s source region. High temporal and high spatial resolution observations reveal that the two adjacent ends of the two filamentary threads are rooted in opposite magnetic polarities within the source region. The two threads approached each other, and then an obvious brightening patch is observed at the interaction position. Subsequently, a pair of hot plasma ejections are observed heading in opposite directions along the paths of the two filamentary threads at a typical speed for two-sided loop jets of the order 150 km s-1. Close to the end of the second jet, we report the formation of a bright hot loop structure at the source region, which suggests the formation of new loops during the interaction. Based on the observational results, we propose that the observed two-sided loop jets are caused by magnetic reconnection between the two adjacent filamentary threads, largely different from the previous scenario that a two-sided loop jet is generated by magnetic reconnection between an emerging bipole and the overlying horizontal magnetic fields.

Identification and analysis of structures in the corona from X-ray photography

NASA Technical Reports Server (NTRS)

Vaiana, G. S.; Krieger, A. S.; Timothy, A. F.

1973-01-01

This paper summarizes the results of a program of rocket observations of the solar corona with grazing incidence X-ray telescopes. A series of five flights of a Kanigen-surfaced telescope with a few arc seconds resolution, together with the first flight of a newer telescope have resulted in the identification of six classes of coronal structures observable in the X-ray photographs. These are: active regions, active region interconnections, large loop structures associated with unipolar magnetic regions, coronal holes, coronal bright points, and the structures surrounding filament cavities. Two solar flares have been observed. The methods involved in deriving coronal temperature and density information from X-ray photographs are described and the analysis of a bright active region (McMath plage 11035) observed at the west limb on November 24, 1970 is presented as an example of these techniques.

Does High Plasma-β Dynamics ``Load'' Active Regions?

NASA Astrophysics Data System (ADS)

McIntosh, Scott W.

2007-03-01

Using long-duration observations in the He II 304 Å passband of SOHO EIT, we investigate the spatial and temporal appearance of impulsive intensity fluctuations in the pixel light curves. These passband intensity fluctuations come from plasma emitting in the chromosphere, in the transition region, and in the lowest portions of the corona. We see that they are spatially tied to the supergranular scale and that their rate of occurrence is tied to the unsigned imbalance of the magnetic field in which they are observed. The signature of the fluctuations (in space and time) is consistent with their creation by magnetoconvection-forced reconnection, which is driven by the flow field in the high-β plasma. The signature of the intensity fluctuations around an active region suggests that the bulk of the mass and energy going into the active region complex observed in the hotter coronal plasma is supplied by this process, dynamically forcing the looped structure from beneath.

Crystal structure of p44, a constitutively active splice variant of visual arrestin.

PubMed

Granzin, Joachim; Cousin, Anneliese; Weirauch, Moritz; Schlesinger, Ramona; Büldt, Georg; Batra-Safferling, Renu

2012-03-09

Visual arrestin specifically binds to photoactivated and phosphorylated rhodopsin and inactivates phototransduction. In contrast, the p44 splice variant can terminate phototransduction by binding to nonphosphorylated light-activated rhodopsin. Here we report the crystal structure of bovine p44 at a resolution of 1.85 Å. Compared to native arrestin, the p44 structure reveals significant differences in regions crucial for receptor binding, namely flexible loop V-VI and polar core regions. Additionally, electrostatic potential is remarkably positive on the N-domain and the C-domain. The p44 structure represents an active conformation that serves as a model to explain the 'constitutive activity' found in arrestin variants. Copyright © 2012 Elsevier Ltd. All rights reserved.

Dynamics of the CMZ - Giant Magnetic Loops Connection in the Galactic Center

NASA Astrophysics Data System (ADS)

Langer, William

2012-10-01

Understanding the mass transfer and dynamics among the Galactic Center, the disk, and the halo of the Milky Way is fundamental to the study of the evolution of galaxies and star formation. Several giant molecular loops (GML), detected in CO maps of the Galactic Center, are likely the result of the magnetic Parker instability. We have new evidence of a possible dynamical connection between these loops and the Central Molecular Zone (CMZ) from a sparse [CII] sampling from our Herschel Open Time Key Project GOT C+. The CMZ-GML region is dynamically active and is likely to have a significant ionized component. However, we have no information on the distribution and dynamics of the ionized gas. The fine-structure lines of [NII] are key probes of the warm ionized medium (WIM) and along with the [CII] can isolate the different ionization components. We have a Herschel OT2 Priority 1 program to map the GML and the CMZ-GML connection in [CII] in more detail. However, we did not propose needed [NII] observations due to an incomplete analysis of our limited GOT C+ data at the time. Here we propose to observe with the SOFIA/GREAT instrument, [NII] in the CMZ-GML interface region using the L1b band, and serendipitously CO (16-15) using band L2. With this data, combined with our Herschel HIFI [CII], Mopra 12CO (1-0) and 13CO (1-0), and HI, we will characterize these important ISM components and their motions in these Galactic Center features. These observations of the nearest such regions of galactic center activity, also have bearing on the dynamics of other galactic nuclei.

NRF2 regulates core and stabilizing circadian clock loops, coupling redox and timekeeping in Mus musculus

PubMed Central

Sutter, Carrie Hayes; Olesen, Kristin M; Kensler, Thomas W

2018-01-01

Diurnal oscillation of intracellular redox potential is known to couple metabolism with the circadian clock, yet the responsible mechanisms are not well understood. We show here that chemical activation of NRF2 modifies circadian gene expression and rhythmicity, with phenotypes similar to genetic NRF2 activation. Loss of Nrf2 function in mouse fibroblasts, hepatocytes and liver also altered circadian rhythms, suggesting that NRF2 stoichiometry and/or timing of expression are important to timekeeping in some cells. Consistent with this concept, activation of NRF2 at a circadian time corresponding to the peak generation of endogenous oxidative signals resulted in NRF2-dependent reinforcement of circadian amplitude. In hepatocytes, activated NRF2 bound specific enhancer regions of the core clock repressor gene Cry2, increased Cry2 expression and repressed CLOCK/BMAL1-regulated E-box transcription. Together these data indicate that NRF2 and clock comprise an interlocking loop that integrates cellular redox signals into tissue-specific circadian timekeeping. PMID:29481323

CK1/Doubletime activity delays transcription activation in the circadian clock

PubMed Central

O'Neil, Jenna L; Merz, Gregory E; Dusad, Kritika; Crane, Brian R; Young, Michael W

2018-01-01

In the Drosophila circadian clock, Period (PER) and Timeless (TIM) proteins inhibit Clock-mediated transcription of per and tim genes until PER is degraded by Doubletime/CK1 (DBT)-mediated phosphorylation, establishing a negative feedback loop. Multiple regulatory delays within this feedback loop ensure ~24 hr periodicity. Of these delays, the mechanisms that regulate delayed PER degradation (and Clock reactivation) remain unclear. Here we show that phosphorylation of certain DBT target sites within a central region of PER affect PER inhibition of Clock and the stability of the PER/TIM complex. Our results indicate that phosphorylation of PER residue S589 stabilizes and activates PER inhibitory function in the presence of TIM, but promotes PER degradation in its absence. The role of DBT in regulating PER activity, stabilization and degradation ensures that these events are chronologically and biochemically linked, and contributes to the timing of an essential delay that influences the period of the circadian clock. PMID:29611807

Interlocked feedforward loops control cell-type-specific Rhodopsin expression in the Drosophila eye.

PubMed

Johnston, Robert J; Otake, Yoshiaki; Sood, Pranidhi; Vogt, Nina; Behnia, Rudy; Vasiliauskas, Daniel; McDonald, Elizabeth; Xie, Baotong; Koenig, Sebastian; Wolf, Reinhard; Cook, Tiffany; Gebelein, Brian; Kussell, Edo; Nakagoshi, Hideki; Desplan, Claude

2011-06-10

How complex networks of activators and repressors lead to exquisitely specific cell-type determination during development is poorly understood. In the Drosophila eye, expression patterns of Rhodopsins define at least eight functionally distinct though related subtypes of photoreceptors. Here, we describe a role for the transcription factor gene defective proventriculus (dve) as a critical node in the network regulating Rhodopsin expression. dve is a shared component of two opposing, interlocked feedforward loops (FFLs). Orthodenticle and Dve interact in an incoherent FFL to repress Rhodopsin expression throughout the eye. In R7 and R8 photoreceptors, a coherent FFL relieves repression by Dve while activating Rhodopsin expression. Therefore, this network uses repression to restrict and combinatorial activation to induce cell-type-specific expression. Furthermore, Dve levels are finely tuned to yield cell-type- and region-specific repression or activation outcomes. This interlocked FFL motif may be a general mechanism to control terminal cell-fate specification. Copyright © 2011 Elsevier Inc. All rights reserved.

Detection of somatic mutations in the mitochondrial DNA control region D-loop in brain tumors: The first report in Malaysian patients.

PubMed

Mohamed Yusoff, Abdul Aziz; Mohd Nasir, Khairol Naaim; Haris, Khalilah; Mohd Khair, Siti Zulaikha Nashwa; Abdul Ghani, Abdul Rahman Izaini; Idris, Zamzuri; Abdullah, Jafri Malin

2017-11-01

Although the role of nuclear-encoded gene alterations has been well documented in brain tumor development, the involvement of the mitochondrial genome in brain tumorigenesis has not yet been fully elucidated and remains controversial. The present study aimed to identify mutations in the mitochondrial DNA (mtDNA) control region D-loop in patients with brain tumors in Malaysia. A mutation analysis was performed in which DNA was extracted from paired tumor tissue and blood samples obtained from 49 patients with brain tumors. The D-loop region DNA was amplified using the PCR technique, and genetic data from DNA sequencing analyses were compared with the published revised Cambridge sequence to identify somatic mutations. Among the 49 brain tumor tissue samples evaluated, 25 cases (51%) had somatic mutations of the mtDNA D-loop, with a total of 48 mutations. Novel mutations that had not previously been identified in the D-loop region (176 A-deletion, 476 C>A, 566 C>A and 16405 A-deletion) were also classified. No significant associations between the D-loop mutation status and the clinicopathological parameters were observed. To the best of our knowledge, the current study presents the first evidence of alterations in the mtDNA D-loop regions in the brain tumors of Malaysian patients. These results may provide an overview and data regarding the incidence of mitochondrial genome alterations in Malaysian patients with brain tumors. In addition to nuclear genome aberrations, these specific mitochondrial genome alterations may also be considered as potential cancer biomarkers for the diagnosis and staging of brain cancers.

FORMATION AND ERUPTION OF A FLUX ROPE FROM THE SIGMOID ACTIVE REGION NOAA 11719 AND ASSOCIATED M6.5 FLARE: A MULTI-WAVELENGTH STUDY

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

Joshi, Bhuwan; Kushwaha, Upendra; Dhara, Sajal Kumar

We investigate the formation, activation, and eruption of a flux rope (FR) from the sigmoid active region NOAA 11719 by analyzing E(UV), X-ray, and radio measurements. During the pre-eruption period of ∼7 hr, the AIA 94 Å images reveal the emergence of a coronal sigmoid through the interaction between two J-shaped bundles of loops, which proceeds with multiple episodes of coronal loop brightenings and significant variations in the magnetic flux through the photosphere. These observations imply that repetitive magnetic reconnections likely play a key role in the formation of the sigmoidal FR in the corona and also contribute toward sustaining themore » temperature of the FR higher than that of the ambient coronal structures. Notably, the formation of the sigmoid is associated with the fast morphological evolution of an S-shaped filament channel in the chromosphere. The sigmoid activates toward eruption with the ascent of a large FR in the corona, which is preceded by the decrease in photospheric magnetic flux through the core flaring region, suggesting tether-cutting reconnection as a possible triggering mechanism. The FR eruption results in a two-ribbon M6.5 flare with a prolonged rise phase of ∼21 minutes. The flare exhibits significant deviation from the standard flare model in the early rise phase, during which a pair of J-shaped flare ribbons form and apparently exhibit converging motions parallel to the polarity inversion line, which is further confirmed by the motions of hard X-ray footpoint sources. In the later stages, the flare follows the standard flare model and the source region undergoes a complete sigmoid-to-arcade transformation.« less

Reverse Transcription of a Self-Primed Retrotransposon Requires an RNA Structure Similar to the U5-IR Stem-Loop of Retroviruses

PubMed Central

Lin, Jia-Hwei; Levin, Henry L.

1998-01-01

An inverted repeat (IR) within the U5 region of the Rous sarcoma virus (RSV) mRNA forms a structure composed of a 7-bp stem and a 5-nucleotide (nt) loop. This U5-IR structure has been shown to be required for the initiation of reverse transcription. The mRNA of Tf1, long terminal repeat-containing retrotransposon from fission yeast (Schizosaccharomyces pombe) contains nucleotides with the potential to form a U5-IR stem-loop that is strikingly similar to that of RSV. The putative U5-IR stem-loop of Tf1 consists of a 7-bp stem and a 25-nt loop. Results from mutagenesis studies indicate that the U5-IR stem-loop in the mRNA of Tf1 does form and that it is required for Tf1 transposition. Although the loop is required for transposition, we were surprised that the specific sequence of the nucleotides within the loop was unimportant for function. Additional investigation indicates that the loss of transposition activity due to a reduction in the loop size to 6 nt could be rescued by increasing the GC content of the stem. This result indicates that the large loop in the Tf1 mRNA relative to that of the RSV allows the formation of the relatively weak U5-IR stem. The levels of Tf1 proteins expressed and the amounts of Tf1 RNA packaged into the virus-like particles were not affected by mutations in the U5-IR structure. However, all of the mutations in the U5-IR structure that caused defects in transposition produced low amounts of reverse transcripts. A unique feature in the initiation of Tf1 reverse transcription is that, instead of a tRNA, the first 11 nt of the Tf1 mRNA serve as the minus-strand primer. Analysis of the 5′ end of Tf1 mRNA revealed that the mutations in the U5-IR stem-loop that resulted in defects in reverse transcription caused a reduction in the cleavage activity required to generate the Tf1 primer. Our results indicate that the U5-IR stems of Tf1 and RSV are conserved in size, position, and function. PMID:9774699

RNA-dependent RNA polymerase of hepatitis C virus binds to its coding region RNA stem-loop structure, 5BSL3.2, and its negative strand.

PubMed

Kanamori, Hiroshi; Yuhashi, Kazuhito; Ohnishi, Shin; Koike, Kazuhiko; Kodama, Tatsuhiko

2010-05-01

The hepatitis C virus NS5B RNA-dependent RNA polymerase (RdRp) is a key enzyme involved in viral replication. Interaction between NS5B RdRp and the viral RNA sequence is likely to be an important step in viral RNA replication. The C-terminal half of the NS5B-coding sequence, which contains the important cis-acting replication element, has been identified as an NS5B-binding sequence. In the present study, we confirm the specific binding of NS5B to one of the RNA stem-loop structures in the region, 5BSL3.2. In addition, we show that NS5B binds to the complementary strand of 5BSL3.2 (5BSL3.2N). The bulge structure of 5BSL3.2N was shown to be indispensable for tight binding to NS5B. In vitro RdRp activity was inhibited by 5BSL3.2N, indicating the importance of the RNA element in the polymerization by RdRp. These results suggest the involvement of the RNA stem-loop structure of the negative strand in the replication process.

THE UBIQUITOUS PRESENCE OF LOOPLIKE FINE STRUCTURE INSIDE SOLAR ACTIVE REGIONS

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

Wang, Y.-M., E-mail: yi.wang@nrl.navy.mil

Although most of the solar surface outside active regions (ARs) is pervaded by small-scale fields of mixed polarity, this magnetic “carpet” or “junkyard” is thought to be largely absent inside AR plages and strong network. However, using extreme-ultraviolet images and line-of-sight magnetograms from the Solar Dynamics Observatory, we find that unipolar flux concentrations, both inside and outside ARs, often have small, loop-shaped Fe ix 17.1 and Fe xii 19.3 nm features embedded within them, even though no minority-polarity flux is visible in the corresponding magnetograms. Such looplike structures, characterized by horizontal sizes of ∼3–5 Mm and varying on timescales ofmore » minutes or less, are seen inside bright 17.1 nm moss, as well as in fainter moss-like regions associated with weaker network outside ARs. We also note a tendency for bright coronal loops to show compact, looplike features at their footpoints. Based on these observations, we suggest that present-day magnetograms may be substantially underrepresenting the amount of minority-polarity flux inside plages and strong network, and that reconnection between small bipoles and the overlying large-scale field could be a major source of coronal heating both in ARs and in the quiet Sun.« less

Deciphering the roles of outer membrane protein A extracellular loops in the pathogenesis of Escherichia coli K1 meningitis.

PubMed

Mittal, Rahul; Krishnan, Subramanian; Gonzalez-Gomez, Ignacio; Prasadarao, Nemani V

2011-01-21

Outer membrane protein A (OmpA) has been implicated as an important virulence factor in several gram-negative bacterial infections such as Escherichia coli K1, a leading cause of neonatal meningitis associated with significant mortality and morbidity. In this study, we generated E. coli K1 mutants that express OmpA in which three or four amino acids from various extracellular loops were changed to alanines, and we examined their ability to survive in several immune cells. We observed that loop regions 1 and 2 play an important role in the survival of E. coli K1 inside neutrophils and dendritic cells, and loop regions 1 and 3 are needed for survival in macrophages. Concomitantly, E. coli K1 mutants expressing loop 1 and 2 mutations were unable to cause meningitis in a newborn mouse model. Of note, mutations in loop 4 of OmpA enhance the severity of the pathogenesis by allowing the pathogen to survive better in circulation and to produce high bacteremia levels. These results demonstrate, for the first time, the roles played by different regions of extracellular loops of OmpA of E. coli K1 in the pathogenesis of meningitis and may help in designing effective preventive strategies against this deadly disease.

RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability.

PubMed

Chang, Emily Yun-Chia; Novoa, Carolina A; Aristizabal, Maria J; Coulombe, Yan; Segovia, Romulo; Chaturvedi, Richa; Shen, Yaoqing; Keong, Christelle; Tam, Annie S; Jones, Steven J M; Masson, Jean-Yves; Kobor, Michael S; Stirling, Peter C

2017-12-04

Sgs1, the orthologue of human Bloom's syndrome helicase BLM, is a yeast DNA helicase functioning in DNA replication and repair. We show that SGS1 loss increases R-loop accumulation and sensitizes cells to transcription-replication collisions. Yeast lacking SGS1 accumulate R-loops and γ-H2A at sites of Sgs1 binding, replication pausing regions, and long genes. The mutation signature of sgs1 Δ reveals copy number changes flanked by repetitive regions with high R-loop-forming potential. Analysis of BLM in Bloom's syndrome fibroblasts or by depletion of BLM from human cancer cells confirms a role for Sgs1/BLM in suppressing R-loop-associated genome instability across species. In support of a potential direct effect, BLM is found physically proximal to DNA:RNA hybrids in human cells, and can efficiently unwind R-loops in vitro. Together, our data describe a conserved role for Sgs1/BLM in R-loop suppression and support an increasingly broad view of DNA repair and replication fork stabilizing proteins as modulators of R-loop-mediated genome instability. © 2017 Chang et al.

Spatial Structure of Multimode Oscillations in a Solar Flare on 14 May 2013 in EUV and Radio Bands

NASA Astrophysics Data System (ADS)

Kolotkov, Dmitry; Nakariakov, Valery; Nisticò, Giuseppe; Shibasaki, Kiyoto; Kupriyanova, Elena

Quasi-periodic pulsations and coronal loop oscillations in an X-class solar flare on 14 May 2013 are considered. Rapidly decaying kink oscillations of coronal loops with periods of several minutes in the flaring active region detected in the EUV band with SDO/AIA after the impulsive phase of the flare. Oscillations of neighbouring loops are excited simultaneously, but get rapidly out of phase. In the impulsive phase, observations in the radio band with the Nobeyama Radioheliograph and Radiopolarimeter show quasi-periodic pulsations that are most pronounced in the 17 GHz band. In the correlation plots and the integrated flux the pulsations have a symmetric triangular shape. The period of pulsations is about 1 min. Analysis of the spatial locations of the radio sources reveal that the triangularity is likely to be caused by superposition of several harmonic modes.

Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes

PubMed Central

Nandy, Suman Kumar; Seal, Alpana

2016-01-01

Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases. PMID:27764212

Modality Specific Cerebro-Cerebellar Activations in Verbal Working Memory: An fMRI Study

PubMed Central

Kirschen, Matthew P.; Chen, S. H. Annabel; Desmond, John E.

2010-01-01

Verbal working memory (VWM) engages frontal and temporal/parietal circuits subserving the phonological loop, as well as, superior and inferior cerebellar regions which have projections from these neocortical areas. Different cerebro-cerebellar circuits may be engaged for integrating aurally- and visually-presented information for VWM. The present fMRI study investigated load (2, 4, or 6 letters) and modality (auditory and visual) dependent cerebro-cerebellar VWM activation using a Sternberg task. FMRI revealed modality-independent activations in left frontal (BA 6/9/44), insular, cingulate (BA 32), and bilateral inferior parietal/supramarginal (BA 40) regions, as well as in bilateral superior (HVI) and right inferior (HVIII) cerebellar regions. Visual presentation evoked prominent activations in right superior (HVI/CrusI) cerebellum, bilateral occipital (BA19) and left parietal (BA7/40) cortex while auditory presentation showed robust activations predominately in bilateral temporal regions (BA21/22). In the cerebellum, we noted a visual to auditory emphasis of function progressing from superior to inferior and from lateral to medial regions. These results extend our previous findings of fMRI activation in cerebro-cerebellar networks during VWM, and demonstrate both modality dependent commonalities and differences in activations with increasing memory load. PMID:20714061

Modality specific cerebro-cerebellar activations in verbal working memory: an fMRI study.

PubMed

Kirschen, Matthew P; Chen, S H Annabel; Desmond, John E

2010-01-01

Verbal working memory (VWM) engages frontal and temporal/parietal circuits subserving the phonological loop, as well as, superior and inferior cerebellar regions which have projections from these neocortical areas. Different cerebro-cerebellar circuits may be engaged for integrating aurally- and visually-presented information for VWM. The present fMRI study investigated load (2, 4, or 6 letters) and modality (auditory and visual) dependent cerebro-cerebellar VWM activation using a Sternberg task. FMRI revealed modality-independent activations in left frontal (BA 6/9/44), insular, cingulate (BA 32), and bilateral inferior parietal/supramarginal (BA 40) regions, as well as in bilateral superior (HVI) and right inferior (HVIII) cerebellar regions. Visual presentation evoked prominent activations in right superior (HVI/CrusI) cerebellum, bilateral occipital (BA19) and left parietal (BA7/40) cortex while auditory presentation showed robust activations predominantly in bilateral temporal regions (BA21/22). In the cerebellum, we noted a visual to auditory emphasis of function progressing from superior to inferior and from lateral to medial regions. These results extend our previous findings of fMRI activation in cerebro-cerebellar networks during VWM, and demonstrate both modality dependent commonalities and differences in activations with increasing memory load.

Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop

PubMed Central

Meng, Yilin; Roux, Benoît

2013-01-01

Molecular dynamics umbrella sampling simulations are used to compare the relative stability of the active conformation of the catalytic domain of c-Src kinase while the tyrosine 416 in the activation loop (A-loop) is either unphosphorylated or phosphorylated. When the A-loop is unphosphorylated, there is considerable flexiblity of the kinase. While the active conformation of the kinase is not forbidden and can be visited transiently, it is not the predominant state. This is consistent with the view that c-Src displays some catalytic activity even when the A-loop is unphosphorylated. In contrast, phosphorylation of the A-loop contributes to stabilize several structural features that are critical for catalysis, such as the hydrophobic regulatory spine, the HRD motif, and the electrostatic switch. In summary, the free energy landscape calculations demonstrate that phosphorylation of tyrosine 416 in the A-loop essentially “locks” the kinase into its catalytically competent conformation. PMID:24103328

OBSERVATIONAL SIGNATURES OF CORONAL LOOP HEATING AND COOLING DRIVEN BY FOOTPOINT SHUFFLING

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

Dahlburg, R. B.; Taylor, B. D.; Einaudi, G.

The evolution of a coronal loop is studied by means of numerical simulations of the fully compressible three-dimensional magnetohydrodynamic equations using the HYPERION code. The footpoints of the loop magnetic field are advected by random motions. As a consequence, the magnetic field in the loop is energized and develops turbulent nonlinear dynamics characterized by the continuous formation and dissipation of field-aligned current sheets: energy is deposited at small scales where heating occurs. Dissipation is nonuniformly distributed so that only a fraction of the coronal mass and volume gets heated at any time. Temperature and density are highly structured at scalesmore » that, in the solar corona, remain observationally unresolved: the plasma of our simulated loop is multithermal, where highly dynamical hotter and cooler plasma strands are scattered throughout the loop at sub-observational scales. Numerical simulations of coronal loops of 50,000 km length and axial magnetic field intensities ranging from 0.01 to 0.04 T are presented. To connect these simulations to observations, we use the computed number densities and temperatures to synthesize the intensities expected in emission lines typically observed with the Extreme Ultraviolet Imaging Spectrometer on Hinode. These intensities are used to compute differential emission measure distributions using the Monte Carlo Markov Chain code, which are very similar to those derived from observations of solar active regions. We conclude that coronal heating is found to be strongly intermittent in space and time, with only small portions of the coronal loop being heated: in fact, at any given time, most of the corona is cooling down.« less

Three Dimensional Structure and Time Development of Radio Emission from Solar Active Regions.

DTIC Science & Technology

1983-01-15

8217 surrounded by a weaker unpolarized halo whose angular extent ranges between 5’ and 9’. The bright (106K) sunspot-associated cores, which were intepreted in...shorter intervals. Examination of the He film indicates that the dominant He emission was stable for periods of at least six hours. Figure 8 and 9 also...the cool loops and may occupy a substantial fraction of the region above sunspots. This intepretation has, in fact, been supported by the model of

Force-Free Magnetic Fields Calculated from Automated Tracing of Coronal Loops with AIA/SDO

NASA Astrophysics Data System (ADS)

Aschwanden, M. J.

2013-12-01

One of the most realistic magnetic field models of the solar corona is a nonlinear force-free field (NLFFF) solution. There exist about a dozen numeric codes that compute NLFFF solutions based on extrapolations of photospheric vector magnetograph data. However, since the photosphere and lower chromosphere is not force-free, a suitable correction has to be applied to the lower boundary condition. Despite of such "pre-processing" corrections, the resulting theoretical magnetic field lines deviate substantially from observed coronal loop geometries. - Here we developed an alternative method that fits an analytical NLFFF approximation to the observed geometry of coronal loops. The 2D coordinates of the geometry of coronal loop structures observed with AIA/SDO are traced with the "Oriented Coronal CUrved Loop Tracing" (OCCULT-2) code, an automated pattern recognition algorithm that has demonstrated the fidelity in loop tracing matching visual perception. A potential magnetic field solution is then derived from a line-of-sight magnetogram observed with HMI/SDO, and an analytical NLFFF approximation is then forward-fitted to the twisted geometry of coronal loops. We demonstrate the performance of this magnetic field modeling method for a number of solar active regions, before and after major flares observed with SDO. The difference of the NLFFF and the potential field energies allows us then to compute the free magnetic energy, which is an upper limit of the energy that is released during a solar flare.

Numerical Simulation of DC Coronal Heating

NASA Astrophysics Data System (ADS)

Dahlburg, Russell B.; Einaudi, G.; Taylor, Brian D.; Ugarte-Urra, Ignacio; Warren, Harry; Rappazzo, A. F.; Velli, Marco

2016-05-01

Recent research on observational signatures of turbulent heating of a coronal loop will be discussed. The evolution of the loop is is studied by means of numerical simulations of the fully compressible three-dimensional magnetohydrodynamic equations using the HYPERION code. HYPERION calculates the full energy cycle involving footpoint convection, magnetic reconnection, nonlinear thermal conduction and optically thin radiation. The footpoints of the loop magnetic field are convected by random photospheric motions. As a consequence the magnetic field in the loop is energized and develops turbulent nonlinear dynamics characterized by the continuous formation and dissipation of field-aligned current sheets: energy is deposited at small scales where heating occurs. Dissipation is non-uniformly distributed so that only a fraction of thecoronal mass and volume gets heated at any time. Temperature and density are highly structured at scales which, in the solar corona, remain observationally unresolved: the plasma of the simulated loop is multi thermal, where highly dynamical hotter and cooler plasma strands are scattered throughout the loop at sub-observational scales. Typical simulated coronal loops are 50000 km length and have axial magnetic field intensities ranging from 0.01 to 0.04 Tesla. To connect these simulations to observations the computed number densities and temperatures are used to synthesize the intensities expected in emission lines typically observed with the Extreme ultraviolet Imaging Spectrometer (EIS) on Hinode. These intensities are then employed to compute differential emission measure distributions, which are found to be very similar to those derived from observations of solar active regions.

Observational Signatures of Coronal Heating

NASA Astrophysics Data System (ADS)

Dahlburg, R. B.; Einaudi, G.; Ugarte-Urra, I.; Warren, H. P.; Rappazzo, A. F.; Velli, M.; Taylor, B.

2016-12-01

Recent research on observational signatures of turbulent heating of a coronal loop will be discussed. The evolution of the loop is is studied by means of numericalsimulations of the fully compressible three-dimensionalmagnetohydrodynamic equations using the HYPERION code. HYPERION calculates the full energy cycle involving footpoint convection, magnetic reconnection,nonlinear thermal conduction and optically thin radiation.The footpoints of the loop magnetic field are convected by random photospheric motions. As a consequence the magnetic field in the loop is energized and develops turbulent nonlinear dynamics characterized by the continuous formation and dissipation of field-aligned current sheets: energy is deposited at small scales where heating occurs. Dissipation is non-uniformly distributed so that only a fraction of thecoronal mass and volume gets heated at any time. Temperature and density are highly structured at scales which, in the solar corona, remain observationally unresolved: the plasma of the simulated loop is multi-thermal, where highly dynamical hotter and cooler plasma strands arescattered throughout the loop at sub-observational scales. Typical simulated coronal loops are 50000 km length and have axial magnetic field intensities ranging from 0.01 to 0.04 Tesla.To connect these simulations to observations the computed numberdensities and temperatures are used to synthesize the intensities expected inemission lines typically observed with the Extreme ultraviolet Imaging Spectrometer(EIS) on Hinode. These intensities are then employed to compute differentialemission measure distributions, which are found to be very similar to those derivedfrom observations of solar active regions.

Evidence for two-loop interaction from IRIS and SDO observations of penumbral brightenings

NASA Astrophysics Data System (ADS)

Alissandrakis, C. E.; Koukras, A.; Patsourakos, S.; Nindos, A.

2017-07-01

Aims: We investigate small scale energy release events which can provide clues on the heating mechanism of the solar corona. Methods: We analyzed spectral and imaging data from the Interface Region Imaging Spectrograph (IRIS), images from the Atmospheric Imaging Assembly (AIA) aboard the Solar Dynamics Observatoty (SDO), and magnetograms from the Helioseismic and Magnetic Imager (HMI) aboard SDO. Results: We report observations of small flaring loops in the penumbra of a large sunspot on July 19, 2013. Our main event consisted of a loop spanning 15'', from the umbral-penumbral boundary to an opposite polarity region outside the penumbra. It lasted approximately 10 min with a two minute impulsive peak and was observed in all AIA/SDO channels, while the IRIS slit was located near its penumbral footpoint. Mass motions with an apparent velocity of 100 km s-1 were detected beyond the brightening, starting in the rise phase of the impulsive peak; these were apparently associated with a higher-lying loop. We interpret these motions in terms of two-loop interaction. IRIS spectra in both the C II and Si iv lines showed very extended wings, up to about 400 km s-1, first in the blue (upflows) and subsequently in the red wing. In addition to the strong lines, emission was detected in the weak lines of Cl I, O I and C I, as well as in the Mg II triplet lines. Absorption features in the profiles of the C II doublet, the Si iv doublet and the Mg II h and k lines indicate the existence of material with a lower source function between the brightening and the observer. We attribute this absorption to the higher loop and this adds further credibility to the two-loop interaction hypothesis. Tilts were detected in the absorption spectra, as well as in the spectra of Cl I, O I, and C I lines, possibly indicating rotational motions from the untwisting of magnetic flux tubes. Conclusions: We conclude that the absorption features in the C II, Si iv and Mg II profiles originate in a higher-lying, descending loop; as this approached the already activated lower-lying loop, their interaction gave rise to the impulsive peak, the very broad line profiles and the mass motions. Movies associated to Figs. A.1-A.3 are available at http://www.aanda.org

A small modified hammerhead ribozyme and its conformational characteristics determined by mutagenesis and lattice calculation.

PubMed Central

Lustig, B; Lin, N H; Smith, S M; Jernigan, R L; Jeang, K T

1995-01-01

A prototypic hammerhead ribozyme has three helices that surround an asymmetrical central core loop. We have mutagenized a hammerhead type ribozyme. In agreement with previous studies, progressive removal of stem-loop II from a three stemmed ribozyme showed that this region is not absolutely critical for catalysis. However, complete elimination of stem II and its loop did reduce, but did not eliminate, function. In a stem-loop II-deleted ribozyme, activity was best preserved when a purine, preferably a G, was present at position 10.1. This G contributed to catalysis irregardless of its role as either one part of a canonical pair with a C residue at 11.1 or a lone nucleotide with C (11.1) deleted. Computational methods using lattices generated 87 million three-dimensional chain forms for a stem-loop II-deleted RNA complex that preserved one potential G.C base pair at positions 10.1 and 11.1. This exhaustive set of chain forms included one major class of structures with G(10.1) being spatially proximal to the GUCX cleavage site of the substrate strand. Strong correlations were observed between colinear arrangement of stems I and III, constraints of base-pairing in the central core loop, and one particular placement of G(10.1) relative to the cleavage site. Our calculations of a stem-loop II-deleted ribozyme indicate that without needing to invoke any other constraints, the inherent asymmetry in the lengths of the two loop strands (3 nt in one and 7 nt in the other) that compose the core and flank G10.1-C11.1 stipulated strongly this particular G placement. This suggests that the hammerhead ribozyme maintains an asymmetry in its internal loop for a necessary structure/function reason. Images PMID:7567466

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

Bae, Brian; Nayak, Dhananjaya; Ray, Ananya

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

A Nanoflare-Based Cellular Automaton Model and the Observed Properties of the Coronal Plasma

NASA Technical Reports Server (NTRS)

Lopez-Fuentes, Marcelo; Klimchuk, James Andrew

2016-01-01

We use the cellular automaton model described in Lopez Fuentes and Klimchuk to study the evolution of coronal loop plasmas. The model, based on the idea of a critical misalignment angle in tangled magnetic fields, produces nanoflares of varying frequency with respect to the plasma cooling time. We compare the results of the model with active region (AR) observations obtained with the Hinode/XRT and SDOAIA instruments. The comparison is based on the statistical properties of synthetic and observed loop light curves. Our results show that the model reproduces the main observational characteristics of the evolution of the plasma in AR coronal loops. The typical intensity fluctuations have amplitudes of 10 percent - 15 percent both for the model and the observations. The sign of the skewness of the intensity distributions indicates the presence of cooling plasma in the loops. We also study the emission measure (EM) distribution predicted by the model and obtain slopes in log(EM) versus log(T) between 2.7 and 4.3, in agreement with published observational values.

