WorldWideScience
 
 
1

CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure.  

UK PubMed Central (United Kingdom)

BACKGROUND: One aim of the in silico characterization of proteins is to identify all residue-positions, which are crucial for function or structure. Several sequence-based algorithms exist, which predict functionally important sites. However, with respect to sequence information, many functionally and structurally important sites are hard to distinguish and consequently a large number of incorrectly predicted functional sites have to be expected. This is why we were interested to design a new classifier that differentiates between functionally and structurally important sites and to assess its performance on representative datasets. RESULTS: We have implemented CLIPS-1D, which predicts a role in catalysis, ligand-binding, or protein structure for residue-positions in a mutually exclusive manner. By analyzing a multiple sequence alignment, the algorithm scores conservation as well as abundance of residues at individual sites and their local neighborhood and categorizes by means of a multiclass support vector machine. A cross-validation confirmed that residue-positions involved in catalysis were identified with state-of-the-art quality; the mean MCC-value was 0.34. For structurally important sites, prediction quality was considerably higher (mean MCC = 0.67). For ligand-binding sites, prediction quality was lower (mean MCC = 0.12), because binding sites and structurally important residue-positions share conservation and abundance values, which makes their separation difficult. We show that classification success varies for residues in a class-specific manner. This is why our algorithm computes residue-specific p-values, which allow for the statistical assessment of each individual prediction. CLIPS-1D is available as a Web service at http://www-bioinf.uni-regensburg.de/. CONCLUSIONS: CLIPS-1D is a classifier, whose prediction quality has been determined separately for catalytic sites, ligand-binding sites, and structurally important sites. It generates hypotheses about residue-positions important for a set of homologous proteins and focuses on conservation and abundance signals. Thus, the algorithm can be applied in cases where function cannot be transferred from well-characterized proteins by means of sequence comparison.

Janda JO; Busch M; Kück F; Porfenenko M; Merkl R

2012-01-01

2

CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background One aim of the in silico characterization of proteins is to identify all residue-positions, which are crucial for function or structure. Several sequence-based algorithms exist, which predict functionally important sites. However, with respect to sequence information, many functionally and structurally important sites are hard to distinguish and consequently a large number of incorrectly predicted functional sites have to be expected. This is why we were interested to design a new classifier that differentiates between functionally and structurally important sites and to assess its performance on representative datasets. Results We have implemented CLIPS-1D, which predicts a role in catalysis, ligand-binding, or protein structure for residue-positions in a mutually exclusive manner. By analyzing a multiple sequence alignment, the algorithm scores conservation as well as abundance of residues at individual sites and their local neighborhood and categorizes by means of a multiclass support vector machine. A cross-validation confirmed that residue-positions involved in catalysis were identified with state-of-the-art quality; the mean MCC-value was 0.34. For structurally important sites, prediction quality was considerably higher (mean MCC = 0.67). For ligand-binding sites, prediction quality was lower (mean MCC = 0.12), because binding sites and structurally important residue-positions share conservation and abundance values, which makes their separation difficult. We show that classification success varies for residues in a class-specific manner. This is why our algorithm computes residue-specific p-values, which allow for the statistical assessment of each individual prediction. CLIPS-1D is available as a Web service at http://www-bioinf.uni-regensburg.de/. Conclusions CLIPS-1D is a classifier, whose prediction quality has been determined separately for catalytic sites, ligand-binding sites, and structurally important sites. It generates hypotheses about residue-positions important for a set of homologous proteins and focuses on conservation and abundance signals. Thus, the algorithm can be applied in cases where function cannot be transferred from well-characterized proteins by means of sequence comparison.

Janda Jan-Oliver; Busch Markus; Kück Fabian; Porfenenko Mikhail; Merkl Rainer

2012-01-01

3

PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences.  

UK PubMed Central (United Kingdom)

Annotation of any newly determined protein sequence depends on the pairwise sequence identity with known sequences. However, for the twilight zone sequences which have only 15-25% identity, the pair-wise comparison methods are inadequate and the annotation becomes a challenging task. Such sequences can be annotated by using methods that recognize their fold. Bowie et al. described a 3D1D profile method in which the amino acid sequences that fold into a known 3D structure are identified by their compatibility to that known 3D structure. We have improved the above method by using the predicted secondary structure information and employ it for fold recognition from the twilight zone sequences. In our Protein Secondary Structure 3D1D (PSS-3D1D) method, a score (w) for the predicted secondary structure of the query sequence is included in finding the compatibility of the query sequence to the known fold 3D structures. In the benchmarks, the PSS-3D1D method shows a maximum of 21% improvement in predicting correctly the ? + ? class of folds from the sequences with twilight zone level of identity, when compared with the 3D1D profile method. Hence, the PSS-3D1D method could offer more clues than the 3D1D method for the annotation of twilight zone sequences. The web based PSS-3D1D method is freely available in the PredictFold server at http://bioinfo.bdu.ac.in/servers/ .

Ganesan K; Parthasarathy S

2011-12-01

4

PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences.  

Science.gov (United States)

Annotation of any newly determined protein sequence depends on the pairwise sequence identity with known sequences. However, for the twilight zone sequences which have only 15-25% identity, the pair-wise comparison methods are inadequate and the annotation becomes a challenging task. Such sequences can be annotated by using methods that recognize their fold. Bowie et al. described a 3D1D profile method in which the amino acid sequences that fold into a known 3D structure are identified by their compatibility to that known 3D structure. We have improved the above method by using the predicted secondary structure information and employ it for fold recognition from the twilight zone sequences. In our Protein Secondary Structure 3D1D (PSS-3D1D) method, a score (w) for the predicted secondary structure of the query sequence is included in finding the compatibility of the query sequence to the known fold 3D structures. In the benchmarks, the PSS-3D1D method shows a maximum of 21% improvement in predicting correctly the ? + ? class of folds from the sequences with twilight zone level of identity, when compared with the 3D1D profile method. Hence, the PSS-3D1D method could offer more clues than the 3D1D method for the annotation of twilight zone sequences. The web based PSS-3D1D method is freely available in the PredictFold server at http://bioinfo.bdu.ac.in/servers/ . PMID:22160493

Ganesan, K; Parthasarathy, S

2011-12-03

5

Tandem repeats modify the structure of the canine CD1D gene.  

UK PubMed Central (United Kingdom)

Among the CD1 proteins that present lipid antigens to T cells, CD1d is the only one that stimulates a population of T cells with an invariant T-cell receptor known as NKT cells. Sequencing of a 722 nucleotide gap in the dog (Canis lupus familiaris) genome revealed that the canine CD1D gene lacks a sequence homologous to exon 2 of human CD1D, coding for the start codon and signal peptide. Also, the canine CD1D gene contains three different short tandem repeats that disrupt the expected gene structure. Because canine CD1D cDNA lacks sequences homologous to human exon 2 and 3, the functionality of canine CD1d protein may be affected, and this could have consequences for the development and activation of canine NKT cells.

Looringh van Beeck FA; Leegwater PA; Herrmann T; Broere F; Rutten VP; Willemse T; Van Rhijn I

2013-06-01

6

Local structure study of vanadium pentoxide 1D-nanostructures  

International Nuclear Information System (INIS)

Vanadium pentoxide (V2O5·nH2O) 1D-nanostructures as nanowires and nanorods have been obtained by decomposition of vanadium peroxide in hydrothermal conditions. Electron microscopy, Raman spectroscopy, and X-ray absorption spectroscopy (XAS) were employed to characterize the morphology and the local structure of as-obtained samples. Scanning transmission electron microscopy (STEM) revealed that the diameter of the nanowires and nanorods were found to be 10–20 and 30–40 nm, respectively. The results demonstrated that a combination of Raman and XAS techniques allowed the accurate characterization of the local structure of V2O5 1D-nanostructures which are related to different morphologies. Analyses of X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectra reveals that the local structure of V in the as-obtained samples is similar to the bulk V2O5 (in orthorhombic phase), except for a higher degree of local symmetry within the structure of the VO5 square pyramid. Additionally, the nanostructures prepared by this technique present a single crystalline nature and could emit visible light at room temperature which is related to the local order of V atoms of the studied samples.

2011-01-01

7

Progress of 1D protein structure prediction at last.  

UK PubMed Central (United Kingdom)

Accuracy of predicting protein secondary structure and solvent accessibility from sequence information has been improved significantly by using information contained in multiple sequence alignments as input to a neural network system. For the Asilomar meeting, predictions for 13 proteins were generated automatically using the publicly available prediction method PHD. The results confirm the estimate of 72% three-state prediction accuracy. The fairly accurate predictions of secondary structure segments made the tool useful as a starting point for modeling of higher dimensional aspects of protein structure.

Rost B; Sander C

1995-11-01

8

Synthesis and structural characterization of 1-(D-glycosyloxy)phthalazines.  

Science.gov (United States)

Coupling of the trimethylsilyl derivative of (2H)phthalazin-1-one with 1,2,3,4,6-penta-O-acetyl-alpha-D-glucopyranose and 1,2,3,4,6-penta-O-acetyl-alpha-D-galactopyranose in the presence of stannic chloride gave the respective glycosides, 2-(per-O-acetyl-D-glycosyloxy)phthalazines, which upon deacetylation gave the respective unprotected analogues. Under the same conditions 1,2,3,5-tetra-O-acetyl-beta-D-ribofuranose gave 1-(2,3,5-tri-O-acetyl-alpha-D-ribofuranosyloxy)phthalazine. Electrospray mass spectrometry aided the structural characterization of this series of 1-(D-glycosylyloxy)phthalazines. Low energy collisionally-induced dissociation tandem mass spectrometry of the protonated molecules confirmed the MS fragmentation routes and the structural identities of this novel series of glycosides. PMID:14572713

Haikal, Abdellfattah Z; El Ashry, El Sayed H; Banoub, Joseph

2003-10-31

9

Chiral-Odd Structure Function $h_1^D(x)$ and Tensor Charge of the Deuteron  

CERN Multimedia

The chiral-odd structure function h_{1}^D(x) and the tensor charge of the deuteron are studied within the Bethe-Salpeter formalism for the deuteron amplitude. Utilizing a simple model for the nucleon structure function, h_1^N, h_1^D(x) is calculated and the nuclear effects are analyzed.

Umnikov, A Yu; Khanna, F C; He, Han-xin

1996-01-01

10

SSViewer: Sequence Structure Viewer  

Directory of Open Access Journals (Sweden)

Full Text Available An important aspect of bioinformatics is sequence. Sequence is a discrete function which contains the combinations of amino acids in proteins and nucleotides in Dna. Important functions of Amino Acids are to serve as the building blocks of proteins, which are linear chains of amino acids. Amino acids can be linked together in varying sequences to form a vast variety of proteins. Twenty-two amino acids are naturally incorporated into polypeptides and are called protein-o-genic or standard amino acids. Of these, 20 are encoded by the universal genetic code. In the case of the DNA sequence A, T, G, C is used to represent DNA. This sequence information is analysed to determine genes that encode polypeptides (proteins), RNA, genes, regulatory sequences, structural motifs, repetitive sequences and DNA sequences can be accurately analysed using computational techniques like BLAST, FASTA which is not possible manually. In the present study we developed a tool to visualize the 3D structure for a given sequence by using programming language Java and HTML.

