NANOGRAIN DENSITY OUTSIDE SATURN’S A RING

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

Johnson, Robert E.; Tseng, Wei-Ling; Elrod, M. K.

The observed disparity between the radial dependence of the ion and electron densities measured by the Cassini plasma (CAPS) and radio (RPWS) science instruments are used to show that the region between the outer edge of Saturn’s main rings and its tenuous G ring is permeated with small charged grains (nanograins). These grains emanate from the edge of the A ring and from the tenuous F and G rings. This is a region of Saturn’s magnetosphere that is relatively unexplored, but will be a focus of Cassini ’s F ring orbits prior to the end of mission in 2017 September.more » Confirmation of the grain densities predicted here will enhance our ability to describe the formation and destruction of material in this important region of Saturn’s magnetosphere.« less

Ring-diameter Ratios for Multi-ring Basins Average 2.0(0.5)D

NASA Technical Reports Server (NTRS)

Pike, R. J.; Spudis, P. D.

1985-01-01

The spacing of the concentric rings of planetary impact basins was studied. It is shown that a radial increment of x (sup 0.5) D, where x is about 2.0 and D = ring diameter, separates both (1) adjacent least-squares groups of rings and arcs of multi-ring basins on Mars, Mercury, and the Moon; and (2) adjacent rings of individual basins on the three planets. Statistics for ratios of ring diameters are presented, the first and most-applied parameter of ring spacing. It is found that ratios excluding rings flanking the main ring also have a mean spacing increment of about 2.0. Ratios including such rings, as for the least-squares groups, and (1) above, have a larger increment, averaging 2.1. The F-test indicates, that these spacings of basin ring locations, and mode of ring formation are controlled by the mechanics of the impact event itself, rather than by crustal properties.

Supra-molecular architecture in a co-crystal of the N(7)-H tautomeric form of N (6)-benzoyl-adenine with adipic acid (1/0.5).

PubMed

Swinton Darious, Robert; Thomas Muthiah, Packianathan; Perdih, Franc

2016-06-01

The asymmetric unit of the title co-crystal, C12H9N5O·0.5C6H10O4, consists of one mol-ecule of N (6)-benzoyl-adenine (BA) and one half-mol-ecule of adipic acid (AA), the other half being generated by inversion symmetry. The dihedral angle between the adenine and phenyl ring planes is 26.71 (7)°. The N (6)-benzoyl-adenine mol-ecule crystallizes in the N(7)-H tautomeric form with three non-protonated N atoms. This tautomeric form is stabilized by intra-molecular N-H⋯O hydrogen bonding between the carbonyl (C=O) group and the N(7)-H hydrogen atom on the Hoogsteen face of the purine ring, forming an S(7) ring motif. The two carboxyl groups of adipic acid inter-act with the Watson-Crick face of the BA mol-ecules through O-H⋯N and N-H⋯O hydrogen bonds, generating an R 2 (2)(8) ring motif. The latter units are linked by N-H⋯N hydrogen bonds, forming layers parallel to (10-5). A weak C-H⋯O hydrogen bond is also present, linking adipic acid mol-ecules in neighbouring layers, enclosing R (2) 2(10) ring motifs and forming a three-dimensional structure. C=O⋯π and C-H⋯π inter-actions are also present in the structure.

The structure of Jupiter’s main ring from New Horizons: A comparison with other ring-moon systems

NASA Astrophysics Data System (ADS)

Chancia, Robert; Hedman, Matthew

2018-04-01

During New Horizon’s Jupiter flyby in 2007, the Long-Range Reconnaissance Imager (LORRI) took several images of the planet’s main ring. The data set contains two extended image-movies of the main ring, along with several brief observations at varying ring azimuths, and a small set of high phase angle images. Thus far, the only published work on the New Horizons Jupiter rings data set found seven bright clumps with sub-km equivalent radii embedded in the main ring (Showalter et al. 2007 Science). In this work, we searched the inner region of the main ring for any structures that might be perturbed at the 3:2 resonances with the rotation of Jupiter’s magnetic field or massive storms. We also examined the structure of the outer main ring in order to assess how it is shaped by the small moons Metis and Adrastea. Some of the features seen in Jupiter’s main ring are similar to those found in other dusty rings around Saturn, Uranus, and Neptune. By comparing these different rings, we can gain a better understanding of how small moons sculpt tenuous rings.

4,5,7,8,17-Penta­hydr­oxy-14,18-dimethyl-6-methyl­ene-3,10-dioxapenta­cyclo­[9.8.0.01,7.04,19.013,18]nona­dec-14-ene-9,16-dione methanol solvate dihydrate

PubMed Central

Teh, Chin Hoe; Teoh, Siew Chin; Yeap, Chin Sing; Chan, Kit Lam; Fun, Hoong-Kun

2009-01-01

The title quassinoid compound, C20H24O9·CH3OH·2H2O, is a natural eurycomanone isolated from the roots of Eurycoma longifolia. The mol­ecules contain a fused five-ring system, with one tetra­hydro­furan ring adopting an envelope conformation, one tetra­hydro­pyran-2-one ring in a screw boat conformation, one cyclo­hexenone ring in a half-chair conformation and two cyclo­hexane rings in chair conformations. Intra­molecular C—H⋯O inter­actions generate S(5) ring motifs and an O—H⋯O inter­action generates an S(7) ring motif. In the crystal, mol­ecules are linked via inter­molecular O—H⋯O inter­actions along the b axis and further stacked along a axis. The absolute configuration of the title compound was inferred from previously solved structures of its analogues. PMID:21582604

2-Amino-5-chloro-pyrimidin-1-ium hydrogen maleate.

PubMed

Fun, Hoong-Kun; Hemamalini, Madhukar; Rajakannan, Venkatachalam

2012-01-01

In the title salt, C(4)H(5)ClN(3) (+)·C(4)H(3)O(4) (-), the 2-amino-5-chloro-pyrimidinium cation is protonated at one of its pyrimidine N atoms. In the roughly planar (r.m.s. deviation = 0.026 Å) hydrogen malate anion, an intra-molecular O-H⋯O hydrogen bond generates an S(7) ring. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl-ate O atoms of the anion via a pair of N-H⋯O hydrogen bonds, forming an R(2) (2)(8) ring motif. The ion pairs are connected via further N-H⋯O hydrogen bonds and a short C-H⋯O inter-action, forming layers lying parallel to the bc plane.

3-(Adamantan-1-yl)-4-ethyl-1-{[4-(2-meth-oxy-phen-yl)piperazin-1-yl]meth-yl}-1H-1,2,4-triazole-5(4H)-thione.

PubMed

El-Emam, Ali A; Al-Tuwaijri, Hanaa M; Al-Abdullah, Ebtehal S; Chidan Kumar, C S; Fun, Hoong-Kun

2014-01-01

In the title compound, C26H37N5OS, the piperazine ring adopts a chair conformation. The triazole ring forms dihedral angles of 67.85 (9) and 59.41 (9)° with the piperazine and benzene rings, respectively, resulting in an approximate V-shaped conformation for the mol-ecule. An intra-molecular C-H⋯O hydrogen bond generates an S(6) ring motif. The crystal structure features C-H⋯π inter-actions, producing a two-dimensional supramolecular architecture.

The RNA recognition motif domains of RBM5 are required for RNA binding and cancer cell proliferation inhibition

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

Zhang, Lei; Zhang, Qing; Yang, Yu

Highlights: • RNA recognition motif domains of RBM5 are essential for cell proliferation inhibition. • RNA recognition motif domains of RBM5 are essential for apoptosis induction. • RNA recognition motif domains of RBM5 are essential for RNA binding. • RNA recognition motif domains of RBM5 are essential for caspase-2 alternative splicing. - Abstract: RBM5 is a known putative tumor suppressor gene that has been shown to function in cell growth inhibition by modulating apoptosis. RBM5 also plays a critical role in alternative splicing as an RNA binding protein. However, it is still unclear which domains of RBM5 are required formore » RNA binding and related functional activities. We hypothesized the two putative RNA recognition motif (RRM) domains of RBM5 spanning from amino acids 98–178 and 231–315 are essential for RBM5-mediated cell growth inhibition, apoptosis regulation, and RNA binding. To investigate this hypothesis, we evaluated the activities of the wide-type and mutant RBM5 gene transfer in low-RBM5 expressing A549 cells. We found that, unlike wild-type RBM5 (RBM5-wt), a RBM5 mutant lacking the two RRM domains (RBM5-ΔRRM), is unable to bind RNA, has compromised caspase-2 alternative splicing activity, lacks cell proliferation inhibition and apoptosis induction function in A549 cells. These data provide direct evidence that the two RRM domains of RBM5 are required for RNA binding and the RNA binding activity of RBM5 contributes to its function on apoptosis induction and cell growth inhibition.« less

An evolving view of Saturn’s dynamic rings

USGS Publications Warehouse

Cuzzi, J.N.; Burns, J.A.; Charnoz, S.; Clark, Roger N.; Colwell, J.E.; Dones, L.; Esposito, L.W.; Filacchione, G.; French, R.G.; Hedman, M.M.; Kempf, S.; Marouf, E.A.; Murray, C.D.; Nicholson, P.D.; Porco, C.C.; Schmidt, J.; Showalter, M.R.; Spilker, L.J.; Spitale, J.; Srama, R.; Srem evi, M.; Tiscareno, M.S.; Weiss, J.

2010-01-01

We review our understanding of Saturn’s rings after nearly 6 years of observations by the Cassini spacecraft. Saturn’s rings are composed mostly of water ice but also contain an undetermined reddish contaminant. The rings exhibit a range of structure across many spatial scales; some of this involves the interplay of the fluid nature and the self-gravity of innumerable orbiting centimeter- to meter-sized particles, and the effects of several peripheral and embedded moonlets, but much remains unexplained. A few aspects of ring structure change on time scales as short as days. It remains unclear whether the vigorous evolutionary processes to which the rings are subject imply a much younger age than that of the solar system. Processes on view at Saturn have parallels in circumstellar disks.

The structure directing effect of organic cations onto the crystal structures of layered thioantimonates(III): Solvothermal synthesis and crystal structures of five new compounds containing the 2∞[Sb 8S 13] 2- anion

NASA Astrophysics Data System (ADS)

Puls, Angela; Näther, Christian; Kiebach, Ragnar; Bensch, Wolfgang

2006-09-01

The five new thioantimonates(III) ( iprH) 2[Sb 8S 13] ( I), (1,2-dapH) 2[Sb 8S 13] ( II), (1,3-dapH 2)[Sb 8S 13] ( III), (dienH 2)[Sb 8S 13]ṡ1.5H 2O ( IV), and (C 6H 9N 2)[Sb 8S 13]ṡ2.5H 2O ( V) were synthesised under solvothermal conditions ( ipr = iso-propylamine; 1,2-dap = 1,2-diaminopropane; 1,3-dap = 1,3-diaminopropane; dien = diethylentriamine; C 6H 9N 2 = 3-(aminoethyl)-pyridine). The structures of compounds I and II are topological very similar and a central motif is a Sb 10S 10 ring. On both sides of this ring Sb 5S 5 rings are condensed. These rings are connected via Sb 4S 4 rings leading to the sequence Sb 10S 10-Sb 5S 5-Sb 4S 4-Sb 5S 5-Sb 10Sb 10 in the [010] direction. Further interconnection into the two-dimensional [Sb 8S 13] 2- anion produces a large central Sb 18S 18 ring with dimensions of 11ṡ11 Å in both compounds. The two atoms thick layers are linear and stacked along the a axis generating large channels running along [010]. The layered anion of compound III is constructed by interconnection of the SbS 3 and SbS 4 units yielding Sb 19S 19, Sb 14S 14, Sb 13S 13, and Sb 8S 8 rings. The linear layers are two atoms thick and are stacked perpendicular to [001] to form channels running along the same direction. The last two compounds IV and V show a similar network topology. The layered anion is constructed by SbS 3 trigonal pyramids and SbS 4 units. The layer contains a Sb 12S 12 rings as the main structural motif. The corrugated layers extending in the (100) plane are two atoms thick and are stacked in a manner that large tunnels run along [100]. The total potential solvent areas are large and range from 20.7% for III to 35% for II.

Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.

PubMed

Martin-Malpartida, Pau; Batet, Marta; Kaczmarska, Zuzanna; Freier, Regina; Gomes, Tiago; Aragón, Eric; Zou, Yilong; Wang, Qiong; Xi, Qiaoran; Ruiz, Lidia; Vea, Angela; Márquez, José A; Massagué, Joan; Macias, Maria J

2017-12-12

Smad transcription factors activated by TGF-β or by BMP receptors form trimeric complexes with Smad4 to target specific genes for cell fate regulation. The CAGAC motif has been considered as the main binding element for Smad2/3/4, whereas Smad1/5/8 have been thought to preferentially bind GC-rich elements. However, chromatin immunoprecipitation analysis in embryonic stem cells showed extensive binding of Smad2/3/4 to GC-rich cis-regulatory elements. Here, we present the structural basis for specific binding of Smad3 and Smad4 to GC-rich motifs in the goosecoid promoter, a nodal-regulated differentiation gene. The structures revealed a 5-bp consensus sequence GGC(GC)|(CG) as the binding site for both TGF-β and BMP-activated Smads and for Smad4. These 5GC motifs are highly represented as clusters in Smad-bound regions genome-wide. Our results provide a basis for understanding the functional adaptability of Smads in different cellular contexts, and their dependence on lineage-determining transcription factors to target specific genes in TGF-β and BMP pathways.

CompariMotif: quick and easy comparisons of sequence motifs.

PubMed

Edwards, Richard J; Davey, Norman E; Shields, Denis C

2008-05-15

CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

Characterization and Promoter Analysis of a Cotton Ring-Type Ubiquitin Ligase (E3) Gene

USDA-ARS?s Scientific Manuscript database

A cotton fiber cDNA, GhRING1, and its corresponding gene have been cloned and characterized. The GhRING1 gene encodes a RING-type ubiquitin ligase (E3) containing 337 amino acids (aa). The GhRING1 protein contains a RING finger motif with conserved cysteine and histine residues at the C-terminus a...

GIV/Girdin activates Gαi and inhibits Gαs via the same motif

PubMed Central

Gupta, Vijay; Bhandari, Deepali; Leyme, Anthony; Aznar, Nicolas; Midde, Krishna K.; Lo, I-Chung; Ear, Jason; Niesman, Ingrid; López-Sánchez, Inmaculada; Blanco-Canosa, Juan Bautista; von Zastrow, Mark; Garcia-Marcos, Mikel; Farquhar, Marilyn G.; Ghosh, Pradipta

2016-01-01

We previously showed that guanine nucleotide-binding (G) protein α subunit (Gα)-interacting vesicle-associated protein (GIV), a guanine-nucleotide exchange factor (GEF), transactivates Gα activity-inhibiting polypeptide 1 (Gαi) proteins in response to growth factors, such as EGF, using a short C-terminal motif. Subsequent work demonstrated that GIV also binds Gαs and that inactive Gαs promotes maturation of endosomes and shuts down mitogenic MAPK–ERK1/2 signals from endosomes. However, the mechanism and consequences of dual coupling of GIV to two G proteins, Gαi and Gαs, remained unknown. Here we report that GIV is a bifunctional modulator of G proteins; it serves as a guanine nucleotide dissociation inhibitor (GDI) for Gαs using the same motif that allows it to serve as a GEF for Gαi. Upon EGF stimulation, GIV modulates Gαi and Gαs sequentially: first, a key phosphomodification favors the assembly of GIV–Gαi complexes and activates GIV’s GEF function; then a second phosphomodification terminates GIV’s GEF function, triggers the assembly of GIV–Gαs complexes, and activates GIV’s GDI function. By comparing WT and GIV mutants, we demonstrate that GIV inhibits Gαs activity in cells responding to EGF. Consequently, the cAMP→PKA→cAMP response element-binding protein signaling axis is inhibited, the transit time of EGF receptor through early endosomes are accelerated, mitogenic MAPK–ERK1/2 signals are rapidly terminated, and proliferation is suppressed. These insights define a paradigm in G-protein signaling in which a pleiotropically acting modulator uses the same motif both to activate and to inhibit G proteins. Our findings also illuminate how such modulation of two opposing Gα proteins integrates downstream signals and cellular responses. PMID:27621449

Non-Linear Dynamics of Saturn’s Rings

NASA Astrophysics Data System (ADS)

Esposito, Larry W.

2015-11-01

Non-linear processes can explain why Saturn’s rings are so active and dynamic. Ring systems differ from simple linear systems in two significant ways: 1. They are systems of granular material: where particle-to-particle collisions dominate; thus a kinetic, not a fluid description needed. We find that stresses are strikingly inhomogeneous and fluctuations are large compared to equilibrium. 2. They are strongly forced by resonances: which drive a non-linear response, pushing the system across thresholds that lead to persistent states.Some of this non-linearity is captured in a simple Predator-Prey Model: Periodic forcing from the moon causes streamline crowding; This damps the relative velocity, and allows aggregates to grow. About a quarter phase later, the aggregates stir the system to higher relative velocity and the limit cycle repeats each orbit.Summary of Halo Results: A predator-prey model for ring dynamics produces transient structures like ‘straw’ that can explain the halo structure and spectroscopy: This requires energetic collisions (v ≈ 10m/sec, with throw distances about 200km, implying objects of scale R ≈ 20km).Transform to Duffing Eqn : With the coordinate transformation, z = M2/3, the Predator-Prey equations can be combined to form a single second-order differential equation with harmonic resonance forcing.Ring dynamics and history implications: Moon-triggered clumping at perturbed regions in Saturn’s rings creates both high velocity dispersion and large aggregates at these distances, explaining both small and large particles observed there. We calculate the stationary size distribution using a cell-to-cell mapping procedure that converts the phase-plane trajectories to a Markov chain. Approximating the Markov chain as an asymmetric random walk with reflecting boundaries allows us to determine the power law index from results of numerical simulations in the tidal environment surrounding Saturn. Aggregates can explain many dynamic aspects

Multiple TPR motifs characterize the Fanconi anemia FANCG protein.

PubMed

Blom, Eric; van de Vrugt, Henri J; de Vries, Yne; de Winter, Johan P; Arwert, Fré; Joenje, Hans

2004-01-05

The genome protection pathway that is defective in patients with Fanconi anemia (FA) is controlled by at least eight genes, including BRCA2. A key step in the pathway involves the monoubiquitylation of FANCD2, which critically depends on a multi-subunit nuclear 'core complex' of at least six FANC proteins (FANCA, -C, -E, -F, -G, and -L). Except for FANCL, which has WD40 repeats and a RING finger domain, no significant domain structure has so far been recognized in any of the core complex proteins. By using a homology search strategy comparing the human FANCG protein sequence with its ortholog sequences in Oryzias latipes (Japanese rice fish) and Danio rerio (zebrafish) we identified at least seven tetratricopeptide repeat motifs (TPRs) covering a major part of this protein. TPRs are degenerate 34-amino acid repeat motifs which function as scaffolds mediating protein-protein interactions, often found in multiprotein complexes. In four out of five TPR motifs tested (TPR1, -2, -5, and -6), targeted missense mutagenesis disrupting the motifs at the critical position 8 of each TPR caused complete or partial loss of FANCG function. Loss of function was evident from failure of the mutant proteins to complement the cellular FA phenotype in FA-G lymphoblasts, which was correlated with loss of binding to FANCA. Although the TPR4 mutant fully complemented the cells, it showed a reduced interaction with FANCA, suggesting that this TPR may also be of functional importance. The recognition of FANCG as a typical TPR protein predicts this protein to play a key role in the assembly and/or stabilization of the nuclear FA protein core complex.

OXP1/YKL215c encodes an ATP-dependent 5-oxoprolinase in Saccharomyces cerevisiae: functional characterization, domain structure and identification of actin-like ATP-binding motifs in eukaryotic 5-oxoprolinases.

PubMed

Kumar, Akhilesh; Bachhawat, Anand Kumar

2010-06-01

OXP1/YKL215c, an uncharacterized ORF of Saccharomyces cerevisiae, encodes a functional ATP-dependent 5-oxoprolinase of 1286 amino acids. The yeast 5-oxoprolinase activity was demonstrated in vivo by utilization of 5-oxoproline as a source of glutamate and OTC, a 5-oxoproline sulfur analogue, as a source of sulfur in cells overexpressing OXP1. In vitro characterization by expression and purification of the recombinant protein in S. cerevisiae revealed that the enzyme exists and functions as a dimer, and has a K(m) of 159 microM and a V(max) of 3.5 nmol h(-1) microg(-1) protein. The enzyme was found to be functionally separable in two distinct domains. An 'actin-like ATPase motif' could be identified in 5-oxprolinases, and mutation of key residues within this motif led to complete loss in ATPase and 5-oxoprolinase activity of the enzyme. The results are discussed in the light of the previously postulated truncated gamma-glutamyl cycle of yeasts.

Rapid motif compliance scoring with match weight sets.

PubMed

Venezia, D; O'Hara, P J

1993-02-01

Most current implementations of motif matching in biological sequences have sacrificed the generality of weight matrix scoring for shorter runtimes. The program MOTIF incorporates a weight matrix and a rapid, backtracking tree-search algorithm to score motif compliance with greatly enhanced performance while placing no constraints on the motif. In addition, any positions within a motif can be marked as 'inviolate', thereby requiring an exact match. MOTIF allows a choice of regular expression formats and can use both motif and sequence libraries as either targets or queries. Nucleic acid sequences can optionally be translated by MOTIF in any frame(s) and used against peptide motifs.

Ring-laser gyroscope system using dispersive element(s)

NASA Technical Reports Server (NTRS)

Smith, David D. (Inventor)

2010-01-01

A ring-laser gyroscope system includes a ring-laser gyroscope (RLG) and at least one dispersive element optically coupled to the RLG's ring-shaped optical path. Each dispersive element has a resonant frequency that is approximately equal to the RLG's lasing frequency. A group index of refraction defined collectively by the dispersive element(s) has (i) a real portion that is greater than zero and less than one, and (ii) an imaginary portion that is less than zero.

MotifNet: a web-server for network motif analysis.

PubMed

Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti

2017-06-15

Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets

PubMed Central

2012-01-01

Background To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. Results We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. Conclusions SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery

Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

PubMed

Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

2012-01-01

To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

Calmodulin Bound to the First IQ Motif Is Responsible for Calcium-dependent Regulation of Myosin 5a*

PubMed Central

Lu, Zekuan; Shen, Mei; Cao, Yang; Zhang, Hai-Man; Yao, Lin-Lin; Li, Xiang-dong

2012-01-01

Myosin 5a is as yet the best-characterized unconventional myosin motor involved in transport of organelles along actin filaments. It is well-established that myosin 5a is regulated by its tail in a Ca2+-dependent manner. The fact that the actin-activated ATPase activity of myosin 5a is stimulated by micromolar concentrations of Ca2+ and that calmodulin (CaM) binds to IQ motifs of the myosin 5a heavy chain indicates that Ca2+ regulates myosin 5a function via bound CaM. However, it is not known which IQ motif and bound CaM are responsible for the Ca2+-dependent regulation and how the head-tail interaction is affected by Ca2+. Here, we found that the CaM in the first IQ motif (IQ1) is responsible for Ca2+ regulation of myosin 5a. In addition, we demonstrate that the C-lobe fragment of CaM in IQ1 is necessary for mediating Ca2+ regulation of myosin 5a, suggesting that the C-lobe fragment of CaM in IQ1 participates in the interaction between the head and the tail. We propose that Ca2+ induces a conformational change of the C-lobe of CaM in IQ1 and prevents interaction between the head and the tail, thus activating motor function. PMID:22437832

Semiconductor ring lasers coupled by a single waveguide

NASA Astrophysics Data System (ADS)

Coomans, W.; Gelens, L.; Van der Sande, G.; Mezosi, G.; Sorel, M.; Danckaert, J.; Verschaffelt, G.

2012-06-01

We experimentally and theoretically study the characteristics of semiconductor ring lasers bidirectionally coupled by a single bus waveguide. This configuration has, e.g., been suggested for use as an optical memory and as an optical neural network motif. The main results are that the coupling can destabilize the state in which both rings lase in the same direction, and it brings to life a state with equal powers at both outputs. These are both undesirable for optical memory operation. Although the coupling between the rings is bidirectional, the destabilization occurs due to behavior similar to an optically injected laser system.

Structure-based design synthesis of functionalized 3-(5-(s-phenyl)-4H-pyrazol-3-yl)-2H-chromen-2-one motifs and indigenous plant extracts and their antimalarial potential

NASA Astrophysics Data System (ADS)

Olayinka, Ajani; Grace, Olasehinde; Titilope, Dokunmu; Ruth, Diji-Geske; Olabode, Onileere; John, Openibo; Oreoluwa, Oluseye; Tochukwu, Chileke; Ezekiel, Adebiyi

2018-04-01

Resistance of the malaria parasite to conventional therapeutic agents calls for increased efforts in antimalarial drug discovery. Current efforts should be targeted at developing safe and affordable new agents to counter the spread of malaria parasites that are resistant to existing therapy. In this study, toxicological and in vivo antiplasmodial properties of 3-(5-(s-phenyl)-4H-pyrazol-3-yl)-42H-chromen-2, Mangifera indica and Tithonia diversifolia in swiss albino mice models, Musmusculus were investigated. 2H-Chromen-2-one also known as coumarin is highly privileged oxygen-containing heterocyclic entity which are present in plant kingdom as secondary metabolites. The maceration technique of crude drug extraction was employed using cold water extraction. Toxicological analysis was carried out using Lorke's method for acute toxicity testing while the chemosuppressive activity was carried out using Peter's four day test on early infection. We also report the synthesis of functionalized 3-(5-(s-phenyl)-4H-pyrazol-3-yl)-2H-chromen-2-one motifs via microwave assisted synthetic approach and isolation of indigenous plant extract in order to investigate their antimalarial efficacy. The condensation reaction of 3-acetylcoumarin with various benzaldehyde derivatives resulted in the formation of 3-[3-acryloyl]-2H-chromen-2-one which was subsequently reaction the hydrazine hydrate via microwave assisted hydrazinolysis to afford the targeted 3-(5-(s-phenyl)-4H-pyrazol-3-yl)-2H-chromen-2-one motifs. The chemical structures were confirmed by analytical data and spectroscopic means such as FT-IR, UV, 1H NMR, 13C NMR and DEPT-135. The microwave assisted reaction was remarkably successful and gave targeted 3-(5-(s-phenyl)-4H-pyrazol-3-yl)-2H-chromen-2-one motifs in higher yields at lesser reaction time compared to conventional heating method. The LD50 of the aqueous extracts of the leaves and stem bark Mangifera indica was established to be ± 707.11 mg/kg b.w., p.o. (body weight

Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability.

PubMed

Nonin, S; Phan, A T; Leroy, J L

1997-09-15

Repetitive cytosine-rich DNA sequences have been identified in telomeres and centromeres of eukaryotic chromosomes. These sequences play a role in maintaining chromosome stability during replication and may be involved in chromosome pairing during meiosis. The C-rich repeats can fold into an 'i-motif' structure, in which two parallel-stranded duplexes with hemiprotonated C.C+ pairs are intercalated. Previous NMR studies of naturally occurring repeats have produced poor NMR spectra. This led us to investigate oligonucleotides, based on natural sequences, to produce higher quality spectra and thus provide further information as to the structure and possible biological function of the i-motif. NMR spectroscopy has shown that d(5mCCTTTACC) forms an i-motif dimer of symmetry-related and intercalated folded strands. The high-definition structure is computed on the basis of the build-up rates of 29 intraresidue and 35 interresidue nuclear Overhauser effect (NOE) connectivities. The i-motif core includes intercalated interstrand C.C+ pairs stacked in the order 2*.8/1.7*/1*.7/2.8* (where one strand is distinguished by an asterisk and the numbers relate to the base positions within the repeat). The TTTA sequences form two loops which span the two wide grooves on opposite sides of the i-motif core; the i-motif core is extended at both ends by the stacking of A6 onto C2.C8+. The lifetimes of pairs C2.C8+ and 5mC1.C7+ are 1 ms and 1 s, respectively, at 15 degrees C. Anomalous exchange properties of the T3 imino proton indicate hydrogen bonding to A6 N7 via a water bridge. The d(5mCCTTTTCC) deoxyoligonucleotide, in which position 6 is occupied by a thymidine instead of an adenine, also forms a symmetric i-motif dimer. However, in this structure the two TTTT loops are located on the same side of the i-motif core and the C.C+ pairs are formed by equivalent cytidines stacked in the order 8*.8/1.1*/7*.7/2.2*. Oligodeoxynucleotides containing two C-rich repeats can fold and dimerize

BayesMotif: de novo protein sorting motif discovery from impure datasets.

PubMed

Hu, Jianjun; Zhang, Fan

2010-01-18

Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of

The Role of BRCA1 Domains and Motifs in Tumor Suppression

DTIC Science & Technology

2010-08-01

contained in this report are those of the author( s ) and should not be construed as an official Department of the Army position, policy or decision...and Motifs in Tumor Suppression 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-08-1-0509 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) Aneliya...Velkova 5d. PROJECT NUMBER Email: aneliya.velkova@moffitt.org 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME( S

1-(4,4''-Difluoro-5'-meth-oxy-1,1':3',1''-terphenyl-4'-yl)ethanone.

PubMed

Fun, Hoong-Kun; Hemamalini, Madhukar; Samshuddin, S; Narayana, B; Sarojini, B K

2012-01-01

In the title compound, C(21)H(16)F(2)O(2), the central benzene ring is inclined at dihedral angles of 30.91 (8) and 46.88 (7)° to the two terminal fluoro-substituted rings. The dihedral angle between the two terminal fluoro-subsituted rings is 68.34 (8)°. An intra-molecular C-H⋯O hydrogen bond generates an S(6) ring motif. The crystal structure is stabilized by weak C-H⋯π inter-actions.

Synchronization properties of network motifs: Influence of coupling delay and symmetry

NASA Astrophysics Data System (ADS)

D'Huys, O.; Vicente, R.; Erneux, T.; Danckaert, J.; Fischer, I.

2008-09-01

We investigate the effect of coupling delays on the synchronization properties of several network motifs. In particular, we analyze the synchronization patterns of unidirectionally coupled rings, bidirectionally coupled rings, and open chains of Kuramoto oscillators. Our approach includes an analytical and semianalytical study of the existence and stability of different in-phase and out-of-phase periodic solutions, complemented by numerical simulations. The delay is found to act differently on networks possessing different symmetries. While for the unidirectionally coupled ring the coupling delay is mainly observed to induce multistability, its effect on bidirectionally coupled rings is to enhance the most symmetric solution. We also study the influence of feedback and conclude that it also promotes the in-phase solution of the coupled oscillators. We finally discuss the relation between our theoretical results on delay-coupled Kuramoto oscillators and the synchronization properties of networks consisting of real-world delay-coupled oscillators, such as semiconductor laser arrays and neuronal circuits.

Synthetic approaches to peptides containing the L-Gln-L-Val-D(S)-Dmt motif.

PubMed

Suaifan, Ghadeer A R Y; Arafat, Tawfiq; Threadgill, Michael D

2007-05-15

The pseudoprolines S-Dmo (5,5-dimethyl-4-oxaproline) and R-Dmt (5,5-dimethyl-4-thiaproline) have been used to study the effects of forcing a fully cis conformation in peptides. Synthesis of peptides containing these (which have the same configuration as L-Pro) is straightforward. However, synthesis of peptides containing S-Dmt is difficult, owing to the rapid cyclisation of L-Aaa-S-Dmt amides and esters to form the corresponding diketopiperazines (DKP); thus the intermediacy of L-Aaa-S-Dmt amides and esters must be avoided in the synthetic sequence. Peptides containing the L-Gln-L-Val-D(S)-Dmt motif are particularly difficult, owing to the insolubility of coupling partners containing Gln. Introduction of Gln as N-Boc-pyroglutamate overcame the latter difficulty and the dipeptide active ester BocPygValOC(6)F(5) coupled in good yield with S-DmtOH. BocPygVal-S- DmtNH(CH(2))(2)C(6)H(4)NO(2) was converted quantitatively to BocGlnVal-S-DmtNH(CH(2))(2)C(6)H(4)NO(2) with ammonia, demonstrating the utility of this approach. Two peptide derivatives (CbzSerLysLeuGlnVal-S-DmtNH(CH(2))(2)C(6)H(4)NO(2) and CbzSerSerLysLeuGlnVal-S- DmtNH(CH(2))(2)C(6)H(4)NO(2)) were assembled, using these new methods of coupling a dipeptide acid active ester with S-DmtOH and introduction of Gln as Pyg, followed by conventional peptide couplings. The presence of the Val caused these peptides to be cleaved very slowly by prostate-specific antigen (PSA) at Leu Gln, rather than the expected Gln Val.

The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer.

PubMed

Sanchez, Jacint G; Okreglicka, Katarzyna; Chandrasekaran, Viswanathan; Welker, Jordan M; Sundquist, Wesley I; Pornillos, Owen

2014-02-18

Tripartite motif (TRIM) proteins make up a large family of coiled-coil-containing RING E3 ligases that function in many cellular processes, particularly innate antiviral response pathways. Both dimerization and higher-order assembly are important elements of TRIM protein function, but the atomic details of TRIM tertiary and quaternary structure have not been fully understood. Here, we present crystallographic and biochemical analyses of the TRIM coiled-coil and show that TRIM proteins dimerize by forming interdigitating antiparallel helical hairpins that position the N-terminal catalytic RING domains at opposite ends of the dimer and the C-terminal substrate-binding domains at the center. The dimer core comprises an antiparallel coiled-coil with a distinctive, symmetric pattern of flanking heptad and central hendecad repeats that appear to be conserved across the entire TRIM family. Our studies reveal how the coiled-coil organizes TRIM25 to polyubiquitylate the RIG-I/viral RNA recognition complex and how dimers of the TRIM5α protein are arranged within hexagonal arrays that recognize the HIV-1 capsid lattice and restrict retroviral replication.

The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer

PubMed Central

Sanchez, Jacint G.; Okreglicka, Katarzyna; Chandrasekaran, Viswanathan; Welker, Jordan M.; Sundquist, Wesley I.; Pornillos, Owen

2014-01-01

Tripartite motif (TRIM) proteins make up a large family of coiled-coil-containing RING E3 ligases that function in many cellular processes, particularly innate antiviral response pathways. Both dimerization and higher-order assembly are important elements of TRIM protein function, but the atomic details of TRIM tertiary and quaternary structure have not been fully understood. Here, we present crystallographic and biochemical analyses of the TRIM coiled-coil and show that TRIM proteins dimerize by forming interdigitating antiparallel helical hairpins that position the N-terminal catalytic RING domains at opposite ends of the dimer and the C-terminal substrate-binding domains at the center. The dimer core comprises an antiparallel coiled-coil with a distinctive, symmetric pattern of flanking heptad and central hendecad repeats that appear to be conserved across the entire TRIM family. Our studies reveal how the coiled-coil organizes TRIM25 to polyubiquitylate the RIG-I/viral RNA recognition complex and how dimers of the TRIM5α protein are arranged within hexagonal arrays that recognize the HIV-1 capsid lattice and restrict retroviral replication. PMID:24550273

[Conserved motifs in voltage sensing proteins].

PubMed

Wang, Chang-He; Xie, Zhen-Li; Lv, Jian-Wei; Yu, Zhi-Dan; Shao, Shu-Li

2012-08-25

This paper was aimed to study conserved motifs of voltage sensing proteins (VSPs) and establish a voltage sensing model. All VSPs were collected from the Uniprot database using a comprehensive keyword search followed by manual curation, and the results indicated that there are only two types of known VSPs, voltage gated ion channels and voltage dependent phosphatases. All the VSPs have a common domain of four helical transmembrane segments (TMS, S1-S4), which constitute the voltage sensing module of the VSPs. The S1 segment was shown to be responsible for membrane targeting and insertion of these proteins, while S2-S4 segments, which can sense membrane potential, for protein properties. Conserved motifs/residues and their functional significance of each TMS were identified using profile-to-profile sequence alignments. Conserved motifs in these four segments are strikingly similar for all VSPs, especially, the conserved motif [RK]-X(2)-R-X(2)-R-X(2)-[RK] was presented in all the S4 segments, with positively charged arginine (R) alternating with two hydrophobic or uncharged residues. Movement of these arginines across the membrane electric field is the core mechanism by which the VSPs detect changes in membrane potential. The negatively charged aspartate (D) in the S3 segment is universally conserved in all the VSPs, suggesting that the aspartate residue may be involved in voltage sensing properties of VSPs as well as the electrostatic interactions with the positively charged residues in the S4 segment, which may enhance the thermodynamic stability of the S4 segments in plasma membrane.

200 MW S-band traveling wave resonant ring development at IHEP

NASA Astrophysics Data System (ADS)

Zhou, Zu-Sheng; Chi, Yun-Long; Git, Meng-Ping; Pei, Guo-Xi

2010-03-01

The resonant-ring is a traveling wave circuit, which is used to produce high peak power with comparatively smaller stored energy. The application to be considered is its use as a high power simulator mainly for testing the klystron ceramic output window, as well as for high power microwave transmission devices. This paper describes the principle of a resonant ring and introduces the structure and property of the newly constructed traveling wave resonant ring at IHEP. Our goal is to produce a 200 MW class resonant ring at 2.856 GHz with a pulse length of 2 μs and repetition rate of 25 Hz. The installation, commissioning and testing of the ring have been completed and a peak power of 200 MW at 3 μs has been achieved. The conditioning results show that all the parameters of the resonant ring reach the design goals.

Motif enrichment tool.

PubMed

Blatti, Charles; Sinha, Saurabh

2014-07-01

The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Unitary circular code motifs in genomes of eukaryotes.

PubMed

El Soufi, Karim; Michel, Christian J

A set X of 20 trinucleotides was identified in genes of bacteria, eukaryotes, plasmids and viruses, which has in average the highest occurrence in reading frame compared to its two shifted frames (Michel, 2015; Arquès and Michel, 1996). This set X has an interesting mathematical property as X is a circular code (Arquès and Michel, 1996). Thus, the motifs from this circular code X, called X motifs, have the property to always retrieve, synchronize and maintain the reading frame in genes. The origin of this circular code X in genes is an open problem since its discovery in 1996. Here, we first show that the unitary circular codes (UCC), i.e. sets of one word, allow to generate unitary circular code motifs (UCC motifs), i.e. a concatenation of the same motif (simple repeats) leading to low complexity DNA. Three classes of UCC motifs are studied here: repeated dinucleotides (D + motifs), repeated trinucleotides (T + motifs) and repeated tetranucleotides (T + motifs). Thus, the D + , T + and T + motifs allow to retrieve, synchronize and maintain a frame modulo 2, modulo 3 and modulo 4, respectively, and their shifted frames (1 modulo 2; 1 and 2 modulo 3; 1, 2 and 3 modulo 4 according to the C 2 , C 3 and C 4 properties, respectively) in the DNA sequences. The statistical distribution of the D + , T + and T + motifs is analyzed in the genomes of eukaryotes. A UCC motif and its comp lementary UCC motif have the same distribution in the eukaryotic genomes. Furthermore, a UCC motif and its complementary UCC motif have increasing occurrences contrary to their number of hydrogen bonds, very significant with the T + motifs. The longest D + , T + and T + motifs in the studied eukaryotic genomes are also given. Surprisingly, a scarcity of repeated trinucleotides (T + motifs) in the large eukaryotic genomes is observed compared to the D + and T + motifs. This result has been investigated and may be explained by two outcomes. Repeated trinucleotides (T + motifs) are identified

Crystal structure and hydrogen-bonding patterns in 5-fluoro-cytosinium picrate.

PubMed

Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D

2017-03-01

In the crystal structure of the title compound, 5-fluoro-cytosinium picrate, C 4 H 5 FN 3 O + ·C 6 H 2 N 3 O 7 - , one N heteroatom of the 5-fluoro-cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA - ) anion. In the crystal, the 5FC + cation inter-acts with the PA - anion through three-centre N-H⋯O hydrogen bonds, forming two conjoined rings having R 2 1 (6) and R 1 2 (6) motifs, and is extended by N-H⋯O hydrogen bonds and C-H⋯O inter-actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C-F⋯π inter-actions.

The 1995 Saturn Ring-Plane Crossings: Ring Thickness and Small Inner Satellites

NASA Astrophysics Data System (ADS)

Poulet, F.; Sicardy, B.

1996-09-01

The May 22() th and August 10() th, 1995, Saturn ring-plane crossings by the Earth were observed from the 2-m and 1-m telescopes at Pic du Midi, the 2.2-m telescope of the University of Hawaii, and with the Adonis adaptive optics camera at the 3.6-m telescope of the European Southern Observatory (ESO). Observations were made with either a 0.9 mu m or 2.2 mu m (short K) methane band filter. The radial brightness profiles of the rings indicate that the outer F ring dominates the apparent edge-on thickness of the system, with a vertically integrated equivalent width of 0.8-1.0 km near a radius of 130,000 km. The photometric behaviors of the A, B, and C rings and of the Cassini Division have been analyzed using a classical radiative transfer code which includes illumination by the Sun and by the planet. The F ring is modelled as a physically thick ribbon (thickness h) composed of large particles embedded in dust. The observed profiles can be explained if the F ring is both optically thick (tau ~ 0.15-0.25), and physically thick (h at least ~ 1.5 km). The large particles dominate the F ring's photometric behavior in backscattered light. Constraints on the particle properties in the other rings have been derived. The dimming of the rings around August 10, 1995 provided ideal conditions to study the small inner satellites. Besides Janus, Epimetheus and Pandora, two unresolved objects were detected in the ESO frames. They have been identified with the objects 1995S5 and 1995S6, detected several hours later by the Hubble Space Telescope (Nicholson et al. 1996, Science 272, 509--515). Combining the ESO and HST data, we derive orbital and photometric parameters for these objects. In particular, we improve the orbital parameters of 1995S5, whose orbital radius is now close to that of the F ring.

Structure of the Mimas 5:3 Bending Wave in Saturn's Rings

NASA Astrophysics Data System (ADS)

Sega, Daniel D.; Colwell, Josh E.

2016-10-01

Saturn's moon Mimas is on an inclined orbit with several strong vertical orbital resonances in Saturn's rings. The 5:3 inner vertical resonance with Mimas lies in the outer A ring and produces a prominent spiral bending wave (BW) that propagates away from Mimas. While dozens of density waves in Saturn's rings have been analyzed to determine local surface mass densities and viscosities, the number of bending waves is limited by the requirement for a moon on an inclined orbit and because, unlike the Lindblad resonances that excite density waves, there can be no first order vertical resonances. The Mimas 5:3 BW is the most prominent in the ring system. Bending wave theory was initially developed by Shu et al. (1983, Icarus, 53, 185-206) following the Voyager encounters with Saturn. Later, Gresh et al. (1986, Icarus, 68, 481-502) modeled radio science occultation data of the Mimas 5:3 BW with an imperfect fit to the theory. The multitude of high resolution stellar occultations observed by Cassini UVIS provides an opportunity to reconstruct the full three-dimensional structure of this wave and learn more about local ring properties. Occultations at high elevation angles out of the ring plane are insensitive to the wave structure due to the small angles of the vertical warping of the rings in the wave. They thus reveal the underlying structure in the wave region. There is a symmetric increase in optical depth throughout the Mimas 5:3 BW region. This may be due to an increase in the abundance of small particles without a corresponding increase in surface mass density. We include this feature in a ray-tracing model of the vertical structure of the wave and fit it to multiple UVIS occultations. The observed amplitude of the wave and its damping behavior of are not well-described by the Shu et al. model, which assumes a fluid-like damping mechanism. A different damping behavior of the ring, perhaps radially varying across the wave region due to differences in the particle

Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.

PubMed

Michael, Sushama; Travé, Gilles; Ramu, Chenna; Chica, Claudia; Gibson, Toby J

2008-02-15

KEN-box-mediated target selection is one of the mechanisms used in the proteasomal destruction of mitotic cell cycle proteins via the APC/C complex. While annotating the Eukaryotic Linear Motif resource (ELM, http://elm.eu.org/), we found that KEN motifs were significantly enriched in human protein entries with cell cycle keywords in the UniProt/Swiss-Prot database-implying that KEN-boxes might be more common than reported. Matches to short linear motifs in protein database searches are not, per se, significant. KEN-box enrichment with cell cycle Gene Ontology terms suggests that collectively these motifs are functional but does not prove that any given instance is so. Candidates were surveyed for native disorder prediction using GlobPlot and IUPred and for motif conservation in homologues. Among >25 strong new candidates, the most notable are human HIPK2, CHFR, CDC27, Dab2, Upf2, kinesin Eg5, DNA Topoisomerase 1 and yeast Cdc5 and Swi5. A similar number of weaker candidates were present. These proteins have yet to be tested for APC/C targeted destruction, providing potential new avenues of research.

Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d.

PubMed

Doxey, Andrew C; Cheng, Zhenyu; Moffatt, Barbara A; McConkey, Brendan J

2010-08-03

Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB) for coplanar aromatic motifs similar to those found in known glycan-binding proteins. The proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO) enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192) in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry. Based on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure.

Ca2+-binding Motif of βγ-Crystallins*

PubMed Central

Srivastava, Shanti Swaroop; Mishra, Amita; Krishnan, Bal; Sharma, Yogendra

2014-01-01

βγ-Crystallin-type double clamp (N/D)(N/D)XX(S/T)S motif is an established but sparsely investigated motif for Ca2+ binding. A βγ-crystallin domain is formed of two Greek key motifs, accommodating two Ca2+-binding sites. βγ-Crystallins make a separate class of Ca2+-binding proteins (CaBP), apparently a major group of CaBP in bacteria. Paralleling the diversity in βγ-crystallin domains, these motifs also show great diversity, both in structure and in function. Although the expression of some of them has been associated with stress, virulence, and adhesion, the functional implications of Ca2+ binding to βγ-crystallins in mediating biological processes are yet to be elucidated. PMID:24567326

Identity and functions of CxxC-derived motifs.

PubMed

Fomenko, Dmitri E; Gladyshev, Vadim N

2003-09-30

Two cysteines separated by two other residues (the CxxC motif) are employed by many redox proteins for formation, isomerization, and reduction of disulfide bonds and for other redox functions. The place of the C-terminal cysteine in this motif may be occupied by serine (the CxxS motif), modifying the functional repertoire of redox proteins. Here we found that the CxxC motif may also give rise to a motif, in which the C-terminal cysteine is replaced with threonine (the CxxT motif). Moreover, in contrast to a view that the N-terminal cysteine in the CxxC motif always serves as a nucleophilic attacking group, this residue could also be replaced with threonine (the TxxC motif), serine (the SxxC motif), or other residues. In each of these CxxC-derived motifs, the presence of a downstream alpha-helix was strongly favored. A search for conserved CxxC-derived motif/helix patterns in four complete genomes representing bacteria, archaea, and eukaryotes identified known redox proteins and suggested possible redox functions for several additional proteins. Catalytic sites in peroxiredoxins were major representatives of the TxxC motif, whereas those in glutathione peroxidases represented the CxxT motif. Structural assessments indicated that threonines in these enzymes could stabilize catalytic thiolates, suggesting revisions to previously proposed catalytic triads. Each of the CxxC-derived motifs was also observed in natural selenium-containing proteins, in which selenocysteine was present in place of a catalytic cysteine.

MotifMark: Finding regulatory motifs in DNA sequences.

PubMed

Hassanzadeh, Hamid Reza; Kolhe, Pushkar; Isbell, Charles L; Wang, May D

2017-07-01

The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

5-Methylpyrazine-2-carboxamide

DOE PAGES

Rillema, D. Paul; Senaratne, Nilmini K.; Moore, Curtis; ...

2017-07-28

The title compound, C 6H 7N 3O, is nearly planar, with a dihedral angle of 2.14 (11)° between the pyrazine ring and the mean plane of the carboxamide group [C—C(=O)—N]. In the crystal, molecules are linked via pairs of N—H...O hydrogen bonds forming inversion dimers with an R 2 2 (8) ring motif. These dimers are further linked by a pair of N—H...N hydrogen bonds, enclosing an R 2 2 (10) ring motif, and C—H...O hydrogen bonds, forming ribbons lying parallel to the ab plane. The ribbons are linked by offset π–π interactions [intercentroid distance = 3.759(1)Å], forming two setsmore » of mutually perpendicular slabs parallel to planes (110) and (1-10).« less

Biotransformation of two β-secretase inhibitors including ring opening and contraction of a pyrimidine ring.

PubMed

Lindgren, Anders; Eklund, Göran; Turek, Dominika; Malmquist, Jonas; Swahn, Britt-Marie; Holenz, Jörg; von Berg, Stefan; Karlström, Sofia; Bueters, Tjerk

2013-05-01

Recently, the discovery of the aminoisoindoles as potent and selective inhibitors of β-secretase was reported, including the close structural analogs compound (S)-1-pyridin-4-yl-4-fluoro-1-(3-(pyrimidin-5-yl)phenyl)-1H-isoindol-3-amine [(S)-25] and (S)-1-(2-(difluoromethyl)pyridin-4-yl)-4-fluoro-1-(3-(pyrimidin-5-yl)phenyl)-1H-isoindol-3-amine hemifumarate (AZD3839), the latter being recently progressed to the clinic. The biotransformation of (S)-25 was investigated in vitro and in vivo in rat, rabbit, and human and compared with AZD3839 to further understand the metabolic fate of these compounds. In vitro, CYP3A4 was the major responsible enzyme and metabolized both compounds to a large extent in the commonly shared pyridine and pyrimidine rings. The main proposed metabolic pathways in various in vitro systems were N-oxidation of the pyridine and/or pyrimidine ring and conversion to 4-pyrimidone and pyrimidine-2,4-dione. Both compounds were extensively metabolized, and more than 90% was excreted in feces after intravenous administration of radiolabeled compound to the rat. Here, the main pathways were N-oxidation of the pyridine and/or pyrimidine ring and a ring contraction of the pyrimidine ring into an imidazole ring. Ring-contracted metabolites accounted for 25% of the total metabolism in the rat for (S)-25, whereas the contribution was much smaller for AZD3839. This metabolic pathway was not foreseen on the basis of the obtained in vitro data. In conclusion, we discovered an unusual metabolic pathway of aryl-pyrimidine-containing compounds by a ring-opening reaction followed by elimination of a carbon atom and a ring closure to form an imidazole ring.

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences.

PubMed

Mehdi, Ahmed M; Sehgal, Muhammad Shoaib B; Kobe, Bostjan; Bailey, Timothy L; Bodén, Mikael

2013-01-01

Local motifs are patterns of DNA or protein sequences that occur within a sequence interval relative to a biologically defined anchor or landmark. Current protein motif discovery methods do not adequately consider such constraints to identify biologically significant motifs that are only weakly over-represented but spatially confined. Using negatives, i.e. sequences known to not contain a local motif, can further increase the specificity of their discovery. This article introduces the method DLocalMotif that makes use of positional information and negative data for local motif discovery in protein sequences. DLocalMotif combines three scoring functions, measuring degrees of motif over-representation, entropy and spatial confinement, specifically designed to discriminatively exploit the availability of negative data. The method is shown to outperform current methods that use only a subset of these motif characteristics. We apply the method to several biological datasets. The analysis of peroxisomal targeting signals uncovers several novel motifs that occur immediately upstream of the dominant peroxisomal targeting signal-1 signal. The analysis of proline-tyrosine nuclear localization signals uncovers multiple novel motifs that overlap with C2H2 zinc finger domains. We also evaluate the method on classical nuclear localization signals and endoplasmic reticulum retention signals and find that DLocalMotif successfully recovers biologically relevant sequence properties. http://bioinf.scmb.uq.edu.au/dlocalmotif/

25Gb/s 1V-driving CMOS ring modulator with integrated thermal tuning.

PubMed

Li, Guoliang; Zheng, Xuezhe; Yao, Jin; Thacker, Hiren; Shubin, Ivan; Luo, Ying; Raj, Kannan; Cunningham, John E; Krishnamoorthy, Ashok V

2011-10-10

We report a high-speed ring modulator that fits many of the ideal qualities for optical interconnect in future exascale supercomputers. The device was fabricated in a 130 nm SOI CMOS process, with 7.5 μm ring radius. Its high-speed section, employing PN junction that works at carrier-depletion mode, enables 25 Gb/s modulation and an extinction ratio >5 dB with only 1V peak-to-peak driving. Its thermal tuning section allows the device to work in broad wavelength range, with a tuning efficiency of 0.19 nm/mW. Based on microwave characterization and circuit modeling, the modulation energy is estimated ~7 fJ/bit. The whole device fits in a compact 400 μm2 footprint.

The T-cell receptor beta chain CDR3 region of BV8S1/BJ1S5 transcripts in type 1 diabetes.

PubMed

Naserke, H E; Durinovic-Bellò, I; Seidel, D; Ziegler, A G

1996-01-01

We recently described the T-cell receptor (TCR) beta chain CDR3 motif S-SDRLG-NQPQH (BV8S1-BJ1S5) in an islet-specific T-cell clone (K2.12) from a type 1 diabetic patient (AS). A similar motif (RLGNQ) was also reported in a T-cell clone of non-obese diabetic (NOD) mice by others. In order to determine the frequency of our motif in selected and unselected T-cell populations, we cloned and sequenced the CDR3 region of BV8S1-BJ1S5 transcripts. These transcripts were derived from unstimulated peripheral blood T lymphocytes from two type 1 diabetic patients (AS and FS) and their non-diabetic sibling (WS), as well as from an islet-specific T-cell line of one of the patients. In addition, we compared the structure and composition of the CDR3 region in BV8S1-BJ1S5 transcripts from peripheral blood T cells between the patients and their non-diabetic sibling (>50 sequences each). We found that 30% of the islet-specific T-cell line cDNA clones expressed the entire sequence-motif, whereas it was absent in the clones of unstimulated peripheral blood T cells from both patients and their non-diabetic sibling. The average length of the CDR3 region was shorter in the patients (mean AS 9.9, FS 9.9, versus WS 10.7, p = 0.0037) and the number of inserted nucleotides in N nucleotide addition at the DJ-junction lower (mean AS 3.5, FS 3. 2, versus WS 5.2, P = <10(-4)) as compared with their non-diabetic sibling. Moreover, the pattern of amino acid usage in the CDR3 region was dissimilar at positions 5 and 6, where polar amino acids predominated in both diabetic siblings. In contrast, basic amino acids are preferentially used at position 5 in the clones of the non-diabetic sibling. These data provide information on the general structure of the TCR(BV8S1-BJ1S5) CDR3 region in type 1 diabetes and may indicate differences in the amino and nucleic acid composition of the TCR beta chain CDR3 region between two type 1 diabetic patients and their non-diabetic sibling.

Crystal structure of 6-chloro-5-iso-propyl-pyrimidine-2,4(1H,3H)-dione.