A NANOFLARE-BASED CELLULAR AUTOMATON MODEL AND THE OBSERVED PROPERTIES OF THE CORONAL PLASMA

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

Fuentes, Marcelo López; Klimchuk, James A., E-mail: lopezf@iafe.uba.ar

2016-09-10

We use the cellular automaton model described in López Fuentes and Klimchuk to study the evolution of coronal loop plasmas. The model, based on the idea of a critical misalignment angle in tangled magnetic fields, produces nanoflares of varying frequency with respect to the plasma cooling time. We compare the results of the model with active region (AR) observations obtained with the Hinode /XRT and SDO /AIA instruments. The comparison is based on the statistical properties of synthetic and observed loop light curves. Our results show that the model reproduces the main observational characteristics of the evolution of the plasmamore » in AR coronal loops. The typical intensity fluctuations have amplitudes of 10%–15% both for the model and the observations. The sign of the skewness of the intensity distributions indicates the presence of cooling plasma in the loops. We also study the emission measure (EM) distribution predicted by the model and obtain slopes in log(EM) versus log(T) between 2.7 and 4.3, in agreement with published observational values.« less

FIP bias in a sigmoidal active region

NASA Astrophysics Data System (ADS)

Baker, D.; Brooks, D. H.; Démoulin, P.; van Driel-Gesztelyi, Lidia; Green, L. M.; Steed, K.; Carlyle, J.

2014-01-01

We investigate first ionization potential (FIP) bias levels in an anemone active region (AR) - coronal hole (CH) complex using an abundance map derived from Hinode/EIS spectra. The detailed, spatially resolved abundance map has a large field of view covering 359'' × 485''. Plasma with high FIP bias, or coronal abundances, is concentrated at the footpoints of the AR loops whereas the surrounding CH has a low FIP bias, ~1, i.e. photospheric abundances. A channel of low FIP bias is located along the AR's main polarity inversion line containing a filament where ongoing flux cancellation is observed, indicating a bald patch magnetic topology characteristic of a sigmoid/flux rope configuration.

Interacting cytoplasmic loops of subunits a and c of Escherichia coli F1F0 ATP synthase gate H+ transport to the cytoplasm.

PubMed

Steed, P Ryan; Kraft, Kaitlin A; Fillingame, Robert H

2014-11-25

H(+)-transporting F1F0 ATP synthase catalyzes the synthesis of ATP via coupled rotary motors within F0 and F1. H(+) transport at the subunit a-c interface in transmembranous F0 drives rotation of a cylindrical c10 oligomer within the membrane, which is coupled to rotation of subunit γ within the α3β3 sector of F1 to mechanically drive ATP synthesis. F1F0 functions in a reversible manner, with ATP hydrolysis driving H(+) transport. ATP-driven H(+) transport in a select group of cysteine mutants in subunits a and c is inhibited after chelation of Ag(+) and/or Cd(+2) with the substituted sulfhydryl groups. The H(+) transport pathway mapped via these Ag(+)(Cd(+2))-sensitive Cys extends from the transmembrane helices (TMHs) of subunits a and c into cytoplasmic loops connecting the TMHs, suggesting these loop regions could be involved in gating H(+) release to the cytoplasm. Here, using select loop-region Cys from the single cytoplasmic loop of subunit c and multiple cytoplasmic loops of subunit a, we show that Cd(+2) directly inhibits passive H(+) transport mediated by F0 reconstituted in liposomes. Further, in extensions of previous studies, we show that the regions mediating passive H(+) transport can be cross-linked to each other. We conclude that the loop-regions in subunits a and c that are implicated in H(+) transport likely interact in a single structural domain, which then functions in gating H(+) release to the cytoplasm.

ABOVE-THE-LOOP-TOP OSCILLATION AND QUASI-PERIODIC CORONAL WAVE GENERATION IN SOLAR FLARES

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

Takasao, Shinsuke; Shibata, Kazunari, E-mail: takasao@kwasan.kyoto-u.ac.jp

Observations revealed that various kinds of oscillations are excited in solar flare regions. Quasi-periodic pulsations (QPPs) in flare emissions are commonly observed in a wide range of wavelengths. Recent observations have found that fast-mode magnetohydrodynamic (MHD) waves are quasi-periodically emitted from some flaring sites (quasi-periodic propagating fast-mode magnetoacoustic waves; QPFs). Both QPPs and QPFs imply a cyclic disturbance originating from the flaring sites. However, the physical mechanisms remain puzzling. By performing a set of two-dimensional MHD simulations of a solar flare, we discovered the local oscillation above the loops filled with evaporated plasma (above-the-loop-top region) and the generation of QPFsmore » from such oscillating regions. Unlike all previous models for QPFs, our model includes essential physics for solar flares such as magnetic reconnection, heat conduction, and chromospheric evaporation. We revealed that QPFs can be spontaneously excited by the above-the-loop-top oscillation. We found that this oscillation is controlled by the backflow of the reconnection outflow. The new model revealed that flare loops and the above-the-loop-top region are full of shocks and waves, which is different from the previous expectations based on a standard flare model and previous simulations. In this paper, we show the QPF generation process based on our new picture of flare loops and will briefly discuss a possible relationship between QPFs and QPPs. Our findings will change the current view of solar flares to a new view in which they are a very dynamic phenomenon full of shocks and waves.« less

Genetic distance of Malaysian mousedeer based on mitochondrial DNA cytochrome oxidase I (COI) and D-loop region sequences

NASA Astrophysics Data System (ADS)

Bakar, Mohamad-Azam Akmal Abu; Rovie-Ryan, Jeffrine Japning; Ampeng, Ahmad; Yaakop, Salmah; Nor, Shukor Md; Md-Zain, Badrul Munir

2018-04-01

Mousedeer is one of the primitive mammals that can be found mainly in Southeast-Asia region. There are two species of mousedeer in Malaysia which are Tragulus kanchil and Tragulus napu. Both species can be distinguish by size, coat coloration, and throat pattern but clear diagnosis still cannot be found. The objective of the study is to show the genetic distance relationship between T. kanchil and T. napu and their population based on mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and D-loop region. There are 42 sample of mousedeer were used in this study collected by PERHILITAN from different locality. Another 29 D-loop sequence were retrieved from Genbank for comparative analysis. All sample were amplified using universal primer and species-specific primer for COI and D-loop genes via PCR process. The amplified sequences were analyzed to determine genetic distance of T. kanchil and T. napu. From the analysis, the average genetic distance between T. kanchil and T. napu based on locus COI and D-loop were 0.145 and 0.128 respectively. The genetic distance between populations of T. kanchil based on locus COI was between 0.003-0.013. For locus D-loop, genetic distance analysis showed distance in relationship between west-coast populations to east-coast population of T. kanchil. COI and D-loop mtDNA region provided a clear picture on the relationship within the mousedeer species. Last but not least, conservation effort toward protecting this species can be done by study the molecular genetics and prevent the extinction of this species.

A phosphatase-independent gain-of-function mutation in PTEN triggers aberrant cell growth in astrocytes through an autocrine IGF-1 loop.

PubMed

Fernández, S; Genis, L; Torres-Alemán, I

2014-08-07

Loss-of-function mutations in the phosphatase PTEN (phosphatase and tensin homolog deleted on chromosome10) contribute to aberrant cell growth in part through upregulation of the mitogenic IGF-1/PI3K/Akt pathway. In turn, this pathway exerts a homeostatic feedback over PTEN. Using mutagenesis analysis to explore a possible impact of this mutual control on astrocyte growth, we found that truncation of the C-terminal region of PTEN (Δ51) associates with a marked increase in NFκB activity, a transcription factor overactivated in astrocyte tumors. Whereas mutations of PTEN are considered to lead to a loss-of-function, PTENΔ51, a truncation that comprises a region frequently mutated in human gliomas, displayed a neomorphic (gain-of-function) activity that was independent of its phosphatase activity. This gain-of-function of PTENΔ51 includes stimulation of IGF-1 synthesis through protein kinase A activation of the IGF-1 promoter. Increased IGF-1 originates an autocrine loop that activates Akt and NFκB. Constitutive activation of NFκB in PTENΔ51-expressing astrocytes leads to aberrant cell growth; astrocytes expressing this mutant PTEN generate colonies in vitro and tumors in vivo. Mutations converting a tumor suppressor such as PTEN into a tumor promoter through a gain-of-function involving IGF-1 production may further our understanding of the role played by this growth factor in glioma growth and help us define druggable targets for personalized therapy.

Trans-activation of the Tetrahymena group I intron ribozyme via a non-native RNA-RNA interaction.

PubMed Central

Ikawa, Y; Shiraishi, H; Inoue, T

1999-01-01

The peripheral P2.1 domain of the Tetrahymena group I intron ribozyme has been shown to be non-essential for splicing. We found, however, that separately prepared P2.1 RNA efficiently accelerates the 3' splice-site-specific hydrolysis reaction of a mutant ribozyme lacking both P2.1 and its upstream region in trans. We report here the unusual properties of this trans-activation. Compensatory mutational analysis revealed that non-native long-range base-pairings between the loop region of P2.1 RNA and L5c region of the mutant ribozyme are needed for the activation in spite of the fact that P2.1 forms base-pairings with P9.1 in the Tetrahymena ribozyme. The trans -activation depends on the non-native RNA-RNA interaction together with the higher order structure of P2.1 RNA. This activation is unique among the known trans-activations that utilize native tertiary interactions or RNA chaperons. PMID:10075996

Successive Two-sided Loop Jets Caused by Magnetic Reconnection between Two Adjacent Filamentary Threads

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

Tian, Zhanjun; Liu, Yu; Shen, Yuandeng

We present observational analysis of two successive two-sided loop jets observed by the ground-based New Vacuum Solar Telescope and the space-borne Solar Dynamics Observatory . The two successive two-sided loop jets manifested similar evolution processes and both were associated with the interaction of two small-scale adjacent filamentary threads, magnetic emerging, and cancellation processes at the jet’s source region. High temporal and high spatial resolution observations reveal that the two adjacent ends of the two filamentary threads are rooted in opposite magnetic polarities within the source region. The two threads approached each other, and then an obvious brightening patch is observedmore » at the interaction position. Subsequently, a pair of hot plasma ejections are observed heading in opposite directions along the paths of the two filamentary threads at a typical speed for two-sided loop jets of the order 150 km s{sup −1}. Close to the end of the second jet, we report the formation of a bright hot loop structure at the source region, which suggests the formation of new loops during the interaction. Based on the observational results, we propose that the observed two-sided loop jets are caused by magnetic reconnection between the two adjacent filamentary threads, largely different from the previous scenario that a two-sided loop jet is generated by magnetic reconnection between an emerging bipole and the overlying horizontal magnetic fields.« less

First Detection of a Strong Magnetic Field on a Bursty Brown Dwarf: Puzzle Solved

NASA Astrophysics Data System (ADS)

Berdyugina, S. V.; Harrington, D. M.; Kuzmychov, O.; Kuhn, J. R.; Hallinan, G.; Kowalski, A. F.; Hawley, S. L.

2017-09-01

We report the first direct detection of a strong, 5 kG magnetic field on the surface of an active brown dwarf. LSR J1835+3259 is an M8.5 dwarf exhibiting transient radio and optical emission bursts modulated by fast rotation. We have detected the surface magnetic field as circularly polarized signatures in the 819 nm sodium lines when an active emission region faced the Earth. Modeling Stokes profiles of these lines reveals the effective temperature of 2800 K and log gravity acceleration of 4.5. These parameters place LSR J1835+3259 on evolutionary tracks as a young brown dwarf with the mass of 55+/- 4{M}{{J}} and age of 22 ± 4 Myr. Its magnetic field is at least 5.1 kG and covers at least 11% of the visible hemisphere. The active region topology recovered using line profile inversions comprises hot plasma loops with a vertical stratification of optical and radio emission sources. These loops rotate with the dwarf in and out of view causing periodic emission bursts. The magnetic field is detected at the base of the loops. This is the first time that we can quantitatively associate brown dwarf non-thermal bursts with a strong, 5 kG surface magnetic field and solve the puzzle of their driving mechanism. This is also the coolest known dwarf with such a strong surface magnetic field. The young age of LSR J1835+3259 implies that it may still maintain a disk, which may facilitate bursts via magnetospheric accretion, like in higher-mass T Tau-type stars. Our results pave a path toward magnetic studies of brown dwarfs and hot Jupiters.

Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice.

PubMed

Dong, Qianli; Li, Ning; Li, Xiaochong; Yuan, Zan; Xie, Dejian; Wang, Xiaofei; Li, Jianing; Yu, Yanan; Wang, Jinbin; Ding, Baoxu; Zhang, Zhibin; Li, Changping; Bian, Yao; Zhang, Ai; Wu, Ying; Liu, Bao; Gong, Lei

2018-06-01

The non-random spatial packing of chromosomes in the nucleus plays a critical role in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate compartment delimitation and extensive TADs (Topologically Associated Domains) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome. We found subtle features including chromatin loops, gene loops, and off-/near-diagonal intensive interaction regions. Gene chromatin loops associated with H3K27me3 could be positively involved in gene expression. In addition to insulated enhancing effects for neighbor gene expression, the identified rice gene loops could bi-directionally (+/-) affect the expression of looped genes themselves. Finally, web-interleaved off-diagonal IHIs/KEEs (Interactive Heterochromatic Islands or KNOT ENGAGED ELEMENTs) could trap transposable elements (TEs) via the enrichment of silencing epigenetic marks. In parallel, the near-diagonal FIREs (Frequently Interacting Regions) could positively affect the expression of involved genes. Our results suggest that the chromatin packing pattern in rice is generally similar to that in Arabidopsis thaliana but with clear differences at specific structural levels. We conclude that genomic composition, epigenetic modification, and transcriptional activity could act in combination to shape global and local chromatin packing in rice. Our results confirm recent observations in rice and A. thaliana but also provide additional insights into the patterns and features of chromatin organization in higher plants. © 2018 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

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

PubMed

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

2016-12-27

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

Closed Field Coronal Heating Models Inspired by Wave Turbulence

NASA Astrophysics Data System (ADS)

Downs, C.; Lionello, R.; Mikic, Z.; Linker, J.; Velli, M. M.

2013-12-01

To simulate the energy balance of coronal plasmas on macroscopic scales, we often require the specification of the coronal heating mechanism in some functional form. To go beyond empirical formulations and to build a more physically motivated heating function, we investigate the wave-turbulence dissipation (WTD) phenomenology for the heating of closed coronal loops. To do so, we employ an implementation of non-WKB equations designed to capture the large-scale propagation, reflection, and dissipation of wave turbulence along a loop. The parameter space of this model is explored by solving the coupled WTD and hydrodynamic equations in 1D for an idealized loop, and the relevance to a range of solar conditions is established by computing solutions for several hundred loops extracted from a realistic 3D coronal field. Due to the implicit dependence of the WTD heating model on loop geometry and plasma properties along the loop and at the footpoints, we find that this model can significantly reduce the number of free parameters when compared to traditional empirical heating models, and still robustly describe a broad range of quiet-sun and active region conditions. The importance of the self-reflection term in producing realistic heating scale heights and thermal non-equilibrium cycles is discussed, and preliminary 3D thermodynamic MHD simulations using this formulation are presented. Research supported by NASA and NSF.

Molecular dynamics simulations of glycosyltransferase LgtC.

PubMed

Snajdrová, Lenka; Kulhánek, Petr; Imberty, Anne; Koca, Jaroslav

2004-04-02

Molecular dynamics simulations have been performed on fully solvated alpha-(1-->4)-galactosyltransferase LgtC from Neisseria meningitidis with and without the donor substrate UDP-Gal and in the presence of the manganese ion. The analysis of the trajectories revealed a limited movement in the loop X (residues 75-80) and a larger conformational change in the loop Y (residues 246-251) in the simulation, when UDP-Gal was not present. In this case, the loops X and Y open by almost 10A, exposing the active site to the solvent. The 'hinge region' responsible for the opening is composed of residues 246-247. We have also analyzed the behavior of the manganese ion in the simulations. The coordination number is 6 when UDP-Gal is present and it increases to 7 when it is absent. In the latter case, three water molecules become coordinated to the ion. In both cases, the coordination is very stable implying that the manganese ion is tightly bound in the active site of the enzyme even if UDP-Gal is not present. Further analysis of the structural water molecules location confirmed that the mobility of water molecules in the active site and the accessibility of this site for solvent are higher in the absence of the substrate.

Behaviour of fractional loop delay zero crossing digital phase locked loop (FR-ZCDPLL)

NASA Astrophysics Data System (ADS)

Nasir, Qassim

2018-01-01

This article analyses the performance of the first-order zero crossing digital phase locked loops (FR-ZCDPLL) when fractional loop delay is added to loop. The non-linear dynamics of the loop is presented, analysed and examined through bifurcation behaviour. Numerical simulation of the loop is conducted to proof the mathematical analysis of the loop operation. The results of the loop simulation show that the proposed FR-ZCDPLL has enhanced the performance compared to the conventional zero crossing DPLL in terms of wider lock range, captured range and stable operation region. In addition, extensive experimental simulation was conducted to find the optimum loop parameters for different loop environmental conditions. The addition of the fractional loop delay network in the conventional loop also reduces the phase jitter and its variance especially when the signal-to-noise ratio is low.

Regulation of TCF ETS-domain transcription factors by helix-loop-helix motifs.

PubMed

Stinson, Julie; Inoue, Toshiaki; Yates, Paula; Clancy, Anne; Norton, John D; Sharrocks, Andrew D

2003-08-15

DNA binding by the ternary complex factor (TCF) subfamily of ETS-domain transcription factors is tightly regulated by intramolecular and intermolecular interactions. The helix-loop-helix (HLH)-containing Id proteins are trans-acting negative regulators of DNA binding by the TCFs. In the TCF, SAP-2/Net/ERP, intramolecular inhibition of DNA binding is promoted by the cis-acting NID region that also contains an HLH-like motif. The NID also acts as a transcriptional repression domain. Here, we have studied the role of HLH motifs in regulating DNA binding and transcription by the TCF protein SAP-1 and how Cdk-mediated phosphorylation affects the inhibitory activity of the Id proteins towards the TCFs. We demonstrate that the NID region of SAP-1 is an autoinhibitory motif that acts to inhibit DNA binding and also functions as a transcription repression domain. This region can be functionally replaced by fusion of Id proteins to SAP-1, whereby the Id moiety then acts to repress DNA binding in cis. Phosphorylation of the Ids by cyclin-Cdk complexes results in reduction in protein-protein interactions between the Ids and TCFs and relief of their DNA-binding inhibitory activity. In revealing distinct mechanisms through which HLH motifs modulate the activity of TCFs, our results therefore provide further insight into the role of HLH motifs in regulating TCF function and how the inhibitory properties of the trans-acting Id HLH proteins are themselves regulated by phosphorylation.

Mitochondria DNA replication and DNA methylation in the metabolic memory associated with continued progression of diabetic retinopathy.

PubMed

Tewari, Shikha; Zhong, Qing; Santos, Julia M; Kowluru, Renu A

2012-07-24

Diabetic retinopathy fails to halt after cessation of hyperglycemic insult, and a vicious cycle of mitochondria damage continues. The aim of our study was to investigate the effect of termination of hyperglycemia on retinal mtDNA replication, and elucidate the mechanism responsible for the continued mtDNA damage. Polymerase gamma 1 (POLG1), the catalytic subunit of the mitochondrial DNA replication enzyme, and the damage to the displacement loop region of mtDNA (D-loop) were analyzed in the retina from streptozotocin-diabetic rats maintained in poor glycemic control (PC, glycated hemoglobin ∼11%) or in good glycemic control (GC, glycated hemoglobin ∼6%) for 6 months, or in PC for three months followed by GC for three months (Rev). To understand the mechanism DNA methylation status of POLG1 promoter was investigated by methylation-specific PCR. The key parameters were confirmed in the isolated retinal endothelial cells exposed to high glucose, followed by normal glucose. POLG1 continued to be down-regulated, the D-loop region damaged, and the CpG islands at the regulatory region of POLG hyper-methylated even after three months of GC that had followed three months of PC (Rev group). Similar results were observed in the retinal endothelial cells exposed to normal glucose after being exposed to high glucose. Continued hypermethylation of the CpG sites at the regulatory region of POLG affects its binding to the mtDNA, compromising the transcriptional activity. Modulation of DNA methylation using pharmaceutic or molecular means could help maintain mitochondria homeostasis, and prevent further progression of diabetic retinopathy.

A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior.

PubMed

Kromann-Hansen, Tobias; Oldenburg, Emil; Yung, Kristen Wing Yu; Ghassabeh, Gholamreza H; Muyldermans, Serge; Declerck, Paul J; Huang, Mingdong; Andreasen, Peter A; Ngo, Jacky Chi Ki

2016-07-15

A peptide segment that binds the active site of a serine protease in a substrate-like manner may behave like an inhibitor or a substrate. However, there is sparse information on which factors determine the behavior a particular peptide segment will exhibit. Here, we describe the first x-ray crystal structure of a nanobody in complex with a serine protease. The nanobody displays a new type of interaction between an antibody and a serine protease as it inserts its complementary determining region-H3 loop into the active site of the protease in a substrate-like manner. The unique binding mechanism causes the nanobody to behave as a strong inhibitor as well as a poor substrate. Intriguingly, its substrate behavior is incomplete, as 30-40% of the nanobody remained intact and inhibitory after prolonged incubation with the protease. Biochemical analysis reveals that an intra-loop interaction network within the complementary determining region-H3 of the nanobody balances its inhibitor versus substrate behavior. Collectively, our results unveil molecular factors, which may be a general mechanism to determine the substrate versus inhibitor behavior of other protease inhibitors. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

A training rule which guarantees finite-region stability for a class of closed-loop neural-network control systems.

PubMed

Kuntanapreeda, S; Fullmer, R R

1996-01-01

A training method for a class of neural network controllers is presented which guarantees closed-loop system stability. The controllers are assumed to be nonlinear, feedforward, sampled-data, full-state regulators implemented as single hidden-layer neural networks. The controlled systems must be locally hermitian and observable. Stability of the closed-loop system is demonstrated by determining a Lyapunov function, which can be used to identify a finite stability region about the regulator point.

Study of the post-flare loops on 29 July 1973. I - Dynamics of the X-ray loops

NASA Technical Reports Server (NTRS)

Nolte, J. T.; Gerassimenko, M.; Krieger, A. S.; Petrasso, R. D.; Svestka, Z.

1979-01-01

We derive an empirical model of the X-ray emitting post-flare loops observed during the decay phase of the 29 July 1973 flare. We find that the loops are elliptical, with the brightest emitting region at the tops. We determine the height, velocity of growth, and ratio of height to width of the loops at times from 3 to 12 hr after the flare onset.

Coronal temperatures of selected active cool stars as derived from low resolution Einstein observations

NASA Technical Reports Server (NTRS)

Vilhu, Osmi; Linsky, Jeffrey L.

1990-01-01

Mean coronal temperatures of some active G-K stars were derived from Rev1-processed Einstein-observatory's IPC-spectra. The combined X-ray and transition region emission line data are in rough agreement with static coronal loop models. Although the sample is too small to derive any statistically significant conclusions, it suggests that the mean coronal temperature depends linearly on the inverse Rossby-number, with saturation at short rotation periods.

Stabilization of a protein conferred by an increase in folded state entropy.

PubMed

Dagan, Shlomi; Hagai, Tzachi; Gavrilov, Yulian; Kapon, Ruti; Levy, Yaakov; Reich, Ziv

2013-06-25

Entropic stabilization of native protein structures typically relies on strategies that serve to decrease the entropy of the unfolded state. Here we report, using a combination of experimental and computational approaches, on enhanced thermodynamic stability conferred by an increase in the configurational entropy of the folded state. The enhanced stability is observed upon modifications of a loop region in the enzyme acylphosphatase and is achieved despite significant enthalpy losses. The modifications that lead to increased stability, as well as those that result in destabilization, however, strongly compromise enzymatic activity, rationalizing the preservation of the native loop structure even though it does not provide the protein with maximal stability or kinetic foldability.

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

Jafarzadeh, S.; Rutten, R. J.; Szydlarski, M.

A dense forest of slender bright fibrils near a small solar active region is seen in high-quality narrowband Ca ii H images from the SuFI instrument onboard the Sunrise balloon-borne solar observatory. The orientation of these slender Ca ii H fibrils (SCF) overlaps with the magnetic field configuration in the low solar chromosphere derived by magnetostatic extrapolation of the photospheric field observed with Sunrise/IMaX and SDO/HMI. In addition, many observed SCFs are qualitatively aligned with small-scale loops computed from a novel inversion approach based on best-fit numerical MHD simulation. Such loops are organized in canopy-like arches over quiet areas thatmore » differ in height depending on the field strength near their roots.« less

Dynamics of flare sprays. [in sun

NASA Technical Reports Server (NTRS)

Tandberg-Hanssen, E.; Martin, S. F.; Hansen, R. T.

1980-01-01

During solar cycle No. 20 new insight into the flare-spray phenomenon has been attained due to several innovations in solar optical-observing techniques (higher spatial resolution cinema-photography, tunable passband filters, multislit spectroscopy and extended angular field coronagraphs). From combined analysis of 13 well-observed sprays which occurred between 1969-1974 it is concluded that (1) the spray material originates from a preexisting active region filament which undergoes increased absorption some tens of minutes prior to the abrupt chromospheric brightening at the 'flare-start', and (2) the spray material is confined within a steadily expanding, loop-shaped (presumable magnetically controlled) envelope with part of the materials draining back down along one or both legs of the loop.

Thermal instability in post-flare plasmas

NASA Technical Reports Server (NTRS)

Antiochos, S. K.

1976-01-01

The cooling of post-flare plasmas is discussed and the formation of loop prominences is explained as due to a thermal instability. A one-dimensional model was developed for active loop prominences. Only the motion and heat fluxes parallel to the existing magnetic fields are considered. The relevant size scales and time scales are such that single-fluid MHD equations are valid. The effects of gravity, the geometry of the field and conduction losses to the chromosphere are included. A computer code was constructed to solve the model equations. Basically, the system is treated as an initial value problem (with certain boundary conditions at the chromosphere-corona transition region), and a two-step time differencing scheme is used.

Functional and structural analysis of the sialic acid-binding domain of rotaviruses.

PubMed Central

Isa, P; López, S; Segovia, L; Arias, C F

1997-01-01

The infectivity of most animal rotaviruses is dependent on the interaction of the virus spike protein VP4 with a sialic acid (SA)-containing cell receptor, and the SA-binding domain of this protein has been mapped between amino acids 93 and 208 of its trypsin cleavage fragment VP8. To identify which residues in this region are essential for the SA-binding activity, we performed alanine mutagenesis of the rotavirus RRV VP8 expressed in bacteria as a fusion polypeptide with glutathione S-transferase. Tyrosines were primarily targeted since tyrosine has been involved in the interaction of other viral hemagglutinins with SA. Of the 15 substitutions carried out, 10 abolished the SA-dependent hemagglutination activity of the protein, as well as its ability to bind to glycophorin A in a solid-phase assay. However, only alanine substitutions for tyrosines 155 and 188 and for serine 190 did not affect the overall conformation of the protein, as judged by their interaction with a panel of conformationally sensitive neutralizing VP8 monoclonal antibodies (MAbs). These findings suggest that these three amino acids play an essential role in the SA-binding activity of the protein, presumably by interacting directly with the SA molecule. The predicted secondary structure of VP8 suggests that it is organized as 11 beta-strands separated by loops; in this model, Tyr-155 maps to loop 7 while Tyr-188 and Ser-190 map to loop 9. The close proximity of these two loops is also supported by previous results from competition experiments with neutralizing MAbs directed at RRV VP8. PMID:9261399

Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster

PubMed Central

Mishiro, Tsuyoshi; Ishihara, Ko; Hino, Shinjiro; Tsutsumi, Shuichi; Aburatani, Hiroyuki; Shirahige, Katsuhiko; Kinoshita, Yoshikazu; Nakao, Mitsuyoshi

2009-01-01

Long-range regulatory elements and higher-order chromatin structure coordinate the expression of multiple genes in cluster, and CTCF/cohesin-mediated chromatin insulator may be a key in this regulation. The human apolipoprotein (APO) A1/C3/A4/A5 gene region, whose alterations increase the risk of dyslipidemia and atherosclerosis, is partitioned at least by three CTCF-enriched sites and three cohesin protein RAD21-enriched sites (two overlap with the CTCF sites), resulting in the formation of two transcribed chromatin loops by interactions between insulators. The C3 enhancer and APOC3/A4/A5 promoters reside in the same loop, where the APOC3/A4 promoters are pointed towards the C3 enhancer, whereas the APOA1 promoter is present in the different loop. The depletion of either CTCF or RAD21 disrupts the chromatin loop structure, together with significant changes in the APO expression and the localization of transcription factor hepatocyte nuclear factor (HNF)-4α and transcriptionally active form of RNA polymerase II at the APO promoters. Thus, CTCF/cohesin-mediated insulators maintain the chromatin loop formation and the localization of transcriptional apparatus at the promoters, suggesting an essential role of chromatin insulation in controlling the expression of clustered genes. PMID:19322193

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

Baker, D.; Van Driel-Gesztelyi, L.; Green, L. M.

Using spectra obtained by the EUV Imaging Spectrometer (EIS) instrument onboard Hinode, we present a detailed spatially resolved abundance map of an active region (AR)-coronal hole (CH) complex that covers an area of 359'' × 485''. The abundance map provides first ionization potential (FIP) bias levels in various coronal structures within the large EIS field of view. Overall, FIP bias in the small, relatively young AR is 2-3. This modest FIP bias is a consequence of the age of the AR, its weak heating, and its partial reconnection with the surrounding CH. Plasma with a coronal composition is concentrated atmore » AR loop footpoints, close to where fractionation is believed to take place in the chromosphere. In the AR, we found a moderate positive correlation of FIP bias with nonthermal velocity and magnetic flux density, both of which are also strongest at the AR loop footpoints. Pathways of slightly enhanced FIP bias are traced along some of the loops connecting opposite polarities within the AR. We interpret the traces of enhanced FIP bias along these loops to be the beginning of fractionated plasma mixing in the loops. Low FIP bias in a sigmoidal channel above the AR's main polarity inversion line, where ongoing flux cancellation is taking place, provides new evidence of a bald patch magnetic topology of a sigmoid/flux rope configuration.« less

Flexibility of the Head-Stalk Linker Domain of Paramyxovirus HN Glycoprotein Is Essential for Triggering Virus Fusion.

PubMed

Adu-Gyamfi, Emmanuel; Kim, Lori S; Jardetzky, Theodore S; Lamb, Robert A

2016-10-15

The Paramyxoviridae comprise a large family of enveloped, negative-sense, single-stranded RNA viruses with significant economic and public health implications. For nearly all paramyxoviruses, infection is initiated by fusion of the viral and host cell plasma membranes in a pH-independent fashion. Fusion is orchestrated by the receptor binding protein hemagglutinin-neuraminidase (HN; also called H or G depending on the virus type) protein and a fusion (F) protein, the latter undergoing a major refolding process to merge the two membranes. Mechanistic details regarding the coupling of receptor binding to F activation are not fully understood. Here, we have identified the flexible loop region connecting the bulky enzymatically active head and the four-helix bundle stalk to be essential for fusion promotion. Proline substitution in this region of HN of parainfluenza virus 5 (PIV5) and Newcastle disease virus HN abolishes cell-cell fusion, whereas HN retains receptor binding and neuraminidase activity. By using reverse genetics, we engineered recombinant PIV5-EGFP viruses with mutations in the head-stalk linker region of HN. Mutations in this region abolished virus recovery and infectivity. In sum, our data suggest that the loop region acts as a "hinge" around which the bulky head of HN swings to-and-fro to facilitate timely HN-mediate F-triggering, a notion consistent with the stalk-mediated activation model of paramyxovirus fusion. Paramyxovirus fusion with the host cell plasma membrane is essential for virus infection. Membrane fusion is orchestrated via interaction of the receptor binding protein (HN, H, or G) with the viral fusion glycoprotein (F). Two distinct models have been suggested to describe the mechanism of fusion: these include "the clamp" and the "provocateur" model of activation. By using biochemical and reverse genetics tools, we have obtained strong evidence in favor of the HN stalk-mediated activation of paramyxovirus fusion. Specifically, our data strongly support the notion that the short linker between the head and stalk plays a role in "conformational switching" of the head group to facilitate F-HN interaction and triggering. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Flexibility of the Head-Stalk Linker Domain of Paramyxovirus HN Glycoprotein Is Essential for Triggering Virus Fusion

PubMed Central

Adu-Gyamfi, Emmanuel; Kim, Lori S.; Jardetzky, Theodore S.