Shyam Perugu,; Harika Jalli,; Dr.Manjula Bhanoori,

2013-01-01

11

Genome Sequence of Bovine Viral Diarrhea Virus Strain 10JJ-SKR, Belonging to Genotype 1d.  

UK PubMed Central (United Kingdom)

Here, we report the complete genome sequence of a bovine viral diarrhea virus (BVDV) belonging to genotype 1d, strain 10JJ-SKR, which was isolated from cattle. The complete genome is 12,267 nucleotides (nt) in length, with a single large open reading frame. This is the first report of a BVDV belonging to genotype 1d and will enable further study of the molecular and epidemiological characteristics of this virus.

Joo SK; Lim SI; Jeoung HY; Song JY; Oem JK; Mun SH; An DJ

2013-01-01

12

The structure of 1D CuI crystals inside SWNTs.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Nanocomposites consisting of one-dimensional CuI crystals inside single-walled carbon nanotubes were obtained using the capillary technique. high-resolution transmission electron microscopy investigations of the atomic structure of the encapsulated 1D CuI crystals revealed two types of 1D CuI crysta...

Kiselev, NA; Zakalyukin, RM; Zhigalina, OM; Grobert, N; Kumskov, AS

13

A 1-D coordination polymer based on a Mn40 octagonal super-structure.  

UK PubMed Central (United Kingdom)

A 1-D coordination polymer, constructed using a combination of diols and phenolic oximes, contains a novel [Mn(9)] sub-unit, a nanosized [Mn(40)] octagonal super-structure and a [Mn(21)] repeating unit.

Manoli M; Inglis R; Manos MJ; Papaefstathiou GS; Brechin EK; Tasiopoulos AJ

2013-02-01

14

Structure and Catalytic Mechanism of Human Steroid 5-Reductase (AKR1D1)  

Energy Technology Data Exchange (ETDEWEB)

Human steroid 5{beta}-reductase (aldo-keto reductase (AKR) 1D1) catalyzes reduction of {Delta}{sup 4}-ene double bonds in steroid hormones and bile acid precursors. We have reported the structures of an AKR1D1-NADP{sup +} binary complex, and AKR1D1-NADP{sup +}-cortisone, AKR1D1-NADP{sup +}-progesterone and AKR1D1-NADP{sup +}-testosterone ternary complexes at high resolutions. Recently, structures of AKR1D1-NADP{sup +}-5{beta}-dihydroprogesterone complexes showed that the product is bound unproductively. Two quite different mechanisms of steroid double bond reduction have since been proposed. However, site-directed mutagenesis supports only one mechanism. In this mechanism, the 4-pro-R hydride is transferred from the re-face of the nicotinamide ring to C5 of the steroid substrate. E120, a unique substitution in the AKR catalytic tetrad, permits a deeper penetration of the steroid substrate into the active site to promote optimal reactant positioning. It participates with Y58 to create a 'superacidic' oxyanion hole for polarization of the C3 ketone. A role for K87 in the proton relay proposed using the AKR1D1-NADP{sup +}-5{beta}-dihydroprogesterone structure is not supported.

Costanzo, L.; Drury, J; Christianson, D; Penning, T

2009-01-01

15

Structure and catalytic mechanism of human steroid 5?-reductase (AKR1D1)  

Science.gov (United States)

Human steroid 5?-reductase (aldo-keto reductase (AKR) 1D1) catalyzes reduction of ?4-ene double bonds in steroid hormones and bile acid precursors. We have reported the structures of an AKR1D1-NADP+ binary complex, and AKR1D1-NADP+-cortisone, AKR1D1-NADP+-progesterone and AKR1D1-NADP+-testosterone ternary complexes at high resolutions. Recently, structures of AKR1D1-NADP+-5?-dihydroprogesterone complexes showed that the product is bound unproductively. Two quite different mechanisms of steroid double bond reduction have since been proposed. However, site-directed mutagenesis supports only one mechanism. In this mechanism, the 4-pro-R hydride is transferred from the re-face of the nicotinamide ring to C5 of the steroid substrate. E120, a unique substitution in the AKR catalytic tetrad, permits a deeper penetration of the steroid substrate into the active site to promote optimal reactant positioning. It participates with Y58 to create a “superacidic” oxyanion hole for polarization of the C3 ketone. A role for K87 in the proton relay proposed using the AKR1D1-NADP+-5?-dihydroprogesterone structure is not supported.

Di Costanzo, Luigi; Drury, Jason E.; Christianson, David W.; Penning, Trevor M.

2009-01-01

16

The structure of 1D CuI crystals inside SWNTs.  

Science.gov (United States)

Nanocomposites consisting of one-dimensional CuI crystals inside single-walled carbon nanotubes were obtained using the capillary technique. high-resolution transmission electron microscopy investigations of the atomic structure of the encapsulated 1D CuI crystals revealed two types of 1D CuI crystals with growth direction and relative to the bulk hexagonal CuI structure. Atomic structure models were proposed based on the high-resolution transmission electron microscopy images. According to the proposed models and image simulations, the main contrast in the 1D crystal images arises from the iodine atoms whereas copper atoms, with lower atomic number giving lower contrast, are thought to be statistically distributed. PMID:19017232

Kiselev, N A; Zakalyukin, R M; Zhigalina, O M; Grobert, N; Kumskov, A S; Grigoriev, Yu V; Chernysheva, M V; Eliseev, A A; Krestinin, A V; Tretyakov, Yu D; Freitag, B; Hutchison, J L

2008-11-01

17

The structure of 1D CuI crystals inside SWNTs.  

UK PubMed Central (United Kingdom)

Nanocomposites consisting of one-dimensional CuI crystals inside single-walled carbon nanotubes were obtained using the capillary technique. high-resolution transmission electron microscopy investigations of the atomic structure of the encapsulated 1D CuI crystals revealed two types of 1D CuI crystals with growth direction <001> and <110> relative to the bulk hexagonal CuI structure. Atomic structure models were proposed based on the high-resolution transmission electron microscopy images. According to the proposed models and image simulations, the main contrast in the 1D crystal images arises from the iodine atoms whereas copper atoms, with lower atomic number giving lower contrast, are thought to be statistically distributed.

Kiselev NA; Zakalyukin RM; Zhigalina OM; Grobert N; Kumskov AS; Grigoriev YV; Chernysheva MV; Eliseev AA; Krestinin AV; Tretyakov YD; Freitag B; Hutchison JL

2008-11-01

18

Vertically integrated ZnO-Based 1D1R structure for resistive switching  

International Nuclear Information System (INIS)

[en] We report a ZnO-based 1D1R structure, which is formed by a vertical integration of a FeZnO/MgO switching resistor (1R) and an Ag/MgZnO Schottky diode (1D). The multifunctional ZnO and its compounds are grown through MOCVD with in situ doping. For the R element, the current ratio of the high-resistance state (HRS) over the low-resistance state (LRS) at 1 V is 2.4 × 106. The conduction mechanisms of the HRS and LRS are Poole–Frenkel emission and resistive conduction, respectively. The D element shows the forward/reverse current ratio at ±1 V to be 2.4 × 107. This 1D1R structure exhibits high RHRS/RLRS ratio, excellent rectifying characteristics and robust retention. (paper)

2013-04-10

19

Vertically integrated ZnO-Based 1D1R structure for resistive switching  

Science.gov (United States)

We report a ZnO-based 1D1R structure, which is formed by a vertical integration of a FeZnO/MgO switching resistor (1R) and an Ag/MgZnO Schottky diode (1D). The multifunctional ZnO and its compounds are grown through MOCVD with in situ doping. For the R element, the current ratio of the high-resistance state (HRS) over the low-resistance state (LRS) at 1 V is 2.4 × 106. The conduction mechanisms of the HRS and LRS are Poole-Frenkel emission and resistive conduction, respectively. The D element shows the forward/reverse current ratio at ±1 V to be 2.4 × 107. This 1D1R structure exhibits high RHRS/RLRS ratio, excellent rectifying characteristics and robust retention.

Zhang, Yang; Duan, Ziqing; Li, Rui; Ku, Chieh-Jen; Reyes, Pavel I.; Ashrafi, Almamun; Zhong, Jian; Lu, Yicheng

2013-04-01

20

The structure of 1D CuI crystals inside SWNTs  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Citation: Kiselev, N. A. et al. (2008). 'The structure of 1D CuI crystals inside SWNTs', Journal of Microscopy, 232(2), 335-342. [The definitive version of the article is available at http://www3.interscience.wiley.com/journal/121496577/abstract]. © 2008 the Authors.

Kiselev, N. A.; Zakalyukin, R. M.; Zhigalina, O. M.; Grobert, N.; Kumskov, A. S.

 
 
 
 
21

Large frequency range of negligible transmission in 1D photonic quantum well structures  

CERN Multimedia

We show that it is possible to enlarge the range of low transmission in 1D photonic crystals by using photonic quantum well structures. If a defect is introduced in the photonic quantum well structures, defect modes with a very high quality factor may appear. The transmission of the defect mode is due to the coupling between the eigenmodes of the defect and those at the band edges of the constituent photonic crystals.

Zi, J; Zhang, C

1998-01-01

22

Hyperfine structures of the nd 1D(n = 3 - 8) states of 3He I  

International Nuclear Information System (INIS)

We have used the beam-foil quantum beat method to measure the hyperfine structure separations F = 3/2 - 5/2 of the 1snd 1D states (n = 3 - 8) of 3He I. We observed the single frequency modulated decay curves of the 1s2p 1P - 1snd 1D transitions for times after excitation up to 50 ns, corresponding to 4 to 5 modulation periods. The frequencies obtained (with a precision of 2 to 5%) are compared with other experiments and theory. The frequencies are determined mainly by the singlet-triplet energy separations and mixing factors for the He I D-states. The results agree with the same parameters obtained from other recent level-crossing measurements in strong magnetic field mixing of the singlet-triplet states

1981-01-01

23

Computational Study and Analysis of Structural Imperfections in 1D and 2D Photonic Crystals  

Energy Technology Data Exchange (ETDEWEB)

Dielectric reflectors that are periodic in one or two dimensions, also known as 1D and 2D photonic crystals, have been widely studied for many potential applications due to the presence of wavelength-tunable photonic bandgaps. However, the unique optical behavior of photonic crystals is based on theoretical models of perfect analogues. Little is known about the practical effects of dielectric imperfections on their technologically useful optical properties. In order to address this issue, a finite-difference time-domain (FDTD) code is employed to study the effect of three specific dielectric imperfections in 1D and 2D photonic crystals. The first imperfection investigated is dielectric interfacial roughness in quarter-wave tuned 1D photonic crystals at normal incidence. This study reveals that the reflectivity of some roughened photonic crystal configurations can change up to 50% at the center of the bandgap for RMS roughness values around 20% of the characteristic periodicity of the crystal. However, this reflectivity change can be mitigated by increasing the index contrast and/or the number of bilayers in the crystal. In order to explain these results, the homogenization approximation, which is usually applied to single rough surfaces, is applied to the quarter-wave stacks. The results of the homogenization approximation match the FDTD results extremely well, suggesting that the main role of the roughness features is to grade the refractive index profile of the interfaces in the photonic crystal rather than diffusely scatter the incoming light. This result also implies that the amount of incoherent reflection from the roughened quarterwave stacks is extremely small. This is confirmed through direct extraction of the amount of incoherent power from the FDTD calculations. Further FDTD studies are done on the entire normal incidence bandgap of roughened 1D photonic crystals. These results reveal a narrowing and red-shifting of the normal incidence bandgap with increasing RMS roughness. Again, the homogenization approximation is able to predict these results. The problem of surface scratches on 1D photonic crystals is also addressed. Although the reflectivity decreases are lower in this study, up to a 15% change in reflectivity is observed in certain scratched photonic crystal structures. However, this reflectivity change can be significantly decreased by adding a low index protective coating to the surface of the photonic crystal. Again, application of homogenization theory to these structures confirms its predictive power for this type of imperfection as well. Additionally, the problem of a circular pores in 2D photonic crystals is investigated, showing that almost a 50% change in reflectivity can occur for some structures. Furthermore, this study reveals trends that are consistent with the 1D simulations: parameter changes that increase the absolute reflectivity of the photonic crystal will also increase its tolerance to structural imperfections. Finally, experimental reflectance spectra from roughened 1D photonic crystals are compared to the results predicted computationally in this thesis. Both the computed and experimental spectra correlate favorably, validating the findings presented herein.