PubMed

Haress, Nadia G; Ghabbour, Hazem A; El-Emam, Ali A; Chidan Kumar, C S; Fun, Hoong-Kun

2014-11-01

In the mol-ecule of the title compound, C7H9ClN2O2, the conformation is determined by intra-molecular C-H⋯O and C-H⋯Cl hydrogen bonds, which generate S(6) and S(5) ring motifs. The isopropyl group is almost perpendicular to the pyrimidine ring with torsion angles of -70.8 (3) and 56.0 (3)°. In the crystal, two inversion-related mol-ecules are linked via a pair of N-H⋯O hydrogen bonds into R 2 (2)(8) dimers; these dimers are connected into chains extending along the bc plane via an additional N-H⋯O hydrogen bond and weaker C-H⋯O hydrogen bonds. The crystal structure is further stabilized by a weak π-π inter-action [3.6465 (10) Å] between adjacent pyrimidine-dione rings arranged in a head-to-tail fashion, producing a three-dimensional network.

THE EFFECTS OF CRACKING ON THE SURFACE POTENTIAL OF ICY GRAINS IN SATURN’S E-RING: LABORATORY STUDIES

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

Bu, Caixia; Bahr, David A.; Dukes, Catherine A.

2016-07-10

Within Saturn's E-ring, dust grains are coated by water vapor co-released with ice grains from the geyser-like eruptions of Enceladus. These ice-coated grains have intrinsic surface potential and interact synergistically with the ions and electrons of Saturn's magnetospheric plasmas. We perform laboratory experiments to investigate the effects of water-ice growth on the surface potential, using amorphous solid water (ASW) films. We estimate the growth of the surface potential to be ∼ 2.5 mV (Earth) yr{sup 1} and 112 mV yr{sup 1} for E-ring grains at ∼4.5 R {sub s} and 3.95 R {sub s} outside Enceladus’s plume, respectively. In addition,more » our measurements show that the linear relationship between the surface potential and the film thickness, as described in previous studies, has an upper limit, where the film spontaneously cracks above a porosity-dependent critical thickness. Heating of the cracked films with (and without) deposited charge shows that significant positive (and negative) surface potentials are retained at temperatures above 110 K, contrary to the minimal values (roughly zero) for thin, transparent ASW films. The significant surface potentials observed on micron-scale cracked ice films after thermal cycling, (5–20) V, are consistent with Cassini measurements, which indicate a negative charge of up to 5 V for E-ring dust particles at ∼5 R {sub s}. Therefore, the native grain surface potential resulting from water-vapor coating must be included in modeling studies of interactions between E-ring icy surfaces and Saturn's magnetospheric plasma.« less

Crystal structure and hydrogen-bonding patterns in 5-fluoro­cytosinium picrate

PubMed Central

Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D.

2017-01-01

In the crystal structure of the title compound, 5-fluoro­cytosinium picrate, C4H5FN3O+·C6H2N3O7 −, one N heteroatom of the 5-fluoro­cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA−) anion. In the crystal, the 5FC+ cation inter­acts with the PA− anion through three-centre N—H⋯O hydrogen bonds, forming two conjoined rings having R 2 1(6) and R 1 2(6) motifs, and is extended by N—H⋯O hydrogen bonds and C—H⋯O inter­actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C—F⋯π inter­actions. PMID:28316809

Two polymorphs of 2,5-dichloro-3,6-bis(dibenzylamino)-p-hydroquinone with flexible dibenzylamino groups.

PubMed

Shin, In Sub; Shimada, Yuta; Horiguchi-Babamoto, Emi; Matsumoto, Shinya

2018-04-01

We obtained two conformational polymorphs of 2,5-dichloro-3,6-bis(dibenzylamino)-p-hydroquinone, C 34 H 30 Cl 2 N 2 O 2 . Both polymorphs have an inversion centre at the centre of the hydroquinone ring (Z' = 1/2), and there are no significant differences between their bond lengths and angles. The most significant structural difference in the molecular conformations was found in the rotation of the phenyl rings of the two crystallographically independent benzyl groups. The crystal structures of the polymorphs were distinguishable with respect to the arrangement of the hydroquinone rings and the packing motif of the phenyl rings that form part of the benzyl groups. The phenyl groups of one polymorph are arranged in a face-to-edge motif between adjacent molecules, with intermolecular C-H...π interactions, whereas the phenyl rings in the other polymorph form a lamellar stacking pattern with no significant intermolecular interactions. We suggest that this partial conformational difference in the molecular structures leads to the significant structural differences observed in their molecular arrangements.

3-Phenyl-6-(2-pyrid-yl)-1,2,4,5-tetra-zine.

PubMed

Chartrand, Daniel; Laverdière, François; Hanan, Garry

2007-12-06

The title compound, C(13)H(9)N(5), is the first asymmetric diaryl-1,2,4,5-tetra-zine to be crystallographically characterized. We have been inter-ested in this motif for incorporation into supra-molecular assemblies based on coordination chemistry. The solid state structure shows a centrosymmetric mol-ecule, forcing a positional disorder of the terminal phenyl and pyridyl rings. The mol-ecule is completely planar, unusual for aromatic rings with N atoms in adjacent ortho positions. The stacking observed is very common in diaryl-tetra-zines and is dominated by π stacking [centroid-to-centroid distance between the tetrazine ring and the aromatic ring of an adjacent molecule is 3.6 Å, perpendicular (centroid-to-plane) distance of about 3.3 Å].

The c-ring stoichiometry of ATP synthase is adapted to cell physiological requirements of alkaliphilic Bacillus pseudofirmus OF4

PubMed Central

Preiss, Laura; Klyszejko, Adriana L.; Hicks, David B.; Liu, Jun; Fackelmayer, Oliver J.; Yildiz, Özkan; Krulwich, Terry A.; Meier, Thomas

2013-01-01

The c-rings of ATP synthases consist of individual c-subunits, all of which harbor a conserved motif of repetitive glycine residues (GxGxGxG) important for tight transmembrane α-helix packing. The c-ring stoichiometry determines the number of ions transferred during enzyme operation and has a direct impact on the ion-to-ATP ratio, a cornerstone parameter of cell bioenergetics. In the extreme alkaliphile Bacillus pseudofirmus OF4, the glycine motif is replaced by AxAxAxA. We performed a structural study on two mutants with alanine-to-glycine changes using atomic force microscopy and X-ray crystallography, and found that mutants form smaller c12 rings compared with the WT c13. The molar growth yields of B. pseudofirmus OF4 cells on malate further revealed that the c12 mutants have a considerably reduced capacity to grow on limiting malate at high pH. Our results demonstrate that the mutant ATP synthases with either c12 or c13 can support ATP synthesis, and also underscore the critical importance of an alanine motif with c13 ring stoichiometry for optimal growth at pH >10. The data indicate a direct connection between the precisely adapted ATP synthase c-ring stoichiometry and its ion-to-ATP ratio on cell physiology, and also demonstrate the bioenergetic challenges and evolutionary adaptation strategies of extremophiles. PMID:23613590

(E)-1-(Pyridin-2-yl)-3-(3,4,5-trimeth­oxy­phen­yl)prop-2-en-1-one

PubMed Central

Fun, Hoong-Kun; Suwunwong, Thitipone; Chantrapromma, Suchada

2011-01-01

In the title heteroaryl chalcone derivative, C17H17NO4, the dihedral angle between the pyridine and benzene rings is 10.82 (5)°. The two meth­oxy groups at the meta positions are essentially coplanar with the attached benzene rings [C—O—C—C torsion angles = −0.97 (14) and 179.47 (9)°], whereas the meth­oxy group at the para position is twisted from the attached ring with a C—O—C—C torsion angle of −104.48 (11)°. A C—H⋯O close contact involving two of the meth­oxy groups generates an S(6) ring motif. In the crystal, mol­ecules are linked by weak C—H⋯O inter­actions into columns along the b axis. PMID:22058997

A Conserved GPG-Motif in the HIV-1 Nef Core Is Required for Principal Nef-Activities

PubMed Central

Martínez-Bonet, Marta; Palladino, Claudia; Briz, Veronica; Rudolph, Jochen M.; Fackler, Oliver T.; Relloso, Miguel; Muñoz-Fernandez, Maria Angeles; Madrid, Ricardo

2015-01-01

To find out new determinants required for Nef activity we performed a functional alanine scanning analysis along a discrete but highly conserved region at the core of HIV-1 Nef. We identified the GPG-motif, located at the 121–137 region of HIV-1 NL4.3 Nef, as a novel protein signature strictly required for the p56Lck dependent Nef-induced CD4-downregulation in T-cells. Since the Nef-GPG motif was dispensable for CD4-downregulation in HeLa-CD4 cells, Nef/AP-1 interaction and Nef-dependent effects on Tf-R trafficking, the observed effects on CD4 downregulation cannot be attributed to structure constraints or to alterations on general protein trafficking. Besides, we found that the GPG-motif was also required for Nef-dependent inhibition of ring actin re-organization upon TCR triggering and MHCI downregulation, suggesting that the GPG-motif could actively cooperate with the Nef PxxP motif for these HIV-1 Nef-related effects. Finally, we observed that the Nef-GPG motif was required for optimal infectivity of those viruses produced in T-cells. According to these findings, we propose the conserved GPG-motif in HIV-1 Nef as functional region required for HIV-1 infectivity and therefore with a potential interest for the interference of Nef activity during HIV-1 infection. PMID:26700863

Helix-packing motifs in membrane proteins.

PubMed

Walters, R F S; DeGrado, W F

2006-09-12

The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd 5 A), allowing 90% of the library to be assigned to clusters consisting of at least five members. Surprisingly, three quarters of the helical pairs belong to one of five tightly clustered motifs whose structural features can be understood in terms of simple principles of helix-helix packing. Thus, the universe of common transmembrane helix-pairing motifs is relatively simple. The largest cluster, which comprises 29% of the library members, consists of an antiparallel motif with left-handed packing angles, and it is frequently stabilized by packing of small side chains occurring every seven residues in the sequence. Right-handed parallel and antiparallel structures show a similar tendency to segregate small residues to the helix-helix interface but spaced at four-residue intervals. Position-specific sequence propensities were derived for the most populated motifs. These structural and sequential motifs should be quite useful for the design and structural prediction of membrane proteins.

4-(4-Bromo-phen-yl)-1-(2,6-difluoro-benz-yl)-3-(3,4,5-trimeth-oxy-phen-yl)-1H-1,2,4-triazole-5(4H)-thione.

PubMed

Fun, Hoong-Kun; Ooi, Chin Wei; Chandrakantha, B; Isloor, Arun M; Shetty, Prakash

2012-01-01

In the title compound, C(24)H(20)BrF(2)N(3)O(3)S, the triazole ring (r.m.s. deviation = 0.0107 Å) makes dihedral angles of 28.18 (14), 63.76 (14) and 77.01 (18)°, respectively, with the trimeth-oxy-, bromo-, and difluoro-substituted benzene rings. The C atoms of the meta meth-oxy groups are roughly coplanar with their ring [displacements = -0.289 (4) and 0.083 (7) Å], whereas the C atom of the para group is displaced [1.117 (3) Å]. In the crystal, inversion dimers linked by two pairs of C-H⋯O hydrogen bonds occur. The ring motif of the two hydrogen bonds to their symmetry-generated O-atom acceptors is R(2) (2)(8).

Loss of ring current O+ ions due to interaction with Pc 5 waves

NASA Astrophysics Data System (ADS)

Hudson, Mary; Chan, Anthony; Roth, Ilan

1993-01-01

The behavior of ring current ions in low-frequency geomagnetic pulsations is investigated analytically and numerically. We focus primarily on ring current O+ ions, whose flux increases dramatically during geomagnetic storms and decays at a rate which is not fully explained by collisional processes. This paper presents a new loss mechanism for the O+ ions due to the combined effects of convection and corotation electric fields and interaction with Pc 5 waves (wave period: 150-600 s) via a magnetic drift-bounce resonance. A test particle code has been developed to calculate the motion of the ring current O+ ions in a time-independent dipole magnetic field, and convection and corotation electric fields, plus Pc 5 wave fields, for which a simple analytical model has been formulated based on spacecraft observations. For given fields, whether a particle gains or loses energy depends on its initial kinetic energy, pitch angle at the equatorial plane, and the position of its guiding center with respect to the azimuthal phase of the wave. The ring current O+ ions show a dispersion in energies and L values with decreasing local time across the dayside, and a bulk shift to lower energies and higher L values. The former is due to the wave-particle interaction causing the ion to gain or lose energy, while the latter is due to the convection electric field. Our simulations show that, due to the interaction with the Pc 5 waves, the particle's kinetic energy can drop below that required to overcome the convection potential and the particle will be lost to the dayside magnetopause by a sunward E×B drift. This may contribute to the loss of O+ ions at intermediate energies (tens of keV) observed during the recovery phase of geomagnetic storms.

The PDZ-binding motif of Yes-associated protein is required for its co-activation of TEAD-mediated CTGF transcription and oncogenic cell transforming activity

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

Shimomura, Tadanori; Miyamura, Norio; Hata, Shoji

2014-01-17

Highlights: •Loss of the PDZ-binding motif inhibits constitutively active YAP (5SA)-induced oncogenic cell transformation. •The PDZ-binding motif of YAP promotes its nuclear localization in cultured cells and mouse liver. •Loss of the PDZ-binding motif inhibits YAP (5SA)-induced CTGF transcription in cultured cells and mouse liver. -- Abstract: YAP is a transcriptional co-activator that acts downstream of the Hippo signaling pathway and regulates multiple cellular processes, including proliferation. Hippo pathway-dependent phosphorylation of YAP negatively regulates its function. Conversely, attenuation of Hippo-mediated phosphorylation of YAP increases its ability to stimulate proliferation and eventually induces oncogenic transformation. The C-terminus of YAP contains amore » highly conserved PDZ-binding motif that regulates YAP’s functions in multiple ways. However, to date, the importance of the PDZ-binding motif to the oncogenic cell transforming activity of YAP has not been determined. In this study, we disrupted the PDZ-binding motif in the YAP (5SA) protein, in which the sites normally targeted by Hippo pathway-dependent phosphorylation are mutated. We found that loss of the PDZ-binding motif significantly inhibited the oncogenic transformation of cultured cells induced by YAP (5SA). In addition, the increased nuclear localization of YAP (5SA) and its enhanced activation of TEAD-dependent transcription of the cell proliferation gene CTGF were strongly reduced when the PDZ-binding motif was deleted. Similarly, in mouse liver, deletion of the PDZ-binding motif suppressed nuclear localization of YAP (5SA) and YAP (5SA)-induced CTGF expression. Taken together, our results indicate that the PDZ-binding motif of YAP is critical for YAP-mediated oncogenesis, and that this effect is mediated by YAP’s co-activation of TEAD-mediated CTGF transcription.« less

Motif discovery and motif finding from genome-mapped DNase footprint data.

PubMed

Kulakovskiy, Ivan V; Favorov, Alexander V; Makeev, Vsevolod J

2009-09-15

Footprint data is an important source of information on transcription factor recognition motifs. However, a footprinting fragment can contain no sequences similar to known protein recognition sites. Inspection of genome fragments nearby can help to identify missing site positions. Genome fragments containing footprints were supplied to a pipeline that constructed a position weight matrix (PWM) for different motif lengths and selected the optimal PWM. Fragments were aligned with the SeSiMCMC sampler and a new heuristic algorithm, Bigfoot. Footprints with missing hits were found for approximately 50% of factors. Adding only 2 bp on both sides of a footprinting fragment recovered most hits. We automatically constructed motifs for 41 Drosophila factors. New motifs can recognize footprints with a greater sensitivity at the same false positive rate than existing models. Also we discuss possible overfitting of constructed motifs. Software and the collection of regulatory motifs are freely available at http://line.imb.ac.ru/DMMPMM.

BOREAS TE-5 Tree Ring and Carbon Isotope Ratio Data

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Curd, Shelaine (Editor); Ehleriinger, Jim; Brooks, J. Renee; Flanagan, Larry

2000-01-01

The BOREAS TE-5 team collected several data sets to investigate the vegetation-atmosphere CO2 and H2O exchange processes. These data include tree ring widths and cellulose carbon isotope data from coniferous trees collected at the BOREAS NSA and SSA in 1993 and 1994 by the BOREAS TE-5 team. Ring width data are provided for both Picea mariana and Pinus banksiana. The carbon isotope data are provided only for Pinus banksiana. The data are provided in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

Synthesis of ( 2S, 4S)-4-phenylamino-5-oxoproline derivatives.

PubMed

Nizova, I A; Krasnov, V P; Levit, G L; Kodess, M I

2002-01-01

The paper describes the synthesis of ( 2S, 4S)-4-(N-Ts)- and ( 2S, 4S)-4-(N-Boc)-phenylamino-5-oxoprolines (pyroglutamic acid). These derivatives have been shown to be useful for synthesis of their amides and peptides in spite of steric hindrances caused by bulky groups adjacent to the reaction centre. Under the conditions applied no lactam ring opening and no loss of stereochemical integrity of any of the chiral centres were observed, which has been confirmed by NMR techniques.

Tyrocidine A Analogues Bearing the Planar d-Phe-2-Abz Turn Motif: How Conformation Impacts Bioactivity.

PubMed

Cameron, Alan J; Edwards, Patrick J B; Harjes, Elena; Sarojini, Vijayalekshmi

2017-12-14

The d-Phe-Pro β-turn of the cyclic β-hairpin antimicrobial decapeptide tyrocidine A, (Tyrc A) was substituted with the d-Phe-2-aminobenzoic acid (2-Abz) motif in a synthetic analogue (1). The NMR structure of 1 demonstrated that compound 1 retained the β-hairpin structure of Tyrc A with additional planarity, resulting in approximately 30-fold reduced hemolysis than Tyrc A. Although antibacterial activity was partially compromised, a single Gln to Lys substitution (2) restored activity equivalent to Tyrc A against S. aureus, enhanced activity against two Gram negative strains and maintained the reduced hemeloysis of 1. Analysis by transmission electron microscopy (TEM) suggested a membrane lytic mechanism of action for these peptides. Compound 2 also exhibits nanomolar antifungal activity in synergy with amphotericin B. The d-Phe-2-Abz turn may serve as a tool for the synthesis of structurally predictable β-hairpin libraries. Unlike traditional β-turn motifs such as d-Pro-Gly, both the 2-Abz and d-Phe rings may be further functionalized.

How the Enceladus dust plume feeds Saturn’s E ring

NASA Astrophysics Data System (ADS)

Kempf, Sascha; Beckmann, Uwe; Schmidt, Jürgen

2010-04-01

Pre-Cassini models of Saturn's E ring [Horányi, M., Burns, J., Hamilton, D., 1992. Icarus 97, 248-259; Juhász, A., Horányi, M., 2002. J. Geophys. Res. 107, 1-10] failed to reproduce its peculiar vertical structure inferred from Earth-bound observations [de Pater, I., Martin, S.C., Showalter, M.R., 2004. Icarus 172, 446-454]. After the discovery of an active ice-volcanism of Saturn's icy moon Enceladus the relevance of the directed injection of particles for the vertical ring structure of the E ring was swiftly recognised [Juhász, A., Horányi, M., Morfill, G.E., 2007. Geophys. Res. Lett. 34, L09104; Kempf, S., Beckmann, U., Moragas-Klostermeyer, G., Postberg, F., Srama, R., Economou, T., Schmidt, J., Spahn, F., Grün, E., 2008. Icarus 193, 420-437]. However, simple models for the delivery of particles from the plume to the ring predict a too small vertical ring thickness and overestimate the amount of the injected dust. Here we report on numerical simulations of grains leaving the plume and populating the dust torus of Enceladus. We run a large number of dynamical simulations including gravity and Lorentz force to investigate the earliest phase of the ring particle life span. The evolution of the electrostatic charge carried by the initially uncharged grains is treated selfconsistently. Freshly ejected plume particles are moving in almost circular orbits because the Enceladus orbital speed exceeds the particles' ejection speeds by far. Only a small fraction of grains that leave the Hill sphere of Enceladus survive the next encounter with the moon. Thus, the flux and size distribution of the surviving grains, replenishing the ring particle reservoir, differs significantly from the flux and size distribution of the particles freshly ejected from the plume. Our numerical simulations reproduce the vertical ring profile measured by the Cassini Cosmic Dust Analyzer (CDA) [Kempf, S., Beckmann, U., Moragas-Klostermeyer, G., Postberg, F., Srama, R., EconoDmou, T

Tripartite motif ligases catalyze polyubiquitin chain formation through a cooperative allosteric mechanism.

PubMed

Streich, Frederick C; Ronchi, Virginia P; Connick, J Patrick; Haas, Arthur L

2013-03-22

Ligation of polyubiquitin chains to proteins is a fundamental post-translational modification, often resulting in targeted degradation of conjugated proteins. Attachment of polyubiquitin chains requires the activities of an E1 activating enzyme, an E2 carrier protein, and an E3 ligase. The mechanism by which polyubiquitin chains are formed remains largely speculative, especially for RING-based ligases. The tripartite motif (TRIM) superfamily of ligases functions in many cellular processes including innate immunity, cellular localization, development and differentiation, signaling, and cancer progression. The present results show that TRIM ligases catalyze polyubiquitin chain formation in the absence of substrate, the rates of which can be used as a functional readout of enzyme function. Initial rate studies under biochemically defined conditions show that TRIM32 and TRIM25 are specific for the Ubc5 family of E2-conjugating proteins and, along with TRIM5α, exhibit cooperative kinetics with respect to Ubc5 concentration, with submicromolar [S]0.5 and Hill coefficients of 3-5, suggesting they possess multiple binding sites for their cognate E2-ubiquitin thioester. Mutation studies reveal a second, non-canonical binding site encompassing the C-terminal Ubc5α-helix. Polyubiquitin chain formation requires TRIM subunit oligomerization through the conserved coiled-coil domain, but can be partially replaced by fusing the catalytic domain to GST to promote dimerization. Other results suggest that TRIM32 assembles polyubiquitin chains as a Ubc5-linked thioester intermediate. These results represent the first detailed mechanistic study of TRIM ligase activity and provide a functional context for oligomerization observed in the superfamily.

Archaea S-layer nanotube from a "black smoker" in complex with cyclo-octasulfur (S8 ) rings.

PubMed

McDougall, Matthew; Francisco, Olga; Harder-Viddal, Candice; Roshko, Roy; Meier, Markus; Stetefeld, Jörg

2017-12-01

Elemental sulfur exists primarily as an S80 ring and serves as terminal electron acceptor for a variety of sulfur-fermenting bacteria. Hyperthermophilic archaea from black smoker vents are an exciting research tool to advance our knowledge of sulfur respiration under extreme conditions. Here, we use a hybrid method approach to demonstrate that the proteinaceous cavities of the S-layer nanotube of the hyperthermophilic archaeon Staphylothermus marinus act as a storage reservoir for cyclo-octasulfur S8. Fully atomistic molecular dynamics (MD) simulations were performed and the method of multiconfigurational thermodynamic integration was employed to compute the absolute free energy for transferring a ring of elemental sulfur S8 from an aqueous bath into the largest hydrophobic cavity of a fragment of archaeal tetrabrachion. Comparisons with earlier MD studies of the free energy of hydration as a function of water occupancy in the same cavity of archaeal tetrabrachion show that the sulfur ring is energetically favored over water. © 2017 Wiley Periodicals, Inc.

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

PubMed Central

Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

2013-01-01

The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

A R/K-rich motif in the C-terminal of the homeodomain is required for complete translocating of NKX2.5 protein into nucleus.

PubMed

Ouyang, Ping; Zhang, He; Fan, Zhaolan; Wei, Pei; Huang, Zhigang; Wang, Sen; Li, Tao

2016-11-05

NKX2.5 plays important roles in heart development. Being a transcription factor, NKX2.5 exerts its biological functions in nucleus. However, the sequence motif that localize NKX2.5 into nucleus is still not clear. Here, we found a R/K-rich sequence motif from Q187 to R197 (QNRRYKCKRQR) was required for exclusive nuclear localization of NKX2.5. Eight truncated plasmids (E109X, Q149X, Q170X, Q187X, Q198X, Y256X, Y259X, and C264X) which were associated with congenital heart disease (CHD) were constructed. Compared with the wild type NKX2.5, the proteins E109X, Q149X, Q170X, Q187X without intact homeodomain (HD) showed no transcriptional activity while Q198X, Y256X, Y259X and C264X with intact HD showed 50 to 66% transcriptional activity. E109X, Q149X, Q170X, Q187X without intact HD localized in the cytoplasm and nucleus simultaneously and Q198X, Y256X, Y259X and C264X with intact HD localized completely in nucleus. These results inferred the indispensability of 187QNRRYKCKRQR197 in exclusive nucleus localization. Additionally, this sequence motif was very conservative among human, mouse and rat, indicating this motif was important for NKX2.5 function. Thus, we concluded that R/K-rich sequence motif 187QNRRYKCKRQR197 played a central role for NKX2.5 nuclear localization. Our findings provided a clue to understand the mechanisms between the truncated NKX2.5 mutants and CHD. Copyright © 2016 Elsevier B.V. All rights reserved.

New observations and a photographic atlas of polar-ring galaxies

NASA Technical Reports Server (NTRS)

Whitmore, Bradley C.; Lucas, Ray A.; Mcelroy, Douglas B.; Steiman-Cameron, Thomas Y.; Sackett, Penny D.

1990-01-01

A photographic atlas of polar-ring galaxies and related objects is presented. The atlas includes kinematically confirmed polar-ring galaxies (category A), good candidates based on their morphological appearance (category B), possible candidates (category C), and possibly related objects (category D). New photometric and kinematic observations are reported for several galaxies in the catalog, including observations that show that UGC 7576 and UGC 9796 ( = II ZW 73) are S0 galaxies with polar rings. Roughly 0.5 percent of all nearby S0 galaxies appear to have polar rings. When corrected for various selection effects (e.g., nonoptimal viewing orientation, possible dimming, or limited lifetime of the ring) the percentage increases to about 5 percent of S0 galaxies which have, or have had a polar ring.

Photochemistry in Saturn’s Ring-Shadowed Atmosphere: Modulation of Hydrocarbons and Aerosols

NASA Astrophysics Data System (ADS)

Edgington, Scott G.; Atreya, Sushil K.; Wilson, Eric H.; Baines, Kevin H.; West, Robert A.; Bjoraker, Gordon L.; Fletcher, Leigh N.; Momary, Tom

2015-11-01

Cassini has been orbiting Saturn for over eleven years now. During this epoch, the ring shadow has moved from covering much of the northern hemisphere (the solar inclination was 24 degrees) to covering a large swath south of the equator and it continues to move southward. At Saturn Orbit Insertion in 2004, the projection of the A-ring onto Saturn reached as far as 40N along the central meridian (52N at the terminator). At its maximum extent, the ring shadow can reach as far as 48N/S (58N/S at the terminator). The net effect is that the intensity of both ultraviolet and visible sunlight penetrating through the rings to any particular latitude will vary depending on both Saturn’s axis relative to the Sun and the optical thickness of each ring system. In essence, the rings act like semi-transparent venetian blinds.Our previous work, examined the variation of the solar flux as a function of solar inclination, i.e. for each 7.25-year season at Saturn. Here, we report on the impact of the oscillating ring shadow on the photolysis and production rates of hydrocarbons (acetylene, ethane, propane, and benzene) and phosphine in Saturn’s stratosphere and upper troposphere. The impact of these production and loss rates on the abundance of long-lived photochemical products leading to haze formation are explored. Similarly, we assess their impact on phosphine abundance, a disequilibrium species whose presence in the upper troposphere can be used as a tracer of convective processes in the deeper atmosphere.We will also present our ongoing analysis of Cassini’s datasets that provide an estimate of the evolving haze content of the northern hemisphere and we will begin to assess the implications for dynamical mixing. In particular, we will examine how the now famous hexagonal jet stream acts like a barrier to transport, isolating Saturn’s north polar region from outside transport of photochemically-generated molecules and haze.The research described in this paper was carried

Evidence for Bs* Bs* production at the Gamma(5S) resonance.

PubMed

Artuso, M; Boulahouache, C; Blusk, S; Butt, J; Dorjkhaidav, O; Li, J; Menaa, N; Mountain, R; Nandakumar, R; Randrianarivony, K; Redjimi, R; Sia, R; Skwarnicki, T; Stone, S; Wang, J C; Zhang, K; Csorna, S E; Bonvicini, G; Cinabro, D; Dubrovin, M; Bornheim, A; Pappas, S P; Weinstein, A J; Briere, R A; Chen, G P; Chen, J; Ferguson, T; Tatishvili, G; Vogel, H; Watkins, M E; Rosner, J L; Adam, N E; Alexander, J P; Berkelman, K; Cassel, D G; Crede, V; Duboscq, J E; Ecklund, K M; Ehrlich, R; Fields, L; Galik, R S; Gibbons, L; Gittelman, B; Gray, R; Gray, S W; Hartill, D L; Heltsley, B K; Hertz, D; Jones, C D; Kandaswamy, J; Kreinick, D L; Kuznetsov, V E; Mahlke-Krüger, H; Meyer, T O; Onyisi, P U E; Patterson, J R; Peterson, D; Phillips, E A; Pivarski, J; Riley, D; Ryd, A; Sadoff, A J; Schwarthoff, H; Shi, X; Shepherd, M R; Stroiney, S; Sun, W M; Urner, D; Wilksen, T; Weaver, K M; Weinberger, M; Athar, S B; Avery, P; Breva-Newell, L; Patel, R; Potlia, V; Stoeck, H; Yelton, J; Rubin, P; Cawlfield, C; Eisenstein, B I; Gollin, G D; Karliner, I; Kim, D; Lowrey, N; Naik, P; Sedlack, C; Selen, M; White, E J; Williams, J; Wiss, J; Asner, D M; Edwards, K W; Besson, D; Pedlar, T K; Cronin-Hennessy, D; Gao, K Y; Gong, D T; Hietala, J; Kubota, Y; Klein, T; Lang, B W; Li, S Z; Poling, R; Scott, A W; Smith, A; Dobbs, S; Metreveli, Z; Seth, K K; Tomaradze, A; Zweber, P; Ernst, J; Arms, K; Severini, H; Dytman, S A; Love, W; Mehrabyan, S; Mueller, J A; Savinov, V; Li, Z; Lopez, A; Mendez, H; Ramirez, J; Huang, G S; Miller, D H; Pavlunin, V; Sanghi, B; Shipsey, I P J; Adams, G S; Cravey, M; Cummings, J P; Danko, I; Napolitano, J; He, Q; Muramatsu, H; Park, C S; Thorndike, E H; Coan, T E; Gao, Y S; Liu, F; Stroynowski, R

2005-12-31

We use data collected by the CLEO III detector at the Cornell Electron Storage Ring to measure the inclusive yields of D(s) mesons as B(Y(5S) --> D(s)X) = (44-7 +/- 4.2 +/- 9.9)% and B(Y(4S) --> D(s)X) = (18.1 +/- 0.5 +/- 2.8)%. From these measurements, we make a model dependent estimate of the ratio of B(s)*B(s)* to the total bb quark pair production of (16.0 +/- 2.6 +/- 5.8)% at the Y(5S) energy.

Expression of 5 S rRNA genes linked to 35 S rDNA in plants, their epigenetic modification and regulatory element divergence

PubMed Central

2012-01-01

Background In plants, the 5 S rRNA genes usually occur as separate tandems (S-type arrangement) or, less commonly, linked to 35 S rDNA units (L-type). The activity of linked genes remains unknown so far. We studied the homogeneity and expression of 5 S genes in several species from family Asteraceae known to contain linked 35 S-5 S units. Additionally, their methylation status was determined using bisulfite sequencing. Fluorescence in situ hybridization was applied to reveal the sub-nuclear positions of rDNA arrays. Results We found that homogenization of L-type units went to completion in most (4/6) but not all species. Two species contained major L-type and minor S-type units (termed Ls-type). The linked genes dominate 5 S rDNA expression while the separate tandems do not seem to be expressed. Members of tribe Anthemideae evolved functional variants of the polymerase III promoter in which a residing C-box element differs from the canonical angiosperm motif by as much as 30%. On this basis, a more relaxed consensus sequence of a plant C-box: (5’-RGSWTGGGTG-3’) is proposed. The 5 S paralogs display heavy DNA methylation similarly as to their unlinked counterparts. FISH revealed the close association of 35 S-5 S arrays with nucleolar periphery indicating that transcription of 5 S genes may occur in this territory. Conclusions We show that the unusual linked arrangement of 5 S genes, occurring in several plant species, is fully compatible with their expression and functionality. This extraordinary 5 S gene dynamics is manifested at different levels, such as variation in intrachromosomal positions, unit structure, epigenetic modification and considerable divergence of regulatory motifs. PMID:22716941

Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires.

PubMed

Bergseng, Elin; Dørum, Siri; Arntzen, Magnus Ø; Nielsen, Morten; Nygård, Ståle; Buus, Søren; de Souza, Gustavo A; Sollid, Ludvig M

2015-02-01

Celiac disease is caused by intolerance to cereal gluten proteins, and HLA-DQ molecules are involved in the disease pathogenesis by presentation of gluten peptides to CD4(+) T cells. The α- or β-chain sharing HLA molecules DQ2.5, DQ2.2, and DQ7.5 display different risks for the disease. It was recently demonstrated that T cells of DQ2.5 and DQ2.2 patients recognize distinct sets of gluten epitopes, suggesting that these two DQ2 variants select different peptides for display. To explore whether this is the case, we performed a comprehensive comparison of the endogenous self-peptides bound to HLA-DQ molecules of B-lymphoblastoid cell lines. Peptides were eluted from affinity-purified HLA molecules of nine cell lines and subjected to quadrupole orbitrap mass spectrometry and MaxQuant software analysis. Altogether, 12,712 endogenous peptides were identified at very different relative abundances. Hierarchical clustering of normalized quantitative data demonstrated significant differences in repertoires of peptides between the three DQ variant molecules. The neural network-based method, NNAlign, was used to identify peptide-binding motifs. The binding motifs of DQ2.5 and DQ7.5 concurred with previously established binding motifs. The binding motif of DQ2.2 was strikingly different from that of DQ2.5 with position P3 being a major anchor having a preference for threonine and serine. This is notable as three recently identified epitopes of gluten recognized by T cells of DQ2.2 celiac patients harbor serine at position P3. This study demonstrates that relative quantitative comparison of endogenous peptides sampled from our protein metabolism by HLA molecules provides clues to understand HLA association with disease.

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

PubMed Central

2014-01-01

Abstract ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data. Reviewers This article was reviewed by Prof. Sandor Pongor, Dr. Yuriy Gusev, and Dr. Shyam Prabhakar (nominated by Prof. Limsoon Wong). PMID:24555784

New patterns in dust off the edge of Saturn’s main rings

NASA Astrophysics Data System (ADS)

Chancia, Robert Ormal; Hedman, Matthew M.; Ye, Shengyi; Kurth, William S.

2017-10-01

The Roche Division is a 3000-km-span of diffuse dust located at the outer edge of Saturn’s main ring system between the A and F rings. Several high-resolution images from Cassini’s orbit insertion revealed two regions with higher concentrations of dust within the Roche Division. These proposed dusty ringlets R/2004 S1 (radius=137,630 km) and R/2004 S2 (radius=138,900 km) lie coincident with the orbit of Atlas and slightly interior to the orbit of Prometheus respectively (Porco et al. 2005a Science). Using several image sequences later obtained by Cassini Hedman et al. 2009 (Icarus) found that these concentrations of dusty ring material are not simple ringlets, but are in fact organized into canted azimuthal brightness variations with a periodicity akin to a 3:4 resonance with Saturn’s rotation rate. The presumed perturbing phenomenon is Saturn’s kilometric radiation (SKR), a strong low wavelength component of the planet’s radio emissions, whose power oscillates near the planet’s rotation rate at a frequency matching the Roche Division structures. However, over the course of the Cassini mission the SKR period has varied by at least 7 minutes. As a result, the location of the resonance moved interior to the edge of the A ring and out of the Roche Division around the time of Saturn’s equinox. Subsequent observations of the Roche Division in the this time period show no evidence of the prominent structures previously observed during the first few years of the Cassini mission. Recently, the 3:4 resonant structures have reappeared in the Roche Division as one of the SKR periods has increased. Here we show that the these dusty Roche Division structures are present in sync with the varying SKR period using images sequences spanning the entire Cassini mission. We also highlight some particularly optimal observations, obtained during Cassini’s F-ring proximal and grand finale orbits, which reveal the dusty structure of the Roche Division in unprecedented

Self-assembling of dihydroxypropyl 5,6-dihydrothymine derivatives

NASA Astrophysics Data System (ADS)

Cetina, Mario; Makarević, Janja; Nura-Lama, Afërdita

2010-09-01

( R, S)-1-(2',3'-Dibenzoyloxypropyl)-5,6-dihydrothymine ( 2) was synthesized from ( R, S)-1-(2',3'-dihydroxypropyl)-5,6-dihydrothymine and its structure has been analyzed by X-ray diffraction, NMR and FTIR spectroscopic methods. The molecular structure and supramolecular assembling of 2 is compared with the structure of its dimesyloxypropyl analogue ( 1). Compound 1 crystallizes as cocrystal of two diastereoisomers, while 2 crystallizes as a racemic mixture. Main hydrogen-bonded motif in both compounds is dimer formed by pair of N sbnd H···O( dbnd C) hydrogen bonds, which are further linked by C sbnd H···O hydrogen bonds. Phenyl rings of dibenzoyl-dihydropyrimidine moieties of 2 participate also in supramolecular aggregation via three C sbnd H···π interactions. Hydrogen bonding as driving force of 2 self-assembly was proving by the NMR and FTIR spectroscopy.

Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase: DAWIDZIAK et al.

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

Dawidziak, Daria M.; Sanchez, Jacint G.; Wagner, Jonathan M.

Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction of the two attendant RING domains. The RING domains themselves bind E2 conjugating enzymes as dimers, implying that an active TRIM ligase requires higher-order oligomerization of the basal coiled-coil dimers. Here, we report crystal structures of the TRIM23 RING domain in isolation and in complex with an E2–ubiquitin conjugate. Our results indicate that TRIM23 enzymatic activity requires RING dimerization, consistent with the general model of TRIM activation.

[Prediction of Promoter Motifs in Virophages].

PubMed

Gong, Chaowen; Zhou, Xuewen; Pan, Yingjie; Wang, Yongjie

2015-07-01

Virophages have crucial roles in ecosystems and are the transport vectors of genetic materials. To shed light on regulation and control mechanisms in virophage--host systems as well as evolution between virophages and their hosts, the promoter motifs of virophages were predicted on the upstream regions of start codons using an analytical tool for prediction of promoter motifs: Multiple EM for Motif Elicitation. Seventeen potential promoter motifs were identified based on the E-value, location, number and length of promoters in genomes. Sputnik and zamilon motif 2 with AT-rich regions were distributed widely on genomes, suggesting that these motifs may be associated with regulation of the expression of various genes. Motifs containing the TCTA box were predicted to be late promoter motif in mavirus; motifs containing the ATCT box were the potential late promoter motif in the Ace Lake mavirus . AT-rich regions were identified on motif 2 in the Organic Lake virophage, motif 3 in Yellowstone Lake virophage (YSLV)1 and 2, motif 1 in YSLV3, and motif 1 and 2 in YSLV4, respectively. AT-rich regions were distributed widely on the genomes of virophages. All of these motifs may be promoter motifs of virophages. Our results provide insights into further exploration of temporal expression of genes in virophages as well as associations between virophages and giant viruses.

Stochastic events lead to accretion in Saturn’s rings

NASA Astrophysics Data System (ADS)

Esposito, L. W.

2009-12-01

UVIS occultations indicate accretion is triggered at the B ring edge, in strong density waves in ring A and in the F ring. Moons may trigger accretion by streamline crowding (Lewis & Stewart); which enhances collisions, leading to accretion; increasing random velocities; leading to more collisions and more accretion. Cassini occultations of these strongly perturbed locations show not only accretion but also disaggregation, with time scales of hours to weeks. The collisions may lead to temporary aggregations via stochastic events: they can compress unconsolidated objects, trigger adhesion or bring small pieces into contact with larger or higher-density seeds. Disaggregation then can follow from disruptive collisions or tidal shedding. In the accretion/disruption balance, increased random motions could eventually give the upper hand to disruption… just as ‘irrational exuberance’ can lead to financial panic in the economy; or the overpopulation of hares can lead to boom-and-bust in the population of foxes. This unstable equilibrium can similarly give rise to episodic cycles in accretion: explaining why the observable ring features that indicate embedded objects have been increasing since the beginning of Cassini’s observations of Saturn in 2004.

Planetary Rings

NASA Astrophysics Data System (ADS)

Esposito, Larry W.

2011-07-01

Preface; 1. Introduction: the allure of ringed planets; 2. Studies of planetary rings 1610-2004; 3. Diversity of planetary rings; 4. Individual ring particles and their collisions; 5. Large-scale ring evolution; 6. Moons confine and sculpt rings; 7. Explaining ring phenomena; 8. N-Body simulations; 9. Stochastic models; 10. Age and evolution of rings; 11. Saturn's mysterious F ring; 12. Neptune's partial rings; 13. Jupiter's ring-moon system after Galileo; 14. Ring photometry; 15. Dusty rings; 16. Cassini observations; 17. Summary: the big questions; Glossary; References; Index.

DMINDA: an integrated web server for DNA motif identification and analyses.

PubMed

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-07-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Planetary Rings

NASA Astrophysics Data System (ADS)

Esposito, Larry

2014-03-01

Preface: a personal view of planetary rings; 1. Introduction: the allure of the ringed planets; 2. Studies of planetary rings 1610-2013; 3. Diversity of planetary rings; 4. Individual ring particles and their collisions; 5. Large-scale ring evolution; 6. Moons confine and sculpt rings; 7. Explaining ring phenomena; 8. N-body simulations; 9. Stochastic models; 10. Age and evolution of rings; 11. Saturn's mysterious F ring; 12. Uranus' rings and moons; 13. Neptune's partial rings; 14. Jupiter's ring-moon system after Galileo and New Horizons; 15. Ring photometry; 16. Dusty rings; 17. Concluding remarks; Afterword; Glossary; References; Index.

Nardo Ring, Italy

NASA Technical Reports Server (NTRS)

2008-01-01

The Nardo Ring is a striking visual feature from space, and astronauts have photographed it several times. The Ring is a race car test track; it is 12.5 kilometers long and steeply banked to reduce the amount of active steering needed by drivers. The Nardo Ring lies in a remote area on the heel of Italy's 'boot,' 50 kilometers east of the naval port of Taranto. The Ring encompasses a number of active (green) and fallow (brown to dark brown) agricultural fields. In this zone of intensive agriculture, farmers gain access to their fields through the Ring via a series of underpasses. Winding features within the southern section of the Ring appear to be smaller, unused race tracks.

The image covers an area of 18.8 x 16.4 km, was acquired on August 17. 2007, and is located at 49.3 degrees north latitude, 17.8 degrees east longitude.

The U.S. science team is located at NASA's Jet Propulsion Laboratory, Pasadena, Calif. The Terra mission is part of NASA's Science Mission Directorate.

Aromaticity of strongly bent benzene rings: persistence of a diatropic ring current and its shielding cone in [5]paracyclophane.

PubMed

Jenneskens, Leonardus W; Havenith, Remco W A; Soncini, Alessandro; Fowler, Patrick W

2011-10-06

Direct evaluation of the induced π current density in [5]paracyclophane (1) shows that, despite the significant non-planarity (α = 23.2°) enforced by the pentamethylene bridge, there is only a modest (ca. 17%) reduction in the π ring current, justifying the use of shielding-cone arguments for the assignment of (1)H NMR chemical shifts of 1 and the claim that the non-planar benzene ring in 1 retains its aromaticity (on the magnetic criterion).

Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation*

PubMed Central

Habisov, Sabrina; Huber, Jessica; Ichimura, Yoshinobu; Akutsu, Masato; Rogova, Natalia; Loehr, Frank; McEwan, David G.; Johansen, Terje; Dikic, Ivan; Doetsch, Volker; Komatsu, Masaaki; Rogov, Vladimir V.; Kirkin, Vladimir

2016-01-01

The covalent conjugation of ubiquitin-fold modifier 1 (UFM1) to proteins generates a signal that regulates transcription, response to cell stress, and differentiation. Ufmylation is initiated by ubiquitin-like modifier activating enzyme 5 (UBA5), which activates and transfers UFM1 to ubiquitin-fold modifier-conjugating enzyme 1 (UFC1). The details of the interaction between UFM1 and UBA5 required for UFM1 activation and its downstream transfer are however unclear. In this study, we described and characterized a combined linear LC3-interacting region/UFM1-interacting motif (LIR/UFIM) within the C terminus of UBA5. This single motif ensures that UBA5 binds both UFM1 and light chain 3/γ-aminobutyric acid receptor-associated proteins (LC3/GABARAP), two ubiquitin (Ub)-like proteins. We demonstrated that LIR/UFIM is required for the full biological activity of UBA5 and for the effective transfer of UFM1 onto UFC1 and a downstream protein substrate both in vitro and in cells. Taken together, our study provides important structural and functional insights into the interaction between UBA5 and Ub-like modifiers, improving the understanding of the biology of the ufmylation pathway. PMID:26929408

The conformational free-energy landscape of β-D-mannopyranose: evidence for a (1)S(5) → B(2,5) → (O)S(2) catalytic itinerary in β-mannosidases.

PubMed

Ardèvol, Albert; Biarnés, Xevi; Planas, Antoni; Rovira, Carme

2010-11-17

The mechanism of glycosidic bond cleavage by glycosidases involves substrate ring distortions in the Michaelis complex that favor catalysis. Retaining β-mannosidases bind the substrate in a (1)S(5) conformation, and recent experiments have proposed an unusual substrate conformational pathway ((1)S(5) → B(2,5) → (O)S(2)) for the hydrolysis reaction. By means of Car-Parrinello metadynamics simulations, we have obtained the conformational free-energy surface (FES) of a β-d-mannopyranose molecule associated with the ideal Stoddart conformational diagram. We have found that (1)S(5) is among the most stable conformers and simultaneously is the most preactivated conformation in terms of elongation/shortening of the C1-O1/C1-O5 bonds, C1-O1 orientation, and charge development at the anomeric carbon. Analysis of the computed FES gives support to the proposed (1)S(5) → B(2,5) → (O)S(2) catalytic itinerary, showing that the degree of preactivation of the substrate in glycoside hydrolases (GHs) is related to the properties of an isolated sugar ring. We introduce a simple preactivation index integrating several structural, electronic, and energetic properties that can be used to predict the conformation of the substrate in the Michaelis complex of any GH.

1-(2,4-Di-nitro-phen-yl)-2-[(E)-(3,4,5-tri-meth-oxy-benzyl-idene)]hydrazine.

PubMed

Chantrapromma, Suchada; Ruanwas, Pumsak; Boonnak, Nawong; Chidan Kumar, C S; Fun, Hoong-Kun

2014-02-01

Mol-ecules of the title compound, C16H16N4O7, are not planar with a dihedral angle of 5.50 (11)° between the substituted benzene rings. The two meta-meth-oxy groups of the 3,4,5-tri-meth-oxy-benzene moiety lie in the plane of the attached ring [Cmeth-yl-O-C-C torsion angles -0.1 (4)° and -3.7 (3)°] while the para-meth-oxy substituent lies out of the plane [Cmeth-yl-O-C-C, -86.0 (3)°]. An intra-molecular N-H⋯O hydrogen bond involving the 2-nitro substituent generates an S(6) ring motif. In the crystal structure, mol-ecules are linked by weak C-H⋯O inter-actions into screw chains, that are arranged into a sheet parallel to the bc plane. These sheets are connected by π-π stacking inter-actions between the nitro and meth-oxy substituted aromatic rings with a centroid-centroid separation of 3.9420 (13) Å. C-H⋯π contacts further stabilize the two-dimensional network.

Saturn's largest ring.

PubMed

Verbiscer, Anne J; Skrutskie, Michael F; Hamilton, Douglas P

2009-10-22

Most planetary rings in the Solar System lie within a few radii of their host body, because at these distances gravitational accelerations inhibit satellite formation. The best known exceptions are Jupiter's gossamer rings and Saturn's E ring, broad sheets of dust that extend outward until they fade from view at five to ten planetary radii. Source satellites continuously supply the dust, which is subsequently lost in collisions or by radial transport. Here we report that Saturn has an enormous ring associated with its outer moon Phoebe, extending from at least 128R(S) to 207R(S) (Saturn's radius R(S) is 60,330 km). The ring's vertical thickness of 40R(S) matches the range of vertical motion of Phoebe along its orbit. Dynamical considerations argue that these ring particles span the Saturnian system from the main rings to the edges of interplanetary space. The ring's normal optical depth of approximately 2 x 10(-8) is comparable to that of Jupiter's faintest gossamer ring, although its particle number density is several hundred times smaller. Repeated impacts on Phoebe, from both interplanetary and circumplanetary particle populations, probably keep the ring populated with material. Ring particles smaller than centimetres in size slowly migrate inward and many of them ultimately strike the dark leading face of Iapetus.

Motif-based analysis of large nucleotide data sets using MEME-ChIP

PubMed Central

Ma, Wenxiu; Noble, William S; Bailey, Timothy L

2014-01-01

MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can analyze peak regions identified by ChIP-seq, cross-linking sites identified by cLIP-seq and related assays, as well as sets of genomic regions selected using other criteria. MEME-ChIP performs de novo motif discovery, motif enrichment analysis, motif location analysis and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. MEME-ChIP performs two complementary types of de novo motif discovery: weight matrix–based discovery for high accuracy; and word-based discovery for high sensitivity. Motif enrichment analysis using DNA or RNA motifs from human, mouse, worm, fly and other model organisms provides even greater sensitivity. MEME-ChIP’s interactive HTML output groups and aligns significant motifs to ease interpretation. this protocol takes less than 3 h, and it provides motif discovery approaches that are distinct and complementary to other online methods. PMID:24853928

WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches

PubMed Central

Romer, Katherine A.; Kayombya, Guy-Richard; Fraenkel, Ernest

2007-01-01

WebMOTIFS provides a web interface that facilitates the discovery and analysis of DNA-sequence motifs. Several studies have shown that the accuracy of motif discovery can be significantly improved by using multiple de novo motif discovery programs and using randomized control calculations to identify the most significant motifs or by using Bayesian approaches. WebMOTIFS makes it easy to apply these strategies. Using a single submission form, users can run several motif discovery programs and score, cluster and visualize the results. In addition, the Bayesian motif discovery program THEME can be used to determine the class of transcription factors that is most likely to regulate a set of sequences. Input can be provided as a list of gene or probe identifiers. Used with the default settings, WebMOTIFS accurately identifies biologically relevant motifs from diverse data in several species. WebMOTIFS is freely available at http://fraenkel.mit.edu/webmotifs. PMID:17584794

Analysis of septins across kingdoms reveals orthology and new motifs.

PubMed

Pan, Fangfang; Malmberg, Russell L; Momany, Michelle

2007-07-01

Septins are cytoskeletal GTPase proteins first discovered in the fungus Saccharomyces cerevisiae where they organize the septum and link nuclear division with cell division. More recently septins have been found in animals where they are important in processes ranging from actin and microtubule organization to embryonic patterning and where defects in septins have been implicated in human disease. Previous studies suggested that many animal septins fell into independent evolutionary groups, confounding cross-kingdom comparison. In the current work, we identified 162 septins from fungi, microsporidia and animals and analyzed their phylogenetic relationships. There was support for five groups of septins with orthology between kingdoms. Group 1 (which includes S. cerevisiae Cdc10p and human Sept9) and Group 2 (which includes S. cerevisiae Cdc3p and human Sept7) contain sequences from fungi and animals. Group 3 (which includes S. cerevisiae Cdc11p) and Group 4 (which includes S. cerevisiae Cdc12p) contain sequences from fungi and microsporidia. Group 5 (which includes Aspergillus nidulans AspE) contains sequences from filamentous fungi. We suggest a modified nomenclature based on these phylogenetic relationships. Comparative sequence alignments revealed septin derivatives of already known G1, G3 and G4 GTPase motifs, four new motifs from two to twelve amino acids long and six conserved single amino acid positions. One of these new motifs is septin-specific and several are group specific. Our studies provide an evolutionary history for this important family of proteins and a framework and consistent nomenclature for comparison of septin orthologs across kingdoms.

Biological network motif detection and evaluation

PubMed Central

2011-01-01

Background Molecular level of biological data can be constructed into system level of data as biological networks. Network motifs are defined as over-represented small connected subgraphs in networks and they have been used for many biological applications. Since network motif discovery involves computationally challenging processes, previous algorithms have focused on computational efficiency. However, we believe that the biological quality of network motifs is also very important. Results We define biological network motifs as biologically significant subgraphs and traditional network motifs are differentiated as structural network motifs in this paper. We develop five algorithms, namely, EDGEGO-BNM, EDGEBETWEENNESS-BNM, NMF-BNM, NMFGO-BNM and VOLTAGE-BNM, for efficient detection of biological network motifs, and introduce several evaluation measures including motifs included in complex, motifs included in functional module and GO term clustering score in this paper. Experimental results show that EDGEGO-BNM and EDGEBETWEENNESS-BNM perform better than existing algorithms and all of our algorithms are applicable to find structural network motifs as well. Conclusion We provide new approaches to finding network motifs in biological networks. Our algorithms efficiently detect biological network motifs and further improve existing algorithms to find high quality structural network motifs, which would be impossible using existing algorithms. The performances of the algorithms are compared based on our new evaluation measures in biological contexts. We believe that our work gives some guidelines of network motifs research for the biological networks. PMID:22784624

Supramolecular architectures in the salt trimethoprimium ferrocene-1-carboxylate and the cocrystal 4-amino-5-chloro-2,6-dimethylpyrimidine-ferrocene-1-carboxylic acid (1/1).

PubMed

Swinton Darious, Robert; Thomas Muthiah, Packianathan; Perdih, Franc

2017-09-01

In the salt trimethoprimium ferrocenecarboxylate [systematic name: 2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidin-1-ium ferrocene-1-carboxylate], (C 14 H 19 N 4 O 3 )[Fe(C 5 H 5 )(C 6 H 4 O 2 )], (I), of the antibacterial compound trimethoprim, the carboxylate group interacts with the protonated aminopyrimidine group of trimethoprim via two N-H...O hydrogen bonds, generating a robust R 2 2 (8) ring motif (heterosynthon). However, in the cocrystal 4-amino-5-chloro-2,6-dimethylpyrimidine-ferrocene-1-carboxylic acid (1/1), [Fe(C 5 H 5 )(C 6 H 5 O 2 )]·C 6 H 8 ClN 3 , (II), the carboxyl-aminopyrimidine interaction [R 2 2 (8) motif] is absent. The carboxyl group interacts with the pyrimidine ring via a single O-H...N hydrogen bond. The pyrimidine rings, however, form base pairs via a pair of N-H...N hydrogen bonds, generating an R 2 2 (8) supramolecular homosynthon. In salt (I), the unsubstituted cyclopentadienyl ring is disordered over two positions, with a refined site-occupation ratio of 0.573 (10):0.427 (10). In this study, the two five-membered cyclopentadienyl (Cp) rings of ferrocene are in a staggered conformation, as is evident from the C...Cg...Cg...C pseudo-torsion angles, which are in the range 36.13-37.53° for (I) and 22.58-23.46° for (II). Regarding the Cp ring of the minor component in salt (I), the geometry of the ferrocene ring is in an eclipsed conformation, as is evident from the C...Cg...Cg...C pseudo-torsion angles, which are in the range 79.26-80.94°. Both crystal structures are further stabilized by weak π-π interactions.