2016-01-01

ABSTRACT The Paramyxoviridae comprise a large family of enveloped, negative-sense, single-stranded RNA viruses with significant economic and public health implications. For nearly all paramyxoviruses, infection is initiated by fusion of the viral and host cell plasma membranes in a pH-independent fashion. Fusion is orchestrated by the receptor binding protein hemagglutinin-neuraminidase (HN; also called H or G depending on the virus type) protein and a fusion (F) protein, the latter undergoing a major refolding process to merge the two membranes. Mechanistic details regarding the coupling of receptor binding to F activation are not fully understood. Here, we have identified the flexible loop region connecting the bulky enzymatically active head and the four-helix bundle stalk to be essential for fusion promotion. Proline substitution in this region of HN of parainfluenza virus 5 (PIV5) and Newcastle disease virus HN abolishes cell-cell fusion, whereas HN retains receptor binding and neuraminidase activity. By using reverse genetics, we engineered recombinant PIV5-EGFP viruses with mutations in the head-stalk linker region of HN. Mutations in this region abolished virus recovery and infectivity. In sum, our data suggest that the loop region acts as a “hinge” around which the bulky head of HN swings to-and-fro to facilitate timely HN-mediate F-triggering, a notion consistent with the stalk-mediated activation model of paramyxovirus fusion. IMPORTANCE Paramyxovirus fusion with the host cell plasma membrane is essential for virus infection. Membrane fusion is orchestrated via interaction of the receptor binding protein (HN, H, or G) with the viral fusion glycoprotein (F). Two distinct models have been suggested to describe the mechanism of fusion: these include “the clamp” and the “provocateur” model of activation. By using biochemical and reverse genetics tools, we have obtained strong evidence in favor of the HN stalk-mediated activation of paramyxovirus fusion. Specifically, our data strongly support the notion that the short linker between the head and stalk plays a role in “conformational switching” of the head group to facilitate F-HN interaction and triggering. PMID:27489276

Insights into factorless translational initiation by the tRNA-like pseudoknot domain of a viral IRES.

PubMed

Au, Hilda H T; Jan, Eric

2012-01-01

The intergenic region internal ribosome entry site (IGR IRES) of the Dicistroviridae family adopts an overlapping triple pseudoknot structure to directly recruit the 80S ribosome in the absence of initiation factors. The pseudoknot I (PKI) domain of the IRES mimics a tRNA-like codon:anticodon interaction in the ribosomal P site to direct translation initiation from a non-AUG initiation codon in the A site. In this study, we have performed a comprehensive mutational analysis of this region to delineate the molecular parameters that drive IRES translation. We demonstrate that IRES-mediated translation can initiate at an alternate adjacent and overlapping start site, provided that basepairing interactions within PKI remain intact. Consistent with this, IGR IRES translation tolerates increases in the variable loop region that connects the anticodon- and codon-like elements within the PKI domain, as IRES activity remains relatively robust up to a 4-nucleotide insertion in this region. Finally, elements from an authentic tRNA anticodon stem-loop can functionally supplant corresponding regions within PKI. These results verify the importance of the codon:anticodon interaction of the PKI domain and further define the specific elements within the tRNA-like domain that contribute to optimal initiator Met-tRNA(i)-independent IRES translation.

Insights into Factorless Translational Initiation by the tRNA-Like Pseudoknot Domain of a Viral IRES

PubMed Central

Au, Hilda H. T.; Jan, Eric

2012-01-01

The intergenic region internal ribosome entry site (IGR IRES) of the Dicistroviridae family adopts an overlapping triple pseudoknot structure to directly recruit the 80S ribosome in the absence of initiation factors. The pseudoknot I (PKI) domain of the IRES mimics a tRNA-like codon:anticodon interaction in the ribosomal P site to direct translation initiation from a non-AUG initiation codon in the A site. In this study, we have performed a comprehensive mutational analysis of this region to delineate the molecular parameters that drive IRES translation. We demonstrate that IRES-mediated translation can initiate at an alternate adjacent and overlapping start site, provided that basepairing interactions within PKI remain intact. Consistent with this, IGR IRES translation tolerates increases in the variable loop region that connects the anticodon- and codon-like elements within the PKI domain, as IRES activity remains relatively robust up to a 4-nucleotide insertion in this region. Finally, elements from an authentic tRNA anticodon stem-loop can functionally supplant corresponding regions within PKI. These results verify the importance of the codon:anticodon interaction of the PKI domain and further define the specific elements within the tRNA-like domain that contribute to optimal initiator Met-tRNAi-independent IRES translation. PMID:23236506

Properties of a large-scale interplanetary loop structure as deduced from low-energy proton anisotropy and magnetic field measurements

NASA Technical Reports Server (NTRS)

Tranquille, C.; Sanderson, T. R.; Marsden, R. G.; Wenzel, K.-P.; Smith, E. J.

1987-01-01

Correlated particle and magnetic field measurements by the ISEE 3 spacecraft are presented for the loop structure behind the interplanetary traveling shock event of Nov. 12, 1978. Following the passage of the turbulent shock region, strong bidirectional streaming of low-energy protons is observed for approximately 6 hours, corresponding to a loop thickness of about 0.07 AU. This region is also characterized by a low relative variance of the magnetic field, a depressed proton intensity, and a reduction in the magnetic power spectral density. Using quasi-linear theory applied to a slab model, a value of 3 AU is derived for the mean free path during the passage of the closed loop. It is inferred from this observation that the proton regime associated with the loop structure is experiencing scatter-free transport and that either the length of the loop is approximately 3 AU between the sun and the earth or else the protons are being reflected at both ends of a smaller loop.

Computer-aided active-site-directed modeling of the Herpes Simplex Virus 1 and human thymidine kinase

NASA Astrophysics Data System (ADS)

Folkers, Gerd; Trumpp-Kallmeyer, Susanne; Gutbrod, Oliver; Krickl, Sabine; Fetzer, Jürgen; Keil, Günther M.

1991-10-01

Thymidine kinase (TK), which is induced by Herpes Simplex Virus 1 (HSV1), plays a key role in the antiviral activity of guanine derivatives such as aciclovir (ACV). In contrast, ACV shows only low affinity to the corresponding host cell enzyme. In order to define the differences in substrate binding of the two enzymes on molecular level, models for the three-dimensional (3-D) structures of the active sites of HSV1-TK and human TK were developed. The reconstruction of the active sites started from primary and secondary structure analysis of various kinases. The results were validated to homologous enzymes with known 3-D structures. The models predict that both enzymes consist of a central core β-sheet structure, connected by loops and α-helices very similar to the overall structure of other nucleotide binding enzymes. The phosphate binding is made up of a highly conserved glycine-rich loop at the N-terminus of the proteins and a conserved region at the C-terminus. The thymidine recognition site was found about 100 amino acids downstream from the phosphate binding loop. The differing substrate specificity of human and HSV1-TK can be explained by amino-acid substitutions in the homologous regions. To achieve a better understanding of the structure of the active site and how the thymidine kinase proteins interact with their substrates, the corresponding complexes of thymidine and dihydroxypropoxyguanine (DHPG) with HSV1 and human TK were built. For the docking of the guanine derivative, the X-ray structure of Elongation Factor Tu (EF-Tu), co-crystallized with guanosine diphosphate, was taken as reference. Fitting of thymidine into the active sites was done with respect to similar interactions found in thymidylate kinase. To complement the analysis of the 3-D structures of the two kinases and the substrate enzyme interactions, site-directed mutagenesis of the thymidine recognition site of HSV1-TK has been undertaken, changing Asp162 in the thymidine recognition site into Asn. First investigations reveal that the enzymatic activity of the mutant protein is destroyed.

Multi-loop positivity of the planar $$ \\mathcal{N} $$ = 4 SYM six-point amplitude

DOE PAGES

Dixon, Lance J.; von Hippel, Matt; McLeod, Andrew J.; ...

2017-02-22

We study the six-point NMHV ratio function in planarmore » $$ \\mathcal{N} $$ = 4 SYM theory in the context of positive geometry. The Amplituhedron construction of the integrand for the amplitudes provides a kinematical region in which the integrand was observed to be positive. It is natural to conjecture that this property survives integration, i.e. that the final result for the ratio function is also positive in this region. Establishing such a result would imply that preserving positivity is a surprising property of the Minkowski contour of integration and it might indicate some deeper underlying structure. We find that the ratio function is positive everywhere we have tested it, including analytic results for special kinematical regions at one and two loops, as well as robust numerical evidence through five loops. There is also evidence for not just positivity, but monotonicity in a “radial” direction. We also investigate positivity of the MHV six-gluon amplitude. While the remainder function ceases to be positive at four loops, the BDS-like normalized MHV amplitude appears to be positive through five loops.« less

Fast de novo discovery of low-energy protein loop conformations.

PubMed

Wong, Samuel W K; Liu, Jun S; Kou, S C

2017-08-01

In the prediction of protein structure from amino acid sequence, loops are challenging regions for computational methods. Since loops are often located on the protein surface, they can have significant roles in determining protein functions and binding properties. Loop prediction without the aid of a structural template requires extensive conformational sampling and energy minimization, which are computationally difficult. In this article we present a new de novo loop sampling method, the Parallely filtered Energy Targeted All-atom Loop Sampler (PETALS) to rapidly locate low energy conformations. PETALS explores both backbone and side-chain positions of the loop region simultaneously according to the energy function selected by the user, and constructs a nonredundant ensemble of low energy loop conformations using filtering criteria. The method is illustrated with the DFIRE potential and DiSGro energy function for loops, and shown to be highly effective at discovering conformations with near-native (or better) energy. Using the same energy function as the DiSGro algorithm, PETALS samples conformations with both lower RMSDs and lower energies. PETALS is also useful for assessing the accuracy of different energy functions. PETALS runs rapidly, requiring an average time cost of 10 minutes for a length 12 loop on a single 3.2 GHz processor core, comparable to the fastest existing de novo methods for generating an ensemble of conformations. Proteins 2017; 85:1402-1412. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations.

PubMed

Jiang, Jun; Aduri, Raviprasad; Chow, Christine S; SantaLucia, John

2014-04-01

Helix 69 (H69) is a 19-nt stem-loop region from the large subunit ribosomal RNA. Three pseudouridine (Ψ) modifications clustered in H69 are conserved across phylogeny and known to affect ribosome function. To explore the effects of Ψ on the conformations of Escherichia coli H69 in solution, nuclear magnetic resonance spectroscopy was used to reveal the structural differences between H69 with (ΨΨΨ) and without (UUU) Ψ modifications. Comparison of the two structures shows that H69 ΨΨΨ has the following unique features: (i) the loop region is closed by a Watson-Crick base pair between Ψ1911 and A1919, which is potentially reinforced by interactions involving Ψ1911N1H and (ii) Ψ modifications at loop residues 1915 and 1917 promote base stacking from Ψ1915 to A1918. In contrast, the H69 UUU loop region, which lacks Ψ modifications, is less organized. Structure modulation by Ψ leads to alteration in conformational behavior of the 5' half of the H69 loop region, observed as broadening of C1914 non-exchangeable base proton resonances in the H69 ΨΨΨ nuclear magnetic resonance spectra, and plays an important biological role in establishing the ribosomal intersubunit bridge B2a and mediating translational fidelity.

Positive And Negative Feedback Loops Coupled By Common Transcription Activator And Repressor

NASA Astrophysics Data System (ADS)

Sielewiesiuk, Jan; Łopaciuk, Agata

2015-03-01

Dynamical systems consisting of two interlocked loops with negative and positive feedback have been studied using the linear analysis of stability and numerical solutions. Conditions for saddle-node bifurcation were formulated in a general form. Conditions for Hopf bifurcations were found in a few symmetrical cases. Auto-oscillations, when they exist, are generated by the negative feedback repressive loop. This loop determines the frequency and amplitude of oscillations. The positive feedback loop of activation slightly modifies the oscillations. Oscillations are possible when the difference between Hilll's coefficients of the repression and activation is sufficiently high. The highly cooperative activation loop with a fast turnover slows down or even makes the oscillations impossible. The system under consideration can constitute a component of epigenetic or enzymatic regulation network.

Evaluation of T-111 forced-convection loop tested with lithium at 1370 C. [free convection

NASA Technical Reports Server (NTRS)

Devan, J. H.; Long, E. L., Jr.

1975-01-01

A T-111 alloy (Ta-8% W-2% Hf) forced-convection loop containing molten lithium was operated 3000 hr at a maximum temperature of 1370 C. Flow velocities up to 6.3 m/sec were used, and the results of this forced-convection loop are very similar to those observed in lower velocity thermal-convection loops of T-111 containing lithium. Weight changes were determined at 93 positions around the loop. The maximum dissolution rate occurred at the maximum wall temperature of the loop and was less than 1.3 microns/year. Mass transfer of hafnium, nitrogen, and, to a lesser extent, carbon occurred from the hotter to cooler regions. Exposed surfaces in the highest temperature region were found to be depleted in hafnium to a depth of 60 microns with no detectable change in tungsten content. There was some loss in room-temperature tensile strength for specimens exposed to lithium at 1370 C, attributable to depletion of hafnium and nitrogen and to attendant grain growth.

Ex-vessel neutron dosimetry analysis for westinghouse 4-loop XL pressurized water reactor plant using the RadTrack{sup TM} Code System with the 3D parallel discrete ordinates code RAPTOR-M3G

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

Chen, J.; Alpan, F. A.; Fischer, G.A.

2011-07-01

Traditional two-dimensional (2D)/one-dimensional (1D) SYNTHESIS methodology has been widely used to calculate fast neutron (>1.0 MeV) fluence exposure to reactor pressure vessel in the belt-line region. However, it is expected that this methodology cannot provide accurate fast neutron fluence calculation at elevations far above or below the active core region. A three-dimensional (3D) parallel discrete ordinates calculation for ex-vessel neutron dosimetry on a Westinghouse 4-Loop XL Pressurized Water Reactor has been done. It shows good agreement between the calculated results and measured results. Furthermore, the results show very different fast neutron flux values at some of the former plate locationsmore » and elevations above and below an active core than those calculated by a 2D/1D SYNTHESIS method. This indicates that for certain irregular reactor internal structures, where the fast neutron flux has a very strong local effect, it is required to use a 3D transport method to calculate accurate fast neutron exposure. (authors)« less

Simulations of Flare Reconnection in Breakout Coronal Mass Ejections

NASA Astrophysics Data System (ADS)

DeVore, C. Richard; Karpen, J. T.; Antiochos, S. K.

2009-05-01

We report 3D MHD simulations of the flare reconnection in the corona below breakout coronal mass ejections (CMEs). The initial setup is a single bipolar active region imbedded in the global-scale background dipolar field of the Sun, forming a quadrupolar magnetic configuration with a coronal null point. Rotational motions applied to the active-region polarities at the base of the atmosphere introduce shear across the polarity inversion line (PIL). Eventually, the magnetic stress and energy reach the critical threshold for runaway breakout reconnection, at which point the sheared core field erupts outward at high speed. The vertical current sheet formed by the stretching of the departing sheared field suffers reconnection that reforms the initial low-lying arcade across the PIL, i.e., creates the flare loops. Our simulation model, the Adaptively Refined MHD Solver, exploits local grid refinement to resolve the detailed structure and evolution of the highly dynamic current sheet. We are analyzing the numerical experiments to identify and interpret observable signatures of the flare reconnection associated with CMEs, e.g., the flare loops and ribbons, coronal jets and shock waves, and possible origins of solar energetic particles. This research was supported by NASA and ONR.

Numerical Simulations of Helicity Condensation in the Solar Corona

NASA Technical Reports Server (NTRS)

Zhao, L.; DeVore, C. R.; Antiochos, S. K.; Zurbuchen, T. H.

2015-01-01

The helicity condensation model has been proposed by Antiochos (2013) to explain the observed smoothness of coronal loops and the observed buildup of magnetic shear at filament channels. The basic hypothesis of the model is that magnetic reconnection in the corona causes the magnetic stress injected by photospheric motions to collect only at those special locations where prominences form. In this work we present the first detailed quantitative MHD simulations of the reconnection evolution proposed by the helicity condensation model. We use the well-known ansatz of modeling the closed corona as an initially uniform field between two horizontal photospheric plates. The system is driven by applying photospheric rotational flows that inject magnetic helicity into the system. The flows are confined to a finite region on the photosphere so as to mimic the finite flux system of, for example, a bipolar active region. The calculations demonstrate that, contrary to common belief, coronal loops having opposite helicity do not reconnect, whereas loops having the same sense of helicity do reconnect. Furthermore, we find that for a given amount of helicity injected into the corona, the evolution of the magnetic shear is insensitive to whether the pattern of driving photospheric motions is fixed or quasi-random. In all cases, the shear propagates via reconnection to the boundary of the flow region while the total magnetic helicity is conserved, as predicted by the model. We discuss the implications of our results for solar observations and for future, more realistic simulations of the helicity condensation process.

HIV1 V3 loop hypermutability is enhanced by the guanine usage bias in the part of env gene coding for it.

PubMed

Khrustalev, Vladislav Victorovich

2009-01-01

Guanine is the most mutable nucleotide in HIV genes because of frequently occurring G to A transitions, which are caused by cytosine deamination in viral DNA minus strands catalyzed by APOBEC enzymes. Distribution of guanine between three codon positions should influence the probability for G to A mutation to be nonsynonymous (to occur in first or second codon position). We discovered that nucleotide sequences of env genes coding for third variable regions (V3 loops) of gp120 from HIV1 and HIV2 have different kinds of guanine usage biases. In the HIV1 reference strain and 100 additionally analyzed HIV1 strains the guanine usage bias in V3 loop coding regions (2G>1G>3G) should lead to elevated nonsynonymous G to A transitions occurrence rates. In the HIV2 reference strain and 100 other HIV2 strains guanine usage bias in V3 loop coding regions (3G>2G>1G) should protect V3 loops from hypermutability. According to the HIV1 and HIV2 V3 alignment, insertion of the sequence enriched with 2G (21 codons in length) occurred during the evolution of HIV1 predecessor, while insertion of the different sequence enriched with 3G (19 codons in length) occurred during the evolution of HIV2 predecessor. The higher is the level of 3G in the V3 coding region, the lower should be the immune escaping mutation occurrence rates. This hypothesis was tested in this study by comparing the guanine usage in V3 loop coding regions from HIV1 fast and slow progressors. All calculations have been performed by our algorithms "VVK In length", "VVK Dinucleotides" and "VVK Consensus" (www.barkovsky.hotmail.ru).

The Prevalence and Use of Walking Loops in Neighborhood Parks: A National Study.

PubMed

Cohen, Deborah A; Han, Bing; Evenson, Kelly R; Nagel, Catherine; McKenzie, Thomas L; Marsh, Terry; Williamson, Stephanie; Harnik, Peter

2017-02-01

Previous studies indicate that the design of streets and sidewalks can influence physical activity among residents. Park features also influence park use and park-based physical activity. Although individuals can walk on streets and sidewalks, walking loops in parks offer a setting to walk in nature and to avoid interruptions from traffic. Here we describe the use of walking loops in parks and compare the number of park users and their physical activity in urban neighborhood parks with and without walking loops. We analyzed data from the National Study of Neighborhood Parks in which a representative sample of neighborhood parks (n = 174) from 25 U.S. cities with > 100,000 population were observed systematically to document facilities and park users by age group and sex. We compared the number of people and their physical activity in parks with and without walking loops, controlling for multiple factors, including park size, facilities, and population density. Overall, compared with parks without walking loops, on average during an hourly observation, parks with walking loops had 80% more users (95% CI: 42, 139%), and levels of moderate-to-vigorous physical activity were 90% higher (95% CI: 49, 145%). The additional park use and park-based physical activity occurred not only on the walking loops but throughout the park. Walking loops may be a promising means of increasing population level physical activity. Further studies are needed to confirm a causal relationship. Citation: Cohen DA, Han B, Evenson KR, Nagel C, McKenzie TL, Marsh T, Williamson S, Harnik P. 2017. The prevalence and use of walking loops in neighborhood parks: a national study. Environ Health Perspect 125:170-174; http://dx.doi.org/10.1289/EHP293.

The Prevalence and Use of Walking Loops in Neighborhood Parks: A National Study

PubMed Central

Cohen, Deborah A.; Han, Bing; Evenson, Kelly R.; Nagel, Catherine; McKenzie, Thomas L.; Marsh, Terry; Williamson, Stephanie; Harnik, Peter

2016-01-01

Background: Previous studies indicate that the design of streets and sidewalks can influence physical activity among residents. Park features also influence park use and park-based physical activity. Although individuals can walk on streets and sidewalks, walking loops in parks offer a setting to walk in nature and to avoid interruptions from traffic. Objectives: Here we describe the use of walking loops in parks and compare the number of park users and their physical activity in urban neighborhood parks with and without walking loops. Methods: We analyzed data from the National Study of Neighborhood Parks in which a representative sample of neighborhood parks (n = 174) from 25 U.S. cities with > 100,000 population were observed systematically to document facilities and park users by age group and sex. We compared the number of people and their physical activity in parks with and without walking loops, controlling for multiple factors, including park size, facilities, and population density. Results: Overall, compared with parks without walking loops, on average during an hourly observation, parks with walking loops had 80% more users (95% CI: 42, 139%), and levels of moderate-to-vigorous physical activity were 90% higher (95% CI: 49, 145%). The additional park use and park-based physical activity occurred not only on the walking loops but throughout the park. Conclusions: Walking loops may be a promising means of increasing population level physical activity. Further studies are needed to confirm a causal relationship. Citation: Cohen DA, Han B, Evenson KR, Nagel C, McKenzie TL, Marsh T, Williamson S, Harnik P. 2017. The prevalence and use of walking loops in neighborhood parks: a national study. Environ Health Perspect 125:170–174; http://dx.doi.org/10.1289/EHP293 PMID:27517530

Role of the Pepino mosaic virus 3'-untranslated region elements in negative-strand RNA synthesis in vitro.

PubMed

Osman, Toba A M; Olsthoorn, René C L; Livieratos, Ioannis C

2014-09-22

Pepino mosaic virus (PepMV) is a mechanically-transmitted positive-strand RNA potexvirus, with a 6410 nt long single-stranded (ss) RNA genome flanked by a 5'-methylguanosine cap and a 3' poly-A tail. Computer-assisted folding of the 64 nt long PepMV 3'-untranslated region (UTR) resulted in the prediction of three stem-loop structures (hp1, hp2, and hp3 in the 3'-5' direction). The importance of these structures and/or sequences for promotion of negative-strand RNA synthesis and binding to the RNA dependent RNA polymerase (RdRp) was tested in vitro using a specific RdRp assay. Hp1, which is highly variable among different PepMV isolates, appeared dispensable for negative-strand synthesis. Hp2, which is characterized by a large U-rich loop, tolerated base-pair changes in its stem as long as they maintained the stem integrity but was very sensitive to changes in the U-rich loop. Hp3, which harbours the conserved potexvirus ACUUAA hexamer motif, was essential for template activity. Template-RNA polymerase binding competition experiments showed that the ACUUAA sequence represents a high-affinity RdRp binding element. Copyright © 2014 Elsevier B.V. All rights reserved.

Organization of the Indian hedgehog--parathyroid hormone-related protein system in the postnatal growth plate.

PubMed

Chau, Michael; Forcinito, Patricia; Andrade, Anenisia C; Hegde, Anita; Ahn, Sohyun; Lui, Julian C; Baron, Jeffrey; Nilsson, Ola

2011-08-01

In embryonic growth cartilage, Indian hedgehog (Ihh) and parathyroid hormone-related protein (PTHrP) participate in a negative feedback loop that regulates chondrocyte differentiation. Postnatally, this region undergoes major structural and functional changes. To explore the organization of the Ihh–PTHrP system in postnatal growth plate, we microdissected growth plates of 7-day-old rats into their constituent zones and assessed expression of genes participating in the h–PTHrP feedback loop. Ihh, Patched 1, Smoothened, Gli1, Gli2, Gli3, and Pthr1 were expressed in regions analogous to the expression domains in embryonic growth cartilage. However, PTHrP was expressed in resting zone cartilage, a site that differs from the embryonic source, the periarticular cells. We then used mice in which lacZ has replaced coding sequences of Gli1 and thus serves as a marker for active hedgehog signaling. At 1, 4, 8, and 12 weeks of age, lacZ expression was detected in a pattern analogous to that of embryonic cartilage. The findings support the hypothesis that the embryonic Ihh–PTHrP feedback loop is maintained in the postnatal growth plate except that the source of PTHrP has shifted to a more proximal location in the resting zone.

Flat microwave spectra seen at X-class flares

NASA Technical Reports Server (NTRS)

Lee, Jeongwoo W.; Gary, Dale E.; Zirin, H.

1994-01-01

We report peculiar spectral activity of four large microwave bursts as obtained from the Solar Arrays at the Owens Valey Radio Observatory during observations of X-class flares on 24 May 1990 and 7, 8, 22 March 1991. Main observational points that we newly uncovered are: (1) flat flux spectra over 1-18 GHz in large amounts of flux ranging from 10(exp 2) to 10(exp 4) s.f.u. at the maximum phase, (2) a common evolutionary pattern in which the spectral region of dominant flux shifts from high frequencies at the initial rise to low frequencies at the decaying phase, and (3) unusual time profiles that are impulsive at high frequencies but more extended at lower frequencies. We carry out the model calculations of microwave spectra under assumptions of gyrosynchrotron mechanism and a dipole field configuration to reproduce the observational characteristics. Our results are summarized as follows. First, a flat microwave spectrum reaching up to 10(exp 2) - 10(exp 4) s.f.u. may occur in a case where a magnetic loop is extended to an angular size of approximately (0.7-7.0) x 10(exp -7) sterad and contains a huge number (N(E greater than 10 keV) approx. 10(exp 36) - 10(exp 38)) of nonthermal electrons with power-law index approx. 3-3.5 over the entire volume. Second, the observed spectral activity could adequately be accounted for by the shrinking of the region of nonthermal electrons to the loop top and by the softening of the power-law spectrum of electrons in a time scale ranging 3-45 min depending on the event. Third, the extended microwave activity at lower frequencies is probably due to electrons trapped in the loop top where magnetic fields are low. Finally, we clarify the physical distinction between these large, extended microwave bursts and the gradual/post-microwave bursts often seen in weak events, both of which are characterized by long-period activity and broadband spectra.

Stepwise Loop Insertion Strategy for Active Site Remodeling to Generate Novel Enzyme Functions.

PubMed

Hoque, Md Anarul; Zhang, Yong; Chen, Liuqing; Yang, Guangyu; Khatun, Mst Afroza; Chen, Haifeng; Hao, Liu; Feng, Yan

2017-05-19

The remodeling of active sites to generate novel biocatalysts is an attractive and challenging task. We developed a stepwise loop insertion strategy (StLois), in which randomized residue pairs are inserted into active site loops. The phosphotriesterase-like lactonase from Geobacillus kaustophilus (GkaP-PLL) was used to investigate StLois's potential for changing enzyme function. By inserting six residues into active site loop 7, the best variant ML7-B6 demonstrated a 16-fold further increase in catalytic efficiency toward ethyl-paraoxon compared with its initial template, that is a 609-fold higher, >10 7 fold substrate specificity shift relative to that of wild-type lactonase. The remodeled variants displayed 760-fold greater organophosphate hydrolysis activity toward the organophosphates parathion, diazinon, and chlorpyrifos. Structure and docking computations support the source of notably inverted enzyme specificity. Considering the fundamental importance of active site loops, the strategy has potential for the rapid generation of novel enzyme functions by loop remodeling.

EVIDENCE FOR EVAPORATION-INCOMPLETE CONDENSATION CYCLES IN WARM SOLAR CORONAL LOOPS

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

Froment, C.; Auchère, F.; Bocchialini, K.

2015-07-10

Quasi-constant heating at the footpoints of loops leads to evaporation and condensation cycles of the plasma: thermal non-equilibrium (TNE). This phenomenon is believed to play a role in the formation of prominences and coronal rain. However, it is often discounted as being involved in the heating of warm loops because the models do not reproduce observations. Recent simulations have shown that these inconsistencies with observations may be due to oversimplifications of the geometries of the models. In addition, our recent observations reveal that long-period intensity pulsations (several hours) are common in solar coronal loops. These periods are consistent with thosemore » expected from TNE. The aim of this paper is to derive characteristic physical properties of the plasma for some of these events to test the potential role of TNE in loop heating. We analyzed three events in detail using the six EUV coronal channels of the Solar Dynamics Observatory/Atmospheric Imaging Assembly. We performed both a differential emission measure (DEM) and a time-lag analysis, including a new method to isolate the relevant signal from the foreground and background emission. For the three events, the DEM undergoes long-period pulsations, which is a signature of periodic heating even though the loops are captured in their cooling phase, as is the bulk of the active regions. We link long-period intensity pulsations to new signatures of loop heating with strong evidence for evaporation and condensation cycles. We thus simultaneously witness widespread cooling and TNE. Finally, we discuss the implications of our new observations for both static and impulsive heating models.« less

Trigger of Successive Filament Eruptions Observed by SDO and STEREO

NASA Astrophysics Data System (ADS)

Dhara, Sajal Kumar; Belur, Ravindra; Kumar, Pankaj; Banyal, Ravinder Kumar; Mathew, Shibu K.; Joshi, Bhuwan

2017-10-01

Using multiwavelength observations from the Solar Dynamics Observatory (SDO) and the Solar Terrestrial Relations Observatory (STEREO), we investigate the mechanism of two successive eruptions (F1 and F2) of a filament in active region NOAA 11444 on 27 March 2012. The filament was inverse J-shaped and lay along a quasi-circular polarity inversion line (PIL). The first part of the filament erupted at ˜2{:}30 UT on 27 March 2012 (F1), the second part at around 4:20 UT on the same day (F2). A precursor or preflare brightening was observed below the filament main axis about 30 min before F1. The brightening was followed by a jet-like ejection below the filament, which triggered its eruption. Before the eruption of F2, the filament seemed to be trapped within the overlying arcade loops for almost 1.5 h before it successfully erupted. Interestingly, we observe simultaneously contraction (˜12 km s^{-1}) and expansion (˜20 km s^{-1}) of arcade loops in the active region before F2. Magnetograms obtained with the Helioseismic and Magnetic Imager (HMI) show converging motion of the opposite polarities, which result in flux cancellation near the PIL. We suggest that flux cancellation at the PIL resulted in a jet-like ejection below the filament main axis, which triggered F1, similar to the tether-cutting process. F2 was triggered by removal of the overlying arcade loops via reconnection. Both filament eruptions produced high-speed (˜1000 km s^{-1}) coronal mass ejections.

Dynamics of the active site loops in catalyzing aminoacylation reaction in seryl and histidyl tRNA synthetases.

PubMed

Dutta, Saheb; Kundu, Soumya; Saha, Amrita; Nandi, Nilashis

2018-03-01

Aminoacylation reaction is the first step of protein biosynthesis. The catalytic reorganization at the active site of aminoacyl tRNA synthetases (aaRSs) is driven by the loop motions. There remain lacunae of understanding concerning the catalytic loop dynamics in aaRSs. We analyzed the functional loop dynamics in seryl tRNA synthetase from Methanopyrus kandleri ( mk SerRS) and histidyl tRNA synthetases from Thermus thermophilus ( tt HisRS), respectively, using molecular dynamics. Results confirm that the motif 2 loop and other active site loops are flexible spots within the catalytic domain. Catalytic residues of the loops form a network of interaction with the substrates to form a reactive state. The loops undergo transitions between closed state and open state and the relaxation of the constituent residues occurs in femtosecond to nanosecond time scale. Order parameters are higher for constituent catalytic residues which form a specific network of interaction with the substrates to form a reactive state compared to the Gly residues within the loop. The development of interaction is supported from mutation studies where the catalytic domain with mutated loop exhibits unfavorable binding energy with the substrates. During the open-close motion of the loops, the catalytic residues make relaxation by ultrafast librational motion as well as fast diffusive motion and subsequently relax rather slowly via slower diffusive motion. The Gly residues act as a hinge to facilitate the loop closing and opening by their faster relaxation behavior. The role of bound water is analyzed by comparing implicit solvent-based and explicit solvent-based simulations. Loops fail to form catalytically competent geometry in absence of water. The present result, for the first time reveals the nature of the active site loop dynamics in aaRS and their influence on catalysis.

Solar burst precursors and energy build-up at microwave wavelengths

NASA Technical Reports Server (NTRS)

Lang, Kenneth R.; Wilson, Robert F.

1986-01-01

We summarize high-resolution microwave observations (VLA) of heating and magnetic triggering in coronal loops. Magnetic changes that precede solar eruptions on time scales of tens of minutes involve primarily emerging coronal loops and the interaction of two or more loops. Thermal cyclotron lines have been detected in coronal loops, suggesting the presence of hot current sheets that enhance emission from relatively thin layers of enhanced temperature and constant magnetic field. These current sheets may play a role in the excitation of solar bursts. A filament-associated source with a high brightness temperature and steep radiation spectrum occurs above a region of apparently weak photospheric field. This source might be attributed to currents that enhance coronal magnetic fields. Compact (phi=5 sec) transient sources with lifetimes of 30 to 60 minutes have also been detected in regions of apparently weak photospheric field. We conclude by comparing VLA observations of coronal loops with simultaneous SMM-XRP observations.

Solar burst precursors and energy build-up at microwave wavelengths

NASA Astrophysics Data System (ADS)

Lang, Kenneth R.; Wilson, Robert F.

We summarize high-resolution microwave observations (VLA) of heating and magnetic triggering in coronal loops. Magnetic changes that precede solar eruptions on time scales of tens of minutes involve primarily emerging coronal loops and the interaction of two or more loops. Thermal cyclotron lines have been detected in coronal loops, suggesting the presence of hot current sheets that enhance emission from relatively thin layers of enhanced temperature and constant magnetic field. These current sheets may play a role in the excitation of solar bursts. A filament-associated source with a high brightness temperature and steep radiation spectrum occurs above a region of apparently weak photospheric field. This source might be attributed to currents that enhance coronal magnetic fields. Compact (phi=5 sec) transient sources with lifetimes of 30 to 60 minutes have also been detected in regions of apparently weak photospheric field. We conclude by comparing VLA observations of coronal loops with simultaneous SMM-XRP observations.