K.R. Maskaly

2005-06-01

24

Semi-analytical method for light interaction with 1D-periodic nanoplasmonic structures.  

UK PubMed Central (United Kingdom)

We present a detailed description of a computationally efficient, semi-analytical method (SAM) to calculate the electomagnetic field distribution in a 1D-periodic, subwavelength-structured metal film placed between dielectric substrates. The method is roughly three orders of magnitude faster than the finite-element method (FEM). SAM is used to study the resonant transmission of light through nanoplasmonic structures, and to analyze the role of fundamental and higher-order Bloch surface plasmons in transmission enhancement. The method is also suitable for solving the eigenvalue problem and finding modes of the structure. Results obtained with SAM, FEM, and the finite-difference time-domain method show very good agreement for various parameters of the structure.

Kobyakov A; Zakharian AR; Mafi A; Darmanyan SA

2008-06-01

25

Second-order parametric interactions in 1-D photonic-crystal microcavity structures.  

Science.gov (United States)

We develop a generalized model for studying second-order parametric interactions in 1-D multilayered photonic structures, accounting for collinear oblique waves and partial pump depletion. This model is used to assess the performance of parametric devices in photonic-crystal microcavity (PCM) structures. Our model shows dramatic enhancement of nonlinear interactions at frequencies for which the waves are localized. Also, we demonstrate the exponential dependence of the conversion efficiency of second harmonic generation (SHG) on the number of layers as was recently pointed out. In addition, in optical parametric amplification (OPA), we find that the gain has a resonance-like dependence on the pump intensity, turning large peak gain into strong attenuation at greater intensities, which suggests that the device can operate as an optical switch. PMID:18542628

Saleh, Mohammed F; Dal Negro, Luca; Saleh, Bahaa E

2008-04-14

26

1D crustal structure from quality seismological data for the Cyprus subduction zone  

Science.gov (United States)

The eastern Mediterranean is a tectonically complex region, where long-term subduction and accretion processes have shaped the overall evolution. Recently, many seismic tomography studies have shown subducted slabs of the Neo-Tethyan lithosphere, continuing its subduction in the Hellenic trench, stalled in the Cyprus trench and being torn near the intersection between them. Antalya bay is a key region located on the western flank of the Cyprus Subduction Zone (CSZ), close to the junction between the Hellenic and Cyprus Arcs. Here deep earthquakes are nucleated, which otherwise cannot be seen anywhere else along the CSZ. For this reason, we focus our attention specifically to the Antalya Bay area but also the remaining parts of the CSZ. Several regional studies have been carried out to define the velocity structure beneath the region but none have been able to locate the CSZ. One of the main reasons for this was the lack of incorporation of a wide seismic network in those regional studies. We compile a large catalog of seismicity and relocate earthquakes to infer 1D local crustal structure using the clusters of seismicity. We used seismic data between 2005 - 2011 which are recorded at more than 335 seismic stations operated by several agencies and portable deployments. The data-set is composed of over 10,000 events and earthquakes can be grouped in several distinct clusters. We defined five of these clusters, where the total number of events is more than 4500, among which we selected over 2000 events with the highest data quality. 1-D local P-wave velocity models are developed using this high quality data-set and the earthquakes are relocated using the local velocity models. The compiled and reanalyzed data will contribute to perform local earthquake tomography. Moreover, obtained local velocity models represent a fundamental step towards an improved seismic tomography studies in a very crucial region in the eastern Mediterranean.

Perk, ?ükran; De?er, Ali; Özbak?r, Karabulut, Hayrullah

2013-04-01

27

A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition.  

Science.gov (United States)

Little is known regarding the basis for selection of the semi-invariant alphabeta T cell receptor (TCR) expressed by natural killer T (NKT) cells or how this mediates recognition of CD1d-glycolipid complexes. We have determined the structures of two human NKT TCRs that differ in their CDR3beta composition and length. Both TCRs contain a conserved, positively charged pocket at the ligand interface that is lined by residues from the invariant TCR alpha- and semi-invariant beta-chains. The cavity is centrally located and ideally suited to interact with the exposed glycosyl head group of glycolipid antigens. Sequences common to mouse and human invariant NKT TCRs reveal a contiguous conserved "hot spot" that provides a basis for the reactivity of NKT cells across species. Structural and functional data suggest that the CDR3beta loop provides a plasticity mechanism that accommodates recognition of a variety of glycolipid antigens presented by CD1d. We propose a model of NKT TCR-CD1d-glycolipid interaction in which the invariant CDR3alpha loop is predicted to play a major role in determining the inherent bias toward CD1d. The findings define a structural basis for the selection of the semi-invariant alphabeta TCR and the unique antigen specificity of NKT cells. PMID:16505140

Kjer-Nielsen, Lars; Borg, Natalie A; Pellicci, Daniel G; Beddoe, Travis; Kostenko, Lyudmila; Clements, Craig S; Williamson, Nicholas A; Smyth, Mark J; Besra, Gurdyal S; Reid, Hugh H; Bharadwaj, Mandvi; Godfrey, Dale I; Rossjohn, Jamie; McCluskey, James

2006-02-27

28

Multiplet structure of the defect modes in 1D helical photonic crystals with twist defects  

International Nuclear Information System (INIS)

We theoretically analyse the defect modes generated by equispaced twist defects in 1D helical (cholesteric-like) structures within their frequency gap which is such that only the first two of the four eigenwaves 1±, 2± are exponentially attenuated. n0 identical defects generate n0 different defect modes, each one represented by a linear combination of the four eigenwaves. The components 1+ and 1- are by far the dominant ones and they are localized near the defect planes. We give exact analytic expressions for the elements of the transfer and scattering matrices of the defect planes, for the functions defining the defect mode when n0 = 1, and for the defect frequencies when n0 = 1, 2, 3. In the particular case n0 = 2 and twist angle ? = ?/2, the difference between the two defect wavelengths ?d2, ?d1 depends exponentially on the distance z1 between the defect planes, going to zero for z1 ? ? and becoming as large as the entire frequency gap for z1 ? 0.

2005-10-14

29

Multiplet structure of the defect modes in 1D helical photonic crystals with twist defects  

Energy Technology Data Exchange (ETDEWEB)

We theoretically analyse the defect modes generated by equispaced twist defects in 1D helical (cholesteric-like) structures within their frequency gap which is such that only the first two of the four eigenwaves 1{sup {+-}}, 2{sup {+-}} are exponentially attenuated. n{sub 0} identical defects generate n{sub 0} different defect modes, each one represented by a linear combination of the four eigenwaves. The components 1{sup +} and 1{sup -} are by far the dominant ones and they are localized near the defect planes. We give exact analytic expressions for the elements of the transfer and scattering matrices of the defect planes, for the functions defining the defect mode when n{sub 0} = 1, and for the defect frequencies when n{sub 0} = 1, 2, 3. In the particular case n{sub 0} = 2 and twist angle {theta} = {pi}/2, the difference between the two defect wavelengths {lambda}{sub d2}, {lambda}{sub d1} depends exponentially on the distance z{sub 1} between the defect planes, going to zero for z{sub 1} {yields} {infinity} and becoming as large as the entire frequency gap for z{sub 1} {yields} 0.

Avendano, C G [Instituto de Fisica, Universidad Nacional Autonoma de Mexico, Apdo. P 20-364 01000, Mexico DF (Mexico); Ponti, S [Dipartimento di Fisica Politecnico di Torino and INFM, Corso Duca degli Abruzzi 24, 10129 Torino (Italy); Reyes, J A [Instituto de Fisica, Universidad Nacional Autonoma de Mexico, Apdo. P 20-364 01000, Mexico DF (Mexico); Oldano, C [Dipartimento di Fisica Politecnico di Torino and INFM, Corso Duca degli Abruzzi 24, 10129 Torino (Italy)

2005-10-14

30

Crystal Structures of Human TBC1D1 and TBC1D4 (AS160) RabGTPase-activating Protein (RabGAP) Domains Reveal Critical Elements for GLUT4 Translocation  

Energy Technology Data Exchange (ETDEWEB)

We have solved the x-ray crystal structures of the RabGAP domains of human TBC1D1 and human TBC1D4 (AS160), at 2.2 and 3.5 {angstrom} resolution, respectively. Like the yeast Gyp1p RabGAP domain, whose structure was solved previously in complex with mouse Rab33B, the human TBC1D1 and TBC1D4 domains both have 16 {alpha}-helices and no {beta}-sheet elements. We expected the yeast Gyp1p RabGAP/mouse Rab33B structure to predict the corresponding interfaces between cognate mammalian RabGAPs and Rabs, but found that residues were poorly conserved. We further tested the relevance of this model by Ala-scanning mutagenesis, but only one of five substitutions within the inferred binding site of the TBC1D1 RabGAP significantly perturbed catalytic efficiency. In addition, substitution of TBC1D1 residues with corresponding residues from Gyp1p did not enhance catalytic efficiency. We hypothesized that biologically relevant RabGAP/Rab partners utilize additional contacts not described in the yeast Gyp1p/mouse Rab33B structure, which we predicted using our two new human TBC1D1 and TBC1D4 structures. Ala substitution of TBC1D1 Met{sup 930}, corresponding to a residue outside of the Gyp1p/Rab33B contact, substantially reduced catalytic activity. GLUT4 translocation assays confirmed the biological relevance of our findings. Substitutions with lowest RabGAP activity, including catalytically dead RK and Met{sup 930} and Leu{sup 1019} predicted to perturb Rab binding, confirmed that biological activity requires contacts between cognate RabGAPs and Rabs beyond those in the yeast Gyp1p RabGAP/mouse Rab33B structure.

S Park; W Jin; S Shoelson

2011-12-31

31

The TBC1D1 gene: structure, function, and association with obesity and related traits.  