Hubble reveals the Ring Nebula’s true shape

NASA Image and Video Library

2017-12-08

Caption: In this composite image, visible-light observations by NASA’s Hubble Space Telescope are combined with infrared data from the ground-based Large Binocular Telescope in Arizona to assemble a dramatic view of the well-known Ring Nebula. Credit: NASA, ESA, C.R. Robert O’Dell (Vanderbilt University), G.J. Ferland (University of Kentucky), W.J. Henney and M. Peimbert (National Autonomous University of Mexico) Credit for Large Binocular Telescope data: David Thompson (University of Arizona) ---- The Ring Nebula's distinctive shape makes it a popular illustration for astronomy books. But new observations by NASA's Hubble Space Telescope of the glowing gas shroud around an old, dying, sun-like star reveal a new twist. "The nebula is not like a bagel, but rather, it's like a jelly doughnut, because it's filled with material in the middle," said C. Robert O'Dell of Vanderbilt University in Nashville, Tenn. He leads a research team that used Hubble and several ground-based telescopes to obtain the best view yet of the iconic nebula. The images show a more complex structure than astronomers once thought and have allowed them to construct the most precise 3-D model of the nebula. "With Hubble's detail, we see a completely different shape than what's been thought about historically for this classic nebula," O'Dell said. "The new Hubble observations show the nebula in much clearer detail, and we see things are not as simple as we previously thought." The Ring Nebula is about 2,000 light-years from Earth and measures roughly 1 light-year across. Located in the constellation Lyra, the nebula is a popular target for amateur astronomers. Read more: 1.usa.gov/14VAOMk 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

3-Phenyl-6-(2-pyrid­yl)-1,2,4,5-tetra­zine

PubMed Central

Chartrand, Daniel; Laverdière, François; Hanan, Garry

2008-01-01

The title compound, C13H9N5, is the first asymmetric diaryl-1,2,4,5-tetra­zine to be crystallographically characterized. We have been inter­ested in this motif for incorporation into supra­molecular assemblies based on coordination chemistry. The solid state structure shows a centrosymmetric mol­ecule, forcing a positional disorder of the terminal phenyl and pyridyl rings. The mol­ecule is completely planar, unusual for aromatic rings with N atoms in adjacent ortho positions. The stacking observed is very common in diaryl­tetra­zines and is dominated by π stacking [centroid-to-centroid distance between the tetrazine ring and the aromatic ring of an adjacent molecule is 3.6 Å, perpendicular (centroid-to-plane) distance of about 3.3 Å]. PMID:21200916

A Gibbs sampler for motif detection in phylogenetically close sequences

NASA Astrophysics Data System (ADS)

Siddharthan, Rahul; van Nimwegen, Erik; Siggia, Eric

2004-03-01

Genes are regulated by transcription factors that bind to DNA upstream of genes and recognize short conserved ``motifs'' in a random intergenic ``background''. Motif-finders such as the Gibbs sampler compare the probability of these short sequences being represented by ``weight matrices'' to the probability of their arising from the background ``null model'', and explore this space (analogous to a free-energy landscape). But closely related species may show conservation not because of functional sites but simply because they have not had sufficient time to diverge, so conventional methods will fail. We introduce a new Gibbs sampler algorithm that accounts for common ancestry when searching for motifs, while requiring minimal ``prior'' assumptions on the number and types of motifs, assessing the significance of detected motifs by ``tracking'' clusters that stay together. We apply this scheme to motif detection in sporulation-cycle genes in the yeast S. cerevisiae, using recent sequences of other closely-related Saccharomyces species.

Atomistic Description of Thiostannate-Capped CdSe Nanocrystals: Retention of Four-Coordinate SnS4 Motif and Preservation of Cd-Rich Stoichiometry

PubMed Central

2016-01-01

Colloidal semiconductor nanocrystals (NCs) are widely studied as building blocks for novel solid-state materials. Inorganic surface functionalization, used to displace native organic capping ligands from NC surfaces, has been a major enabler of electronic solid-state devices based on colloidal NCs. At the same time, very little is known about the atomistic details of the organic-to-inorganic ligand exchange and binding motifs at the NC surface, severely limiting further progress in designing all-inorganic NCs and NC solids. Taking thiostannates (K4SnS4, K4Sn2S6, K6Sn2S7) as typical examples of chalcogenidometallate ligands and oleate-capped CdSe NCs as a model NC system, in this study we address these questions through the combined application of solution 1H NMR spectroscopy, solution and solid-state 119Sn NMR spectroscopy, far-infrared and X-ray absorption spectroscopies, elemental analysis, and by DFT modeling. We show that through the X-type oleate-to-thiostannate ligand exchange, CdSe NCs retain their Cd-rich stoichiometry, with a stoichiometric CdSe core and surface Cd adatoms serving as binding sites for terminal S atoms of the thiostannates ligands, leading to all-inorganic (CdSe)core[Cdm(Sn2S7)yK(6y-2m)]shell (taking Sn2S76– ligand as an example). Thiostannates SnS44– and Sn2S76– retain (distorted) tetrahedral SnS4 geometry upon binding to NC surface. At the same time, experiments and simulations point to lower stability of Sn2S64– (and SnS32–) in most solvents and its lower adaptability to the NC surface caused by rigid Sn2S2 rings. PMID:25597625

Analysis of a Triple Star System Occulted By Saturn’s Rings

NASA Astrophysics Data System (ADS)

Bratcher, Allison; Colwell, J. E.; Bolin, B.

2012-10-01

On January 4, 2012, the Ultraviolet Imaging Spectrograph aboard the Cassini Spacecraft observed Saturn’s rings as they occulted the triple star system, Iota Orionis. Remarkably, the brightest star was occulted by the moon Prometheus, and we provide the timing information of first and last contact for navigation purposes and a chord across the moon. The large separation of the individual stars projected in the ring plane makes it possible to measure the profiles of narrow features in the rings as they were occulted by each of the three stars. This occultation thus provides a unique opportunity to measure short-scale longitudinal variations in narrow ringlets with stellar occultation data that usually provide only a single longitudinal sample. Iota Orionis has a low elevation angle (B=1.4 degrees) above the plane of the rings, enhancing the sensitivity of the occultation (by a factor of 1/sin(B)=41) to the optically thin regions of the rings such as the C Ring and the Cassini Division as well as faint ringlets in the Encke gap. We distinguished the three signals by creating a model triple star signal using data from another occultation. We were able to identify several faint, narrow ringlets, including two in the Encke gap, occulted by two of the three stars and more prominent ringlets, such as the Huygens ringlet, in all three stellar light curves. We present the equivalent widths of these ringlets in the data from this triple star system and limits on ring variability over the azimuthal separation of the stars that ranges from 6000 km at the inner C ring to 200 km at the outer A ring.

Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.

PubMed

Michel, Christian J; Ngoune, Viviane Nguefack; Poch, Olivier; Ripp, Raymond; Thompson, Julie D

2017-12-03

A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X, in the complete genome of the yeast Saccharomyces cerevisiae . Several properties of X motifs are identified by basic statistics (at the frequency level), and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R. We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae . We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae , but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions). This property is true for all cardinalities of X motifs (from 4 to 20) and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non-X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together, represent the first

Hydrogen-bonding patterns in 5-fluoro-cytosine-melamine co-crystal (4/1).

PubMed

Mohana, Marimuthu; Muthiah, Packianathan Thomas; Sanjeewa, Liurukara D; McMillen, Colin D

2016-04-01

The asymmetric unit of the title compound, 4C4H4FN3O·C3H6N6, comprises of two independent 5-fluoro-cytosine (5FC) mol-ecules (A and B) and one half-mol-ecule of melamine (M). The other half of the melamine mol-ecule is generated by a twofold axis. 5FC mol-ecules A and B are linked through two different homosynthons [R 2 (2)(8) ring motif]; one is formed via a pair of N-H⋯O hydrogen bonds and the second via a pair of N-H⋯N hydrogen bonds. In addition to this pairing, the O atoms of 5FC mol-ecules A and B inter-act with the N2 amino group on both sides of the melamine mol-ecule, forming a DDAA array of quadruple hydrogen bonds and generating a supra-molecular pattern. The 5FC (mol-ecules A and B) and two melamine mol-ecules inter-act via N-H⋯O, N-H⋯N and N-H⋯O, N-H⋯N, C-H⋯F hydrogen bonds forming R 6 (6)(24) and R 4 (4)(15) ring motifs. The crystal structure is further strengthened by C-H⋯F, C-F⋯π and π-π stacking inter-actions.

Searching RNA motifs and their intermolecular contacts with constraint networks.

PubMed

Thébault, P; de Givry, S; Schiex, T; Gaspin, C

2006-09-01

Searching RNA gene occurrences in genomic sequences is a task whose importance has been renewed by the recent discovery of numerous functional RNA, often interacting with other ligands. Even if several programs exist for RNA motif search, none exists that can represent and solve the problem of searching for occurrences of RNA motifs in interaction with other molecules. We present a constraint network formulation of this problem. RNA are represented as structured motifs that can occur on more than one sequence and which are related together by possible hybridization. The implemented tool MilPat is used to search for several sRNA families in genomic sequences. Results show that MilPat allows to efficiently search for interacting motifs in large genomic sequences and offers a simple and extensible framework to solve such problems. New and known sRNA are identified as H/ACA candidates in Methanocaldococcus jannaschii. http://carlit.toulouse.inra.fr/MilPaT/MilPat.pl.

Photochemistry in Saturn’s Ring-Shadowed Atmosphere: Photochemistry and Haze Observations

NASA Astrophysics Data System (ADS)

Edgington, Scott G.; Atreya, Sushil K.; Baines, Kevin H.; West, Robert A.; Bjoraker, Gordon L.; Fletcher, Leigh; Momary, Thomas W.; Wilson, Eric; CIRS, ISS, UVIS, VIMS

2017-10-01

After 13 years of observing Saturn, Cassini would have ended nearly a half Saturnian year. During this epoch, the ring shadow has moved from covering much of the northern hemisphere to covering a large swath southern hemisphere. The net effect is that the intensity of both ultraviolet and visible sunlight penetrating through the rings to any particular latitude will vary depending on both Saturn’s axis relative to the Sun and the optical thickness of each ring system. In essence, the rings act like semi-transparent venetian blinds. This effect magnifies the effect due to axial tilt alone and acts to turn off photochemistry and haze generation. This effect is seen in both the presence of a bluish Rayleigh-scattering atmosphere in 2004 in the northern hemisphere and color change to blue in the northern hemisphere.Previous work examined the variation of the solar flux as a function of solar inclination, i.e. for each 7.25-year season at Saturn. We report on the impact of the oscillating ring shadow, in addition to variation due to axial tilt, on photolysis and production rates of hydrocarbons and phosphine in Saturn’s stratosphere and upper troposphere. The impact of these production and loss rates on the abundance of long-lived photochemical products leading to haze formation are explored. We assess their impact on a disequilibrium species whose presence in the upper troposphere can be used as a tracer of convective processes in the deeper atmosphere.We will also present our ongoing analysis of Cassini’s CIRS, UVIS, and VIMS datasets that provide an estimate of the evolving haze content. In particular, we will examine how the region inside Saturn’s famous hexagonal jet stream changes over time from a relatively clear atmosphere to a hazy one. We also explore how the hexagon acts like a barrier to transport, isolating Saturn’s north polar region from outside influences of photochemically-generated molecules and haze.The research described in this paper was

Resveratrol and para-coumarate serve as ring precursors for coenzyme Q biosynthesis[S

PubMed Central

Xie, Letian X.; Williams, Kevin J.; He, Cuiwen H.; Weng, Emily; Khong, San; Rose, Tristan E.; Kwon, Ohyun; Bensinger, Steven J.; Marbois, Beth N.; Clarke, Catherine F.

2015-01-01

Coenzyme Q (Q or ubiquinone) is a redox-active polyisoprenylated benzoquinone lipid essential for electron and proton transport in the mitochondrial respiratory chain. The aromatic ring 4-hydroxybenzoic acid (4HB) is commonly depicted as the sole aromatic ring precursor in Q biosynthesis despite the recent finding that para-aminobenzoic acid (pABA) also serves as a ring precursor in Saccharomyces cerevisiae Q biosynthesis. In this study, we employed aromatic 13C6-ring-labeled compounds including 13C6-4HB, 13C6-pABA, 13C6-resveratrol, and 13C6-coumarate to investigate the role of these small molecules as aromatic ring precursors in Q biosynthesis in Escherichia coli, S. cerevisiae, and human and mouse cells. In contrast to S. cerevisiae, neither E. coli nor the mammalian cells tested were able to form 13C6-Q when cultured in the presence of 13C6-pABA. However, E. coli cells treated with 13C6-pABA generated 13C6-ring-labeled forms of 3-octaprenyl-4-aminobenzoic acid, 2-octaprenyl-aniline, and 3-octaprenyl-2-aminophenol, suggesting UbiA, UbiD, UbiX, and UbiI are capable of using pABA or pABA-derived intermediates as substrates. E. coli, S. cerevisiae, and human and mouse cells cultured in the presence of 13C6-resveratrol or 13C6-coumarate were able to synthesize 13C6-Q. Future evaluation of the physiological and pharmacological responses to dietary polyphenols should consider their metabolism to Q. PMID:25681964

Efficient exact motif discovery.

PubMed

Marschall, Tobias; Rahmann, Sven

2009-06-15

The motif discovery problem consists of finding over-represented patterns in a collection of biosequences. It is one of the classical sequence analysis problems, but still has not been satisfactorily solved in an exact and efficient manner. This is partly due to the large number of possibilities of defining the motif search space and the notion of over-representation. Even for well-defined formalizations, the problem is frequently solved in an ad hoc manner with heuristics that do not guarantee to find the best motif. We show how to solve the motif discovery problem (almost) exactly on a practically relevant space of IUPAC generalized string patterns, using the p-value with respect to an i.i.d. model or a Markov model as the measure of over-representation. In particular, (i) we use a highly accurate compound Poisson approximation for the null distribution of the number of motif occurrences. We show how to compute the exact clump size distribution using a recently introduced device called probabilistic arithmetic automaton (PAA). (ii) We define two p-value scores for over-representation, the first one based on the total number of motif occurrences, the second one based on the number of sequences in a collection with at least one occurrence. (iii) We describe an algorithm to discover the optimal pattern with respect to either of the scores. The method exploits monotonicity properties of the compound Poisson approximation and is by orders of magnitude faster than exhaustive enumeration of IUPAC strings (11.8 h compared with an extrapolated runtime of 4.8 years). (iv) We justify the use of the proposed scores for motif discovery by showing our method to outperform other motif discovery algorithms (e.g. MEME, Weeder) on benchmark datasets. We also propose new motifs on Mycobacterium tuberculosis. The method has been implemented in Java. It can be obtained from http://ls11-www.cs.tu-dortmund.de/people/marschal/paa_md/.

Identification of sequence motifs significantly associated with antisense activity.

PubMed

McQuisten, Kyle A; Peek, Andrew S

2007-06-07

Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the model to be efficient we must know what properties do not associate significantly and can be omitted from the model. This paper will discuss the results of a randomization procedure to find motifs that associate significantly with either high or low antisense suppression activity, analysis of their properties, as well as the results of support vector machine modelling using these significant motifs as features. We discovered 155 motifs that associate significantly with high antisense suppression activity and 202 motifs that associate significantly with low suppression activity. The motifs range in length from 2 to 5 bases, contain several motifs that have been previously discovered as associating highly with antisense activity, and have thermodynamic properties consistent with previous work associating thermodynamic properties of sequences with their antisense activity. Statistical analysis revealed no correlation between a motif's position within an antisense sequence and that sequences antisense activity. Also, many significant motifs existed as subwords of other significant motifs. Support vector regression experiments indicated that the feature set of significant motifs increased correlation compared to all possible motifs as well as several subsets of the significant motifs. The thermodynamic properties of the significantly associated motifs support existing data correlating the thermodynamic properties of the antisense oligonucleotide with antisense efficiency, reinforcing our hypothesis that antisense suppression is strongly associated with probe/target thermodynamics, as there are no enzymatic mediators to speed the process along like the RNA Induced

Counting motifs in dynamic networks.

PubMed

Mukherjee, Kingshuk; Hasan, Md Mahmudul; Boucher, Christina; Kahveci, Tamer

2018-04-11

A network motif is a sub-network that occurs frequently in a given network. Detection of such motifs is important since they uncover functions and local properties of the given biological network. Finding motifs is however a computationally challenging task as it requires solving the costly subgraph isomorphism problem. Moreover, the topology of biological networks change over time. These changing networks are called dynamic biological networks. As the network evolves, frequency of each motif in the network also changes. Computing the frequency of a given motif from scratch in a dynamic network as the network topology evolves is infeasible, particularly for large and fast evolving networks. In this article, we design and develop a scalable method for counting the number of motifs in a dynamic biological network. Our method incrementally updates the frequency of each motif as the underlying network's topology evolves. Our experiments demonstrate that our method can update the frequency of each motif in orders of magnitude faster than counting the motif embeddings every time the network changes. If the network evolves more frequently, the margin with which our method outperforms the existing static methods, increases. We evaluated our method extensively using synthetic and real datasets, and show that our method is highly accurate(≥ 96%) and that it can be scaled to large dense networks. The results on real data demonstrate the utility of our method in revealing interesting insights on the evolution of biological processes.

Direct AUC optimization of regulatory motifs.

PubMed

Zhu, Lin; Zhang, Hong-Bo; Huang, De-Shuang

2017-07-15

The discovery of transcription factor binding site (TFBS) motifs is essential for untangling the complex mechanism of genetic variation under different developmental and environmental conditions. Among the huge amount of computational approaches for de novo identification of TFBS motifs, discriminative motif learning (DML) methods have been proven to be promising for harnessing the discovery power of accumulated huge amount of high-throughput binding data. However, they have to sacrifice accuracy for speed and could fail to fully utilize the information of the input sequences. We propose a novel algorithm called CDAUC for optimizing DML-learned motifs based on the area under the receiver-operating characteristic curve (AUC) criterion, which has been widely used in the literature to evaluate the significance of extracted motifs. We show that when the considered AUC loss function is optimized in a coordinate-wise manner, the cost function of each resultant sub-problem is a piece-wise constant function, whose optimal value can be found exactly and efficiently. Further, a key step of each iteration of CDAUC can be efficiently solved as a computational geometry problem. Experimental results on real world high-throughput datasets illustrate that CDAUC outperforms competing methods for refining DML motifs, while being one order of magnitude faster. Meanwhile, preliminary results also show that CDAUC may also be useful for improving the interpretability of convolutional kernels generated by the emerging deep learning approaches for predicting TF sequences specificities. CDAUC is available at: https://drive.google.com/drive/folders/0BxOW5MtIZbJjNFpCeHlBVWJHeW8 . dshuang@tongji.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Beam vacuum system of Brookhaven`s muon storage ring

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

Hseuth, H.C.; Snydstrup, L.; Mapes, M.

1995-11-01

A storage ring with a circumference of 45 m is being built at Brookhaven to measure the g-2 value of the muons to an accuracy of 0.35 ppm.. The beam vacuum system of the storage ring will operate at 10{sup -7} Torr and has to be completely non-magnetic. It consists of twelve sector chambers. The chambers are constructed of aluminum and are approximately 3.5 m in length with a rectangular cross-section of 16.5 cm high by 45 cm at the widest point. The design features, fabrication techniques and cleaning methods for these chambers are described. The beam vacuum system willmore » be pumped by forty eight non-magnetic distributed ion pumps with a total pumping speed of over 2000 {ell}/sec. Monte Carlo simulations of the pressure distribution in the muon storage region are presented.« less

Allosteric Breakage of the Hydrogen Bond within the Dual-Histidine Motif in the Active Site of Human Pin1 PPIase.

PubMed

Wang, Jing; Tochio, Naoya; Kawasaki, Ryosuke; Tamari, Yu; Xu, Ning; Uewaki, Jun-Ichi; Utsunomiya-Tate, Naoko; Tate, Shin-Ichi

2015-08-25

Intimate cooperativity among active site residues in enzymes is a key factor for regulating elaborate reactions that would otherwise not occur readily. Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) is the phosphorylation-dependent cis-trans peptidyl-prolyl isomerase (PPIase) that specifically targets phosphorylated Ser/Thr-Pro motifs. Residues C113, H59, H157, and T152 form a hydrogen bond network in the active site, as in the noted connection. Theoretical studies have shown that protonation to thiolate C113 leads to rearrangement of this hydrogen bond network, with switching of the tautomeric states of adjacent histidines (H59 and H157) [Barman, A., and Hamelberg, D. (2014) Biochemistry 53, 3839-3850]. This is called the "dual-histidine motif". Here, C113A and C113S Pin1 mutants were found to alter the protonation states of H59 according to the respective residue type replaced at C113, and the mutations resulted in disruption of the hydrogen bond within the dual-histidine motif. In the C113A mutant, H59 was observed to be in exchange between ε- and δ-tautomers, which widened the entrance of the active site cavity, as seen by an increase in the distance between residues A113 and S154. The C113S mutant caused H59 to exchange between the ε-tautomer and imidazolium while not changing the active site structure. Moreover, the imidazole ring orientations of H59 and H157 were changed in the C113S mutant. These results demonstrated that a mutation at C113 modulates the hydrogen bond network dynamics. Thus, C113 acts as a pivot to drive the concerted function among the residues in the hydrogen bond network, as theoretically predicted.

Molecular Interaction Between Smurfl WW2 Domain and PPXY Motifs of Smadl, Smad5, and Smad6-Modeling and Analysis.

PubMed

Sangadala, Sreedhara; Rao Metpally, Raghu Prasad; B Reddy, Boojala Vijay

2007-08-01

Abstract The ubiquitin-proteasome proteolytic pathway is essential for various important biological processes including cell cycle progression, gene transcription, and signal transduction. One of the important regulatory mechanisms by which the bone-inducing activity of the bone morphogenetic protein (BMP) signaling is modulated involves ubiquitin-mediated proteasomal degradation. The BMP induced receptor signal is transmitted intracellularly by phosphorylation of Smad proteins by the activated receptor I. The phosphorylated Smads 1, 5, and 8 (R-Smads) oligomerize with the co-Smad (Smad4). The complex, thus, formed translocates to the nucleus and interacts with other cofactors to regulate the expression of downstream target genes. R-Smads contain PPXY motif in the linker region that interacts with Smad ubiquitin regulatory factor 1 (Smurf1), an E3 ubiquitin ligase that catalyzes ubiquitination of target proteins for proteasomal degradation. Smurf1 contains a HECT domain, a C2 domain, and 2 WW domains (WW1, WW2). The PPXY motif in target proteins and its interaction with Smurf1 may form the basis for regulation of steady-state levels of Smads in controlling BMP-responsiveness of cells. Here, we present a homology-based model of the Smurf1 WW2 domain and the target octa-peptides containing PPXY motif of Smurf1- interacting Smads. We carried out docking of Smurf1 WW2 domain with the PPXY motifs of Smadl, Smad5, and Smad6 and identified the key amino acid residues involved in interaction. Furthermore, we present experimental evidence that WW2 domain of Smurf1 does indeed interact with the Smad proteins and that the deletion of WW2 domain of Smurf1 results in loss of its binding to Smads using the purified recombinant proteins. Finally, we also present data confirming that the deletion of WW2 domain in Smurf1 abolishes its ubiquitination activity on Smad1 in an in vitro ubiquitination assay. It shows that the interaction between the WW domain and Smad PPXY motif is a

Phosphorylation of PPP(S/T)P motif of the free LRP6 intracellular domain is not required to activate the Wnt/beta-catenin pathway and attenuate GSK3beta activity.

PubMed

Beagle, Brandon; Mi, Kaihong; Johnson, Gail V W

2009-11-01

The canonical Wnt/beta-catenin signaling pathway plays a critical role in numerous physiological and pathological processes. LRP6 is an essential co-receptor for Wnt/beta-catenin signaling; as transduction of the Wnt signal is strongly dependent upon GSK3beta-mediated phosphorylation of multiple PPP(S/T)P motifs within the membrane-anchored LRP6 intracellular domain. Previously, we showed that the free LRP6 intracellular domain (LRP6-ICD) can activate the Wnt/beta-catenin pathway in a beta-catenin and TCF/LEF-1 dependent manner, as well as interact with and attenuate GSK3beta activity. However, it is unknown if the ability of LRP6-ICD to attenuate GSK3beta activity and modulate activation of the Wnt/beta-catenin pathway requires phosphorylation of the LRP6-ICD PPP(S/T)P motifs, in a manner similar to the membrane-anchored LRP6 intracellular domain. Here we provide evidence that the LRP6-ICD does not have to be phosphorylated at its PPP(S/T)P motif by GSK3beta to stabilize endogenous cytosolic beta-catenin resulting in activation of TCF/LEF-1 and the Wnt/beta-catenin pathway. LRP6-ICD and a mutant in which all 5 PPP(S/T)P motifs were changed to PPP(A)P motifs equivalently interacted with and attenuated GSK3beta activity in vitro, and both constructs inhibited the in situ GSK3beta-mediated phosphorylation of beta-catenin and tau to the same extent. These data indicate that the LRP6-ICD attenuates GSK3beta activity similar to other GSK3beta binding proteins, and is not a result of it being a GSK3beta substrate. Our findings suggest the functional and regulatory mechanisms governing the free LRP6-ICD may be distinct from membrane-anchored LRP6, and that release of the LRP6-ICD may provide a complimentary signaling cascade capable of modulating Wnt-dependent gene expression. (c) 2009 Wiley-Liss, Inc.

Appearance of Saturn’s F ring azimuthal channels for the anti-alignment configuration between the ring and Prometheus

NASA Astrophysics Data System (ADS)

Chavez, Carlos E.

2009-09-01

In this article we explore the aspect of the F ring with respect to the anti-alignment configuration between the ring and Prometheus. We focus our attention on the shape of the F ring's azimuthal channels which were first reported by Porco et al. (Porco, C.C., Baker, E., Barbara, J., Beurle, K., Brahic, A., Burns, J.A., Charnoz, S., Cooper, N., Dawson, D.D., Del Genio, A.D., Denk, T., Dones, L., Dyudina, U., Evans, M.W., Giese, B., Grazier, K., Helfenstein, P., Ingersoll, A.P., Jacobson, R.A., Johnson, T.V., McEwen, A., Murray, C.D., Neukum, G., Owen, W.M., Perry, J., Roatsch, T., Spitale, J., Squyres, S., Thomas, P., Tiscareno, M., Turtle, E., Vasavada, A.R., Veverka, J., Wagner, R., West, R. [2005] Science, 307, 1226-1236) and numerically explored by Murray et al. (Murray, C.D., Chavez, C., Beurle, K., Cooper, N., Evans, M.W., Burns, J.A., Porco, C.C. [2005] Nature 437, 1326-1329) who found excellent agreement between Cassini's ISS reprojected images and their numerical model via a direct comparison. We find that for anti-alignment the channels are wider and go deeper inside the ring material. From our numerical model we find a new feature, an island in the middle of the channel. This island is made up of the particles that have been perturbed the most by Prometheus and only appears when this satellite is close to apoapsis. In addition, plots of the anti-alignment configuration for different orbital stages of Prometheus are obtained and discussed here.

The Particle Size Distribution in Saturn’s C Ring from UVIS and VIMS Stellar Occultations and RSS Radio Occultations

NASA Astrophysics Data System (ADS)

Jerousek, Richard Gregory; Colwell, Josh; Hedman, Matthew M.; French, Richard G.; Marouf, Essam A.; Esposito, Larry; Nicholson, Philip D.

2017-10-01

The Cassini Ultraviolet Imaging Spectrograph (UVIS) and Visual and Infrared Mapping Spectrometer (VIMS) have measured ring optical depths over a wide range of viewing geometries at effective wavelengths of 0.15 μm and 2.9 μm respectively. Using Voyager S and X band radio occultations and the direct inversion of the forward scattered S band signal, Marouf et al. (1982), (1983), and Zebker et al. (1985) determined the power-law size distribution parameters assuming a minimum particle radius of 1 mm. Many further studies have also constrained aspects of the particle size distribution throughout the main rings. Marouf et al. (2008a) determined the smallest ring particles to have radii of 4-5 mm using Cassini RSS data. Harbison et al. (2013) used VIMS solar occultations and also found minimum particle sizes of 4-5 mm in the C ring with q ~ 3.1, where n(a)da=Ca^(-q)da is the assumed differential power-law size distribution for particles of radius a. Recent studies of excess variance in stellar signal by Colwell et al. (2017, submitted) constrain the cross-section-weighted effective particle radius to 1 m to several meters. Using the wide range of viewing geometries available to VIMS and UVIS stellar occultations we find that normal optical depth does not strongly depend on viewing geometry at 10km resolution (which would be the case if self-gravity wakes were present). Throughout the C ring, we fit power-law derived optical depths to those measured by UVIS, VIMS, and by the Cassini Radio Science Subsystem (RSS) at 0.94 and 3.6 cm wavelengths to constrain the four parameters of the size distribution at 10km radial resolution. We find significant amounts of particle size sorting throughout the region with a positive correlation between maximum particles size (amax) and normal optical depth with a mean value of amax ~ 3 m in the background C ring. This correlation is negative in the C ring plateaus. We find an inverse correlation in minimum particle radius with normal

1-(2,4-Dinitro­phen­yl)-2-(1,2,3,4-tetra­hydro­naphthalen-1-yl­idene)hydrazine

PubMed Central

Danish, M.; Hamid, Masood; Tahir, M. Nawaz; Ahmad, Nazir; Ghafoor, Sabiha

2010-01-01

In the title compound, C14H14N4O4, the dihedral angle between the benzene rings is 10.42 (8)°. The nitro groups make dihedral angles of 5.3 (2) and 6.47 (15)° with their parent ring and are oriented at 11.2 (3)° with respect to each other. An intra­molecular N—H⋯O hydrogen bond completes an S(6) ring motif. In the crystal, mol­ecules are linked by C—H⋯O inter­actions, thus forming (010) chains in which R 2 2(13) ring motifs are present. There also exist aromatic π–π stacking inter­actions [centroid–centroid separation = 3.7046 (9) Å]. PMID:21588393

Ynamides in Ring Forming Transformations

PubMed Central

WANG, XIAO-NA; YEOM, HYUN-SUK; FANG, LI-CHAO; HE, SHUZHONG; MA, ZHI-XIONG; KEDROWSKI, BRANT L.; HSUNG, RICHARD P.

2013-01-01

Conspectus The ynamide functional group activates carbon-carbon triple bonds through an attached nitrogen atom that bears an electron-withdrawing group. As a result, the alkyne has both electrophilic and nucleophilic properties. Through the selection of the electron-withdrawing group attached to nitrogen chemists can modulate the electronic properties and reactivity of ynamides, making these groups versatile synthetic building blocks. The reactions of ynamides also lead directly to nitrogen-containing products, which provides access to important structural motifs found in natural products and molecules of medicinal interest. Therefore, researchers have invested increasing time and research in the chemistry of ynamides in recent years. This Account surveys and assesses new organic transformations involving ynamides developed in our laboratory and in others around the world. We showcase the synthetic power of ynamides for rapid assembly of complex molecular structures. Among the recent reports of ynamide transformations, ring-forming reactions provide a powerful tool for generating molecular complexity quickly. In addition to their synthetic utility, such reactions are mechanistically interesting. Therefore, we focus primarily on the cyclization chemistry of ynamides. This Account highlights ynamide reactions that are useful in the rapid synthesis of cyclic and polycyclic structural manifolds. We discuss the mechanisms active in the ring formations and describe representative examples that demonstrate the scope of these reactions and provide mechanistic insights. In this discussion we feature examples of ynamide reactions involving radical cyclizations, ring-closing metathesis, transition metal and non-transition metal mediated cyclizations, cycloaddition reactions, and rearrangements. The transformations presented rapidly introduce structural complexity and include nitrogen within, or in close proximity to, a newly formed ring (or rings). Thus, ynamides have emerged

The Methionine-aromatic Motif Plays a Unique Role in Stabilizing Protein Structure*

PubMed Central

Valley, Christopher C.; Cembran, Alessandro; Perlmutter, Jason D.; Lewis, Andrew K.; Labello, Nicholas P.; Gao, Jiali; Sachs, Jonathan N.

2012-01-01

Of the 20 amino acids, the precise function of methionine (Met) remains among the least well understood. To establish a determining characteristic of methionine that fundamentally differentiates it from purely hydrophobic residues, we have used in vitro cellular experiments, molecular simulations, quantum calculations, and a bioinformatics screen of the Protein Data Bank. We show that approximately one-third of all known protein structures contain an energetically stabilizing Met-aromatic motif and, remarkably, that greater than 10,000 structures contain this motif more than 10 times. Critically, we show that as compared with a purely hydrophobic interaction, the Met-aromatic motif yields an additional stabilization of 1–1.5 kcal/mol. To highlight its importance and to dissect the energetic underpinnings of this motif, we have studied two clinically relevant TNF ligand-receptor complexes, namely TRAIL-DR5 and LTα-TNFR1. In both cases, we show that the motif is necessary for high affinity ligand binding as well as function. Additionally, we highlight previously overlooked instances of the motif in several disease-related Met mutations. Our results strongly suggest that the Met-aromatic motif should be exploited in the rational design of therapeutics targeting a range of proteins. PMID:22859300

The heptanucleotide motif GAGACGC is a key component of a cis-acting promoter element that is critical for SnSAG1 expression in Sarcocystis neurona.

PubMed

Gaji, Rajshekhar Y; Howe, Daniel K

2009-07-01

The apicomplexan parasite Sarcocystis neurona undergoes a complex process of intracellular development, during which many genes are temporally regulated. The described study was undertaken to begin identifying the basic promoter elements that control gene expression in S. neurona. Sequence analysis of the 5'-flanking region of five S. neurona genes revealed a conserved heptanucleotide motif GAGACGC that is similar to the WGAGACG motif described upstream of multiple genes in Toxoplasma gondii. The promoter region for the major surface antigen gene SnSAG1, which contains three heptanucleotide motifs within 135 bases of the transcription start site, was dissected by functional analysis using a dual luciferase reporter assay. These analyses revealed that a minimal promoter fragment containing all three motifs was sufficient to drive reporter molecule expression, with the presence and orientation of the 5'-most heptanucleotide motif being absolutely critical for promoter function. Further studies should help to identify additional sequence elements important for promoter function and for controlling gene expression during intracellular development by this apicomplexan pathogen.

De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes.

PubMed

Zolotarov, Yevgen; Strömvik, Martina

2015-01-01

Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes, de novo motif discovery was performed on 350 dehydrin promoter sequences from a total of 51 plant genomes. Overrepresented motifs were identified in the promoters of five dehydrin classes. The Kn dehydrin promoters contain motifs linked with meristem specific expression, as well as motifs linked with cold/dehydration and abscisic acid response. KS dehydrin promoters contain a motif with a GATA core. SKn and YnSKn dehydrin promoters contain motifs that match elements connected with cold/dehydration, abscisic acid and light response. YnKn dehydrin promoters contain motifs that match abscisic acid and light response elements, but not cold/dehydration response elements. Conserved promoter motifs are present in the dehydrin classes and across different plant lineages, indicating that dehydrin gene regulation is likely also conserved.

Variations in Ring Particle Cooling across Saturn's Rings with Cassini CIRS

NASA Astrophysics Data System (ADS)

Brooks, S. M.; Spilker, L. J.; Pilorz, S.; Edgington, S. G.; Déau, E.; Altobelli, N.

2010-12-01

Cassini's Composite Infrared Spectrometer has recorded over two million of spectra of Saturn's rings in the far infrared since arriving at Saturn in 2004. CIRS records far infrared radiation between 10 and 600 cm-1 ( 16.7 and 1000 μ {m} ) at focal plane 1 (FP1), which has a field of view of 3.9 mrad. Thermal emission from Saturn’s rings peaks in this wavelength range. Ring temperatures can be inferred from FP1 data. By tracking how ring temperatures vary, we can determine the thermal inertia of the rings. Previous studies have shown that the rings' thermal inertia, a measure of their response to changes in the thermal environment, varies from ring to ring. Thermal inertia can provide insight into the physical structure of Saturn's ring particles and their regoliths. Low thermal inertia and rapidly changing temperatures are suggestive of ring particles that have more porous or fluffy regoliths or that are riddled with cracks. Solid particles can be expected to have higher thermal inertias. Ferrari et al. (2005) fit thermal inertia values of 5218 {Jm)-2 {K}-1 {s}-1/2 to their B ring data and 6412 {Jm)-2 {K}-1 {s}-1/2 to their C ring data. In this work we focus on CIRS observations of the shadowed portion of Saturn's rings. The rings’ thermal budget is dominated by its absorption of solar radiation. As a result, ring particles abruptly cool as they traverse Saturn's shadow. From these shadow observations we can create cooling curves at specific locations across the rings. We will show that the rings' cooling curves and thus their thermal inertia vary not only from ring to ring, but by location within the individual rings. This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. Copyright 2010 California Institute of Technology. Government sponsorship acknowledged.

Jupiter's Main Ring/Ring Halo

NASA Technical Reports Server (NTRS)

1997-01-01

A mosaic of four images taken through the clear filter (610 nanometers) of the solid state imaging (CCD) system aboard NASA's Galileo spacecraft on November 8, 1996, at a resolution of approximately 46 kilometers (28.5 miles) per picture element (pixel) along Jupiter's rings. Because the spacecraft was only about 0.5 degrees above the ring plane, the image is highly foreshortened in the vertical direction. The images were obtained when Galileo was in Jupiter's shadow, peering back toward the Sun; the ring was approximately 2.3 million kilometers (1.4 million miles) away. The arc on the far right of the image is produced when sunlight is scattered by small particles comprising Jupiter's upper atmospheric haze. The ring also efficiently scatters light, indicating that much of its brightness is due to particles that are microns or less in diameter. Such small particles are believed to have human-scale lifetimes, i.e., very brief compared to the solar system's age.

Jupiter's ring system is composed of three parts - - a flat main ring, a lenticular halo interior to the main ring, and the gossamer ring, outside the main ring. The near and far arms of Jupiter's main ring extend horizontally across the mosaic, joining together at the ring's ansa, on the figure's far left side. The near arm of the ring appears to be abruptly truncated close to the planet, at the point where it passes into Jupiter's shadow. Some radial structure is barely visible across the ring's ansa (top image). A faint mist of particles can be seen above and below the main rings. This vertically extended 'halo' is unusual in planetary rings, and is probably caused by electromagnetic forces pushing the smallest grains out of the ring plane. Because of shadowing, the halo is not visible close to Jupiter in the lower right part of the mosaic. To accentuate faint features in the bottom image of the ring halo, different brightnesses are shown through color. Brightest features are white or yellow and the

Chitin-induced and CHITIN ELICITOR RECEPTOR KINASE1 (CERK1) phosphorylation-dependent endocytosis of Arabidopsis thaliana LYSIN MOTIF-CONTAINING RECEPTOR-LIKE KINASE5 (LYK5).

PubMed

Erwig, Jan; Ghareeb, Hassan; Kopischke, Michaela; Hacke, Ronja; Matei, Alexandra; Petutschnig, Elena; Lipka, Volker

2017-07-01

To detect potential pathogens, plants perceive the fungal polysaccharide chitin through receptor complexes containing lysin motif receptor-like kinases (LysM-RLKs). To investigate the ligand-induced spatial dynamics of chitin receptor components, we studied the subcellular behaviour of two Arabidopsis thaliana LysM-RLKs involved in chitin signalling, CHITIN ELICITOR RECEPTOR KINASE1 (CERK1) and LYSIN MOTIF-CONTAINING RECEPTOR-LIKE KINASE5. We performed standard and quantitative confocal laser scanning microscopy on stably transformed A. thaliana plants expressing fluorescently tagged CERK1 and LYK5 from their native promoters. Microscopy approaches were complemented by biochemical analyses in plants and in vitro. Both CERK1 and LYK5 localized to the plasma membrane and showed constitutive endomembrane trafficking. After chitin treatment, however, CERK1 remained at the plasma membrane while LYK5 relocalized into mobile intracellular vesicles. Detailed analyses revealed that chitin perception transiently induced the internalization of LYK5 into late endocytic compartments. Plants that lacked CERK1 or expressed an enzymatically inactive CERK1 variant did not exhibit chitin-induced endocytosis of LYK5. CERK1 could phosphorylate LYK5 in vitro and chitin treatment induced CERK1-dependent phosphorylation of LYK5 in planta. Our results suggest that chitin-induced phosphorylation by CERK1 triggers LYK5 internalization. Thus, our work identifies phosphorylation as a key regulatory step in endocytosis of plant RLKs and also provides evidence for receptor complex dissociation after ligand perception. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

TAE+ 5.2 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.2 (SUN4 VERSION WITH MOTIF)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

programs to display and control the user interfaces. Since the WPTs access the workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides a means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System and the Open Software Foundation's Motif. The HP 9000 Series 700/800 version of TAE 5.2 requires Version 11 Release 5 of the X Window System. All other machine versions of TAE 5.2 require Version 11, Release 4 of the X Window System. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus was developed in 1989 and version 5.2 was released in 1993. TAE Plus 5.2 is available on media suitable for five different machine platforms: (1) IBM RS/6000 series workstations running AIX (.25 inch tape cartridge in UNIX tar format), (2) DEC RISC

Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair

PubMed Central

Lee, Byung Il; Kim, Kyoung Hoon; Park, Soo Jeong; Eom, Soo Hyun; Song, Hyun Kyu; Suh, Se Won

2004-01-01

RecR, together with RecF and RecO, facilitates RecA loading in the RecF pathway of homologous recombinational DNA repair in procaryotes . The human Rad52 protein is a functional counterpart of RecFOR. We present here the crystal structure of RecR from Deinococcus radiodurans (DR RecR). A monomer of DR RecR has a two-domain structure: the N-terminal domain with a helix–hairpin–helix (HhH) motif and the C-terminal domain with a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif. Four such monomers form a ring-shaped tetramer of 222 symmetry with a central hole of 30−35 Å diameter. In the crystal, two tetramers are concatenated, implying that the RecR tetramer is capable of opening and closing. We also show that DR RecR binds to both dsDNA and ssDNA, and that its HhH motif is essential for DNA binding. PMID:15116069

3-Fluoro­salicylaldoxime at 6.5 GPa

PubMed Central

Wood, Peter A.; Forgan, Ross S.; Parsons, Simon; Pidcock, Elna; Tasker, Peter A.

2009-01-01

3-Fluoro­salicylaldoxime, C7H6FNO2, unlike many salicylaldoxime derivatives, forms a crystal structure containing hydrogen-bonded chains rather than centrosymmetric hydrogen-bonded ring motifs. Each chain inter­acts with two chains above and two chains below via π–π stacking contacts [shortest centroid–centroid distance = 3.295 (1) Å]. This structure at 6.5 GPa represents the final point in a single-crystal compression study. PMID:21583672

Detection and Preliminary Analysis of Motifs in Promoters of Anaerobically Induced Genes of Different Plant Species

PubMed Central

MOHANTY, BIJAYALAXMI; KRISHNAN, S. P. T.; SWARUP, SANJAY; BAJIC, VLADIMIR B.

2005-01-01

• Background and Aims Plants can suffer from oxygen limitation during flooding or more complete submergence and may therefore switch from Kreb's cycle respiration to fermentation in association with the expression of anaerobically inducible genes coding for enzymes involved in glycolysis and fermentation. The aim of this study was to clarify mechanisms of transcriptional regulation of these anaerobic genes by identifying motifs shared by their promoter regions. • Methods Statistically significant motifs were detected by an in silico method from 13 promoters of anaerobic genes. The selected motifs were common for the majority of analysed promoters. Their significance was evaluated by searching for their presence in transcription factor-binding site databases (TRANSFAC, PlantCARE and PLACE). Using several negative control data sets, it was tested whether the motifs found were specific to the anaerobic group. • Key Results Previously, anaerobic response elements have been identified in maize (Zea mays) and arabidopsis (Arabidopsis thaliana) genes. Known functional motifs were detected, such as GT and GC motifs, but also other motifs shared by most of the genes examined. Five motifs detected have not been found in plants hitherto but are present in the promoters of animal genes with various functions. The consensus sequences of these novel motifs are 5′-AAACAAA-3′, 5′-AGCAGC-3′, 5′-TCATCAC-3′, 5′-GTTT(A/C/T)GCAA-3′ and 5′-TTCCCTGTT-3′. • Conclusions It is believed that the promoter motifs identified could be functional by conferring anaerobic sensitivity to the genes that possess them. This proposal now requires experimental verification. PMID:16027132

Seasonal and radial trends in Saturn’s thermal plasma between the main rings and Enceladus

NASA Astrophysics Data System (ADS)

Elrod, M. K.; Tseng, W.-L.; Woodson, A. K.; Johnson, R. E.

2014-11-01

A goal of Cassini's extended mission is to examine the seasonal variations of Saturn's magnetosphere, moons, and rings. Recently we showed that the thermal plasma between the main rings and Enceladus exhibited a time dependence that we attributed to a seasonally variable source of oxygen from the main rings (Elrod, M.K., Tseng, W.-L., Wilson, R.J., Johnson, R.E. [2012]. J. Geophys. Res. 117, A03207. http://dx.doi.org/10.1029/2011JA017332). Such a temporal variation was subsequently seen in the energetic ion composition (Christon, S.P., Hamilton, D.C., DiFabio, R.D., Mitchel, D.G., Krimigis, S.M., Jontof-Hutter, D.S. [2013]. J. Geophys. Res. 28. http://dx.doi.org/10.1002/jgra.50383; Christon, S.P., Hamilton, D.C., Mitchell, D.G., DiFabio, R.D., Krimigis, S.M. [2014]. J. Geophys. Res., submitted for publication). Here we incorporate the most recent measurements by the Cassini Plasma Spectrometer (CAPS) into our earlier analysis (Elrod, M.K., Tseng, W.-L., Wilson, R.J., Johnson, R.E. [2012]. J. Geophys. Res. 117, A03207. http://dx.doi.org/10.1029/2011JA017332) and our modeling (Tseng, W.-L., Johnson, R.E., Elrod, M.K. [2013a]. Planet. Space Sci. 77, 126-135) of the thermal plasma in the region between the main rings and the orbit of Enceladus. Data taken in 2012, well past equinox for which the northern side of the main rings were illuminated, appear consistent with a seasonal variation. Although the thermal plasma in this region comes from two sources that have very different radial and temporal trends, the extended ring atmosphere and the Enceladus torus, the heavy ion density is found to exhibit a steep radial dependence that is similar for the years examined. Using our chemical model, we show that this dependence requires either a radial dependence for Enceladus torus that differs significantly from recent models or, as we suggest here, enhanced heavy ion quenching/neutralization with decreasing distance from the edge of the main rings. We examine the possible

CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks

NASA Astrophysics Data System (ADS)

Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng

2014-12-01

Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

Assessment of composite motif discovery methods.

PubMed

Klepper, Kjetil; Sandve, Geir K; Abul, Osman; Johansen, Jostein; Drablos, Finn

2008-02-26

Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have addressed the problem of single motif discovery - discovering binding motifs for individual transcription factors. In higher organisms, however, transcription factors usually act in combination with nearby bound factors to induce specific regulatory behaviours. Hence, recent focus has shifted from single motifs to the discovery of sets of motifs bound by multiple cooperating transcription factors, so called composite motifs or cis-regulatory modules. Given the large number and diversity of methods available, independent assessment of methods becomes important. Although there have been several benchmark studies of single motif discovery, no similar studies have previously been conducted concerning composite motif discovery. We have developed a benchmarking framework for composite motif discovery and used it to evaluate the performance of eight published module discovery tools. Benchmark datasets were constructed based on real genomic sequences containing experimentally verified regulatory modules, and the module discovery programs were asked to predict both the locations of these modules and to specify the single motifs involved. To aid the programs in their search, we provided position weight matrices corresponding to the binding motifs of the transcription factors involved. In addition, selections of decoy matrices were mixed with the genuine matrices on one dataset to test the response of programs to varying levels of noise. Although some of the methods tested tended to score somewhat better than others overall, there were still large variations between individual datasets and no single method performed consistently better than the rest in all situations. The variation in performance on individual datasets also shows that the new benchmark datasets represents a

5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4.

PubMed

Khund-Sayeed, Syed; He, Ximiao; Holzberg, Timothy; Wang, Jun; Rajagopal, Divya; Upadhyay, Shriyash; Durell, Stewart R; Mukherjee, Sanjit; Weirauch, Matthew T; Rose, Robert; Vinson, Charles

2016-09-12

We evaluated DNA binding of the B-HLH family members TCF4 and USF1 using protein binding microarrays (PBMs) containing double-stranded DNA probes with cytosine on both strands or 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC) on one DNA strand and cytosine on the second strand. TCF4 preferentially bound the E-box motif (CAN|NTG) with strongest binding to the 8-mer CAG|GTGGT. 5mC uniformly decreases DNA binding of both TCF4 and USF1. The bulkier 5hmC also inhibited USF1 binding to DNA. In contrast, 5hmC dramatically enhanced TCF4 binding to E-box motifs ACAT|GTG and ACAC|GTG, being better bound than any 8-mer containing cytosine. Examination of X-ray structures of the closely related TCF3 and USF1 bound to DNA suggests TCF3 can undergo a conformational shift to preferentially bind to 5hmC while the USF1 basic region is bulkier and rigid precluding a conformation shift to bind 5hmC. These results greatly expand the regulatory DNA sequence landscape bound by TCF4.

Hydrogen-bonding patterns in 5-fluoro­cytosine–melamine co-crystal (4/1)

PubMed Central

Mohana, Marimuthu; Muthiah, Packianathan Thomas; Sanjeewa, Liurukara D.; McMillen, Colin D.

2016-01-01

The asymmetric unit of the title compound, 4C4H4FN3O·C3H6N6, comprises of two independent 5-fluoro­cytosine (5FC) mol­ecules (A and B) and one half-mol­ecule of melamine (M). The other half of the melamine mol­ecule is generated by a twofold axis. 5FC mol­ecules A and B are linked through two different homosynthons [R 2 2(8) ring motif]; one is formed via a pair of N—H⋯O hydrogen bonds and the second via a pair of N—H⋯N hydrogen bonds. In addition to this pairing, the O atoms of 5FC mol­ecules A and B inter­act with the N2 amino group on both sides of the melamine mol­ecule, forming a DDAA array of quadruple hydrogen bonds and generating a supra­molecular pattern. The 5FC (mol­ecules A and B) and two melamine mol­ecules inter­act via N—H⋯O, N—H⋯N and N—H⋯O, N—H⋯N, C—H⋯F hydrogen bonds forming R 6 6(24) and R 4 4(15) ring motifs. The crystal structure is further strengthened by C—H⋯F, C—F⋯π and π–π stacking inter­actions. PMID:27375887

In situ measurements of Saturn’s ionosphere show that it is dynamic and interacts with the rings

NASA Astrophysics Data System (ADS)

Wahlund, J.-E.; Morooka, M. W.; Hadid, L. Z.; Persoon, A. M.; Farrell, W. M.; Gurnett, D. A.; Hospodarsky, G.; Kurth, W. S.; Ye, S.-Y.; Andrews, D. J.; Edberg, N. J. T.; Eriksson, A. I.; Vigren, E.

2018-01-01

The ionized upper layer of Saturn’s atmosphere, its ionosphere, provides a closure of currents mediated by the magnetic field to other electrically charged regions (for example, rings) and hosts ion-molecule chemistry. In 2017, the Cassini spacecraft passed inside the planet’s rings, allowing in situ measurements of the ionosphere. The Radio and Plasma Wave Science instrument detected a cold, dense, and dynamic ionosphere at Saturn that interacts with the rings. Plasma densities reached up to 1000 cubic centimeters, and electron temperatures were below 1160 kelvin near closest approach. The density varied between orbits by up to two orders of magnitude. Saturn’s A- and B-rings cast a shadow on the planet that reduced ionization in the upper atmosphere, causing a north-south asymmetry.

Structural and functional analysis of a FeoB A143S G5 loop mutant explains the accelerated GDP release rate.

PubMed

Guilfoyle, Amy P; Deshpande, Chandrika N; Vincent, Kimberley; Pedroso, Marcelo M; Schenk, Gerhard; Maher, Megan J; Jormakka, Mika

2014-05-01

GTPases (G proteins) hydrolyze the conversion of GTP to GDP and free phosphate, comprising an integral part of prokaryotic and eukaryotic signaling, protein biosynthesis and cell division, as well as membrane transport processes. The G protein cycle is brought to a halt after GTP hydrolysis, and requires the release of GDP before a new cycle can be initiated. For eukaryotic heterotrimeric Gαβγ proteins, the interaction with a membrane-bound G protein-coupled receptor catalyzes the release of GDP from the Gα subunit. Structural and functional studies have implicated one of the nucleotide binding sequence motifs, the G5 motif, as playing an integral part in this release mechanism. Indeed, a Gαs G5 mutant (A366S) was shown to have an accelerated GDP release rate, mimicking a G protein-coupled receptor catalyzed release state. In the present study, we investigate the role of the equivalent residue in the G5 motif (residue A143) in the prokaryotic membrane protein FeoB from Streptococcus thermophilus, which includes an N-terminal soluble G protein domain. The structure of this domain has previously been determined in the apo and GDP-bound states and in the presence of a transition state analogue, revealing conformational changes in the G5 motif. The A143 residue was mutated to a serine and analyzed with respect to changes in GTPase activity, nucleotide release rate, GDP affinity and structural alterations. We conclude that the identity of the residue at this position in the G5 loop plays a key role in the nucleotide release rate by allowing the correct positioning and hydrogen bonding of the nucleotide base. © 2014 FEBS.

Crystal structure and absolute configuration of (3aS,4S,5R,7aR)-2,2,7-trimethyl-3a,4,5,7a-tetra-hydro-1,3-benzodioxole-4,5-diol.

PubMed

Macías, Mario A; Suescun, Leopoldo; Pandolfi, Enrique; Schapiro, Valeria; Tibhe, Gaurao D; Mombrú, Álvaro W

2015-09-01

The absolute configuration of the title compound, C10H16O4, determined as 3aS,4S,5R,7aR on the basis of the synthetic pathway, was confirmed by X-ray diffraction. The mol-ecule contains a five- and a six-membered ring that adopt twisted and envelope conformations, respectively. The dihedral angle between the mean planes of the rings is 76.80 (11)° as a result of their cis-fusion. In the crystal, mol-ecules are linked by two pairs of O-H⋯O hydrogen bonds, forming chains along [010]. These chains are further connected by weaker C-H⋯O inter-actions along [100], creating (001) sheets that inter-act only by weak van der Waals forces.