Human Y-Family DNA Polymerase κ Is More Tolerant to Changes in Its Active Site Loop than Its Ortholog Escherichia coli DinB.

PubMed

Antczak, Nicole M; Packer, Morgan R; Lu, Xueguang; Zhang, Ke; Beuning, Penny J

2017-11-20

DNA damage is a constant threat and can be bypassed in a process called translesion synthesis, which is typically carried out by Y-family DNA polymerases. Y-family DNA polymerases are conserved in all domains of life and tend to have specificity for certain types of DNA damage. Escherichia coli DinB and its human ortholog pol κ can bypass specific minor groove deoxyguanine adducts efficiently and are inhibited by major groove adducts, as Y-family DNA polymerases make contacts with the minor groove side of the DNA substrate and lack contacts with the major groove at the nascent base pair. DinB is inhibited by major groove adducts more than pol κ, and they each have active site loops of different lengths, with four additional amino acids in the DinB loop. We previously showed that the R35A active site loop mutation in DinB allows for bypass of the major groove adduct N 6 -furfuryl-dA. These observations led us to investigate the different active site loops by creating loop swap chimeras of DinB with a pol κ loop and vice versa by changing the loop residues in a stepwise fashion. We then determined their activity with undamaged DNA or DNA containing N 2 -furfuryl-dG or N 6 -furfuryl-dA. The DinB proteins with the pol kappa loop have low activity on all templates but have decreased misincorporation compared to either wild-type protein. The kappa proteins with the DinB loop retain activity on all templates and have decreased misincorporation compared to either wild-type protein. We assessed the thermal stability of the proteins and observed an increase in stability in the presence of all DNA templates and additional increases generally only in the presence of the undamaged and N 2 -furfuryl-dG adduct and dCTP, which correlates with activity. Overall we find that pol κ is more tolerant to changes in the active site loop than DinB.

Manipulations of extracellular Loop 2 in α1 GlyR ultra-sensitive ethanol receptors (USERs) enhance receptor sensitivity to isoflurane, ethanol, and lidocaine, but not propofol

PubMed Central

Naito, Anna; Muchhala, Karan H.; Trang, Janice; Asatryan, Liana; Trudell, James R.; Homanics, Gregg E.; Alkana, Ronald L.; Davies, Daryl L.

2015-01-01

We recently developed Ultra-Sensitive Ethanol Receptors (USERs) as a novel tool for investigation of single receptor subunit populations sensitized to extremely low ethanol concentrations that do not affect other receptors in the nervous system. To this end, we found that mutations within the extracellular Loop 2 region of glycine receptors (GlyRs) and γ-aminobutyric acid type A receptors (GABAARs) can significantly increase receptor sensitivity to micro-molar concentrations of ethanol resulting in up to a 100-fold increase in ethanol sensitivity relative to wild type (WT) receptors. The current study investigated: 1) Whether structural manipulations of Loop 2 in α1 GlyRs could similarly increase receptor sensitivity to other anesthetics; and 2) If mutations exclusive to the C-terminal end of Loop 2 are sufficient to impart these changes. We expressed α1 GlyR USERs in Xenopus oocytes and tested the effects of three classes of anesthetics, isoflurane (volatile), propofol (intravenous), and lidocaine (local), known to enhance glycine-induced chloride currents using two-electrode voltage clamp electrophysiology. Loop 2 mutations produced a significant 10-fold increase in isoflurane and lidocaine sensitivity, but no increase in propofol sensitivity compared to WT α1 GlyRs. Interestingly, we also found that structural manipulations in the C-terminal end of Loop 2 were sufficient and selective for α1 GlyR modulation by ethanol, isoflurane, and lidocaine. These studies are the first to report the extracellular region of α1 GlyRs as a site of lidocaine action. Overall, the findings suggest that Loop 2 of α1 GlyRs is a key region that mediates isoflurane and lidocaine modulation. Moreover, the results identify important amino acids in Loop 2 that regulate isoflurane, lidocaine, and ethanol action. Collectively, these data indicate the commonality of the sites for isoflurane, lidocaine, and ethanol action, and the structural requirements for allosteric modulation on α1 GlyRs within the extracellular Loop 2 region. PMID:25827497

Cyclotron Line in Solar Microwave Radiation by Radio Telescope RATAN-600 Observations of the Solar Active Region NOAA 12182

NASA Astrophysics Data System (ADS)

Peterova, N. G.; Topchilo, N. A.

2017-12-01

This paper presents the results of observation of a rare phenomenon—a narrowband increase in the brightness of cyclotron radiation of one of the structural details of a radio source located in the solar corona above the solar active region NOAA 12182 in October 2014 at a frequency of 4.2 ± 0.1 GHz. The brightness of radiation in the maximum of the phenomenon has reached 10 MK; its duration was equal to 3 s. The exact location of the source of the narrowband cyclotron radiation is indicated: it is a corona above a fragmented (4-nuclear) sunspot, on which a small UV flare loop was closed.

The Yohkoh mission for high-energy solar physics

NASA Technical Reports Server (NTRS)

Acton, L.; Tsuneta, S.; Ogawara, Y.; Bentley, R.; Bruner, M.; Canfield, R.; Culhane, L.; Doschek, G.; Hiei, E.; Hirayama, T.

1992-01-01

Data on solar flare mechanisms and the sun's corona will be generated by Japan's Yohkoh satellite's X-ray imaging sensors and X-ray and gamma-ray spectrometers. It is noted that the X-ray corona above active regions expands, in some cases almost continually, in contradiction of the widely accepted model of magnetohydrostatic equilibrium in such regions. Flaring X-ray bright points have been discovered to often involve ejecta into an adjacent, much larger and fainter magnetic loop, which brightens along its length at speeds up to 1000 km/sec.

The YOHKOH mission for high-energy solar physics

NASA Astrophysics Data System (ADS)

Acton, L.; Tsuneta, S.; Ogawara, Y.; Bentley, R.; Bruner, M.; Canfield, R.; Culhane, L.; Doschek, G.; Hiei, E.; Hirayama, T.

1992-10-01

Data on solar flare mechanisms and the sun's corona will be generated by Japan's Yohkoh satellite's X-ray imaging sensors and X-ray and gamma-ray spectrometers. It is noted that the X-ray corona above active regions expands, in some cases almost continually, in contradiction of the widely accepted model of magnetohydrostatic equilibrium in such regions. Flaring X-ray bright points have been discovered to often involve ejecta into an adjacent, much larger and fainter magnetic loop, which brightens along its length at speeds up to 1000 km/sec.

Comparative assessment of the efficacy of closed helical loop and T-loop for space closure in lingual orthodontics-a finite element study.

PubMed

Chacko, Ajay; Tikku, Tripti; Khanna, Rohit; Maurya, Rana Pratap; Srivastava, Kamna

2018-05-28

Retraction in lingual orthodontics has biomechanical differences when compared to labial orthodontics, which is not yet established. Thus, we have intended to compare the biomechanical characteristics of closed helical loop and T-loop on 1 mm activation with 30° of compensatory curvatures during retraction in lingual orthodontics. STb lingual brackets were indirectly bonded to maxillary typhodont model that was scanned to obtain FEM model. Closed helical loop (2 × 7 mm) and T-loop (6 × 2 × 7 mm) of 0.016″ × 0.016″ TMA wire were modeled without preactivation bends. Preactivation bends at 30° were given in the software. Boundary conditions were set. The force (F) and moment (M) of both the loops were determined on 1 mm activation, using ANSYS software. M/F ratio was also calculated for both the loops. T-loop exerted less force, thus increased M/F ratio as compared to closed helical loop on 1 mm activation. When torque has to be preserved in the anterior segment during retraction in lingual orthodontics, T-loop can be preferred over closed helical loop.

A Bayesian Approach to Period Searching in Solar Coronal Loops

NASA Astrophysics Data System (ADS)

Scherrer, Bryan; McKenzie, David

2017-03-01

We have applied a Bayesian generalized Lomb-Scargle period searching algorithm to movies of coronal loop images obtained with the Hinode X-ray Telescope (XRT) to search for evidence of periodicities that would indicate resonant heating of the loops. The algorithm makes as its only assumption that there is a single sinusoidal signal within each light curve of the data. Both the amplitudes and noise are taken as free parameters. It is argued that this procedure should be used alongside Fourier and wavelet analyses to more accurately extract periodic intensity modulations in coronal loops. The data analyzed are from XRT Observation Program #129C: “MHD Wave Heating (Thin Filters),” which occurred during 2006 November 13 and focused on active region 10293, which included coronal loops. The first data set spans approximately 10 min with an average cadence of 2 s, 2″ per pixel resolution, and used the Al-mesh analysis filter. The second data set spans approximately 4 min with a 3 s average cadence, 1″ per pixel resolution, and used the Al-poly analysis filter. The final data set spans approximately 22 min at a 6 s average cadence, and used the Al-poly analysis filter. In total, 55 periods of sinusoidal coronal loop oscillations between 5.5 and 59.6 s are discussed, supporting proposals in the literature that resonant absorption of magnetic waves is a viable mechanism for depositing energy in the corona.

A Bayesian Approach to Period Searching in Solar Coronal Loops

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

Scherrer, Bryan; McKenzie, David

2017-03-01

We have applied a Bayesian generalized Lomb–Scargle period searching algorithm to movies of coronal loop images obtained with the Hinode X-ray Telescope (XRT) to search for evidence of periodicities that would indicate resonant heating of the loops. The algorithm makes as its only assumption that there is a single sinusoidal signal within each light curve of the data. Both the amplitudes and noise are taken as free parameters. It is argued that this procedure should be used alongside Fourier and wavelet analyses to more accurately extract periodic intensity modulations in coronal loops. The data analyzed are from XRT Observation Programmore » 129C: “MHD Wave Heating (Thin Filters),” which occurred during 2006 November 13 and focused on active region 10293, which included coronal loops. The first data set spans approximately 10 min with an average cadence of 2 s, 2″ per pixel resolution, and used the Al-mesh analysis filter. The second data set spans approximately 4 min with a 3 s average cadence, 1″ per pixel resolution, and used the Al-poly analysis filter. The final data set spans approximately 22 min at a 6 s average cadence, and used the Al-poly analysis filter. In total, 55 periods of sinusoidal coronal loop oscillations between 5.5 and 59.6 s are discussed, supporting proposals in the literature that resonant absorption of magnetic waves is a viable mechanism for depositing energy in the corona.« less

Parametric Loop Division for 3D Localization in Wireless Sensor Networks

PubMed Central

Ahmad, Tanveer

2017-01-01

Localization in Wireless Sensor Networks (WSNs) has been an active topic for more than two decades. A variety of algorithms were proposed to improve the localization accuracy. However, they are either limited to two-dimensional (2D) space, or require specific sensor deployment for proper operations. In this paper, we proposed a three-dimensional (3D) localization scheme for WSNs based on the well-known parametric Loop division (PLD) algorithm. The proposed scheme localizes a sensor node in a region bounded by a network of anchor nodes. By iteratively shrinking that region towards its center point, the proposed scheme provides better localization accuracy as compared to existing schemes. Furthermore, it is cost-effective and independent of environmental irregularity. We provide an analytical framework for the proposed scheme and find its lower bound accuracy. Simulation results shows that the proposed algorithm provides an average localization accuracy of 0.89 m with a standard deviation of 1.2 m. PMID:28737714

Neutral-Line Magnetic Shear and Enhanced Coronal Heating in Solar Active Regions

NASA Technical Reports Server (NTRS)

Falconer, D. A.; Moore, R. L.; Porter, J. G.; Gary, G. A.; Shimizu, T.

1997-01-01

By examining the magnetic structure at sites in the bright coronal interiors of active regions that are not flaring but exhibit persistent strong coronal heating, we establish some new characteristics of the magnetic origins of this heating. We have examined the magnetic structure of these sites in five active regions, each of which was well observed by both the Yohkoh SXT and the Marshall Space Flight Center Vector Magnetograph and showed strong shear in its magnetic field along part of at least one neutral line (polarity inversion). Thus, we can assess whether this form of nonpotential field structure in active regions is a characteristic of the enhanced coronal heating and vice versa. From 27 orbits' worth of Yohkoh SXT images of the five active regions, we have obtained a sample of 94 persistently bright coronal features (bright in all images from a given orbit), 40 long (greater than or approximately equals 20,000 km) neutral-line segments having strong magnetic shear throughout (shear angle greater than 45 deg), and 39 long neutral-line segments having weak magnetic shear throughout (shear angle less than 45 deg). From this sample, we find that: (1) all of our persistently bright coronal features are rooted in magnetic fields that are stronger than 150 G; (2) nearly all (95%) of these enhanced coronal features are rooted near neutral lines (closer than 10,000 km); (3) a great majority (80%) of the bright features are rooted near strong-shear portions of neutral lines; (4) a great majority (85%) of long strong-shear segments of neutral lines have persistently bright coronal features rooted near them; (5) a large minority (40%) of long weak-shear segments of neutral lines have persistently bright coronal features rooted near them; and (6) the brightness of a persistently bright Coronal feature often changes greatly over a few hours. From these results, we conclude that most persistent enhanced heating of coronal loops in active regions: (1) requires the presence of a polarity inversion in the magnetic field near at least one of the loop footpoints; (2) is greatly aided by the presence of strong shear in the core magnetic field along that neutral line; and (3) is controlled by some variable process that acts in this magnetic environment. We infer that this variable process is low-lying reconnection accompanying flux cancellation.

Diacylglycerol Acyltransferase 1 Is Regulated by Its N-Terminal Domain in Response to Allosteric Effectors.

PubMed

Caldo, Kristian Mark P; Acedo, Jeella Z; Panigrahi, Rashmi; Vederas, John C; Weselake, Randall J; Lemieux, M Joanne

2017-10-01

Diacylglycerol acyltransferase 1 (DGAT1) is an integral membrane enzyme catalyzing the final and committed step in the acyl-coenzyme A (CoA)-dependent biosynthesis of triacylglycerol (TAG). The biochemical regulation of TAG assembly remains one of the least understood areas of primary metabolism to date. Here, we report that the hydrophilic N-terminal domain of Brassica napus DGAT1 (BnaDGAT1 1-113 ) regulates activity based on acyl-CoA/CoA levels. The N-terminal domain is not necessary for acyltransferase activity and is composed of an intrinsically disordered region and a folded segment. We show that the disordered region has an autoinhibitory function and a dimerization interface, which appears to mediate positive cooperativity, whereas the folded segment of the cytosolic region was found to have an allosteric site for acyl-CoA/CoA. Under increasing acyl-CoA levels, the binding of acyl-CoA with this noncatalytic site facilitates homotropic allosteric activation. Enzyme activation, on the other hand, is prevented under limiting acyl-CoA conditions (low acyl-CoA-to-CoA ratio), whereby CoA acts as a noncompetitive feedback inhibitor through interaction with the same folded segment. The three-dimensional NMR solution structure of the allosteric site revealed an α-helix with a loop connecting a coil fragment. The conserved amino acid residues in the loop interacting with CoA were identified, revealing details of this important regulatory element for allosteric regulation. Based on these results, a model is proposed illustrating the role of the N-terminal domain of BnaDGAT1 as a positive and negative modulator of TAG biosynthesis. © 2017 American Society of Plant Biologists. All Rights Reserved.

Akinetic-rigid and tremor-dominant Parkinson's disease patients show different patterns of intrinsic brain activity.

PubMed

Zhang, Jiuquan; Wei, Luqing; Hu, Xiaofei; Xie, Bing; Zhang, Yanling; Wu, Guo-Rong; Wang, Jian

2015-01-01

Parkinson's disease (PD) is a surprisingly heterogeneous neurodegenerative disorder. It is well established that different subtypes of PD present with different clinical courses and prognoses. However, the neural mechanism underlying these disparate presentations is uncertain. Here we used resting-state fMRI (rs-fMRI) and the regional homogeneity (ReHo) method to determine neural activity patterns in the two main clinical subgroups of PD (akinetic-rigid and tremor-dominant). Compared with healthy controls, akinetic-rigid (AR) subjects had increased ReHo mainly in right amygdala, left putamen, bilateral angular gyrus, bilateral medial prefrontal cortex (MPFC), and decreased ReHo in left post cingulate gyrus/precuneus (PCC/PCu) and bilateral thalamus. In contrast, tremor-dominant (TD) patients showed higher ReHo mostly in bilateral angular gyrus, left PCC, cerebellum_crus1, and cerebellum_6, while ReHo was decreased in right putamen, primary sensory cortex (S1), vermis_3, and cerebellum_4_5. These results indicate that AR and TD subgroups both represent altered spontaneous neural activity in default-mode regions and striatum, and AR subjects exhibit more changed neural activity in the mesolimbic cortex (amygdala) but TD in the cerebellar regions. Of note, direct comparison of the two subgroups revealed a distinct ReHo pattern primarily located in the striatal-thalamo-cortical (STC) and cerebello-thalamo-cortical (CTC) loops. Overall, our findings highlight the involvement of default mode network (DMN) and STC circuit both in AR and TD subtypes, but also underscore the importance of integrating mesolimbic-striatal and CTC loops in understanding neural systems of akinesia and rigidity, as well as resting tremor in PD. This study provides improved understanding of the pathophysiological models of different subtypes of PD. Copyright © 2014 Elsevier Ltd. All rights reserved.

Inhibition of Cav3.2 T-type Calcium Channels by Its Intracellular I-II Loop*

PubMed Central

Monteil, Arnaud; Chausson, Patrick; Boutourlinsky, Katia; Mezghrani, Alexandre; Huc-Brandt, Sylvaine; Blesneac, Iulia; Bidaud, Isabelle; Lemmers, Céline; Leresche, Nathalie; Lambert, Régis C.; Lory, Philippe

2015-01-01

Voltage-dependent calcium channels (Cav) of the T-type family (Cav3.1, Cav3.2, and Cav3.3) are activated by low threshold membrane depolarization and contribute greatly to neuronal network excitability. Enhanced T-type channel activity, especially Cav3.2, contributes to disease states, including absence epilepsy. Interestingly, the intracellular loop connecting domains I and II (I-II loop) of Cav3.2 channels is implicated in the control of both surface expression and channel gating, indicating that this I-II loop plays an important regulatory role in T-type current. Here we describe that co-expression of this I-II loop or its proximal region (Δ1-Cav3.2; Ser423–Pro542) together with recombinant full-length Cav3.2 channel inhibited T-type current without affecting channel expression and membrane incorporation. Similar T-type current inhibition was obtained in NG 108-15 neuroblastoma cells that constitutively express Cav3.2 channels. Of interest, Δ1-Cav3.2 inhibited both Cav3.2 and Cav3.1 but not Cav3.3 currents. Efficacy of Δ1-Cav3.2 to inhibit native T-type channels was assessed in thalamic neurons using viral transduction. We describe that T-type current was significantly inhibited in the ventrobasal neurons that express Cav3.1, whereas in nucleus reticularis thalami neurons that express Cav3.2 and Cav3.3 channels, only the fast inactivating T-type current (Cav3.2 component) was significantly inhibited. Altogether, these data describe a new strategy to differentially inhibit Cav3 isoforms of the T-type calcium channels. PMID:25931121

The SH2 domain of Abl kinases regulates kinase autophosphorylation by controlling activation loop accessibility.

PubMed

Lamontanara, Allan Joaquim; Georgeon, Sandrine; Tria, Giancarlo; Svergun, Dmitri I; Hantschel, Oliver

2014-11-17

The activity of protein kinases is regulated by multiple molecular mechanisms, and their disruption is a common driver of oncogenesis. A central and almost universal control element of protein kinase activity is the activation loop that utilizes both conformation and phosphorylation status to determine substrate access. In this study, we use recombinant Abl tyrosine kinases and conformation-specific kinase inhibitors to quantitatively analyse structural changes that occur after Abl activation. Allosteric SH2-kinase domain interactions were previously shown to be essential for the leukemogenesis caused by the Bcr-Abl oncoprotein. We find that these allosteric interactions switch the Abl activation loop from a closed to a fully open conformation. This enables the trans-autophosphorylation of the activation loop and requires prior phosphorylation of the SH2-kinase linker. Disruption of the SH2-kinase interaction abolishes activation loop phosphorylation. Our analysis provides a molecular mechanism for the SH2 domain-dependent activation of Abl that may also regulate other tyrosine kinases.

The SH2 domain of Abl kinases regulates kinase autophosphorylation by controlling activation loop accessibility

NASA Astrophysics Data System (ADS)

Lamontanara, Allan Joaquim; Georgeon, Sandrine; Tria, Giancarlo; Svergun, Dmitri I.; Hantschel, Oliver

2014-11-01

The activity of protein kinases is regulated by multiple molecular mechanisms, and their disruption is a common driver of oncogenesis. A central and almost universal control element of protein kinase activity is the activation loop that utilizes both conformation and phosphorylation status to determine substrate access. In this study, we use recombinant Abl tyrosine kinases and conformation-specific kinase inhibitors to quantitatively analyse structural changes that occur after Abl activation. Allosteric SH2-kinase domain interactions were previously shown to be essential for the leukemogenesis caused by the Bcr-Abl oncoprotein. We find that these allosteric interactions switch the Abl activation loop from a closed to a fully open conformation. This enables the trans-autophosphorylation of the activation loop and requires prior phosphorylation of the SH2-kinase linker. Disruption of the SH2-kinase interaction abolishes activation loop phosphorylation. Our analysis provides a molecular mechanism for the SH2 domain-dependent activation of Abl that may also regulate other tyrosine kinases.

WHAT IS THE SOURCE OF QUIET SUN TRANSITION REGION EMISSION?

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

Schmit, D. J.; De Pontieu, Bart

Dating back to the first observations of the on-disk corona, there has been a qualitative link between the photosphere’s magnetic network and enhanced transition-temperature plasma emission. These observations led to the development of a general model that describes emission structures through the partitioning of the atmospheric volume with different magnetic loop geometries that exhibit different energetic equilibria. Does the internetwork produce transition-temperature emission? What fraction of network flux connects to the corona? How does quiet Sun emission compare with low-activity Sun-like stars? In this work, we revisit the canonical model of the quiet Sun, with high-resolution observations from the Interfacemore » Region Imaging Spectrograph ( IRIS ) and HMI in hand, to address those questions. We use over 900 deep exposures of Si iv 1393 Å from IRIS along with nearly simultaneous HMI magnetograms to quantify the correlation between transition-temperature emission structures and magnetic field concentrations through a number of novel statistics. Our observational results are coupled with analysis of the Bifrost MHD model and a large-scale potential field model. Our results paint a complex portrait of the quiet Sun. We measure an emission signature in the distant internetwork that cannot be attributed to network contribution. We find that the dimmest regions of emission are not linked to the local vertical magnetic field. Using the MHD simulation, we categorize the emission contribution from cool mid-altitude loops and high-altitude coronal loops and discuss the potential emission contribution of spicules. Our results provide new constraints on the coupled solar atmosphere so that we can build on our understanding of how dynamic thermal and magnetic structures generate the observed phenomena in the transition region.« less

The discrete and localized nature of the variable emission from active regions

NASA Technical Reports Server (NTRS)

Arndt, Martina Belz; Habbal, Shadia Rifai; Karovska, Margarita

1994-01-01

Using data from the Extreme Ultraviolet (EUV) Spectroheliometer on Skylab, we study the empirical characteristics of the variable emission in active regions. These simultaneous multi-wavelength observations clearly confirm that active regions consist of a complex of loops at different temperatures. The variable emission from this complex has very well-defined properties that can be quantitatively summarized as follows: (1) It is localized predominantly around the footpoints where it occurs at discrete locations. (2) The strongest variability does not necessarily coincide with the most intense emission. (3) The fraction of the area of the footpoints, (delta n)/N, that exhibits variable emission, varies by +/- 15% as a function of time, at any of the wavelengths measured. It also varies very little from footpoint to footpoint. (4) This fractional variation is temperature dependent with a maximum around 10(exp 5) K. (5) The ratio of the intensity of the variable to the average background emission, (delta I)/(bar-I), also changes with temperature. In addition, we find that these distinctive characteristics persist even when flares occur within the active region.

Decreased functional brain activation in Friedreich ataxia using the Simon effect task.

PubMed

Georgiou-Karistianis, N; Akhlaghi, H; Corben, L A; Delatycki, M B; Storey, E; Bradshaw, J L; Egan, G F

2012-08-01

The present study applied the Simon effect task to examine the pattern of functional brain reorganization in individuals with Friedreich ataxia (FRDA), using functional magnetic resonance imaging (fMRI). Thirteen individuals with FRDA and 14 age and sex matched controls participated, and were required to respond to either congruent or incongruent arrow stimuli, presented either to the left or right of a screen, via laterally-located button press responses. Although the Simon effect (incongruent minus congruent stimuli) showed common regions of activation in both groups, including the superior and middle prefrontal cortices, insulae, superior and inferior parietal lobules (LPs, LPi), occipital cortex and cerebellum, there was reduced functional activation across a range of brain regions (cortical, subcortical and cerebellar) in individuals with FRDA. The greater Simon effect behaviourally in individuals with FRDA, compared with controls, together with concomitant reductions in functional brain activation and reduced functional connectivity between cortical and sub-cortical regions, implies a likely disruption of cortico-cerebellar loops and ineffective engagement of cognitive/attention regions required for response suppression. Copyright © 2012 Elsevier Inc. All rights reserved.

Upwelling and downwelling induced by mesoscale circulation in the DeSoto Canyon region

NASA Astrophysics Data System (ADS)

Nguyen, T. T.; Chassignet, E.; Morey, S. L.; Dukhovskoy, D. S.

2014-12-01

Ocean dynamics are complex over irregular topography areas, and the northeastern Gulf of Mexico, specifically the DeSoto Canyon region, is a challenge for modelers and oceanographers. Vertical movement of waters, especially upwelling, is observed to take place over the canyon's head and along the coast; however, it is not well understood. We focus on upwelling/downwelling processes induced by the Loop Current and its associated eddy field using multi-decadal Hybrid Coordinate Ocean Model simulations. The Loop Current, part of the Gulf Stream, can develop northward into the Gulf through the Yucatan Channel and exit through the Florida Straits. It can reach the continental slope of the study domain and directly depress the isopycnals. Cyclonic eddies in front of the Loop Current also induce upwelling underneath. On the other hand, the Loop Current sometimes impinges on the West Florida Shelf and generates a high pressure disturbance, which travels northward along the shelf into the study region. Consequently, large-scale downwelling occurs across the continental slopes. Our analysis of sea surface height shows that the Loop Current pressure disturbance tends to propagate along the shallow isobaths of 100 to 300 m in the topographic wave direction from south of the West Florida Shelf to the Mississippi Delta. In addition, after shedding a large anticyclonic eddy, the Loop Current retracts southward and can touch the southeastern corner of the West Florida Shelf. This can result in a higher pressure disturbance, and therefore stronger large-scale downwelling in the DeSoto Canyon region.

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

Wemmer, D.E.; Kumar, N.V.; Metrione, R.M.

Toxin II from Radianthus paumotensis (Rp/sub II/) has been investigated by high-resolution NMR and chemical sequencing methods. Resonance assignments have been obtained for this protein by the sequential approach. NMR assignments could not be made consistent with the previously reported primary sequence for this protein, and chemical methods have been used to determine a sequence with which the NMR data are consistent. Analysis of the 2D NOE spectra shows that the protein secondary structure is comprised of two sequences of ..beta..-sheet, probably joined into a distorted continuous sheet, connected by turns and extended loops, without any regular ..cap alpha..-helical segments.more » The residues previously implicated in activity in this class of proteins, D8 and R13, occur in a loop region.« less

Mechanism of action of chromogranin A on catecholamine release: molecular modeling of the catestatin region reveals a β-strand/loop/β-strand structure secured by hydrophobic interactions and predictive of activity

PubMed Central

Tsigelny, Igor; Mahata, Sushil K.; Taupenot, Laurent; Preece, Nicholas E.; Mahata, Manjula; Khan, Imran; Parmer, Robert J.; O’Connor, Daniel T.

2009-01-01

A novel fragment of chromogranin A, known as ‘catestatin’ (bovine chromogranin A344–364), inhibits catecholamine release from chromaffin cells and noradrenergic neurons by acting as a non-competitive nicotinic cholinergic antagonist, and may therefore constitute an endogenous autocrine feedback regulator of sympathoadrenal activity. To characterize how this activity depends on the peptide’s structure, we searched for common 3-dimensional motifs for this primary structure or its homologs. Catestatin’s primary structure bore significant (29–35.5% identity, general alignment score 44–57) sequence homology to fragment sequences within three homologs of known 3-dimensional structures, based on solved X-ray crystals: 8FAB, 1PKM, and 2IG2. Each of these sequences exists in nature as a β-strand/loop/β-strand structure, stabilized by hydrophobic interactions between the β-strands. The catestatin structure was stable during molecular dynamics simulations. The catestatin loop contains three Arg residues, whose electropositive side chains form the terminus of the structure, and give rise to substantial uncompensated charge asymmetry in the molecule. A hydrophobic moment plot revealed that catestatin is the only segment of chromogranin A predicted to contain amphiphilic β-strand. Circular dichroism in the far ultraviolet showed substantial (63%) β-sheet structure, especially in a hydrophobic environment. Alanine-substitution mutants of catestatin established a crucial role for the three central arginine residues in the loop (Arg351, Arg353, and Arg358), though not for two arginine residues in the strand region toward the amino-terminus. [125I]Catestatin bound to Torpedo membranes at a site other than the nicotinic agonist binding site. When the catestatin structure was ‘docked’ with the extracellular domain of the Torpedo nicotinic cholinergic receptor, it interacted principally with the β and δ subunits, in a relatively hydrophobic region of the cation pore extracellular orifice, and the complex of ligand and receptor largely occluded the cation pore, providing a structural basis for the non-competitive nicotinic cholinergic antagonist properties of the peptide. We conclude that a homology model of catestatin correctly predicts actual features of the peptide, both physical and biological. The model suggests particular spatial and charge features of the peptide which may serve as starting points in the development of non-peptide mimetics of this endogenous nicotinic cholinergic antagonist. PMID:9809795

Visualizing Active-Site Dynamics in Single Crystals of HePTP: Opening of the WPD Loop Involves Coordinated Movement of the E Loop

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

D Critton; L Tautz; R Page

2011-12-31

Phosphotyrosine hydrolysis by protein tyrosine phosphatases (PTPs) involves substrate binding by the PTP loop and closure over the active site by the WPD loop. The E loop, located immediately adjacent to the PTP and WPD loops, is conserved among human PTPs in both sequence and structure, yet the role of this loop in substrate binding and catalysis is comparatively unexplored. Hematopoietic PTP (HePTP) is a member of the kinase interaction motif (KIM) PTP family. Compared to other PTPs, KIM-PTPs have E loops that are unique in both sequence and structure. In order to understand the role of the E loopmore » in the transition between the closed state and the open state of HePTP, we identified a novel crystal form of HePTP that allowed the closed-state-to-open-state transition to be observed within a single crystal form. These structures, which include the first structure of the HePTP open state, show that the WPD loop adopts an 'atypically open' conformation and, importantly, that ligands can be exchanged at the active site, which is critical for HePTP inhibitor development. These structures also show that tetrahedral oxyanions bind at a novel secondary site and function to coordinate the PTP, WPD, and E loops. Finally, using both structural and kinetic data, we reveal a novel role for E-loop residue Lys182 in enhancing HePTP catalytic activity through its interaction with Asp236 of the WPD loop, providing the first evidence for the coordinated dynamics of the WPD and E loops in the catalytic cycle, which, as we show, is relevant to multiple PTP families.« less

SAROS: Solar Active Region Observations from Spacelab

NASA Technical Reports Server (NTRS)

Krieger, A. S.

1985-01-01

A definition study of the SAROS investigation was conducted. An instrument design and mode of operation was established which was consistent with the capabilities of the Space Transportation System. Upon completion of the definition phase study the program was placed on hold for approximately five years before being terminated. Consequently, the promise which this investigation held for understanding the heating processes in coronal loops remains unfulfilled.

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

Chatterjee, Achintya K.; Nandy, Nilmadhab; Bari, Md. Washimul

The anomalous behavior of D-layer preparation time of the ionosphere are observed only before, during and after the earthquakes, which took place in the neighbouring region by monitoring the Very Low Frequency (VLF) signal using Gyrator II loop antenna. The anomalies were also observed in the sunrise terminator times during seismically active days. These anomalous behavior may be due to the Lithosphere-Ionosphere coupling. These anomalies may be a precursor of earthquake.

Simultaneous SMM flat crystal spectrometer and Very Large Array observations of solar active regions

NASA Technical Reports Server (NTRS)

Lang, Kenneth R.; Willson, Robert F.; Smith, Kermit L.; Strong, Keith T.

1987-01-01

High-resolution images of the quiescent emission from two solar active regions at 20 cm (VLA) and soft X-ray (SMM FCS) wavelengths are compared. There are regions where the X-ray coronal loops have been completely imaged at 20 cm wavelength. In other regions, the X-ray radiation was detected without detectable 20 cm radiation, and vice versa. The X-ray data were used to infer average electron temperatures of about 3-million K and average electron densities of about 2.5 x 10 to the 9th/cu cm for the X-ray emitting plasma in the two active regions. The thermal bremsstrahlung of the X-ray emitting plasma is optically thin at 20 cm wavelength. The 20 cm brightness temperatures were always less than T(e), which is consistent with optically thin bremsstrahlung. The low T(B) can be explained if a higher, cooler plasma covers the hotter X-ray emitting plasma. Thermal gyroresonance radiation must account for the intense 20 cm radiation near and above sunspots where no X-ray radiation is detected.

Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations

PubMed Central

Jiang, Jun; Aduri, Raviprasad; Chow, Christine S.; SantaLucia, John

2014-01-01

Helix 69 (H69) is a 19-nt stem-loop region from the large subunit ribosomal RNA. Three pseudouridine (Ψ) modifications clustered in H69 are conserved across phylogeny and known to affect ribosome function. To explore the effects of Ψ on the conformations of Escherichia coli H69 in solution, nuclear magnetic resonance spectroscopy was used to reveal the structural differences between H69 with (ΨΨΨ) and without (UUU) Ψ modifications. Comparison of the two structures shows that H69 ΨΨΨ has the following unique features: (i) the loop region is closed by a Watson–Crick base pair between Ψ1911 and A1919, which is potentially reinforced by interactions involving Ψ1911N1H and (ii) Ψ modifications at loop residues 1915 and 1917 promote base stacking from Ψ1915 to A1918. In contrast, the H69 UUU loop region, which lacks Ψ modifications, is less organized. Structure modulation by Ψ leads to alteration in conformational behavior of the 5' half of the H69 loop region, observed as broadening of C1914 non-exchangeable base proton resonances in the H69 ΨΨΨ nuclear magnetic resonance spectra, and plays an important biological role in establishing the ribosomal intersubunit bridge B2a and mediating translational fidelity. PMID:24371282

Modulation of activation-loop phosphorylation by JAK inhibitors is binding mode dependent

PubMed Central

Bonenfant, Débora; Rubert, Joëlle; Vangrevelinghe, Eric; Scheufler, Clemens; Marque, Fanny; Régnier, Catherine H.; De Pover, Alain; Ryckelynck, Hugues; Bhagwat, Neha; Koppikar, Priya; Goel, Aviva; Wyder, Lorenza; Tavares, Gisele; Baffert, Fabienne; Pissot-Soldermann, Carole; Manley, Paul W.; Gaul, Christoph; Voshol, Hans; Levine, Ross L.; Sellers, William R.; Hofmann, Francesco; Radimerski, Thomas

2016-01-01

JAK inhibitors are being developed for the treatment of rheumatoid arthritis, psoriasis, myeloproliferative neoplasms and leukemias. Most of these drugs target the ATP-binding pocket and stabilize the active conformation of the JAK kinases. This type-I binding mode leads to an increase in JAK activation-loop phosphorylation, despite blockade of kinase function. Here we report that stabilizing the inactive state via type-II inhibition acts in the opposite manner, leading to a loss of activation-loop phosphorylation. We used X-ray crystallography to corroborate the binding mode and report for the first time the crystal structure of the JAK2 kinase domain in an inactive conformation. Importantly, JAK inhibitor-induced activation-loop phosphorylation requires receptor interaction, as well as intact kinase and pseudokinase domains. Hence, depending on the respective conformation stabilized by a JAK inhibitor, hyperphosphorylation of the activation-loop may or may not be elicited. PMID:22684457

Entrainment and high-density three-dimensional mapping in right atrial macroreentry provide critical complementary information: Entrainment may unmask "visual reentry" as passive.

PubMed

Pathik, Bhupesh; Lee, Geoffrey; Nalliah, Chrishan; Joseph, Stephen; Morton, Joseph B; Sparks, Paul B; Sanders, Prashanthan; Kistler, Peter M; Kalman, Jonathan M

2017-10-01

With the recent advent of high-density (HD) 3-dimensional (3D) mapping, the utility of entrainment is uncertain. However, the limitations of visual representation and interpretation of these high-resolution 3D maps are unclear. The purpose of this study was to determine the strengths and limitations of both HD 3D mapping and entrainment mapping during mapping of right atrial macroreentry. Fifteen patients were studied. The number and type of circuits accounting for ≥90% of the tachycardia cycle length using HD 3D mapping were verified using systematic entrainment mapping. Entrainment sites with an unexpectedly long postpacing interval despite proximity to the active circuit were evaluated. Based on HD 3D mapping, 27 circuits were observed: 12 peritricuspid, 2 upper loop reentry, 10 lower loop reentry, and 3 lateral wall circuits. With entrainment, 17 of the 27 circuits were active: all 12 peritricuspid and 2 upper loop reentry. However, lower loop reentry was confirmed in only 3 of 10, and none of the 3 lateral wall circuits were present. Mean percentage of tachycardia cycle length covered by active circuits was 98% ± 1% vs 97% ± 2% for passive circuits (P = .09). None of the 345 entrainment runs terminated tachycardia or changed tachycardia mechanism. In 8 of 15 patients, 13 examples of unexpectedly long postpacing interval were observed at entrainment sites located distal to localized zones of slow conduction seen on HD 3D mapping. Using HD 3D mapping, "visual reentry" may be due to passive circuitous propagation rather than a critical reentrant circuit. HD 3D mapping provides new insights into regional conduction and helps explain unusual entrainment phenomena. Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Effect of subthalamic nucleus stimulation during exercise on the mesolimbocortical dopaminergic region in Parkinson's disease: a positron emission tomography study.

PubMed

Nozaki, Takao; Sugiyama, Kenji; Yagi, Shunsuke; Yoshikawa, Etsuji; Kanno, Toshihiko; Asakawa, Tetsuya; Ito, Tae; Terada, Tatsuhiro; Namba, Hiroki; Ouchi, Yasuomi

2013-03-01

To elucidate the dynamic effects of deep brain stimulation (DBS) in the subthalamic nucleus (STN) during activity on the dopaminergic system, 12 PD patients who had STN-DBS operations at least 1 month prior, underwent two positron emission tomography scans during right-foot movement in DBS-off and DBS-on conditions. To quantify motor performance changes, the motion speed and mobility angle of the foot at the ankle were measured twice. Estimations of the binding potential of [(11)C]raclopride (BP(ND)) were based on the Logan plot method. Significant motor recovery was found in the DBS-on condition. The STN-DBS during exercise significantly reduced the [(11)C]raclopride BP(ND) in the caudate and the nucleus accumbens (NA), but not in the dorsal or ventral putamen. The magnitude of dopamine release in the NA correlated negatively with the magnitude of motor load, indicating that STN-DBS facilitated motor behavior more smoothly and at less expense to dopamine neurons in the region. The lack of dopamine release in the putamen and the significant dopamine release in the ventromedial striatum by STN-DBS during exercise indicated dopaminergic activation occurring in the motivational circuit during action, suggesting a compensatory functional activation of the motor loop from the nonmotor to the motor loop system.

Molecular dynamics simulations of certain RGD-based peptides from Kistrin provide insight into the higher activity of REI-RGD34 protein at higher temperature.

PubMed

Upadhyay, Sanjay K

2014-05-01

To determine the bioactive conformation required to bind with receptor aIIbb3, the peptide sequence RIPRGDMP from Kistrin was inserted into CDR 1 loop region of REI protein, resulting in REI-RGD34. The activity of REI-RGD34 was observed to increase at higher temperature towards the receptor aIIbb3. It could be justified in either way: the modified complex forces the restricted peptide to adapt bioactive conformation or it unfolds the peptide in a way that opens its binding surface with high affinity for receptor. Here, we model the conformational preference of RGD sequence in RIPRGDMP at 25 and 42 °C using multiple MD simulations. Further, we model the peptide sequence RGD, PRGD and PRGDMP from kistrin to observe the effect of flanking residues on conformational sampling of RGD. The presence of flanking residues around RGD peptide greatly influenced the conformational sampling. A transition from bend to turn conformation was observed for RGD sequence at 42 °C. The turn conformation shows pharmacophoric parameters required to recognize the receptor aIIbb3. Thus, the temperaturedependent activity of RIPRGDMP when inserted into the loop region of REI can be explained by the presence of the turn conformation. This study will help in designing potential antagonist for the receptor aIIbb3.

Effect of substrate RNA sequence on the cleavage reaction by a short ribozyme.

PubMed Central

Ohmichi, T; Okumoto, Y; Sugimoto, N

1998-01-01

Leadzyme is a ribozyme that requires Pb2+. The catalytic sequence, CUGGGAGUCC, binds to an RNA substrate, GGACC downward arrowGAGCCAG, cleaving the RNA substrate at one site. We have investigated the effect of the substrate sequence on the cleavage activity of leadzyme using mutant substrates in order to structurally understand the RNA catalysis. The results showed that leadzyme acted as a catalyst for single site cleavage of a C5 deletion mutant substrate, GGAC downward arrowGAGCCAG, as well as the wild-type substrate. However, a mutant substrate GGACCGACCAG, which had G8 deleted from the wild-type substrate, was not cleaved. Kinetic studies by surface plasmon resonance indicated that the difference between active and inactive structures reflected the slow association and dissociation rate constants of complex formation induced by Pb2+rather than differences in complex stability. CD spectra showed that the active form of the substrate-leadzyme complex was rearranged by Pb2+binding. The G8 of the wild-type substrate, which was absent in the inactive complex, is not near the cleavage site. Thus, these results show that the active substrate-leadzyme complex has a Pb2+binding site at the junction between the unpaired region (asymmetric internal loop) and the stem region, which is distal to the cleavage site. Pb2+may play a role in rearranging the bases in the asymmetric internal loop to the correct position for catalysis. PMID:9837996

Stabilization and analytical tuning rule of double-loop control scheme for unstable dead-time process

NASA Astrophysics Data System (ADS)

Ugon, B.; Nandong, J.; Zang, Z.

2017-06-01

The presence of unstable dead-time systems in process plants often leads to a daunting challenge in the design of standard PID controllers, which are not only intended to provide close-loop stability but also to give good performance-robustness overall. In this paper, we conduct stability analysis on a double-loop control scheme based on the Routh-Hurwitz stability criteria. We propose to use this unstable double-loop control scheme which employs two P/PID controllers to control first-order or second-order unstable dead-time processes typically found in process industries. Based on the Routh-Hurwitz stability necessary and sufficient criteria, we establish several stability regions which enclose within them the P/PID parameter values that guarantee close-loop stability of the double-loop control scheme. A systematic tuning rule is developed for the purpose of obtaining the optimal P/PID parameter values within the established regions. The effectiveness of the proposed tuning rule is demonstrated using several numerical examples and the result are compared with some well-established tuning methods reported in the literature.

MHD Modeling of Coronal Loops: the Transition Region Throat

NASA Technical Reports Server (NTRS)

Guarrasi, M.; Reale, F.; Orlando, S.; Mignone, A.; Klimchuk, J. A.

2014-01-01

Context. The expansion of coronal loops in the transition region may considerably influence the diagnostics of the plasma emission measure. The cross-sectional area of the loops is expected to depend on the temperature and pressure, and might be sensitive to the heating rate. Aims. The approach here is to study the area response to slow changes in the coronal heating rate, and check the current interpretation in terms of steady heating models. Methods. We study the area response with a time-dependent 2D magnetohydrodynamic (MHD) loop model, including the description of the expanding magnetic field, coronal heating and losses by thermal conduction, and radiation from optically thin plasma. We run a simulation for a loop 50 Mm long and quasi-statically heated to about 4 millikelvin. Results. We find that the area can change substantially with the quasi-steady heating rate, e.g., by approx. 40% at 0.5 millikelvin as the loop temperature varies between 1 millikelvin and 4 millikelvin, and, therefore, affects the interpretation of the differential emission measure vs. temperature (DEM(T)) curves.

Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity

PubMed Central

Chauvot de Beauchêne, Isaure; Allain, Ariane; Panel, Nicolas; Laine, Elodie; Trouvé, Alain; Dubreuil, Patrice; Tchertanov, Luba

2014-01-01

Receptor tyrosine kinase KIT controls many signal transduction pathways and represents a typical allosterically regulated protein. The mutation-induced deregulation of KIT activity impairs cellular physiological functions and causes serious human diseases. The impact of hotspots mutations (D816H/Y/N/V and V560G/D) localized in crucial regulatory segments, the juxtamembrane region (JMR) and the activation (A-) loop, on KIT internal dynamics was systematically studied by molecular dynamics simulations. The mutational outcomes predicted in silico were correlated with in vitro and in vivo activation rates and drug sensitivities of KIT mutants. The allosteric regulation of KIT in the native and mutated forms is described in terms of communication between the two remote segments, JMR and A-loop. A strong correlation between the communication profile and the structural and dynamical features of KIT in the native and mutated forms was established. Our results provide new insight on the determinants of receptor KIT constitutive activation by mutations and resistance of KIT mutants to inhibitors. Depiction of an intra-molecular component of the communication network constitutes a first step towards an integrated description of vast communication pathways established by KIT in physiopathological contexts. PMID:25079768

Radio physics of the sun; Proceedings of the Symposium, University of Maryland, College Park, Md., August 7-10, 1979

NASA Technical Reports Server (NTRS)

Kundu, M. R. (Editor); Gergely, T. E.

1980-01-01

Papers are presented in the areas of the radio characteristics of the quiet sun and active regions, the centimeter, meter and decameter wavelength characteristics of solar bursts, space observations of low-frequency bursts, theoretical interpretations of solar active regions and bursts, joint radio, visual and X-ray observations of active regions and bursts, and the similarities of stellar radio characteristics to solar radio phenomena. Specific topics include the centimeter and millimeter wave characteristics of the quiet sun, radio fluctuations arising upon the transit of shock waves through the transition region, microwave, EUV and X-ray observations of active region loops and filaments, interferometric observations of 35-GHz radio bursts, emission mechanisms for radio bursts, the spatial structure of microwave bursts, observations of type III bursts, the statistics of type I bursts, and the numerical simulation of type III bursts. Attention is also given to the theory of type IV decimeter bursts, Voyager observations of type II and III bursts at kilometric wavelengths, radio and whitelight observations of coronal transients, and the possibility of obtaining radio observations of current sheets on the sun.

THE NONPOTENTIALITY OF CORONAE OF SOLAR ACTIVE REGIONS, THE DYNAMICS OF THE SURFACE MAGNETIC FIELD, AND THE POTENTIAL FOR LARGE FLARES

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

Schrijver, Carolus J., E-mail: schrijver@lmsal.com

Flares and eruptions from solar active regions (ARs) are associated with atmospheric electrical currents accompanying distortions of the coronal field away from a lowest-energy potential state. In order to better understand the origin of these currents and their role in M- and X-class flares, I review all AR observations made with Solar Dynamics Observatory (SDO)/Helioseismic and Magnetic Imager and SDO/Atmospheric Imaging Assembly from 2010 May through 2014 October within ≈40° from the disk center. I select the roughly 4% of all regions that display a distinctly nonpotential coronal configuration in loops with a length comparable to the scale of themore » AR, and all that emit GOES X-class flares. The data for 41 regions confirm, with a single exception, that strong-field, high-gradient polarity inversion lines (SHILs) created during emergence of magnetic flux into, and related displacement within, pre-existing ARs are associated with X-class flares. Obvious nonpotentiality in the AR-scale loops occurs in six of ten selected regions with X-class flares, all with relatively long SHILs along their primary polarity inversion line, or with a long internal filament there. Nonpotentiality can exist in ARs well past the flux-emergence phase, often with reduced or absent flaring. I conclude that the dynamics of the flux involved in the compact SHILs is of pre-eminent importance for the large-flare potential of ARs within the next day, but that their associated currents may not reveal themselves in AR-scale nonpotentiality. In contrast, AR-scale nonpotentiality, which can persist for many days, may inform us about the eruption potential other than those from SHILs which is almost never associated with X-class flaring.« less

Can Thermal Nonequilibrium Explain Coronal Loops?

NASA Technical Reports Server (NTRS)

Klimchuk, James A.; Karpen, Judy T.; Antiochos, Spiro K.

2010-01-01

Any successful model of coronal loops must explain a number of observed properties. For warm (approx. 1 MK) loops, these include: 1. excess density, 2. flat temperature profile, 3. super-hydrostatic scale height, 4. unstructured intensity profile, and 5. 1000-5000 s lifetime. We examine whether thermal nonequilibrium can reproduce the observations by performing hydrodynamic simulations based on steady coronal heating that decreases exponentially with height. We consider both monolithic and multi-stranded loops. The simulations successfully reproduce certain aspects of the observations, including the excess density, but each of them fails in at least one critical way. -Xonolithic models have far too much intensity structure, while multi-strand models are either too structured or too long-lived. Storms of nanoflares remain the only viable explanation for warm loops that has been proposed so far. Our results appear to rule out the widespread existence of heating that is both highly concentrated low in the corona and steady or quasi-steady (slowly varying or impulsive with a rapid cadence). Active regions would have a very different appearance if the dominant heating mechanism had these properties. Thermal nonequilibrium may nonetheless play an important role in prominences and catastrophic cooling e(veen.gts..,coronal rain) that occupy a small fraction of the coronal volume. However, apparent inconsistencies between the models and observations of cooling events have yet to be understood.

EVOLUTION OF MAGNETIC FIELD AND ENERGY IN A MAJOR ERUPTIVE ACTIVE REGION BASED ON SDO/HMI OBSERVATION

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

Sun Xudong; Hoeksema, J. Todd; Liu, Yang

We report the evolution of the magnetic field and its energy in NOAA active region 11158 over five days based on a vector magnetogram series from the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamic Observatory (SDO). Fast flux emergence and strong shearing motion led to a quadrupolar sunspot complex that produced several major eruptions, including the first X-class flare of Solar Cycle 24. Extrapolated nonlinear force-free coronal fields show substantial electric current and free energy increase during early flux emergence near a low-lying sigmoidal filament with a sheared kilogauss field in the filament channel. The computed magneticmore » free energy reaches a maximum of {approx}2.6 Multiplication-Sign 10{sup 32} erg, about 50% of which is stored below 6 Mm. It decreases by {approx}0.3 Multiplication-Sign 10{sup 32} erg within 1 hr of the X-class flare, which is likely an underestimation of the actual energy loss. During the flare, the photospheric field changed rapidly: the horizontal field was enhanced by 28% in the core region, becoming more inclined and more parallel to the polarity inversion line. Such change is consistent with the conjectured coronal field 'implosion' and is supported by the coronal loop retraction observed by the Atmospheric Imaging Assembly (AIA). The extrapolated field becomes more 'compact' after the flare, with shorter loops in the core region, probably because of reconnection. The coronal field becomes slightly more sheared in the lowest layer, relaxes faster with height, and is overall less energetic.« less

Analysis of Inter-Moss Loops in the Solar Region with IRIS and SDO AIA: Automatic Event Detection and Characterization

NASA Technical Reports Server (NTRS)

Fayock, Brian; Winebarger, Amy; De Pontieu, Bart; Alexander, Caroline

2016-01-01

The Interface Region Imaging Spectrograph (IRIS), launched in the summer of 2013, is designed specifically to observe and investigate the transition region and adjacent layers of the solar atmosphere, obtaining images in high spatial, temporal, and spectral resolution. Our particular work is focused on the evolution of inter-moss loops, which have been detected in the lower corona by the Atmospheric Imaging Assembly (AIA) and the High-Resolution Coronal Imager (Hi- C), but are known to have foot points below the transition region. With the high-resolution capabilities of IRIS and its Si IV pass band, which measures activity in the upper chromosphere, we can study these magnetic loops in detail and compare their characteristic length and time scales to those obtained from several AIA image sets, particularly the 171, 193, and 211 pass bands. By comparing the results between these four data sets, one can potentially establish a measure of the ionization equilibrium for the location in question. To explore this idea, we found a large, sit-and-stare observation within the IRIS database that fit our specifications. This data set contained a number of well-defined inter-moss loops (by visual inspection) with a cadence less than or equal to that of AIA (approximately 12 seconds). This particular data set was recorded on October 23, 2013 at 07:09:30, lasting for 3219 seconds with a field of view of 120.6 by 128.1 arcseconds, centered on -53.9 by 59.1 arcseconds from disk center. For ease of comparison, the AIA data has been interpolated to match the IRIS cadence and resolution. In the main portion of the poster, we demonstrate the detection of events, the information collected, and the immediate results to the right, showing the progress of an event with green as the start, blue as the peak, and red as the end. Below here, we demonstrate how pixels are combined to form groups. The 3D results are shown to the right

Analysis of Inter-Moss Loops in the Solar Region with IRIS and SDO AIA: Automatic Event Detection and Characterization

NASA Technical Reports Server (NTRS)

Fayock, Brian; Winebarger, Amy; De Pontieu, Bart

2014-01-01

The Interface Region Imaging Spectrograph (IRIS), launched in the summer of 2013, is designed specifically to observe and investigate the transition region and adjacent layers of the solar atmosphere, obtaining images in high spatial, temporal, and spectral resolution. Our particular work is focused on the evolution of inter-moss loops, which have been detected in the lower corona by the Atmospheric Imaging Assembly (AIA) and the High-Resolution Coronal Imager (Hi- C), but are known to have foot points below the transition region. With the high-resolution capabilities of IRIS and its Si IV pass band, which measures activity in the upper chromosphere, we can study these magnetic loops in detail and compare their characteristic length and time scales to those obtained from several AIA image sets, particularly the 171, 193, and 211 pass bands. By comparing the results between these four data sets, one can potentially establish a measure of the ionization equilibrium for the location in question. To explore this idea, we found a large, sit-and-stare observation within the IRIS database that fit our specifications. This data set contained a number of well-defined inter-moss loops (by visual inspection) with a cadence less than or equal to that of AIA (approximately 12 seconds). This particular data set was recorded on October 23, 2013 at 07:09:30, lasting for 3219 seconds with a field of view of 120.6 by 128.1 arcseconds, centered on -53.9 by 59.1 arcseconds from disk center. For ease of comparison, the AIA data has been interpolated to match the IRIS cadence and resolution. In the main portion of the poster, we demonstrate the detection of events, the information collected, and the immediate results to the right, showing the progress of an event with green as the start, blue as the peak, and red as the end. Below here, we demonstrate how pixels are combined to form groups. The 3D results are shown to the right.

Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family.

PubMed

Contessa, Gian Marco; Orsale, Maria; Melino, Sonia; Torre, Vincent; Paci, Maurizio; Desideri, Alessandro; Cicero, Daniel O

2005-03-01

The NMR high-resolution structure of calmodulin complexed with a fragment of the olfactory cyclic-nucleotide gated channel is described. This structure shows features that are unique for this complex, including an active role of the linker connecting the N- and C-lobes of calmodulin upon binding of the peptide. Such linker is not only involved in the formation of an hydrophobic pocket to accommodate a bulky peptide residue, but it also provides a positively charged region complementary to a negative charge of the target. This complex of calmodulin with a target not belonging to the kinase family was used to test the residual dipolar coupling (RDC) approach for the determination of calmodulin binding modes to peptides. Although the complex here characterized belongs to the (1--14) family, high Q values were obtained with all the 1:1 complexes for which crystalline structures are available. Reduction of the RDC data set used for the correlation analysis to structured regions of the complex allowed a clear identification of the binding mode. Excluded regions comprise calcium binding loops and loops connecting the EF-hand motifs.

Explaining observed red and blue-shifts using multi-stranded coronal loops

NASA Astrophysics Data System (ADS)

Regnier, S.; Walsh, R. W.; Pearson, J.

2012-03-01

Magnetic plasma loops have been termed the building blocks of the solar atmosphere. However, it must be recognised that if the range of loop structures we can observe do consist of many ''sub-resolution'' elements, then current one-dimensional hydrodynamic models are really only applicable to an individual plasma element or strand. Thus a loop should be viewed is an amalgamation of these strands. They could operate in thermal isolation from one another with a wide range of temperatures occurring across the structural elements. This scenario could occur when the energy release mechanism consists of localised, discrete bursts of energy that are due to small scale reconnection sites within the coronal magnetic field- the nanoflare coronal heating mechanism. These energy bursts occur in a time-dependent manner, distributed along the loop/strand length, giving a heating function that depends on space and time. An important observational discovery with the Hinode/EIS spectrometer is the existence of red and blue-shifts in coronal loops depending on the location of the footpoints (inner or outer parts of the active region), and the temperature of the emission line in which the Doppler shifts are measured. Based on the multi-stranded model developed by Sarkar and Walsh (2008, ApJ, 683, 516), we show that red and blue-shifts exist in different simulated Hinode/EIS passbands: cooler lines (OV-SiVII) being dominated by red-shifts, whilst hotter lines (FeXV-CaXVII) are a combination of both. The distribution of blue-shifts depends on the energy input and not so much on the heating location. Characteristic Doppler shifts generated fit well with observed values. We also simulate the Hinode/EIS rasters to closely compare our simulation with the observations. Even if not statistically significant, loops can have footpoints with opposite Doppler shifts.

Is there an association between the use of heeled footwear and schizophrenia?

PubMed

Flensmark, Jarl

2004-01-01

Existing etiological and pathogenetical theories of schizophrenia have only been able to find support in some epidemiological, clinical, and pathophysiological facts. A selective literature review and synthesis is used to present a hypothesis that finds support in all facts and is contradicted by none. Heeled footwear began to be used more than a 1000 years ago, and led to the occurrence of the first cases of schizophrenia. Industrialization of shoe production increased schizophrenia prevalence. Mechanization of the production started in Massachusetts, spread from there to England and Germany, and then to the rest of Western Europe. A remarkable increase in schizophrenia prevalence followed the same pattern. In Baden in Germany the increasing stream of young patients more or less hastily progrediating to a severe state of cognitive impairment made it possible for Kraepelin to delineate dementia praecox as a nosological entity. The patients continued to use heeled shoes after they were admitted to the hospitals and the disease progrediated. High rates of schizophrenia are found among first-generation immigrants from regions with a warmer climate to regions with a colder climate, where the use of shoes is more common. Still higher rates among second-generation immigrants are caused by the use of shoes during the onset of walking at an age of about 11-12 months. Other findings point to the importance of this in the later development of schizophrenia. A child born in January-March begins to walk in December-March, when it's cold outside and the chances of going barefoot are smaller. They are also smaller in urban settings. During walking synchronised stimuli from mechanoreceptors in the lower extremities increase activity in cerebello-thalamo-cortico-cerebellar loops through their action on NMDA-receptors. Using heeled shoes leads to weaker stimulation of the loops. Reduced cortical activity changes dopaminergic function which involves the basal ganglia-thalamo-cortical-nigro-basal ganglia loops. Bicycle riding reduces depression in schizophrenia due to stronger stimulation by improved lengthening contractions of the triceps surae muscles. Electrode stimulation of cerebellar loops normally stimulated by mechanoreceptors in the lower extremities could improve functioning in schizophrenia. Cross-sectional prevalence studies of the association between the use of heeled footwear and schizophrenia should be made in immigrants from regions with a warmer climate or in groups of people who began to wear shoes at different ages. Copyright 2004 Elsevier Ltd.

Mass and energy supply of a cool coronal loop near its apex

NASA Astrophysics Data System (ADS)

Yan, Limei; Peter, Hardi; He, Jiansen; Xia, Lidong; Wang, Linghua

2018-03-01

Context. Different models for the heating of solar corona assume or predict different locations of the energy input: concentrated at the footpoints, at the apex, or uniformly distributed. The brightening of a loop could be due to the increase in electron density ne, the temperature T, or a mixture of both. Aim. We investigate possible reasons for the brightening of a cool loop at transition region temperatures through imaging and spectral observation. Methods: We observed a loop with the Interface Region Imaging Spectrograph (IRIS) and used the slit-jaw images together with spectra taken at a fixed slit position to study the evolution of plasma properties in and below the loop. We used spectra of Si IV, which forms at around 80 000 K in equilibrium, to identify plasma motions and derive electron densities from the ratio of inter-combination lines of O IV. Additional observations from the Solar Dynamics Observatory (SDO) were employed to study the response at coronal temperatures (Atmospheric Imaging Assembly, AIA) and to investigate the surface magnetic field below the loop (Helioseismic and Magnetic Imager, HMI). Results: The loop first appears at transition region temperatures and later also at coronal temperatures, indicating a heating of the plasma in the loop. The appearance of hot plasma in the loop coincides with a possible accelerating upflow seen in Si IV, with the Doppler velocity shifting continuously from -70 km s-1 to -265 km s-1. The 3D magnetic field lines extrapolated from the HMI magnetogram indicate possible magnetic reconnection between small-scale magnetic flux tubes below or near the loop apex. At the same time, an additional intensity enhancement near the loop apex is visible in the IRIS slit-jaw images at 1400 Å. These observations suggest that the loop is probably heated by the interaction between the loop and the upflows, which are accelerated by the magnetic reconnection between small-scale magnetic flux tubes at lower altitudes. Before and after the possible heating phase, the intensity changes in the optically thin (Si IV) and optical thick line (C II) are mainly contributed by the density variation without significant heating. Conclusions: We therefore provide evidence for the heating of an envelope loop that is affected by accelerating upflows, which are probably launched by magnetic reconnection between small-scale magnetic flux tubes underneath the envelope loop. This study emphasizes that in the complex upper atmosphere of the Sun, the dynamics of the 3D coupled magnetic field and flow field plays a key role in thermalizing 1D structures such as coronal loops. An animation associated to Fig. 1 is available at http://https://www.aanda.org

Myosin 3A Kinase Activity Is Regulated by Phosphorylation of the Kinase Domain Activation Loop*

PubMed Central

Quintero, Omar A.; Unrath, William C.; Stevens, Stanley M.; Manor, Uri; Kachar, Bechara; Yengo, Christopher M.

2013-01-01

Class III myosins are unique members of the myosin superfamily in that they contain both a motor and kinase domain. We have found that motor activity is decreased by autophosphorylation, although little is known about the regulation of the kinase domain. We demonstrate by mass spectrometry that Thr-178 and Thr-184 in the kinase domain activation loop and two threonines in the loop 2 region of the motor domain are autophosphorylated (Thr-908 and Thr-919). The kinase activity of MYO3A 2IQ with the phosphomimic (T184E) or phosphoblock (T184A) mutations demonstrates that kinase activity is reduced 30-fold as a result of the T184A mutation, although the Thr-178 site only had a minor impact on kinase activity. Interestingly, the actin-activated ATPase activity of MYO3A 2IQ is slightly reduced as a result of the T178A and T184A mutations suggesting coupling between motor and kinase domains. Full-length GFP-tagged T184A and T184E MYO3A constructs transfected into COS7 cells do not disrupt the ability of MYO3A to localize to filopodia structures. In addition, we demonstrate that T184E MYO3A reduces filopodia elongation in the presence of espin-1, whereas T184A enhances filopodia elongation in a similar fashion to kinase-dead MYO3A. Our results suggest that as MYO3A accumulates at the tips of actin protrusions, autophosphorylation of Thr-184 enhances kinase activity resulting in phosphorylation of the MYO3A motor and reducing motor activity. The differential regulation of the kinase and motor activities allows for MYO3A to precisely self-regulate its concentration in the actin bundle-based structures of cells. PMID:24214986

Myosin 3A kinase activity is regulated by phosphorylation of the kinase domain activation loop.

PubMed

Quintero, Omar A; Unrath, William C; Stevens, Stanley M; Manor, Uri; Kachar, Bechara; Yengo, Christopher M

2013-12-27

Class III myosins are unique members of the myosin superfamily in that they contain both a motor and kinase domain. We have found that motor activity is decreased by autophosphorylation, although little is known about the regulation of the kinase domain. We demonstrate by mass spectrometry that Thr-178 and Thr-184 in the kinase domain activation loop and two threonines in the loop 2 region of the motor domain are autophosphorylated (Thr-908 and Thr-919). The kinase activity of MYO3A 2IQ with the phosphomimic (T184E) or phosphoblock (T184A) mutations demonstrates that kinase activity is reduced 30-fold as a result of the T184A mutation, although the Thr-178 site only had a minor impact on kinase activity. Interestingly, the actin-activated ATPase activity of MYO3A 2IQ is slightly reduced as a result of the T178A and T184A mutations suggesting coupling between motor and kinase domains. Full-length GFP-tagged T184A and T184E MYO3A constructs transfected into COS7 cells do not disrupt the ability of MYO3A to localize to filopodia structures. In addition, we demonstrate that T184E MYO3A reduces filopodia elongation in the presence of espin-1, whereas T184A enhances filopodia elongation in a similar fashion to kinase-dead MYO3A. Our results suggest that as MYO3A accumulates at the tips of actin protrusions, autophosphorylation of Thr-184 enhances kinase activity resulting in phosphorylation of the MYO3A motor and reducing motor activity. The differential regulation of the kinase and motor activities allows for MYO3A to precisely self-regulate its concentration in the actin bundle-based structures of cells.

Computational study of β-N-acetylhexosaminidase from Talaromyces flavus, a glycosidase with high substrate flexibility.

PubMed

Kulik, Natallia; Slámová, Kristýna; Ettrich, Rüdiger; Křen, Vladimír

2015-01-28

β-N-Acetylhexosaminidase (GH20) from the filamentous fungus Talaromyces flavus, previously identified as a prominent enzyme in the biosynthesis of modified glycosides, lacks a high resolution three-dimensional structure so far. Despite of high sequence identity to previously reported Aspergillus oryzae and Penicilluim oxalicum β-N-acetylhexosaminidases, this enzyme tolerates significantly better substrate modification. Understanding of key structural features, prediction of effective mutants and potential substrate characteristics prior to their synthesis are of general interest. Computational methods including homology modeling and molecular dynamics simulations were applied to shad light on the structure-activity relationship in the enzyme. Primary sequence analysis revealed some variable regions able to influence difference in substrate affinity of hexosaminidases. Moreover, docking in combination with consequent molecular dynamics simulations of C-6 modified glycosides enabled us to identify the structural features required for accommodation and processing of these bulky substrates in the active site of hexosaminidase from T. flavus. To access the reliability of predictions on basis of the reported model, all results were confronted with available experimental data that demonstrated the principal correctness of the predictions as well as the model. The main variable regions in β-N-acetylhexosaminidases determining difference in modified substrate affinity are located close to the active site entrance and engage two loops. Differences in primary sequence and the spatial arrangement of these loops and their interplay with active site amino acids, reflected by interaction energies and dynamics, account for the different catalytic activity and substrate specificity of the various fungal and bacterial β-N-acetylhexosaminidases.

Regional acetylcholinesterase activity and its correlation with behavioral performances in 15-month old transgenic mice expressing the human C99 fragment of APP.

PubMed

Dumont, M; Lalonde, R; Ghersi-Egea, J-F; Fukuchi, K; Strazielle, C

2006-09-01

In addition to Abeta plaques and neurofibrillary tangles, Alzheimer's disease (AD) is characterized by increased brain levels of APP C-terminal fragments. In the present investigation, the cholinergic innervation in forebrain regions of transgenic mice (Tg13592) expressing the human betaAPP C99 fragment was compared to that of non-transgenic controls by measuring the activity of the non-specific catabolic enzyme, acetylcholinesterase (AChE). The AchE activity of Tg13592 mice was altered in several regions implicated in the functional loop of regulation between septum and hippocampus, vulnerable in Alzheimer pathology and critically involved in cognitive functions. In particular, AChE activity was upregulated in three basal forebrain regions containing cholinergic cell bodies, prelimbic cortex, anterior subiculum, and paraventricular thalamus, but downregulated in lateral septum and reticular thalamus. The increased activity in medial septum and anterior subiculum was linearly correlated with poor performances in a spatial learning task, possibly due to cell stress mechanisms. Because of some similarities in terms of neurochemistry and behavior, this mouse model may be of use for studying prodromal AD.