UK PubMed Central (United Kingdom)

This review summarizes what is currently known on the TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1 (TBC1D1) gene and gives an overview of its links with human obesity and related traits, taking also information from other animals. Several studies indicated that TBC1D1 contributes to the development of obesity by regulating skeletal muscle insulin sensitivity. A polymorphic site (p.R125W) in the human gene has been associated with female body mass index (BMI) in a few different cohorts. Few other polymorphisms in this gene were associated with BMI and diabetic nephropathy. Following a candidate gene approach, polymorphisms in the pig TBC1D1 gene were associated with fat deposition traits. In chicken, a few quantitative trait loci for growth and fat deposition were localized in the region containing TBC1D1. These complementary results could contribute to further understand the role of TBC1D1 in developing obesity.

Fontanesi L; Bertolini F

2013-01-01

32

Hyperfine structure evolution in an electric field and determination of tensor polarizabilities in He (4 and 5 1D)  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Variations of hyperfine structure in 3He (n 1D) are calculated as a function of an applied electric field. Using a quantum beat method on a fast helium beam excited and aligned by a thin carbon foil, we observe the time evolution of the alignment for a set of static electric fields. Tensor polarizab...

Denis, A.; Ouerdane, Y.; Docao, G.; Désesquelles, J.

33

Phase structure of (2+1)d strongly coupled lattice gauge theories  

CERN Document Server

We study the chiral phase transition in (2+1)d strongly coupled U(N) lattice gauge theories with staggered fermions. We show with high precision simulations performed directly in the chiral limit that these models undergo a Berezinski-Kosterlitz-Thouless (BKT) transition. We also show that this universality class is unaffected even in the large N limit.

Strouthos, C G

2003-01-01

34

Coulomb drag in phase-coherent mesoscopic structures - Numerical study of disordered 1D-wires  

CERN Multimedia

We study Coulomb drag between two parallel disordered mesoscopic 1D-wires. By numerical ensemble averaging we calculate the statistical properties of the transconductance G_21 including its distribution. For wires with mutually uncorrelated disorder potentials we find that the mean value is finite, but with comparable fluctuations so that sign-reversal is possible. For identical disorder potentials the mean value and the fluctuations nare enhanced compared to the case of uncorrelated disorder.

Mortensen, N A; Jauho, A P; Mortensen, Niels Asger; Flensberg, Karsten; Jauho, Antti-Pekka

2001-01-01

35

Inhibition of Human Steroid 5-Reductase (AKR1D1) by Finasteride and Structure of the Enzyme-Inhibitor Complex  

Energy Technology Data Exchange (ETDEWEB)

The {Delta}{sup 4}-3-ketosteroid functionality is present in nearly all steroid hormones apart from estrogens. The first step in functionalization of the A-ring is mediated in humans by steroid 5{alpha}- or 5{beta}-reductase. Finasteride is a mechanism-based inactivator of 5{alpha}-reductase type 2 with subnanomolar affinity and is widely used as a therapeutic for the treatment of benign prostatic hyperplasia. It is also used for androgen deprivation in hormone-dependent prostate carcinoma, and it has been examined as a chemopreventive agent in prostate cancer. The effect of finasteride on steroid 5{beta}-reductase (AKR1D1) has not been previously reported. We show that finasteride competitively inhibits AKR1D1 with low micromolar affinity but does not act as a mechanism-based inactivator. The structure of the AKR1D1 {center_dot} NADP{sup +} {center_dot} finasteride complex determined at 1.7 {angstrom} resolution shows that it is not possible for NADPH to reduce the {Delta}{sup 1-2}-ene of finasteride because the cofactor and steroid are not proximal to each other. The C3-ketone of finasteride accepts hydrogen bonds from the catalytic residues Tyr-58 and Glu-120 in the active site of AKR1D1, providing an explanation for the competitive inhibition observed. This is the first reported structure of finasteride bound to an enzyme involved in steroid hormone metabolism.

Drury, J.; Di Costanzo, L; Penning, T; Christianson, D

2009-01-01

36

Inhibition of Human Steroid 5?-Reductase (AKR1D1) by Finasteride and Structure of the Enzyme-Inhibitor Complex*  

Science.gov (United States)

The ?4-3-ketosteroid functionality is present in nearly all steroid hormones apart from estrogens. The first step in functionalization of the A-ring is mediated in humans by steroid 5?- or 5?-reductase. Finasteride is a mechanism-based inactivator of 5?-reductase type 2 with subnanomolar affinity and is widely used as a therapeutic for the treatment of benign prostatic hyperplasia. It is also used for androgen deprivation in hormone-de pend ent prostate carcinoma, and it has been examined as a chemopreventive agent in prostate cancer. The effect of finasteride on steroid 5?-reductase (AKR1D1) has not been previously reported. We show that finasteride competitively inhibits AKR1D1 with low micromolar affinity but does not act as a mechanism-based inactivator. The structure of the AKR1D1·NADP+·finasteride complex determined at 1.7 ? resolution shows that it is not possible for NADPH to reduce the ?1-2-ene of finasteride because the cofactor and steroid are not proximal to each other. The C3-ketone of finasteride accepts hydrogen bonds from the catalytic residues Tyr-58 and Glu-120 in the active site of AKR1D1, providing an explanation for the competitive inhibition observed. This is the first reported structure of finasteride bound to an enzyme involved in steroid hormone metabolism.

Drury, Jason E.; Di Costanzo, Luigi; Penning, Trevor M.; Christianson, David W.

2009-01-01

37

A revised 1-D electrical conductivity reference structure beneath North Pacific obtained by semi-global induction study  

International Nuclear Information System (INIS)

Complete text of publication follows. One dimensional (1-D) electrical conductivity structure in the mid-mantle beneath the northern Pacific is revised in order to discuss the mean state of the mantle and to obtain a credible starting model for 3-D inversions. Semi-global geomagnetic depth sounding (GDS) responses obtained at 13 stations and submarine cable magnetotelluric (MT) responses for 8 cables in the period range 1.7 to 113 days were used to obtain the revised structure. We employed an iterative scheme combining surface layer correction to remove the effect of ocean-land heterogeneity in the responses and 1-D inversion to obtain the revised structure. The validity of the scheme is examined by making synthetic tests: We confirmed that the structure obtained using this scheme not only represents the model which explains the corrected response the best but also reflects the actual mean conductivity structure in the mid-mantle depths. The obtained 1-D conductivity in the transition zone by supposing jumps at 400 and 650 km depths (2-jump model) is higher than that of dry Wadsleyite and Ringwoodite measured experimentally by Yoshino et al. (2008). If the high conductivity is entirely due to the effect of water in the transition zone, the region contains 0.5 wt% of water. However, if an additional discontinuity of electrical conductivity is allowed at 500 km depth in the 1-D inversion, the obtained model has lower conductivity than the 2-jump model in the upper 100 km of the transition zone. In this case, the conductivity in the layer is rather close to that of dry Wadsleyite.

2009-01-01

38

A novel 1D non-periodic photonic band-gap structure  

Science.gov (United States)

In this paper, the development and filter characteristic of photonic band-gap (PBG) structure and defected ground structure (DGS) are analyzed. The non-periodic structure has simpler structure, smaller size and smaller ripple compared to the periodic structure. Though the stop band of non-periodic structure is narrower, it can meet the application. What's more, C-shaped structure with two stop bands can realize selection in special frequency band. So it can meet the need of two stop bands.

Li, Yuan; Li, Huancai; Ding, Ronglin

2005-12-01

39

Hyperfine structures of the nd /sup 1/D(n = 3 - 8) states of /sup 3/He I  

Energy Technology Data Exchange (ETDEWEB)

We have used the beam-foil quantum beat method to measure the hyperfine structure separations F = 3/2 - 5/2 of the 1snd /sup 1/D states (n = 3 - 8) of /sup 3/He I. We observed the single frequency modulated decay curves of the 1s2p /sup 1/P - 1snd /sup 1/D transitions for times after excitation up to 50 ns, corresponding to 4 to 5 modulation periods. The frequencies obtained (with a precision of 2 to 5%) are compared with other experiments and theory. The frequencies are determined mainly by the singlet-triplet energy separations and mixing factors for the He I D-states. The results agree with the same parameters obtained from other recent level-crossing measurements in strong magnetic field mixing of the singlet-triplet states.

Brooks, R.L.; Streif, V.F.; Berry, H.G.

1981-01-01

40

Solid-state structural transformations and photoreactivity of 1D-ladder coordination polymers of Pb(II).  

UK PubMed Central (United Kingdom)

An attempt has been made to design double-stranded ladder-like coordination polymers (CPs) of hemidirected Pb(II) . Four CPs, [Pb(?-bpe)(O2 C-C6 H5 )2 ]?2H2 O (1), [Pb2 (?-bpe)2 (?-O2 C-C6 H5 )2 (O2 C-C6 H5 )2 ] (2), [Pb2 (?-bpe)2 (?-O2 C-p-Tol)2 (O2 C-p-Tol)2 ]? 1.5?H2 O (3) and [Pb2 (?-bpe)2 (?-O2 C-m-Tol)2 (O2 C-m-Tol)2 ] (4) (bpe=1,2-bis(4'-pyridyl)ethylene), have been synthesised and investigated for their solid-state photoreactivity. CPs 2-4, having a parallel orientation of bpe molecules in their ladder structures and being bridged by carboxylates, were found to be photoreactive, whereas CP 1 is a linear one-dimensional (1D) CP with guest water molecules aggregating to form a hydrogen-bonded 1D structure. The linear strands of 1 were found to pair up upon eliminating lattice water molecules by heating, which led to the solid-state structural transformation of photostable linear 1D CP 1 into photoreactive ladder CP 2. In the construction of the double-stranded ladder-like structures, the parallel alignment of C?C bonds in 2-4 is dictated by the chelating and ?2 -?(2) :?(1) bridging modes of the benzoate and toluate ligands. The role of solvents in the formation of such double-stranded ladder-like structures has also been investigated. A single-crystal-to-single-crystal transformation occurred when 4 was irradiated under UV light to form [Pb2 (rctt-tpcb)(?-O2 C-m-Tol)2 (O2 C-m-Tol)2 ] (5).

Kole GK; Peedikakkal AM; Toh BM; Vittal JJ

2013-03-01

 
 
 
 
41

Mapping of the serotonin 5-HT{sub 1D{beta}} autoreceptor gene on chromosome 6 and direct analysis for sequence variants  

Energy Technology Data Exchange (ETDEWEB)

Abnormal brain serotonin function may be characteristic of several neuropsychiatric disorders. Thus, it is important to identify polymorphic genes and screen for functional variants at loci coding for genes that control normal serotonin functions. 5-HT{sub 1D{beta}} is a terminal serotonin autoreceptor which may play a role in regulating serotonin synthesis and release. Using an SSCP technique we screened for 5-HT{sub 1D{beta}} coding sequence variants in psychiatrically interviewed populations, which included controls, alcoholics, and alcoholic arsonists and alcoholic violent offenders with low CSF concentrations of the main serotonin metabolite 5-HIAA. A common polymorphism was identified in the 5-HT{sub 1D{beta}} gene with allele frequencies of 0.72 and 0.28. The SSCP variant was caused by a silent G to C substitution at nucleotide 861 of the coding region. This polymorphism could also be detected as a HincII RFLP of amplified DNA. DNAs from informative CEPH families were typed for the HincII RFLP and analyzed with respect to 20 linked markers on chromosome 6. Multipoint analysis placed the 5-HT{sub 1D{beta}} receptor gene between markers D6S286 and D6S275. A maximum two-point lod score of 10.90 was obtained to D6S26, which had been previously localized on 6q14-15. Chromosomal aberrations involving this region have been previously shown to cause retinal anomalies, developmental delay, and abnormal brain development. This region also contains the gene for North Carolina-type macular dystrophy. 34 refs., 3 figs., 1 tab.