Statistical tests to compare motif count exceptionalities

PubMed Central

Robin, Stéphane; Schbath, Sophie; Vandewalle, Vincent

2007-01-01

Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use. PMID:17346349

Thomson's Jumping Ring over a Long Coil

ERIC Educational Resources Information Center

Jeffery, Rondo N.; Amiri, Farhang

2018-01-01

The classic jumping ring apparatus consists of a coil with an iron core that extends out of the coil. A copper or aluminum ring placed over the iron core jumps upward when AC power is applied to the coil. In this paper we will examine a modified design of the jumping ring apparatus, called the "long-coil design." It allows the ring to…

FY2017 status report: Model 9975 O-ring fixture long-term leak performance

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

Daugherty, W. L.

A series of experiments to monitor the aging performance of Viton® GLT and GLT-S O-rings used in the Model 9975 shipping package has been ongoing since 2004 at the Savannah River National Laboratory. One approach has been to periodically evaluate the leak performance of O-rings being aged in mock-up 9975 Primary Containment Vessels (PCVs) at elevated temperature. Other methods such as compression-stress relaxation (CSR) tests and field surveillance are also on-going to evaluate O-ring behavior. Seventy tests using PCV mock-ups with GLT O-rings were assembled and heated to temperatures ranging from 200 to 450 ºF. They were leak-tested initially andmore » have been tested periodically to determine if they continue to meet the leak-tightness criterion defined in ANSI standard N14.5-97. Due to material substitution, a smaller test matrix with fourteen additional tests was initiated in 2008 with GLT-S O-rings heated to temperatures ranging from 200 to 400 ºF. Leak test failures have been experienced in all of the GLT O-ring fixtures aging at 350 ºF and higher temperatures, and in 8 fixtures aging at 300 ºF. The 300 °F GLT O-ring fixtures failed after 2.8 to 5.7 years at temperature. The remaining GLT O-ring fixtures aging at 300 ºF were retired from testing following more than 5 years at temperature without failure. No failures have yet been observed in GLT O-ring fixtures aging at 200 ºF for 9 to 10.5 years, or in GLT O-ring fixtures aging at 270 ºF for 5.7 years. These aging temperatures bound O-ring temperatures anticipated during normal storage in K-Area Complex (KAC). Leak test failures have been experienced in all of the GLT-S O-ring fixtures aging at 300 ºF and above. No failures have yet been observed in GLT-S O-ring fixtures aging at 200 and 250 ºF for 6.9 to 7.5 years. Data from the O-ring fixtures are generally consistent with results from compression stress relaxation testing, and provide confidence in the predictive models based on those

Oligomeric ferrocene rings

NASA Astrophysics Data System (ADS)

Inkpen, Michael S.; Scheerer, Stefan; Linseis, Michael; White, Andrew J. P.; Winter, Rainer F.; Albrecht, Tim; Long, Nicholas J.

2016-09-01

Cyclic oligomers comprising strongly interacting redox-active monomer units represent an unknown, yet highly desirable class of nanoscale materials. Here we describe the synthesis and properties of the first family of molecules belonging to this compound category—differently sized rings comprising only 1,1‧-disubstituted ferrocene units (cyclo[n], n = 5-7, 9). Due to the close proximity and connectivity of centres (covalent Cp-Cp linkages; Cp = cyclopentadienyl) solution voltammograms exhibit well-resolved, separated 1e- waves. Theoretical interrogations into correlations based on ring size and charge state are facilitated using values of the equilibrium potentials of these transitions, as well as their relative spacing. As the interaction free energies between the redox centres scale linearly with overall ring charge and in conjunction with fast intramolecular electron transfer (˜107 s-1), these molecules can be considered as uniformly charged nanorings (diameter ˜1-2 nm).

Prestressed Ring Beam in the Church of St. Peter’s and Paul’s in Bodzanow, Design and Realization

NASA Astrophysics Data System (ADS)

Szydlowski, Rafal; Labuzek, Barbara; Turcza, Monika

2017-10-01

The present trend in architecture is designing thin. slender and spacious architectural forms. It has become the reason for searching for new solutions and finding new ways of use of the existing construction ones. Recently, the first time in Poland, the post-tensioning has been used in realization of church building. In the Church of St. Peter’s and Paul’s in Bodzanow (near Cracow) was designed circumferential ring beam post-tensioned with 4 unbounded tendons to transfer peripheral tensile forces from the roof. Thanks to the use of a prestressed ring beam hidden in the wall, large cross-section of roof girders was possible to be avoided, as well as a massive reinforced concrete ring or additional steel tie-rods. The paper presents the applied solutions in details with the theoretical calculated results as well as the results of prestressing measured in site during tensioning of tendons. Based on presented results some conclusions have been drawn.

Finding specific RNA motifs: Function in a zeptomole world?

PubMed Central

KNIGHT, ROB; YARUS, MICHAEL

2003-01-01

We have developed a new method for estimating the abundance of any modular (piecewise) RNA motif within a longer random region. We have used this method to estimate the size of the active motifs available to modern SELEX experiments (picomoles of unique sequences) and to a plausible RNA World (zeptomoles of unique sequences: 1 zmole = 602 sequences). Unexpectedly, activities such as specific isoleucine binding are almost certainly present in zeptomoles of molecules, and even ribozymes such as self-cleavage motifs may appear (depending on assumptions about the minimal structures). The number of specified nucleotides is not the only important determinant of a motif’s rarity: The number of modules into which it is divided, and the details of this division, are also crucial. We propose three maxims for easily isolated motifs: the Maxim of Minimization, the Maxim of Multiplicity, and the Maxim of the Median. These maxims together state that selected motifs should be small and composed of as many separate, equally sized modules as possible. For evenly divided motifs with four modules, the largest accessible activity in picomole scale (1–1000 pmole) pools of length 100 is about 34 nucleotides; while for zeptomole scale (1–1000 zmole) pools it is about 20 specific nucleotides (50% probability of occurrence). This latter figure includes some ribozymes and aptamers. Consequently, an RNA metabolism apparently could have begun with only zeptomoles of RNA molecules. PMID:12554865

Cassini Radio Occultations of Saturn's Rings: Scattered Signal and Particle Sizes

NASA Astrophysics Data System (ADS)

Thomson, F.; Wong, K.; Marouf, E.; French, R.; Rappaport, N.; McGhee, C.; Anabtawi, A.; Asmar, S.; Barbinis, E.; Fleischman, D.; Goltz, G.; Johnston, D.; Rochblatt, D.

2005-08-01

Eight Cassini radio occultations of Saturn's rings were conducted from May 3 to September 5, 2005. During any given occultation, Cassini transmits Ka-, X-, and S-band sinusoidal signals (0.94, 3.6, and 13 cm-wavelength) through the rings. Spectral analysis of the perturbed signals received at stations of the Deep Space Network (DSN) reveals two distinct signal components. The first is the direct signal, a narrowband component representing the incident sinusoid emerging from the rings reduced in amplitude and changed in phase. The second is the scattered signal, a broadband component, representing near-forward scattering by ring particles. After reconstruction to remove diffraction effects, time history of the direct signal yields profiles of ring structure at resolution approaching ˜50 m. Of primary concern here is the broadband component. For the first time ever, clearly detectable scattered signals were observed at all three (Ka/X/S) bands. A single X/S radio occultation by Voyager 1 in 1980 detected scattered signal at X-band only, primarily because of the small ring opening angle B=5.9o at the time, compared with 19.1 ≤ B ≤ 23.6o for Cassini. Time histories of the observed spectra (spectrograms) and their dependence on wavelength provide important information about physical ring properties, including abundance of meter-size particles, particle crowding, clustering, spatial anisotropy, vertical ring profile and thickness. Cassini occultation orbits were optimized to map scattering by individual ring features into nearly non-overlapping spectral bands, allowing unambiguous identification of the contribution of ring features to the computed spectrograms. We present Ka/X/S spectrograms over the full extent of the ring system and relate their behavior to observed ring structure. The spectrograms imply presence of meters-size particles throughout the ring system. Preliminary results regarding the particle size distribution and vertical ring profile of selected

Discriminative motif optimization based on perceptron training

PubMed Central

Patel, Ronak Y.; Stormo, Gary D.

2014-01-01

Motivation: Generating accurate transcription factor (TF) binding site motifs from data generated using the next-generation sequencing, especially ChIP-seq, is challenging. The challenge arises because a typical experiment reports a large number of sequences bound by a TF, and the length of each sequence is relatively long. Most traditional motif finders are slow in handling such enormous amount of data. To overcome this limitation, tools have been developed that compromise accuracy with speed by using heuristic discrete search strategies or limited optimization of identified seed motifs. However, such strategies may not fully use the information in input sequences to generate motifs. Such motifs often form good seeds and can be further improved with appropriate scoring functions and rapid optimization. Results: We report a tool named discriminative motif optimizer (DiMO). DiMO takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. We use area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner. Using DiMO, on a large test set of 87 TFs from human, drosophila and yeast, we show that it is possible to significantly improve motifs identified by nine motif finders. The motifs are generated/optimized using training sets and evaluated on test sets. The AUC is improved for almost 90% of the TFs on test sets and the magnitude of increase is up to 39%. Availability and implementation: DiMO is available at http://stormo.wustl.edu/DiMO Contact: rpatel@genetics.wustl.edu, ronakypatel@gmail.com PMID:24369152

Earth: A Ringed Planet?

NASA Astrophysics Data System (ADS)

Hancock, L. O.; Povenmire, H.

2010-12-01

Among the most beautiful findings of the Space Age have been the discoveries of planetary rings. Not only Saturn but also Jupiter, Uranus and Neptune have rings; Saturn’s ring system has structures newly discovered; even Saturn's moon Rhea itself has a ring. All these are apparently supplied by material from the planetary moons (Rhea's ring by Rhea itself). The question naturally arises, why should the Earth not have a ring, and on the other hand, if it does, why has it not been observed? No rings have yet been observed in the inner solar system, but after all, rings in the inner solar system might simply tend to be fainter and more transient than those of the outer solar system: the inner solar system is more affected by the solar wind, and the Sun’s perturbing gravitational influence is greater. J.A. O’Keefe first suggested (1980) that Earth might have a ring system of its own. An Earth ring could account for some climate events. O’Keefe remarked that formation or thickening of a ring system in Earth’s equatorial plane could drive glaciation by deepening the chill of the winter hemisphere. (It is very well established that volcanic dust is an effective agent for the extinction of sunlight; this factor can be overwhelmingly apparent in eclipse observations.) O’Keefe died in 2000 and the speculation was not pursued, but the idea of an Earth ring has a prima facie reasonableness that calls for its renewed consideration. The program of this note is to hypothesize that, as O’Keefe proposed: (a) an Earth ring system exists; (b) it affects Earth's weather and climate; (c) the tektite strewn fields comprise filaments of the ring fallen to Earth's surface on various occasions of disturbance by comets or asteroids. On this basis, and drawing on the world's weather records, together with the Twentieth Century Reanalysis by NCEP/CIRES covering the period 1870-2010 and the geology of the tektite strewn fields, we herein propose the hypothesized Earth ring

Identifying the scale-dependent motifs in atmospheric surface layer by ordinal pattern analysis

NASA Astrophysics Data System (ADS)

Li, Qinglei; Fu, Zuntao

2018-07-01

Ramp-like structures in various atmospheric surface layer time series have been long studied, but the presence of motifs with the finer scale embedded within larger scale ramp-like structures has largely been overlooked in the reported literature. Here a novel, objective and well-adapted methodology, the ordinal pattern analysis, is adopted to study the finer-scaled motifs in atmospheric boundary-layer (ABL) time series. The studies show that the motifs represented by different ordinal patterns take clustering properties and 6 dominated motifs out of the whole 24 motifs account for about 45% of the time series under particular scales, which indicates the higher contribution of motifs with the finer scale to the series. Further studies indicate that motif statistics are similar for both stable conditions and unstable conditions at larger scales, but large discrepancies are found at smaller scales, and the frequencies of motifs "1234" and/or "4321" are a bit higher under stable conditions than unstable conditions. Under stable conditions, there are great changes for the occurrence frequencies of motifs "1234" and "4321", where the occurrence frequencies of motif "1234" decrease from nearly 24% to 4.5% with the scale factor increasing, and the occurrence frequencies of motif "4321" change nonlinearly with the scale increasing. These great differences of dominated motifs change with scale can be taken as an indicator to quantify the flow structure changes under different stability conditions, and motif entropy can be defined just by only 6 dominated motifs to quantify this time-scale independent property of the motifs. All these results suggest that the defined scale of motifs with the finer scale should be carefully taken into consideration in the interpretation of turbulence coherent structures.

Record of the Solar Activity and of Other Geophysical Phenomenons in Tree Ring

NASA Astrophysics Data System (ADS)

Rigozo, Nivaor Rodolfo

1999-01-01

Tree ring studies are usually used to determine or verify climatic factors which prevail in a given place or region and may cause tree ring width variations. Few studies are dedicated to the geophysical phenomena which may underlie these tree ring width variations. In order to look for periodicities which may be associated to the solar activity and/or to other geophysical phenomena which may influence tree ring growth, a new interactive image analysis method to measure tree ring width was developed and is presented here. This method makes use of a computer and a high resolution flatbed scanner; a program was also developed in Interactive Data Language (IDL 5.0) to study ring digitized images and transform them into time series. The main advantage of this method is the tree ring image interactive analysis without needing complex and high cost instrumentation. Thirty-nine samples were collected: 12 from Concordia - S. C., 9 from Canela - R. S., 14 from Sao Francisco de Paula - R. S., one from Nova Petropolis - R. S., 2 from Sao Martinho da Serra - R. S. e one from Chile. Fit functions are applied to ring width time series to obtain the best long time range trend (growth rate of every tree) curves and are eliminated through a standardization process that gives the tree ring index time series from which is performed spectral analysis by maximum entropy method and iterative regression. The results obtained show periodicities close to 11 yr, 22 yr Hale solar cycles and 5.5 yr for all sampling locations 52 yr and Gleissberg cycles for Concordia - S. C. and Chile samples. El Nino events were also observed with periods around 4 e 7 yr.

Molecular interaction between Smurf1 WW2 domain and PPXY motifs of Smad1, Smad5, and Smad6--modeling and analysis.

PubMed

Sangadala, Sreedhara; Metpally, Raghu Prasad Rao; Reddy, Boojala Vijay B

2007-08-01

The ubiquitin-proteasome proteolytic pathway is essential for various important biological processes including cell cycle progression, gene transcription, and signal transduction. One of the important regulatory mechanisms by which the bone-inducing activity of the bone morphogenetic protein (BMP) signaling is modulated involves ubiquitin-mediated proteasomal degradation. The BMP induced receptor signal is transmitted intracellularly by phosphorylation of Smad proteins by the activated receptor I. The phosphorylated Smads 1, 5, and 8 (R-Smads) oligomerize with the co-Smad (Smad4). The complex, thus, formed translocates to the nucleus and interacts with other cofactors to regulate the expression of downstream target genes. R-Smads contain PPXY motif in the linker region that interacts with Smad ubiquitin regulatory factor 1 (Smurf1), an E3 ubiquitin ligase that catalyzes ubiquitination of target proteins for proteasomal degradation. Smurf1 contains a HECT domain, a C2 domain, and 2 WW domains (WW1, WW2). The PPXY motif in target proteins and its interaction with Smurf1 may form the basis for regulation of steady-state levels of Smads in controlling BMP-responsiveness of cells. Here, we present a homology-based model of the Smurf1 WW2 domain and the target octa-peptides containing PPXY motif of Smurf1-interacting Smads. We carried out docking of Smurf1 WW2 domain with the PPXY motifs of Smad1, Smad5, and Smad6 and identified the key amino acid residues involved in interaction. Furthermore, we present experimental evidence that WW2 domain of Smurf1 does indeed interact with the Smad proteins and that the deletion of WW2 domain of Smurf1 results in loss of its binding to Smads using the purified recombinant proteins. Finally, we also present data confirming that the deletion of WW2 domain in Smurf1 abolishes its ubiquitination activity on Smad1 in an in vitro ubiquitination assay. It shows that the interaction between the WW domain and Smad PPXY motif is a key step in

Identification in a pseudoknot of a U.G motif essential for the regulation of the expression of ribosomal protein S15.

PubMed

Bénard, L; Mathy, N; Grunberg-Manago, M; Ehresmann, B; Ehresmann, C; Portier, C

1998-03-03

The ribosomal protein S15 from Escherichia coli binds to a pseudoknot in its own messenger. This interaction is an essential step in the mechanism of S15 translational autoregulation. In a previous study, a recognition determinant for S15 autoregulation, involving a U.G wobble pair, was located in the center of stem I of the pseudoknot. In this study, an extensive mutagenesis analysis has been conducted in and around this U.G pair by comparing the effects of these mutations on the expression level of S15. The results show that the U.G wobble pair cannot be substituted by A.G, C.A, A.C, G.U, or C.G without loss of the autocontrol. In addition, the base pair C.G, adjacent to the 5' side of U, cannot be flipped or changed to another complementary base pair without also inducing derepression of translation. A unique motif, made of only two adjacent base pairs, U.G/C.G, is essential for S15 autoregulation and is presumably involved in direct recognition by the S15 protein.

Identification in a pseudoknot of a U⋅G motif essential for the regulation of the expression of ribosomal protein S15

PubMed Central

Bénard, Lionel; Mathy, Nathalie; Grunberg-Manago, Marianne; Ehresmann, Bernard; Ehresmann, Chantal; Portier, Claude

1998-01-01

The ribosomal protein S15 from Escherichia coli binds to a pseudoknot in its own messenger. This interaction is an essential step in the mechanism of S15 translational autoregulation. In a previous study, a recognition determinant for S15 autoregulation, involving a U⋅G wobble pair, was located in the center of stem I of the pseudoknot. In this study, an extensive mutagenesis analysis has been conducted in and around this U⋅G pair by comparing the effects of these mutations on the expression level of S15. The results show that the U⋅G wobble pair cannot be substituted by A⋅G, C⋅A, A⋅C, G⋅U, or C⋅G without loss of the autocontrol. In addition, the base pair C⋅G, adjacent to the 5′ side of U, cannot be flipped or changed to another complementary base pair without also inducing derepression of translation. A unique motif, made of only two adjacent base pairs, U⋅G/C⋅G, is essential for S15 autoregulation and is presumably involved in direct recognition by the S15 protein. PMID:9482926

Structural Analysis of the Bacterial Proteasome Activator Bpa in Complex with the 20S Proteasome.

PubMed

Bolten, Marcel; Delley, Cyrille L; Leibundgut, Marc; Boehringer, Daniel; Ban, Nenad; Weber-Ban, Eilika

2016-12-06

Mycobacterium tuberculosis harbors proteasomes that recruit substrates for degradation through an ubiquitin-like modification pathway. Recently, a non-ATPase activator termed Bpa (bacterial proteasome activator) was shown to support an alternate proteasomal degradation pathway. Here, we present the cryo-electron microscopy (cryo-EM) structure of Bpa in complex with the 20S core particle (CP). For docking into the cryo-EM density, we solved the X-ray structure of Bpa, showing that it forms tight four-helix bundles arranged into a 12-membered ring with a 40 Å wide central pore and the C-terminal helix of each protomer protruding from the ring. The Bpa model was fitted into the cryo-EM map of the Bpa-CP complex, revealing its architecture and striking symmetry mismatch. The Bpa-CP interface was resolved to 3.5 Å, showing the interactions between the C-terminal GQYL motif of Bpa and the proteasome α-rings. This docking mode is related to the one observed for eukaryotic activators with features specific to the bacterial complex. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element.

PubMed

Fukunaga, Junichi; Nomura, Yusuke; Tanaka, Yoichiro; Amano, Ryo; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Sakamoto, Taiichi; Kozu, Tomoko

2013-07-01

AML1 (RUNX1) is a key transcription factor for hematopoiesis that binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. Aberrations in the AML1 gene are frequently found in human leukemia. To better understand AML1 and its potential utility for diagnosis and therapy, we obtained RNA aptamers that bind specifically to the AML1 Runt domain. Enzymatic probing and NMR analyses revealed that Apt1-S, which is a truncated variant of one of the aptamers, has a CACG tetraloop and two stem regions separated by an internal loop. All the isolated aptamers were found to contain the conserved sequence motif 5'-NNCCAC-3' and 5'-GCGMGN'N'-3' (M:A or C; N and N' form Watson-Crick base pairs). The motif contains one AC mismatch and one base bulged out. Mutational analysis of Apt1-S showed that three guanines of the motif are important for Runt binding as are the three guanines of RDE, which are directly recognized by three arginine residues of the Runt domain. Mutational analyses of the Runt domain revealed that the amino acid residues used for Apt1-S binding were similar to those used for RDE binding. Furthermore, the aptamer competed with RDE for binding to the Runt domain in vitro. These results demonstrated that the Runt domain of the AML1 protein binds to the motif of the aptamer that mimics DNA. Our findings should provide new insights into RNA function and utility in both basic and applied sciences.

[Personal motif in art].

PubMed

Gerevich, József

2015-01-01

One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy.

The polarization of the G-protein activated potassium channel GIRK5 to the vegetal pole of Xenopus laevis oocytes is driven by a di-leucine motif.

PubMed

Díaz-Bello, Beatriz; Rangel-García, Claudia I; Salvador, Carolina; Carrisoza-Gaytán, Rolando; Escobar, Laura I

2013-01-01

The G protein-coupled inwardly-rectifying potassium channels (known as GIRK or Kir3) form functional heterotetramers gated by G-βγ subunits. GIRK channels participate in heart rate modulation and neuronal postsynaptic inhibition in mammals. In Xenopus laevis oocytes, GIRK5 is a functional homomultimer. Previously, we found that phosphorylation of a tyrosine (Y16) at its N-terminus downregulates the surface expression of GIRK5. In this work, we elucidated the subcellular localization and trafficking of GIRK5 in oocytes. Several EGFP-GIRK5 chimeras were produced and an ECFP construct was used to identify the endoplasmic reticulum (ER). Whereas GIRK5-WT was retained in the ER at the animal pole, the phospho-null GIRK5-Y16A was localized to the vegetal pole. Interestingly, a construct with an N-terminal Δ25 deletion produced an even distribution of the channel in the whole oocyte. Through an alanine-scan, we identified an acidic cluster/di-leucine sorting-signal recognition motif between E17 and I22. We quantified the effect of each amino acid residue within this di-leucine motif in determining the distribution of GIRK5 to the animal and vegetal poles. We found that Y16 and I22 contributed to functional expression and were dominant in the polarization of GIRK5. We thus conclude that the N-terminal acidic di-leucine motif of GIRK5 determines its retention and polarized trafficking within Xl oocytes.

The Polarization of the G-Protein Activated Potassium Channel GIRK5 to the Vegetal Pole of Xenopus laevis Oocytes Is Driven by a Di-Leucine Motif

PubMed Central

Díaz-Bello, Beatriz; Rangel-García, Claudia I.; Salvador, Carolina; Carrisoza-Gaytán, Rolando; Escobar, Laura I.

2013-01-01

The G protein-coupled inwardly-rectifying potassium channels (known as GIRK or Kir3) form functional heterotetramers gated by G-βγ subunits. GIRK channels participate in heart rate modulation and neuronal postsynaptic inhibition in mammals. In Xenopus laevis oocytes, GIRK5 is a functional homomultimer. Previously, we found that phosphorylation of a tyrosine (Y16) at its N-terminus downregulates the surface expression of GIRK5. In this work, we elucidated the subcellular localization and trafficking of GIRK5 in oocytes. Several EGFP-GIRK5 chimeras were produced and an ECFP construct was used to identify the endoplasmic reticulum (ER). Whereas GIRK5-WT was retained in the ER at the animal pole, the phospho-null GIRK5-Y16A was localized to the vegetal pole. Interestingly, a construct with an N-terminal Δ25 deletion produced an even distribution of the channel in the whole oocyte. Through an alanine-scan, we identified an acidic cluster/di-leucine sorting-signal recognition motif between E17 and I22. We quantified the effect of each amino acid residue within this di-leucine motif in determining the distribution of GIRK5 to the animal and vegetal poles. We found that Y16 and I22 contributed to functional expression and were dominant in the polarization of GIRK5. We thus conclude that the N-terminal acidic di-leucine motif of GIRK5 determines its retention and polarized trafficking within Xl oocytes. PMID:23717539

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

PubMed Central

Frith, Martin C.; Saunders, Neil F. W.; Kobe, Bostjan; Bailey, Timothy L.

2008-01-01

Biology is encoded in molecular sequences: deciphering this encoding remains a grand scientific challenge. Functional regions of DNA, RNA, and protein sequences often exhibit characteristic but subtle motifs; thus, computational discovery of motifs in sequences is a fundamental and much-studied problem. However, most current algorithms do not allow for insertions or deletions (indels) within motifs, and the few that do have other limitations. We present a method, GLAM2 (Gapped Local Alignment of Motifs), for discovering motifs allowing indels in a fully general manner, and a companion method GLAM2SCAN for searching sequence databases using such motifs. glam2 is a generalization of the gapless Gibbs sampling algorithm. It re-discovers variable-width protein motifs from the PROSITE database significantly more accurately than the alternative methods PRATT and SAM-T2K. Furthermore, it usefully refines protein motifs from the ELM database: in some cases, the refined motifs make orders of magnitude fewer overpredictions than the original ELM regular expressions. GLAM2 performs respectably on the BAliBASE multiple alignment benchmark, and may be superior to leading multiple alignment methods for “motif-like” alignments with N- and C-terminal extensions. Finally, we demonstrate the use of GLAM2 to discover protein kinase substrate motifs and a gapped DNA motif for the LIM-only transcriptional regulatory complex: using GLAM2SCAN, we identify promising targets for the latter. GLAM2 is especially promising for short protein motifs, and it should improve our ability to identify the protein cleavage sites, interaction sites, post-translational modification attachment sites, etc., that underlie much of biology. It may be equally useful for arbitrarily gapped motifs in DNA and RNA, although fewer examples of such motifs are known at present. GLAM2 is public domain software, available for download at http://bioinformatics.org.au/glam2. PMID:18437229

Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20.

PubMed

Maio, N; Rouault, T A

2016-10-01

Iron-sulfur (Fe-S) clusters are inorganic cofactors that are fundamental to several biological processes in all three kingdoms of life. In most organisms, Fe-S clusters are initially assembled on a scaffold protein, ISCU, and subsequently transferred to target proteins or to intermediate carriers by a dedicated chaperone/co-chaperone system. The delivery of assembled Fe-S clusters to recipient proteins is a crucial step in the biogenesis of Fe-S proteins, and, in mammals, it relies on the activity of a multiprotein transfer complex that contains the chaperone HSPA9, the co-chaperone HSC20 and the scaffold ISCU. How the transfer complex efficiently engages recipient Fe-S target proteins involves specific protein interactions that are not fully understood. This mini review focuses on recent insights into the molecular mechanism of amino acid motif recognition and discrimination by the co-chaperone HSC20, which guides Fe-S cluster delivery.

Beyond Atg8 binding: The role of AIM/LIR motifs in autophagy.

PubMed

Fracchiolla, Dorotea; Sawa-Makarska, Justyna; Martens, Sascha

2017-05-04

Selective macroautophagy/autophagy mediates the selective delivery of cytoplasmic cargo material via autophagosomes into the lytic compartment for degradation. This selectivity is mediated by cargo receptor molecules that link the cargo to the phagophore (the precursor of the autophagosome) membrane via their simultaneous interaction with the cargo and Atg8 proteins on the membrane. Atg8 proteins are attached to membrane in a conjugation reaction and the cargo receptors bind them via short peptide motifs called Atg8-interacting motifs/LC3-interacting regions (AIMs/LIRs). We have recently shown for the yeast Atg19 cargo receptor that the AIM/LIR motifs also serve to recruit the Atg12-Atg5-Atg16 complex, which stimulates Atg8 conjugation, to the cargo. We could further show in a reconstituted system that the recruitment of the Atg12-Atg5-Atg16 complex is sufficient for cargo-directed Atg8 conjugation. Our results suggest that AIM/LIR motifs could have more general roles in autophagy.

TAE+ 5.1 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.1 (SUN3 VERSION WITH MOTIF)

NASA Technical Reports Server (NTRS)

TAE SUPPORT OFFICE

1994-01-01

workbench-generated resource files during each execution, details such as color, font, location, and object type remain independent from the application code, allowing changes to the user interface without recompiling and relinking. The Silicon Graphics version of TAE Plus now has a font caching scheme and a color caching scheme to make color allocation more efficient. In addition to WPTs, TAE Plus can control interaction of objects from the interpreted TAE Command Language. TCL provides an extremely powerful means for the more experienced developer to quickly prototype an application's use of TAE Plus interaction objects and add programming logic without the overhead of compiling or linking. TAE Plus requires MIT's X Window System, Version 11 Release 4, and the Open Software Foundation's Motif Toolkit 1.1 or 1.1.1. The Workbench and WPTs are written in C++ and the remaining code is written in C. TAE Plus is available by license for an unlimited time period. The licensed program product includes the TAE Plus source code and one set of supporting documentation. Additional documentation may be purchased separately at the price indicated below. The amount of disk space required to load the TAE Plus tar format tape is between 35Mb and 67Mb depending on the machine version. The recommended minimum memory is 12Mb. Each TAE Plus platform delivery tape includes pre-built libraries and executable binary code for that particular machine, as well as source code, so users do not have to do an installation. Users wishing to recompile the source will need both a C compiler and either GNU's C++ Version 1.39 or later, or a C++ compiler based on AT&T 2.0 cfront. TAE Plus comes with InterViews and idraw, two software packages developed by Stanford University and integrated in TAE Plus. TAE Plus was developed in 1989 and version 5.1 was released in 1991. TAE Plus is currently available on media suitable for eight different machine platforms: 1) DEC VAX computers running VMS 5.3 or higher (TK

A Compact Trench-Assisted Multi-Orbital-Angular-Momentum Multi-Ring Fiber for Ultrahigh-Density Space-Division Multiplexing (19 Rings × 22 Modes)

PubMed Central

Li, Shuhui; Wang, Jian

2014-01-01

We present a compact (130 μm cladding diameter) trench-assisted multi-orbital-angular-momentum (OAM) multi-ring fiber with 19 rings each supporting 22 modes with 18 OAM ones. Using the high-contrast-index ring and trench designs, the trench-assisted multi-OAM multi-ring fiber (TA-MOMRF) features both low-level inter-mode crosstalk and inter-ring crosstalk within a wide wavelength range (1520 to 1630 nm), which can potentially enable Pbit/s total transmission capacity and hundreds bit/s/Hz spectral efficiency in a single TA-MOMRF. Moreover, the effective refractive index difference of even and odd fiber eigenmodes induced by the ellipticity of ring and fiber bending and their impacts on the purity of OAM mode and mode coupling/crosstalk are analyzed. It is found that high-order OAM modes show preferable tolerance to the ring ellipticity and fiber bending. The designed fiber offers favorable tolerance to both small ellipticity of ring (<−22 dB crosstalk under an ellipticity of 0.5%) and small bend radius (<−20 dB crosstalk under a bend radius of 2 cm). PMID:24458159

On the formation of vortex rings in coaxial tubes

NASA Astrophysics Data System (ADS)

Gan, Lian

2011-11-01

The formation of vortex rings within coaxial tubes of different diameter is investigated experimentally and numerically. PIV measurements were carried out in a water tank equipped with a piston-cylinder apparatus used to generate vortex rings inside a series of coaxial tubes with tube to piston diameter ratios, DT / D , ranging from 4 to 1.5. In order to distinguish between the effect confinement has on the formation of isolated vortex rings from those formed with a trailing jet flow, non- dimensional stroke ratios below and above the formation number were investigated, L / D = 2 . 5 and 10 respectively. For DT / D > 2 and L / D s below the formation number the kinematics of the vortex rings follow classical inviscid theory in so much as their self-induced velocity decreases linearly with decreasing tube diameter in accordance with the image theorem. For DT / D <= 2 boundary layer separation along the tube wall begins to interfere with the vortex during its roll-up phase. For vortex rings below the formation number, the vortex core is briefly arrested upon completion of the piston stroke. On the other hand, long L / D s give rise to even more complex dynamics. When DT / D = 2 the interaction between boundary layer and the starting jet acts to suppress vortex ring formation altogether. However, as confinement is increased further to DT / D = 1 . 5 the formation of a lead vortex ring re-appears but with a circulation lower than the formation number before rapidly decaying.

SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data

PubMed Central

Dotu, Ivan; Adamson, Scott I.; Coleman, Benjamin; Fournier, Cyril; Ricart-Altimiras, Emma; Eyras, Eduardo

2018-01-01

RNA-protein binding is critical to gene regulation, controlling fundamental processes including splicing, translation, localization and stability, and aberrant RNA-protein interactions are known to play a role in a wide variety of diseases. However, molecular understanding of RNA-protein interactions remains limited; in particular, identification of RNA motifs that bind proteins has long been challenging, especially when such motifs depend on both sequence and structure. Moreover, although RNA binding proteins (RBPs) often contain more than one binding domain, algorithms capable of identifying more than one binding motif simultaneously have not been developed. In this paper we present a novel pipeline to determine binding peaks in crosslinking immunoprecipitation (CLIP) data, to discover multiple possible RNA sequence/structure motifs among them, and to experimentally validate such motifs. At the core is a new semi-automatic algorithm SARNAclust, the first unsupervised method to identify and deconvolve multiple sequence/structure motifs simultaneously. SARNAclust computes similarity between sequence/structure objects using a graph kernel, providing the ability to isolate the impact of specific features through the bulge graph formalism. Application of SARNAclust to synthetic data shows its capability of clustering 5 motifs at once with a V-measure value of over 0.95, while GraphClust achieves only a V-measure of 0.083 and RNAcontext cannot detect any of the motifs. When applied to existing eCLIP sets, SARNAclust finds known motifs for SLBP and HNRNPC and novel motifs for several other RBPs such as AGGF1, AKAP8L and ILF3. We demonstrate an experimental validation protocol, a targeted Bind-n-Seq-like high-throughput sequencing approach that relies on RNA inverse folding for oligo pool design, that can validate the components within the SLBP motif. Finally, we use this protocol to experimentally interrogate the SARNAclust motif predictions for protein ILF3. Our

Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20

PubMed Central

Maio, N.; Rouault, T. A.

2017-01-01

Iron-sulfur (Fe-S) clusters are inorganic cofactors that are fundamental to several biological processes in all three kingdoms of life. In most organisms, Fe-S clusters are initially assembled on a scaffold protein, ISCU, and subsequently transferred to target proteins or to intermediate carriers by a dedicated chaperone/co-chaperone system. The delivery of assembled Fe-S clusters to recipient proteins is a crucial step in the biogenesis of Fe-S proteins, and, in mammals, it relies on the activity of a multiprotein transfer complex that contains the chaperone HSPA9, the co-chaperone HSC20 and the scaffold ISCU. How the transfer complex efficiently engages recipient Fe-S target proteins involves specific protein interactions that are not fully understood. This mini review focuses on recent insights into the molecular mechanism of amino acid motif recognition and discrimination by the co-chaperone HSC20, which guides Fe-S cluster delivery. PMID:27714045

Physiological Responses during Cycling With Oval Chainrings (Q-Ring) and Circular Chainrings.

PubMed

Cordova, Alfredo; Latasa, Iban; Seco, Jesus; Villa, Gerardo; Rodriguez-Falces, Javier

2014-05-01

The aim of this study was to compare the physiological responses of cyclists using round (C-ring) or oval (Q-ring) chainrings during an incremental test until exhaustion. Following a randomized design, twelve male elite cyclists [age (mean ± SD): 21.1 ± 2.1 yr; VO2max: 78.1 ± 5.3 mL·kg(-1)min(-1)] performed two incremental maximal tests separated by 48 h (one with C-rings, the other with Q-rings). Starting at 100 W, the workload was increased by 25 W every 3 min until volitional exhaustion. Maximal heart rate, power output and oxygen consumption were compared. Blood lactate was monitored throughout the test. After the incremental test, 4 intermittent 20-s maximal sprints with a 60-s recovery period in between were performed. Maximal isometric voluntary contractions were performed at rest and immediately after each 20-s maximal sprint, and the force and EMG RMS amplitude were recorded from the vastus medialis and vastus lateralis muscles. For the incremental exercise test, no significant differences were found in the maximal power output (P=0.12), oxygen consumption (P=0.39), and heart rate (P=0.32) between Q-rings and C-rings. Throughout the incremental test, lactate levels were comparable when using both the C-rings and Q-rings (P=0.47). During the short sprints, power output was 2.5-6.5% greater for Q-rings than for C-rings (P=0.22). The decline in EMG RMS amplitude observed during the incremental tests was comparable for Q-rings and C-rings (0.42). These findings indicate that the oval chainring design, presented here as "Q-rings", did not significantly influence the physiological response to an incremental exercise test as compared to a conventional chainring. Key pointsDuring the incremental exercise test, no significant differences were found in power output, oxygen consumption or heart rate between oval "Q-rings" and conventional chainrings.Over the course of the incremental test, blood lactate levels were comparable for the oval "Q-rings" and

Radial Profiles of Saturn’s Phoebe Ring

NASA Astrophysics Data System (ADS)

Tamayo, Daniel; Markham, Stephen; Hedman, Matthew M.; Burns, Joseph A.

2015-11-01

In 2009, the Spitzer observatory discovered a vast circumplanetary dust ring around Saturn, sourced by its swarm of irregular satellites. This material had been hypothesized to exist, in order to blanket Iapetus’ leading face and create its stark hemispherical dichotomy. Unfortunately, observations from near-Earth space cannot probe how far inward the Phoebe ring extends, as they are overwhelmed by scattered light from the planet. Additionally, to date, such measurements have only been achieved of thermal emission in the mid-infrared.By contrast, we present results from recent observations with the Cassini spacecraft (in orbit about Saturn) at optical wavelengths. Using a novel observational technique that exploits the moving shadow cast by Saturn, we mitigate the scattered light and background, and have been able to clearly extract the exceedingly faint Phoebe ring signal (line-of-sight optical depth of 10e-9, surface brightness of roughly 27 mag/arcsec^2).Our extracted albedos are consistent with dark material liberated from the irregular satellites. Additionally, we present reconstructed radial profiles over the broad range of distances from Saturn spanned by our observations. We also connect these results to theoretical models of the size-dependent dynamics of Phoebe ring dust grains under the action of the relevant perturbations.

The RING domain of the scaffold protein Ste5 adopts a molten globular character with high thermal and chemical stability.

PubMed

Walczak, Michal J; Samatanga, Brighton; van Drogen, Frank; Peter, Matthias; Jelesarov, Ilian; Wider, Gerhard

2014-01-27

Ste5 is a scaffold protein that controls the pheromone response of the MAP-kinase cascade in yeast cells. Upon pheromone stimulation, Ste5 (through its RING-H2 domain) interacts with the β and γ subunits of an activated heterodimeric G protein and promotes activation of the MAP-kinase cascade. With structural and biophysical studies, we show that the Ste5 RING-H2 domain exists as a molten globule under native buffer conditions, in yeast extracts, and even in denaturing conditions containing urea (7 M). Furthermore, it exhibits high thermal stability in native conditions. Binding of the Ste5 RING-H2 domain to the physiological Gβ/γ (Ste4/Ste18) ligand is accompanied by a conformational transition into a better folded, more globular structure. This study reveals novel insights into the folding mechanism and recruitment of binding partners by the Ste5 RING-H2 domain. We speculate that many RING domains may share a similar mechanism of substrate recognition and molten-globule-like character. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interconnected network motifs control podocyte morphology and kidney function.

PubMed

Azeloglu, Evren U; Hardy, Simon V; Eungdamrong, Narat John; Chen, Yibang; Jayaraman, Gomathi; Chuang, Peter Y; Fang, Wei; Xiong, Huabao; Neves, Susana R; Jain, Mohit R; Li, Hong; Ma'ayan, Avi; Gordon, Ronald E; He, John Cijiang; Iyengar, Ravi

2014-02-04

Podocytes are kidney cells with specialized morphology that is required for glomerular filtration. Diseases, such as diabetes, or drug exposure that causes disruption of the podocyte foot process morphology results in kidney pathophysiology. Proteomic analysis of glomeruli isolated from rats with puromycin-induced kidney disease and control rats indicated that protein kinase A (PKA), which is activated by adenosine 3',5'-monophosphate (cAMP), is a key regulator of podocyte morphology and function. In podocytes, cAMP signaling activates cAMP response element-binding protein (CREB) to enhance expression of the gene encoding a differentiation marker, synaptopodin, a protein that associates with actin and promotes its bundling. We constructed and experimentally verified a β-adrenergic receptor-driven network with multiple feedback and feedforward motifs that controls CREB activity. To determine how the motifs interacted to regulate gene expression, we mapped multicompartment dynamical models, including information about protein subcellular localization, onto the network topology using Petri net formalisms. These computational analyses indicated that the juxtaposition of multiple feedback and feedforward motifs enabled the prolonged CREB activation necessary for synaptopodin expression and actin bundling. Drug-induced modulation of these motifs in diseased rats led to recovery of normal morphology and physiological function in vivo. Thus, analysis of regulatory motifs using network dynamics can provide insights into pathophysiology that enable predictions for drug intervention strategies to treat kidney disease.

Interconnected Network Motifs Control Podocyte Morphology and Kidney Function

PubMed Central

Azeloglu, Evren U.; Hardy, Simon V.; Eungdamrong, Narat John; Chen, Yibang; Jayaraman, Gomathi; Chuang, Peter Y.; Fang, Wei; Xiong, Huabao; Neves, Susana R.; Jain, Mohit R.; Li, Hong; Ma’ayan, Avi; Gordon, Ronald E.; He, John Cijiang; Iyengar, Ravi

2014-01-01

Podocytes are kidney cells with specialized morphology that is required for glomerular filtration. Diseases, such as diabetes, or drug exposure that causes disruption of the podocyte foot process morphology results in kidney pathophysiology. Proteomic analysis of glomeruli isolated from rats with puromycin-induced kidney disease and control rats indicated that protein kinase A (PKA), which is activated by adenosine 3′,5′-monophosphate (cAMP), is a key regulator of podocyte morphology and function. In podocytes, cAMP signaling activates cAMP response element–binding protein (CREB) to enhance expression of the gene encoding a differentiation marker, synaptopodin, a protein that associates with actin and promotes its bundling. We constructed and experimentally verified a β-adrenergic receptor–driven network with multiple feedback and feedforward motifs that controls CREB activity. To determine how the motifs interacted to regulate gene expression, we mapped multicompartment dynamical models, including information about protein subcellular localization, onto the network topology using Petri net formalisms. These computational analyses indicated that the juxtaposition of multiple feedback and feedforward motifs enabled the prolonged CREB activation necessary for synaptopodin expression and actin bundling. Drug-induced modulation of these motifs in diseased rats led to recovery of normal morphology and physiological function in vivo. Thus, analysis of regulatory motifs using network dynamics can provide insights into pathophysiology that enable predictions for drug intervention strategies to treat kidney disease. PMID:24497609

1-(2,4-Di­nitro­phen­yl)-2-[(E)-(3,4,5-tri­meth­oxy­benzyl­idene)]hydrazine

PubMed Central

Chantrapromma, Suchada; Ruanwas, Pumsak; Boonnak, Nawong; Chidan Kumar, C. S.; Fun, Hoong-Kun

2014-01-01

Mol­ecules of the title compound, C16H16N4O7, are not planar with a dihedral angle of 5.50 (11)° between the substituted benzene rings. The two meta-meth­oxy groups of the 3,4,5-tri­meth­oxy­benzene moiety lie in the plane of the attached ring [Cmeth­yl–O–C–C torsion angles −0.1 (4)° and −3.7 (3)°] while the para-meth­oxy substituent lies out of the plane [Cmeth­yl—O—C—C, −86.0 (3)°]. An intra­molecular N—H⋯O hydrogen bond involving the 2-nitro substituent generates an S(6) ring motif. In the crystal structure, mol­ecules are linked by weak C—H⋯O inter­actions into screw chains, that are arranged into a sheet parallel to the bc plane. These sheets are connected by π–π stacking inter­actions between the nitro and meth­oxy substituted aromatic rings with a centroid–centroid separation of 3.9420 (13) Å. C—H⋯π contacts further stabilize the two-dimensional network. PMID:24764900

(E)-2-[(E)-3-(Hy-droxy-imino)-butan-2-yl-idene]-N-methyl-hydrazinecarbothio-amide.

PubMed

Abduelftah, Halema Shaban; Ali, Amna Qasem; Eltayeb, Naser Eltaher; Teoh, Siang Guan; Fun, Hoong-Kun

2012-01-01

In the title compound, C(6)H(12)N(4)OS, an intra-molecular N-H⋯N hydrogen-bond is present giving rise to an S(5) ring motif. In the crystal, double-stranded chains propagating along [10[Formula: see text

Does Saturn have rings outside 10 R(s)?

NASA Technical Reports Server (NTRS)

Cheng, A. F.; Lanzerotti, L. J.; Maclennan, C. G.

1985-01-01

Voyager ion and electron data in the energy range 30-1000 keV as measured by the Low Energy Charged Particle experiment are reviewed to check suggestions based on star occultation data that there are additional tenuous rings of Saturn beyond 10 Saturn radii from that planet. In the Voyager data, there is no convincing evidence for such ring matter. Features in the charged particle fluxes in the regions in question are more readily explained by temporal variations and/or spatial structure unrelated to ring matter, such as the mantle on the dayside and/or detached plasma sheets.

The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element

PubMed Central

Fukunaga, Junichi; Nomura, Yusuke; Tanaka, Yoichiro; Amano, Ryo; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Sakamoto, Taiichi; Kozu, Tomoko

2013-01-01

AML1 (RUNX1) is a key transcription factor for hematopoiesis that binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. Aberrations in the AML1 gene are frequently found in human leukemia. To better understand AML1 and its potential utility for diagnosis and therapy, we obtained RNA aptamers that bind specifically to the AML1 Runt domain. Enzymatic probing and NMR analyses revealed that Apt1-S, which is a truncated variant of one of the aptamers, has a CACG tetraloop and two stem regions separated by an internal loop. All the isolated aptamers were found to contain the conserved sequence motif 5′-NNCCAC-3′ and 5′-GCGMGN′N′-3′ (M:A or C; N and N′ form Watson–Crick base pairs). The motif contains one AC mismatch and one base bulged out. Mutational analysis of Apt1-S showed that three guanines of the motif are important for Runt binding as are the three guanines of RDE, which are directly recognized by three arginine residues of the Runt domain. Mutational analyses of the Runt domain revealed that the amino acid residues used for Apt1-S binding were similar to those used for RDE binding. Furthermore, the aptamer competed with RDE for binding to the Runt domain in vitro. These results demonstrated that the Runt domain of the AML1 protein binds to the motif of the aptamer that mimics DNA. Our findings should provide new insights into RNA function and utility in both basic and applied sciences. PMID:23709277

A common antigenic motif recognized by naturally occurring human VH5-51/VL4-1 anti-tau antibodies with distinct functionalities.

PubMed

Apetri, Adrian; Crespo, Rosa; Juraszek, Jarek; Pascual, Gabriel; Janson, Roosmarijn; Zhu, Xueyong; Zhang, Heng; Keogh, Elissa; Holland, Trevin; Wadia, Jay; Verveen, Hanneke; Siregar, Berdien; Mrosek, Michael; Taggenbrock, Renske; Ameijde, Jeroenvan; Inganäs, Hanna; van Winsen, Margot; Koldijk, Martin H; Zuijdgeest, David; Borgers, Marianne; Dockx, Koen; Stoop, Esther J M; Yu, Wenli; Brinkman-van der Linden, Els C; Ummenthum, Kimberley; van Kolen, Kristof; Mercken, Marc; Steinbacher, Stefan; de Marco, Donata; Hoozemans, Jeroen J; Wilson, Ian A; Koudstaal, Wouter; Goudsmit, Jaap

2018-05-31

Misfolding and aggregation of tau protein are closely associated with the onset and progression of Alzheimer's Disease (AD). By interrogating IgG + memory B cells from asymptomatic donors with tau peptides, we have identified two somatically mutated V H 5-51/V L 4-1 antibodies. One of these, CBTAU-27.1, binds to the aggregation motif in the R3 repeat domain and blocks the aggregation of tau into paired helical filaments (PHFs) by sequestering monomeric tau. The other, CBTAU-28.1, binds to the N-terminal insert region and inhibits the spreading of tau seeds and mediates the uptake of tau aggregates into microglia by binding PHFs. Crystal structures revealed that the combination of V H 5-51 and V L 4-1 recognizes a common Pro-X n -Lys motif driven by germline-encoded hotspot interactions while the specificity and thereby functionality of the antibodies are defined by the CDR3 regions. Affinity improvement led to improvement in functionality, identifying their epitopes as new targets for therapy and prevention of AD.

An arginine-rich motif of ring finger protein 4 (RNF4) oversees the recruitment and degradation of the phosphorylated and SUMOylated Krüppel-associated box domain-associated protein 1 (KAP1)/TRIM28 protein during genotoxic stress.

PubMed

Kuo, Ching-Ying; Li, Xu; Kong, Xiang-Qian; Luo, Cheng; Chang, Che-Chang; Chung, Yiyin; Shih, Hsiu-Ming; Li, Keqin Kathy; Ann, David K

2014-07-25

Krüppel-associated box domain-associated protein 1 (KAP1) is a universal transcriptional corepressor that undergoes multiple posttranslational modifications (PTMs), including SUMOylation and Ser-824 phosphorylation. However, the functional interplay of KAP1 PTMs in regulating KAP1 turnover during DNA damage response remains unclear. To decipher the role and cross-talk of multiple KAP1 PTMs, we show here that DNA double strand break-induced KAP1 Ser-824 phosphorylation promoted the recruitment of small ubiquitin-like modifier (SUMO)-targeted ubiquitin E3 ligase, ring finger protein 4 (RNF4), and subsequent RNF4-mediated, SUMO-dependent degradation. Besides the SUMO interacting motif (SIM), a previously unrecognized, but evolutionarily conserved, arginine-rich motif (ARM) in RNF4 acts as a novel recognition motif for selective target recruitment. Results from combined mutagenesis and computational modeling studies suggest that RNF4 utilizes concerted bimodular recognition, namely SIM for Lys-676 SUMOylation and ARM for Ser(P)-824 of simultaneously phosphorylated and SUMOylated KAP1 (Ser(P)-824-SUMO-KAP1). Furthermore, we proved that arginines 73 and 74 within the ARM of RNF4 are required for efficient recruitment to KAP1 or accelerated degradation of promyelocytic leukemia protein (PML) under stress. In parallel, results of bimolecular fluorescence complementation assays validated the role of the ARM in recognizing Ser(P)-824 in living cells. Taken together, we establish that the ARM is required for RNF4 to efficiently target Ser(P)-824-SUMO-KAP1, conferring ubiquitin Lys-48-mediated proteasomal degradation in the context of double strand breaks. The conservation of such a motif may possibly explain the requirement for timely substrate selectivity determination among a myriad of SUMOylated proteins under stress conditions. Thus, the ARM dynamically regulates the SIM-dependent recruitment of targets to RNF4, which could be critical to dynamically fine-tune the

An Arginine-rich Motif of Ring Finger Protein 4 (RNF4) Oversees the Recruitment and Degradation of the Phosphorylated and SUMOylated Krüppel-associated Box Domain-associated Protein 1 (KAP1)/TRIM28 Protein during Genotoxic Stress*

PubMed Central

Kuo, Ching-Ying; Li, Xu; Kong, Xiang-Qian; Luo, Cheng; Chang, Che-Chang; Chung, Yiyin; Shih, Hsiu-Ming; Li, Keqin Kathy; Ann, David K.

2014-01-01

Krüppel-associated box domain-associated protein 1 (KAP1) is a universal transcriptional corepressor that undergoes multiple posttranslational modifications (PTMs), including SUMOylation and Ser-824 phosphorylation. However, the functional interplay of KAP1 PTMs in regulating KAP1 turnover during DNA damage response remains unclear. To decipher the role and cross-talk of multiple KAP1 PTMs, we show here that DNA double strand break-induced KAP1 Ser-824 phosphorylation promoted the recruitment of small ubiquitin-like modifier (SUMO)-targeted ubiquitin E3 ligase, ring finger protein 4 (RNF4), and subsequent RNF4-mediated, SUMO-dependent degradation. Besides the SUMO interacting motif (SIM), a previously unrecognized, but evolutionarily conserved, arginine-rich motif (ARM) in RNF4 acts as a novel recognition motif for selective target recruitment. Results from combined mutagenesis and computational modeling studies suggest that RNF4 utilizes concerted bimodular recognition, namely SIM for Lys-676 SUMOylation and ARM for Ser(P)-824 of simultaneously phosphorylated and SUMOylated KAP1 (Ser(P)-824-SUMO-KAP1). Furthermore, we proved that arginines 73 and 74 within the ARM of RNF4 are required for efficient recruitment to KAP1 or accelerated degradation of promyelocytic leukemia protein (PML) under stress. In parallel, results of bimolecular fluorescence complementation assays validated the role of the ARM in recognizing Ser(P)-824 in living cells. Taken together, we establish that the ARM is required for RNF4 to efficiently target Ser(P)-824-SUMO-KAP1, conferring ubiquitin Lys-48-mediated proteasomal degradation in the context of double strand breaks. The conservation of such a motif may possibly explain the requirement for timely substrate selectivity determination among a myriad of SUMOylated proteins under stress conditions. Thus, the ARM dynamically regulates the SIM-dependent recruitment of targets to RNF4, which could be critical to dynamically fine-tune the

Discovery of phosphorylation motif mixtures in phosphoproteomics data

PubMed Central

Ritz, Anna; Shakhnarovich, Gregory; Salomon, Arthur R.; Raphael, Benjamin J.

2009-01-01

Motivation: Modification of proteins via phosphorylation is a primary mechanism for signal transduction in cells. Phosphorylation sites on proteins are determined in part through particular patterns, or motifs, present in the amino acid sequence. Results: We describe an algorithm that simultaneously discovers multiple motifs in a set of peptides that were phosphorylated by several different kinases. Such sets of peptides are routinely produced in proteomics experiments.Our motif-finding algorithm uses the principle of minimum description length to determine a mixture of sequence motifs that distinguish a foreground set of phosphopeptides from a background set of unphosphorylated peptides. We show that our algorithm outperforms existing motif-finding algorithms on synthetic datasets consisting of mixtures of known phosphorylation sites. We also derive a motif specificity score that quantifies whether or not the phosphoproteins containing an instance of a motif have a significant number of known interactions. Application of our motif-finding algorithm to recently published human and mouse proteomic studies recovers several known phosphorylation motifs and reveals a number of novel motifs that are enriched for interactions with a particular kinase or phosphatase. Our tools provide a new approach for uncovering the sequence specificities of uncharacterized kinases or phosphatases. Availability: Software is available at http:/cs.brown.edu/people/braphael/software.html. Contact: aritz@cs.brown.edu; braphael@cs.brown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18996944

A compact 5.5 GHz band-rejected UWB antenna using complementary split ring resonators.