System Control for the Transitional DCS.

DTIC Science & Technology

1978-12-01

hour. The equipment destroyed includes the TTC-39 switch, all RF and multiplex equipment, emergency power equipment, distribution frames, antennal and...switch executes loop test to Rhein Main ULS, activating a local alarm at Donnersberg. Since restoral activity has not already been completed, alarm is...ITEM COMMENTS (BYTES) Loop ID Switch number and physical loop number 6 (BCD). Loop circuit CCSD 8 Telephone number 3 Location Physical location of

The mitochondrial intermembrane loop region of rat carnitine palmitoyltransferase 1A is a major determinant of its malonyl-CoA sensitivity.

PubMed

Borthwick, Karen; Jackson, Vicky N; Price, Nigel T; Zammit, Victor A

2006-11-03

Carnitine palmitoyltransferase (CPT) 1A adopts a polytopic conformation within the mitochondrial outer membrane, having both the N- and C-terminal segments on the cytosolic aspect of the membrane and a loop region connecting the two transmembrane (TM) segments protruding into the inter membrane space. In this study we demonstrate that the loop exerts major effects on the sensitivity of the enzyme to its inhibitor, malonyl-CoA. Insertion of a 16-residue spacer between the C-terminal part of the loop sequence (i.e. between residues 100 and 101) and TM2 (which is predicted to start at residue 102) increased the sensitivity to malonyl-CoA inhibition of the resultant mutant protein by more than 10-fold. By contrast, the same insertion made between TM1 and the loop had no effects on the kinetic properties of the enzyme, indicating that effects on the catalytic C-terminal segment were specifically induced by loop-TM2 interactions. Enhanced sensitivity was also observed in all mutants in which the native TM2-loop pairing was disrupted either by making chimeras in which the loops and TM2 segments of CPT 1A and CPT 1B were exchanged or by deleting successive 9-residue segments from the loop sequence. The data suggest that the sequence spanning the loop-TM2 boundary determines the disposition of this TM in the membrane so as to alter the conformation of the C-terminal segment and thus affect its interaction with malonyl-CoA.

An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase

NASA Astrophysics Data System (ADS)

Pucheta-Martínez, Encarna; Saladino, Giorgio; Morando, Maria Agnese; Martinez-Torrecuadrada, Jorge; Lelli, Moreno; Sutto, Ludovico; D'Amelio, Nicola; Gervasio, Francesco Luigi

2016-04-01

Phosphorylation of the activation loop is a fundamental step in the activation of most protein kinases. In the case of the Src tyrosine kinase, a prototypical kinase due to its role in cancer and its historic importance, phosphorylation of tyrosine 416 in the activation loop is known to rigidify the structure and contribute to the switch from the inactive to a fully active form. However, whether or not phosphorylation is able per-se to induce a fully active conformation, that efficiently binds ATP and phosphorylates the substrate, is less clear. Here we employ a combination of solution NMR and enhanced-sampling molecular dynamics simulations to fully map the effects of phosphorylation and ATP/ADP cofactor loading on the conformational landscape of Src tyrosine kinase. We find that both phosphorylation and cofactor binding are needed to induce a fully active conformation. What is more, we find a complex interplay between the A-loop and the hinge motion where the phosphorylation of the activation-loop has a significant allosteric effect on the dynamics of the C-lobe.

Entanglement entropy and correlations in loop quantum gravity

NASA Astrophysics Data System (ADS)

Feller, Alexandre; Livine, Etera R.

2018-02-01

Black hole entropy is one of the few windows into the quantum aspects of gravitation, and its study over the years has highlighted the holographic nature of gravity. At the non-perturbative level in quantum gravity, promising explanations are being explored in terms of the entanglement entropy between regions of space. In the context of loop quantum gravity, this translates into an analysis of the correlations between the regions of the spin network states defining the quantum state of the geometry of space. In this paper, we explore a class of states, motivated by results in condensed matter physics, satisfying an area law for entanglement entropy and having non-trivial correlations. We highlight that entanglement comes from holonomy operators acting on loops crossing the boundary of the region.

Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models

NASA Astrophysics Data System (ADS)

Dodani, Sheel C.; Kiss, Gert; Cahn, Jackson K. B.; Su, Ye; Pande, Vijay S.; Arnold, Frances H.

2016-05-01

The dynamic motions of protein structural elements, particularly flexible loops, are intimately linked with diverse aspects of enzyme catalysis. Engineering of these loop regions can alter protein stability, substrate binding and even dramatically impact enzyme function. When these flexible regions are unresolvable structurally, computational reconstruction in combination with large-scale molecular dynamics simulations can be used to guide the engineering strategy. Here we present a collaborative approach that consists of both experiment and computation and led to the discovery of a single mutation in the F/G loop of the nitrating cytochrome P450 TxtE that simultaneously controls loop dynamics and completely shifts the enzyme's regioselectivity from the C4 to the C5 position of L-tryptophan. Furthermore, we find that this loop mutation is naturally present in a subset of homologous nitrating P450s and confirm that these uncharacterized enzymes exclusively produce 5-nitro-L-tryptophan, a previously unknown biosynthetic intermediate.

Solar-burst precursors and energy buildup at microwave wavelengths

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

Lang, K.R.; Willson, R.F.

High-resolution microwave observations (VLA) of heating and magnetic triggering in coronal loops are summarized. Magnetic changes that precede solar eruptions on time scales of tens of minutes involve primarily emerging coronal loops and the interaction of two or more loops. Thermal cyclotron lines were detected in coronal loops, suggesting the presence of hot current sheets that enhance emission from relatively thin layers of enhanced temperature and constant magnetic field. These current sheets may play a role in the excitation of solar bursts. A filament-associated source with a high brightness temperature and steep radiation spectrum occurs above a region of apparentlymore » weak photospheric field. This source might be attributed to currents that enhance coronal magnetic fields. Compact (phi=5 sec) transient sources with lifetimes of 30 to 60 minutes were also detected in regions of apparently weak photospheric field. VLA observations of coronal loops are compared with simultaneous SMM-XRP observations in conclusion.« less

An Actomyosin-Arf-GEF Negative Feedback Loop for Tissue Elongation under Stress.

PubMed

West, Junior J; Zulueta-Coarasa, Teresa; Maier, Janna A; Lee, Donghoon M; Bruce, Ashley E E; Fernandez-Gonzalez, Rodrigo; Harris, Tony J C

2017-08-07

In response to a pulling force, a material can elongate, hold fast, or fracture. During animal development, multi-cellular contraction of one region often stretches neighboring tissue. Such local contraction occurs by induced actomyosin activity, but molecular mechanisms are unknown for regulating the physical properties of connected tissue for elongation under stress. We show that cytohesins, and their Arf small G protein guanine nucleotide exchange activity, are required for tissues to elongate under stress during both Drosophila dorsal closure (DC) and zebrafish epiboly. In Drosophila, protein localization, laser ablation, and genetic interaction studies indicate that the cytohesin Steppke reduces tissue tension by inhibiting actomyosin activity at adherens junctions. Without Steppke, embryogenesis fails, with epidermal distortions and tears resulting from myosin misregulation. Remarkably, actomyosin network assembly is necessary and sufficient for local Steppke accumulation, where live imaging shows Steppke recruitment within minutes. This rapid negative feedback loop provides a molecular mechanism for attenuating the main tension generator of animal tissues. Such attenuation relaxes tissues and allows orderly elongation under stress. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structure and Dynamics Analysis on Plexin-B1 Rho GTPase Binding Domain as a Monomer and Dimer

PubMed Central

2015-01-01

Plexin-B1 is a single-pass transmembrane receptor. Its Rho GTPase binding domain (RBD) can associate with small Rho GTPases and can also self-bind to form a dimer. In total, more than 400 ns of NAMD molecular dynamics simulations were performed on RBD monomer and dimer. Different analysis methods, such as root mean squared fluctuation (RMSF), order parameters (S2), dihedral angle correlation, transfer entropy, principal component analysis, and dynamical network analysis, were carried out to characterize the motions seen in the trajectories. RMSF results show that after binding, the L4 loop becomes more rigid, but the L2 loop and a number of residues in other regions become slightly more flexible. Calculating order parameters (S2) for CH, NH, and CO bonds on both backbone and side chain shows that the L4 loop becomes essentially rigid after binding, but part of the L1 loop becomes slightly more flexible. Backbone dihedral angle cross-correlation results show that loop regions such as the L1 loop including residues Q25 and G26, the L2 loop including residue R61, and the L4 loop including residues L89–R91, are highly correlated compared to other regions in the monomer form. Analysis of the correlated motions at these residues, such as Q25 and R61, indicate two signal pathways. Transfer entropy calculations on the RBD monomer and dimer forms suggest that the binding process should be driven by the L4 loop and C-terminal. However, after binding, the L4 loop functions as the motion responder. The signal pathways in RBD were predicted based on a dynamical network analysis method using the pathways predicted from the dihedral angle cross-correlation calculations as input. It is found that the shortest pathways predicted from both inputs can overlap, but signal pathway 2 (from F90 to R61) is more dominant and overlaps all of the routes of pathway 1 (from F90 to P111). This project confirms the allosteric mechanism in signal transmission inside the RBD network, which was in part proposed in the previous experimental study. PMID:24901636

Evidence of Significant Energy Input in the Late Phase of a Solar Flare from NuSTAR X-Ray Observations

NASA Astrophysics Data System (ADS)

Kuhar, Matej; Krucker, Säm; Hannah, Iain G.; Glesener, Lindsay; Saint-Hilaire, Pascal; Grefenstette, Brian W.; Hudson, Hugh S.; White, Stephen M.; Smith, David M.; Marsh, Andrew J.; Wright, Paul J.; Boggs, Steven E.; Christensen, Finn E.; Craig, William W.; Hailey, Charles J.; Harrison, Fiona A.; Stern, Daniel; Zhang, William W.

2017-01-01

We present observations of the occulted active region AR 12222 during the third Nuclear Spectroscopic Telescope ARray (NuSTAR) solar campaign on 2014 December 11, with concurrent Solar Dynamics Observatory (SDO)/AIA and FOXSI-2 sounding rocket observations. The active region produced a medium-size solar flare 1 day before the observations, at ˜18 UT on 2014 December 10, with the post-flare loops still visible at the time of NuSTAR observations. The time evolution of the source emission in the SDO/AIA 335 Å channel reveals the characteristics of an extreme-ultraviolet late-phase event, caused by the continuous formation of new post-flare loops that arch higher and higher in the solar corona. The spectral fitting of NuSTAR observations yields an isothermal source, with temperature 3.8-4.6 MK, emission measure (0.3-1.8) × 1046 cm-3, and density estimated at (2.5-6.0) × 108 cm-3. The observed AIA fluxes are consistent with the derived NuSTAR temperature range, favoring temperature values in the range of 4.0-4.3 MK. By examining the post-flare loops’ cooling times and energy content, we estimate that at least 12 sets of post-flare loops were formed and subsequently cooled between the onset of the flare and NuSTAR observations, with their total thermal energy content an order of magnitude larger than the energy content at flare peak time. This indicates that the standard approach of using only the flare peak time to derive the total thermal energy content of a flare can lead to a large underestimation of its value.

EVIDENCE OF SIGNIFICANT ENERGY INPUT IN THE LATE PHASE OF A SOLAR FLARE FROM NuSTAR X-RAY OBSERVATIONS

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

Kuhar, Matej; Krucker, Säm; Hannah, Iain G.

We present observations of the occulted active region AR 12222 during the third Nuclear Spectroscopic Telescope ARray ( NuSTAR ) solar campaign on 2014 December 11, with concurrent Solar Dynamics Observatory ( SDO )/AIA and FOXSI-2 sounding rocket observations. The active region produced a medium-size solar flare 1 day before the observations, at ∼18 UT on 2014 December 10, with the post-flare loops still visible at the time of NuSTAR observations. The time evolution of the source emission in the SDO/ AIA 335 Å channel reveals the characteristics of an extreme-ultraviolet late-phase event, caused by the continuous formation of newmore » post-flare loops that arch higher and higher in the solar corona. The spectral fitting of NuSTAR observations yields an isothermal source, with temperature 3.8–4.6 MK, emission measure (0.3–1.8) × 10{sup 46} cm{sup −3}, and density estimated at (2.5–6.0) × 10{sup 8} cm{sup −3}. The observed AIA fluxes are consistent with the derived NuSTAR temperature range, favoring temperature values in the range of 4.0–4.3 MK. By examining the post-flare loops’ cooling times and energy content, we estimate that at least 12 sets of post-flare loops were formed and subsequently cooled between the onset of the flare and NuSTAR observations, with their total thermal energy content an order of magnitude larger than the energy content at flare peak time. This indicates that the standard approach of using only the flare peak time to derive the total thermal energy content of a flare can lead to a large underestimation of its value.« less

Functional and structural characterization of the pentapeptide insertion of Theileria annulata lactate dehydrogenase by site-directed mutagenesis, comparative modeling and molecular dynamics simulations.

PubMed

Erdemir, Aysegul; Mutlu, Ozal

2017-06-01

Lactate dehydrogenase (LDH) is an important metabolic enzyme in glycolysis and it has been considered as the main energy source in many organisms including apicomplexan parasites. Differences at the active site loop of the host and parasite LDH's makes this enzyme an attractive target for drug inhibitors. In this study, five amino acid insertions in the active site pocket of Theileria annulata LDH (TaLDH) were deleted by PCR-based site-directed mutagenesis, expression and activity analysis of mutant and wild type TaLDH enzymes were performed. Removal of the insertion at the active site loop caused production of an inactive enzyme. Furthermore, structures of wild and mutant enzymes were predicted by comparative modeling and the importance of the insertions at the active site loop were also assigned by molecular docking and dynamics simulations in order to evaluate essential role of this loop for the enzymatic activity. Pentapeptide insertion removal resulted in loss of LDH activity due to deletion of Trp96 and conformational change of Arg98 because of loop instability. Analysis of wild type and mutant enzymes with comparative molecular dynamics simulations showed that the fluctuations of the loop residues increase in mutant enzyme. Together with in silico studies, in vitro results revealed that active site loop has a vital role in the enzyme activity and our findings promise hope for the further drug design studies against theileriosis and other apicomplexan parasite diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

Flexibility and mutagenic resiliency of glycosyltransferases.

PubMed

Bay, Marie Lund; Cuesta-Seijo, Jose A; Weadge, Joel T; Persson, Mattias; Palcic, Monica M

2014-10-01

The human blood group A and B antigens are synthesized by two highly homologous enzymes, glycosyltransferase A (GTA) and glycosyltransferase B (GTB), respectively. These enzymes catalyze the transfer of either GalNAc or Gal from their corresponding UDP-donors to αFuc1-2βGal-R terminating acceptors. GTA and GTB differ at only four of 354 amino acids (R176G, G235S, L266M, G268A), which alter the donor specificity from UDP-GalNAc to UDP-Gal. Blood type O individuals synthesize truncated or non-functional enzymes. The cloning, crystallization and X-ray structure elucidations for GTA and GTB have revealed key residues responsible for donor discrimination and acceptor binding. Structural studies suggest that numerous conformational changes occur during the catalytic cycle. Over 300 ABO alleles are tabulated in the blood group antigen mutation database (BGMUT) that provides a framework for structure-function studies. Natural mutations are found in all regions of GTA and GTB from the active site, flexible loops, stem region and surfaces remote from the active site. Our characterizations of natural mutants near a flexible loop (V175M), on a remote surface site (P156L), in the metal binding motif (M212V) and near the acceptor binding site (L232P) demonstrate the resiliency of GTA and GTB to mutagenesis.

Studies of Xenopus laevis mitochondrial DNA: D-loop mapping and characterization of DNA-binding proteins

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

Cairns, S.S.

1987-01-01

In X. laevis oocytes, mitochondrial DNA accumulates to 10/sup 5/ times the somatic cell complement, and is characterized by a high frequency of a triple-stranded displacement hoop structure at the origin of replication. To map the termini of the single strands, it was necessary to correct the nucleotide sequence of the D-loop region. The revised sequence of 2458 nucleotides contains 54 discrepancies in comparison to a previously published sequence. Radiolabeling of the nascent strands of the D-loop structure either at the 5' end or at the 3' end identifies a major species with a length of 1670 nucleotides. Cleavage ofmore » the 5' labeled strands reveals two families of ends located near several matches to an element, designated CSB-1, that is conserved in this location in several vertebrate genomes. Cleavage of 3' labeled strands produced one fragment. The unique 3' end maps to about 15 nucleotides preceding the tRNA/sup Pro/ gene. A search for proteins which may bind to mtDNA in this region to regulate nucleic acid synthesis has identified three activities in lysates of X. laevis mitochondria. The DNA-binding proteins were assayed by monitoring their ability to retard the migration of labeled double- or single-stranded DNA fragments in polyacrylamide gels. The DNA binding preference was determined by competition with an excess of either ds- or ssDNA.« less

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

PubMed Central

Smith, Emily M.; Lajoie, Bryan R.; Jain, Gaurav; Dekker, Job

2016-01-01

Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation. PMID:26748519

Effects of human chromosome 12 on interactions between Tat and TAR of human immunodeficiency virus type 1.

PubMed Central

Alonso, A; Cujec, T P; Peterlin, B M

1994-01-01

Rates of transcriptions of the human immunodeficiency virus are greatly increased by the viral trans activator Tat. In vitro, Tat binds to the 5' bulge of the trans-activation response (TAR) RNA stem-loop, which is present in all viral transcripts. In human cells, the central loop in TAR and its cellular RNA-binding proteins are also critical for the function of Tat. Previously, we demonstrated that in rodent cells (CHO cells), but not in those which contain the human chromosome 12 (CHO12 cells), Tat-TAR interactions are compromised. In this study, we examined the roles of the bulge and loop in TAR in Tat trans activation in these cells. Whereas low levels of trans activation depended solely on interactions between Tat and the bulge in CHO cells, high levels of trans activation depended also on interactions between Tat and the loop in CHO12 cells. Since the TAR loop binding proteins in these two cell lines were identical and different from their human counterpart, the human chromosome 12 does not encode TAR loop binding proteins. In vivo binding competition studies with TAR decoys confirmed that the binding of Tat to TAR is more efficient in CHO12 cells. Thus, the protein(s) encoded on human chromosome 12 helps to tether Tat to TAR via its loop, which results in high levels of trans activation. Images PMID:8083988

Complex folding and misfolding effects of deer-specific amino acid substitutions in the β2-α2 loop of murine prion protein

NASA Astrophysics Data System (ADS)

Agarwal, Sonya; Döring, Kristina; Gierusz, Leszek A.; Iyer, Pooja; Lane, Fiona M.; Graham, James F.; Goldmann, Wilfred; Pinheiro, Teresa J. T.; Gill, Andrew C.

2015-10-01

The β2-α2 loop of PrPC is a key modulator of disease-associated prion protein misfolding. Amino acids that differentiate mouse (Ser169, Asn173) and deer (Asn169, Thr173) PrPC appear to confer dramatically different structural properties in this region and it has been suggested that amino acid sequences associated with structural rigidity of the loop also confer susceptibility to prion disease. Using mouse recombinant PrP, we show that mutating residue 173 from Asn to Thr alters protein stability and misfolding only subtly, whilst changing Ser to Asn at codon 169 causes instability in the protein, promotes oligomer formation and dramatically potentiates fibril formation. The doubly mutated protein exhibits more complex folding and misfolding behaviour than either single mutant, suggestive of differential effects of the β2-α2 loop sequence on both protein stability and on specific misfolding pathways. Molecular dynamics simulation of protein structure suggests a key role for the solvent accessibility of Tyr168 in promoting molecular interactions that may lead to prion protein misfolding. Thus, we conclude that ‘rigidity’ in the β2-α2 loop region of the normal conformer of PrP has less effect on misfolding than other sequence-related effects in this region.

DETECTION OF SUPERSONIC DOWNFLOWS AND ASSOCIATED HEATING EVENTS IN THE TRANSITION REGION ABOVE SUNSPOTS

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

Kleint, L.; Martínez-Sykora, J.; Antolin, P.

Interface Region Imaging Spectrograph data allow us to study the solar transition region (TR) with an unprecedented spatial resolution of 0.''33. On 2013 August 30, we observed bursts of high Doppler shifts suggesting strong supersonic downflows of up to 200 km s{sup –1} and weaker, slightly slower upflows in the spectral lines Mg II h and k, C II 1336, Si IV 1394 Å, and 1403 Å, that are correlated with brightenings in the slitjaw images (SJIs). The bursty behavior lasts throughout the 2 hr observation, with average burst durations of about 20 s. The locations of these short-lived events appear to bemore » the umbral and penumbral footpoints of EUV loops. Fast apparent downflows are observed along these loops in the SJIs and in the Atmospheric Imaging Assembly, suggesting that the loops are thermally unstable. We interpret the observations as cool material falling from coronal heights, and especially coronal rain produced along the thermally unstable loops, which leads to an increase of intensity at the loop footpoints, probably indicating an increase of density and temperature in the TR. The rain speeds are on the higher end of previously reported speeds for this phenomenon, and possibly higher than the free-fall velocity along the loops. On other observing days, similar bright dots are sometimes aligned into ribbons, resembling small flare ribbons. These observations provide a first insight into small-scale heating events in sunspots in the TR.« less

Structural Characterizations of Glycerol Kinase: Unraveling Phosphorylation-Induced Long-Range Activation

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

Yeh, Joanne I.; Kettering, Regina; Saxl, Ruth

2009-09-11

Glycerol metabolism provides a central link between sugar and fatty acid catabolism. In most bacteria, glycerol kinase plays a crucial role in regulating channel/facilitator-dependent uptake of glycerol into the cell. In the firmicute Enterococcus casseliflavus, this enzyme's activity is enhanced by phosphorylation of the histidine residue (His232) located in its activation loop, approximately 25 A from its catalytic cleft. We reported earlier that some mutations of His232 altered enzyme activities; we present here the crystal structures of these mutant GlpK enzymes. The structure of a mutant enzyme with enhanced enzymatic activity, His232Arg, reveals that residues at the catalytic cleft aremore » more optimally aligned to bind ATP and mediate phosphoryl transfer. Specifically, the position of Arg18 in His232Arg shifts by approximately 1 A when compared to its position in wild-type (WT), His232Ala, and His232Glu enzymes. This new conformation of Arg18 is more optimally positioned at the presumed gamma-phosphate location of ATP, close to the glycerol substrate. In addition to structural changes exhibited at the active site, the conformational stability of the activation loop is decreased, as reflected by an approximately 35% increase in B factors ('thermal factors') in a mutant enzyme displaying diminished activity, His232Glu. Correlating conformational changes to alteration of enzymatic activities in the mutant enzymes identifies distinct localized regions that can have profound effects on intramolecular signal transduction. Alterations in pairwise interactions across the dimer interface can communicate phosphorylation states over 25 A from the activation loop to the catalytic cleft, positioning Arg18 to form favorable interactions at the beta,gamma-bridging position with ATP. This would offset loss of the hydrogen bonds at the gamma-phosphate of ATP during phosphoryl transfer to glycerol, suggesting that appropriate alignment of the second substrate of glycerol kinase, the ATP molecule, may largely determine the rate of glycerol 3-phosphate production.« less

R-loops cause genomic instability in T helper lymphocytes from patients with Wiskott-Aldrich syndrome.

PubMed

Sarkar, Koustav; Han, Seong-Su; Wen, Kuo-Kuang; Ochs, Hans D; Dupré, Loïc; Seidman, Michael M; Vyas, Yatin M

2017-12-15

Wiskott-Aldrich syndrome (WAS), X-linked thrombocytopenia (XLT), and X-linked neutropenia, which are caused by WAS mutations affecting Wiskott-Aldrich syndrome protein (WASp) expression or activity, manifest in immunodeficiency, autoimmunity, genomic instability, and lymphoid and other cancers. WASp supports filamentous actin formation in the cytoplasm and gene transcription in the nucleus. Although the genetic basis for XLT/WAS has been clarified, the relationships between mutant forms of WASp and the diverse features of these disorders remain ill-defined. We sought to define how dysfunctional gene transcription is causally linked to the degree of T H cell deficiency and genomic instability in the XLT/WAS clinical spectrum. In human T H 1- or T H 2-skewing cell culture systems, cotranscriptional R-loops (RNA/DNA duplex and displaced single-stranded DNA) and DNA double-strand breaks (DSBs) were monitored in multiple samples from patients with XLT and WAS and in normal T cells depleted of WASp. WASp deficiency provokes increased R-loops and R-loop-mediated DSBs in T H 1 cells relative to T H 2 cells. Mechanistically, chromatin occupancy of serine 2-unphosphorylated RNA polymerase II is increased, and that of topoisomerase 1, an R-loop preventing factor, is decreased at R-loop-enriched regions of IFNG and TBX21 (T H 1 genes) in T H 1 cells. These aberrations accompany increased unspliced (intron-retained) and decreased spliced mRNA of IFNG and TBX21 but not IL13 (T H 2 gene). Significantly, increased cellular load of R-loops and DSBs, which are normalized on RNaseH1-mediated suppression of ectopic R-loops, inversely correlates with disease severity scores. Transcriptional R-loop imbalance is a novel molecular defect causative in T H 1 immunodeficiency and genomic instability in patients with WAS. The study proposes that cellular R-loop load could be used as a potential biomarker for monitoring symptom severity and prognostic outcome in the XLT-WAS clinical spectrum and could be targeted therapeutically. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. All rights reserved.

THE LITTLEST HIGGS MODEL AND ONE-LOOP ELECTROWEAK PRECISION CONSTRAINTS.

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

CHEN, M.C.; DAWSON,S.

2004-06-16

We present in this talk the one-loop electroweak precision constraints in the Littlest Higgs model, including the logarithmically enhanced contributions from both fermion and scalar loops. We find the one-loop contributions are comparable to the tree level corrections in some regions of parameter space. A low cutoff scale is allowed for a non-zero triplet VEV. Constraints on various other parameters in the model are also discussed. The role of triplet scalars in constructing a consistent renormalization scheme is emphasized.

Structure and dynamics of coronal plasmas

NASA Technical Reports Server (NTRS)

Golub, Leon

1995-01-01

The Normal Incidence X-ray Telescope (NIXT) obtained a unique set of high resolution full disk solar images which were exposed simultaneously by X-rays in a passband at 63.5 A and by visible light. The perfect alignment of a photospheric visible light image with a coronal X-ray image enables us to present observations of X-ray intensity vs an accurately determined height above the visible limb. The height at which the observed X-ray intensity peak varies from 4000 km in active regions to 9000 km in quiet regions of the sun. The interpretation of the observations stems from the previously established fact that, for the coronal loops, emission in the NIXT bandpass peaks sharply just above the footpoints. Because there is not a sharp peak in the observed X-ray intensity vs off limb height, we conclude that the loop footpoints, when viewed at the limb, are obscured by absorption in chromospheric material along the line of sight. We calculate the X-ray intensity vs height predicted by a number of different idealizations of the solar atmosphere, and we compare these calculations with the observed X-ray intensity vs height. The calculations use existing coronal and chromospheric models. In order for the calculations to reproduce the observed off limb X-ray intensities, we are forced to assume an atmosphere in which the footpoints of coronal loops are interspersed along the line of sight with cooler chromospheric material extending to heights well above the loop footpoints. We argue that the absorption coefficient for NIXT X-rays by chromospheric material is roughly proportional to the neutral hydrogen density, and we estimate an average neutral hydrogen density and scale height implied by the data.

Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage

PubMed Central

Bozek, Katarzyna; Lengauer, Thomas; Sierra, Saleta; Kaiser, Rolf; Domingues, Francisco S.

2013-01-01

The relationship of HIV tropism with disease progression and the recent development of CCR5-blocking drugs underscore the importance of monitoring virus coreceptor usage. As an alternative to costly phenotypic assays, computational methods aim at predicting virus tropism based on the sequence and structure of the V3 loop of the virus gp120 protein. Here we present a numerical descriptor of the V3 loop encoding its physicochemical and structural properties. The descriptor allows for structure-based prediction of HIV tropism and identification of properties of the V3 loop that are crucial for coreceptor usage. Use of the proposed descriptor for prediction results in a statistically significant improvement over the prediction based solely on V3 sequence with 3 percentage points improvement in AUC and 7 percentage points in sensitivity at the specificity of the 11/25 rule (95%). We additionally assessed the predictive power of the new method on clinically derived ‘bulk’ sequence data and obtained a statistically significant improvement in AUC of 3 percentage points over sequence-based prediction. Furthermore, we demonstrated the capacity of our method to predict therapy outcome by applying it to 53 samples from patients undergoing Maraviroc therapy. The analysis of structural features of the loop informative of tropism indicates the importance of two loop regions and their physicochemical properties. The regions are located on opposite strands of the loop stem and the respective features are predominantly charge-, hydrophobicity- and structure-related. These regions are in close proximity in the bound conformation of the loop potentially forming a site determinant for the coreceptor binding. The method is available via server under http://structure.bioinf.mpi-inf.mpg.de/. PMID:23555214

Creation of a Ligand-Dependent Enzyme by Fusing Circularly Permuted Antibody Variable Region Domains.

PubMed

Iwai, Hiroto; Kojima-Misaizu, Miki; Dong, Jinhua; Ueda, Hiroshi

2016-04-20

Allosteric control of enzyme activity with exogenous substances has been hard to achieve, especially using antibody domains that potentially allow control by any antigens of choice. Here, in order to attain this goal, we developed a novel antibody variable region format introduced with circular permutations, called Clampbody. The two variable-region domains of the antibone Gla protein (BGP) antibody were each circularly permutated to have novel termini at the loops near their domain interface. Through their attachment to the N- and C-termini of a circularly permutated TEM-1 β-lactamase (cpBLA), we created a molecular switch that responds to the antigen peptide. The fusion protein specifically recognized the antigen, and in the presence of some detergent or denaturant, its catalytic activity was enhanced up to 4.7-fold in an antigen-dependent manner, due to increased resistance to these reagents. Hence, Clampbody will be a powerful tool for the allosteric regulation of enzyme and other protein activities and especially useful to design robust biosensors.

X-ray and microwave observations of active regions

NASA Technical Reports Server (NTRS)

Webb, D. F.; Davis, J. M.; Kundu, M. R.; Velusamy, T.

1983-01-01

Coordinated high-resolution (1-3 arcsec) observations of two active solar regions (H 421 and H 419) on November 16, 1979, are reported: soft-X-ray filtergrams from a sounding rocket flight, VLA total-intensity and circular-polarization microwave (6-cm) radio maps, KPNO full-disk photospheric magnetograms, and BBSO H-alpha data. The images were converted to 4.8-arcsec/mm-scale transparencies and coaligned on the basis of sunspot positions for comparison. The two active regions are characterized in detail, and intensity, size, and polarization data for the brightest microwave components (BMC) are listed. It is found that 19 of the 32 BMC are farther than 5 arcsec from any sunspot, and that X-ray-emitting structures only rarely correspond to sunspots, or BMC. About one third of the BMC are located at the feet or legs of coronal loops smaller than about 50,000 km. The limitations implied by these obervations for proposed thermal-bremsstrahlung, thermal-gyro-resonance, and nonthermal microwave-emission mechanisms are discussed.

NMR and Bioinformatics Discovery of Exosites That Tune Metalloelastase Specificity for Solubilized Elastin and Collagen Triple Helices*

PubMed Central

Palmier, Mark O.; Fulcher, Yan G.; Bhaskaran, Rajagopalan; Duong, Vinh Q.; Fields, Gregg B.; Van Doren, Steven R.

2010-01-01

The catalytic domain of metalloelastase (matrix metalloproteinase-12 or MMP-12) is unique among MMPs in exerting high proteolytic activity upon fibrils that resist hydrolysis, especially elastin from lungs afflicted with chronic obstructive pulmonary disease or arteries with aneurysms. How does the MMP-12 catalytic domain achieve this specificity? NMR interface mapping suggests that α-elastin species cover the primed subsites, a strip across the β-sheet from β-strand IV to the II–III loop, and a broad bowl from helix A to helix C. The many contacts may account for the comparatively high affinity, as well as embedding of MMP-12 in damaged elastin fibrils in vivo. We developed a strategy called BINDSIght, for bioinformatics and NMR discovery of specificity of interactions, to evaluate MMP-12 specificity without a structure of a complex. BINDSIght integration of the interface mapping with other ambiguous information from sequences guided choice mutations in binding regions nearer the active site. Single substitutions at each of ten locations impair specific activity toward solubilized elastin. Five of them impair release of peptides from intact elastin fibrils. Eight lesions also impair specific activity toward triple helices from collagen IV or V. Eight sites map to the “primed” side in the III–IV, V–B, and S1′ specificity loops. Two map to the “unprimed” side in the IV–V and B–C loops. The ten key residues circumscribe the catalytic cleft, form an exosite, and are distinctive features available for targeting by new diagnostics or therapeutics. PMID:20663866

The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.

PubMed

Tsuchiya, Yuko; Mizuguchi, Kenji

2016-04-01

Of the complementarity-determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen-binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen-binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen-binding tendencies of all the CDR loops. © 2016 The Protein Society.

Alfvén Wave Heating Model of an Active Region and Comparisons with the EIS Observations

NASA Astrophysics Data System (ADS)

Lawless, A. P.; Asgari-Targhi, M.