Lappalainen, J.; Dean, M.; Virkkunen, M. [National Cancer Institute, Fredrick, MD (United States)] [and others

1995-04-24

42

Measurement of the Deuteron Spin Structure Function g1d(x) for 1 (GeV/c)2 2 2  

International Nuclear Information System (INIS)

New measurements are reported on the deuteron spin structure function g1d. These results were obtained from deep inelastic scattering of 48.3 GeV electrons on polarized deuterons in the kinematic range 0.01 2 2. These are the first high dose electron scattering data obtained using lithium deuteride (6Li2H) as the target material. Extrapolations of the data were performed to obtain moments of g1d, including ?1d, and the net quark polarization ? ?.

1999-01-01

43

Reversible supra-channel effects: 3D kagome structure and catalysis via a molecular array of 1D coordination polymers.  

UK PubMed Central (United Kingdom)

Self-assembly of CuX2 (X(-) = ClO4(-) and BF4(-)) with 2,3-bis(nicotinoyloxy)naphthalene yields a 1D loop-chain skeleton. The loop-chains form an ensemble constituting a unique 3D kagome-type structure with both hexagonal and trigonal supra-channels. The unprecedented supra-channel effects on the catalytic oxidation of 3,5-di-tert-butylcatechol to 3,5-di-tert-butylbenzoquinone were investigated.

Lee H; Noh TH; Jung OS

2013-10-01

44

Reversible supra-channel effects: 3D kagome structure and catalysis via a molecular array of 1D coordination polymers.  

Science.gov (United States)

Self-assembly of CuX2 (X(-) = ClO4(-) and BF4(-)) with 2,3-bis(nicotinoyloxy)naphthalene yields a 1D loop-chain skeleton. The loop-chains form an ensemble constituting a unique 3D kagome-type structure with both hexagonal and trigonal supra-channels. The unprecedented supra-channel effects on the catalytic oxidation of 3,5-di-tert-butylcatechol to 3,5-di-tert-butylbenzoquinone were investigated. PMID:23989602

Lee, Haeri; Noh, Tae Hwan; Jung, Ok-Sang

2013-08-29

45

Properties of Floquet-Bloch space harmonics in 1D periodic magneto-dielectric structures  

DEFF Research Database (Denmark)

Recent years have witnessed a significant research interest in Floquet-Bloch analysis for determining the homogenized permittivity and permeability of metamaterials consisting of periodic structures. This work investigates fundamental properties of the Floquet-Bloch space harmonics in a 1-dimensional magneto-dielectric lossless structure supporting a transverse-electric-magnetic Floquet-Bloch wave; in particular, the space harmonic permittivity and permeability, as well as the space harmonic Poynting vector.

Breinbjerg, O.

2012-01-01

46

Electronic and structural properties of 3D, 2D and 1D materials  

Science.gov (United States)

In this work several applications of the ab initio pseudopotential density functional theory method are presented. With this method it is possible to calculate the electronic ground state properties of many systems like bulk solids, surfaces, nanotubes, and nanowires, and draw conclusions about the systems structural and electronic properties. With modifications of this approach excited states can also be treated. The first chapter of this thesis gives a brief description of the computational techniques employed. The second chapter describes results of calculations on the structural and electronic properties of carbon and germanium. We try to shed some light on a still poorly understood structural phase transition of graphite under pressure at low temperatures, which is different from the high temperature regime. Next, we study the phase transition path of germanium under pressure and predict the existence of a new phase. The following chapter explores the possibility of superconductivity in the graphite-like compound BC3 since there are many similarities between the electronic structure of this material and the 39 K superconductor MgB2. Subsequently, results of calculations on the adsorption of indium atoms on carbon nanotubes and graphite-like surfaces are presented. These studies explain some very interesting experimental results of In migration on nanotubes in an electrical potential. In the following chapters the electronic properties of very thin metallic MoSe nanowires are studied, and the different regimes of stability of metallic monatomic chains of Au, Al, Ag, Pd, Rh, and Ru are investigated and compared. Chapter 7 addresses the possible polymerization of C60 molecules inside carbon and boron nitride nanotubes. Finally, the propagation of a light signal in a medium with gains and losses is investigated, and the possibility of a discontinuity in the index of refraction is discussed.

Ribeiro, Filipe Joao

47

Local duality in spin structure functions g1(p) and g1(d)  

International Nuclear Information System (INIS)

Inclusive double spin asymmetries obtained by scattering polarized electrons off polarized protons and deuterons have been analyzed to address the issue of quark hadron duality in the polarized spin structure functions gp 1 and gd 1. A polarized electron beam, solid polarized NH3 and ND3 targets and the CEBAF Large Acceptance Spectrometer (CLAS) in Hall B were used to collect the data. The resulting gp 1 and gd 1 were averaged over the nucleon resonance energy region (M

2006-01-01

48

Local duality in spin structure functions g1(p) and g1(d)  

Energy Technology Data Exchange (ETDEWEB)

Inclusive double spin asymmetries obtained by scattering polarized electrons off polarized protons and deuterons have been analyzed to address the issue of quark hadron duality in the polarized spin structure functions gp 1 and gd 1. A polarized electron beam, solid polarized NH3 and ND3 targets and the CEBAF Large Acceptance Spectrometer (CLAS) in Hall B were used to collect the data. The resulting gp 1 and gd 1 were averaged over the nucleon resonance energy region (M

Yelena Prok

2006-02-01

49

Extension of the classical Fabry-Perot formula to 1D multilayered structures  

Science.gov (United States)

In any field theory the interaction of a wave packet with a multilayered potential is of high theoretical and practical relevance. In the present work we show an extension to any number of layers of the classical Fabry-Perot formula that works for any level of absorption, any thickness of the composing layers, any number of layers, any angle of incidence and for evanescent waves as well. More specifically, the ability of dealing with input evanescent waves and complex metal-based structures is of special interest for superlenses analysis and design. Some explicit examples in electromagnetism are also discussed.

Gawhary, O. El; Dheur, M. C.; Pereira, S. F.; Braat, J. J. M.

2013-06-01

50

Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques  

Science.gov (United States)

In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques (1H, 13C, APT, DEPT, NOE/NOESY, 1H 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.

Topcu, Gulacti; Ulubelen, Ayhan

2007-05-01

51

Perception of structure in short melodic sequences.  

UK PubMed Central (United Kingdom)

Three experiments studied the perception of tone sequences having various degrees of musical structure. Ratings of perceived structure and ease of recognition in transposition were both influenced by harmonic progression (as defined by music theory), the contour (directional changes in pitch), and the excursion or repetition pattern within the sequence. The relation between the original and transposed sequence also affected ease of recognition in accordance with the number of tones shared between the two sequences. The results are described in terms of the abstraction and analysis of levels of pitch relations, an analysis conducted even by musically untrained listeners. The conceptual framework emphasizes the application of musical rules as an illustration of rules governing auditory sequences in general.

Cuddy LL; Cohen AJ; Mewhort DJ

1981-08-01

52

Perception of structure in short melodic sequences.  

Science.gov (United States)

Three experiments studied the perception of tone sequences having various degrees of musical structure. Ratings of perceived structure and ease of recognition in transposition were both influenced by harmonic progression (as defined by music theory), the contour (directional changes in pitch), and the excursion or repetition pattern within the sequence. The relation between the original and transposed sequence also affected ease of recognition in accordance with the number of tones shared between the two sequences. The results are described in terms of the abstraction and analysis of levels of pitch relations, an analysis conducted even by musically untrained listeners. The conceptual framework emphasizes the application of musical rules as an illustration of rules governing auditory sequences in general. PMID:6457099

Cuddy, L L; Cohen, A J; Mewhort, D J

1981-08-01

53

Syntheses, structures, spectroscopic and electrochemical properties of two 1D organic-inorganic CuII-LnIII heterometallic germanotungstates.  

UK PubMed Central (United Kingdom)

Two organic-inorganic hybrid copper-lanthanide heterometallic germanotungstates KNa2H7[enH2]3[Cu(en)2(H2O)]2[Cu(en)2]2{Cu(en)2[Eu(?-GeW11O39)2]2}·13H2O (1) and Na2H4[Cu(en)2(H2O)]2[Cu(en)2]6[Cu(en)2]{Cu(en)2[La(?-GeW11O39)2]2}·12H2O (2) have been hydrothermally synthesized by reaction of K8Na2[A-?-GeW9O34]·25H2O with CuCl2·2H2O and EuCl3/LaCl3 in the presence of en (en=ethylenediamine) and structurally characterized by elemental analyses, IR spectra and single-crystal X-ray diffraction. 1 exhibits the 1D chain motif built by tetrameric {[Cu(en)2(H2O)]2[Cu(en)2]2{Cu(en)2[Eu(?-GeW11O39)2]2}}(16-) moieties through square antiprismatic K(+) cations while 2 displays the 1D architecture made by tetrameric [[Cu(en)2]6[Cu(en)2]{Cu(en)2[La(?-GeW11O39)2]2}](10-) units via octahedral [Cu(en)2](2+) cations. Furthermore, the solid-state electrochemical and electrocatalytic properties of 1 have been investigated and 1 indicates the good electrocatalytic activity for nitrite reduction. In addition, the photoluminescence property of 1 has been investigated.

Zhang J; Li J; Li L; Zhao H; Ma P; Zhao J; Chen L

2013-10-01

54

Syntheses, structures, spectroscopic and electrochemical properties of two 1D organic-inorganic CuII-LnIII heterometallic germanotungstates.  