PubMed

Islam, M M; Faruque, M R I; Islam, M T

2014-01-01

A band-removal property employing microwave frequencies using complementary split ring resonators (CSRRs) is applied to design a compact UWB antenna wishing for the rejection of some frequency band, which is meanwhile exercised by the existing wireless applications. The reported antenna comprises optimization of a circular radiating patch, in which slotted complementary SRRs are implanted. It is printed on low dielectric FR4 substrate material fed by a partial ground plane and a microstrip line. Validated results exhibit that the reported antenna shows a wide bandwidth covering from 3.45 to more than 12 GHz, with a compact dimension of 22 × 26 mm(2), and VSWR < 2, observing band elimination of 5.5 GHz WLAN band.

A generic motif discovery algorithm for sequential data.

PubMed

Jensen, Kyle L; Styczynski, Mark P; Rigoutsos, Isidore; Stephanopoulos, Gregory N

2006-01-01

Motif discovery in sequential data is a problem of great interest and with many applications. However, previous methods have been unable to combine exhaustive search with complex motif representations and are each typically only applicable to a certain class of problems. Here we present a generic motif discovery algorithm (Gemoda) for sequential data. Gemoda can be applied to any dataset with a sequential character, including both categorical and real-valued data. As we show, Gemoda deterministically discovers motifs that are maximal in composition and length. As well, the algorithm allows any choice of similarity metric for finding motifs. Finally, Gemoda's output motifs are representation-agnostic: they can be represented using regular expressions, position weight matrices or any number of other models for any type of sequential data. We demonstrate a number of applications of the algorithm, including the discovery of motifs in amino acids sequences, a new solution to the (l,d)-motif problem in DNA sequences and the discovery of conserved protein substructures. Gemoda is freely available at http://web.mit.edu/bamel/gemoda

RING1 is associated with the polycomb group protein complex and acts as a transcriptional repressor.

PubMed

Satijn, D P; Gunster, M J; van der Vlag, J; Hamer, K M; Schul, W; Alkema, M J; Saurin, A J; Freemont, P S; van Driel, R; Otte, A P

1997-07-01

The Polycomb (Pc) protein is a component of a multimeric, chromatin-associated Polycomb group (PcG) protein complex, which is involved in stable repression of gene activity. The identities of components of the PcG protein complex are largely unknown. In a two-hybrid screen with a vertebrate Pc homolog as a target, we identify the human RING1 protein as interacting with Pc. RING1 is a protein that contains the RING finger motif, a specific zinc-binding domain, which is found in many regulatory proteins. So far, the function of the RING1 protein has remained enigmatic. Here, we show that RING1 coimmunoprecipitates with a human Pc homolog, the vertebrate PcG protein BMI1, and HPH1, a human homolog of the PcG protein Polyhomeotic (Ph). Also, RING1 colocalizes with these vertebrate PcG proteins in nuclear domains of SW480 human colorectal adenocarcinoma and Saos-2 human osteosarcoma cells. Finally, we show that RING1, like Pc, is able to repress gene activity when targeted to a reporter gene. Our findings indicate that RING1 is associated with the human PcG protein complex and that RING1, like PcG proteins, can act as a transcriptional repressor.

Physics of planetary rings

NASA Astrophysics Data System (ADS)

Gorkavyi, N.

2007-08-01

image from the Hubble Space Telescope (STIS, observation of team by Sara Heap, our co-author) and results of our simulation of scattered light from warped disk will be compared [4]. The direct signatures of this planet were discovered on 2002 by Keck telescope observations. References: 1. Fridman, A.M. and Gorkavyi, N.N. Physics of Planetary Rings (Celestial Mechanics of a Continuous Media). Springer-Verlag, 1999, 436 p. 2. Gorkavyi, N.N., Taidakova, T.A. The Model for Formation of Jupiter, Saturn and Neptune Satellite Systems, Astronomy Letters., 1995, v. 21 (6). pp.939-945; Discovered Saturnian and undiscovered Neptuanian retrograde satellites, BAAS, v.33, N4, 1403; The New Model of the Origin of the Moon, BAAS, 2004, 36, #2 3. Ozernoy, L.M., Gorkavyi, N.N., Mather, J.C. & Taidakova, T. 2000, Signatures of Exo-solar Planets in Dust Debris Disks, ApJ, 537:L147-L151, 2000 July 10. 4. Gorkavyi, N.N., Heap S.R., Ozernoy, L.M., Taidakova, T.A., and Mather, J.C. Indicator of Exo-Solar Planet(s) in the Circumstellar Disk Around Beta Pictoris. In:"Planetary Systems in the Universe: Observation, Formation, and Evolution". Proc. IAU Symp. No. 202, 2004, ASP Conf. Series, p.331-334. 5. Gorkavyi, N., Taidakova, T. Outermost planets of Beta Pictoris, Vega and Epsilon Eridani: goals for direct imaging. In: "Direct Imaging of Exoplanets: Science and Techniques" (C. Aime and F. Vakili, eds.). Proc. IAU Coll. No. 200, 2005, p.47-51.

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

PubMed

Castro-Mondragon, Jaime Abraham; Jaeger, Sébastien; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2017-07-27

Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Polarization Studies for the eRHIC Electron Storage Ring

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

Gianfelice-Wendt, Eliana; Tepikian, S.

A hadron/lepton collider with polarized beams has been under consideration by the scientific community since some years, in the U.S. and Europe. Among the various proposals, those by JLAB and BNL with polarized electron and proton beams are currently under closer study in the U.S. Experimenters call for the simultaneous storage of electron bunches with both spin helicity. In the BNL based Ring-Ring design, electrons are stored at top energy in a ring to be accommodated in the existing RHIC tunnel. The transversely polarized electron beam is injected into the storage ring at variable energies, between 5 and 18 GeV.more » Polarization is brought into the longitudinal direction at the IP by a couple of spin rotators. In this paper results of first studies of the attainable beam polarization level and lifetime in the storage ring at 18 GeV are presented.« less

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

PubMed Central

Krestel, Ralf; Ohler, Uwe; Vingron, Martin; Marsico, Annalisa

2017-01-01

Abstract RNA-binding proteins (RBPs) play an important role in RNA post-transcriptional regulation and recognize target RNAs via sequence-structure motifs. The extent to which RNA structure influences protein binding in the presence or absence of a sequence motif is still poorly understood. Existing RNA motif finders either take the structure of the RNA only partially into account, or employ models which are not directly interpretable as sequence-structure motifs. We developed ssHMM, an RNA motif finder based on a hidden Markov model (HMM) and Gibbs sampling which fully captures the relationship between RNA sequence and secondary structure preference of a given RBP. Compared to previous methods which output separate logos for sequence and structure, it directly produces a combined sequence-structure motif when trained on a large set of sequences. ssHMM’s model is visualized intuitively as a graph and facilitates biological interpretation. ssHMM can be used to find novel bona fide sequence-structure motifs of uncharacterized RBPs, such as the one presented here for the YY1 protein. ssHMM reaches a high motif recovery rate on synthetic data, it recovers known RBP motifs from CLIP-Seq data, and scales linearly on the input size, being considerably faster than MEMERIS and RNAcontext on large datasets while being on par with GraphProt. It is freely available on Github and as a Docker image. PMID:28977546

Deciphering functional glycosaminoglycan motifs in development.

PubMed

Townley, Robert A; Bülow, Hannes E

2018-03-23

Glycosaminoglycans (GAGs) such as heparan sulfate, chondroitin/dermatan sulfate, and keratan sulfate are linear glycans, which when attached to protein backbones form proteoglycans. GAGs are essential components of the extracellular space in metazoans. Extensive modifications of the glycans such as sulfation, deacetylation and epimerization create structural GAG motifs. These motifs regulate protein-protein interactions and are thereby repsonsible for many of the essential functions of GAGs. This review focusses on recent genetic approaches to characterize GAG motifs and their function in defined signaling pathways during development. We discuss a coding approach for GAGs that would enable computational analyses of GAG sequences such as alignments and the computation of position weight matrices to describe GAG motifs. Copyright © 2018 Elsevier Ltd. All rights reserved.

A motif for infinite metal atom wires.

PubMed

Yin, Xi; Warren, Steven A; Pan, Yung-Tin; Tsao, Kai-Chieh; Gray, Danielle L; Bertke, Jeffery; Yang, Hong

2014-12-15

A new motif for infinite metal atom wires with tunable compositions and properties is developed based on the connection between metal paddlewheel and square planar complex moieties. Two infinite Pd chain compounds, [Pd4(CO)4(OAc)4Pd(acac)2] 1 and [Pd4(CO)4(TFA)4Pd(acac)2] 2, and an infinite Pd-Pt heterometallic chain compound, [Pd4(CO)4(OAc)4Pt(acac)2] 3, are identified by single-crystal X-ray diffraction analysis. In these new structures, the paddlewheel moiety is a Pd four-membered ring coordinated by bridging carboxylic ligands and μ2 carbonyl ligands. The planar moiety is either Pd(acac)2 or Pt(acac)2 (acac = acetylacetonate). These moieties are connected by metallophilic interactions. The results showed that these one-dimensional metal wire compounds have photoluminescent properties that are tunable by changing ligands and metal ions. 3 can also serve as a single source precursor for making Pd4Pt bimetallic nanostructures with precise control of metal composition. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydrogen bonding motifs, spectral characterization, theoretical computations and anticancer studies on chloride salt of 6-mercaptopurine: An assembly of corrugated lamina shows enhanced solubility

NASA Astrophysics Data System (ADS)

Suresh Kumar, S.; Athimoolam, S.; Sridhar, B.

2015-10-01

6-Mercaptopurine (an anti cancer drug), is coming under the class II Biopharmaceutics Classification System (BCS). In order to enhance the solubility with retained physiochemical/pharmaceutical properties, the present work was attempted with its salt form. The single crystals of 6-mercaptopurinium chloride (6MPCl) were successfully grown by slow evaporation technique under ambient temperature. The X-ray diffraction study shows that the crystal packing is dominated by N-H⋯Cl classical hydrogen bonds leading to corrugated laminar network. The hydrogen bonds present in the lamina can be dismantled as three chain C21(6), C21(7) and C21(8) motifs running along ab-diagonal of the unit cell. These primary chain motifs are interlinked to each other forming ring R63(21) motifs. These chain and ring motifs are aggregated like a dendrimer structure leading to the above said corrugated lamina. This low dimensional molecular architecture differs from the ladder like arrays in pure drug though it possess lattice water molecule in lieu of the chloride anion in the present compound. Geometrical optimizations of 6MPCl were done by Density Functional Theory (DFT) using B3LYP function with two different basis sets. The optimized molecular geometries and computed vibrational spectra are compared with their experimental counterparts. The Natural Bond Orbital (NBO) analysis was carried out to interpret hyperconjugative interaction and Intramolecular Charge Transfer (ICT). The chemical hardness, electronegativity, chemical potential and electrophilicity index of 6MPCl were found along with the HOMO-LUMO plot. The lower band gap value obtained from the Frontier Molecular Orbital (FMO) analysis reiterates the pharmaceutical activity of the compound. The anticancer studies show that 6MPCl retains its activity against human cervical cancer cell line (HeLa). Hence, this anticancer efficacy and improved solubility demands 6MPCl towards the further pharmaceutical applications.

Constraints on Particle Sizes in Saturn's G Ring from Ring Plane Crossing Observations

NASA Astrophysics Data System (ADS)

Throop, H. B.; Esposito, L. W.

1996-09-01

The ring plane crossings in 1995--96 allowed earth-based observations of Saturn's diffuse rings (Nicholson et al., Nature 272, 1996; De Pater et al. Icarus 121, 1996) at a phase angle of alpha ~ 5 deg . We calculate the G ring reflectance for steady state distributions of dust to km-sized bodies from a range of physical models which track the evolution of the G ring from its initial formation following the disruption of a progenitor satellite (Canup & Esposito 1996, \\ Icarus,\\ in press). We model scattering from the ring's small particles using an exact T-matrix method for nonspherical, absorptive particles (Mishchenko et al. 1996, \\ JGR Atmo., in press), large particles using the phase function and spectrum of Europa, and intermediate particles using a linear combination of the small and large limits. Two distinct particle size distributions from the CE96 model fit the observed spectrum. The first is that of a dusty ring, with the majority of ring reflectance in dust particles of relatedly shallow power law size distribution exponent q ~ 2.5. The second has equal reflectances from a) dust in the range q ~ 3.5 -- 6.5 and b) macroscopic bodies > 1 mm. In this second case, the respective slightly blue and red components combine to form the observed relatively flat spectrum. Although light scattering in backscatter is not sufficient to completely constrain the G ring size distribution, the distributions predicted by the CE96 model can explain the earth-based observations.

The Saturn Ring Observer: In situ studies of planetary rings

NASA Astrophysics Data System (ADS)

Nicholson, P. D.; Tiscareno, M. S.; Spilker, L. J.

2010-12-01

As part of the Planetary Science Decadal Survey recently undertaken by the NRC's Space Studies Board for the National Academy of Sciences, studies were commissioned for a number of potential missions to outer planet targets. One of these studies examined the technological feasibility of a mission to carry out in situ studies of Saturn's rings, from a spacecraft placed in a circular orbit above the ring plane: the Saturn Ring Observer. The technical findings and background are discussed in a companion poster by T. R. Spilker et al. Here we outline the science goals of such a mission. Most of the fundamental interactions in planetary rings occur on spatial scales that are unresolved by flyby or orbiter spacecraft. Typical particle sizes in the rings of Saturn are in the 1 cm - 10 m range, and average interparticle spacings are a few meters. Indirect evidence indicates that the vertical thickness of the rings is as little as 5 - 10 m, which implies a velocity dispersion of only a few mm/sec. Theories of ring structure and evolution depend on the unknown characteristics of interparticle collisions and on the size distribution of the ring particles. The SRO could provide direct measurements of both the coefficient of restitution -- by monitoring individual collisions -- and the particles’ velocity dispersion. High-resolution observations of individual ring particles should also permit estimates of their spin states. Numerical simulations of Saturn’s rings incorporating both collisions and self-gravity predict that the ring particles are not uniformly distributed, but are instead clustered into elongated structures referred to as “self-gravity wakes”, which are continually created and destroyed on an orbital timescale. Theory indicates that the average separation between wakes in the A ring is of order 30-100 m. Direct imaging of self-gravity wakes, including their formation and subsequent dissolution, would provide critical validation of these models. Other

Biomechanical and morphological differences between the sclera canal ring and a peripheral sclera ring in the porcine eye.

PubMed

Terai, Naim; Schlötzer-Schrehardt, Ursula; Spoerl, Eberhard; Hornykewycz, Karin; Haentzschel, Janek; Haustein, Michael; Pillunat, Lutz E

2012-01-01

To investigate a possible association between the biomechanical load and unload behaviour and the elastin content of the sclera canal ring (SCR) and a superiorly localized sclera ring (SPS) in the porcine eye. Two sclera rings were trephined from each of 40 porcine eyes, one containing the SCR and the other an SPS. The load and the unload curves were measured in the extension range of 0-2.0 mm by a biomaterial tester. Hysteresis was determined from the area enclosed by the loading and unloading curve. Histochemical staining with resorcin-fuchsin and morphometric analysis of paraffin-embedded sections of both rings were performed to detect the area occupied by elastin fibres. At 1 mm extension, the mean load of the SCR was 0.89 ± 0.22 N and that of the SPS 1.13 ± 0.19 N, which was not significantly different between both rings (p > 0.05). Mean hysteresis in the SCR was 1.55 ± 0.30 N × mm and 1.90 ± 0.18 N × mm in the SPS, which was significantly different between both rings (p = 0.01). Mean sclera thickness was 986 μm in the SCR (range: 900-1,060 μm) and 971 μm in the SPS (range: 800-1,200 μm) without a statistically significant difference between both sclera rings (p = 0.78). The area occupied by elastin fibres was 15.5 ± 3.4% in the SCR and 4.5 ± 1.5% in the SPS, which was significantly different between both rings (p = 0.0001). Hysteresis in the SCR was significantly lower than in the SPS, indicating a higher elasticity of the SCR in the porcine eye. This effect could be explained by a higher content of elastin in the surrounding ring of the peripapillary optic nerve head providing reversible contraction in cases of intra-ocular pressure variations. Copyright © 2011 S. Karger AG, Basel.

Climatic significance of the bristlecone pine latewood frost-ring record at Almagre Mountain, Colorado, U.S.A.

USGS Publications Warehouse

Brunstein, F. Craig

1996-01-01

From 1900 to 1993, latewood frost rings occurred in 1903, 1912, 1941, 1961, and 1965 in 10 to 21% of the sampled bristlecone pines at Almagre Mountain, Colorado. In early to mid September in each of those years, a severe outbreak of unseasonably cold air from higher latitudes produced a memorable or historic late-summer snowstorm in the western United States. Record subfreezing temperatures during these snowstorms probably caused the latewood frost rings, shortened (by about 1 mo in 1912) already colder than normal growing seasons, and caused crop damage in parts of the Western United States. Latewood frost rings recorded in relatively high percentages of the sampled trees (such as the 1805 event in 61% of sampled trees) were probably caused by multiple severe outbreaks of unseasonably cold air from higher latitudes that occurred from early September (possibly as early as mid- or late August) to mid-September. Analyses of 1900-1992 temperature data for two widely separated Colorado stations, Fort Collins and Colorado Springs, show that average summer (June-September) temperatures during latewood frost-ring years in this century were 1.5 and 2.0°C cooler than normal, respectively. Mountain snowpack probably persisted through these cool summers and was subsequently buried by the earlier than normal snowfall in September. Latewood frost-ring, ring-width, historical, and other data suggest that severe to cataclysmic volcanic eruptions from 1812 to 1835 triggered (1) an extended period of climatic cooling from as early as 1816 or 1817 through the early 1850s in the Southern Rocky Mountains, (2) catastrophic winters in Colorado and Wyoming in 1842-43 and 1844-45, and in the Great Salt Lake Basin in 1836-37, that caused large-scale destruction of bison and other large plains animals, and (3) Little Ice Age alpine glacial advances in about 1850-60 in the western United States.

A private DNA motif finding algorithm.

PubMed

Chen, Rui; Peng, Yun; Choi, Byron; Xu, Jianliang; Hu, Haibo

2014-08-01

With the increasing availability of genomic sequence data, numerous methods have been proposed for finding DNA motifs. The discovery of DNA motifs serves a critical step in many biological applications. However, the privacy implication of DNA analysis is normally neglected in the existing methods. In this work, we propose a private DNA motif finding algorithm in which a DNA owner's privacy is protected by a rigorous privacy model, known as ∊-differential privacy. It provides provable privacy guarantees that are independent of adversaries' background knowledge. Our algorithm makes use of the n-gram model and is optimized for processing large-scale DNA sequences. We evaluate the performance of our algorithm over real-life genomic data and demonstrate the promise of integrating privacy into DNA motif finding. Copyright © 2014 Elsevier Inc. All rights reserved.

Metal ring on 4th or 5th finger markedly increases both cardiac troponin I at left ventricle and cancer-related parameters such as oncogen C-fosAb2 & integrin α₅β₁[corrected] by 4-12 times. Thus these metal rings appear to promote both heart problems & cancer.

PubMed

Omura, Yoshiaki; Hines, Howard; Jones, Marilyn; O'Young, Brian; Duvvi, Harsha; Lu, Dominic P; Pallos, Andrew; Shimotsuura, Yasuhiro; Ohki, Motomu

2010-01-01

We examined patients wearing a metal ring on the left 4th finger with abnormally increased Cardiac Troponin I (which is known to increase in the presence of myocardial injury or left ventricular hypertrophy) of 5-14ng BDORT units (depending on the ring and individual) at left ventricle compared with normal value of 1ng BDORT units or less. Although shape of the ECG does not change significantly regardless of whether metal rings are on or not, when rings are on, the Bi-Digital O-Ring Test evaluation of trace of ECG revealed "Vulnerable Period of Rising Part of T-wave" of ECG waves (which correspond to the left ventricle and AV node) become abnormal with increased Cardiac Troponin I. DHEA in various parts of the body reduced significantly and maximum decrease in DHEA was found when metal ring was on the left 4th and 5th fingers. Telomere reduced with each of the 5 fingers, but the 2nd, 4th, and 5th fingers produced the maximum reduction of telomere. When metal ring was inserted onto the left 1st finger and left 2nd finger, Cardiac Troponin I did not change significantly. Additional abnormality was found when patients with cancer wore metal ring(s); namely both Cardiac Troponin I and cancer parameters, such as Integrin α₅β₁[corrected] and Oncogen C-fos Ab2, increase anywhere between 4-12 times. However, when the ring was cut, creating a 1mm or longer empty space, no increase in cancer markers and Cardiac Troponin I were observed. Similar findings were found with metal bracelets.

Findings on rings and inner satellites of Saturn of Pioneer 11

NASA Astrophysics Data System (ADS)

van Allen, J. A.

1982-09-01

The introductory part of this paper gives a short account of the theory of absorption by planetary rings and satellites of energetic charged particles that are trapped in a planet's magnetic field and describes the observable consequences of such absorption processes. The previously published University of Iowa observations of absorption features during Pioneer 11's passage through Saturn's inner radiation belt on 1 September 1979 are critically reanalyzed and related to other evidence on rings and satellites inside 2.9 Saturn radii, especially that from the imaging system on Voyagers 1 and 2. It is found (a) that satellites 1979 S1, 1979 S2, and 1980 S3 are almost certainly identical; (b) that the evidence for 1979 S4 is weak to nonexistent; (c) that 1979 S5 and two other nearby absorption features and 1979 S6 and one other nearby absorption feature are probably caused by longitudinal and radial structure of Ring F and not by satellites; and (d) that absorption feature 1979 S3 at 169,200 + or - 600 km is identified with the optically observed Ring G.

Cassini imaging observations of Jupiter's rings

NASA Astrophysics Data System (ADS)

Throop, H. B.; Porco, C. C.; West, R. A.; Burns, J. A.; Showalter, M. R.; Nicholson, P. D.

2003-05-01

Cassini's Imaging Science Subsystem (ISS) instrument took nearly 1200 images of the Jupiter ring system during the spacecraft's 6-month encounter with Jupiter. These observations constitute the most complete dataset of the ring taken by a single instrument, both in phase angle (0.5 - 120° at seven angles) and wavelength (0.45 - 0.93 μ {m} through eight filters). The main ring was detected in all targeted exposures; the halo and gossamer rings were too faint to be observed above the planet's stray light. The optical depth and radial profile of the main ring are unchanged from that of previous studies. No evidence for broad asymmetries within the ring were found; we did identify possible evidence for 1000 km-scale clumps within the ring. Cassini observations at a phase angle of 64° place an upper limit on the ring's full thickness of 80 km. We have combined the Cassini ISS and VIMS observations with those from Voyager, HST, Keck, Galileo, Palomar, and IRTF. We have fit the entire suite of data using a photometric model that includes microscopic silicate dust grains as well as larger, long-lived `parent bodies' that engender this dust. Our dust grain model considers a range of spheroidal particle shapes computed using the T-matrix method (Mishchenko & Travis 1998). Our best-fit model to all the data indicates an optical depth of small particles of τ s = 4.7x 10-6 and large bodies τ l = 1.3x 10-6. The dust is concentrated about a radius of 15 μ {m}. The data are fit significantly better using non-spherical rather than spherical dust grains. The parent bodies themselves must be very red from 0.4--2.5 μ {m} and may have absorption features near 0.9 μ {m} and 2.2 μ {m}.

A Compact 5.5 GHz Band-Rejected UWB Antenna Using Complementary Split Ring Resonators

PubMed Central

Islam, M. M.; Faruque, M. R. I.; Islam, M. T.

2014-01-01

A band-removal property employing microwave frequencies using complementary split ring resonators (CSRRs) is applied to design a compact UWB antenna wishing for the rejection of some frequency band, which is meanwhile exercised by the existing wireless applications. The reported antenna comprises optimization of a circular radiating patch, in which slotted complementary SRRs are implanted. It is printed on low dielectric FR4 substrate material fed by a partial ground plane and a microstrip line. Validated results exhibit that the reported antenna shows a wide bandwidth covering from 3.45 to more than 12 GHz, with a compact dimension of 22 × 26 mm2, and VSWR < 2, observing band elimination of 5.5 GHz WLAN band. PMID:24971379

The radii of Uranian rings alpha, beta, gamma, delta, epsilon, eta, 4, 5, and 6 from their occultations of SAO 158687

NASA Technical Reports Server (NTRS)

Elliot, J. L.; Dunham, E.; Wasserman, L. H.; Millis, R. L.; Churms, J.

1978-01-01

All available timing data for the occultations of SAO 158687 on March 10, 1977, by the cited rings of Uranus are analyzed. Least-squares fits to the data are performed using a model which postulates that rings alpha, beta, gamma, and delta are circular and coplanar. A solution obtained under the assumption that the ring plane coincides with the plane of the satellite orbits is adopted which yields radii of 44,844 km for ring alpha, 45,799 km for ring beta, 47,746 km for ring gamma, and 48,423 km for ring delta. The uncertainties in these values are discussed along with the apparent shapes and inclinations of these main rings. The mean radii estimated for the other rings are: 47,323 km for ring eta, 42,663 km for ring 4, 42,360 km for ring 5, and 41,980 km for ring 6.

Loss of ring current O(+) ions due to interaction with Pc 5 waves

NASA Astrophysics Data System (ADS)

Li, Xinlin; Hudson, Mary; Chan, Anthony; Roth, Ilan

1993-01-01

A test particle code is used here to investigate ring current ion interaction with Pc 5 waves, combined with convection and corotation electric fields, with emphasis on the loss of O(+) ions over the dayside magnetosphere. A new loss mechanism for the O(+) ions due to the combined effects of convection and corotation electric fields and interactions with Pc 5 waves via a magnetic drift-bound resonance is presented. For given fields, whether a particle gains or losses energy depends on its initial kinetic energy, pitch angle at the equatorial plane, and the position of its guiding center with respect to the azimuthal phase of the wave. The ring current O(+) ions show a dispersion in energies and L values with decreasing local time across the dayside, and a bulk shift to lower energies and higher L values. Due to interaction with the Pc 5 waves, the particle's kinetic energy can drop below that required to overcome the convection potential and the particle is lost to the dayside magnetopause by a sunward E x B drift.

Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals

PubMed Central

2014-01-01

Background The polyadenylation of RNA is critical for gene functioning, but the conserved sequence motifs (often called signal or signature motifs), motif locations and abundances, and base composition patterns around mRNA polyadenylation [poly(A)] sites are still uncharacterized in most species. The evolutionary tendency for poly(A) site selection is still largely unknown. Results We analyzed the poly(A) site regions of 31 species or phyla. Different groups of species showed different poly(A) signal motifs: UUACUU at the poly(A) site in the parasite Trypanosoma cruzi; UGUAAC (approximately 13 bases upstream of the site) in the alga Chlamydomonas reinhardtii; UGUUUG (or UGUUUGUU) at mainly the fourth base downstream of the poly(A) site in the parasite Blastocystis hominis; and AAUAAA at approximately 16 bases and approximately 19 bases upstream of the poly(A) site in animals and plants, respectively. Polyadenylation signal motifs are usually several hundred times more abundant around poly(A) sites than in whole genomes. These predominant motifs usually had very specific locations, whether upstream of, at, or downstream of poly(A) sites, depending on the species or phylum. The poly(A) site was usually an adenosine (A) in all analyzed species except for B. hominis, and there was weak A predominance in C. reinhardtii. Fungi, animals, plants, and the protist Phytophthora infestans shared a general base abundance pattern (or base composition pattern) of “U-rich—A-rich—U-rich—Poly(A) site—U-rich regions”, or U-A-U-A-U for short, with some variation for each kingdom or subkingdom. Conclusion This study identified the poly(A) signal motifs, motif locations, and base composition patterns around mRNA poly(A) sites in protists, fungi, plants, and animals and provided insight into poly(A) site evolution. PMID:25052519

Chemokine (C-C motif) receptor 5-using envelopes predominate in dual/mixed-tropic HIV from the plasma of drug-naive individuals.

PubMed

Irlbeck, David M; Amrine-Madsen, Heather; Kitrinos, Kathryn M; Labranche, Celia C; Demarest, James F

2008-07-31

HIV-1 utilizes CD4 and either chemokine (C-C motif) receptor 5 (CCR5) or chemokine (C-X-C motif) receptor 4 (CXCR4) to gain entry into host cells. Small molecule CCR5 antagonists are currently being developed for the treatment of HIV-1 infection. Because HIV-1 may also use CXCR4 for entry, the use of CCR5 entry inhibitors is controversial for patients harboring CCR5-using and CXCR4-using (dual/mixed-tropic) viruses. The goal of the present study was to determine the proportion of CCR5-tropic and CXCR4-tropic viruses in dual/mixed-tropic virus isolates from drug-naïve patients and the phenotypic and genotypic relationships of viruses that use CCR5 or CXCR4 or both. Fourteen antiretroviral-naive HIV-1-infected patients were identified as having population coreceptor tropism readout of dual/mixed-tropic viruses. Intrapatient comparisons of coreceptor tropism and genotype of env clones were conducted on plasma virus from each patient. Population HIV-1 envelope tropism and susceptibility to the CCR5 entry inhibitor, aplaviroc, were performed using the Monogram Biosciences Trofile Assay. Twelve env clones from each patient were analyzed for coreceptor tropism, aplaviroc sensitivity, genotype, and intrapatient phylogenetic relationships. Viral populations from antiretroviral-naive patients with dual/mixed-tropic virus are composed primarily of CCR5-tropic env clones mixed with those that use both coreceptors (R5X4-tropic) and, occasionally, CXCR4-tropic env clones. Interestingly, the efficiency of CXCR4 use by R5X4-tropic env clones varied with their genetic relationships to CCR5-tropic env clones from the same patient. These data show that the majority of viruses in these dual/mixed-tropic populations use CCR5 and suggest that antiretroviral-naive patients may benefit from combination therapy that includes CCR5 entry inhibitors.

Chaotic Motifs in Gene Regulatory Networks

PubMed Central

Zhang, Zhaoyang; Ye, Weiming; Qian, Yu; Zheng, Zhigang; Huang, Xuhui; Hu, Gang

2012-01-01

Chaos should occur often in gene regulatory networks (GRNs) which have been widely described by nonlinear coupled ordinary differential equations, if their dimensions are no less than 3. It is therefore puzzling that chaos has never been reported in GRNs in nature and is also extremely rare in models of GRNs. On the other hand, the topic of motifs has attracted great attention in studying biological networks, and network motifs are suggested to be elementary building blocks that carry out some key functions in the network. In this paper, chaotic motifs (subnetworks with chaos) in GRNs are systematically investigated. The conclusion is that: (i) chaos can only appear through competitions between different oscillatory modes with rivaling intensities. Conditions required for chaotic GRNs are found to be very strict, which make chaotic GRNs extremely rare. (ii) Chaotic motifs are explored as the simplest few-node structures capable of producing chaos, and serve as the intrinsic source of chaos of random few-node GRNs. Several optimal motifs causing chaos with atypically high probability are figured out. (iii) Moreover, we discovered that a number of special oscillators can never produce chaos. These structures bring some advantages on rhythmic functions and may help us understand the robustness of diverse biological rhythms. (iv) The methods of dominant phase-advanced driving (DPAD) and DPAD time fraction are proposed to quantitatively identify chaotic motifs and to explain the origin of chaotic behaviors in GRNs. PMID:22792171

Sequential visibility-graph motifs

NASA Astrophysics Data System (ADS)

Iacovacci, Jacopo; Lacasa, Lucas

2016-04-01

Visibility algorithms transform time series into graphs and encode dynamical information in their topology, paving the way for graph-theoretical time series analysis as well as building a bridge between nonlinear dynamics and network science. In this work we introduce and study the concept of sequential visibility-graph motifs, smaller substructures of n consecutive nodes that appear with characteristic frequencies. We develop a theory to compute in an exact way the motif profiles associated with general classes of deterministic and stochastic dynamics. We find that this simple property is indeed a highly informative and computationally efficient feature capable of distinguishing among different dynamics and robust against noise contamination. We finally confirm that it can be used in practice to perform unsupervised learning, by extracting motif profiles from experimental heart-rate series and being able, accordingly, to disentangle meditative from other relaxation states. Applications of this general theory include the automatic classification and description of physical, biological, and financial time series.

Occurrence probability of structured motifs in random sequences.

PubMed

Robin, S; Daudin, J-J; Richard, H; Sagot, M-F; Schbath, S

2002-01-01

The problem of extracting from a set of nucleic acid sequences motifs which may have biological function is more and more important. In this paper, we are interested in particular motifs that may be implicated in the transcription process. These motifs, called structured motifs, are composed of two ordered parts separated by a variable distance and allowing for substitutions. In order to assess their statistical significance, we propose approximations of the probability of occurrences of such a structured motif in a given sequence. An application of our method to evaluate candidate promoters in E. coli and B. subtilis is presented. Simulations show the goodness of the approximations.

Distinct cagA EPIYA motifs are associated with ethnic diversity in Malaysia and Singapore.

PubMed

Schmidt, Heather-Marie A; Goh, Khean-Lee; Fock, Kwong Ming; Hilmi, Ida; Dhamodaran, Subbiah; Forman, David; Mitchell, Hazel

2009-08-01

In vitro studies have shown that the biologic activity of CagA is influenced by the number and class of EPIYA motifs present in its variable region as these motifs correspond to the CagA phosphorylation sites. It has been hypothesized that strains possessing specific combinations of these motifs may be responsible for gastric cancer development. This study investigated the prevalence of cagA and the EPIYA motifs with regard to number, class, and patterns in strains from the three major ethnic groups within the Malaysian and Singaporean populations in relation to disease development. Helicobacter pylori isolates from 49 Chinese, 43 Indian, and 14 Malay patients with functional dyspepsia (FD) and 21 gastric cancer (GC) cases were analyzed using polymerase chain reaction for the presence of cagA and the number, type, and pattern of EPIYA motifs. Additionally, the EPIYA motifs of 47 isolates were sequenced. All 126 isolates possessed cagA, with the majority encoding EPIYA-A (97.6%) and all encoding EPIYA-B. However, while the cagA of 93.0% of Indian FD isolates encoded EPIYA-C as the third motif, 91.8% of Chinese FD isolates and 81.7% of Chinese GC isolates encoded EPIYA-D (p < .001). Of Malay FD isolates, 61.5% and 38.5% possessed EPIYA-C and EPIYA-D, respectively. The majority of isolates possessed three EPIYA motifs; however, Indian isolates were significantly more likely to have four or more (p < .05). Although, H. pylori strains with distinct cagA-types are circulating within the primary ethnic groups resident in Malaysia and Singapore, these genotypes appear unassociated with the development of GC in the ethnic Chinese population. The phenomenon of distinct strains circulating within different ethnic groups, in combination with host and certain environmental factors, may help to explain the rates of GC development in Malaysia.

Propellers in Saturn's rings

NASA Astrophysics Data System (ADS)

Sremcevic, M.; Stewart, G. R.; Albers, N.; Esposito, L. W.

2013-12-01

Theoretical studies and simulations have demonstrated the effects caused by objects embedded in planetary rings. Even if the objects are too small to be directly observed, each creates a much larger gravitational imprint on the surrounding ring material. These strongly depend on the mass of the object and range from "S" like propeller-shaped structures for about 100m-sized icy bodies to the opening of circumferential gaps as in the case of the embedded moons Pan and Daphnis and their corresponding Encke and Keeler Gaps. Since the beginning of the Cassini mission many of these smaller objects (~<500m in size) have been indirectly identified in Saturn's A ring through their propeller signature in the images. Furthermore, recent Cassini observations indicate the possible existence of objects embedded even in Saturn's B and C ring. In this paper we present evidence for the existence of propellers in Saturn's B ring by combining data from Cassini Ultraviolet Imaging Spectrograph (UVIS) and Imaging Science Subsystem (ISS) experiments. We show evidence that B ring seems to harbor two distinct populations of propellers: "big" propellers covering tens of degrees in azimuth situated in the densest part of B ring, and "small" propellers in less dense inner B ring that are similar in size and shape to known A ring propellers. The population of "big" propellers is exemplified with a single object which is observed for 5 years of Cassini data. The object is seen as a very elongated bright stripe (40 degrees wide) in unlit Cassini images, and dark stripe in lit geometries. In total we report observing the feature in images at 18 different epochs between 2005 and 2010. In UVIS occultations we observe this feature as an optical depth depletion in 14 out of 93 occultation cuts at corrotating longitudes compatible with imaging data. Combining the available Cassini data we infer that the object is a partial gap located at r=112,921km embedded in the high optical depth region of the B

Dynamics of the Uranian Rings

NASA Technical Reports Server (NTRS)

Dermott, S. F.

1984-01-01

Some of the problems of the shepherding satellite model of Goldreich ant tremaine are discussed. The following topics are studied: (1) optical depths of the all the observed narrow rings; (2) satellite and ring separation timescales; (3) ring edge sharpness; (4) shock formation in narrow rings; (5) the existence of small satellites near the Uranian rings; and (6) the apse and node alignments of the eccentric and inclined rings.

Neptune - full ring system

NASA Technical Reports Server (NTRS)

1989-01-01

This pair of Voyager 2 images (FDS 11446.21 and 11448.10), two 591-s exposures obtained through the clear filter of the wide angle camera, show the full ring system with the highest sensitivity. Visible in this figure are the bright, narrow N53 and N63 rings, the diffuse N42 ring, and (faintly) the plateau outside of the N53 ring (with its slight brightening near 57,500 km).

Molecular cloning and characterization of a novel RING zinc-finger protein gene up-regulated under in vitro salt stress in cassava.

PubMed

dos Reis, Sávio Pinho; Tavares, Liliane de Souza Conceição; Costa, Carinne de Nazaré Monteiro; Brígida, Aílton Borges Santa; de Souza, Cláudia Regina Batista

2012-06-01

Cassava (Manihot esculenta Crantz) is one of the world's most important food crops. It is cultivated mainly in developing countries of tropics, since its root is a major source of calories for low-income people due to its high productivity and resistance to many abiotic and biotic factors. A previous study has identified a partial cDNA sequence coding for a putative RING zinc finger in cassava storage root. The RING zinc finger protein is a specialized type of zinc finger protein found in many organisms. Here, we isolated the full-length cDNA sequence coding for M. esculenta RZF (MeRZF) protein by a combination of 5' and 3' RACE assays. BLAST analysis showed that its deduced amino acid sequence has a high level of similarity to plant proteins of RZF family. MeRZF protein contains a signature sequence motif for a RING zinc finger at its C-terminal region. In addition, this protein showed a histidine residue at the fifth coordination site, likely belonging to the RING-H2 subgroup, as confirmed by our phylogenetic analysis. There is also a transmembrane domain in its N-terminal region. Finally, semi-quantitative RT-PCR assays showed that MeRZF expression is increased in detached leaves treated with sodium chloride. Here, we report the first evidence of a RING zinc finger gene of cassava showing potential role in response to salt stress.

The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity.

PubMed

Yang, Lingna; Wang, Chongyuan; Li, Fudong; Zhang, Jiahai; Nayab, Anam; Wu, Jihui; Shi, Yunyu; Gong, Qingguo

2017-09-29

MEX-3 is a K-homology (KH) domain-containing RNA-binding protein first identified as a translational repressor in Caenorhabditis elegans , and its four orthologs (MEX-3A-D) in human and mouse were subsequently found to have E3 ubiquitin ligase activity mediated by a RING domain and critical for RNA degradation. Current evidence implicates human MEX-3C in many essential biological processes and suggests a strong connection with immune diseases and carcinogenesis. The highly conserved dual KH domains in MEX-3 proteins enable RNA binding and are essential for the recognition of the 3'-UTR and post-transcriptional regulation of MEX-3 target transcripts. However, the molecular mechanisms of translational repression and the consensus RNA sequence recognized by the MEX-3C KH domain are unknown. Here, using X-ray crystallography and isothermal titration calorimetry, we investigated the RNA-binding activity and selectivity of human MEX-3C dual KH domains. Our high-resolution crystal structures of individual KH domains complexed with a noncanonical U-rich and a GA-rich RNA sequence revealed that the KH1/2 domains of human MEX-3C bound MRE10, a 10-mer RNA (5'-CAGAGUUUAG-3') consisting of an eight-nucleotide MEX-3-recognition element (MRE) motif, with high affinity. Of note, we also identified a consensus RNA motif recognized by human MEX-3C. The potential RNA-binding sites in the 3'-UTR of the human leukocyte antigen serotype ( HLA-A2 ) mRNA were mapped with this RNA-binding motif and further confirmed by fluorescence polarization. The binding motif identified here will provide valuable information for future investigations of the functional pathways controlled by human MEX-3C and for predicting potential mRNAs regulated by this enzyme. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Using SCOPE to identify potential regulatory motifs in coregulated genes.

PubMed

Martyanov, Viktor; Gross, Robert H

2011-05-31

SCOPE is an ensemble motif finder that uses three component algorithms in parallel to identify potential regulatory motifs by over-representation and motif position preference. Each component algorithm is optimized to find a different kind of motif. By taking the best of these three approaches, SCOPE performs better than any single algorithm, even in the presence of noisy data. In this article, we utilize a web version of SCOPE to examine genes that are involved in telomere maintenance. SCOPE has been incorporated into at least two other motif finding programs and has been used in other studies. The three algorithms that comprise SCOPE are BEAM, which finds non-degenerate motifs (ACCGGT), PRISM, which finds degenerate motifs (ASCGWT), and SPACER, which finds longer bipartite motifs (ACCnnnnnnnnGGT). These three algorithms have been optimized to find their corresponding type of motif. Together, they allow SCOPE to perform extremely well. Once a gene set has been analyzed and candidate motifs identified, SCOPE can look for other genes that contain the motif which, when added to the original set, will improve the motif score. This can occur through over-representation or motif position preference. Working with partial gene sets that have biologically verified transcription factor binding sites, SCOPE was able to identify most of the rest of the genes also regulated by the given transcription factor. Output from SCOPE shows candidate motifs, their significance, and other information both as a table and as a graphical motif map. FAQs and video tutorials are available at the SCOPE web site which also includes a "Sample Search" button that allows the user to perform a trial run. Scope has a very friendly user interface that enables novice users to access the algorithm's full power without having to become an expert in the bioinformatics of motif finding. As input, SCOPE can take a list of genes, or FASTA sequences. These can be entered in browser text fields, or read from

Saturn Ring

NASA Image and Video Library

2007-12-12

Like Earth, Saturn has an invisible ring of energetic ions trapped in its magnetic field. This feature is known as a "ring current." This ring current has been imaged with a special camera on Cassini sensitive to energetic neutral atoms. This is a false color map of the intensity of the energetic neutral atoms emitted from the ring current through a processed called charged exchange. In this process a trapped energetic ion steals and electron from cold gas atoms and becomes neutral and escapes the magnetic field. The Cassini Magnetospheric Imaging Instrument's ion and neutral camera records the intensity of the escaping particles, which provides a map of the ring current. In this image, the colors represent the intensity of the neutral emission, which is a reflection of the trapped ions. This "ring" is much farther from Saturn (roughly five times farther) than Saturn's famous icy rings. Red in the image represents the higher intensity of the particles, while blue is less intense. Saturn's ring current had not been mapped before on a global scale, only "snippets" or areas were mapped previously but not in this detail. This instrument allows scientists to produce movies (see PIA10083) that show how this ring changes over time. These movies reveal a dynamic system, which is usually not as uniform as depicted in this image. The ring current is doughnut shaped but in some instances it appears as if someone took a bite out of it. This image was obtained on March 19, 2007, at a latitude of about 54.5 degrees and radial distance 1.5 million kilometres (920,000 miles). Saturn is at the center, and the dotted circles represent the orbits of the moon's Rhea and Titan. The Z axis points parallel to Saturn's spin axis, the X axis points roughly sunward in the sun-spin axis plane, and the Y axis completes the system, pointing roughly toward dusk. The ion and neutral camera's field of view is marked by the white line and accounts for the cut-off of the image on the left. The

Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants.

PubMed

Al-Momani, Shireen; Qi, Da; Ren, Zhe; Jones, Andrew R

2018-06-15

Phosphorylation is one of the most prevalent post-translational modifications and plays a key role in regulating cellular processes. We carried out a bioinformatics analysis of pre-existing phosphoproteomics data, to profile two model species representing the largest subclasses in flowering plants the dicot Arabidopsis thaliana and the monocot Oryza sativa, to understand the extent to which phosphorylation signaling and function is conserved across evolutionary divergent plants. We identified 6537 phosphopeptides from 3189 phosphoproteins in Arabidopsis and 2307 phosphopeptides from 1613 phosphoproteins in rice. We identified phosphorylation motifs, finding nineteen pS motifs and two pT motifs shared in rice and Arabidopsis. The majority of shared motif-containing proteins were mapped to the same biological processes with similar patterns of fold enrichment, indicating high functional conservation. We also identified shared patterns of crosstalk between phosphoserines with enrichment for motifs pSXpS, pSXXpS and pSXXXpS, where X is any amino acid. Lastly, our results identified several pairs of motifs that are significantly enriched to co-occur in Arabidopsis proteins, indicating cross-talk between different sites, but this was not observed in rice. Our results demonstrate that there are evolutionary conserved mechanisms of phosphorylation-mediated signaling in plants, via analysis of high-throughput phosphorylation proteomics data from key monocot and dicot species: rice and Arabidposis thaliana. The results also suggest that there is increased crosstalk between phosphorylation sites in A. thaliana compared with rice. The results are important for our general understanding of cell signaling in plants, and the ability to use A. thaliana as a general model for plant biology. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Multiple Dileucine-like Motifs Direct VGLUT1 Trafficking

PubMed Central

Foss, Sarah M.; Li, Haiyan; Santos, Magda S.; Edwards, Robert H.

2013-01-01

The vesicular glutamate transporters (VGLUTs) package glutamate into synaptic vesicles, and the two principal isoforms VGLUT1 and VGLUT2 have been suggested to influence the properties of release. To understand how a VGLUT isoform might influence transmitter release, we have studied their trafficking and previously identified a dileucine-like endocytic motif in the C terminus of VGLUT1. Disruption of this motif impairs the activity-dependent recycling of VGLUT1, but does not eliminate its endocytosis. We now report the identification of two additional dileucine-like motifs in the N terminus of VGLUT1 that are not well conserved in the other isoforms. In the absence of all three motifs, rat VGLUT1 shows limited accumulation at synaptic sites and no longer responds to stimulation. In addition, shRNA-mediated knockdown of clathrin adaptor proteins AP-1 and AP-2 shows that the C-terminal motif acts largely via AP-2, whereas the N-terminal motifs use AP-1. Without the C-terminal motif, knockdown of AP-1 reduces the proportion of VGLUT1 that responds to stimulation. VGLUT1 thus contains multiple sorting signals that engage distinct trafficking mechanisms. In contrast to VGLUT1, the trafficking of VGLUT2 depends almost entirely on the conserved C-terminal dileucine-like motif: without this motif, a substantial fraction of VGLUT2 redistributes to the plasma membrane and the transporter's synaptic localization is disrupted. Consistent with these differences in trafficking signals, wild-type VGLUT1 and VGLUT2 differ in their response to stimulation. PMID:23804088

Multiple dileucine-like motifs direct VGLUT1 trafficking.

PubMed

Foss, Sarah M; Li, Haiyan; Santos, Magda S; Edwards, Robert H; Voglmaier, Susan M

2013-06-26

The vesicular glutamate transporters (VGLUTs) package glutamate into synaptic vesicles, and the two principal isoforms VGLUT1 and VGLUT2 have been suggested to influence the properties of release. To understand how a VGLUT isoform might influence transmitter release, we have studied their trafficking and previously identified a dileucine-like endocytic motif in the C terminus of VGLUT1. Disruption of this motif impairs the activity-dependent recycling of VGLUT1, but does not eliminate its endocytosis. We now report the identification of two additional dileucine-like motifs in the N terminus of VGLUT1 that are not well conserved in the other isoforms. In the absence of all three motifs, rat VGLUT1 shows limited accumulation at synaptic sites and no longer responds to stimulation. In addition, shRNA-mediated knockdown of clathrin adaptor proteins AP-1 and AP-2 shows that the C-terminal motif acts largely via AP-2, whereas the N-terminal motifs use AP-1. Without the C-terminal motif, knockdown of AP-1 reduces the proportion of VGLUT1 that responds to stimulation. VGLUT1 thus contains multiple sorting signals that engage distinct trafficking mechanisms. In contrast to VGLUT1, the trafficking of VGLUT2 depends almost entirely on the conserved C-terminal dileucine-like motif: without this motif, a substantial fraction of VGLUT2 redistributes to the plasma membrane and the transporter's synaptic localization is disrupted. Consistent with these differences in trafficking signals, wild-type VGLUT1 and VGLUT2 differ in their response to stimulation.

Molecular Signaling Network Motifs Provide a Mechanistic Basis for Cellular Threshold Responses

PubMed Central

Bhattacharya, Sudin; Conolly, Rory B.; Clewell, Harvey J.; Kaminski, Norbert E.; Andersen, Melvin E.

2014-01-01

Background: Increasingly, there is a move toward using in vitro toxicity testing to assess human health risk due to chemical exposure. As with in vivo toxicity testing, an important question for in vitro results is whether there are thresholds for adverse cellular responses. Empirical evaluations may show consistency with thresholds, but the main evidence has to come from mechanistic considerations. Objectives: Cellular response behaviors depend on the molecular pathway and circuitry in the cell and the manner in which chemicals perturb these circuits. Understanding circuit structures that are inherently capable of resisting small perturbations and producing threshold responses is an important step towards mechanistically interpreting in vitro testing data. Methods: Here we have examined dose–response characteristics for several biochemical network motifs. These network motifs are basic building blocks of molecular circuits underpinning a variety of cellular functions, including adaptation, homeostasis, proliferation, differentiation, and apoptosis. For each motif, we present biological examples and models to illustrate how thresholds arise from specific network structures. Discussion and Conclusion: Integral feedback, feedforward, and transcritical bifurcation motifs can generate thresholds. Other motifs (e.g., proportional feedback and ultrasensitivity)produce responses where the slope in the low-dose region is small and stays close to the baseline. Feedforward control may lead to nonmonotonic or hormetic responses. We conclude that network motifs provide a basis for understanding thresholds for cellular responses. Computational pathway modeling of these motifs and their combinations occurring in molecular signaling networks will be a key element in new risk assessment approaches based on in vitro cellular assays. Citation: Zhang Q, Bhattacharya S, Conolly RB, Clewell HJ III, Kaminski NE, Andersen ME. 2014. Molecular signaling network motifs provide a

RNA motif search with data-driven element ordering.

PubMed

Rampášek, Ladislav; Jimenez, Randi M; Lupták, Andrej; Vinař, Tomáš; Brejová, Broňa

2016-05-18

In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .

Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics.

PubMed

Li, Sanshu; Breaker, Ronald R

2017-10-13

With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies. We have adapted a bioinformatics pipeline for discovering bacterial ncRNAs to systematically analyze many fungal genomes. This comparative genomics pipeline integrates information on conserved RNA sequence and structural features with alternative splicing information to reveal fungal RNA motifs that are candidate regulatory domains, or that might have other possible functions. A total of 15 prominent classes of structured ncRNA candidates were identified, including variant HDV self-cleaving ribozyme representatives, atypical snoRNA candidates, and possible structured antisense RNA motifs. Candidate regulatory motifs were also found associated with genes for ribosomal proteins, S-adenosylmethionine decarboxylase (SDC), amidase, and HexA protein involved in Woronin body formation. We experimentally confirm that the variant HDV ribozymes undergo rapid self-cleavage, and we demonstrate that the SDC RNA motif reduces the expression of SAM decarboxylase by translational repression. Furthermore, we provide evidence that several other motifs discovered in this study are likely to be functional ncRNA elements. Systematic screening of fungal genomes using a computational discovery pipeline has revealed the existence of a variety of novel structured ncRNAs. Genome contexts and similarities to known ncRNA motifs provide strong evidence for the biological and biochemical functions of some newly found ncRNA motifs

The ER-bound RING finger protein 5 (RNF5/RMA1) causes degenerative myopathy in transgenic mice and is deregulated in inclusion body myositis.

PubMed

Delaunay, Agnès; Bromberg, Kenneth D; Hayashi, Yukiko; Mirabella, Massimiliano; Burch, Denise; Kirkwood, Brian; Serra, Carlo; Malicdan, May C; Mizisin, Andrew P; Morosetti, Roberta; Broccolini, Aldobrando; Guo, Ling T; Jones, Stephen N; Lira, Sergio A; Puri, Pier Lorenzo; Shelton, G Diane; Ronai, Ze'ev

2008-02-13

Growing evidence supports the importance of ubiquitin ligases in the pathogenesis of muscular disorders, although underlying mechanisms remain largely elusive. Here we show that the expression of RNF5 (aka RMA1), an ER-anchored RING finger E3 ligase implicated in muscle organization and in recognition and processing of malfolded proteins, is elevated and mislocalized to cytoplasmic aggregates in biopsies from patients suffering from sporadic-Inclusion Body Myositis (sIBM). Consistent with these findings, an animal model for hereditary IBM (hIBM), but not their control littermates, revealed deregulated expression of RNF5. Further studies for the role of RNF5 in the pathogenesis of s-IBM and more generally in muscle physiology were performed using RNF5 transgenic and KO animals. Transgenic mice carrying inducible expression of RNF5, under control of beta-actin or muscle specific promoter, exhibit an early onset of muscle wasting, muscle degeneration and extensive fiber regeneration. Prolonged expression of RNF5 in the muscle also results in the formation of fibers containing congophilic material, blue-rimmed vacuoles and inclusion bodies. These phenotypes were associated with altered expression and activity of ER chaperones, characteristic of myodegenerative diseases such as s-IBM. Conversely, muscle regeneration and induction of ER stress markers were delayed in RNF5 KO mice subjected to cardiotoxin treatment. While supporting a role for RNF5 Tg mice as model for s-IBM, our study also establishes the importance of RNF5 in muscle physiology and its deregulation in ER stress associated muscular disorders.