2013-12-01

We study the generation and dissipation of Alfvén waves in open and closed field lines using the images from the Solar Dynamics Observatory's (SDO) Atmospheric Imaging Assembly (AIA) (van Ballegouijen et al. 2011; Asgari-Targhi & van Ballegouijen 2012; Asgari et al. 2013). The goal is to search for observational evidence of Alfvén waves in the solar corona and to understand their role in coronal heating. We focus on one particular active region on the 10th of December 2007. Using the MDI magnetogram and the potential field modeling of this region, we create three-dimensional MHD models for several open and closed field lines in different locations in the active region. For each model, we compute the temperature, pressure, magnetic field strength, average heating rate, and other parameters along the loop. We then compare these results with the EIS observations. This research is supported by the NSF grant for the Solar physics REU Program at the Smithsonian Astrophysical Observatory (AGS-1263241) and contract SP02H1701R from Lockheed-Martin to SAO.

MHD modeling of coronal loops: the transition region throat

NASA Astrophysics Data System (ADS)

Guarrasi, M.; Reale, F.; Orlando, S.; Mignone, A.; Klimchuk, J. A.

2014-04-01

Context. The expansion of coronal loops in the transition region may considerably influence the diagnostics of the plasma emission measure. The cross-sectional area of the loops is expected to depend on the temperature and pressure, and might be sensitive to the heating rate. Aims: The approach here is to study the area response to slow changes in the coronal heating rate, and check the current interpretation in terms of steady heating models. Methods: We study the area response with a time-dependent 2D magnetohydrodynamic (MHD) loop model, including the description of the expanding magnetic field, coronal heating and losses by thermal conduction, and radiation from optically thin plasma. We run a simulation for a loop 50 Mm long and quasi-statically heated to about 4 MK. Results: We find that the area can change substantially with the quasi-steady heating rate, e.g., by ~40% at 0.5 MK as the loop temperature varies between 1 MK and 4 MK, and, therefore, affects the interpretation of the differential emission measure vs. temperature (DEM(T)) curves. The movie associated to Fig. 4 is available in electronic form at http://www.aanda.org

Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling.

PubMed

Afriat-Jurnou, Livnat; Jackson, Colin J; Tawfik, Dan S

2012-08-07

Only decades after the introduction of organophosphate pesticides, bacterial phosphotriesterases (PTEs) have evolved to catalyze their degradation with remarkable efficiency. Their closest known relatives, lactonases, with promiscuous phosphotriasterase activity, dubbed PTE-like lactonases (PLLs), share only 30% sequence identity and also differ in the configuration of their active-site loops. PTE was therefore presumed to have evolved from a yet unknown PLL whose primary activity was the hydrolysis of quorum sensing homoserine lactones (HSLs) (Afriat et al. (2006) Biochemistry 45, 13677-13686). However, how PTEs diverged from this presumed PLL remains a mystery. In this study we investigated loop remodeling as a means of reconstructing a homoserine lactonase ancestor that relates to PTE by few mutational steps. Although, in nature, loop remodeling is a common mechanism of divergence of enzymatic functions, reproducing this process in the laboratory is a challenge. Structural and phylogenetic analyses enabled us to remodel one of PTE's active-site loops into a PLL-like configuration. A deletion in loop 7, combined with an adjacent, highly epistatic, point mutation led to the emergence of an HSLase activity that is undetectable in PTE (k(cat)/K(M) values of up to 2 × 10(4)). The appearance of the HSLase activity was accompanied by only a minor decrease in PTE's paraoxonase activity. This specificity change demonstrates the potential role of bifunctional intermediates in the divergence of new enzymatic functions and highlights the critical contribution of loop remodeling to the rapid divergence of new enzyme functions.

Noncoherent pseudonoise code tracking performance of spread spectrum receivers

NASA Technical Reports Server (NTRS)

Simon, M. K.

1977-01-01

The optimum design and performance of two noncoherent PN tracking loop configurations, namely, the delay-locked loop and tau-dither loop, are described. In particular, the bandlimiting effects of the bandpass arm filters are considered by demonstrating that for a fixed data rate and data signal-to-noise ratio, there exists an optimum filter bandwidth in the sense of minimizing the loop's tracking jitter. Both the linear and nonlinear loop analyses are presented, and the region of validity of the former relative to the latter is indicated. In addition, numerical results are given for several filter types. For example, assuming ideal bandpass arm filters, it is shown that the tau-dither loop requires approximately 1 dB more signal-to-noise ratio than the delay-locked loop for equal rms tracking jitters.

Using coronal seismology to estimate the magnetic field strength in a realistic coronal model

NASA Astrophysics Data System (ADS)

Chen, F.; Peter, H.

2015-09-01

Aims: Coronal seismology is used extensively to estimate properties of the corona, e.g. the coronal magnetic field strength is derived from oscillations observed in coronal loops. We present a three-dimensional coronal simulation, including a realistic energy balance in which we observe oscillations of a loop in synthesised coronal emission. We use these results to test the inversions based on coronal seismology. Methods: From the simulation of the corona above an active region, we synthesise extreme ultraviolet emission from the model corona. From this, we derive maps of line intensity and Doppler shift providing synthetic data in the same format as obtained from observations. We fit the (Doppler) oscillation of the loop in the same fashion as done for observations to derive the oscillation period and damping time. Results: The loop oscillation seen in our model is similar to imaging and spectroscopic observations of the Sun. The velocity disturbance of the kink oscillation shows an oscillation period of 52.5 s and a damping time of 125 s, which are both consistent with the ranges of periods and damping times found in observations. Using standard coronal seismology techniques, we find an average magnetic field strength of Bkink = 79 G for our loop in the simulation, while in the loop the field strength drops from roughly 300 G at the coronal base to 50 G at the apex. Using the data from our simulation, we can infer what the average magnetic field derived from coronal seismology actually means. It is close to the magnetic field strength in a constant cross-section flux tube, which would give the same wave travel time through the loop. Conclusions: Our model produced a realistic looking loop-dominated corona, and provides realistic information on the oscillation properties that can be used to calibrate and better understand the result from coronal seismology. A movie associated with Fig. 1 is available in electronic form at http://www.aanda.org

Voice loops as coordination aids in space shuttle mission control.

PubMed

Patterson, E S; Watts-Perotti, J; Woods, D D

1999-01-01

Voice loops, an auditory groupware technology, are essential coordination support tools for experienced practitioners in domains such as air traffic management, aircraft carrier operations and space shuttle mission control. They support synchronous communication on multiple channels among groups of people who are spatially distributed. In this paper, we suggest reasons for why the voice loop system is a successful medium for supporting coordination in space shuttle mission control based on over 130 hours of direct observation. Voice loops allow practitioners to listen in on relevant communications without disrupting their own activities or the activities of others. In addition, the voice loop system is structured around the mission control organization, and therefore directly supports the demands of the domain. By understanding how voice loops meet the particular demands of the mission control environment, insight can be gained for the design of groupware tools to support cooperative activity in other event-driven domains.

Voice loops as coordination aids in space shuttle mission control

NASA Technical Reports Server (NTRS)

Patterson, E. S.; Watts-Perotti, J.; Woods, D. D.

1999-01-01

Voice loops, an auditory groupware technology, are essential coordination support tools for experienced practitioners in domains such as air traffic management, aircraft carrier operations and space shuttle mission control. They support synchronous communication on multiple channels among groups of people who are spatially distributed. In this paper, we suggest reasons for why the voice loop system is a successful medium for supporting coordination in space shuttle mission control based on over 130 hours of direct observation. Voice loops allow practitioners to listen in on relevant communications without disrupting their own activities or the activities of others. In addition, the voice loop system is structured around the mission control organization, and therefore directly supports the demands of the domain. By understanding how voice loops meet the particular demands of the mission control environment, insight can be gained for the design of groupware tools to support cooperative activity in other event-driven domains.

Simulations of fully deformed oscillating flux tubes

NASA Astrophysics Data System (ADS)

Karampelas, K.; Van Doorsselaere, T.

2018-02-01

Context. In recent years, a number of numerical studies have been focusing on the significance of the Kelvin-Helmholtz instability in the dynamics of oscillating coronal loops. This process enhances the transfer of energy into smaller scales, and has been connected with heating of coronal loops, when dissipation mechanisms, such as resistivity, are considered. However, the turbulent layer is expected near the outer regions of the loops. Therefore, the effects of wave heating are expected to be confined to the loop's external layers, leaving their denser inner parts without a heating mechanism. Aim. In the current work we aim to study the spatial evolution of wave heating effects from a footpoint driven standing kink wave in a coronal loop. Methods: Using the MPI-AMRVAC code, we performed ideal, three dimensional magnetohydrodynamic simulations of footpoint driven transverse oscillations of a cold, straight coronal flux tube, embedded in a hotter environment. We have also constructed forward models for our simulation using the FoMo code. Results: The developed transverse wave induced Kelvin-Helmholtz (TWIKH) rolls expand throughout the tube cross-section, and cover it entirely. This turbulence significantly alters the initial density profile, leading to a fully deformed cross section. As a consequence, the resistive and viscous heating rate both increase over the entire loop cross section. The resistive heating rate takes its maximum values near the footpoints, while the viscous heating rate at the apex. Conclusions: We conclude that even a monoperiodic driver can spread wave heating over the whole loop cross section, potentially providing a heating source in the inner loop region. Despite the loop's fully deformed structure, forward modelling still shows the structure appearing as a loop. A movie attached to Fig. 1 is available at http://https://www.aanda.org

What triggers differential DNA methylation of genes and TEs: contribution of body methylation?

PubMed

Inagaki, S; Kakutani, T

2012-01-01

Transposable elements (TEs) are epigenetically silenced with extensive DNA methylation. The silent epigenetic marks should, however, be excluded from active genes. By genetic approaches, we study mechanisms to remove the heterochromatin marks from transcribed genes. Based on our observations on control of TE transcription, we propose a possible trigger for the TE-specific accumulation of DNA methylation. A critical difference between TEs and genes could be their responses to the DNA methylation in the internal part of transcribed regions. When their internal region is methylated, genes are still transcribed, but TEs could be silenced, which may reflect the obligatory position of every critical cis-acting element within the TE itself. This initial difference of TEs and genes will be amplified by positive feedback loops to stabilize active or silent states. Thus, the mechanisms to accumulate heterochromatin marks within transcribed regions could provide a trigger to induce differential DNA methylation between genes and TEs.

Not even wrong: A philosophical, historical and ultimately a scientific inquiry into the Schmidt Law

NASA Astrophysics Data System (ADS)

Madore, Barry F.; Carlson, Erika K.

2017-03-01

We introduce a novel approach to interpreting the well-known spatial correlation of gas densities with on-going star formation. Treated as a closed-loop process involving two physically distinct phases the data can be subdivided into regions that are active and those that are quiescent. The active regions can be distinguished by the presence of high-mass, short-lived, but recently-formed OB stars; the quiescent regions are marked by an absence of these stars and they are considered to be recovering from the last star-formation event and are re-collapsing. The relative (areal) frequencies of those two phases are directly proportional to the relative timescales. For four Local Group galaxies, NGC 6822, the Large & Small Magellanic Clouds, and M33, the cloud assembly/collapse timescales are all found to be monotonically decreasing power-law functions of density, with as yet to be explained differences.

Mini-filament Eruptions Triggering Confined Solar Flares Observed by ONSET and SDO

NASA Astrophysics Data System (ADS)

Yang, Shuhong; Zhang, Jun

2018-06-01

Using the observations from the Optical and Near-infrared Solar Eruption Tracer (ONSET) and the Solar Dynamics Observatory (SDO), we study an M5.7 flare in AR 11476 on 2012 May 10 and a micro-flare in the quiet Sun on 2017 March 23. Before the onset of each flare, there is a reverse S-shaped filament above the polarity inversion line, then the filaments become unstable and begin to rise. The rising filaments gain the upper hand over the tension force of the dome-like overlying loops and thus successfully erupt outward. The footpoints of the reconnecting overlying loops successively brighten and are observed as two flare ribbons, while the newly formed low-lying loops appear as post-flare loops. These eruptions are similar to the classical model of successful filament eruptions associated with coronal mass ejections (CMEs). However, the erupting filaments in this study move along large-scale lines and eventually reach the remote solar surface; i.e., no filament material is ejected into the interplanetary space. Thus, both the flares are confined. These results reveal that some successful filament eruptions can trigger confined flares. Our observations also imply that this kind of filament eruption may be ubiquitous on the Sun, from active regions (ARs) with large flares to the quiet Sun with micro-flares.

Conformational transition in signal transduction: metastable states and transition pathways in the activation of a signaling protein.

PubMed

Banerjee, Rahul; Yan, Honggao; Cukier, Robert I

2015-06-04

Signal transduction is of vital importance to the growth and adaptation of living organisms. The key to understand mechanisms of biological signal transduction is elucidation of the conformational dynamics of its signaling proteins, as the activation of a signaling protein is fundamentally a process of conformational transition from an inactive to an active state. A predominant form of signal transduction for bacterial sensing of environmental changes in the wild or inside their hosts is a variety of two-component systems, in which the conformational transition of a response regulator (RR) from an inactive to an active state initiates responses to the environmental changes. Here, RR activation has been investigated using RR468 as a model system by extensive unbiased all-atom molecular dynamics (MD) simulations in explicit solvent, starting from snapshots along a targeted MD trajectory that covers the conformational transition. Markov state modeling, transition path theory, and geometric analyses of the wealth of the MD data have provided a comprehensive description of the RR activation. It involves a network of metastable states, with one metastable state essentially the same as the inactive state and another very similar to the active state that are connected via a small set of intermediates. Five major pathways account for >75% of the fluxes of the conformational transition from the inactive to the active-like state. The thermodynamic stability of the states and the activation barriers between states are found, to identify rate-limiting steps. The conformal transition is initiated predominantly by movements of the β3α3 loop, followed by movements of the β4α4-loop and neighboring α4 helix region, and capped by additional movements of the β3α3 loop. A number of transient hydrophobic and hydrogen bond interactions are revealed, and they may be important for the conformational transition.

Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains.

PubMed

Krieger, Florian; Möglich, Andreas; Kiefhaber, Thomas

2005-03-16

Glycine and proline residues are frequently found in turn and loop structures of proteins and are believed to play an important role during chain compaction early in folding. We investigated their effect on the dynamics of intrachain loop formation in various unstructured polypeptide chains. Loop formation is significantly slower around trans prolyl peptide bonds and faster around glycine residues compared to any other amino acid. However, short loops are formed fastest around cis prolyl bonds with a time constant of 6 ns for end-to-end contact formation in a four-residue loop. Formation of short loops encounters activation energies in the range of 15 to 30 kJ/mol. The altered dynamics around glycine and trans prolyl bonds can be mainly ascribed to their effects on the activation energy. The fast dynamics around cis prolyl bonds, in contrast, originate in a higher Arrhenius pre-exponential factor, which compensates for an increased activation energy for loop formation compared to trans isomers. All-atom simulations of proline-containing peptides indicate that the conformational space for cis prolyl isomers is largely restricted compared to trans isomers. This leads to decreased average end-to-end distances and to a smaller loss in conformational entropy upon loop formation in cis isomers. The results further show that glycine and proline residues only influence formation of short loops containing between 2 and 10 residues, which is the typical loop size in native proteins. Formation of larger loops is not affected by the presence of a single glycine or proline residue.

Velocity vector imaging fails to quantify regional myocardial dysfunction in a mouse model of isoprenaline-induced cardiotoxicity.

PubMed

Täng, Margareta Scharin; Redfors, Bjorn; Shao, Yangzhen; Omerovic, Elmir

2012-08-01

Regional myocardial deformation patterns are important in a variety of cardiac diseases, including stress-induced cardiomyopathy. Velocity-vector-based imaging is a speckle-tracking echocardiography (STE)-based algorithm that has been shown to allow in-depth cardiac phenotyping in humans. Regional posterior wall myocardial dysfunction occurs during severe isoprenaline stress in mice. We have previously shown that regional posterior wall end-systolic transmural strain decreases after severe isoprenaline toxicity in mice. We hypothesize that STE can detect and further quantify these perturbations. Twenty-three mice underwent echocardiographic examination using the VEVO2100 system. Regional transmural radial strain and strain rate were calculated in both parasternal short-axis and parasternal long-axis cine loops using the VisualSonics VEVO 2100 velocity vector imaging (VVI) STE algorithm. Eight C57BL/6 mice underwent baseline echocardiographic examination using the VisualSonics VEVO 770 system, which can acquire >1,000 frames/s cine loops. In a parasternal short-axis cine loop, the heart was divided into six segments, and regional fractional wall thickening (FWT) was assessed manually. The same protocols were also performed 90 minutes post 400 mg/kg intraperitoneally isoprenaline. Regional myocardial FWT is uniform at baseline but increases significantly in anterolateral segments, whereas it decreases significantly in posterior segments (P < 0.05). A similar pattern is seen using the VVI algorithm although the variance is larger, and differences are smaller and fail to reach significance. VVI is less sensitive in detecting regional perturbations in myocardial function than manual tracing, possibly due to the low frame rate in the cine loops used. © 2012, Wiley Periodicals, Inc.

Coronal rain in magnetic bipolar weak fields

NASA Astrophysics Data System (ADS)

Xia, C.; Keppens, R.; Fang, X.

2017-07-01

Aims: We intend to investigate the underlying physics for the coronal rain phenomenon in a representative bipolar magnetic field, including the formation and the dynamics of coronal rain blobs. Methods: With the MPI-AMRVAC code, we performed three dimensional radiative magnetohydrodynamic (MHD) simulation with strong heating localized on footpoints of magnetic loops after a relaxation to quiet solar atmosphere. Results: Progressive cooling and in-situ condensation starts at the loop top due to radiative thermal instability. The first large-scale condensation on the loop top suffers Rayleigh-Taylor instability and becomes fragmented into smaller blobs. The blobs fall vertically dragging magnetic loops until they reach low-β regions and start to fall along the loops from loop top to loop footpoints. A statistic study of the coronal rain blobs finds that small blobs with masses of less than 1010 g dominate the population. When blobs fall to lower regions along the magnetic loops, they are stretched and develop a non-uniform velocity pattern with an anti-parallel shearing pattern seen to develop along the central axis of the blobs. Synthetic images of simulated coronal rain with Solar Dynamics Observatory Atmospheric Imaging Assembly well resemble real observations presenting dark falling clumps in hot channels and bright rain blobs in a cool channel. We also find density inhomogeneities during a coronal rain "shower", which reflects the observed multi-stranded nature of coronal rain. Movies associated to Figs. 3 and 7 are available at http://www.aanda.org

ON THE STRENGTH OF THE HEMISPHERIC RULE AND THE ORIGIN OF ACTIVE-REGION HELICITY

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

Wang, Y.-M., E-mail: yi.wang@nrl.navy.mil

Vector magnetograph and morphological observations have shown that the solar magnetic field tends to have negative (positive) helicity in the northern (southern) hemisphere, although only ∼60%-70% of active regions appear to obey this 'hemispheric rule'. In contrast, at least ∼80% of quiescent filaments and filament channels that form during the decay of active regions follow the rule. We attribute this discrepancy to the difficulty in determining the helicity sign of newly emerged active regions, which are dominated by their current-free component; as the transverse field is canceled at the polarity inversion lines, however, the axial component becomes dominant there, allowingmore » a more reliable determination of the original active-region chirality. We thus deduce that the hemispheric rule is far stronger than generally assumed, and cannot be explained by stochastic processes. Earlier studies have shown that the twist associated with the axial tilt of active regions is too small to account for the observed helicity; here, both tilt and twist are induced by the Coriolis force acting on the diverging flow in the emerging flux tube. However, in addition to this east-west expansion about the apex of the loop, each of its legs must expand continually in cross section during its rise through the convection zone, thereby acquiring a further twist through the Coriolis force. Since this transverse pressure effect is not limited by drag or tension forces, the final twist depends mainly on the rise time, and may be large enough to explain the observed active-region helicity.« less

Predicted stem-loop structures and variation in nucleotide sequence of 3' noncoding regions among animal calicivirus genomes.

PubMed

Seal, B S; Neill, J D; Ridpath, J F

1994-07-01

Caliciviruses are nonenveloped with a polyadenylated genome of approximately 7.6 kb and a single capsid protein. The "RNA Fold" computer program was used to analyze 3'-terminal noncoding sequences of five feline calicivirus (FCV), rabbit hemorrhagic disease virus (RHDV), and two San Miguel sea lion virus (SMSV) isolates. The FCV 3'-terminal sequences are 40-46 nucleotides in length and 72-91% similar. The FCV sequences were predicted to contain two possible duplex structures and one stem-loop structure with free energies of -2.1 to -18.2 kcal/mole. The RHDV genomic 3'-terminal RNA sequences are 54 nucleotides in length and share 49% sequence similarity to homologous regions of the FCV genome. The RHDV sequence was predicted to form two duplex structures in the 3'-terminal noncoding region with a single stem-loop structure, resembling that of FCV. In contrast, the SMSV 1 and 4 genomic 3'-terminal noncoding sequences were 185 and 182 nucleotides in length, respectively. Ten possible duplex structures were predicted with an average structural free energy of -35 kcal/mole. Sequence similarity between the two SMSV isolates was 75%. Furthermore, extensive cloverleaflike structures are predicted in the 3' noncoding region of the SMSV genome, in contrast to the predicted single stem-loop structures of FCV or RHDV.

Far UV Observations of Interstellar Shocks

NASA Technical Reports Server (NTRS)

Raymond, John C.

1998-01-01

This grant covered analysis of Hopkins Ultraviolet Telescope data from the Astro-2 mission. The proposed research was aimed primarily at SNR shock waves, but the ASTRO-2 GO program was intended to make the GOs part of the instrument teams. The grant therefore covered extensive travel to Marshall Space Flight Center for mission simulations and the mission itself. In keeping with the unique nature of the ASTRO-2 GO program, I participated actively in the instrument team's investigations of HH objects and cataclysmic variables. Over the course of the Astro-2 mission, we obtained good observations of the supernova remnants SN1006 (1 position), Vela (3 positions), the Cygnus Loop (7 positions) and 0519-69 in the LMC (1 position) as part of this GI program, along with Puppis A (1 position), Vela (1 position), the Cygnus Loop (7 positions) and the Schweizer- Middleditch star (HUT PI program on SNRS). We also observed the Herbig-Haro object HH2 and about a dozen cataclysmic variables, including magnetic systems and dwarf novae. This GI grant covered modest travel for data analysis. We anticipate submitting papers on the non-radiative shock in northern Cygnus Loop, on the LMC Balmer-dominated remnant LMC 0519-69, on the radiative shocks in the Eastern Cygnus Loop (the XA region), and on the cataclysmic variable YZ Cnc over the course of the coming year. We have obtained extensive supporting data from ground-based telescopes for the Cygnus Loop spectra.

Manipulation of the extrastriate frontal loop can resolve visual disability in blindsight patients.

PubMed

Badgaiyan, Rajendra D

2012-12-01

Patients with blindsight are not consciously aware of visual stimuli in the affected field of vision but retain nonconscious perception. This disability can be resolved if nonconsciously perceived information can be brought to their conscious awareness. It can be accomplished by manipulating neural network of visual awareness. To understand this network, we studied the pattern of cortical activity elicited during processing of visual stimuli with or without conscious awareness. The analysis indicated that a re-entrant signaling loop between the area V3A (located in the extrastriate cortex) and the frontal cortex is critical for processing conscious awareness. The loop is activated by visual signals relayed in the primary visual cortex, which is damaged in blindsight patients. Because of the damage, V3A-frontal loop is not activated and the signals are not processed for conscious awareness. These patients however continue to receive visual signals through the lateral geniculate nucleus. Since these signals do not activate the V3A-frontal loop, the stimuli are not consciously perceived. If visual input from the lateral geniculate nucleus is appropriately manipulated and made to activate the V3A-frontal loop, blindsight patients can regain conscious vision. Published by Elsevier Ltd.

Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum.

PubMed

Borisova, Anna S; Eneyskaya, Elena V; Jana, Suvamay; Badino, Silke F; Kari, Jeppe; Amore, Antonella; Karlsson, Magnus; Hansson, Henrik; Sandgren, Mats; Himmel, Michael E; Westh, Peter; Payne, Christina M; Kulminskaya, Anna A; Ståhlberg, Jerry

2018-01-01

The ascomycete fungus Trichoderma reesei is the predominant source of enzymes for industrial conversion of lignocellulose. Its glycoside hydrolase family 7 cellobiohydrolase (GH7 CBH) Tre Cel7A constitutes nearly half of the enzyme cocktail by weight and is the major workhorse in the cellulose hydrolysis process. The orthologs from Trichoderma atroviride ( Tat Cel7A) and Trichoderma harzianum ( Tha Cel7A) show high sequence identity with Tre Cel7A, ~ 80%, and represent naturally evolved combinations of cellulose-binding tunnel-enclosing loop motifs, which have been suggested to influence intrinsic cellobiohydrolase properties, such as endo-initiation, processivity, and off-rate. The Tat Cel7A, Tha Cel7A, and Tre Cel7A enzymes were characterized for comparison of function. The catalytic domain of Tat Cel7A was crystallized, and two structures were determined: without ligand and with thio-cellotriose in the active site. Initial hydrolysis of bacterial cellulose was faster with Tat Cel7A than either Tha Cel7A or Tre Cel7A. In synergistic saccharification of pretreated corn stover, both Tat Cel7A and Tha Cel7A were more efficient than Tre Cel7A, although Tat Cel7A was more sensitive to thermal inactivation. Structural analyses and molecular dynamics (MD) simulations were performed to elucidate important structure/function correlations. Moreover, reverse conservation analysis (RCA) of sequence diversity revealed divergent regions of interest located outside the cellulose-binding tunnel of Trichoderma spp. GH7 CBHs. We hypothesize that the combination of loop motifs is the main determinant for the observed differences in Cel7A activity on cellulosic substrates. Fine-tuning of the loop flexibility appears to be an important evolutionary target in Trichoderma spp., a conclusion supported by the RCA data. Our results indicate that, for industrial use, it would be beneficial to combine loop motifs from Tat Cel7A with the thermostability features of Tre Cel7A. Furthermore, one region implicated in thermal unfolding is suggested as a primary target for protein engineering.

Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum

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

Borisova, Anna S.; Eneyskaya, Elena V.; Jana, Suvamay

The ascomycete fungus Trichoderma reesei is the predominant source of enzymes for industrial conversion of lignocellulose. Its glycoside hydrolase family 7 cellobiohydrolase (GH7 CBH) TreCel7A constitutes nearly half of the enzyme cocktail by weight and is the major workhorse in the cellulose hydrolysis process. The orthologs from Trichoderma atroviride (TatCel7A) and Trichoderma harzianum (ThaCel7A) show high sequence identity with TreCel7A, ~ 80%, and represent naturally evolved combinations of cellulose-binding tunnel-enclosing loop motifs, which have been suggested to influence intrinsic cellobiohydrolase properties, such as endo-initiation, processivity, and off-rate. The TatCel7A, ThaCel7A, and TreCel7A enzymes were characterized for comparison of function. Themore » catalytic domain of TatCel7A was crystallized, and two structures were determined: without ligand and with thio-cellotriose in the active site. Initial hydrolysis of bacterial cellulose was faster with TatCel7A than either ThaCel7A or TreCel7A. In synergistic saccharification of pretreated corn stover, both TatCel7A and ThaCel7A were more efficient than TreCel7A, although TatCel7A was more sensitive to thermal inactivation. Structural analyses and molecular dynamics (MD) simulations were performed to elucidate important structure/function correlations. Moreover, reverse conservation analysis (RCA) of sequence diversity revealed divergent regions of interest located outside the cellulose-binding tunnel of Trichoderma spp. GH7 CBHs. We hypothesize that the combination of loop motifs is the main determinant for the observed differences in Cel7A activity on cellulosic substrates. Fine-tuning of the loop flexibility appears to be an important evolutionary target in Trichoderma spp., a conclusion supported by the RCA data. Our results indicate that, for industrial use, it would be beneficial to combine loop motifs from TatCel7A with the thermostability features of TreCel7A. Furthermore, one region implicated in thermal unfolding is suggested as a primary target for protein engineering.« less

Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum

DOE PAGES

Borisova, Anna S.; Eneyskaya, Elena V.; Jana, Suvamay; ...

2018-01-13

The ascomycete fungus Trichoderma reesei is the predominant source of enzymes for industrial conversion of lignocellulose. Its glycoside hydrolase family 7 cellobiohydrolase (GH7 CBH) TreCel7A constitutes nearly half of the enzyme cocktail by weight and is the major workhorse in the cellulose hydrolysis process. The orthologs from Trichoderma atroviride (TatCel7A) and Trichoderma harzianum (ThaCel7A) show high sequence identity with TreCel7A, ~ 80%, and represent naturally evolved combinations of cellulose-binding tunnel-enclosing loop motifs, which have been suggested to influence intrinsic cellobiohydrolase properties, such as endo-initiation, processivity, and off-rate. The TatCel7A, ThaCel7A, and TreCel7A enzymes were characterized for comparison of function. Themore » catalytic domain of TatCel7A was crystallized, and two structures were determined: without ligand and with thio-cellotriose in the active site. Initial hydrolysis of bacterial cellulose was faster with TatCel7A than either ThaCel7A or TreCel7A. In synergistic saccharification of pretreated corn stover, both TatCel7A and ThaCel7A were more efficient than TreCel7A, although TatCel7A was more sensitive to thermal inactivation. Structural analyses and molecular dynamics (MD) simulations were performed to elucidate important structure/function correlations. Moreover, reverse conservation analysis (RCA) of sequence diversity revealed divergent regions of interest located outside the cellulose-binding tunnel of Trichoderma spp. GH7 CBHs. We hypothesize that the combination of loop motifs is the main determinant for the observed differences in Cel7A activity on cellulosic substrates. Fine-tuning of the loop flexibility appears to be an important evolutionary target in Trichoderma spp., a conclusion supported by the RCA data. Our results indicate that, for industrial use, it would be beneficial to combine loop motifs from TatCel7A with the thermostability features of TreCel7A. Furthermore, one region implicated in thermal unfolding is suggested as a primary target for protein engineering.« less

Maternal Betaine Supplementation during Gestation Enhances Expression of mtDNA-Encoded Genes through D-Loop DNA Hypomethylation in the Skeletal Muscle of Newborn Piglets.

PubMed

Jia, Yimin; Song, Haogang; Gao, Guichao; Cai, Demin; Yang, Xiaojing; Zhao, Ruqian

2015-11-25

Betaine has been widely used in animal and human nutrition to promote muscle growth and performance, yet it remains unknown whether maternal betaine supplementation during gestation affects the metabolic characteristics of neonatal skeletal muscles. In the present study, feeding sows with betaine-supplemented diets throughout gestation significantly upregulated the expression of mtDNA-encoded OXPHOS genes (p < 0.05), including COX1, COX2, and ND5, in the muscle of newborn piglets, which was associated with enhanced mitochondrial COX enzyme activity (p < 0.05). Concurrently, maternal betaine supplementation increased the plasma betaine concentration and muscle expression of methyl transfer enzymes (p < 0.05), BHMT and GNMT, in offspring piglets. Nevertheless, Dnmt3a was downregulated at the level of both mRNA and protein, which was associated with a hypomethylated mtDNA D-loop region (p < 0.05). These results suggest that maternal betaine supplementation during gestation enhances expression of mtDNA-encoded genes through D-loop DNA hypomethylation in the skeletal muscle of newborn piglets.

3D Studies of the Solar Corona and its Evolution with SOHO/EIT

NASA Astrophysics Data System (ADS)

Portier-Fozzani, F.

This thesis deals with 3D evolution of coronal structures based upon the ultraviolet telescope of SOHO : EIT. Anaglyphs and incertainties on a complete stereovision reconstruction are described. Stereoscopic methods for loop reconstruction were successfully made to find 3D parameters. With dynamical stereoscopy, physical conditions were derived for 30 loops of temperature around 1MK. A method which is able to derive twist variation were also built. Emerging loops were found highly twisted and they detwist as they grow. According to helicity conservation, this correspond to a transfert of twist into expansion. Long time twist evolution of magnetic flux tubes are followed in relation with flares as relaxation. Interaction between magnetic field lines were analysed. An example of reconnection between open and closed field line were observed. Other interactions were found with multi-wavelength observations : coronal holes borders (and thus CH) are better defined when an active region nearby is growing. Other imaging techniques were used to better take profit as possible of SOHO/EIT. A multiscale vision model (MVM) was applied with success to show small coronal structures evolutions hidden by the noise level.

Conformation Changes, N-terminal Involvement, and cGMP Signal Relay in the Phosphodiesterase-5 GAF Domain*

PubMed Central

Wang, Huanchen; Robinson, Howard; Ke, Hengming

2010-01-01

The activity of phosphodiesterase-5 (PDE5) is specific for cGMP and is regulated by cGMP binding to GAF-A in its regulatory domain. To better understand the regulatory mechanism, x-ray crystallographic and biochemical studies were performed on constructs of human PDE5A1 containing the N-terminal phosphorylation segment, GAF-A, and GAF-B. Superposition of this unliganded GAF-A with the previously reported NMR structure of cGMP-bound PDE5 revealed dramatic conformational differences and suggested that helix H4 and strand B3 probably serve as two lids to gate the cGMP-binding pocket in GAF-A. The structure also identified an interfacial region among GAF-A, GAF-B, and the N-terminal loop, which may serve as a relay of the cGMP signal from GAF-A to GAF-B. N-terminal loop 98–147 was physically associated with GAF-B domains of the dimer. Biochemical analyses showed an inhibitory effect of this loop on cGMP binding and its involvement in the cGMP-induced conformation changes. PMID:20861010

Closed-loop separation control over a sharp edge ramp using genetic programming

NASA Astrophysics Data System (ADS)

Debien, Antoine; von Krbek, Kai A. F. F.; Mazellier, Nicolas; Duriez, Thomas; Cordier, Laurent; Noack, Bernd R.; Abel, Markus W.; Kourta, Azeddine

2016-03-01

We experimentally perform open and closed-loop control of a separating turbulent boundary layer downstream from a sharp edge ramp. The turbulent boundary layer just above the separation point has a Reynolds number Re_{θ }≈ 3500 based on momentum thickness. The goal of the control is to mitigate separation and early re-attachment. The forcing employs a spanwise array of active vortex generators. The flow state is monitored with skin-friction sensors downstream of the actuators. The feedback control law is obtained using model-free genetic programming control (GPC) (Gautier et al. in J Fluid Mech 770:442-457, 2015). The resulting flow is assessed using the momentum coefficient, pressure distribution and skin friction over the ramp and stereo PIV. The PIV yields vector field statistics, e.g. shear layer growth, the back-flow area and vortex region. GPC is benchmarked against the best periodic forcing. While open-loop control achieves separation reduction by locking-on the shedding mode, GPC gives rise to similar benefits by accelerating the shear layer growth. Moreover, GPC uses less actuation energy.