Science.gov (United States)

Two organic-inorganic hybrid copper-lanthanide heterometallic germanotungstates KNa2H7[enH2]3[Cu(en)2(H2O)]2[Cu(en)2]2{Cu(en)2[Eu(?-GeW11O39)2]2}·13H2O (1) and Na2H4[Cu(en)2(H2O)]2[Cu(en)2]6[Cu(en)2]{Cu(en)2[La(?-GeW11O39)2]2}·12H2O (2) have been hydrothermally synthesized by reaction of K8Na2[A-?-GeW9O34]·25H2O with CuCl2·2H2O and EuCl3/LaCl3 in the presence of en (en=ethylenediamine) and structurally characterized by elemental analyses, IR spectra and single-crystal X-ray diffraction. 1 exhibits the 1D chain motif built by tetrameric {[Cu(en)2(H2O)]2[Cu(en)2]2{Cu(en)2[Eu(?-GeW11O39)2]2}}(16-) moieties through square antiprismatic K(+) cations while 2 displays the 1D architecture made by tetrameric [[Cu(en)2]6[Cu(en)2]{Cu(en)2[La(?-GeW11O39)2]2}](10-) units via octahedral [Cu(en)2](2+) cations. Furthermore, the solid-state electrochemical and electrocatalytic properties of 1 have been investigated and 1 indicates the good electrocatalytic activity for nitrite reduction. In addition, the photoluminescence property of 1 has been investigated. PMID:23786977

Zhang, Jingli; Li, Jie; Li, Lijie; Zhao, Haozhe; Ma, Pengtao; Zhao, Junwei; Chen, Lijuan

2013-05-29

55

Measurement of the Deuteron Spin Structure Function $g_{1}^{d(x)}$ for $1(GeV/c)^{2} < Q^{2} < 40 (GeV/c)^{2}$  

CERN Multimedia

New measurements are reported on the deuteron spin structure function g_1^d. These results were obtained from deep inelastic scattering of 48.3 GeV electrons on polarized deuterons in the kinematic range 0.01 < x < 0.9 and 1 < Q^2 < 40 (GeV/c)^2. These are the first high dose electron scattering data obtained using lithium deuteride (6Li2H) as the target material. Extrapolations of the data were performed to obtain moments of g_1^d, including Gamma_1^d, and the net quark polarization Delta Sigma.

Anthony, P L; Averett, T; Band, H R; Berisso, M C; Borel, H; Bosted, P E; Bultmann, S L; Buénerd, M; Chupp, T E; Churchwell, S; Court, G R; Crabb, D; Day, D; Decowski, P; De Pietro, P; Erbacher, R; Erickson, R; Feltham, A; Fonvieille, H; Frlez, E; Gearhart, R A; Ghazikhanian, V; Gómez, J; Griffioen, K A; Harris, C; Houlden, M A; Hughes, E W; Hyde-Wright, C E; Igo, G; Incerti, S; Jensen, J; Johnson, J R; King, P M; Kolomensky, Yu G; Kuhn, S E; Lindgren, R; Lombard-Nelsen, R M; Marroncle, J; McCarthy, J; McKee, P; Meyer, Werner T; Mitchell, G; Mitchell, J; Olson, M; Penttila, S; Peterson, G; Petratos, G G; Pitthan, R; Pocanic, D; Prepost, R; Prescott, C; Qin, L M; Raue, B A; Reyna, D; Rochester, L S; Rock, S E; Rondon-Aramayo, O A; Sabatie, F; Sick, I; Smith, T; Sorrell, L; Staley, F; Lorant, S St; Stuart, L M; Szalata, Z M; Terrien, Y; Tobias, A; Todor, L; Toole, T; Trentalange, S; Walz, D; Welsh, R C; Wesselmann, F R; Wright, T R; Young, C C; Zeier, M; Zhu, H; Zihlmann, B

1999-01-01

56

From 1D chain to 3D framework uranyl diphosphonates: syntheses, crystal structures, and selective ion exchange.  

Science.gov (United States)

In this work, we demonstrate a family of new inorganic-organic hybrid uranyl diphosphonates based on 1-hydroxyethylidenediphosphonic acid (H(4)L) linker by using hydrothermal method. These compounds, (Hbpi)[(UO(2))(H(2)O)(HL)]·H(2)O (UP-1), represents 1D structure, (Hbpi)[(UO(2))(H(2)O)(HL)] (UP-2), (H(2)dib)(0.5)[(UO(2))(H(2)O)(HL)] (UP-3), and [(UO(2))(H(2)O)(H(2)L)]·2H(2)O (UP-4) feature 2D architectures, (H(2)bipy){[(UO(2))(H(2)O)](2)[(UO(2))(H(2)O)(2)](L)(2)}·2H(2)O (UP-5), and (H(3)O)(2){[(UO(2))(H(2)O)](3)(L)(2)}·2H(2)O (UP-6) adopt 3D networks (bpi: 1-(biphenyl-4-yl)-1H-imidazole, dib: 1,4-di(1H-imidazol-1-yl)benzene, bipy: 2,2'-bipyridine). Among them, UP-1, UP-2, UP-3, and UP-4 possess the same structural building unit but with different structures. UP-5 and UP-6 feature the same UO(2)/L ratio of 3:2 but a different structural building unit. Photoluminescence studies reveal that UP-5 displays characteristic emissions of uranyl cations. Ion-exchange experiments demonstrate that the H(3)O(+) in UP-6 can be easily and selectively exchanged by monovalent cations including Na(+), K(+), Cs(+), and Ag(+) cations, whereas the framework retains identical as confirmed by single-crystal X-ray diffractions. PMID:23094669

Yang, Weiting; Wu, Hong-Yue; Wang, Run-Xue; Pan, Qing-Jiang; Sun, Zhong-Ming; Zhang, Hongjie

2012-10-24

57

X-ray diffraction and Raman scattering studies on large-area array and nanobranched structure of 1D MoO{sub 2} nanorods  

Energy Technology Data Exchange (ETDEWEB)

One-dimensional (1D) MoO{sub 2} nanorods in the form of a large-area array and nanobranched structure were prepared by hot-filament metal-oxide vapour deposition at low and high pressures in atmospheric argon flows respectively. The x-ray diffraction (XRD) patterns of both as-synthesized samples show that the 1D MoO{sub 2} nanorods are monoclinic crystals in space group P 2{sub 1}/c. The Raman spectrum of the large-area array of 1D MoO{sub 2} nanorods appears to be the same as that of a two-dimensional (2D) MoO{sub 2} thin film. The Raman spectrum of the nanobranched structure of 1D MoO{sub 2} nanorods showed a downshift and asymmetric broadening of the Raman first-order TO peak when compared with the bulk (q = 0) mode. The Raman shift and broadening were attributed to phonon confinement effect in the 1D nanorods. The in situ Raman spectra of laser-induced oxidation of the nanobranched structure of 1D MoO{sub 2} nanorods demonstrate that they can be oxidized easily and more strongly than the 3D bulk MoO{sub 2} powder.

Kumari, Latha [Department of Physics, National Dong Hwa University, Hualien 974, Taiwan (China); Ma, Y-R [Department of Physics, National Dong Hwa University, Hualien 974, Taiwan (China); Tsai, C-C [Department of Physics, National Dong Hwa University, Hualien 974, Taiwan (China); Lin, Y-W [Department of Physics, National Dong Hwa University, Hualien 974, Taiwan (China); Wu, S Y [Department of Physics, National Dong Hwa University, Hualien 974, Taiwan (China); Cheng, K-W [Institute of Physics, Academia Sinica, Taipei 1159, Taiwan (China); Liou Yung [Institute of Physics, Academia Sinica, Taipei 1159, Taiwan (China)

2007-03-21

58

X-ray diffraction and Raman scattering studies on large-area array and nanobranched structure of 1D MoO2 nanorods  

International Nuclear Information System (INIS)

One-dimensional (1D) MoO2 nanorods in the form of a large-area array and nanobranched structure were prepared by hot-filament metal-oxide vapour deposition at low and high pressures in atmospheric argon flows respectively. The x-ray diffraction (XRD) patterns of both as-synthesized samples show that the 1D MoO2 nanorods are monoclinic crystals in space group P 21/c. The Raman spectrum of the large-area array of 1D MoO2 nanorods appears to be the same as that of a two-dimensional (2D) MoO2 thin film. The Raman spectrum of the nanobranched structure of 1D MoO2 nanorods showed a downshift and asymmetric broadening of the Raman first-order TO peak when compared with the bulk (q = 0) mode. The Raman shift and broadening were attributed to phonon confinement effect in the 1D nanorods. The in situ Raman spectra of laser-induced oxidation of the nanobranched structure of 1D MoO2 nanorods demonstrate that they can be oxidized easily and more strongly than the 3D bulk MoO2 powder

2007-03-21

59

On maximal eigenfrequency separation in two-material structures: the 1D and 2D scalar cases  

DEFF Research Database (Denmark)

We present a method to maximize the separation of two adjacent eigenfrequencies in structures with two material components. The method is based on finite element analysis and topology optimization in which an iterative algorithm is used to find the optimal distribution of the materials. Results are presented for eigenvalue problems based on the 1D and 2D scalar wave equations. Two different objectives are used in the optimization, the difference between two adjacent eigenfrequencies and the ratio between the squared eigenfrequencies. In the ID case, we use simple interpolation of material parameters but in the 2D case the use of a more involved interpolation is needed, and results obtained with a new interpolation function are shown. In the 2D case, the objective is reformulated into a double-bound formulation due to the complication from multiple eigenfrequencies. It is shown that some general conclusions can be drawn that relate the material parameters to the obtainable objective values and the optimized designs.

Jensen, Jakob SØndergaard; Pedersen, Niels Leergaard

2006-01-01

60

X-Ray crystal structure of [HSm{V(IV)O(TPPS)}]n and encapsulation of nitrogen molecules in 1-D channels.  

UK PubMed Central (United Kingdom)

The crystal structure of an N(2)-encapusulated MOF, which is stable under open-air conditions at ambient temperature, was determined by single-crystal X-ray diffraction at 123 K. The crystal MOF of [HSm{V(IV)O(TPPS)}](n) designed to have 1-D channels periodically constricted by porphyrins planes adsorbed N(2) at 77 K. The adsorbed N(2) molecules remained in the 1-D channels even after warming to ambient temperature. The single-crystal structure of [HSm{V(IV)O(TPPS)}](n)?N(2) determined by X-ray diffraction indicated that N(2) molecules trapped in the constricted parts block other N(2) molecules in 1-D channels from escaping from the MOF. Such a unique encapsulation mode provides a promising approach toward designing novel MOFs with high gas storage capacity at ambient temperature.

Chen WT; Yamada Y; Liu GN; Kubota A; Ichikawa T; Kojima Y; Guo GC; Fukuzumi S

2011-12-01

 
 
 
 
61

X-Ray crystal structure of [HSm{V(IV)O(TPPS)}]n and encapsulation of nitrogen molecules in 1-D channels.  

Science.gov (United States)

The crystal structure of an N(2)-encapusulated MOF, which is stable under open-air conditions at ambient temperature, was determined by single-crystal X-ray diffraction at 123 K. The crystal MOF of [HSm{V(IV)O(TPPS)}](n) designed to have 1-D channels periodically constricted by porphyrins planes adsorbed N(2) at 77 K. The adsorbed N(2) molecules remained in the 1-D channels even after warming to ambient temperature. The single-crystal structure of [HSm{V(IV)O(TPPS)}](n)?N(2) determined by X-ray diffraction indicated that N(2) molecules trapped in the constricted parts block other N(2) molecules in 1-D channels from escaping from the MOF. Such a unique encapsulation mode provides a promising approach toward designing novel MOFs with high gas storage capacity at ambient temperature. PMID:22012574

Chen, Wen-Tong; Yamada, Yusuke; Liu, Guang-Ning; Kubota, Akira; Ichikawa, Takayuki; Kojima, Yoshitsugu; Guo, Guo-Cong; Fukuzumi, Shunichi

2011-10-19

62

Electronic structure of Cr1-dS (d=0,0.17) with NiAs-type crystal structure  

CERN Multimedia

Valence-band and conduction-band electronic structure of CrS (d=0) and Cr5S6 (d=0.17) has been investigated by means of photoemission and inverse-photoemission spectroscopies. Bandwidth of the valence bands of Cr5S6 (8.5 eV) is wider than that of CrS (8.1 eV), though the Cr 3d partial density of states evaluated from the Cr 3p-3d resonant photoemission spectroscopy is almost unchanged between the two compounds with respect to the shapes including binding energies. The Cr 3d (t2g) exchange splitting energies of CrS and Cr5S6 are determined to be 3.9 and 3.3 eV, respectively.