The ER-Bound RING Finger Protein 5 (RNF5/RMA1) Causes Degenerative Myopathy in Transgenic Mice and Is Deregulated in Inclusion Body Myositis

PubMed Central

Delaunay, Agnès; Bromberg, Kenneth D.; Hayashi, Yukiko; Mirabella, Massimiliano; Burch, Denise; Kirkwood, Brian; Serra, Carlo; Malicdan, May C.; Mizisin, Andrew P.; Morosetti, Roberta; Broccolini, Aldobrando; Guo, Ling T.; Jones, Stephen N.; Lira, Sergio A.; Puri, Pier Lorenzo; Shelton, G. Diane; Ronai, Ze'ev

2008-01-01

Growing evidence supports the importance of ubiquitin ligases in the pathogenesis of muscular disorders, although underlying mechanisms remain largely elusive. Here we show that the expression of RNF5 (aka RMA1), an ER-anchored RING finger E3 ligase implicated in muscle organization and in recognition and processing of malfolded proteins, is elevated and mislocalized to cytoplasmic aggregates in biopsies from patients suffering from sporadic-Inclusion Body Myositis (sIBM). Consistent with these findings, an animal model for hereditary IBM (hIBM), but not their control littermates, revealed deregulated expression of RNF5. Further studies for the role of RNF5 in the pathogenesis of s-IBM and more generally in muscle physiology were performed using RNF5 transgenic and KO animals. Transgenic mice carrying inducible expression of RNF5, under control of β-actin or muscle specific promoter, exhibit an early onset of muscle wasting, muscle degeneration and extensive fiber regeneration. Prolonged expression of RNF5 in the muscle also results in the formation of fibers containing congophilic material, blue-rimmed vacuoles and inclusion bodies. These phenotypes were associated with altered expression and activity of ER chaperones, characteristic of myodegenerative diseases such as s-IBM. Conversely, muscle regeneration and induction of ER stress markers were delayed in RNF5 KO mice subjected to cardiotoxin treatment. While supporting a role for RNF5 Tg mice as model for s-IBM, our study also establishes the importance of RNF5 in muscle physiology and its deregulation in ER stress associated muscular disorders. PMID:18270596

A DFT investigation of a bulky biomimetic model catalyzing the 5'-outer ring deiodination of thyroxine.

PubMed

Fortino, Mariagrazia; Marino, Tiziana; Russo, Nino; Sicilia, Emilia

2016-12-01

This paper illustrates the outcomes of a density functional theory investigation aimed at unraveling mechanistic aspects of the 5'-outer ring deiodination process of thyroxine (T4) assisted by the sterically protected organoselenol compound BpqSeH. BpqSeH, which was previously synthesized and tested for its deiodinase activity, is able to afford the active hormone 3,5,3'-tetraiodothyronine (T3) by selective outer-ring deiodination of T4, and to protect the SeH moiety inside the nano-sized molecular cavity from further reactivity, allowing its isolation and characterization. Calculations were also performed including an imidazole ring that, mimicking a His residue in the active site of the original enzyme, plays an crucial role in deprotonating the selenol moiety. Both the suggested enol/keto tautomerization and the previously proven formation of an intermediate whose main characteristic is the presence of a Se⋯I⋯C halogen bond, were examined along the pathway leading to 5'-outer ring deiodination. The calculated potential energy surface showed that neither the pathway encompassing enol/keto tautomerism nor the formation of a halogen bond paving the way to C-I bond breaking and chalcogen-I bond forming is viable. The exergonic formation of the final selenenyl iodide product confirms the stabilization effect of the molecular cavity. Graphical Abstract Computed free energy profile describing the 5'-outer deiodination of thyroxine assisted by the steric hindered organoselenol BpqSH compound. The molecular electrostatic potential map reoported for the INT1 intermediate shows the non-covalent Se-I interaction, due to the attraction between charges of opposite sign, that weakens the C-I bond and prepares the formation of the new Se-I bond.

Supra­molecular inter­actions in 2,6-di­amino-4-chloro­pyrimidin-1-ium 5-chloro­salicylate and bis­(2,6-di­amino-4-chloro­pyrimidin-1-ium) naphthalene-1,5-di­sulfonate

PubMed Central

Swinton Darious, Robert; Thomas Muthiah, Packianathan

2018-01-01

The crystals of two new salts, 2,6-di­amino-4-chloro­pyrimidin-1-ium 5-chloro­salicylate, C4H6ClN4 +·C7H4ClO3 −, (I), and bis­(2,6-di­amino-4-chloro­pyrimidin-1-ium) naphthalene-1,5-di-sulfonate, 2C4H6ClN4 +·C10H6O6S2 2−, (II), have been synthesized and characterized by single-crystal X-ray diffraction. In both compounds, the N atom of the pyrimidine group in between the amino substituents is protonated and the pyrimidinium cation forms a pair of N—H⋯O hydrogen bonds with the carboxyl­ate/sulfonate ion, leading to a robust R 2 2(8) motif (supra­molecular heterosynthon). In compound (I), a self-complementary base pairing involving the other pyrimidinium ring nitro­gen atom and one of the amino groups via a pair of N—H⋯N hydrogen bonds [R 2 2(8) homosynthon] is also present. In compound (II), the crystallographic inversion centre coincides with the inversion centre of the naphthalene-1,5-di­sulfonate ion and all the sulfonate O atoms are hydrogen-bond acceptors, generating fused-ring motifs and a quadruple DDAA array. A halogen-bond (Cl⋯Cl) inter­action is present in (I) with a distance and angle of 3.3505 (12) Å and 151.37 (10)°, respectively. In addition, a C—Cl⋯π inter­action and a π–π inter­action in (I) and a π–π inter­action in (II) further stabilize these crystal structures. PMID:29850062

Fluorescence decay of naphthalene studied in an electrostatic storage ring, the Mini-Ring

NASA Astrophysics Data System (ADS)

Martin, S.; Matsumoto, J.; Kono, N.; Ji, M.-C.; Brédy, R.; Bernard, J.; Cassimi, A.; Chen, L.

2017-10-01

The cooling of naphthalene cations (C10H8)+ has been studied in a compact electrostatic ion storage ring, the Mini-Ring. A nano second laser pulse of 532 nm (2.33 eV) was used to probe the internal energy distribution every millisecond during the storage time up to 5 ms. The evolution of the internal energy distribution of the stored ions was simulated with a model taking into account the dissociation and the radiative decay processes. Calculated decay curves were fitted to the corresponding laser induced neutral decays. For a laser power of 200 μJ/pulse, a good agreement between experiment and modeling was found using an initial Gaussian energy distribution centered to 5.9 eV and a fluorescence decay rate varying from 200 to 300 s-1 in the energy range from 6 to 7 eV. This fast decay was attributed to the delayed Poincaré fluorescence process.

Characteristic motifs for families of allergenic proteins

PubMed Central

Ivanciuc, Ovidiu; Garcia, Tzintzuni; Torres, Miguel; Schein, Catherine H.; Braun, Werner

2008-01-01

The identification of potential allergenic proteins is usually done by scanning a database of allergenic proteins and locating known allergens with a high sequence similarity. However, there is no universally accepted cut-off value for sequence similarity to indicate potential IgE cross-reactivity. Further, overall sequence similarity may be less important than discrete areas of similarity in proteins with homologous structure. To identify such areas, we first classified all allergens and their subdomains in the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/) to their closest protein families as defined in Pfam, and identified conserved physicochemical property motifs characteristic of each group of sequences. Allergens populate only a small subset of all known Pfam families, as all allergenic proteins in SDAP could be grouped to only 130 (of 9318 total) Pfams, and 31 families contain more than four allergens. Conserved physicochemical property motifs for the aligned sequences of the most populated Pfam families were identified with the PCPMer program suite and catalogued in the webserver Motif-Mate (http://born.utmb.edu/motifmate/summary.php). We also determined specific motifs for allergenic members of a family that could distinguish them from non-allergenic ones. These allergen specific motifs should be most useful in database searches for potential allergens. We found that sequence motifs unique to the allergens in three families (seed storage proteins, Bet v 1, and tropomyosin) overlap with known IgE epitopes, thus providing evidence that our motif based approach can be used to assess the potential allergenicity of novel proteins. PMID:18951633

Implications of Liebig’s law of the minimum for tree-ring reconstructions of climate

NASA Astrophysics Data System (ADS)

Stine, A. R.; Huybers, P.

2017-11-01

A basic principle of ecology, known as Liebig’s Law of the Minimum, is that plant growth reflects the strongest limiting environmental factor. This principle implies that a limiting environmental factor can be inferred from historical growth and, in dendrochronology, such reconstruction is generally achieved by averaging collections of standardized tree-ring records. Averaging is optimal if growth reflects a single limiting factor and noise but not if growth also reflects locally variable stresses that intermittently limit growth. In this study a collection of Arctic tree ring records is shown to follow scaling relationships that are inconsistent with the signal-plus-noise model of tree growth but consistent with Liebig’s Law acting at the local level. Also consistent with law-of-the-minimum behavior is that reconstructions based on the least-stressed trees in a given year better-follow variations in temperature than typical approaches where all tree-ring records are averaged. Improvements in reconstruction skill occur across all frequencies, with the greatest increase at the lowest frequencies. More comprehensive statistical-ecological models of tree growth may offer further improvement in reconstruction skill.

The amylase inhibitor montbretin A reveals a new glycosidase inhibition motif.

PubMed

Williams, Leslie K; Zhang, Xiaohua; Caner, Sami; Tysoe, Christina; Nguyen, Nham T; Wicki, Jacqueline; Williams, David E; Coleman, John; McNeill, John H; Yuen, Violet; Andersen, Raymond J; Withers, Stephen G; Brayer, Gary D

2015-09-01

The complex plant flavonol glycoside montbretin A is a potent (Ki = 8 nM) and specific inhibitor of human pancreatic α-amylase with potential as a therapeutic for diabetes and obesity. Controlled degradation studies on montbretin A, coupled with inhibition analyses, identified an essential high-affinity core structure comprising the myricetin and caffeic acid moieties linked via a disaccharide. X-ray structural analyses of the montbretin A-human α-amylase complex confirmed the importance of this core structure and revealed a novel mode of glycosidase inhibition wherein internal π-stacking interactions between the myricetin and caffeic acid organize their ring hydroxyls for optimal hydrogen bonding to the α-amylase catalytic residues D197 and E233. This novel inhibitory motif can be reproduced in a greatly simplified analog, offering potential for new strategies for glycosidase inhibition and therapeutic development.

Comparing CTH Simulations and Experiments on Explosively Loaded Rings

NASA Astrophysics Data System (ADS)

Braithwaite, C. H.; Aydelotte, B.; Thadhani, N. N.; Williamson, D. M.

2011-06-01

A series of experiments were conducted on explosively loaded rings for the purpose of studying fragmentation. In addition to the collection of fragments for analysis, the radial velocity of the expanding ring was measured with PDV and the arrangement was imaged using a high speed camera. Both the ring material and the material used as the explosive container were altered and the results compared with simulations performed in CTH. Good agreement was found between the simulations and the experiments. The maximum radial velocity attained was approximately 450 m/s, which was achieved through loading with a 5g PETN based charge.

Classification and assessment tools for structural motif discovery algorithms.

PubMed

Badr, Ghada; Al-Turaiki, Isra; Mathkour, Hassan

2013-01-01

Motif discovery is the problem of finding recurring patterns in biological data. Patterns can be sequential, mainly when discovered in DNA sequences. They can also be structural (e.g. when discovering RNA motifs). Finding common structural patterns helps to gain a better understanding of the mechanism of action (e.g. post-transcriptional regulation). Unlike DNA motifs, which are sequentially conserved, RNA motifs exhibit conservation in structure, which may be common even if the sequences are different. Over the past few years, hundreds of algorithms have been developed to solve the sequential motif discovery problem, while less work has been done for the structural case. In this paper, we survey, classify, and compare different algorithms that solve the structural motif discovery problem, where the underlying sequences may be different. We highlight their strengths and weaknesses. We start by proposing a benchmark dataset and a measurement tool that can be used to evaluate different motif discovery approaches. Then, we proceed by proposing our experimental setup. Finally, results are obtained using the proposed benchmark to compare available tools. To the best of our knowledge, this is the first attempt to compare tools solely designed for structural motif discovery. Results show that the accuracy of discovered motifs is relatively low. The results also suggest a complementary behavior among tools where some tools perform well on simple structures, while other tools are better for complex structures. We have classified and evaluated the performance of available structural motif discovery tools. In addition, we have proposed a benchmark dataset with tools that can be used to evaluate newly developed tools.

DynaMIT: the dynamic motif integration toolkit

PubMed Central

Dassi, Erik; Quattrone, Alessandro

2016-01-01

De-novo motif search is a frequently applied bioinformatics procedure to identify and prioritize recurrent elements in sequences sets for biological investigation, such as the ones derived from high-throughput differential expression experiments. Several algorithms have been developed to perform motif search, employing widely different approaches and often giving divergent results. In order to maximize the power of these investigations and ultimately be able to draft solid biological hypotheses, there is the need for applying multiple tools on the same sequences and merge the obtained results. However, motif reporting formats and statistical evaluation methods currently make such an integration task difficult to perform and mostly restricted to specific scenarios. We thus introduce here the Dynamic Motif Integration Toolkit (DynaMIT), an extremely flexible platform allowing to identify motifs employing multiple algorithms, integrate them by means of a user-selected strategy and visualize results in several ways; furthermore, the platform is user-extendible in all its aspects. DynaMIT is freely available at http://cibioltg.bitbucket.org. PMID:26253738

cWINNOWER Algorithm for Finding Fuzzy DNA Motifs

NASA Technical Reports Server (NTRS)

Liang, Shoudan

2003-01-01

The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in protein-binding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if multiple mutated copies of the motif (i.e., the signals) are present in the DNA sequence in sufficient abundance. The cWINNOWER algorithm substantially improves the sensitivity of the winnower method of Pevzner and Sze by imposing a consensus constraint, enabling it to detect much weaker signals. We studied the minimum number of detectable motifs qc as a function of sequence length N for random sequences. We found that qc increases linearly with N for a fast version of the algorithm based on counting three-member sub-cliques. Imposing consensus constraints reduces qc, by a factor of three in this case, which makes the algorithm dramatically more sensitive. Our most sensitive algorithm, which counts four-member sub-cliques, needs a minimum of only 13 signals to detect motifs in a sequence of length N = 12000 for (l,d) = (15,4).

[Dynamic characters of sulphur and heavy metals concentrations in Pinus taiwanensis growth rings].

PubMed

Wu, Zemin; Gao, Jian; Huang, Chenglin; Hong, Shuyuan

2005-05-01

Based on the concentration analyses of S, Mn, Fe, Zn, Cu and Pb in the growth ring set of Pinus taiwanensis at the summit (1,400-1,600 m alt.) of Huangshan Mountains during past 80 years, this paper studied the dynamic characters of element concentrations in the ring set, and their relationships with atmospheric environment. The results showed that there were three levels of S concentration in the growth ring set, i.e., low concentration (less than 2 mg.kg(-1)), accounted for 58.5% of the ring set; medium (3.65-6.0 mg.kg(-1)), accounted for 24.4%; and high ( > 11.0 mg.kg(-1)), accounted for 17.1%. The dynamic change of S accumulation in the ring set displayed an obvious fluctuation, which could be divided into 3 major types, i.e., fluctuation during 1917-1960, relatively stable during 1961-1980, and gradual increase after 1981. In the growth ring set of 1935-1938, 1959-1960, and recent 10 years, the S accumulation concentrations were all higher than 11 mg.kg(-1), suggesting the relatively high atmospheric S concentration in those periods. There was a significant correlation between the increase of tourist amount in Huangshan scenic spot and the S concentration in growth ring set. The fuel fume centralized in some places might result in the atmospheric pollution at local scale, which in turn, might influence the S accumulation in growth ring set. The Pb accumulation concentration in the ring set was less than the background value in soil. The accumulation concentrations of Mn, Fe, Zn and Cu showed fluctuation characteristics, with independence of each other. The accumulation of Zn and Cu in growth rings had no correlation with tree age, while that of Mn and Fe was in adverse. The Mn concentration in the growth ring set decreased with tree age but increased in recent growth rings, while the Fe concentration was on the contrary, which needed further study.

Chemicals from Biomass: Combining Ring-Opening Tautomerization and Hydrogenation Reactions to Produce 1,5-Pentanediol from Furfural.

PubMed

Brentzel, Zachary J; Barnett, Kevin J; Huang, Kefeng; Maravelias, Christos T; Dumesic, James A; Huber, George W

2017-04-10

A process for the synthesis of 1,5-pentanediol (1,5-PD) with 84 % yield from furfural is developed, utilizing dehydration/hydration, ring-opening tautomerization, and hydrogenation reactions. Although this process has more reaction steps than the traditional direct hydrogenolysis of tetrahydrofurfuryl alcohol (THFA), techno-economic analyses demonstrate that this process is the economically preferred route for the synthesis of biorenewable 1,5-PD. 2-Hydroxytetrahydropyran (2-HY-THP) is the key reaction pathway intermediate that allows for a decrease in the minimum selling price of 1,5-PD. The reactivity of 2-HY-THP is 80 times greater than that of THFA over a bimetallic hydrogenolysis catalyst. This enhanced reactivity is a result of the ring-opening tautomerization to 5-hydoxyvaleraldehyde and subsequent hydrogenation to 1,5-PD. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

SVM2Motif—Reconstructing Overlapping DNA Sequence Motifs by Mimicking an SVM Predictor

PubMed Central

Vidovic, Marina M. -C.; Görnitz, Nico; Müller, Klaus-Robert; Rätsch, Gunnar; Kloft, Marius

2015-01-01

Identifying discriminative motifs underlying the functionality and evolution of organisms is a major challenge in computational biology. Machine learning approaches such as support vector machines (SVMs) achieve state-of-the-art performances in genomic discrimination tasks, but—due to its black-box character—motifs underlying its decision function are largely unknown. As a remedy, positional oligomer importance matrices (POIMs) allow us to visualize the significance of position-specific subsequences. Although being a major step towards the explanation of trained SVM models, they suffer from the fact that their size grows exponentially in the length of the motif, which renders their manual inspection feasible only for comparably small motif sizes, typically k ≤ 5. In this work, we extend the work on positional oligomer importance matrices, by presenting a new machine-learning methodology, entitled motifPOIM, to extract the truly relevant motifs—regardless of their length and complexity—underlying the predictions of a trained SVM model. Our framework thereby considers the motifs as free parameters in a probabilistic model, a task which can be phrased as a non-convex optimization problem. The exponential dependence of the POIM size on the oligomer length poses a major numerical challenge, which we address by an efficient optimization framework that allows us to find possibly overlapping motifs consisting of up to hundreds of nucleotides. We demonstrate the efficacy of our approach on a synthetic data set as well as a real-world human splice site data set. PMID:26690911

Modeling gene regulatory network motifs using statecharts

PubMed Central

2012-01-01

Background Gene regulatory networks are widely used by biologists to describe the interactions among genes, proteins and other components at the intra-cellular level. Recently, a great effort has been devoted to give gene regulatory networks a formal semantics based on existing computational frameworks. For this purpose, we consider Statecharts, which are a modular, hierarchical and executable formal model widely used to represent software systems. We use Statecharts for modeling small and recurring patterns of interactions in gene regulatory networks, called motifs. Results We present an improved method for modeling gene regulatory network motifs using Statecharts and we describe the successful modeling of several motifs, including those which could not be modeled or whose models could not be distinguished using the method of a previous proposal. We model motifs in an easy and intuitive way by taking advantage of the visual features of Statecharts. Our modeling approach is able to simulate some interesting temporal properties of gene regulatory network motifs: the delay in the activation and the deactivation of the "output" gene in the coherent type-1 feedforward loop, the pulse in the incoherent type-1 feedforward loop, the bistability nature of double positive and double negative feedback loops, the oscillatory behavior of the negative feedback loop, and the "lock-in" effect of positive autoregulation. Conclusions We present a Statecharts-based approach for the modeling of gene regulatory network motifs in biological systems. The basic motifs used to build more complex networks (that is, simple regulation, reciprocal regulation, feedback loop, feedforward loop, and autoregulation) can be faithfully described and their temporal dynamics can be analyzed. PMID:22536967

Uranus rings and two moons

NASA Technical Reports Server (NTRS)

1986-01-01

Voyager 2 has discovered two 'shepherd' satellites associated with the rings of Uranus. The two moons -- designated 1986U7 and 1986U8 -- are seen here on either side of the bright epsilon ring; all nine of the known Uranian rings are visible. The image was taken Jan. 21, 1986, at a distance of 4.1 million kilometers (2.5 million miles) and resolution of about 36 km (22 mi). The image was processed to enhance narrow features. The epsilon ring appears surrounded by a dark halo as a result of this processing; occasional blips seen on the ring are also artifacts. Lying inward from the epsilon ring are the delta, gamma and eta rings; then the beta and alpha rings; and finally the barely visible 4, 5 and 6 rings. The rings have been studied since their discovery in 1977, through observations of how they diminish the light of stars they pass in front of. This image is the first direct observation of all nine rings in reflected sunlight. They range in width from about 100 km (60 mi) at the widest part of the epsilon ring to only a few kilometers for most of the others. The discovery of the two ring moons 1986U7 and 1986U8 is a major advance in our understanding of the structure of the Uranian rings and is in good agreement with theoretical predictions of how these narrow rings are kept from spreading out. Based on likely surface brightness properties, the moons are of roughly 2O- and 3O-km diameter, respectively. The Voyager project is managed for NASA by the Jet Propulsion Laboratory.

FPGA implementation of motifs-based neuronal network and synchronization analysis

NASA Astrophysics Data System (ADS)

Deng, Bin; Zhu, Zechen; Yang, Shuangming; Wei, Xile; Wang, Jiang; Yu, Haitao

2016-06-01

Motifs in complex networks play a crucial role in determining the brain functions. In this paper, 13 kinds of motifs are implemented with Field Programmable Gate Array (FPGA) to investigate the relationships between the networks properties and motifs properties. We use discretization method and pipelined architecture to construct various motifs with Hindmarsh-Rose (HR) neuron as the node model. We also build a small-world network based on these motifs and conduct the synchronization analysis of motifs as well as the constructed network. We find that the synchronization properties of motif determine that of motif-based small-world network, which demonstrates effectiveness of our proposed hardware simulation platform. By imitation of some vital nuclei in the brain to generate normal discharges, our proposed FPGA-based artificial neuronal networks have the potential to replace the injured nuclei to complete the brain function in the treatment of Parkinson's disease and epilepsy.

Cavity-locked ring down spectroscopy

DOEpatents

Zare, Richard N.; Paldus, Barbara A.; Harb, Charles C.; Spence, Thomas

2000-01-01

Distinct locking and sampling light beams are used in a cavity ring-down spectroscopy (CRDS) system to perform multiple ring-down measurements while the laser and ring-down cavity are continuously locked. The sampling and locking light beams have different frequencies, to ensure that the sampling and locking light are decoupled within the cavity. Preferably, the ring-down cavity is ring-shaped, the sampling light is s-polarized, and the locking light is p-polarized. Transmitted sampling light is used for ring-down measurements, while reflected locking light is used for locking in a Pound-Drever scheme.

DMINDA: an integrated web server for DNA motif identification and analyses

PubMed Central

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-01-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. PMID:24753419

Redetermined structure, inter-molecular inter-actions and absolute configuration of royleanone.

PubMed

Fun, Hoong-Kun; Chantrapromma, Suchada; Salae, Abdul Wahab; Razak, Ibrahim Abdul; Karalai, Chatchanok

2011-05-01

The structure of the title diterpenoid, C(20)H(28)O(3), {systematic name: (4bS,8aS)-3-hy-droxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octa-hydro-phenanthrene-1,4-dione} is confirmed [Eugster et al. (1993 ▶). Private communication (refcode HACGUN). CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclo-hexane ring adopts a chair conformation whereas the other cyclo-hexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intra-molecular O-H⋯O hydrogen bond generates an S(5) ring motif. In the crystal, mol-ecules are linked into chains along [010] by O-H⋯O hydrogen bonds and weak C-H⋯O inter-actions. The packing also features C⋯O [3.131 (3) Å] short contacts.

SCOPE: a web server for practical de novo motif discovery.

PubMed

Carlson, Jonathan M; Chakravarty, Arijit; DeZiel, Charles E; Gross, Robert H

2007-07-01

SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three component algorithms, each designed to identify a particular class of motifs. Using an ensemble learning approach, SCOPE identifies the best candidate motifs from its component algorithms. In tests on experimentally determined datasets, SCOPE identified motifs with a significantly higher level of accuracy than a number of other web-based motif finders run with their default parameters. Because SCOPE has no adjustable parameters, the web server has an intuitive interface, requiring only a set of gene names or FASTA sequences and a choice of species. The most significant motifs found by SCOPE are displayed graphically on the main results page with a table containing summary statistics for each motif. Detailed motif information, including the sequence logo, PWM, consensus sequence and specific matching sites can be viewed through a single click on a motif. SCOPE's efficient, parameter-free search strategy has enabled the development of a web server that is readily accessible to the practising biologist while providing results that compare favorably with those of other motif finders. The SCOPE web server is at .

Identifying novel sequence variants of RNA 3D motifs

PubMed Central

Zirbel, Craig L.; Roll, James; Sweeney, Blake A.; Petrov, Anton I.; Pirrung, Meg; Leontis, Neocles B.

2015-01-01

Predicting RNA 3D structure from sequence is a major challenge in biophysics. An important sub-goal is accurately identifying recurrent 3D motifs from RNA internal and hairpin loop sequences extracted from secondary structure (2D) diagrams. We have developed and validated new probabilistic models for 3D motif sequences based on hybrid Stochastic Context-Free Grammars and Markov Random Fields (SCFG/MRF). The SCFG/MRF models are constructed using atomic-resolution RNA 3D structures. To parameterize each model, we use all instances of each motif found in the RNA 3D Motif Atlas and annotations of pairwise nucleotide interactions generated by the FR3D software. Isostericity relations between non-Watson–Crick basepairs are used in scoring sequence variants. SCFG techniques model nested pairs and insertions, while MRF ideas handle crossing interactions and base triples. We use test sets of randomly-generated sequences to set acceptance and rejection thresholds for each motif group and thus control the false positive rate. Validation was carried out by comparing results for four motif groups to RMDetect. The software developed for sequence scoring (JAR3D) is structured to automatically incorporate new motifs as they accumulate in the RNA 3D Motif Atlas when new structures are solved and is available free for download. PMID:26130723

A flexible motif search technique based on generalized profiles.

PubMed

Bucher, P; Karplus, K; Moeri, N; Hofmann, K

1996-03-01

A flexible motif search technique is presented which has two major components: (1) a generalized profile syntax serving as a motif definition language; and (2) a motif search method specifically adapted to the problem of finding multiple instances of a motif in the same sequence. The new profile structure, which is the core of the generalized profile syntax, combines the functions of a variety of motif descriptors implemented in other methods, including regular expression-like patterns, weight matrices, previously used profiles, and certain types of hidden Markov models (HMMs). The relationship between generalized profiles and other biomolecular motif descriptors is analyzed in detail, with special attention to HMMs. Generalized profiles are shown to be equivalent to a particular class of HMMs, and conversion procedures in both directions are given. The conversion procedures provide an interpretation for local alignment in the framework of stochastic models, allowing for clear, simple significance tests. A mathematical statement of the motif search problem defines the new method exactly without linking it to a specific algorithmic solution. Part of the definition includes a new definition of disjointness of alignments.

Triadic motifs in the dependence networks of virtual societies.

PubMed

Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

2014-06-10

In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

Triadic motifs in the dependence networks of virtual societies

NASA Astrophysics Data System (ADS)

Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

2014-06-01

In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

Triadic motifs in the dependence networks of virtual societies

PubMed Central

Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

2014-01-01

In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs. PMID:24912755

The conserved RNA recognition motif and C3H1 domain of the Not4 ubiquitin ligase regulate in vivo ligase function.

PubMed

Chen, Hongfeng; Sirupangi, Tirupataiah; Wu, Zhao-Hui; Johnson, Daniel L; Laribee, R Nicholas

2018-05-25

The Ccr4-Not complex controls RNA polymerase II (Pol II) dependent gene expression and proteasome function. The Not4 ubiquitin ligase is a Ccr4-Not subunit that has both a RING domain and a conserved RNA recognition motif and C3H1 domain (referred to as the RRM-C domain) with unknown function. We demonstrate that while individual Not4 RING or RRM-C mutants fail to replicate the proteasomal defects found in Not4 deficient cells, mutation of both exhibits a Not4 loss of function phenotype. Transcriptome analysis revealed that the Not4 RRM-C affects a specific subset of Pol II-regulated genes, including those involved in transcription elongation, cyclin-dependent kinase regulated nutrient responses, and ribosomal biogenesis. The Not4 RING, RRM-C, or RING/RRM-C mutations cause a generalized increase in Pol II binding at a subset of these genes, yet their impact on gene expression does not always correlate with Pol II recruitment which suggests Not4 regulates their expression through additional mechanisms. Intriguingly, we find that while the Not4 RRM-C is dispensable for Ccr4-Not association with RNA Pol II, the Not4 RING domain is required for these interactions. Collectively, these data elucidate previously unknown roles for the conserved Not4 RRM-C and RING domains in regulating Ccr4-Not dependent functions in vivo.

Inhomogeneous molecular ring around the B[e] supergiant LHA 120-S 73

NASA Astrophysics Data System (ADS)

Kraus, M.; Cidale, L. S.; Arias, M. L.; Maravelias, G.; Nickeler, D. H.; Torres, A. F.; Borges Fernandes, M.; Aret, A.; Curé, M.; Vallverdú, R.; Barbá, R. H.

2016-10-01

line profile is strongly variable in both width and shape and resembles of those seen in non-radially pulsating stars. A proper determination of the real underlying stellar rotation velocity is hence not possible. Conclusions: The existence of multiple stable and clumpy rings of alternating density recalls ring structures around planets. Although there is currently insufficient observational evidence, it is tempting to propose a scenario with one (or more) minor bodies or planets revolving around LHA 120-S 73 and stabilizing the ring system, in analogy to the shepherd moons in planetary systems. Based on observations: (1) with the 1.52-m and 2.2-m telescopes at the European Southern Observatory (La Silla, Chile), under the programme 076.D-0609(A) and under the agreement with the Observatório Nacional-MCT (Brazil); (2) at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the Science and Technology Facilities Council (United Kingdom), the National Research Council (Canada), CONICYT (Chile), the Australian Research Council (Australia), Ministério da Ciência, Tecnologia e Inovação (Brazil) and Ministerio de Ciencia, Tecnología e Innovación Productiva (Argentina), under the programmes GS-2004B-Q-54, GS-2010B-Q-31, and GS-2012B-Q-90; (3) at Complejo Astronómico El Leoncito operated under agreement between the Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina and the National Universities of La Plata, Córdoba and San Juan (Visiting Astronomer: A.F.T.); and (4) with the du Pont Telescope at Las Campanas Observatory, Chile, under the programme CNTAC 2008-02 (Visiting Astronomer: R.B. and A.F.T.).Presented spectroscopic data are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http

Unravelling daily human mobility motifs

PubMed Central

Schneider, Christian M.; Belik, Vitaly; Couronné, Thomas; Smoreda, Zbigniew; González, Marta C.

2013-01-01

Human mobility is differentiated by time scales. While the mechanism for long time scales has been studied, the underlying mechanism on the daily scale is still unrevealed. Here, we uncover the mechanism responsible for the daily mobility patterns by analysing the temporal and spatial trajectories of thousands of persons as individual networks. Using the concept of motifs from network theory, we find only 17 unique networks are present in daily mobility and they follow simple rules. These networks, called here motifs, are sufficient to capture up to 90 per cent of the population in surveys and mobile phone datasets for different countries. Each individual exhibits a characteristic motif, which seems to be stable over several months. Consequently, daily human mobility can be reproduced by an analytically tractable framework for Markov chains by modelling periods of high-frequency trips followed by periods of lower activity as the key ingredient. PMID:23658117

Cassini First Diametric Radio Occultation of Saturn's Rings

NASA Astrophysics Data System (ADS)

Marouf, E.; French, R.; Rappaport, N.; Kliore, A.; Flasar, M.; Nagy, A.; Ambrosini, R.; McGhee, C.; Schinder, P.; Anabtawi, A.; Barbinis, E.; Goltz, G.; Thomson, F.; Wong, K.

2005-05-01

We present preliminary results expected from the first planned Cassini radio occultation observation of Saturn's rings, to be conducted on May 3rd, 2005. The path of Cassini as seen from Earth (the occultation track) has been designed to cross the rings from the west to the east ansa almost diametrically, allowing for occultation of all major ring features at two widely separated longitudes (about 180 deg apart). The duration of the geometric occultation is about 1.5 hours on each side. During the occultation, Cassini transmits through the rings three coherent monochromatic radio signals of wavelength 0.94, 3.6, and 13 cm (Ka-, X-, and S-band respectively), a capability unique to Cassini. The perturbed signals received at the Earth are recorded at the NASA DSN complexes at Goldstone and Canberra. Both direct and forward-scattered components of the signal may be identified in spectrograms of the received signals. The time history of the extinction of the direct signal is expected to yield high-spatial-resolution optical depth and phase shift profiles of ring structure. The timing of the occultation was optimized to allow probing the rings when the ring-opening-angle B (the angle between the line-of-sight and the ring plane) is relatively large (B = 23 deg), hence maximizing chances of measuring for the first time the structure of the relatively optically thick Ring B. In a similar experiment by Voyager in 1980, excessive signal attenuation along the long path within the nearly closed rings (B = 5.9 deg) limited the utility of the observations in relatively thick ring regions, in particular the main Ring B. For the Cassini optimized occultation geometry, a large B, slow radial velocity along the occultation track, and much improved phase stability of the reference ultrastable oscillator (USO) on board Cassini combine to promise achievable radial resolution approaching 100 m over a good fraction of the rings. Measurement of the amplitude and phase of the diffracted

Cathepsin K activity-dependent regulation of osteoclast actin ring formation and bone resorption.

PubMed

Wilson, Susan R; Peters, Christoph; Saftig, Paul; Brömme, Dieter

2009-01-23

Cathepsin K is responsible for the degradation of type I collagen in osteoclast-mediated bone resorption. Collagen fragments are known to be biologically active in a number of cell types. Here, we investigate their potential to regulate osteoclast activity. Mature murine osteoclasts were seeded on type I collagen for actin ring assays or dentine discs for resorption assays. Cells were treated with cathepsins K-, L-, or MMP-1-predigested type I collagen or soluble bone fragments for 24 h. The presence of actin rings was determined fluorescently by staining for actin. We found that the percentage of osteoclasts displaying actin rings and the area of resorbed dentine decreased significantly on addition of cathepsin K-digested type I collagen or bone fragments, but not with cathepsin L or MMP-1 digests. Counterintuitively, actin ring formation was found to decrease in the presence of the cysteine proteinase inhibitor LHVS and in cathepsin K-deficient osteoclasts. However, cathepsin L deficiency or the general MMP inhibitor GM6001 had no effect on the presence of actin rings. Predigestion of the collagen matrix with cathepsin K, but not by cathepsin L or MMP-1 resulted in an increased actin ring presence in cathepsin K-deficient osteoclasts. These studies suggest that cathepsin K interaction with type I collagen is required for 1) the release of cryptic Arg-Gly-Asp motifs during the initial attachment of osteoclasts and 2) termination of resorption via the creation of autocrine signals originating from type I collagen degradation.

User's guide to computer programs JET 5A and CIVM-JET 5B to calculate the large elastic-plastic dynamically-induced deformations of multilayer partial and/or complete structural rings

NASA Technical Reports Server (NTRS)

Wu, R. W. H.; Stagliano, T. R.; Witmer, E. A.; Spilker, R. L.

1978-01-01

These structural ring deflections lie essentially in one plane and, hence, are called two-dimensional (2-d). The structural rings may be complete or partial; the former may be regarded as representing a fragment containment ring while the latter may be viewed as a 2-d fragment-deflector structure. These two types of rings may be either free or supported in various ways (pinned-fixed, locally clamped, elastic-foundation supported, mounting-bracket supported, etc.). The initial geometry of each ring may be circular or arbitrarily curved; uniform-thickness or variable-thickness rings may be analyzed. Strain-hardening and strain-rate effects of initially-isotropic material are taken into account. An approximate analysis utilizing kinetic energy and momentum conservation relations is used to predict the after-impact velocities of each fragment and of the impact-affected region of the ring; this procedure is termed the collision-imparted velocity method (CIVM) and is used in the CIVM-JET 5 B program. This imparted-velocity information is used in conjunction with a finite-element structural response computation code to predict the transient, large-deflection, elastic-plastic responses of the ring. Similarly, the equations of motion of each fragment are solved in small steps in time. Provisions are made in the CIVM-JET 5B code to analyze structural ring response to impact attack by from 1 to 3 fragments, each with its own size, mass, translational velocity components, and rotational velocity. The effects of friction between each fragment and the impacted ring are included.

Warped Disks and Inclined Rings around Galaxies

NASA Astrophysics Data System (ADS)

Casertano, Stefano; Sackett, Penny D.; Briggs, Franklin H.

2006-11-01

Preface; Acknowledgements; Workshop participants; Group photograph; 1. The intergalactic HI supply F. Briggs; 2. Neutral gas infall into NGC 628 J. Kamphuis and F. Briggs; 3. VLA HI observations of the radio galaxy Centaurus A J. M. van der Hulst, J. H. van Gorkom, A. D. Haschick and A. D. Tubbs; 4. A geometric model for the dust-band of Centaurus A R. A. Nicholson, K. Taylor and J. Bland; 5. The circumgalactic ring of gas in Leo S. E. Schneider; 6. Using gas kinematics to measure M/L in elliptical galaxies T. de Zeeuw; 7. Velocity fields of disks in triaxial potentials P. J. Teuben; 8. Modeling the atomic gas in NGC 4278 J. F. Lees; 9. A few statistics from the catalog of polar-ring galaxies B. C. Whitmore; 10. Dynamics of polar rings L. S. Sparke; 11. Mergers and the structure of disk galaxies L. Hernquist; 12. Formation of polar rings H.-W. Rix and N. Katz; 13. Gas-dynamical models of settling disks D. Christodoulou and J. E. Tohline; 14. Evolutionary processes affecting galactic accretion disks T. Steiman-Cameron; 15. Particle simulations of polar rings T. Quinn; 16. A bending instability in prolate stellar systems D. Merritt; 17. The Milky Way: lopsided or barred? K. Kuijken; 18. Merger origin of starburst galaxies L. Hernquist; 19. Warped and flaring HI disks A. Bosma; 20. Behaviour of warps in extended disks F. Briggs and J. Kamphuis; 21. Observational constraints for the explanation of warps E. Battaner, E. Florido, M.-L. Sanchez-Saavedra and M. Prieto; 22. Warps in S0s: observations versus theories G. Galletta; 23. Warps and bulges J. Pitesky; 24. Time evolution of galactic warps P. Hofner and L. S. Sparke; 25. Are warps normal modes? S. Casertano; 26. Disk warping in a slewing potential E. C. Ostriker; 27. Concluding discussion Moderator: K. C. Freeman; Name index; Object index; Subject index.

Crystal structures of three indole derivatives: 3-ethnyl-2-methyl-1-phenyl­sulfonyl-1H-indole, 4-phenyl­sulfonyl-3H,4H-cyclo­penta­[b]indol-1(2H)-one and 1-{2-[(E)-2-(5-chloro-2-nitro­phen­yl)ethen­yl]-1-phenyl­sulfonyl-1H-indol-3-yl}ethan-1-one chloro­form monosolvate

PubMed Central

Gopinath, S.; Sethusankar, K.; Ramalingam, Bose Muthu; Mohanakrishnan, Arasambattu K.

2015-01-01

The title compounds, C17H13NO2S, (I), C17H13NO3S, (II), and C24H17ClN2O5S·CHCl3, (III), are indole derivatives. Compounds (I) and (II) crystalize with two independent mol­ecules in the asymmetric unit. The indole ring systems in all three structures deviate only slightly from planarity, with dihedral angles between the planes of the pyrrole and benzene rings spanning the tight range 0.20 (9)–1.65 (9)°. These indole ring systems, in turn, are almost orthogonal to the phenyl­sulfonyl rings [range of dihedral angles between mean planes = 77.21 (8)–89.26 (8)°]. In the three compounds, the mol­ecular structure is stabilized by intra­molecular C—H⋯O hydrogen bonds, generating S(6) ring motifs with the sulfone O atom. In compounds (I) and (II), the two independent mol­ecules are linked by C—H⋯O hydrogen bonds and C—H⋯π inter­actions, while in compound (III), the mol­ecules are linked by C—H⋯O hydrogen bonds, generating R 2 2(22) inversion dimers. PMID:26396842

N′-[(E)-4-Hydr­oxy-3-methoxy­benzyl­idene]pyridine-4-carbohydrazide

PubMed Central

Shafiq, Zahid; Yaqub, Muhammad; Tahir, M. Nawaz; Hussain, Abid; Iqbal, M. Saeed

2009-01-01

In the title compound, C14H13N3O3, the two six-membered rings are oriented at a dihedral angle of 15.17 (11)° and an intra­molecular O—H⋯O hydrogen bond occurs. In the crystal, mol­ecules inter­act by way of N—H⋯O, O—H⋯N and C—H⋯O hydrogen bonds, thereby generating S(5) chain and R 2 1(7) ring motifs. PMID:21578481

What Confines the Rings of Saturn?

NASA Astrophysics Data System (ADS)

Tajeddine, Radwan; Nicholson, Philip D.; Longaretti, Pierre-Yves; El Moutamid, Maryame; Burns, Joseph A.

2017-10-01

The viscous spreading of planetary rings is believed to be counteracted by satellite torques, through either an individual resonance or overlapping resonances. For the A ring of Saturn, it has been commonly believed that the satellite Janus alone can prevent the ring from spreading, via its 7:6 Lindblad resonance. We discuss this common misconception and show that, in reality, the A ring is confined by the contributions from the group of satellites Pan, Atlas, Prometheus, Pandora, Janus, Epimetheus, and Mimas, whose cumulative torques from various resonances gradually decrease the angular momentum flux transported outward through the ring via density and bending waves. We further argue that this decrease in angular momentum flux occurs through “flux reversal.” Furthermore, we use the magnitude of the satellites’ resonance torques to estimate the effective viscosity profile across the A ring, showing that it decreases with radius from ˜50 cm2 s-1 to less than ˜10 cm2 s-1. The gradual estimated decrease of the angular momentum flux and effective viscosity are roughly consistent with results obtained by balancing the shepherding torques from Pan and Daphnis with the viscous torque at the edges of the Encke and Keeler gaps, as well as the edge of the A ring. On the other hand, the Mimas 2:1 Lindblad resonance alone seems to be capable of confining the edge of the B ring, and contrary to the situation in the A ring, we show that the effective viscosity across the B ring is relatively constant at ˜24-30 cm2 s-1.

Helix–hairpin–helix motifs confer salt resistance and processivity on chimeric DNA polymerases

PubMed Central

Pavlov, Andrey R.; Belova, Galina I.; Kozyavkin, Sergei A.; Slesarev, Alexei I.

2002-01-01

Helix–hairpin–helix (HhH) is a widespread motif involved in sequence-nonspecific DNA binding. The majority of HhH motifs function as DNA-binding modules with typical occurrence of one HhH motif or one or two (HhH)2 domains in proteins. We recently identified 24 HhH motifs in DNA topoisomerase V (Topo V). Although these motifs are dispensable for the topoisomerase activity of Topo V, their removal narrows the salt concentration range for topoisomerase activity tenfold. Here, we demonstrate the utility of Topo V's HhH motifs for modulating DNA-binding properties of the Stoffel fragment of TaqDNA polymerase and Pfu DNA polymerase. Different HhH cassettes fused with either NH2 terminus or COOH terminus of DNA polymerases broaden the salt concentration range of the polymerase activity significantly (up to 0.5 M NaCl or 1.8 M potassium glutamate). We found that anions play a major role in the inhibition of DNA polymerase activity. The resistance of initial extension rates and the processivity of chimeric polymerases to salts depend on the structure of added HhH motifs. Regardless of the type of the construct, the thermal stability of chimeric Taq polymerases increases under the optimal ionic conditions, as compared with that of TaqDNA polymerase or its Stoffel fragment. Our approach to raise the salt tolerance, processivity, and thermostability of Taq and Pfu DNA polymerases may be applied to all pol1- and polB-type polymerases, as well as to other DNA processing enzymes. PMID:12368475

A dinucleotide motif in oligonucleotides shows potent immunomodulatory activity and overrides species-specific recognition observed with CpG motif.

PubMed

Kandimalla, Ekambar R; Bhagat, Lakshmi; Zhu, Fu-Gang; Yu, Dong; Cong, Yan-Ping; Wang, Daqing; Tang, Jimmy X; Tang, Jin-Yan; Knetter, Cathrine F; Lien, Egil; Agrawal, Sudhir

2003-11-25

Bacterial and synthetic DNAs containing CpG dinucleotides in specific sequence contexts activate the vertebrate immune system through Toll-like receptor 9 (TLR9). In the present study, we used a synthetic nucleoside with a bicyclic heterobase [1-(2'-deoxy-beta-d-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine; R] to replace the C in CpG, resulting in an RpG dinucleotide. The RpG dinucleotide was incorporated in mouse- and human-specific motifs in oligodeoxynucleotides (oligos) and 3'-3-linked oligos, referred to as immunomers. Oligos containing the RpG motif induced cytokine secretion in mouse spleen-cell cultures. Immunomers containing RpG dinucleotides showed activity in transfected-HEK293 cells stably expressing mouse TLR9, suggesting direct involvement of TLR9 in the recognition of RpG motif. In J774 macrophages, RpG motifs activated NF-kappa B and mitogen-activated protein kinase pathways. Immunomers containing the RpG dinucleotide induced high levels of IL-12 and IFN-gamma, but lower IL-6 in time- and concentration-dependent fashion in mouse spleen-cell cultures costimulated with IL-2. Importantly, immunomers containing GTRGTT and GARGTT motifs were recognized to a similar extent by both mouse and human immune systems. Additionally, both mouse- and human-specific RpG immunomers potently stimulated proliferation of peripheral blood mononuclear cells obtained from diverse vertebrate species, including monkey, pig, horse, sheep, goat, rat, and chicken. An immunomer containing GTRGTT motif prevented conalbumin-induced and ragweed allergen-induced allergic inflammation in mice. We show that a synthetic bicyclic nucleotide is recognized in the C position of a CpG dinucleotide by immune cells from diverse vertebrate species without bias for flanking sequences, suggesting a divergent nucleotide motif recognition pattern of TLR9.

Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints.

PubMed

Niv, Masha Y; Skrabanek, Lucy; Roberts, Richard J; Scheraga, Harold A; Weinstein, Harel

2008-05-01

Restriction endonucleases (REases) are DNA-cleaving enzymes that have become indispensable tools in molecular biology. Type II REases are highly divergent in sequence despite their common structural core, function and, in some cases, common specificities towards DNA sequences. This makes it difficult to identify and classify them functionally based on sequence, and has hampered the efforts of specificity-engineering. Here, we define novel REase sequence motifs, which extend beyond the PD-(D/E)XK hallmark, and incorporate secondary structure information. The automated search using these motifs is carried out with a newly developed fast regular expression matching algorithm that accommodates long patterns with optional secondary structure constraints. Using this new tool, named Scan2S, motifs derived from REases with specificity towards GATC- and CGGG-containing DNA sequences successfully identify REases of the same specificity. Notably, some of these sequences are not identified by standard sequence detection tools. The new motifs highlight potential specificity-determining positions that do not fully overlap for the GATC- and the CCGG-recognizing REases and are candidates for specificity re-engineering.

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance.

PubMed

Casimiro, Ana C; Vinga, Susana; Freitas, Ana T; Oliveira, Arlindo L

2008-02-07

Motif finding algorithms have developed in their ability to use computationally efficient methods to detect patterns in biological sequences. However the posterior classification of the output still suffers from some limitations, which makes it difficult to assess the biological significance of the motifs found. Previous work has highlighted the existence of positional bias of motifs in the DNA sequences, which might indicate not only that the pattern is important, but also provide hints of the positions where these patterns occur preferentially. We propose to integrate position uniformity tests and over-representation tests to improve the accuracy of the classification of motifs. Using artificial data, we have compared three different statistical tests (Chi-Square, Kolmogorov-Smirnov and a Chi-Square bootstrap) to assess whether a given motif occurs uniformly in the promoter region of a gene. Using the test that performed better in this dataset, we proceeded to study the positional distribution of several well known cis-regulatory elements, in the promoter sequences of different organisms (S. cerevisiae, H. sapiens, D. melanogaster, E. coli and several Dicotyledons plants). The results show that position conservation is relevant for the transcriptional machinery. We conclude that many biologically relevant motifs appear heterogeneously distributed in the promoter region of genes, and therefore, that non-uniformity is a good indicator of biological relevance and can be used to complement over-representation tests commonly used. In this article we present the results obtained for the S. cerevisiae data sets.

Comparing CTH simulations and experiments on explosively loaded rings

NASA Astrophysics Data System (ADS)

Braithwaite, C. H.; Aydelotte, Brady; Collins, Adam; Thadhani, Naresh; Williamson, David Martin

2012-03-01

A series of experiments were conducted on explosively loaded metallic rings for the purpose of studying fragmentation. In addition to the collection of fragments for analysis, the radial velocity of the expanding ring was measured with photon Doppler velocimetry (PDV) and the arrangement was imaged using high speed photography. Both the ring material and the material used as the explosive container were altered and the results compared with simulations performed in CTH. Good agreement was found between the simulations and the experiments. The maximum radial velocity attained was approximately 380 m/s, which was achieved through loading with a 5g PETN based charge.

Strength Performance Assessment in a Simulated Men’s Gymnastics Still Rings Cross

PubMed Central

Dunlavy, Jennifer K.; Sands, William A.; McNeal, Jeni R.; Stone, Michael H.; Smith, Sarah L.; Jemni, Monem; Haff, G. Gregory

2007-01-01

Athletes in sports such as the gymnastics who perform the still rings cross position are disadvantaged due to a lack of objective and convenient measurement methods. The gymnastics “cross ”is a held isometric strength position considered fundamental to all still rings athletes. The purpose of this investigation was to determine if two small force platforms (FPs) placed on supports to simulate a cross position could demonstrate the fidelity necessary to differentiate between athletes who could perform a cross from those who could not. Ten gymnasts (5 USA Gymnastics, Senior National Team, and 5 Age Group Level Gymnasts) agreed to participate. The five Senior National Team athletes were grouped as cross Performers; the Age Group Gymnasts could not successfully perform the cross position and were grouped as cross Non- Performers. The two small FPs were first tested for reliability and validity and were then used to obtain a force-time record of a simulated cross position. The simulated cross test consisted of standing between two small force platforms placed on top of large solid gymnastics spotting blocks. The gymnasts attempted to perform a cross position by placing their hands at the center of the FPs and pressing downward with sufficient force that they could remove the support of their feet from the floor. Force-time curves (100 Hz) were obtained and analyzed for the sum of peak and mean arm ground reaction forces. The summed arm forces, mean and peak, were compared to body weight to determine how close the gymnasts came to achieving forces equal to body weight and thus the ability to perform the cross. The mean and peak summed arm forces were able to statistically differentiate between athletes who could perform the cross from those who could not (p < 0.05). The force-time curves and small FPs showed sufficient fidelity to differentiate between Performer and Non- Performer groups. This experiment showed that small and inexpensive force platforms may serve as

Acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicyclo[2.2.1]hept-5-ene with alcohols.

PubMed

Tait, Katrina; Horvath, Alysia; Blanchard, Nicolas; Tam, William

2017-01-01

The acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicylic alkene using alcohol nucleophiles were investigated. Although this acid-catalyzed ring-opening reaction did not cleave the cyclopropane unit as planned, this represent the first examples of ring-openings of cyclopropanated 3-aza-2-oxabicyclo[2.2.1]alkenes that lead to the cleavage of the C-O bond instead of the N-O bond. Different acid catalysts were tested and it was found that pyridinium toluenesulfonate in methanol gave the best yields in the ring-opening reactions. The scope of the reaction was successfully expanded to include primary, secondary, and tertiary alcohol nucleophiles. Through X-ray crystallography, the stereochemistry of the product was determined which confirmed an S N 2-like mechanism to form the ring-opened product.

RING E3 mechanism for ubiquitin ligation to a disordered substrate visualized for human anaphase-promoting complex

DOE PAGES

Brown, Nicholas G.; VanderLinden, Ryan; Watson, Edmond R.; ...

2015-03-30

For many E3 ligases, a mobile RING (Really Interesting New Gene) domain stimulates ubiquitin (Ub) transfer from a thioester-linked E2~Ub intermediate to a lysine on a remotely bound disordered substrate. One such E3 is the gigantic, multisubunit 1.2-MDa anaphase-promoting complex/cyclosome (APC), which controls cell division by ubiquitinating cell cycle regulators to drive their timely degradation. Intrinsically disordered substrates are typically recruited via their KEN-box, D-box, and/or other motifs binding to APC and a coactivator such as CDH1. On the opposite side of the APC, the dynamic catalytic core contains the cullin-like subunit APC2 and its RING partner APC11, which collaboratesmore » with the E2 UBCH10 (UBE2C) to ubiquitinate substrates. However, how dynamic RING–E2~Ub catalytic modules such as APC11–UBCH10~Ub collide with distally tethered disordered substrates remains poorly understood. In this paper, we report structural mechanisms of UBCH10 recruitment to APC CDH1 and substrate ubiquitination. Unexpectedly, in addition to binding APC11’s RING, UBCH10 is corecruited via interactions with APC2, which we visualized in a trapped complex representing an APC CDH1–UBCH10~Ub–substrate intermediate by cryo-electron microscopy, and in isolation by X-ray crystallography. To our knowledge, this is the first structural view of APC, or any cullin–RING E3, with E2 and substrate juxtaposed, and it reveals how tripartite cullin–RING–E2 interactions establish APC’s specificity for UBCH10 and harness a flexible catalytic module to drive ubiquitination of lysines within an accessible zone. Finally, we propose that multisite interactions reduce the degrees of freedom available to dynamic RING E3–E2~Ub catalytic modules, condense the search radius for target lysines, increase the chance of active-site collision with conformationally fluctuating substrates, and enable regulation.« less

STEME: A Robust, Accurate Motif Finder for Large Data Sets

PubMed Central

Reid, John E.; Wernisch, Lorenz

2014-01-01

Motif finding is a difficult problem that has been studied for over 20 years. Some older popular motif finders are not suitable for analysis of the large data sets generated by next-generation sequencing. We recently published an efficient approximation (STEME) to the EM algorithm that is at the core of many motif finders such as MEME. This approximation allows the EM algorithm to be applied to large data sets. In this work we describe several efficient extensions to STEME that are based on the MEME algorithm. Together with the original STEME EM approximation, these extensions make STEME a fully-fledged motif finder with similar properties to MEME. We discuss the difficulty of objectively comparing motif finders. We show that STEME performs comparably to existing prominent discriminative motif finders, DREME and Trawler, on 13 sets of transcription factor binding data in mouse ES cells. We demonstrate the ability of STEME to find long degenerate motifs which these discriminative motif finders do not find. As part of our method, we extend an earlier method due to Nagarajan et al. for the efficient calculation of motif E-values. STEME's source code is available under an open source license and STEME is available via a web interface. PMID:24625410

SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana.