20-Hydroxyecdysone (20E) Primary Response Gene E75 Isoforms Mediate Steroidogenesis Autoregulation and Regulate Developmental Timing in Bombyx*

PubMed Central

Li, Kang; Tian, Ling; Guo, Zhongjian; Guo, Sanyou; Zhang, Jianzhen; Gu, Shi-Hong; Palli, Subba R.; Cao, Yang; Li, Sheng

2016-01-01

The temporal control mechanisms that precisely control animal development remain largely elusive. The timing of major developmental transitions in insects, including molting and metamorphosis, is coordinated by the steroid hormone 20-hydroxyecdysone (20E). 20E involves feedback loops to maintain pulses of ecdysteroid biosynthesis leading to its upsurge, whereas the underpinning molecular mechanisms are not well understood. Using the silkworm Bombyx mori as a model, we demonstrated that E75, the 20E primary response gene, mediates a regulatory loop between ecdysteroid biosynthesis and 20E signaling. E75 isoforms A and C directly bind to retinoic acid receptor-related response elements in Halloween gene promoter regions to induce gene expression thus promoting ecdysteroid biosynthesis and developmental transition, whereas isoform B antagonizes the transcriptional activity of isoform A/C through physical interaction. As the expression of E75 isoforms is differentially induced by 20E, the E75-mediated regulatory loop represents a fine autoregulation of steroidogenesis, which contributes to the precise control of developmental timing. PMID:27365399

Conformation changes, N-terminal involvement and cGMP signal relay in phosphodiesterase-5 GAF domain

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

Wang, H.; Robinson, H.; Ke, H.

2010-12-03

The activity of phosphodiesterase-5 (PDE5) is specific for cGMP and is regulated by cGMP binding to GAF-A in its regulatory domain. To better understand the regulatory mechanism, x-ray crystallographic and biochemical studies were performed on constructs of human PDE5A1 containing the N-terminal phosphorylation segment, GAF-A, and GAF-B. Superposition of this unliganded GAF-A with the previously reported NMR structure of cGMP-bound PDE5 revealed dramatic conformational differences and suggested that helix H4 and strand B3 probably serve as two lids to gate the cGMP-binding pocket in GAF-A. The structure also identified an interfacial region among GAF-A, GAF-B, and the N-terminal loop, whichmore » may serve as a relay of the cGMP signal from GAF-A to GAF-B. N-terminal loop 98-147 was physically associated with GAF-B domains of the dimer. Biochemical analyses showed an inhibitory effect of this loop on cGMP binding and its involvement in the cGMP-induced conformation changes.« less

Conformation Changes N-terminal Involvement and cGMP Signal Relay in the Phosphodiesterase-5 GAF Domain

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

H Wang; H Robinson; H Ke

2011-12-31

The activity of phosphodiesterase-5 (PDE5) is specific for cGMP and is regulated by cGMP binding to GAF-A in its regulatory domain. To better understand the regulatory mechanism, x-ray crystallographic and biochemical studies were performed on constructs of human PDE5A1 containing the N-terminal phosphorylation segment, GAF-A, and GAF-B. Superposition of this unliganded GAF-A with the previously reported NMR structure of cGMP-bound PDE5 revealed dramatic conformational differences and suggested that helix H4 and strand B3 probably serve as two lids to gate the cGMP-binding pocket in GAF-A. The structure also identified an interfacial region among GAF-A, GAF-B, and the N-terminal loop, whichmore » may serve as a relay of the cGMP signal from GAF-A to GAF-B. N-terminal loop 98-147 was physically associated with GAF-B domains of the dimer. Biochemical analyses showed an inhibitory effect of this loop on cGMP binding and its involvement in the cGMP-induced conformation changes.« less

LOOP: Linking Outcomes to Organizational Planning, First Quarterly Report: 25 School Board Priorities.

ERIC Educational Resources Information Center

Ligon, Glynn; Wicker, Maria L. R.

The Austin Independent School District Superintendent of Schools required a process for monitoring district activities. The Office of Research and Evaluation developed LOOP (Linking Outcomes to Organizational Planning). LOOP is a management information system through which progress in a number of activities within the school system may be…

An Anomalous Composition in Slow Solar Wind as a Signature of Magnetic Reconnection in its Source Region

NASA Astrophysics Data System (ADS)

Zhao, L.; Landi, E.; Lepri, S. T.; Kocher, M.; Zurbuchen, T. H.; Fisk, L. A.; Raines, J. M.

2017-01-01

In this paper, we study a subset of slow solar winds characterized by an anomalous charge state composition and ion temperatures compared to average solar wind distributions, and thus referred to as an “Outlier” wind. We find that although this wind is slower and denser than normal slow wind, it is accelerated from the same source regions (active regions and quiet-Sun regions) as the latter and its occurrence rate depends on the solar cycle. The defining property of the Outlier wind is that its charge state composition is the same as that of normal slow wind, with the only exception being a very large decrease in the abundance of fully charged species (He2+, C6+, N7+, O8+, Mg12+), resulting in a significant depletion of the He and C element abundances. Based on these observations, we suggest three possible scenarios for the origin of this wind: (1) local magnetic waves preferentially accelerating non-fully stripped ions over fully stripped ions from a loop opened by reconnection; (2) depleted fully stripped ions already contained in the corona magnetic loops before they are opened up by reconnection; or (3) fully stripped ions depleted by Coulomb collision after magnetic reconnection in the solar corona. If any one of these three scenarios is confirmed, the Outlier wind represents a direct signature of slow wind release through magnetic reconnection.

Structure-function analyses of human kallikrein-related peptidase 2 establish the 99-loop as master regulator of activity.

PubMed

Skala, Wolfgang; Utzschneider, Daniel T; Magdolen, Viktor; Debela, Mekdes; Guo, Shihui; Craik, Charles S; Brandstetter, Hans; Goettig, Peter

2014-12-05

Human kallikrein-related peptidase 2 (KLK2) is a tryptic serine protease predominantly expressed in prostatic tissue and secreted into prostatic fluid, a major component of seminal fluid. Most likely it activates and complements chymotryptic KLK3 (prostate-specific antigen) in cleaving seminal clotting proteins, resulting in sperm liquefaction. KLK2 belongs to the "classical" KLKs 1-3, which share an extended 99- or kallikrein loop near their non-primed substrate binding site. Here, we report the 1.9 Å crystal structures of two KLK2-small molecule inhibitor complexes. In both structures discontinuous electron density for the 99-loop indicates that this loop is largely disordered. We provide evidence that the 99-loop is responsible for two biochemical peculiarities of KLK2, i.e. reversible inhibition by micromolar Zn(2+) concentrations and permanent inactivation by autocatalytic cleavage. Indeed, several 99-loop mutants of KLK2 displayed an altered susceptibility to Zn(2+), which located the Zn(2+) binding site at the 99-loop/active site interface. In addition, we identified an autolysis site between residues 95e and 95f in the 99-loop, whose elimination prevented the mature enzyme from limited autolysis and irreversible inactivation. An exhaustive comparison of KLK2 with related structures revealed that in the KLK family the 99-, 148-, and 220-loop exist in open and closed conformations, allowing or preventing substrate access, which extends the concept of conformational selection in trypsin-related proteases. Taken together, our novel biochemical and structural data on KLK2 identify its 99-loop as a key player in activity regulation. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Structure-Function Analyses of Human Kallikrein-related Peptidase 2 Establish the 99-Loop as Master Regulator of Activity*

PubMed Central

Skala, Wolfgang; Utzschneider, Daniel T.; Magdolen, Viktor; Debela, Mekdes; Guo, Shihui; Craik, Charles S.; Brandstetter, Hans; Goettig, Peter

2014-01-01

Human kallikrein-related peptidase 2 (KLK2) is a tryptic serine protease predominantly expressed in prostatic tissue and secreted into prostatic fluid, a major component of seminal fluid. Most likely it activates and complements chymotryptic KLK3 (prostate-specific antigen) in cleaving seminal clotting proteins, resulting in sperm liquefaction. KLK2 belongs to the “classical” KLKs 1–3, which share an extended 99- or kallikrein loop near their non-primed substrate binding site. Here, we report the 1.9 Å crystal structures of two KLK2-small molecule inhibitor complexes. In both structures discontinuous electron density for the 99-loop indicates that this loop is largely disordered. We provide evidence that the 99-loop is responsible for two biochemical peculiarities of KLK2, i.e. reversible inhibition by micromolar Zn2+ concentrations and permanent inactivation by autocatalytic cleavage. Indeed, several 99-loop mutants of KLK2 displayed an altered susceptibility to Zn2+, which located the Zn2+ binding site at the 99-loop/active site interface. In addition, we identified an autolysis site between residues 95e and 95f in the 99-loop, whose elimination prevented the mature enzyme from limited autolysis and irreversible inactivation. An exhaustive comparison of KLK2 with related structures revealed that in the KLK family the 99-, 148-, and 220-loop exist in open and closed conformations, allowing or preventing substrate access, which extends the concept of conformational selection in trypsin-related proteases. Taken together, our novel biochemical and structural data on KLK2 identify its 99-loop as a key player in activity regulation. PMID:25326387

Chimeric Proton-Pumping Rhodopsins Containing the Cytoplasmic Loop of Bovine Rhodopsin

PubMed Central

Sasaki, Kengo; Yamashita, Takahiro; Yoshida, Kazuho; Inoue, Keiichi; Shichida, Yoshinori; Kandori, Hideki

2014-01-01

G-protein-coupled receptors (GPCRs) transmit stimuli to intracellular signaling systems. Rhodopsin (Rh), which is a prototypical GPCR, possesses an 11-cis retinal. Photoisomerization of 11-cis to all-trans leads to structural changes in the protein of cytoplasmic loops, activating G-protein. Microbial rhodopsins are similar heptahelical membrane proteins that function as bacterial sensors, light-driven ion-pumps, or light-gated channels. They possess an all-trans retinal, and photoisomerization to 13-cis triggers structural changes in protein. Despite these similarities, there is no sequence homology between visual and microbial rhodopsins, and microbial rhodopsins do not activate G-proteins. In this study, new chimeric proton-pumping rhodopsins, proteorhodopsin (PR) and Gloeobacter rhodopsin (GR) were designed by replacing cytoplasmic loops with bovine Rh loops. Although G-protein was not activated by the PR chimeras, all 12 GR chimeras activated G-protein. The GR chimera containing the second cytoplasmic loop of bovine Rh did not activate G-protein. However, the chimera with a second and third double-loop further enhanced G-protein activation. Introduction of an E132Q mutation slowed the photocycle 30-fold and enhanced activation. The highest catalytic activity of the GR chimera was still 3,200 times lower than bovine Rh but only 64 times lower than amphioxus Go-rhodopsin. This GR chimera showed a strong absorption change of the amide-I band on a light-minus-dark difference FTIR spectrum which could represent a larger helical opening, important for G-protein activation. The light-dependent catalytic activity of this GR chimera makes it a potential optogenetic tool for enzymatic activation by light. PMID:24621599

The architecture of the spliceosomal U4/U6.U5 tri-snRNP

PubMed Central

Nguyen, Thi Hoang Duong; Galej, Wojciech P.; Bai, Xiao-chen; Savva, Christos G.; Newman, Andrew J.; Scheres, Sjors H. W.; Nagai, Kiyoshi

2015-01-01

U4/U6.U5 tri-snRNP is a 1.5 MDa pre-assembled spliceosomal complex comprising U5 snRNA, extensively base-paired U4/U6 snRNAs and >30 proteins, including the key components Prp8, Brr2 and Snu114. The tri-snRNP combines with a pre-mRNA substrate bound to U1 and U2 snRNPs and transforms into a catalytically active spliceosome following extensive compositional and conformational changes triggered by unwinding of the U4/U6 snRNAs. CryoEM single-particle reconstruction of yeast tri-snRNP at 5.9Å resolution reveals the essentially complete organization of its RNA and protein components. The single-stranded region of U4 snRNA between its 3′-stem-loop and the U4/U6 snRNA stem I is loaded into the Brr2 helicase active site ready for unwinding. Snu114 and the N-terminal domain of Prp8 position U5 snRNA to insert its Loop I, which aligns the exons for splicing, into the Prp8 active site cavity. The structure provides crucial insights into the activation process and the active site of the spliceosome. PMID:26106855

Evidence and age-related distribution of mtDNA D-loop point mutations in skeletal muscle from healthy subjects and mitochondrial patients.

PubMed

Del Bo, Roberto; Bordoni, Andreina; Martinelli Boneschi, Filippo; Crimi, Marco; Sciacco, Monica; Bresolin, Nereo; Scarlato, Guglielmo; Comi, Giacomo Pietri

2002-10-15

The progressive accumulation of mitochondrial DNA (mtDNA) alterations, ranging from single mutations to large-scale deletions, in both the normal ageing process and pathological conditions is a relevant phenomenon in terms of frequency and heteroplasmic degree. Recently, two point mutations (A189G and T408A) within the Displacement loop (D-loop) region, the control region for mtDNA replication, were shown to occur in skeletal muscles from aged individuals. We evaluated the presence and the heteroplasmy levels of these two mutations in muscle biopsies from 91 unrelated individuals of different ages (21 healthy subjects and 70 patients affected by mitochondrial encephalomyopathies). Overall, both mutations significantly accumulate with age. However, a different relationship was discovered among the different subgroups of patients: a higher number of A189G positive subjects younger than 53 years was detected in the subgroup of multiple-deleted patients; furthermore, a trend towards an increased risk for the mutations was evidenced among patients carrying multiple deletions when compared to healthy controls. These findings support the idea that a common biological mechanism determines the accumulation of somatic point mutations in the D-loop region, both in healthy subjects and in mitochondrial myopathy patients. At the same time, it appears that disorders caused by mutations of nuclear genes controlling mtDNA replication (the "mtDNA multiple deletions" syndromes) present a temporal advantage to mutate in the D-loop region. This observation may be relevant to the definition of the molecular pathogenesis of these latter syndromes. Copyright 2002 Elsevier Science B.V.

Engineering a hyper-catalytic enzyme by photo-activated conformation modulation

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

Agarwal, Pratul K

2012-01-01

Enzyme engineering for improved catalysis has wide implications. We describe a novel chemical modification of Candida antarctica lipase B that allows modulation of the enzyme conformation to promote catalysis. Computational modeling was used to identify dynamical enzyme regions that impact the catalytic mechanism. Surface loop regions located distal to active site but showing dynamical coupling to the reaction were connected by a chemical bridge between Lys136 and Pro192, containing a derivative of azobenzene. The conformational modulation of the enzyme was achieved using two sources of light that alternated the azobenzene moiety in cis and trans conformations. Computational model predicted thatmore » mechanical energy from the conformational fluctuations facilitate the reaction in the active-site. The results were consistent with predictions as the activity of the engineered enzyme was found to be enhanced with photoactivation. Preliminary estimations indicate that the engineered enzyme achieved 8-52 fold better catalytic activity than the unmodulated enzyme.« less

Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin.

PubMed

Peacock, Riley B; Davis, Jessie R; Markwick, Phineus R L; Komives, Elizabeth A

2018-05-08

Thrombin normally cleaves fibrinogen to promote coagulation; however, binding of thrombomodulin to thrombin switches the specificity of thrombin toward protein C, triggering the anticoagulation pathway. The W215A thrombin mutant was reported to have decreased activity toward fibrinogen without significant loss of activity toward protein C. To understand how mutation of Trp215 may alter thrombin specificity, hydrogen-deuterium exchange experiments (HDXMS), accelerated molecular dynamics (AMD) simulations, and activity assays were carried out to compare the dynamics of Trp215 mutants with those of wild type (WT) thrombin. Variation in NaCl concentration had no detectable effect on the sodium-binding (220s CT ) loop, but appeared to affect other surface loops. Trp215 mutants showed significant increases in amide exchange in the 170s CT loop consistent with a loss of H-bonding in this loop identified by the AMD simulations. The W215A thrombin showed increased amide exchange in the 220s CT loop and in the N-terminus of the heavy chain. The AMD simulations showed that a transient conformation of the W215A thrombin has a distorted catalytic triad. HDXMS experiments revealed that mutation of Phe227, which engages in a π-stacking interaction with Trp215, also caused significantly increased amide exchange in the 170s CT loop. Activity assays showed that only the F227V mutant had wild type catalytic activity, whereas all other mutants showed markedly lower activity. Taken together, the results explain the reduced pro-coagulant activity of the W215A mutant and demonstrate the allosteric connection between Trp215, the sodium-binding loop, and the active site.

Usage of mitochondrial D-loop variation to predict risk for Huntington disease.

PubMed

Mousavizadeh, Kazem; Rajabi, Peyman; Alaee, Mahsa; Dadgar, Sepideh; Houshmand, Massoud

2015-08-01

Huntington's disease (HD) is an inherited autosomal neurodegenerative disease caused by the abnormal expansion of the CAG repeats in the Huntingtin (Htt) gene. It has been proven that mitochondrial dysfunction is contributed to the pathogenesis of Huntington's disease. The mitochondrial displacement loop (D-loop) is proven to accumulate mutations at a higher rate than other regions of mtDNA. Thus, we hypothesized that specific SNPs in the D-loop may contribute to the pathogenesis of Huntington's disease. In the present study, 30 patients with Huntington's disease and 463 healthy controls were evaluated for mitochondrial mutation sites within the D-loop region using PCR-sequencing method. Sequence analysis revealed 35 variations in HD group from Cambridge Mitochondrial Sequences. A significant difference (p < 0.05) was seen between patients and control group in eight SNPs. Polymorphisms at C16069T, T16126C, T16189C, T16519C and C16223T were correlated with an increased risk of HD while SNPs at C16150T, T16086C and T16195C were associated with a decreased risk of Huntington's disease.

Limit cycles in piecewise-affine gene network models with multiple interaction loops

NASA Astrophysics Data System (ADS)

Farcot, Etienne; Gouzé, Jean-Luc

2010-01-01

In this article, we consider piecewise affine differential equations modelling gene networks. We work with arbitrary decay rates, and under a local hypothesis expressed as an alignment condition of successive focal points. The interaction graph of the system may be rather complex (multiple intricate loops of any sign, multiple thresholds, etc.). Our main result is an alternative theorem showing that if a sequence of region is periodically visited by trajectories, then under our hypotheses, there exists either a unique stable periodic solution, or the origin attracts all trajectories in this sequence of regions. This result extends greatly our previous work on a single negative feedback loop. We give several examples and simulations illustrating different cases.

Evidence that the X-Ray Plasma in Microflares is in a Sequence of Subresolution Magnetic Tubes

NASA Technical Reports Server (NTRS)

Moore, Ronald L.; Falconer, D. A.; Porter, Jason G.

1998-01-01

We analyze the cooling of the X-ray emitting thermal plasma in microflares observed in active regions by the Yohkoh Soft X-ray Telescope. A typical microflare appears to be a transient brightening of an entire small magnetic loop, often having a diameter near the limit of resolution (approximately 2 x 10(exp 8) cm) (Shimizu 1995, PASJ, 47, 251). The X-ray plasma in the loop cools by emission of XUV radiation and by heat conduction to the cooler plasma at the feet of the loop. The cooling rate is determined by the plasma temperature and density and the loop length. The plasma density is determined from the observed X-ray brightness of the loop in combination with the temperature, the loop diameter, and the filling factor. The filling factor is the volume fraction of the loop occupied by the subset of magnetic tubes that is filled by the X-ray plasma and that contains practically all of the X-ray plasma present in the microflare loop. Taking typical values from the hundreds of microflares measured by Shimizu (1995) (X-ray brightness through the thin aluminum filter approximately 4 x 10(exp 3) DN/s/pixel, lifetime approximately 5 min, temperature approximately 6 x 10(exp 6) K, loop length approximately 10(exp 9) cm, loop diameter approximately 3 x 10(exp 8) cm), we find that for filling factors greater than approximately 1% (1) the cooling time is much shorter than the duration of the microflare, and (2) conductive cooling strongly dominates over radiative cooling. Because the cooling time is so short and because the conductive heat flux goes mainly into increasing the plasma density via chromospheric evaporation, we are compelled to conclude that (1) heating to X-ray temperatures continues through nearly the entire life of a microflare, (2) the heating keeps changing to different field lines, so that any one magnetic tube in the sequence of heated tubes emits X-rays only briefly in the life of the microflare, and (3) at any instant during the microflare the tubes filled with X-ray plasma occupy only a small fraction (less than approximately 10%) of the microflare loop. Hence, we expect that coronal X-ray images with spatial resolution 2-3 times better than from Yohkoh will show plenty of rapidly changing filamentary substructure in microflares.

An extreme ultraviolet wave associated with a failed eruption observed by the Solar Dynamics Observatory

NASA Astrophysics Data System (ADS)

Zheng, R.; Jiang, Y.; Yang, J.; Bi, Y.; Hong, J.; Yang, B.; Yang, D.

2012-05-01

Aims: Taking advantage of the high temporal and spatial resolution of the Solar Dynamics Observatory (SDO) observations, we present an extreme ultraviolet (EUV) wave associated with a failed filament eruption that generated no coronal mass ejection (CME) on 2011 March 1. We aim at understanding the nature and origin of this EUV wave. Methods: Combining the high-quality observations in the photosphere, the chromosphere, and the corona, we studied the characteristics of the wave and its relations to the associated eruption. Results: The event occurred at an ephemeral region near a small active region. The continuous magnetic flux cancelation in the ephemeral region produced pre-eruption brightenings and two EUV jets, and excited the filament eruption, accompanying it with a microflare. After the eruption, the filament material appeared far from the eruption center, and the ambient loops seemed to be intact. It was evident that the filament eruption had failed and was not associated with a CME. The wave happened just after the north jet arrived, and apparently emanated ahead of the north jet, far from the eruption center. The wave propagated at nearly constant velocities in the range of 260-350 km s-1, with a slight negative acceleration in the last phase. Remarkably, the wave continued to propagate, and a loop in its passage was intact when wave and loop met. Conclusions: Our analysis confirms that the EUV wave is a true wave, which we interpret as a fast-mode wave. In addition, the close temporal and spatial relationship between the wave and the jet provides evidence that the wave was likely triggered by the jet when the CME failed to happen. Three movies are available in electronic form at http://www.aanda.org

Second-order electron self-energy loop-after-loop correction for low- Z hydrogen-like ions

NASA Astrophysics Data System (ADS)

Goidenko, Igor; Labzowsky, Leonti; Plunien, Günter; Soff, Gerhard

2005-07-01

The second-order electron self-energy loop-after-loop correction is investigated for hydrogen-like ions in the region of low nuclear charge numbers Z. Both irreducible and reducible parts of this correction are evaluated for the 1s1/2-state within the Fried-Yennie gauge. We confirm the result obtained first by Mallampalli and Sapirstein. The reducible part of this correction is evaluated numerically for the first time and it is consistent with the corresponding analytical αZ-expansion.

A media player causes clinically significant telemetry interference with implantable loop recorders.

PubMed

Thaker, Jay P; Patel, Mehul B; Shah, Ashok J; Liepa, Valdis V; Jongnarangsin, Krit; Thakur, Ranjan K

2009-03-01

The implantable loop recorder is a useful diagnostic tool for intermittent cardiovascular symptoms because it can automatically record arrhythmias as well as a patient-triggered ECG. Media players have been shown to cause telemetry interference with pacemakers. Telemetry interference may be important in patients with implantable loop recorders because capturing a patient-triggered ECG requires a telemetry link between a hand-held activator and the implanted device. The purpose of this study was to determine if a media player causes interference with implantable loop recorders. Fourteen patients with implantable loop recorders underwent evaluation for interference with a 15 GB third generation iPod (Apple, Inc.) media player. All patients had the Reveal Plus (Medtronic, Inc.) implantable loop recorder. We tested for telemetry interference on the programmer by first establishing a telemetry link with the loop recorder and then, the media player was placed next to it, first turned off and then, on. We evaluated for telemetry interference between the activator and the implanted device by placing the activator over the device (normal use) and the media player next to it, first turned off and then, on. We made 5 attempts to capture a patient-triggered ECG by depressing the activator switch 5 times while the media player was off or on. Telemetry interference on the programmer screen, consisting of either high frequency spikes or blanking of the ECG channel was seen in all patients. Telemetry interference with the activator resulted in failure to capture an event in 7 patients. In one of these patients, a green indicator light on the activator suggested that a patient-triggered event was captured, but loop recorder interrogation did not show a captured event. In the remaining 7 patients, an event was captured and appropriately recognized by the device at least 1 out of 5 times. A media player playing in close proximity to an implanted loop recorder may interfere with capture of a patient-triggered event. Patients should be advised to keep media players away from their implanted loop recorder.

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

Antolin, P.; Vissers, G.; Shibata, K., E-mail: antolin@astro.uio.n, E-mail: g.j.m.vissers@astro.uio.n, E-mail: shibata@kwasan.kyoto-u.ac.j

Reported observations in H{alpha}, Ca II H, and K or other chromospheric lines of coronal rain trace back to the days of the Skylab mission. Corresponding to cool and dense plasma, coronal rain is often observed falling down along coronal loops in active regions. A physical explanation for this spectacular phenomenon has been put forward thanks to numerical simulations of loops with footpoint-concentrated heating, a heating scenario in which cool condensations naturally form in the corona. This effect has been termed 'catastrophic cooling' and is the predominant explanation for coronal rain. In this work, we further investigate the link betweenmore » this phenomenon and the heating mechanisms acting in the corona. We start by analyzing observations of coronal rain at the limb in the Ca II H line performed by the Hinode satellite, and derive interesting statistical properties concerning the dynamics. We then compare the observations with 1.5-dimensional MHD simulations of loops being heated by small-scale discrete events concentrated toward the footpoints (that could come, for instance, from magnetic reconnection events), and by Alfven waves generated at the photospheric level. Both our observation and simulation results suggest that coronal rain is a far more common phenomenon than previously thought. Also, we show that the structure and dynamics of condensations are far more sensitive to the internal pressure changes in loops than to gravity. Furthermore, it is found that if a loop is predominantly heated from Alfven waves, coronal rain is inhibited due to the characteristic uniform heating they produce. Hence, coronal rain may not only point to the spatial distribution of the heating in coronal loops but also to the agent of the heating itself. We thus propose coronal rain as a marker for coronal heating mechanisms.« less

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.

PubMed

Smith, Emily M; Lajoie, Bryan R; Jain, Gaurav; Dekker, Job

2016-01-07

Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation. Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

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

PubMed

Kumar, Sandeep; Sharma, Deepak; Kumar, Rajesh

2014-03-01

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

Exposure to subliminal arousing stimuli induces robust activation in the amygdala, hippocampus, anterior cingulate, insular cortex and primary visual cortex: a systematic meta-analysis of fMRI studies.

PubMed

Brooks, S J; Savov, V; Allzén, E; Benedict, C; Fredriksson, R; Schiöth, H B

2012-02-01

Functional Magnetic Resonance Imaging (fMRI) demonstrates that the subliminal presentation of arousing stimuli can activate subcortical brain regions independently of consciousness-generating top-down cortical modulation loops. Delineating these processes may elucidate mechanisms for arousal, aberration in which may underlie some psychiatric conditions. Here we are the first to review and discuss four Activation Likelihood Estimation (ALE) meta-analyses of fMRI studies using subliminal paradigms. We find a maximum of 9 out of 12 studies using subliminal presentation of faces contributing to activation of the amygdala, and also a significantly high number of studies reporting activation in the bilateral anterior cingulate, bilateral insular cortex, hippocampus and primary visual cortex. Subliminal faces are the strongest modality, whereas lexical stimuli are the weakest. Meta-analyses independent of studies using Regions of Interest (ROI) revealed no biasing effect. Core neuronal arousal in the brain, which may be at first independent of conscious processing, potentially involves a network incorporating primary visual areas, somatosensory, implicit memory and conflict monitoring regions. These data could provide candidate brain regions for the study of psychiatric disorders associated with aberrant automatic emotional processing. Copyright © 2011 Elsevier Inc. All rights reserved.

Neutron activation analysis system

DOEpatents

Taylor, M.C.; Rhodes, J.R.

1973-12-25

A neutron activation analysis system for monitoring a generally fluid media, such as slurries, solutions, and fluidized powders, including two separate conduit loops for circulating fluid samples within the range of radiation sources and detectors is described. Associated with the first loop is a neutron source that emits s high flux of slow and thermal neutrons. The second loop employs a fast neutron source, the flux from which is substantially free of thermal neutrons. Adjacent to both loops are gamma counters for spectrographic determination of the fluid constituents. Other gsmma sources and detectors are arranged across a portion of each loop for deterMining the fluid density. (Official Gazette)

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

Antolin, P.; Rouppe van der Voort, L., E-mail: patrick.antolin@astro.uio.no, E-mail: v.d.v.l.rouppe@astro.uio.no

Observed in cool chromospheric lines, such as H{alpha} or Ca II H, coronal rain corresponds to cool and dense plasma falling from coronal heights. Considered as a peculiar sporadic phenomenon of active regions, it has not received much attention since its discovery more than 40 years ago. Yet, it has been shown recently that a close relationship exists between this phenomenon and the coronal heating mechanism. Indeed, numerical simulations have shown that this phenomenon is most likely due to a loss of thermal equilibrium ensuing from a heating mechanism acting mostly toward the footpoints of loops. We present here onemore » of the first high-resolution spectroscopic observations of coronal rain, performed with the CRisp Imaging Spectro Polarimeter (CRISP) instrument at the Swedish Solar Telescope. This work constitutes the first attempt to assess the importance of coronal rain in the understanding of the coronal magnetic field in active regions. With the present resolution, coronal rain is observed to literally invade the entire field of view. A large statistical set is obtained in which dynamics (total velocities and accelerations), shapes (lengths and widths), trajectories (angles of fall of the blobs), and thermodynamic properties (temperatures) of the condensations are derived. Specifically, we find that coronal rain is composed of small and dense chromospheric cores with average widths and lengths of {approx}310 km and {approx}710 km, respectively, average temperatures below 7000 K, displaying a broad distribution of falling speeds with an average of {approx}70 km s{sup -1}, and accelerations largely below the effective gravity along loops. Through estimates of the ion-neutral coupling in the blobs we show that coronal rain acts as a tracer of the coronal magnetic field, thus supporting the multi-strand loop scenario, and acts as a probe of the local thermodynamic conditions in loops. We further elucidate its potential in coronal heating. We find that the cooling in neighboring strands occurs simultaneously in general suggesting a similar thermodynamic evolution among strands, which can be explained by a common footpoint heating process. Constraints for coronal heating models of loops are thus provided. Estimates of the fraction of coronal volume with coronal rain give values between 7% and 30%. Estimates of the occurrence time of the phenomenon in loops set times between 5 and 20 hr, implying that coronal rain may be a common phenomenon, in agreement with the frequent observations of cool downflows in extreme-ultraviolet lines. The coronal mass drain rate in the form of coronal rain is estimated to be on the order of 5 Multiplication-Sign 10{sup 9} g s{sup -1}, a significant quantity compared to the estimate of mass flux into the corona from spicules.« less

DNA–DNA kissing complexes as a new tool for the assembly of DNA nanostructures

PubMed Central

Barth, Anna; Kobbe, Daniela; Focke, Manfred

2016-01-01

Kissing-loop annealing of nucleic acids occurs in nature in several viruses and in prokaryotic replication, among other circumstances. Nucleobases of two nucleic acid strands (loops) interact with each other, although the two strands cannot wrap around each other completely because of the adjacent double-stranded regions (stems). In this study, we exploited DNA kissing-loop interaction for nanotechnological application. We functionalized the vertices of DNA tetrahedrons with DNA stem-loop sequences. The complementary loop sequence design allowed the hybridization of different tetrahedrons via kissing-loop interaction, which might be further exploited for nanotechnology applications like cargo transport and logical elements. Importantly, we were able to manipulate the stability of those kissing-loop complexes based on the choice and concentration of cations, the temperature and the number of complementary loops per tetrahedron either at the same or at different vertices. Moreover, variations in loop sequences allowed the characterization of necessary sequences within the loop as well as additional stability control of the kissing complexes. Therefore, the properties of the presented nanostructures make them an important tool for DNA nanotechnology. PMID:26773051

Structural and mechanistic insights into Mps1 kinase activation.

PubMed

Wang, Wei; Yang, Yuting; Gao, Yuefeng; Xu, Quanbin; Wang, Feng; Zhu, Songcheng; Old, William; Resing, Katheryn; Ahn, Natalie; Lei, Ming; Liu, Xuedong

2009-08-01

Mps1 is one of the several essential kinases whose activation is required for robust mitotic spindle checkpoint signalling. The activity of Mps1 is tightly regulated and increases dramatically during mitosis or in response to spindle damage. To understand the molecular mechanism underlying Mps1 regulation, we determined the crystal structure of the kinase domain of Mps1. The 2.7-A-resolution crystal structure shows that the Mps1 kinase domain adopts a unique inactive conformation. Intramolecular interactions between the key Glu residue in the C helix of the N-terminal lobe and the backbone amides in the catalytic loop lock the kinase in the inactive conformation. Autophosphorylation appears to be a priming event for kinase activation. We identified Mps1 autophosphorylation sites in the activation and the P+1 loops. Whereas activation loop autophosphorylation enhances kinase activity, autophosphorylation at the P+1 loop (T686) is associated with the active kinase. Mutation of T686 autophosphorylation site impairs both autophosphorylation and transphosphorylation. Furthermore, we demonstrated that phosphorylation of T676 may be a priming event for phosphorylation at T686. Finally, we identified two critical lysine residues in the loop between helices EF and F that are essential for substrate recruitment and maintaining high levels of kinase activity. Our studies reveal critical biochemical mechanisms for Mps1 kinase regulation.