Koyama, M; Ueda, Y; Hirai, C; Taniguchi, M

2002-01-01

63

A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Little is known regarding the basis for selection of the semi-invariant ?? T cell receptor (TCR) expressed by natural killer T (NKT) cells or how this mediates recognition of CD1d–glycolipid complexes. We have determined the structures of two human NKT TCRs that differ in their CDR3? composition and...

Kjer-Nielsen, Lars; Borg, Natalie A.; Pellicci, Daniel G.; Beddoe, Travis; Kostenko, Lyudmila; Clements, Craig S.

64

Modeling of Subject Arterial Segments Using 3D Fluid Structure Interaction and 1D-0D Arterial Tree Network Boundary Condition  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Modeling of Subject Specific Arterial Segments Using 3D Fluid Structure Interaction and a 1D-0D Arterial Tree Network Boundary Condition   Magnus Andersson, Jonas Lantz , Matts Karlsson   Department of Management and Engineering, Linköping University, SE-581 83 Linköping, Sweden   Introduction In ...

Andersson, Magnus; Lantz, Jonas; Karlsson, Matts

65

Augmented GARCH sequences: Dependence structure and asymptotics  

CERN Multimedia

The augmented GARCH model is a unification of numerous extensions of the popular and widely used ARCH process. It was introduced by Duan and besides ordinary (linear) GARCH processes, it contains exponential GARCH, power GARCH, threshold GARCH, asymmetric GARCH, etc. In this paper, we study the probabilistic structure of augmented $\\mathrm {GARCH}(1,1)$ sequences and the asymptotic distribution of various functionals of the process occurring in problems of statistical inference. Instead of using the Markov structure of the model and implied mixing properties, we utilize independence properties of perturbed GARCH sequences to directly reduce their asymptotic behavior to the case of independent random variables. This method applies for a very large class of functionals and eliminates the fairly restrictive moment and smoothness conditions assumed in the earlier theory. In particular, we derive functional CLTs for powers of the augmented GARCH variables, derive the error rate in the CLT and obtain asymptotic res...

Hörmann, Siegfried

2008-01-01

66

A novel 1D silver(I) coordination polymer constructed from indol-3-butyric acid: Synthesis, crystal structure and natural bond orbital analysis by DFT  

Science.gov (United States)

A novel one-dimensional Ag(I) coordination polymer with formula [Ag(IBA)]n(1) (IBA = indol-3-butyric acid) has been synthesized and structurally characterized by infrared spectroscopy (IR), elemental analysis and single crystal X-ray diffraction techniques. X-ray crystallographic study revealed that 1 crystallizes in monoclinic space group C2/c with unit cell parameters of a = 25.6863(7) Å, b = 7.5837(2) Å, c = 10.9065(3) Å, ? = 103.296(2)°, V = 2067.61(10) Å3 and shows 1D wave-like one-dimensional coordination polymer. In the crystal structure, 1D chains are formed by Ag2:L2 dimers connected by argentophilic Ag⋯Ag interactions. The adjacent 1D polymeric chains are further assembled by hydrogen bond (NH⋯O), Ag⋯C, Ag⋯?, CH⋯? and weak ?⋯? interactions into a three-dimensional framework. The complex also exhibits the intermolecular pseudo-agostic (IPA) interaction (C-H⋯Ag). The spontaneous formation of the 1D assembly of complex 1 was investigated with density functional theory (DFT) method.

Zorlu, Yunus; Can, Hatice

2013-04-01

67

Structure Prediction of Partial-Length Protein Sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Protein structure information is essential to understand protein function. Computational methods to accurately predict protein structure from the sequence have primarily been evaluated on protein sequences representing full-length native proteins. Here, we demonstrate that top-performing structure prediction methods can accurately predict the partial structures of proteins encoded by sequences that contain approximately 50% or more of the full-length protein sequence. We hypothesize that structure prediction may be useful for predicting functions of proteins whose corresponding genes are mapped expressed sequence tags (ESTs) that encode partial-length amino acid sequences. Additionally, we identify a confidence score representing the quality of a predicted structure as a useful means of predicting the likelihood that an arbitrary polypeptide sequence represents a portion of a foldable protein sequence (“foldability”). This work has ramifications for the prediction of protein structure with limited or noisy sequence information, as well as genome annotation.

Adrian Laurenzi; Ling-Hong Hung; Ram Samudrala

2013-01-01

68

Structure prediction of partial-length protein sequences.  

UK PubMed Central (United Kingdom)

Protein structure information is essential to understand protein function. Computational methods to accurately predict protein structure from the sequence have primarily been evaluated on protein sequences representing full-length native proteins. Here, we demonstrate that top-performing structure prediction methods can accurately predict the partial structures of proteins encoded by sequences that contain approximately 50% or more of the full-length protein sequence. We hypothesize that structure prediction may be useful for predicting functions of proteins whose corresponding genes are mapped expressed sequence tags (ESTs) that encode partial-length amino acid sequences. Additionally, we identify a confidence score representing the quality of a predicted structure as a useful means of predicting the likelihood that an arbitrary polypeptide sequence represents a portion of a foldable protein sequence ("foldability"). This work has ramifications for the prediction of protein structure with limited or noisy sequence information, as well as genome annotation.

Laurenzi A; Hung LH; Samudrala R

2013-01-01

69

Nonlinear deterministic structures and the randomness of protein sequences  

CERN Multimedia

To clarify the randomness of protein sequences, we make a detailed analysis of a set of typical protein sequences representing each structural classes by using nonlinear prediction method. No deterministic structures are found in these protein sequences and this implies that they behave as random sequences. We also give an explanation to the controversial results obtained in previous investigations.

Huang Yan Zhao

2003-01-01

70

EURDYN-1D: a computer code for the one-dimensional non-linear dynamic analysis of structural systems. Description and users' manual (release 1)  

International Nuclear Information System (INIS)

The goal of the present report is to provide for a comprehensive users' manual describing the capabilities of the computer code EURDYN-1D. It includes information and examples about the type of problems which can be solved with the code and explanation on how to prepare input data and, how to interpret output results. The field of applications of EURDYN-1D is the one dimensional dynamic analysis of general structural systems and the code is particularly suited for fast transient events involving propagation of longitudinal mechanical waves (subsonic) in structures. Both geometrical and physical non-linearities can be taken into account. Typical examples are impact problems, fast dynamic loading due the explosions or sudden release for initial loads due to failures, etc. To these classes belong many problems encountered in the reactor safety field as well as in more common and general technological applications

1985-01-01

71

Novel 1D coordination polymer {Tm(Piv)3}n: Synthesis, structure, magnetic properties and thermal behavior  

International Nuclear Information System (INIS)

The new 1D coordination polymer {Tm(Piv)3}n (1), where Piv=OOCBut?, was synthesized in high yield (>95%) by the reaction of thulium acetate with pivalic acid in air at 100 °S. According to the X-ray diffraction data, the metal atoms in compound 1 are in an octahedral ligand environment unusual for lanthanides. The magnetic and luminescence properties of polymer 1, it’s the solid-phase thermal decomposition in air and under argon, and the thermal behavior in the temperature range of ?50…+50 °S were investigated. The vaporization process of complex 1 was studied by the Knudsen effusion method combined with mass-spectrometric analysis of the gas-phase composition in the temperature range of 570–680 K. - Graphical Abstract: Novel 1D coordination polymer {Tm(Piv)3}n was synthesized and studied by X-ray diffraction. The magnetic, luminescence properties, the thermal behavior and the volatility for the compound {Tm(Piv)3}n were investigated.? Highlights: ? We synthesized the coordination polymer {Tm(Piv)3}n. ? Tm atoms in polymer have the coordination number 6. ? Polymer exhibits blue-color emission at room temperature. ? Polymer shows high thermal stability and volatility. ? Polymer has no phase transitions in the range of ?50…+50 °S.

2012-01-01

72

Metastable Se6 as a ligand for Ag+: from isolated molecular to polymeric 1D and 2D structures.  

UK PubMed Central (United Kingdom)

Attempts to prepare the hitherto unknown Se(6)(2+) cation by the reaction of elemental selenium and Ag[A] ([A](-) = [Sb(OTeF(5))(6)](-), [Al(OC(CF(3))(3))(4)](-)) in SO(2) led to the formation of [(OSO)Ag(Se(6))Ag(OSO)][Sb(OTeF(5))(6)](2)1 and [(OSO)(2)Ag(Se(6))Ag(OSO)(2)][Al(OC(CF(3))(3))(4)](2)2a. 1 could only be prepared by using bromine as co-oxidant, however, bulk 2b (2a with loss of SO(2)) was accessible from Ag[Al(OC(CF(3))(3))(4)] and grey Se in SO(2) (chem. analysis). The reactions of Ag[MF(6)] (M = As, Sb) and elemental selenium led to crystals of 1/?{[Ag(Se(6))](?)[Ag(2)(SbF(6))(3)](?)} 3 and {1/?[Ag(Se(6))Ag](?)}[AsF(6)](2)4. Pure bulk 4 was best prepared by the reaction of Se(4)[AsF(6)](2), silver metal and elemental selenium. Attempts to prepare bulk 1 and 3 were unsuccessful. 1-4 were characterized by single-crystal X-ray structure determinations, 2b and 4 additionally by chemical analysis and 4 also by X-ray powder diffraction, FT-Raman and FT-IR spectroscopy. Application of the PRESTO III sequence allowed for the first time (109)Ag MAS NMR investigations of 4 as well as AgF, AgF(2), AgMF(6) and {1/?[Ag(I(2))](?)}[MF(6)] (M = As, Sb). Compounds 1 and 2a/b, with the very large counter ions, contain isolated [Ag(Se(6))Ag](2+) heterocubane units consisting of a Se(6) molecule bicapped by two silver cations (local D(3d) sym). 3 and 4, with the smaller anions, contain close packed stacked arrays of Se(6) rings with Ag(+) residing in octahedral holes. Each Ag(+) ion coordinates to three selenium atoms of each adjacent Se(6) ring. 4 contains [Ag(Se(6))(+)](?) stacks additionally linked by Ag(2)(+) into a two dimensional network. 3 features a remarkable 3-dimensional [Ag(2)(SbF(6))(3)](-) anion held together by strong Sb-FAg contacts between the component Ag(+) and [SbF(6)](-) ions. The hexagonal channels formed by the [Ag(2)(SbF(6))(3)](-) anions are filled by stacks of [Ag(Se(6))(+)](?) cations. Overall 1-4 are new members of the rare class of metal complexes of neutral main group elemental clusters, in which the main group element is positively polarized due to coordination to a metal ion. Notably, 1 to 4 include the commonly metastable Se(6) molecule as a ligand. The structure, bonding and thermodynamics of 1 to 4 were investigated with the help of quantum chemical calculations (PBE0/TZVPP and (RI-)MP2/TZVPP, in part including COSMO solvation) and Born-Fajans-Haber-cycle calculations. From an analysis of all the available data it appears that the formation of the usually metastable Se(6) molecule from grey selenium is thermodynamically driven by the coordination to the Ag(+) ions.