PubMed

Wu, Wenjuan; Liu, Sheng; Ruwe, Hannes; Zhang, Delin; Melonek, Joanna; Zhu, Yajuan; Hu, Xupeng; Gusewski, Sandra; Yin, Ping; Small, Ian D; Howell, Katharine A; Huang, Jirong

2016-03-01

Ribosomal RNA processing is essential for plastid ribosome biogenesis, but is still poorly understood in higher plants. Here, we show that SUPPRESSOR OF THYLAKOID FORMATION1 (SOT1), a plastid-localized pentatricopeptide repeat (PPR) protein with a small MutS-related domain, is required for maturation of the 23S-4.5S rRNA dicistron. Loss of SOT1 function leads to slower chloroplast development, suppression of leaf variegation, and abnormal 23S and 4.5S processing. Predictions based on the PPR motif sequences identified the 5' end of the 23S-4.5S rRNA dicistronic precursor as a putative SOT1 binding site. This was confirmed by electrophoretic mobility shift assay, and by loss of the abundant small RNA 'footprint' associated with this site in sot1 mutants. We found that more than half of the 23S-4.5S rRNA dicistrons in sot1 mutants contain eroded and/or unprocessed 5' and 3' ends, and that the endonucleolytic cleavage product normally released from the 5' end of the precursor is absent in a sot1 null mutant. We postulate that SOT1 binding protects the 5' extremity of the 23S-4.5S rRNA dicistron from exonucleolytic attack, and favours formation of the RNA structure that allows endonucleolytic processing of its 5' and 3' ends. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Enhanced thermal and mechanical properties of PLA/MoS2 nanocomposites synthesized via the in-situ ring-opening polymerization

NASA Astrophysics Data System (ADS)

Chen, Pengpeng; Liang, Xiao; Xu, Ying; Zhou, Yifeng; Nie, Wangyan

2018-05-01

In this work, MoS2 nanosheets were employed to reinforce PLA. In order to promote the homogeneous dispersion of MoS2 in PLA and form a strong interface between MoS2 and PLA, the MoS2 nanosheets were firstly modified by mercapto-ethylamine, and then functionalized with PLA chains through ring-opening polymerization of poly(L-lactide). The XRD, XPS, TGA and 1H NMR characterizations confirmed the successful amino and PLA functionalization of MoS2 nanosheets. The obtained MoS2-g-PLA nanosheets were then introduced to reinforce PLA. SEM images displayed that the MoS2-g-PLA nanosheets were dispersed in PLA matrix uniformly. TGA results showed that initial decomposition temperature was improved from 275.6 °C to 334.8 °C with 0.5 wt% of MoS2-g-PLA nanosheets. The storage modulus of PLA/MoS2-g-PLA-0.5 wt% in the glass state and rubber state were both greatly enhanced compared with neat PLA.

Cometabolic Degradation of Naproxen by Planococcus sp. Strain S5.

PubMed

Domaradzka, Dorota; Guzik, Urszula; Hupert-Kocurek, Katarzyna; Wojcieszyńska, Danuta

Naproxen is a non-steroidal anti-inflammatory drug frequently detected in the influent and effluent of sewage treatment plants. The Gram-positive strain Planococcus sp. S5 was able to remove approximately 30 % of naproxen after 35 days of incubation in monosubstrate culture. Under cometabolic conditions, with glucose or phenol as a growth substrate, the degradation efficiency of S5 increased. During 35 days of incubation, 75.14 ± 1.71 % and 86.27 ± 2.09 % of naproxen was degraded in the presence of glucose and phenol, respectively. The highest rate of naproxen degradation observed in the presence of phenol may be connected with the fact that phenol is known to induce enzymes responsible for aromatic ring cleavage. The activity of phenol monooxygenase, naphthalene monooxygenase, and hydroxyquinol 1,2-dioxygenase was indicated in Planococcus sp. S5 culture with glucose or phenol as a growth substrate. It is suggested that these enzymes may be engaged in naproxen degradation.

2-Hy-droxy-16-[(E)-4-methyl-benzyl-idene]-13-(4-methyl-phen-yl)-12-phenyl-1,11-diaza-penta-cyclo-[12.3.1.0.0.0]octa-deca-3(8),4,6-triene-9,15-dione.

PubMed

Kumar, Raju Suresh; Osman, Hasnah; Abdul Rahim, Aisyah Saad; Goh, Jia Hao; Fun, Hoong-Kun

2010-07-24

In the title compound, C(37)H(32)N(2)O(3), an intra-molecular O-H⋯N hydrogen bond generates a five-membered ring, producing an S(5) motif. The piperidone ring adopts a half-chair conformation. The two fused pyrrolidine rings have similar envelope conformations. The interplanar angles between the benzene rings A/B and C/D are 75.68 (7) and 30.22 (6)°, respectively. In the crystal structure, adjacent mol-ecules are inter-connected into chains propagating along the [010] direction via inter-molecular C-H⋯O hydrogen bonds. Further stabilization is provided by weak C-H⋯π inter-actions.

ATtRACT-a database of RNA-binding proteins and associated motifs.

PubMed

Giudice, Girolamo; Sánchez-Cabo, Fátima; Torroja, Carlos; Lara-Pezzi, Enrique

2016-01-01

RNA-binding proteins (RBPs) play a crucial role in key cellular processes, including RNA transport, splicing, polyadenylation and stability. Understanding the interaction between RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation in a global manner. Despite advances in recent years, a unified non-redundant resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this information is lacking. Here, we developed a database named ATtRACT (available athttp://attract.cnic.es) that compiles information on 370 RBPs and 1583 RBP consensus binding motifs, 192 of which are not present in any other database. To populate ATtRACT we (i) extracted and hand-curated experimentally validated data from CISBP-RNA, SpliceAid-F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein-RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discoveringde novomotifs enriched in a set of related sequences and compare them with the motifs included in the database.Database URL:http:// attract. cnic. es. © The Author(s) 2016. Published by Oxford University Press.

DNA motif alignment by evolving a population of Markov chains.

PubMed

Bi, Chengpeng

2009-01-30

Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

Automatic annotation of protein motif function with Gene Ontology terms.

PubMed

Lu, Xinghua; Zhai, Chengxiang; Gopalakrishnan, Vanathi; Buchanan, Bruce G

2004-09-02

Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, a much needed and important task is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO) project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. This paper presents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifs is viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association is found to be a very useful feature. We take advantage of the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correct association. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about the functions of newly discovered candidate protein motifs.

Basin-ring spacing on the Moon, Mercury, and Mars

USGS Publications Warehouse

Pike, R.J.; Spudis, P.D.

1987-01-01

Radial spacing between concentric rings of impact basins that lack central peaks is statistically similar and nonrandom on the Moon, Mercury, and Mars, both inside and outside the main ring. One spacing interval, (2.0 ?? 0.3)0.5D, or an integer multiple of it, dominates most basin rings. Three analytical approaches yield similar results from 296 remapped or newly mapped rings of 67 multi-ringed basins: least-squares of rank-grouped rings, least-squares of rank and ring diameter for each basin, and averaged ratios of adjacent rings. Analysis of 106 rings of 53 two-ring basins by the first and third methods yields an integer multiple (2 ??) of 2.00.5D. There are two exceptions: (1) Rings adjacent to the main ring of multi-ring basins are consistently spaced at a slightly, but significantly, larger interval, (2.1 ?? 0.3)0.5D; (2) The 88 rings of 44 protobasins (large peak-plus-inner-ring craters) are spaced at an entirely different interval (3.3 ?? 0.6)0.5D. The statistically constant and target-invariant spacing of so many rings suggests that this characteristic may constrain formational models of impact basins on the terrestrial planets. The key elements of such a constraint include: (1) ring positions may not have been located by the same process(es) that formed ring topography; (2) ring location and emplacement of ring topography need not be coeval; (3) ring location, but not necessarily the mode of ring emplacement, reflects one process that operated at the time of impact; and (4) the process yields similarly-disposed topographic features that are spatially discrete at 20.5D intervals, or some multiple, rather than continuous. These four elements suggest that some type of wave mechanism dominates the location, but not necessarily the formation, of basin rings. The waves may be standing, rather than travelling. The ring topography itself may be emplaced at impact by this and/or other mechanisms and may reflect additional, including post-impact, influences. ?? 1987

Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

PubMed Central

Chatterjee, Raghunath; Zhao, Jianfei; He, Ximiao; Shlyakhtenko, Andrey; Mann, Ishminder; Waterfall, Joshua J.; Meltzer, Paul; Sathyanarayana, B. K.; FitzGerald, Peter C.; Vinson, Charles

2012-01-01

Previously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promoters and grouped them into known transcription factor binding sites (TFBS). We now examine split 8-mers consisting of two 4-mers separated by 1-bp to 30-bps (X4-N1-30-X4) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif (C/GCCGGAAGCGGAA) and the ETS⇔CRE motif (C/GCGGAAGTGACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETS⇔CRE motif can be bound simultaneously by both the ETS and the B-ZIP domains without protein-protein clashes. The electrophoretic mobility shift assay (EMSA) shows that the ETS protein GABPα and the B-ZIP protein CREB preferentially bind to the ETS⇔CRE motif only when the two TFBS overlap precisely. In contrast, the ETS domain of ETV5 and CREB interfere with each other for binding the ETS⇔CRE. The 11-mer (CGGAAGTGACG), the conserved part of the ETS⇔CRE motif, occurs 226 times in the human genome and 83% are in known regulatory regions. In vivo GABPα and CREB ChIP-seq peaks identified the ETS⇔CRE as the most enriched motif occurring in promoters of genes involved in mRNA processing, cellular catabolic processes, and stress response, suggesting that a specific class of genes is regulated by this composite motif. PMID:23050235

Cassini RSS occultation observations of density waves in Saturn's rings

NASA Astrophysics Data System (ADS)

McGhee, C. A.; French, R. G.; Marouf, E. A.; Rappaport, N. J.; Schinder, P. J.; Anabtawi, A.; Asmar, S.; Barbinis, E.; Fleischman, D.; Goltz, G.; Johnston, D.; Rochblatt, D.

2005-08-01

On May 3, 2005, the first of a series of eight nearly diametric occultations by Saturn's rings and atmosphere took place, observed by the Cassini Radio Science (RSS) team. Simultaneous high SNR measurements at the Deep Space Network (DSN) at S, X, and Ka bands (λ = 13, 3.6, and 0.9 cm) have provided a remarkably detailed look at the radial structure and particle scattering behavior of the rings. By virtue of the relatively large ring opening angle (B=-23.6o), the slant path optical depth of the rings was much lower than during the Voyager epoch (B=5.9o), making it possible to detect many density waves and other ring features in the Cassini RSS data that were lost in the noise in the Voyager RSS experiment. Ultimately, diffraction correction of the ring optical depth profiles will yield radial resolution as small as tens of meters for the highest SNR data. At Ka band, the Fresnel scale is only 1--1.5 km, and thus even without diffraction correction, the ring profiles show a stunning array of density waves. The A ring is replete with dozens of Pandora and Prometheus inner Lindblad resonance features, and the Janus 2:1 density wave in the B ring is revealed with exceptional clarity for the first time at radio wavelengths. Weaker waves are abundant as well, and multiple occultation chords sample a variety of wave phases. We estimate the surface mass density of the rings from linear density wave models of the weaker waves. For stronger waves, non-linear models are required, providing more accurate estimates of the wave dispersion relation, the ring surface mass density, and the angular momentum exchange between the rings and satellite. We thank the DSN staff for their superb support of these complex observations.

What confines the rings of Saturn?

NASA Astrophysics Data System (ADS)

Tajeddine, Radwan; Nicholson, Philip D.; El Moutamid, Maryame; Longaretti, Pierre-Yves; Burns, Joseph A.

2017-10-01

The viscous spreading of planetary rings is believed to be counteracted by satellite torques, either through an individual resonance or through overlapping resonances (when the satellite is close to the ring edge). For the A ring of Saturn, it has been commonly believed that the satellite Janus alone can prevent the ring from spreading via its 7:6 Lindblad resonance. We discuss this common misconception and show that, in reality, the A ring is confined by the contributions from the group of satellites Pan, Atlas, Prometheus, Pandora, Janus, Epimetheus, and Mimas, whose resonances gradually decrease the angular momentum flux transported outward through the ring via density and bending waves. We further argue that this decrease in angular momentum flux occurs through the mechanism of ‘flux reversal’.We find that the Janus 7:6 torque is relatively feeble, as is the comparable torque of the nearby small satellite Atlas, each amounting to less than one-tenth of the angular momentum transport carried by the A ring. But the cumulative torques of the many other satellite resonances in the A ring sufficiently reduce the angular momentum flux through the rings so that the torques due to Janus and Atlas are effective in confining the outer edge of the ring.Furthermore, we use the magnitude of the satellites’ resonance torques to estimate the effective viscosity profile across the A ring, showing that it decreases from ~50 cm2 s-1 at the inner edge to less than ~11 cm2 s-1 at the outer edge. The gradual estimated decrease of the angular momentum flux and effective viscosity are roughly consistent with results obtained by balancing the shepherding torques from Pan and Daphnis with the viscous torque at the edges of the Encke and Keeler gaps, as well as the edge of the A ring.On the other hand, the Mimas 2:1 Lindblad resonance alone seems to be capable of confining the edge of the B ring, and contrary to the situation in the A ring, we show that the effective viscosity

A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching.

PubMed

Romero, José R; Carballido, Jessica A; Garbus, Ingrid; Echenique, Viviana C; Ponzoni, Ignacio

2016-01-01

The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow the discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. In this study, a de novo strategy for detecting patterns that represent nested motifs was designed based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories, motifs within other motifs, motifs flanked by other motifs, and motifs of large size. The methodology used in this study, applied to genomic sequences from the plant species Aegilops tauschii and Oryza sativa , revealed that it is possible to identify putative nested TEs by detecting these three types of patterns. The results were validated through BLAST alignments, which revealed the efficacy and usefulness of the new method, which is called Mamushka.

Motif discovery with data mining in 3D protein structure databases: discovery, validation and prediction of the U-shape zinc binding ("Huf-Zinc") motif.

PubMed

Maurer-Stroh, Sebastian; Gao, He; Han, Hao; Baeten, Lies; Schymkowitz, Joost; Rousseau, Frederic; Zhang, Louxin; Eisenhaber, Frank

2013-02-01

Data mining in protein databases, derivatives from more fundamental protein 3D structure and sequence databases, has considerable unearthed potential for the discovery of sequence motif--structural motif--function relationships as the finding of the U-shape (Huf-Zinc) motif, originally a small student's project, exemplifies. The metal ion zinc is critically involved in universal biological processes, ranging from protein-DNA complexes and transcription regulation to enzymatic catalysis and metabolic pathways. Proteins have evolved a series of motifs to specifically recognize and bind zinc ions. Many of these, so called zinc fingers, are structurally independent globular domains with discontinuous binding motifs made up of residues mostly far apart in sequence. Through a systematic approach starting from the BRIX structure fragment database, we discovered that there exists another predictable subset of zinc-binding motifs that not only have a conserved continuous sequence pattern but also share a characteristic local conformation, despite being included in totally different overall folds. While this does not allow general prediction of all Zn binding motifs, a HMM-based web server, Huf-Zinc, is available for prediction of these novel, as well as conventional, zinc finger motifs in protein sequences. The Huf-Zinc webserver can be freely accessed through this URL (http://mendel.bii.a-star.edu.sg/METHODS/hufzinc/).

Electronic and geometric structures of Au30 clusters: a network of 2e-superatom Au cores protected by tridentate protecting motifs with u3-S

NASA Astrophysics Data System (ADS)

Tian, Zhimei; Cheng, Longjiu

2015-12-01

Density functional theory calculations have been performed to study the experimentally synthesized Au30S(SR)18 and two related Au30(SR)18 and Au30S2(SR)18 clusters. The patterns of thiolate ligands on the gold cores for the three thiolate-protected Au30 nanoclusters are on the basis of the ``divide and protect'' concept. A novel extended protecting motif with u3-S, S(Au2(SR)2)2AuSR, is discovered, which is termed the tridentate protecting motif. The Au cores of Au30S(SR)18, Au30(SR)18 and Au30S2(SR)18 clusters are Au17, Au20 and Au14, respectively. The superatom-network (SAN) model and the superatom complex (SAC) model are used to explain the chemical bonding patterns, which are verified by chemical bonding analysis based on the adaptive natural density partitioning (AdNDP) method and aromatic analysis on the basis of the nucleus-independent chemical shift (NICS) method. The Au17 core of the Au30S(SR)18 cluster can be viewed as a SAN of one Au6 superatom and four Au4 superatoms. The shape of the Au6 core is identical to that revealed in the recently synthesized Au18(SR)14 cluster. The Au20 core of the Au30(SR)18 cluster can be viewed as a SAN of two Au6 superatoms and four Au4 superatoms. The Au14 core of Au30S2(SR)18 can be regarded as a SAN of two pairs of two vertex-sharing Au4 superatoms. Meanwhile, the Au14 core is an 8e-superatom with 1S21P6 configuration. Our work may aid understanding and give new insights into the chemical synthesis of thiolate-protected Au clusters.Density functional theory calculations have been performed to study the experimentally synthesized Au30S(SR)18 and two related Au30(SR)18 and Au30S2(SR)18 clusters. The patterns of thiolate ligands on the gold cores for the three thiolate-protected Au30 nanoclusters are on the basis of the ``divide and protect'' concept. A novel extended protecting motif with u3-S, S(Au2(SR)2)2AuSR, is discovered, which is termed the tridentate protecting motif. The Au cores of Au30S(SR)18, Au30(SR)18 and Au30S

Observation of Bs production at the Y(5S) resonance.

PubMed

Bonvicini, G; Cinabro, D; Dubrovin, M; Lincoln, A; Bornheim, A; Pappas, S P; Weinstein, A J; Asner, D M; Edwards, K W; Briere, R A; Chen, G P; Chen, J; Ferguson, T; Tatishvili, G; Vogel, H; Watkins, M E; Rosner, J L; Adam, N E; Alexander, J P; Berkelman, K; Cassel, D G; Crede, V; Duboscq, J E; Ecklund, K M; Ehrlich, R; Fields, L; Gibbons, L; Gittelman, B; Gray, R; Gray, S W; Hartill, D L; Heltsley, B K; Hertz, D; Jones, C D; Kandaswamy, J; Kreinick, D L; Kuznetsov, V E; Mahlke-Krüger, H; Meyer, T O; Onyisi, P U E; Patterson, J R; Peterson, D; Phillips, E A; Pivarski, J; Riley, D; Ryd, A; Sadoff, A J; Schwarthoff, H; Shi, X; Shepherd, M R; Stroiney, S; Sun, W M; Urner, D; Wilksen, T; Weaver, K M; Weinberger, M; Athar, S B; Avery, P; Breva-Newell, L; Patel, R; Potlia, V; Stoeck, H; Yelton, J; Rubin, P; Cawlfield, C; Eisenstein, B I; Gollin, G D; Karliner, I; Kim, D; Lowrey, N; Naik, P; Sedlack, C; Selen, M; White, E J; Williams, J; Wiss, J; Besson, D; Pedlar, T K; Cronin-Hennessy, D; Gao, K Y; Gong, D T; Hietala, J; Kubota, Y; Klein, T; Lang, B W; Li, S Z; Poling, R; Scott, A W; Smith, A; Dobbs, S; Metreveli, Z; Seth, K K; Tomaradze, A; Zweber, P; Ernst, J; Arms, K; Severini, H; Dytman, S A; Love, W; Mehrabyan, S; Mueller, J A; Savinov, V; Li, Z; Lopez, A; Mendez, H; Ramirez, J; Huang, G S; Miller, D H; Pavlunin, V; Sanghi, B; Shipsey, I P J; Adams, G S; Anderson, M; Cummings, J P; Danko, I; Napolitano, J; He, Q; Muramatsu, H; Park, C S; Thorndike, E H; Coan, T E; Gao, Y S; Liu, F; Maravin, Y; Artuso, M; Boulahouache, C; Blusk, S; Butt, J; Dorjkhaidav, O; Li, J; Menaa, N; Mountain, R; Nandakumar, R; Randrianarivony, K; Redjimi, R; Sia, R; Skwarnicki, T; Stone, S; Wang, J C; Zhang, K; Csorna, S E

2006-01-20

Using the CLEO detector at the Cornell Electron Storage Ring, we have observed the Bs meson in e+e- annihilation at the Y(5S) resonance. We find 14 candidates consistent with Bs decays into final states with a J/psi or a Ds(*)- . The probability that we have observed a background fluctuation is less than 8 x 10(-10) . We have established that at the energy of the Y(5S) resonance Bs production proceeds predominantly through the creation of Bs*Bs* pairs. We find sigma(e+e- --> Bs*Bs*) = [0.11(-0.03))(+0.04)(stat) +/- 0.02(syst)]nb , and set the following limits: sigma(e+e- --> BsBs)/ sigma(e+ e- --> Bs*Bs*) <0.16 and [sigma(e+e- --> BsBs*) + sigma(e+e- --> Bs*Bs)]/sigma(e+e- -->Bs*Bs*) < 0.16 (90% C.L.). The mass of the Bs* meson is measured to be M(Bs*) = [5.414+/- 0.001(stat) +/- 0.003(syst)] GeV/c2 .

meso-4,4′-Dimeth­oxy-2,2′-{[(3aR,7aS)-2,3,3a,4,5,6,7,7a-octa­hydro-1H-benz­imidazole-1,3-di­yl]bis­(methyl­ene)}diphenol

PubMed Central

Rivera, Augusto; Quiroga, Diego; Ríos-Motta, Jaime; Kučeraková, Monika; Dušek, Michal

2013-01-01

The title compound, C23H30N2O4, a di-Mannich base derived from 4-meth­oxy­phenol and cis-1,2-di­amine­cyclo­hexane, has a perhydro­benzimidazolidine nucleus, in which the cyclo­hexane ring adopts a chair conformation and the heterocyclic ring has a half-chair conformation with a C—N—C—C torsion angles of −48.14 (15) and −14.57 (16)°. The mean plane of the heterocycle makes dihedral angles of 86.29 (6) and 78.92 (6)° with the pendant benzene rings. The mol­ecular structure of the title compound shows the presence of two inter­actions between the N atoms of the imidazolidine ring and the hydroxyl groups through intra­molecular O—H⋯N hydrogen bonds with graph-set motif S(6). The unobserved lone pairs of the N atoms are presumed to be disposed in a syn conformation, being only the second example of an exception to the typical ‘rabbit-ears’ effect in 1,2-di­amines. PMID:24046631

DNA motif elucidation using belief propagation.

PubMed

Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

2013-09-01

Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.

BlockLogo: visualization of peptide and sequence motif conservation

PubMed Central

Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian; Sun, Jing; Schönbach, Christian; Reinherz, Ellis L.; Zhang, Guang Lan; Brusic, Vladimir

2013-01-01

BlockLogo is a web-server application for visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online application and have demonstrated its utility through examples that show visualization of T-cell epitopes and B-cell epitopes (both continuous and discontinuous). Our additional example shows a visualization and analysis of structural motifs that determine specificity of peptide binding to HLA-DR molecules. The BlockLogo server also employs selected experimentally validated prediction algorithms to enable on-the-fly prediction of MHC binding affinity to 15 common HLA class I and class II alleles as well as visual analysis of discontinuous epitopes from multiple sequence alignments. It enables the visualization and analysis of structural and functional motifs that are usually described as regular expressions. It provides a compact view of discontinuous motifs composed of distant positions within biological sequences. BlockLogo is available at: http://research4.dfci.harvard.edu/cvc/blocklogo/ and http://methilab.bu.edu/blocklogo/ PMID:24001880

Motivated Proteins: A web application for studying small three-dimensional protein motifs

PubMed Central

Leader, David P; Milner-White, E James

2009-01-01

Background Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motifs, asx-motifs, asx-turns, β-bulges, β-bulge loops, β-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns. We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. Description The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. Conclusion Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema. PMID:19210785

Molecular pathogenesis of H5 highly pathogenic avian influenza: the role of the haemagglutinin cleavage site motif

PubMed Central

Luczo, Jasmina M.; Stambas, John; Durr, Peter A.; Michalski, Wojtek P.

2015-01-01

Summary The emergence of H5N1 highly pathogenic avian influenza has caused a heavy socio‐economic burden through culling of poultry to minimise human and livestock infection. Although human infections with H5N1 have to date been limited, concerns for the pandemic potential of this zoonotic virus have been greatly intensified following experimental evidence of aerosol transmission of H5N1 viruses in a mammalian infection model. In this review, we discuss the dominance of the haemagglutinin cleavage site motif as a pathogenicity determinant, the host‐pathogen molecular interactions driving cleavage activation, reverse genetics manipulations and identification of residues key to haemagglutinin cleavage site functionality and the mechanisms of cell and tissue damage during H5N1 infection. We specifically focus on the disease in chickens, as it is in this species that high pathogenicity frequently evolves and from which transmission to the human population occurs. With >75% of emerging infectious diseases being of zoonotic origin, it is necessary to understand pathogenesis in the primary host to explain spillover events into the human population. © 2015 The Authors. Reviews in Medical Virology published by John Wiley & Sons Ltd. PMID:26467906

Mechanisms Regulating the Secretion of the Promalignancy Chemokine CCL5 by Breast Tumor Cells: CCL5's 40s Loop and Intracellular Glycosaminoglycans12

PubMed Central

Soria, Gali; Lebel-Haziv, Yaeli; Ehrlich, Marcelo; Meshel, Tsipi; Suez, Adva; Avezov, Edward; Rozenberg, Perri; Ben-Baruch, Adit

2012-01-01

The chemokine CCL5 (RANTES) plays active promalignancy roles in breast malignancy. The secretion of CCL5 by breast tumor cells is an important step in its tumor-promoting activities; therefore, inhibition of CCL5 secretion may have antitumorigenic effects. We demonstrate that, in breast tumor cells, CCL5 secretion necessitated the trafficking of CCL5-containing vesicles on microtubules from the endoplasmic reticulum (ER) to the post-Golgi stage, and CCL5 release was regulated by the rigidity of the actin cytoskeleton. Focusing on the 40s loop of CCL5, we found that the 43TRKN46 sequence of CCL5 was indispensable for its inclusion in motile vesicles, and for its secretion. The TRKN-mutated chemokine reached the Golgi, but trafficked along the ER-to-post-Golgi route differently than the wild-type (WT) chemokine. Based on the studies showing that the 40s loop of CCL5 mediates its binding to glycosaminoglycans (GAG), we analyzed the roles of GAG in regulating CCL5 secretion. TRKN-mutated CCL5 had lower propensity for colocalization with GAG in the Golgi compared to the WT chemokine. Secretion of WT CCL5 was significantly reduced in CHO mutant cells deficient in GAG synthesis, and the WT chemokine acquired an ER-like distribution in these cells, similar to that of TRKN-mutated CCL5 in GAG-expressing cells. The release of WT CCL5 was also reduced after inhibition of GAG presence/synthesis by intracellular expression of heparanase, inhibition of GAG sulfation, and sulfate deprivation. The need for a 43TRKN46 motif and for a GAG-mediated process in CCL5 secretion may enable the future design of modalities that prevent CCL5 release by breast tumor cells. PMID:22355269

DNA containing CpG motifs induces angiogenesis

NASA Astrophysics Data System (ADS)

Zheng, Mei; Klinman, Dennis M.; Gierynska, Malgorzata; Rouse, Barry T.

2002-06-01

New blood vessel formation in the cornea is an essential step in the pathogenesis of a blinding immunoinflammatory reaction caused by ocular infection with herpes simplex virus (HSV). By using a murine corneal micropocket assay, we found that HSV DNA (which contains a significant excess of potentially bioactive "CpG" motifs when compared with mammalian DNA) induces angiogenesis. Moreover, synthetic oligodeoxynucleotides containing CpG motifs attract inflammatory cells and stimulate the release of vascular endothelial growth factor (VEGF), which in turn triggers new blood vessel formation. In vitro, CpG DNA induces the J774A.1 murine macrophage cell line to produce VEGF. In vivo CpG-induced angiogenesis was blocked by the administration of anti-mVEGF Ab or the inclusion of "neutralizing" oligodeoxynucleotides that specifically oppose the stimulatory activity of CpG DNA. These findings establish that DNA containing bioactive CpG motifs induces angiogenesis, and suggest that CpG motifs in HSV DNA may contribute to the blinding lesions of stromal keratitis.

TOPDOM: database of conservatively located domains and motifs in proteins.

PubMed

Varga, Julia; Dobson, László; Tusnády, Gábor E

2016-09-01

The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in α-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins. TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer. tusnady.gabor@ttk.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Jupiter Ring Halo

NASA Image and Video Library

1998-03-26

A mosaic of four images taken through the clear filter (610 nanometers) of the solid state imaging (CCD) system aboard NASA's Galileo spacecraft on November 8, 1996, at a resolution of approximately 46 kilometers (km) per picture element (pixel) along the rings; however, because the spacecraft was only about 0.5 degrees above the ring plane, the image is highly foreshortened in the vertical direction. The images were obtained when Galileo was in Jupiter's shadow peering back toward the Sun; the ring was approximately 2,300,000 kilometers (km) away. The arc on the far right of the image is produced by sunlight scattered by small particles comprising Jupiter's upper atmospheric haze. The ring also efficiently scatters light, indicating that much of its brightness is due to particles that are microns or less in diameter. Such small particles are believed to have human-scale lifetimes, i.e., very brief compared to the solar system's age. Jupiter's ring system is composed of three parts -- a flat main ring, a lenticular halo interior to the main ring, and the gossamer ring, which lies exterior to the main ring. The near and far arms of Jupiter's main ring extend horizontally across the mosaic, joining together at the ring's ansa, on the far left side of the figure. The near arm of the ring appears to be abruptly truncated close to the planet, at the point where it passes into Jupiter's shadow. A faint mist of particles can be seen above and below the main rings; this vertically extended, toroidal "halo" is unusual in planetary rings, and is probably caused by electromagnetic forces which can push small grains out of the ring plane. Halo material is present across this entire image, implying that it reaches more than 27,000 km above the ring plane. Because of shadowing, the halo is not visible close to Jupiter in the lower right part of the mosaic. In order to accentuate faint features in the image, different brightnesses are shown through color, with the brightest being

Tricuspid annuloplasty with the MC3 ring and septal plication technique.

PubMed

Isomura, Tadashi; Hirota, Masanori; Hoshino, Joji; Fukada, Yasuhisa; Kondo, Taichi; Takahashi, Yu

2015-01-01

Functional tricuspid regurgitation is caused by annular dilation mainly in the posterior annulus. However, ring annuloplasty does not always prevent the recurrence of tricuspid regurgitation due to dilation of the septal annulus. We developed a septal plication technique with a 3-dimensional MC3 ring. Between 2006 and 2011, 76 patients (male/female 30/46; mean age 68 ± 11 years) with functional tricuspid regurgitation received tricuspid ring annuloplasty. After placement of the annular sutures, the 3 commissural ring portions were fixed on the equivalent commissures to plicate the anterior and posterior annulus. The end of the septal ring portion was fixed at the optimal annular position to obtain minimal tricuspid regurgitation. All patients were followed-up for a mean of 47 ± 18 months; the longest duration was 79 months. Although there was no operative death, one patient died of sepsis during hospitalization (hospital mortality 1.3%). After implantation of the MC3 ring (mean size 31.0 ± 3.3 mm), additional edge-to-edge sutures were required for minor leakage in 5 (7%) patients. The degree of tricuspid regurgitation was significantly reduced at discharge (0.5 ± 0.6) and midterm (0.6 ± 0.6) compared to 2.5 ± 0.7 before the operation (p < 0.0001). The surgical durability of the MC3 ring was satisfactory at early and midterm follow-up, suggesting that correct plication of the septal annulus is effective for tricuspid ring annuloplasty with a 3-dimensional MC3 ring. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Rheology modification with ring polymers

NASA Astrophysics Data System (ADS)

Vlassopoulos, Dimitris

It is now established that experimental unconcatenated ring polymers can be purified effectively by means of fractionation at the critical condition. For molecular weights well above the entanglement threshold, purified rings relax stress via power-law (with an exponent of about -0.4), sharply departing from their linear counterparts. Experimental results are in harmony with modeling predictions and simulations. Here, we present results from recent interdisciplinary efforts and discuss two challenges: (i) the nonlinear shear rheology of purified ring melts is also very different from that of unlinked chains. Whereas the latter exhibit features that can be explained, to a first approach, in the framework in the tube model, the former behave akin to unentangled chains with finite extensibility and exhibit much small deformation at steady state. (ii) blends of rings and linear polymers exhibit unique features in different regimes: The addition of minute amounts of linear chains drastically affects ring dynamics. This relates to ring purity and the ability of unlinked linear chains to thread rings. With the help of simulations, it is possible to rationalize the observed surprisingly slow viscoelastic relaxation, which is attributed to ring-linear and ring-ring penetrations. On the other hand, adding small amounts of rings to linear polymers of different molecular weights influences their linear and nonlinear rheology in an unprecedented way. The blend viscosity exceeds that of the slower component (linear) in this non-interacting mixture, and its dependencies on composition and molecular weight ratio are examined, whereas the role of molecular architecture is also addressed. Consequently, closing the ends of a linear chain can serve as a powerful means for molecular manipulation of its rheology. This presentation reflects collaborative efforts with S. Costanzo, Z-C. Yan, R. Pasquino, M. Kaliva, S. Kamble, Y. Jeong, P. Lutz, J. Allgaier, T. Chang, D. Talikis, V

Clinical and molecular cytogenetic studies in ring chromosome 5: report of a child with congenital abnormalities.

PubMed

Basinko, Audrey; Giovannucci Uzielli, Maria Luisa; Scarselli, Gloria; Priolo, Manuela; Timpani, Giuseppina; De Braekeleer, Marc

2012-02-01

We report here a child with a ring chromosome 5 (r(5)) associated with facial dysmorphology and multiple congenital abnormalities. Fluorescent in situ hybridization (FISH) using bacterial artificial chromosome (BAC) clones was performed to determine the breakpoints involved in the r(5). The 5p deletion extended from 5p13.2-3 to 5pter and measured 34.61 Mb (range: 33.7-35.52 Mb) while the 5q deletion extended from 5q35.3 to 5qter and measured 2.44 Mb (range: 2.31-2.57 Mb). The patient presented signs such as microcephaly, hypertelorism, micrognathia and epicanthal folds, partially recalling those of a deletion of the short arm of chromosome 5 and the "cri-du-chat" syndrome. The most striking phenotypic features were the congenital heart abnormalities which have been frequently reported in deletions of the distal part of the long arm of chromosome 5 and in rings leading to a 5q35-5qter deletion. However, the NKX2-5 gene, which has been related to congenital heart defects, was not deleted in our patient, nor presumably to some other patients with 5q35.3-5qter deletion. We propose that VEGFR3, deleted in our patient, could be a candidate gene for the congenital heart abnormalities observed. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

C-C motif ligand 5 promotes migration of prostate cancer cells in the prostate cancer bone metastasis microenvironment.

PubMed

Urata, Satoko; Izumi, Kouji; Hiratsuka, Kaoru; Maolake, Aerken; Natsagdorj, Ariunbold; Shigehara, Kazuyoshi; Iwamoto, Hiroaki; Kadomoto, Suguru; Makino, Tomoyuki; Naito, Renato; Kadono, Yoshifumi; Lin, Wen-Jye; Wufuer, Guzailinuer; Narimoto, Kazutaka; Mizokami, Atsushi

2018-03-01

Chemokines and their receptors have key roles in cancer progression. The present study investigated chemokine activity in the prostate cancer bone metastasis microenvironment. Growth and migration of human prostate cancer cells were assayed in cocultures with bone stromal cells. The migration of LNCaP cells significantly increased when co-cultured with bone stromal cells isolated from prostate cancer bone metastases. Cytokine array analysis of conditioned medium from bone stromal cell cultures identified CCL5 as a concentration-dependent promoter of LNCaP cell migration. The migration of LNCaP cells was suppressed when C-C motif ligand 5 (CCL5) neutralizing antibody was added to cocultures with bone stromal cells. Knockdown of androgen receptor with small interfering RNA increased the migration of LNCaP cells compared with control cells, and CCL5 did not promote the migration of androgen receptor knockdown LNCaP. Elevated CCL5 secretion in bone stromal cells from metastatic lesions induced prostate cancer cell migration by a mechanism consistent with CCL5 activity upstream of androgen receptor signaling. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

Dynamics of Centaur Chariklo and evolution of its rings

NASA Astrophysics Data System (ADS)

Kondratyev, B. P.

2016-12-01

It follows from observations that the asteroid Chariklo has two outer rings. The purpose of this paper is constructing the equilibrium model of asteroid and developing the kinetic mechanism of evolution of its rings. We have specified for Chariklo the density ρ0 ≈ 2.71 g/cm3, the mass M0 ≈ 8.817 × 10^{21} g, and the average radius R0 ≈ 128.16 km. Its rings are modeled by circular gravitating tori consisting of the small rock-ice particles that orbit the asteroid. The method does not imply the presence of hidden satellites close to the asteroid, and the equilibrium of the rings is determined by the small velocity dispersion and gravity of particles. The problem of expansion of the internal torus gravitational potential in series in powers of its geometrical parameter is solved. This enables the gravitational energy of Chariklo's rings to be found and to express their masses in terms of the mass of the asteroid M0. We calculated the mass of the inner ring to be M_{r1} ≈ 9.8 × 10^{18} g, and its relation to the mass of the asteroid is M_{r1}/M0 ≈ 0.001; similarly, for the outer ring M_{r2} ≈ 10^{18} g, and M_{r2}/M0 ≈ 0.0001. The mass ratio M_{r1}/M_{r2} ≈ 10 is typical for satellites of other asteroids and dwarf planets. The velocity dispersion of particles in rings υ1 ≈ 1 m/s and υ2 ≈ 45 cm/s is no greater than 1 div 2 % of its rotational velocity υ_{rot} ≈ 40 m/s. The particle of medium radius rp = 25 cm has the mean free path λ ≈ 7 m, and its diffusion time from center line on the surface of the torus is T'1/T_{rot1} ≈ 13 and T'2/T_{rot2} ≈ 5. The dissipation rate equation for Chariklo's rings is derived. From this equation a surprising result follows: the time of energy dissipation (the time of evolution of rings) is only T_{d1} ≈ 103 div 104 years, which by astronomical measures is a very short time scale. We adduce the arguments supporting the idea that these rings in near future can become Chariklo's satellites, and that

Structural and functional analysis of the GABARAP interaction motif (GIM)

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

Rogov, Vladimir V.; Stolz, Alexandra; Ravichandran, Arvind C.

Through the canonical LC3 interaction motif (LIR), [W/F/Y]–X 1–X 2[I/L/V], protein complexes are recruited to autophagosomes to perform their functions as either autophagy adaptors or receptors. How these adaptors/receptors selectively interact with either LC3 or GABARAP families remains unclear. Herein, we determine the range of selectivity of 30 known core LIR motifs towards individual LC3s and GABARAPs. From these, we define a GABARAP Interaction Motif (GIM) sequence ([W/F]–[V/I]–X 2–V) that the adaptor protein PLEKHM1 tightly conforms to. Using biophysical and structural approaches, we show that the PLEKHM1–LIR is indeed 11–fold more specific for GABARAP than LC3B. Selective mutation of themore » X 1 and X 2 positions either completely abolished the interaction with all LC3 and GABARAPs or increased PLEKHM1–GIM selectivity 20–fold towards LC3B. Finally, we show that conversion of p62/SQSTM1, FUNDC1 and FIP200 LIRs into our newly defined GIM, by introducing two valine residues, enhances their interaction with endogenous GABARAP over LC3B. In conclusion, the identification of a GABARAP–specific interaction motif will aid the identification and characterization of the expanding array of autophagy receptor and adaptor proteins and their in vivo functions.« less

Structural and functional analysis of the GABARAP interaction motif (GIM)

DOE PAGES

Rogov, Vladimir V.; Stolz, Alexandra; Ravichandran, Arvind C.; ...

2017-06-27

Through the canonical LC3 interaction motif (LIR), [W/F/Y]–X 1–X 2[I/L/V], protein complexes are recruited to autophagosomes to perform their functions as either autophagy adaptors or receptors. How these adaptors/receptors selectively interact with either LC3 or GABARAP families remains unclear. Herein, we determine the range of selectivity of 30 known core LIR motifs towards individual LC3s and GABARAPs. From these, we define a GABARAP Interaction Motif (GIM) sequence ([W/F]–[V/I]–X 2–V) that the adaptor protein PLEKHM1 tightly conforms to. Using biophysical and structural approaches, we show that the PLEKHM1–LIR is indeed 11–fold more specific for GABARAP than LC3B. Selective mutation of themore » X 1 and X 2 positions either completely abolished the interaction with all LC3 and GABARAPs or increased PLEKHM1–GIM selectivity 20–fold towards LC3B. Finally, we show that conversion of p62/SQSTM1, FUNDC1 and FIP200 LIRs into our newly defined GIM, by introducing two valine residues, enhances their interaction with endogenous GABARAP over LC3B. In conclusion, the identification of a GABARAP–specific interaction motif will aid the identification and characterization of the expanding array of autophagy receptor and adaptor proteins and their in vivo functions.« less

Mutations in the Putative Zinc-Binding Motif of UL52 Demonstrate a Complex Interdependence between the UL5 and UL52 Subunits of the Human Herpes Simplex Virus Type 1 Helicase/Primase Complex

PubMed Central

Chen, Yan; Carrington-Lawrence, Stacy D.; Bai, Ping; Weller, Sandra K.

2005-01-01

Herpes simplex virus type 1 (HSV-1) encodes a heterotrimeric helicase-primase (UL5/8/52) complex. UL5 contains seven motifs found in helicase superfamily 1, and UL52 contains conserved motifs found in primases. The contributions of each subunit to the biochemical activities of the complex, however, remain unclear. We have previously demonstrated that a mutation in the putative zinc finger at UL52 C terminus abrogates not only primase but also ATPase, helicase, and DNA-binding activities of a UL5/UL52 subcomplex, indicating a complex interdependence between the two subunits. To test this hypothesis and to further investigate the role of the zinc finger in the enzymatic activities of the helicase-primase, a series of mutations were constructed in this motif. They differed in their ability to complement a UL52 null virus: totally defective, partial complementation, and potentiating. In this study, four of these mutants were studied biochemically after expression and purification from insect cells infected with recombinant baculoviruses. All mutants show greatly reduced primase activity. Complementation-defective mutants exhibited severe defects in ATPase, helicase, and DNA-binding activities. Partially complementing mutants displayed intermediate levels of these activities, except that one showed a wild-type level of helicase activity. These data suggest that the UL52 zinc finger motif plays an important role in the activities of the helicase-primase complex. The observation that mutations in UL52 affected helicase, ATPase, and DNA-binding activities indicates that UL52 binding to DNA via the zinc finger may be necessary for loading UL5. Alternatively, UL5 and UL52 may share a DNA-binding interface. PMID:15994803

Mutations in the putative zinc-binding motif of UL52 demonstrate a complex interdependence between the UL5 and UL52 subunits of the human herpes simplex virus type 1 helicase/primase complex.

PubMed

Chen, Yan; Carrington-Lawrence, Stacy D; Bai, Ping; Weller, Sandra K

2005-07-01

Herpes simplex virus type 1 (HSV-1) encodes a heterotrimeric helicase-primase (UL5/8/52) complex. UL5 contains seven motifs found in helicase superfamily 1, and UL52 contains conserved motifs found in primases. The contributions of each subunit to the biochemical activities of the complex, however, remain unclear. We have previously demonstrated that a mutation in the putative zinc finger at UL52 C terminus abrogates not only primase but also ATPase, helicase, and DNA-binding activities of a UL5/UL52 subcomplex, indicating a complex interdependence between the two subunits. To test this hypothesis and to further investigate the role of the zinc finger in the enzymatic activities of the helicase-primase, a series of mutations were constructed in this motif. They differed in their ability to complement a UL52 null virus: totally defective, partial complementation, and potentiating. In this study, four of these mutants were studied biochemically after expression and purification from insect cells infected with recombinant baculoviruses. All mutants show greatly reduced primase activity. Complementation-defective mutants exhibited severe defects in ATPase, helicase, and DNA-binding activities. Partially complementing mutants displayed intermediate levels of these activities, except that one showed a wild-type level of helicase activity. These data suggest that the UL52 zinc finger motif plays an important role in the activities of the helicase-primase complex. The observation that mutations in UL52 affected helicase, ATPase, and DNA-binding activities indicates that UL52 binding to DNA via the zinc finger may be necessary for loading UL5. Alternatively, UL5 and UL52 may share a DNA-binding interface.

The chemistry of (ring)Ru sup 2+ (ring = tetramethylthiophene, p-cymene)

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

Ganja, E.A.; Rauchfuss, T.B.; Stern, C.L.

1991-01-01

Described are the compounds ((ring)Ru(OTf){sub 2}){sub x}, where ring = 2,3,4,5-tetramethylthiophene (TMT, 1), and p-cymene (2). These electrophilic reagents serve as precursors to ((ring)RuL{sub 3}){sup 2+}, where L{sub 3} = (H{sub 2}O){sub 3}, (NH{sub 3}){sub 3}, and (PH{sub 3}){sub 3}. Solutions of 1 and 2 react with carbon monoxide to give (ring)Ru(CO)(OTf){sub 2}. The addition of thiophenes to CH{sub 2}Cl{sub 2} solutions of 1 or 2 leads to the precipitation of the sandwich compounds ((ring)(SC{sub 4}R{sub 4})Ru)(OTf){sub 2}, where SC{sub 4}R{sub 4} = thiophene, 2,5-dimethylthiophene, and TMT. ((TMT)Ru(H{sub 2}O){sub 3})(OTf){sub 2} was characterized by single-crystal X-ray crystallography, which established amore » piano-stool geometry with a planar TMT ligand. ((TMT)Ru(D{sub 2}O){sub 3})(OTf){sub 2} decomposes in D{sub 2}O solution at 150C to give ((TMT){sub 2}Ru){sup 2+}, which undergoes selective deuteration at the 2,5-methyl groups. D{sub 2}O solutions of ((TMT){sub 2}Ru){sup 2+} undergo photochemical loss of one TMT ligand in water to give ((TMT)Ru(H{sub 2}O){sub 3}){sup 2+}. A procedure is described for the reversible loading of 1 onto {gamma}-alumina, which in turn was characterized by {sup 13}C CP-MAS NMR spectroscopy.« less

Bioconjugatable Porphyrins Bearing a Compact Swallowtail Motif for Water Solubility

PubMed Central

Borbas, K. Eszter; Mroz, Pawel; Hamblin, Michael R.; Lindsey, Jonathan S.

2011-01-01

A broad range of applications requires access to water-soluble, bioconjugatable porphyrins. Branched alkyl groups attached at the branching site to the porphyrin meso position are known to impart high organic solubility. Such “swallowtail” motifs bearing a polar group (hydroxy, dihydroxyphosphoryl, dihydroxyphosphoryloxy) at the terminus of each branch have now been incorporated at a meso site in trans-AB-porphyrins. The incorporation of the swallowtail motif relies on rational synthetic methods whereby a 1,9-bis(N-propylimino)dipyrromethane (bearing a bioconjugatable tether at the 5-position) is condensed with a dipyrromethane (bearing a protected 1,5-dihydroxypent-3-yl unit at the 5-position). The two hydroxy groups in the swallowtail motif of each of the resulting zinc porphyrins can be transformed to the corresponding diphosphate or diphosphonate product. A 4-(carboxymethyloxy)phenyl group provides the bioconjugatable tether. The six such porphyrins reported here are highly water-soluble (≥20 mM at room temperature in water at pH 7) as determined by visual inspection, UV–vis absorption spectroscopy, or 1H NMR spectroscopy. Covalent attachment was carried out in aqueous solution with the unprotected porphyrin diphosphonate and a monoclonal antibody against the T-cell receptor CD3ε. The resulting conjugate performed comparably to a commercially available fluorescein isothiocyanate-labeled antibody with Jurkat cells in flow cytometry and fluorescence microscopy assays. Taken together, this work enables preparation of useful quantities of water-soluble, bioconjugatable porphyrins in a compact architecture for applications in the life sciences. PMID:16704201

Gelation or molecular recognition; is the bis-(α,β-dihydroxy ester)s motif an omnigelator?

PubMed

Griffiths, Peter C; Knight, David W; Morgan, Ian R; Ford, Amy; Brown, James; Davies, Ben; Heenan, Richard K; King, Stephen M; Dalgliesh, Robert M; Tomkinson, John; Prescott, Stuart; Schweins, Ralf; Paul, Alison

2010-11-18

Understanding the gelation of liquids by low molecular weight solutes at low concentrations gives an insight into many molecular recognition phenomena and also offers a simple route to modifying the physical properties of the liquid. Bis-(α,β-dihydroxy ester)s are shown here to gel thermoreversibly a wide range of solvents, raising interesting questions as to the mechanism of gelation. At gelator concentrations of 5-50 mg ml⁻¹, gels were successfully formed in acetone, ethanol/water mixtures, toluene, cyclohexane and chloroform (the latter, albeit at a higher gelator concentration). A range of neutron techniques - in particular small-angle neutron scattering (SANS) - have been employed to probe the structure of a selection of these gels. The universality of gelation in a range of solvent types suggests the gelation mechanism is a feature of the bis-(α,β-dihydroxy ester) motif, with SANS demonstrating the presence of regular structures in the 30-40 Å range. A correlation between the apparent rodlike character of the structures formed and the polarity of the solvent is evident. Preliminary spin-echo neutron scattering studies (SESANS) indicated the absence of any larger scale structures. Inelastic neutron spectroscopy (INS) studies demonstrated that the solvent is largely unaffected by gelation, but does reveal insights into the thermal history of the samples. Further neutron studies of this kind (particularly SESANS and INS) are warranted, and it is hoped that this work will stimulate others to pursue this line of research.

Gibbs motif sampling: detection of bacterial outer membrane protein repeats.

PubMed Central

Neuwald, A. F.; Liu, J. S.; Lawrence, C. E.

1995-01-01

The detection and alignment of locally conserved regions (motifs) in multiple sequences can provide insight into protein structure, function, and evolution. A new Gibbs sampling algorithm is described that detects motif-encoding regions in sequences and optimally partitions them into distinct motif models; this is illustrated using a set of immunoglobulin fold proteins. When applied to sequences sharing a single motif, the sampler can be used to classify motif regions into related submodels, as is illustrated using helix-turn-helix DNA-binding proteins. Other statistically based procedures are described for searching a database for sequences matching motifs found by the sampler. When applied to a set of 32 very distantly related bacterial integral outer membrane proteins, the sampler revealed that they share a subtle, repetitive motif. Although BLAST (Altschul SF et al., 1990, J Mol Biol 215:403-410) fails to detect significant pairwise similarity between any of the sequences, the repeats present in these outer membrane proteins, taken as a whole, are highly significant (based on a generally applicable statistical test for motifs described here). Analysis of bacterial porins with known trimeric beta-barrel structure and related proteins reveals a similar repetitive motif corresponding to alternating membrane-spanning beta-strands. These beta-strands occur on the membrane interface (as opposed to the trimeric interface) of the beta-barrel. The broad conservation and structural location of these repeats suggests that they play important functional roles. PMID:8520488

Antifungal properties of peptidomimetics with an arginine-[β-(2,5,7-tri-tert-butylindol-3-yl)alanine]-arginine motif against Saccharomyces cerevisiae and Zygosaccharomyces bailii.

PubMed

Larsen, Camilla Eggert; Larsen, Camilla Josephine; Franzyk, Henrik; Regenberg, Birgitte

2015-05-01

Due to increased occurrence of infections and food spoilage caused by yeast, there is an unmet need for new antifungal agents. The arginine-β-(2,5,7-tri-tert-butylindol-3-yl) alanine-arginine (R-Tbt-R) motif was previously proved useful in the design of an antifungal tripeptide. Here, an array of peptidomimetics based on this motif was investigated for antifungal and hemolytic activity. The five most promising modified tetrapeptide analogues ( 6: and 9-12: contain an additional C-terminal hydrophobic residue, and these were found to exhibit antifungal activity against Saccharomyces cerevisiae (MIC 6 and 12 μg mL(-1)) and Zygosaccharomyces bailii (MIC 6-25 μg mL(-1)). Four compounds ( 6: and 9-11: , had limited hemolytic activity (<10% hemolysis at 8 × MIC). Determination of their killing kinetics revealed that compound 9: displayed fungicidal effect. Testing against cells from an S. cerevisiae deletion mutant library indicated that interaction with yeast-specific fungal sphingolipids, most likely constitutes a crucial step in the mode of action. Interestingly, a lack of activity of peptidomimetics 6: and 9-11: towards Candida spp. was shown to be due to degradation or sequestering by the yeast. Due to their ultrashort nature, antifungal activity and low toxicity, the four compounds may have potential as leads for novel preservatives. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

ELM: the status of the 2010 eukaryotic linear motif resource

PubMed Central

Gould, Cathryn M.; Diella, Francesca; Via, Allegra; Puntervoll, Pål; Gemünd, Christine; Chabanis-Davidson, Sophie; Michael, Sushama; Sayadi, Ahmed; Bryne, Jan Christian; Chica, Claudia; Seiler, Markus; Davey, Norman E.; Haslam, Niall; Weatheritt, Robert J.; Budd, Aidan; Hughes, Tim; Paś, Jakub; Rychlewski, Leszek; Travé, Gilles; Aasland, Rein; Helmer-Citterich, Manuela; Linding, Rune; Gibson, Toby J.

2010-01-01

Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported. Although clearly very abundant, linear motifs are difficult to predict de novo in protein sequences due to the difficulty of obtaining robust statistical assessments. The ELM resource at http://elm.eu.org/ provides an expanding knowledge base, currently covering 146 known motifs, with annotation that includes >1300 experimentally reported instances. ELM is also an exploratory tool for suggesting new candidates of known linear motifs in proteins of interest. Information about protein domains, protein structure and native disorder, cellular and taxonomic contexts is used to reduce or deprecate false positive matches. Results are graphically displayed in a ‘Bar Code’ format, which also displays known instances from homologous proteins through a novel ‘Instance Mapper’ protocol based on PHI-BLAST. ELM server output provides links to the ELM annotation as well as to a number of remote resources. Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation. PMID:19920119

A theoretical investigation into the strength of N-NO2 bonds, ring strain and electrostatic potential upon formation of intermolecular H-bonds between HF and the nitro group in nitrogen heterocyclic rings C n H2n N-NO2 (n = 2-5), RDX and HMX.

PubMed

Wang, Bao-Guo; Ren, Fu-de; Shi, Wen-Jing

2015-11-01

Changes in N-NO2 bond strength, ring strain energy and electrostatic potential upon formation of intermolecular H-bonds between HF and the nitro group in nitrogen heterocyclic rings C n H2n N-NO2 (n = 2-5), RDX and HMX were investigated using DFT-B3LYP and MP2(full) methods with the 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. Analysis of electron density shifts was also carried out. The results indicate that H-bonding energy correlates well with the increment of ring strain energy. Upon complex formation, the strength of the N-NO2 trigger-bond is enhanced, suggesting reduced sensitivity, while judged by the increased ring strain energy, sensitivity is increased. However, some features of the molecular surface electrostatic potential, such as a local maximum above the N-NO2 bond and ring, σ + (2) and electrostatic balance parameter ν, remain essentially unchanged upon complex formation, and only a small change in the impact sensitivity h 50 is suggested. It is not sufficient to determine sensitivity solely on the basis of trigger bond or ring strain; as a global feature of a molecule, the molecular surface electrostatic potential is available to help judge the change of sensitivity in H-bonded complexes. Graphical Abstract The strengthened N-NO2 bond suggests reduced sensitivity, while it is reverse by theincreased ring strain energy upon the complex formation. However, the molecular surfaceelectrostatic potential (V S) shows the little change of h 50. The V S should be taken into accountin the analysis of explosive sensitivity in the H-bonded complex.

Recurring sequence-structure motifs in (βα)8-barrel proteins and experimental optimization of a chimeric protein designed based on such motifs.

PubMed

Wang, Jichao; Zhang, Tongchuan; Liu, Ruicun; Song, Meilin; Wang, Juncheng; Hong, Jiong; Chen, Quan; Liu, Haiyan

2017-02-01

An interesting way of generating novel artificial proteins is to combine sequence motifs from natural proteins, mimicking the evolutionary path suggested by natural proteins comprising recurring motifs. We analyzed the βα and αβ modules of TIM barrel proteins by structure alignment-based sequence clustering. A number of preferred motifs were identified. A chimeric TIM was designed by using recurring elements as mutually compatible interfaces. The foldability of the designed TIM protein was then significantly improved by six rounds of directed evolution. The melting temperature has been improved by more than 20°C. A variety of characteristics suggested that the resulting protein is well-folded. Our analysis provided a library of peptide motifs that is potentially useful for different protein engineering studies. The protein engineering strategy of using recurring motifs as interfaces to connect partial natural proteins may be applied to other protein folds. Copyright © 2016 Elsevier B.V. All rights reserved.

Functional Motifs Responsible for Human Metapneumovirus M2-2-mediated Innate Immune Evasion

PubMed Central

Chen, Yu; Deng, Xiaoling; Deng, Junfang; Zhou, Jiehua; Ren, Yuping; Liu, Shengxuan; Prusak, Deborah J.; Wood, Thomas G.; Bao, Xiaoyong

2016-01-01

Human metapneumovirus (hMPV) is a major cause of lower respiratory infection in young children. Repeated infections occur throughout life, but its immune evasion mechanisms are largely unknown. We recently found that hMPV M2-2 protein elicits immune evasion by targeting mitochondrial antiviral-signaling protein (MAVS), an antiviral signaling molecule. However, the molecular mechanisms underlying such inhibition are not known. Our mutagenesis studies revealed that PDZ-binding motifs, 29-DEMI-32 and 39-KEALSDGI-46, located in an immune inhibitory region of M2-2, are responsible for M2-2-mediated immune evasion. We also found both motifs prevent TRAF5 and TRAF6, the MAVS downstream adaptors, to be recruited to MAVS, while the motif 39-KEALSDGI-46 also blocks TRAF3 migrating to MAVS. In parallel, these TRAFs are important in activating transcription factors NF-kB and/or IRF-3 by hMPV. Our findings collectively demonstrate that M2-2 uses its PDZ motifs to launch the hMPV immune evasion through blocking the interaction of MAVS and its downstream TRAFs. PMID:27743962

S5H/DMR6 Encodes a Salicylic Acid 5-Hydroxylase That Fine-Tunes Salicylic Acid Homeostasis

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

Zhang, Yanjun; Zhao, Li; Zhao, Jiangzhe

The phytohormone salicylic acid (SA) plays essential roles in biotic and abiotic responses, plant development, and leaf senescence. 2,5-Dihydroxybenzoic acid (2,5-DHBA or gentisic acid) is one of the most commonly occurring aromatic acids in green plants and is assumed to be generated from SA, but the enzymes involved in its production remain obscure. DMR6 (Downy Mildew Resistant 6, At5g24530) has been proven essential in plant immunity of Arabidopsis, but its biochemical properties are not well understood. Here in this paper, we report the discovery and functional characterization of DMR6 as a SA 5-hydroxylase (S5H) that catalyzes the formation of 2,5-DHBAmore » by hydroxylating SA at the C5 position of its phenyl ring in Arabidopsis. S5H/DMR6 specifically converts SA to 2,5-DHBA in vitro and displays higher catalytic efficiency (K cat/K m=4.96×10 4 M -1s -1) than the previously reported SA 3-hydroxylase (S3H, K cat/K m=6.09 × 10 3 M -1s -1) for SA. Interestingly, S5H/DMR6 displays a substrate inhibition property that may enable automatic control of its enzyme activities. The s5h mutant and s5hs3h double mutant over accumulate SA and display phenotypes such as a smaller growth size, early senescence and a loss of susceptibility to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). S5H/DMR6 is sensitively induced by SA/pathogen treatment and is widely expressed from young seedlings to senescing plants, whereas S3H is more specifically expressed at the mature and senescing stages. Collectively, our results disclose the identity of the enzyme required for 2,5-DHBA formation and reveal a mechanism by which plants fine-tune SA homeostasis by mediating SA 5-hydroxylation.« less

S5H/DMR6 Encodes a Salicylic Acid 5-Hydroxylase That Fine-Tunes Salicylic Acid Homeostasis

DOE PAGES

Zhang, Yanjun; Zhao, Li; Zhao, Jiangzhe; ...

2017-09-12

The phytohormone salicylic acid (SA) plays essential roles in biotic and abiotic responses, plant development, and leaf senescence. 2,5-Dihydroxybenzoic acid (2,5-DHBA or gentisic acid) is one of the most commonly occurring aromatic acids in green plants and is assumed to be generated from SA, but the enzymes involved in its production remain obscure. DMR6 (Downy Mildew Resistant 6, At5g24530) has been proven essential in plant immunity of Arabidopsis, but its biochemical properties are not well understood. Here in this paper, we report the discovery and functional characterization of DMR6 as a SA 5-hydroxylase (S5H) that catalyzes the formation of 2,5-DHBAmore » by hydroxylating SA at the C5 position of its phenyl ring in Arabidopsis. S5H/DMR6 specifically converts SA to 2,5-DHBA in vitro and displays higher catalytic efficiency (K cat/K m=4.96×10 4 M -1s -1) than the previously reported SA 3-hydroxylase (S3H, K cat/K m=6.09 × 10 3 M -1s -1) for SA. Interestingly, S5H/DMR6 displays a substrate inhibition property that may enable automatic control of its enzyme activities. The s5h mutant and s5hs3h double mutant over accumulate SA and display phenotypes such as a smaller growth size, early senescence and a loss of susceptibility to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). S5H/DMR6 is sensitively induced by SA/pathogen treatment and is widely expressed from young seedlings to senescing plants, whereas S3H is more specifically expressed at the mature and senescing stages. Collectively, our results disclose the identity of the enzyme required for 2,5-DHBA formation and reveal a mechanism by which plants fine-tune SA homeostasis by mediating SA 5-hydroxylation.« less

Dynamics of planetary rings

NASA Technical Reports Server (NTRS)

Araki, Suguru

1991-01-01

The modeling of the dynamics of particle collisions within planetary rings is discussed. Particles in the rings collide with one another because they have small random motions in addition to their orbital velocity. The orbital speed is roughly 10 km/s, while the random motions have an average speed of about a tenth of a millimeter per second. As a result, the particle collisions are very gentle. Numerical analysis and simulation of the ring dynamics, performed with the aid of a supercomputer, is outlined.

Hopkins with SPHERES RINGS

NASA Image and Video Library

2013-11-04

ISS037-E-025870 (4 Nov. 2013) --- In the International Space Station?s Kibo laboratory, NASA astronaut Michael Hopkins, Expedition 37 flight engineer, conducts a session with a pair of bowling-ball-sized free-flying satellites known as Synchronized Position Hold, Engage, Reorient, Experimental Satellites, or SPHERES. Surrounding the two SPHERES mini-satellites is ring-shaped hardware known as the Resonant Inductive Near-field Generation System, or RINGS. SPHERES-RINGS seeks to demonstrate wireless power transfer between satellites at a distance for enhanced operations.

Hopkins with SPHERES RINGS

NASA Image and Video Library

2013-11-04

ISS037-E-025868 (4 Nov. 2013) --- In the International Space Station?s Kibo laboratory, NASA astronaut Michael Hopkins, Expedition 37 flight engineer, conducts a session with a pair of bowling-ball-sized free-flying satellites known as Synchronized Position Hold, Engage, Reorient, Experimental Satellites, or SPHERES. Surrounding the two SPHERES mini-satellites is ring-shaped hardware known as the Resonant Inductive Near-field Generation System, or RINGS. SPHERES-RINGS seeks to demonstrate wireless power transfer between satellites at a distance for enhanced operations.

Hopkins with SPHERES RINGS

NASA Image and Video Library

2013-11-04

ISS037-E-025866 (4 Nov. 2013) --- In the International Space Station?s Kibo laboratory, NASA astronaut Michael Hopkins, Expedition 37 flight engineer, conducts a session with a pair of bowling-ball-sized free-flying satellites known as Synchronized Position Hold, Engage, Reorient, Experimental Satellites, or SPHERES. Surrounding the two SPHERES mini-satellites is ring-shaped hardware known as the Resonant Inductive Near-field Generation System, or RINGS. SPHERES-RINGS seeks to demonstrate wireless power transfer between satellites at a distance for enhanced operations.

Hopkins with SPHERES RINGS

NASA Image and Video Library

2013-11-04

ISS037-E-025872 (4 Nov. 2013) --- In the International Space Station?s Kibo laboratory, NASA astronaut Michael Hopkins, Expedition 37 flight engineer, conducts a session with a pair of bowling-ball-sized free-flying satellites known as Synchronized Position Hold, Engage, Reorient, Experimental Satellites, or SPHERES. Surrounding the two SPHERES mini-satellites is ring-shaped hardware known as the Resonant Inductive Near-field Generation System, or RINGS. SPHERES-RINGS seeks to demonstrate wireless power transfer between satellites at a distance for enhanced operations.

Hopkins with SPHERES RINGS

NASA Image and Video Library

2013-11-04

ISS037-E-025879 (4 Nov. 2013) --- In the International Space Station?s Kibo laboratory, NASA astronaut Michael Hopkins, Expedition 37 flight engineer, conducts a session with a pair of bowling-ball-sized free-flying satellites known as Synchronized Position Hold, Engage, Reorient, Experimental Satellites, or SPHERES. Surrounding the two SPHERES mini-satellites is ring-shaped hardware known as the Resonant Inductive Near-field Generation System, or RINGS. SPHERES-RINGS seeks to demonstrate wireless power transfer between satellites at a distance for enhanced operations.

Synthesis and X-ray structural investigation of (5R*,6S*)-1-benzoyl-5-methylthio-6-methoxy-1-azapenam

NASA Astrophysics Data System (ADS)

Krajewski, J. W.; Gluziński, P.; Grochowski, E.; Pupek, K.; Mishnyov, A.; Kemme, A.

1992-08-01

The compound (5R*,6S*)-1-benzoyl-5-methylthio-6-methoxy-1-azapenam ( 3) has been synthesized and its structure investigated by X-ray diffraction. The compound crystallizes in a monoclinic system, space group Cc, Z = 4, a = 12.01(1), b = 16.51(1), c = 8.048(6) Å, β = 115.87(6)°. The structure was solved by direct methods and refined by a full-matrix, least-squares procedure to give R = 0.070, Rw = 0.046, w = 1.34/(σ 2F). The expected cis configuration around the β-lactam ring was fully confirmed.

Oscillations at B Ring Edge

NASA Image and Video Library

2010-11-01

This image obtained by NASA Cassini spacecraft of the outer edge of Saturn?s B ring, reveals the combined effects of a tugging moon and oscillations that can naturally occur in disks like Saturn rings and spiral galaxies.

The opposition and tilt effects of Saturn’s rings from HST observations

NASA Astrophysics Data System (ADS)

Salo, Heikki; French, Richard G.

2010-12-01

The two major factors contributing to the opposition brightening of Saturn's rings are (i) the intrinsic brightening of particles due to coherent backscattering and/or shadow hiding on their surfaces, and (ii) the reduced interparticle shadowing when the solar phase angle α → 0°. We utilize the extensive set of Hubble Space Telescope observations (Cuzzi, J.N., French, R.G., Dones, L. [2002]. Icarus 158, 199-223) for different elevation angles B and wavelengths λ to disentangle these contributions. We assume that the intrinsic contribution is independent of B, so that any B dependence of the phase curves is due to interparticle shadowing, which must also act similarly for all λ's. Our study complements that of Poulet et al. (Poulet, F., Cuzzi, J.N., French, R.G., Dones, L. [2002]. Icarus 158, 224), who used a subset of data for a single B ˜ 10°, and the French et al. (French, R.G., Verbiscer, A., Salo, H., McGhee, C.A., Dones, L. [2007b] PASP 119, 623-642) study for the B ˜ 23° data set that included exact opposition. We construct a grid of dynamical/photometric simulation models, with the method of Salo and Karjalainen (Salo and Karjalainen [2003]. Icarus 164, 428-460), and use these simulations to fit the elevation-dependent part of opposition brightening. Eliminating the modeled interparticle component yields the intrinsic contribution to the opposition effect: for the B and A rings it is almost entirely due to coherent backscattering; for the C ring, an intraparticle shadow hiding contribution may also be present. Based on our simulations, the width of the interparticle shadowing effect is roughly proportional to B. This follows from the observation that as B decreases, the scattering is primarily from the rarefied low filling factor upper ring layers, whereas at larger B's the dense inner parts are visible. Vertical segregation of particle sizes further enhances this effect. The elevation angle dependence of interparticle shadowing also explains most

Accidental ingestion of BiTine ring and a note on inefficient ring separation forceps.

PubMed

Baghele, Om Nemichand; Baghele, Mangala Om

2011-01-01

Accidental ingestion of medium-to-large instruments is relatively uncommon during dental treatment but can be potentially dangerous. A case of BiTine ring ingestion is presented with a note on inefficient ring separation forceps. A 28-year-old male patient accidentally ingested the BiTine ring (2 cm diameter, 0.5 cm outward projections) while it was being applied to a distoproximal cavity in tooth # 19. The ring placement forceps were excessively flexible; bending of the beaks towards the ring combined with a poor no-slippage mechanism led to sudden disengagement of the ring and accelerated movement towards the pharynx. We followed the patient with bulk forming agents and radiographs. Fortunately the ring passed out without any complications. Checking equipment and methods is as important as taking precautions against any preventable medical emergency. It is the responsibility of the clinician to check, verify and then use any instrument/equipment.

Low Optical Depth Features in Saturn's Rings: The Occultation of GSC5249-01240 by Saturn and Its Rings

NASA Astrophysics Data System (ADS)

Bosh, A. S.; Olkin, C. B.

1996-06-01

On 21 November 1995, Saturn and its rings occulted the star GSC5249-01240 (Bosh & McDonald 1992, Astron. J. 103, 983). Although the star is relatively faint (V = 11.9), other circumstances conspired to make this an excellent event: (i) the normally-bright rings were dark because the sun was crossing through the ring plane, reducing the amount of ring contribution to the background noise and therefore increasing the observed S/N, (ii) the ring opening angle was small (B ~ 3deg ), enhancing detection of low-optical-depth material, and (iii) the low sky-plane velocity allowed longer integration times without loss of spatial resolution. Thus this occultation was particularly well-suited to produce high S/N detections of low-tau ring material. We observed this atmosphere and ring occultation with the Faint Object Spectrograph (FOS) on the Hubble Space Telescope. Using the FOS in its high-speed mode, we sampled the starlight with the G650L grating, recording the stellar signal as a function of both wavelength and time. For the initial analysis of these data, the spectral information was sacrificed by binning all wavelengths together; this in turn increased the detected S/N. We performed a geometric solution for the event, using the known locations of circular ring features as fiducials (Elliot et al., Astron. J. 106, 2544). The scattered light from Saturn and the rings was modelled and subtracted from the light curves to obtain line-of-sight optical depth as a function of ring-plane radius. With these processed data we have made the first occultation detection of Saturn's innermost and very tenuous D ring. We find a line-of-sight optical depth for the thickest part of this ring of tau_ {obs} ~ 0.02. The location and morphology of this feature will be discussed. Comparison of the observed structure will be made with the previous Voyager imaging detection of this ring (Smith et al. 1981, Science 212, 163; Marley & Porco 1993, Icarus 106, 508).

NINTH INTERIM STATUS REPORT: MODEL 9975 PCV O-RING FIXTURE LONG-TERM LEAK PERFORMANCE

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

Daugherty, W.

2014-08-06

A series of experiments to monitor the aging performance of Viton® GLT O-rings used in the Model 9975 package has been ongoing since 2004 at the Savannah River National Laboratory. One approach has been to periodically evaluate the leak performance of O-rings being aged in mock-up 9975 Primary Containment Vessels (PCVs) at elevated temperatures. Other methods such as compression-stress relaxation (CSR) tests and field surveillance are also on-going to evaluate O-ring behavior. Seventy tests using PCV mock-ups were assembled and heated to temperatures ranging from 200 to 450 ºF. They were leak-tested initially and have been tested periodically to determinemore » if they continue to meet the leak-tightness criterion defined in ANSI standard N14.5-97. Due to material substitution, fourteen additional tests were initiated in 2008 with GLT-S O-rings heated to temperatures ranging from 200 to 400 ºF. High temperature aging continues for 23 GLT O-ring fixtures at 200 – 270 ºF. Room temperature leak test failures have been experienced in all of the GLT O-ring fixtures aging at 350 ºF and higher temperatures, and in 8 fixtures aging at 300 ºF. The earliest 300 °F GLT O-ring fixture failure was observed at 34 months. The remaining GLT O-ring fixtures aging at 300 ºF have been retired from testing following more than 5 years at temperature without failure. No failures have yet been observed in GLT O-ring fixtures aging at 200 ºF for 72 - 96 months, which bounds O-ring temperatures anticipated during storage in K-Area Complex (KAC). Based on expectations that the 200 ºF fixtures will remain leak-tight for a significant period yet to come, 2 additional fixtures began aging in 2011 at 270 ºF, with hopes that they may reach a failure condition before the 200 ºF fixtures, thus providing additional time to failure data. High temperature aging continues for 6 GLT-S O-ring fixtures at 200 – 300 ºF. Room temperature leak test failures have been experienced in all 8

2-[4-(4,5-Dihydro-1H-pyrrol-2-yl)phen­yl]-4,5-dihydro-1H-imidazole

PubMed Central

Kia, Reza; Fun, Hoong-Kun; Kargar, Hadi

2008-01-01

The mol­ecule of the title compound, C12H14N4, lies about a crystallographic inversion centre. The five- and six-membered rings are twisted from each other, forming a dihedral angle of 18.06 (7)°. In the crystal structure, neighbouring mol­ecules are linked by inter­molecular N—H⋯N hydrogen bonds into one-dimensional infinite chains forming 18-membered rings with R 2 2(18) motifs. The crystal structure is further stabilized by weak inter­molecular π–π stacking [centroid–centroid distance = 3.8254 (6) Å] and C—H⋯π inter­actions. PMID:21581375

An experimental test of a fundamental food web motif.

PubMed

Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

2010-06-07

Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

Oxygen Abundances in the Rings of Polar-Ring Galaxies

NASA Astrophysics Data System (ADS)

Radtke, I. R.; Eskridge, P. B.; Pogge, R. W.

2003-05-01

Polar ring galaxies (PRGs) are typically early-type (S0 or E) galaxies surrounded by rings of gas, dust, and stars orbiting nearly perpendicular to the principle plane of the host galaxy (Whitmore et al. 1990 AJ 100 1489). Given that PRGs have two separate, perpendicular axes of rotation, it is clear on dynamical grounds that PRGs are the products of merger events between two galaxies, but are observed in a state where two distinct kinematic and morphological structures are still apparent. As such, they present a unique opportunity to study merger events in systems where the debris is not confused with material from the host. Our understanding of the relative importance of polar ring systems in the overall process of galaxy evolution is confounded by our lack of knowledge regarding the typical lifetimes and evolutionary histories of polar rings. A crucial factor for understanding the formation and evolution of PRGs is information regarding the elemental abundances of the ring material. Polar rings are typically rich in {\\protectH 2} regions. Optical spectroscopy of these {\\protectH 2} regions can tell us their density, temperature, and oxygen abundance. Our earlier work (Eskridge & Pogge 1997 ApJ 486 259) revealed roughly Solar oxygen abundances for {\\protectH 2} regions in the polar ring of NGC 2685. We have extended this project, and now have spectra for six PRGs. Analysis of the data for II Zw 73 and UGC 7576 reveal the polar rings of these galaxies to have {\\protectH 2} region oxygen abundances in the range 0.3 to 0.6 Solar, substantially less than found for NGC 2685. Abundances in this range are much easier to explain with conventional models of chemical enrichment and polar ring formation. We shall present results for our full sample. Taken as a whole, this sample will provide a clear foundation for the typical chemical enrichment patterns in polar rings, and thus provide a clearer understanding of the formation and evolution of these curious objects. We

AM 2217-490: A polar ring galaxy under construction

NASA Astrophysics Data System (ADS)

Freitas-Lemes, P.; Rodrigues, I.; Faúndez-Abans, M.; Dors, O.

2014-10-01

This work is part of a series of case studies of Polar Ring Galaxies (PRGs) (see also Posters GAL-1: 163, GAL-2: 178). A PRG is formed by an early type host galaxy (e.g. lenticular or elliptical), surrounded by a ring of gas and stars orbiting approximately at the polar plane of the host galaxy. AM2217-490 is an interesting case of PRG in formation, with a still asymmetrical ring that surrounds the host galaxy. Apparently, this bluish structure (characteristic of the rings of PRGs), is not yet in equilibrium with the host galaxy. This study is based on spectra on the range 6250-7250 Å obtained with the CTIO 1.5 m telescope - Chile. From them, we measure a heliocentric radial velocity of 9152± 18 km/s. The value of the ionization parameter (log U = -3.5) is similar to that in interacting galaxies (Freitas-Lemes et al. 2013, submitted to MNRAS; and Krabbe et al. 2013, MNRAS Accepted), and lower than that of isolated ones. The electron density shows little variation along the major axis of the host galaxy, and a mean value typical of interacting galaxies. Diagnostic diagrams show that the nuclear region harbors an AGN, following a trend among polar ring galaxies. The low-resolution images of the SDSS show no tails or bridges connecting the galaxy to other objects, however, in a radius of 5 arcmin there are three other galaxies with similar speeds, featuring a group. A plausible hypothesis is that one of these galaxies may have interacted with AM2217-490, donating material to form the ring.

Nuclear localization of the dehydrin OpsDHN1 is determined by histidine-rich motif.

PubMed

Hernández-Sánchez, Itzell E; Maruri-López, Israel; Ferrando, Alejandro; Carbonell, Juan; Graether, Steffen P; Jiménez-Bremont, Juan F

2015-01-01

The cactus OpsDHN1 dehydrin belongs to a large family of disordered and highly hydrophilic proteins known as Late Embryogenesis Abundant (LEA) proteins, which accumulate during the late stages of embryogenesis and in response to abiotic stresses. Herein, we present the in vivo OpsDHN1 subcellular localization by N-terminal GFP translational fusion; our results revealed a cytoplasmic and nuclear localization of the GFP::OpsDHN1 protein in Nicotiana benthamiana epidermal cells. In addition, dimer assembly of OpsDHN1 in planta using a Bimolecular Fluorescence Complementation (BiFC) approach was demonstrated. In order to understand the in vivo role of the histidine-rich motif, the OpsDHN1-ΔHis version was produced and assayed for its subcellular localization and dimer capability by GFP fusion and BiFC assays, respectively. We found that deletion of the OpsDHN1 histidine-rich motif restricted its localization to cytoplasm, but did not affect dimer formation. In addition, the deletion of the S-segment in the OpsDHN1 protein affected its nuclear localization. Our data suggest that the deletion of histidine-rich motif and S-segment show similar effects, preventing OpsDHN1 from getting into the nucleus. Based on these results, the histidine-rich motif is proposed as a targeting element for OpsDHN1 nuclear localization.

Nuclear localization of the dehydrin OpsDHN1 is determined by histidine-rich motif

PubMed Central

Hernández-Sánchez, Itzell E.; Maruri-López, Israel; Ferrando, Alejandro; Carbonell, Juan; Graether, Steffen P.; Jiménez-Bremont, Juan F.

2015-01-01

The cactus OpsDHN1 dehydrin belongs to a large family of disordered and highly hydrophilic proteins known as Late Embryogenesis Abundant (LEA) proteins, which accumulate during the late stages of embryogenesis and in response to abiotic stresses. Herein, we present the in vivo OpsDHN1 subcellular localization by N-terminal GFP translational fusion; our results revealed a cytoplasmic and nuclear localization of the GFP::OpsDHN1 protein in Nicotiana benthamiana epidermal cells. In addition, dimer assembly of OpsDHN1 in planta using a Bimolecular Fluorescence Complementation (BiFC) approach was demonstrated. In order to understand the in vivo role of the histidine-rich motif, the OpsDHN1-ΔHis version was produced and assayed for its subcellular localization and dimer capability by GFP fusion and BiFC assays, respectively. We found that deletion of the OpsDHN1 histidine-rich motif restricted its localization to cytoplasm, but did not affect dimer formation. In addition, the deletion of the S-segment in the OpsDHN1 protein affected its nuclear localization. Our data suggest that the deletion of histidine-rich motif and S-segment show similar effects, preventing OpsDHN1 from getting into the nucleus. Based on these results, the histidine-rich motif is proposed as a targeting element for OpsDHN1 nuclear localization. PMID:26442018

Moonlet induced wakes in planetary rings: Analytical model including eccentric orbits of moon and ring particles

NASA Astrophysics Data System (ADS)

Seiß, M.; Spahn, F.; Schmidt, Jürgen

2010-11-01

Saturn's rings host two known moons, Pan and Daphnis, which are massive enough to clear circumferential gaps in the ring around their orbits. Both moons create wake patterns at the gap edges by gravitational deflection of the ring material (Cuzzi, J.N., Scargle, J.D. [1985]. Astrophys. J. 292, 276-290; Showalter, M.R., Cuzzi, J.N., Marouf, E.A., Esposito, L.W. [1986]. Icarus 66, 297-323). New Cassini observations revealed that these wavy edges deviate from the sinusoidal waveform, which one would expect from a theory that assumes a circular orbit of the perturbing moon and neglects particle interactions. Resonant perturbations of the edges by moons outside the ring system, as well as an eccentric orbit of the embedded moon, may partly explain this behavior (Porco, C.C., and 34 colleagues [2005]. Science 307, 1226-1236; Tiscareno, M.S., Burns, J.A., Hedman, M.M., Spitale, J.N., Porco, C.C., Murray, C.D., and the Cassini Imaging team [2005]. Bull. Am. Astron. Soc. 37, 767; Weiss, J.W., Porco, C.C., Tiscareno, M.S., Burns, J.A., Dones, L. [2005]. Bull. Am. Astron. Soc. 37, 767; Weiss, J.W., Porco, C.C., Tiscareno, M.S. [2009]. Astron. J. 138, 272-286). Here we present an extended non-collisional streamline model which accounts for both effects. We describe the resulting variations of the density structure and the modification of the nonlinearity parameter q. Furthermore, an estimate is given for the applicability of the model. We use the streamwire model introduced by Stewart (Stewart, G.R. [1991]. Icarus 94, 436-450) to plot the perturbed ring density at the gap edges. We apply our model to the Keeler gap edges undulated by Daphnis and to a faint ringlet in the Encke gap close to the orbit of Pan. The modulations of the latter ringlet, induced by the perturbations of Pan (Burns, J.A., Hedman, M.M., Tiscareno, M.S., Nicholson, P.D., Streetman, B.J., Colwell, J.E., Showalter, M.R., Murray, C.D., Cuzzi, J.N., Porco, C.C., and the Cassini ISS team [2005]. Bull. Am

Mechanisms of Zero-Lag Synchronization in Cortical Motifs

PubMed Central

Gollo, Leonardo L.; Mirasso, Claudio; Sporns, Olaf; Breakspear, Michael

2014-01-01

Zero-lag synchronization between distant cortical areas has been observed in a diversity of experimental data sets and between many different regions of the brain. Several computational mechanisms have been proposed to account for such isochronous synchronization in the presence of long conduction delays: Of these, the phenomenon of “dynamical relaying” – a mechanism that relies on a specific network motif – has proven to be the most robust with respect to parameter mismatch and system noise. Surprisingly, despite a contrary belief in the community, the common driving motif is an unreliable means of establishing zero-lag synchrony. Although dynamical relaying has been validated in empirical and computational studies, the deeper dynamical mechanisms and comparison to dynamics on other motifs is lacking. By systematically comparing synchronization on a variety of small motifs, we establish that the presence of a single reciprocally connected pair – a “resonance pair” – plays a crucial role in disambiguating those motifs that foster zero-lag synchrony in the presence of conduction delays (such as dynamical relaying) from those that do not (such as the common driving triad). Remarkably, minor structural changes to the common driving motif that incorporate a reciprocal pair recover robust zero-lag synchrony. The findings are observed in computational models of spiking neurons, populations of spiking neurons and neural mass models, and arise whether the oscillatory systems are periodic, chaotic, noise-free or driven by stochastic inputs. The influence of the resonance pair is also robust to parameter mismatch and asymmetrical time delays amongst the elements of the motif. We call this manner of facilitating zero-lag synchrony resonance-induced synchronization, outline the conditions for its occurrence, and propose that it may be a general mechanism to promote zero-lag synchrony in the brain. PMID:24763382

The effect of orthology and coregulation on detecting regulatory motifs.

PubMed

Storms, Valerie; Claeys, Marleen; Sanchez, Aminael; De Moor, Bart; Verstuyf, Annemieke; Marchal, Kathleen

2010-02-03

Computational de novo discovery of transcription factor binding sites is still a challenging problem. The growing number of sequenced genomes allows integrating orthology evidence with coregulation information when searching for motifs. Moreover, the more advanced motif detection algorithms explicitly model the phylogenetic relatedness between the orthologous input sequences and thus should be well adapted towards using orthologous information. In this study, we evaluated the conditions under which complementing coregulation with orthologous information improves motif detection for the class of probabilistic motif detection algorithms with an explicit evolutionary model. We designed datasets (real and synthetic) covering different degrees of coregulation and orthologous information to test how well Phylogibbs and Phylogenetic sampler, as representatives of the motif detection algorithms with evolutionary model performed as compared to MEME, a more classical motif detection algorithm that treats orthologs independently. Under certain conditions detecting motifs in the combined coregulation-orthology space is indeed more efficient than using each space separately, but this is not always the case. Moreover, the difference in success rate between the advanced algorithms and MEME is still marginal. The success rate of motif detection depends on the complex interplay between the added information and the specificities of the applied algorithms. Insights in this relation provide information useful to both developers and users. All benchmark datasets are available at http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Storms_Valerie_PlosONE.

Deletion of transcription factor binding motifs using the CRISPR/spCas9 system in the β-globin LCR.

PubMed

Kim, Yea Woon; Kim, AeRi

2017-07-20

Transcription factors play roles in gene transcription through direct binding to their motifs in genome, and inhibiting this binding provides an effective strategy for studying their roles. Here we applied the CRISPR/spCas9 system to mutate the binding motifs of transcription factors. Binding motifs for erythroid specific transcription factors were mutated in the locus control region hypersensitive sites of the human β-globin locus. Guide RNAs targeting binding motifs were cloned into lentiviral CRISPR vector containing the spCas9 gene, and transduced into MEL/ch11 cells carrying a human chromosome 11. DNA mutations in clonal cells were initially screened by quantitative PCR in genomic DNA and then clarified by sequencing. Mutations in binding motifs reduced occupancy by transcription factors in a chromatin environment. Characterization of mutations revealed that the CRISPR/spCas9 system mainly induced deletions in short regions of <20 bp and preferentially deleted nucleotides around the fifth nucleotide upstream of Protospacer adjacent motifs. These results indicate that the CRISPR/Cas9 system is suitable for mutating the binding motifs of transcription factors, and, consequently, would contribute to elucidate the direct roles of transcription factors. ©2017 The Author(s).

Ca2+-Induced Rigidity Change of the Myosin VIIa IQ Motif-Single α Helix Lever Arm Extension.

PubMed

Li, Jianchao; Chen, Yiyun; Deng, Yisong; Unarta, Ilona Christy; Lu, Qing; Huang, Xuhui; Zhang, Mingjie

2017-04-04

Several unconventional myosins contain a highly charged single α helix (SAH) immediately following the calmodulin (CaM) binding IQ motifs, functioning to extend lever arms of these myosins. How such SAH is connected to the IQ motifs and whether the conformation of the IQ motifs-SAH segments are regulated by Ca 2+ fluctuations are not known. Here, we demonstrate by solving its crystal structure that the predicted SAH of myosin VIIa (Myo7a) forms a stable SAH. The structure of Myo7a IQ5-SAH segment in complex with apo-CaM reveals that the SAH sequence can extend the length of the Myo7a lever arm. Although Ca 2+ -CaM remains bound to IQ5-SAH, the Ca 2+ -induced CaM binding mode change softens the conformation of the IQ5-SAH junction, revealing a Ca 2+ -induced lever arm flexibility change for Myo7a. We further demonstrate that the last IQ motif of several other myosins also binds to both apo- and Ca 2+ -CaM, suggesting a common Ca 2+ -induced conformational regulation mechanism. Copyright © 2017 Elsevier Ltd. All rights reserved.

cWINNOWER algorithm for finding fuzzy dna motifs

NASA Technical Reports Server (NTRS)

Liang, S.; Samanta, M. P.; Biegel, B. A.

2004-01-01

The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in protein-binding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if a clique consisting of a sufficiently large number of mutated copies of the motif (i.e., the signals) is present in the DNA sequence. The cWINNOWER algorithm substantially improves the sensitivity of the winnower method of Pevzner and Sze by imposing a consensus constraint, enabling it to detect much weaker signals. We studied the minimum detectable clique size qc as a function of sequence length N for random sequences. We found that qc increases linearly with N for a fast version of the algorithm based on counting three-member sub-cliques. Imposing consensus constraints reduces qc by a factor of three in this case, which makes the algorithm dramatically more sensitive. Our most sensitive algorithm, which counts four-member sub-cliques, needs a minimum of only 13 signals to detect motifs in a sequence of length N = 12,000 for (l, d) = (15, 4). Copyright Imperial College Press.

SELEX and SHAPE reveal that sequence motifs and an extended hairpin in the 5' portion of Turnip crinkle virus satellite RNA C mediate fitness in plants.

PubMed

Bayne, Charlie F; Widawski, Max E; Gao, Feng; Masab, Mohammed H; Chattopadhyay, Maitreyi; Murawski, Allison M; Sansevere, Robert M; Lerner, Bryan D; Castillo, Rinaldys J; Griesman, Trevor; Fu, Jiantao; Hibben, Jennifer K; Garcia-Perez, Alma D; Simon, Anne E; Kushner, David B

2018-07-01

Noncoding RNAs use their sequence and/or structure to mediate function(s). The 5' portion (166 nt) of the 356-nt noncoding satellite RNA C (satC) of Turnip crinkle virus (TCV) was previously modeled to contain a central region with two stem-loops (H6 and H7) and a large connecting hairpin (H2). We now report that in vivo functional selection (SELEX) experiments assessing sequence/structure requirements in H2, H6, and H7 reveal that H6 loop sequence motifs were recovered at nonrandom rates and only some residues are proposed to base-pair with accessible complementary sequences within the 5' central region. In vitro SHAPE of SELEX winners indicates that the central region is heavily base-paired, such that along with the lower stem and H2 region, one extensive hairpin exists composing the entire 5' region. As these SELEX winners are highly fit, these characteristics facilitate satRNA amplification in association with TCV in plants. Copyright © 2018 Elsevier Inc. All rights reserved.

SPHERES-RINGS Time Lapse

NASA Image and Video Library

2014-07-10

ISS040-E-059344 (10 July 2014) --- In the International Space Station’s Kibo laboratory, NASA astronaut Reid Wiseman (left) and European Space Agency astronaut Alexander Gerst, both Expedition 40 flight engineers, conduct a session with a pair of bowling-ball-sized free-flying satellites known as Synchronized Position Hold, Engage, Reorient, Experimental Satellites, or SPHERES. Surrounding the two SPHERES mini-satellites is ring-shaped hardware known as the Resonant Inductive Near-field Generation System, or RINGS. SPHERES-RINGS seeks to demonstrate wireless power transfer between satellites at a distance for enhanced operations.

DNA motifs associated with aberrant CpG island methylation.

PubMed

Feltus, F Alex; Lee, Eva K; Costello, Joseph F; Plass, Christoph; Vertino, Paula M

2006-05-01

Epigenetic silencing involving the aberrant methylation of promoter region CpG islands is widely recognized as a tumor suppressor silencing mechanism in cancer. However, the molecular pathways underlying aberrant DNA methylation remain elusive. Recently we showed that, on a genome-wide level, CpG island loci differ in their intrinsic susceptibility to aberrant methylation and that this susceptibility can be predicted based on underlying sequence context. These data suggest that there are sequence/structural features that contribute to the protection from or susceptibility to aberrant methylation. Here we use motif elicitation coupled with classification techniques to identify DNA sequence motifs that selectively define methylation-prone or methylation-resistant CpG islands. Motifs common to 28 methylation-prone or 47 methylation-resistant CpG island-containing genomic fragments were determined using the MEME and MAST algorithms (). The five most discriminatory motifs derived from methylation-prone sequences were found to be associated with CpG islands in general and were nonrandomly distributed throughout the genome. In contrast, the eight most discriminatory motifs derived from the methylation-resistant CpG islands were randomly distributed throughout the genome. Interestingly, this latter group tended to associate with Alu and other repetitive sequences. Used together, the frequency of occurrence of these motifs successfully discriminated methylation-prone and methylation-resistant CpG island groups with an accuracy of 87% after 10-fold cross-validation. The motifs identified here are candidate methylation-targeting or methylation-protection DNA sequences.

Rotavirus NSP1 Requires Casein Kinase II-Mediated Phosphorylation for Hijacking of Cullin-RING Ligases.

PubMed

Davis, Kaitlin A; Morelli, Marco; Patton, John T

2017-08-29

The rotavirus nonstructural protein NSP1 repurposes cullin-RING E3 ubiquitin ligases (CRLs) to antagonize innate immune responses. By functioning as substrate adaptors of hijacked CRLs, NSP1 causes ubiquitination and proteasomal degradation of host proteins that are essential for expression of interferon (IFN) and IFN-stimulated gene products. The target of most human and porcine rotaviruses is the β-transducin repeat-containing protein (β-TrCP), a regulator of NF-κB activation. β-TrCP recognizes a phosphorylated degron (DSGΦXS) present in the inhibitor of NF-κB (IκB); phosphorylation of the IκB degron is mediated by IκB kinase (IKK). Because NSP1 contains a C-terminal IκB-like degron (ILD; DSGXS) that recruits β-TrCP, we investigated whether the NSP1 ILD is similarly activated by phosphorylation and whether this modification is required to trigger the incorporation of NSP1 into CRLs. Based on mutagenesis and phosphatase treatment studies, we found that both serine residues of the NSP1 ILD are phosphorylated, a pattern mimicking phosphorylation of IκB. A three-pronged approach using small-molecule inhibitors, small interfering RNAs, and mutagenesis demonstrated that NSP1 phosphorylation is mediated by the constitutively active casein kinase II (CKII), rather than IKK. In coimmunoprecipitation assays, we found that this modification was essential for NSP1 recruitment of β-TrCP and induced changes involving the NSP1 N-terminal RING motif that allowed formation of Cul3-NSP1 complexes. Taken together, our results indicate a highly regulated stepwise process in the formation of NSP1-Cul3 CRLs that is initiated by CKII phosphorylation of NSP1, followed by NSP1 recruitment of β-TrCP and ending with incorporation of the NSP1-β-TrCP complex into the CRL via interactions dependent on the highly conserved NSP1 RING motif. IMPORTANCE Rotavirus is a segmented double-stranded RNA virus that causes severe diarrhea in young children. A primary mechanism used by the

EIGHTH INTERIM STATUS REPORT: MODEL 9975 PCV O-RING FIXTURE LONG-TERM LEAK PERFORMANCE

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

Daugherty, W. L.

2013-09-03

A series of experiments to monitor the aging performance of Viton® GLT O-rings used in the Model 9975 package has been ongoing since 2004 at the Savannah River National Laboratory. Seventy tests using mock-ups of 9975 Primary Containment Vessels (PCVs) were assembled and heated to temperatures ranging from 200 to 450 ºF. They were leak-tested initially and have been tested periodically to determine if they meet the criterion of leak-tightness defined in ANSI standard N14.5-97. Fourteen additional tests were initiated in 2008 with GLT-S O-rings heated to temperatures ranging from 200 to 400 ºF. High temperature aging continues for 23more » GLT O-ring fixtures at 200 – 270 ºF. Room temperature leak test failures have been experienced in all of the GLT O-ring fixtures aging at 350 ºF and higher temperatures, and in 8 fixtures aging at 300 ºF. The remaining GLT O-ring fixtures aging at 300 ºF have been retired from testing following more than 5 years at temperature without failure. No failures have yet been observed in GLT O-ring fixtures aging at 200 ºF for 61 - 85 months, which is still bounding to O-ring temperatures during storage in KArea Complex (KAC). Based on expectations that the fixtures aging at 200 ºF will remain leaktight for a significant period yet to come, 2 additional fixtures began aging in 2011 at an intermediate temperature of 270 ºF, with hopes that they may reach a failure condition before the 200 ºF fixtures. High temperature aging continues for 6 GLT-S O-ring fixtures at 200 – 300 ºF. Room temperature leak test failures have been experienced in all 8 of the GLT-S O-ring fixtures aging at 350 and 400 ºF. No failures have yet been observed in GLT-S O-ring fixtures aging at 200 - 300 ºF for 41 - 45 months. Aging and periodic leak testing will continue for the remaining PCV fixtures.« less

Discriminative motif discovery via simulated evolution and random under-sampling.

PubMed

Song, Tao; Gu, Hong

2014-01-01

Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs) training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

The Consequences of Saturn’s Rotating Asymmetric Ring Current

NASA Astrophysics Data System (ADS)

Southwood, D. J.; Kivelson, M. G.

2009-12-01

The plasma and field behavior in the dipolar region of the Saturnian magnetosphere is described, based primarily on interpretation of the magnetic field behavior measured by the Cassini spacecraft. Previous authors, such as Provan and Khurana, have pointed out that the regular pulses in field strength at around 10.8 hrs period detected in this region imply the existence not only of a symmetric ring current but also of a partial ring current. Once spacecraft motion in local time has been allowed for, one finds a close to sinusoidal variation with azimuth and time of the magnetic signal. Hence the partial ring current appears to quasi-rigidly rotate about the planetary axis at the same 10.8 hr period as the pulsing of the Saturn kilometric radiation. We point out that, independent of whether the excess current is due to asymmetry in flux tube population or in plasma beta (pressure normalized to field pressure), such a current gives rise to a rotating circulation system. The compressional field pattern is consistent with an m = 1 pattern of circulation. The fairly uniform inner magnetosphere cam magnetic signature predicted on the basis of inner magnetosphere transverse field components in our past work is modified in a systematic way by the partial ring current effects. The circulation due to the partial ring current has its own set of distributed field aligned currents (FACs). The rotating transverse perturbation field components are twisted by the FACs so that the radial field is reduced at low L-shells and increased at larger L. Overall the cam field is depressed at low L and enhanced as one approaches the boundary of the cam region at L = 10-12. In practice the system must also respond to some local time effects. Loss of plasma is easier on the night-side and flanks than on the day-side and so a day-night asymmetry is imposed tending to increase the perturbation field amplitudes by night. The FACs driven by the asymmetric ring current should be broadly

Saturn's Rings and Associated Ring Plasma Cavity: Evidence for Slow Ring Erosion

NASA Technical Reports Server (NTRS)

Farrell, W. M.; Kurth, W. S.; Gurnett, D. A.; Persoon, A. M.; MacDowall, R. J.

2017-01-01

We re-examine the radio and plasma wave observations obtained during the Cassini Saturn orbit insertion period, as the spacecraft flew over the northern ring surface into a radial distance of 1.3 Rs (over the C-ring). Voyager era studies suggest the rings are a source of micro-meteoroid generated plasma and dust, with theorized peak impact-created plasma outflows over the densest portion of the rings (central B-ring). In sharp contrast, the Cassini Radio and Plasma Wave System (RPWS) observations identify the presence of a ring-plasma cavity located in the central portion of the B-ring, with little evidence of impact-related plasma. While previous Voyager era studies have predicted unstable ion orbits over the C- ring, leading to field-aligned plasma transport to Saturns ionosphere, the Cassini RPWS observations do not reveal evidence for such instability-created plasma fountains. Given the passive ring loss processes observed by Cassini, we find that the ring lifetimes should extend >10(exp 9) years, and that there is limited evidence for prompt destruction (loss in <100 Myrs).

Saturn's rings and associated ring plasma cavity: Evidence for slow ring erosion

NASA Astrophysics Data System (ADS)

Farrell, W. M.; Kurth, W. S.; Gurnett, D. A.; Persoon, A. M.; MacDowall, R. J.

2017-08-01

We re-examine the radio and plasma wave observations obtained during the Cassini Saturn orbit insertion period, as the spacecraft flew over the northern ring surface into a radial distance of 1.3 Rs (over the C-ring). Voyager era studies suggest the rings are a source of micro-meteoroid generated plasma and dust, with theorized peak impact-created plasma outflows over the densest portion of the rings (central B-ring). In sharp contrast, the Cassini Radio and Plasma Wave System (RPWS) observations identify the presence of a ring-plasma cavity located in the central portion of the B-ring, with little evidence of impact-related plasma. While previous Voyager era studies have predicted unstable ion orbits over the C-ring, leading to field-aligned plasma transport to Saturn's ionosphere, the Cassini RPWS observations do not reveal evidence for such instability-created plasma 'fountains'. Given the passive ring loss processes observed by Cassini, we find that the ring lifetimes should extend >109 years, and that there is limited evidence for prompt destruction (loss in <100 Myrs).

Crystal structure of diethyl 2-amino-6-[(thio­phen-3-yl)ethyn­yl]azulene-1,3-di­carboxyl­ate

PubMed Central

Förster, Sebastian; Seichter, Wilhelm; Weber, Edwin

2015-01-01

The title compound, C22H19NO4S, has an almost planar geometry supported by intra­molecular N—H⋯O and C—H⋯O hydrogen bonds. The thio­phene ring is inclined to the azulene ring by 4.85 (16)°, while the eth­oxy­carbonyl groups are inclined to the azulene ring by 7.0 (2) and 5.7 (2)°. In the crystal, mol­ecules are linked by pairs of N—H⋯O hydrogen bonds, forming inversion dimers with an R 2 2(12) ring motif. The dimers are linked via C—H⋯π inter­actions, forming sheets parallel to (10-1). PMID:25844254

Sequence information gain based motif analysis.

PubMed

Maynou, Joan; Pairó, Erola; Marco, Santiago; Perera, Alexandre

2015-11-09

The detection of regulatory regions in candidate sequences is essential for the understanding of the regulation of a particular gene and the mechanisms involved. This paper proposes a novel methodology based on information theoretic metrics for finding regulatory sequences in promoter regions. This methodology (SIGMA) has been tested on genomic sequence data for Homo sapiens and Mus musculus. SIGMA has been compared with different publicly available alternatives for motif detection, such as MEME/MAST, Biostrings (Bioconductor package), MotifRegressor, and previous work such Qresiduals projections or information theoretic based detectors. Comparative results, in the form of Receiver Operating Characteristic curves, show how, in 70% of the studied Transcription Factor Binding Sites, the SIGMA detector has a better performance and behaves more robustly than the methods compared, while having a similar computational time. The performance of SIGMA can be explained by its parametric simplicity in the modelling of the non-linear co-variability in the binding motif positions. Sequence Information Gain based Motif Analysis is a generalisation of a non-linear model of the cis-regulatory sequences detection based on Information Theory. This generalisation allows us to detect transcription factor binding sites with maximum performance disregarding the covariability observed in the positions of the training set of sequences. SIGMA is freely available to the public at http://b2slab.upc.edu.

Investigation of steric influences on hydrogen-bonding motifs in cyclic ureas by using X-ray, neutron, and computational methods.

PubMed

McCormick, Laura J; McDonnell-Worth, Ciaran; Platts, James A; Edwards, Alison J; Turner, David R

2013-11-01

A series of urea-derived heterocycles, 5N-substituted hexahydro-1,3,5-triazin-2-ones, has been prepared and their structures have been determined for the first time. This family of compounds only differ in their substituent at the 5-position (which is derived from the corresponding primary amine), that is, methyl (1), ethyl (2), isopropyl (3), tert-butyl (4), benzyl (5), N,N-(diethyl)ethylamine (6), and 2-hydroxyethyl (7). The common heterocyclic core of these molecules is a cyclic urea, which has the potential to form a hydrogen-bonding tape motif that consists of self-associative R₂²(8) dimers. The results from X-ray crystallography and, where possible, Laue neutron crystallography show that the hydrogen-bonding motifs that are observed and the planarity of the hydrogen bonds appear to depend on the steric hindrance at the α-carbon atom of the N substituent. With the less-hindered substituents, methyl and ethyl, the anticipated tape motif is observed. When additional methyl groups are added onto the α-carbon atom, as in the isopropyl and tert-butyl derivatives, a different 2D hydrogen-bonding motif is observed. Despite the bulkiness of the substituents, the benzyl and N,N-(diethyl)ethylamine derivatives have methylene units at the α-carbon atom and, therefore, display the tape motif. The introduction of a competing hydrogen-bond donor/acceptor in the 2-hydroxyethyl derivative disrupts the tape motif, with a hydroxy group interrupting the N-H···O=C interactions. The geometry around the hydrogen-bearing nitrogen atoms, whether planar or non-planar, has been confirmed for compounds 2 and 5 by using Laue neutron diffraction and rationalized by using computational methods, thus demonstrating that distortion of O-C-N-H torsion angles occurs to maintain almost-linear hydrogen-bonding interactions. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Density Waves in Saturn's Rings from Cassini Radio Occultations

NASA Astrophysics Data System (ADS)

French, R. G.; Rappaport, N. J.; Marouf, E. A.; McGhee, C. A.

2005-12-01

The Cassini Radio Science Team conducted a set of optimized diametric occultations by Saturn and its rings from May to September 2005, providing 11 separate probes of Saturn's ionosphere and atmosphere, and 12 optical depth profiles of the complete ring system. Each event was observed by the stations of the Deep Space Net (DSN) at three radio frequencies (S, X, Ka bands, with corresponding wavelengths of ? = 13, 3.6, and 0.9 cm). Very accurate pointing by the spacecraft and ground antennas resulted in stable baseline signal levels, and the relatively large ring opening angle (B=19-25°) permitted us to probe even quite dense ring regions with excellent SNR. The RSS occultation technique enables us to recover very fine detailed radial structure by correcting for diffraction effects. Multiple occultation chords, covering a variety of ring longitudes and ring opening angles, reveal the structure of the rings in remarkable detail, including density and bending waves, satellite wakes, and subtle variations at the 100-m radius scale. Janus and Epimetheus are responsible for a particularly rich set of density waves, and their coorbital interactions result in a complex interplay of time-variable ring structure over the 8-year libration period of the two satellites. We compare the first-order 2:1, 4:3, 5:4, and 6:5 coorbital density waves from multiple occultation chords to linear density wave models based on a dynamical model of the orbital exchange between the moons. From the observed dispersion relation of the wave crests, we infer the surface mass density and eccentricity gradient of particle streamlines, and match the detailed shapes of the wave crests using a non-linear analysis. Second-order coorbital features are also evident, and there are even hints of third-order density waves in the high SNR radio occultation data.

RNA 3D Structural Motifs: Definition, Identification, Annotation, and Database Searching

NASA Astrophysics Data System (ADS)

Nasalean, Lorena; Stombaugh, Jesse; Zirbel, Craig L.; Leontis, Neocles B.

Structured RNA molecules resemble proteins in the hierarchical organization of their global structures, folding and broad range of functions. Structured RNAs are composed of recurrent modular motifs that play specific functional roles. Some motifs direct the folding of the RNA or stabilize the folded structure through tertiary interactions. Others bind ligands or proteins or catalyze chemical reactions. Therefore, it is desirable, starting from the RNA sequence, to be able to predict the locations of recurrent motifs in RNA molecules. Conversely, the potential occurrence of one or more known 3D RNA motifs may indicate that a genomic sequence codes for a structured RNA molecule. To identify known RNA structural motifs in new RNA sequences, precise structure-based definitions are needed that specify the core nucleotides of each motif and their conserved interactions. By comparing instances of each recurrent motif and applying base pair isosteriCity relations, one can identify neutral mutations that preserve its structure and function in the contexts in which it occurs.

The 5S rDNA in two Abracris grasshoppers (Ommatolampidinae: Acrididae): molecular and chromosomal organization.

PubMed

Bueno, Danilo; Palacios-Gimenez, Octavio Manuel; Martí, Dardo Andrea; Mariguela, Tatiane Casagrande; Cabral-de-Mello, Diogo Cavalcanti

2016-08-01

The 5S ribosomal DNA (rDNA) sequences are subject of dynamic evolution at chromosomal and molecular levels, evolving through concerted and/or birth-and-death fashion. Among grasshoppers, the chromosomal location for this sequence was established for some species, but little molecular information was obtained to infer evolutionary patterns. Here, we integrated data from chromosomal and nucleotide sequence analysis for 5S rDNA in two Abracris species aiming to identify evolutionary dynamics. For both species, two arrays were identified, a larger sequence (named type-I) that consisted of the entire 5S rDNA gene plus NTS (non-transcribed spacer) and a smaller (named type-II) with truncated 5S rDNA gene plus short NTS that was considered a pseudogene. For type-I sequences, the gene corresponding region contained the internal control region and poly-T motif and the NTS presented partial transposable elements. Between the species, nucleotide differences for type-I were noticed, while type-II was identical, suggesting pseudogenization in a common ancestor. At chromosomal point to view, the type-II was placed in one bivalent, while type-I occurred in multiple copies in distinct chromosomes. In Abracris, the evolution of 5S rDNA was apparently influenced by the chromosomal distribution of clusters (single or multiple location), resulting in a mixed mechanism integrating concerted and birth-and-death evolution depending on the unit.