Aris D; Beck J; Decken A; Dionne I; Schmedt auf der Günne J; Hoffbauer W; Köchner T; Krossing I; Passmore J; Rivard E; Steden F; Wang X

2011-06-01

73

Metastable Se6 as a ligand for Ag+: from isolated molecular to polymeric 1D and 2D structures.  

Science.gov (United States)

Attempts to prepare the hitherto unknown Se(6)(2+) cation by the reaction of elemental selenium and Ag[A] ([A](-) = [Sb(OTeF(5))(6)](-), [Al(OC(CF(3))(3))(4)](-)) in SO(2) led to the formation of [(OSO)Ag(Se(6))Ag(OSO)][Sb(OTeF(5))(6)](2)1 and [(OSO)(2)Ag(Se(6))Ag(OSO)(2)][Al(OC(CF(3))(3))(4)](2)2a. 1 could only be prepared by using bromine as co-oxidant, however, bulk 2b (2a with loss of SO(2)) was accessible from Ag[Al(OC(CF(3))(3))(4)] and grey Se in SO(2) (chem. analysis). The reactions of Ag[MF(6)] (M = As, Sb) and elemental selenium led to crystals of 1/?{[Ag(Se(6))](?)[Ag(2)(SbF(6))(3)](?)} 3 and {1/?[Ag(Se(6))Ag](?)}[AsF(6)](2)4. Pure bulk 4 was best prepared by the reaction of Se(4)[AsF(6)](2), silver metal and elemental selenium. Attempts to prepare bulk 1 and 3 were unsuccessful. 1-4 were characterized by single-crystal X-ray structure determinations, 2b and 4 additionally by chemical analysis and 4 also by X-ray powder diffraction, FT-Raman and FT-IR spectroscopy. Application of the PRESTO III sequence allowed for the first time (109)Ag MAS NMR investigations of 4 as well as AgF, AgF(2), AgMF(6) and {1/?[Ag(I(2))](?)}[MF(6)] (M = As, Sb). Compounds 1 and 2a/b, with the very large counter ions, contain isolated [Ag(Se(6))Ag](2+) heterocubane units consisting of a Se(6) molecule bicapped by two silver cations (local D(3d) sym). 3 and 4, with the smaller anions, contain close packed stacked arrays of Se(6) rings with Ag(+) residing in octahedral holes. Each Ag(+) ion coordinates to three selenium atoms of each adjacent Se(6) ring. 4 contains [Ag(Se(6))(+)](?) stacks additionally linked by Ag(2)(+) into a two dimensional network. 3 features a remarkable 3-dimensional [Ag(2)(SbF(6))(3)](-) anion held together by strong Sb-FAg contacts between the component Ag(+) and [SbF(6)](-) ions. The hexagonal channels formed by the [Ag(2)(SbF(6))(3)](-) anions are filled by stacks of [Ag(Se(6))(+)](?) cations. Overall 1-4 are new members of the rare class of metal complexes of neutral main group elemental clusters, in which the main group element is positively polarized due to coordination to a metal ion. Notably, 1 to 4 include the commonly metastable Se(6) molecule as a ligand. The structure, bonding and thermodynamics of 1 to 4 were investigated with the help of quantum chemical calculations (PBE0/TZVPP and (RI-)MP2/TZVPP, in part including COSMO solvation) and Born-Fajans-Haber-cycle calculations. From an analysis of all the available data it appears that the formation of the usually metastable Se(6) molecule from grey selenium is thermodynamically driven by the coordination to the Ag(+) ions. PMID:21552624

Aris, Damian; Beck, Johannes; Decken, Andreas; Dionne, Isabelle; Schmedt auf der Günne, Jörn; Hoffbauer, Wilfried; Köchner, Tobias; Krossing, Ingo; Passmore, Jack; Rivard, Eric; Steden, Folker; Wang, Xinping

2011-05-09

74

Syntheses, crystal structures and properties of two 1-D cadmium(II) coordination polymers based on 1,1'-(1,3-propanediyl)bis-1H-benzimidazole  

International Nuclear Information System (INIS)

[en] The combination of framework-builders 1,1'-(1,3-propanediyl)bis-1H-benzimidazole (pbbm), Cd(II) ion and framework-regulator ClO4- or SO42- provides two new coordination polymers [Cd(pbbm)2(ClO4)2]n(1) and {[Cd(pbbm)SO4(H2O)2].CH3OH}n(2). Both of them display 1-D chain framework, but their detailed structures are clearly different from each other. 1 displays a 1-D ribbon of rings framework, 2 features an interesting infinite 1-D looped chain structure composed of two kinds of rings, the smaller 8-membered ring and the larger 20-membered ring. The antimicrobial activities of the two polymers were tested by the agar diffusion method and the results indicated that they exhibited antimicrobial activities against bacterial strands. The measurement of the non-isothermal kinetics of the thermal decomposition of 2 reveals that there are at least three steps that occur in its decomposition process. - Graphical abstract: Two new Cd(II)-containing complexes have been synthesized and characterized by single-crystal X-ray diffraction. The antimicrobial activity and the non-isothermal kinetics of the thermal decomposition of the polymers were also investigated. Display Omitted

2008-01-01

75

Expanding the 2,2'-bipyrimidine bridged 1D homonuclear coordination polymers family: [M(II)(bpym)Cl2] (M = Fe, Co) magnetic and structural characterization.  

UK PubMed Central (United Kingdom)

One pot reaction of hydrated chloride salts of Fe(II) and Co(II) with stoichiometric amounts of 2,2'-bipyrimidine (bpym) in a methanol-acetonitrile mixture afforded the corresponding 1D homonuclear coordination polymers, [?-(bpym)MCl2]n. Crystal structures of both complexes are isomorphous in the highly symmetric orthorhombic space group Fddd. The 1D coordination polymers are composed of almost orthogonal alternating bipyrimidine bridges linking the {MCl2} units. The magnetic behaviour of the Fe(II) compound can be well understood as a uniform S = 2 chain with an antiferromagnetic exchange interaction between metal ion sites. In the case of the Co(II) ion, also an antiferromagnetic interaction is operative along the uniform chain, while at low temperatures a long range-ordering is observed due to spin canting originating from the anisotropic behaviour of the Co(II) lowest energy Kramers doublets.

Alborés P; Rentschler E

2013-07-01

76

Expanding the 2,2'-bipyrimidine bridged 1D homonuclear coordination polymers family: [M(II)(bpym)Cl2] (M = Fe, Co) magnetic and structural characterization.  

Science.gov (United States)

One pot reaction of hydrated chloride salts of Fe(II) and Co(II) with stoichiometric amounts of 2,2'-bipyrimidine (bpym) in a methanol-acetonitrile mixture afforded the corresponding 1D homonuclear coordination polymers, [?-(bpym)MCl2]n. Crystal structures of both complexes are isomorphous in the highly symmetric orthorhombic space group Fddd. The 1D coordination polymers are composed of almost orthogonal alternating bipyrimidine bridges linking the {MCl2} units. The magnetic behaviour of the Fe(II) compound can be well understood as a uniform S = 2 chain with an antiferromagnetic exchange interaction between metal ion sites. In the case of the Co(II) ion, also an antiferromagnetic interaction is operative along the uniform chain, while at low temperatures a long range-ordering is observed due to spin canting originating from the anisotropic behaviour of the Co(II) lowest energy Kramers doublets. PMID:23676951

Alborés, Pablo; Rentschler, Eva

2013-05-15

77

Syntheses, crystal structures and luminescent properties of two new 1D d 1 coordination polymers constructed from 2,2'-bibenzimidazole and 1,4-benzenedicarboxylate  

International Nuclear Information System (INIS)

[en] Two novel interesting d 1 metal coordination polymers, [Zn(H2bibzim)(BDC)] n (1) and [Cd(H2bibzim)(BDC)] n (2) [H2bibzim=2,2'-bibenzimidazole, BDC=1,4-benzenedicarboxylate] have been synthesized under solvothermal conditions and structurally characterized. Both 1 and 2 are constructed from infinite neutral zigzag-like one-dimensional (1D) chains. The ?-? interactions and interchain hydrogen-bonding interactions further extend the 1D arrangement to generate a 3D supramolecular architecture for 1 and 2. Both complexes have high thermal stability and display strong blue fluorescent emissions in the solid state upon photo-excitation at 365 nm at room temperature. They are the first two examples that 2,2'-bibenzimidazole has been introduced into the d 1 coordination polymeric framework

2005-01-01

78

A polythreading array formed by a (3,5)-connected 3D anionic network and 1D cationic chains: synthesis, structure, and catalytic properties.  

Science.gov (United States)

An unusual copper(II) coordination polymer {[Cu(tmtz)(H2O)4][Cu2(tmtz)2(sip)2]·4H2O}n (1) (tmtz = 1,4-bis(1,2,4-triazol-1-ylmethyl)-2,3,4,5-tetramethylbenzene, sip = 5-sulfoisophthalate) is synthesized by the hydrothermal reaction. X-Ray structural analysis shows that 1 is comprised of two distinct and crystallographically independent polymeric motifs polythreading together. The first motif of 1 is an unusual (3,5)-connected 3D anionic network [Cu2(tmtz)2(sip)2]. The second motif in 1 is the [Cu(tmtz)(H2O)4]n 1D cationic chain. A polythreading array formed by a (3,5)-connected 3D anionic network and 1D cationic chains. The catalytic performance exhibits that 1 is active as a catalyst for the degradation of methyl orange. The thermal analysis is also observed. PMID:23689914

Li, Min; Zhao, Shan; Peng, Yan-Fen; Li, Bao-Long; Li, Hai-Yan

2013-05-21

79

A polythreading array formed by a (3,5)-connected 3D anionic network and 1D cationic chains: synthesis, structure, and catalytic properties.  

UK PubMed Central (United Kingdom)

An unusual copper(II) coordination polymer {[Cu(tmtz)(H2O)4][Cu2(tmtz)2(sip)2]·4H2O}n (1) (tmtz = 1,4-bis(1,2,4-triazol-1-ylmethyl)-2,3,4,5-tetramethylbenzene, sip = 5-sulfoisophthalate) is synthesized by the hydrothermal reaction. X-Ray structural analysis shows that 1 is comprised of two distinct and crystallographically independent polymeric motifs polythreading together. The first motif of 1 is an unusual (3,5)-connected 3D anionic network [Cu2(tmtz)2(sip)2]. The second motif in 1 is the [Cu(tmtz)(H2O)4]n 1D cationic chain. A polythreading array formed by a (3,5)-connected 3D anionic network and 1D cationic chains. The catalytic performance exhibits that 1 is active as a catalyst for the degradation of methyl orange. The thermal analysis is also observed.

Li M; Zhao S; Peng YF; Li BL; Li HY

2013-07-01

80

MSACompro: Improving Multiple Protein Sequence Alignment by Predicted Structural Features.  

Science.gov (United States)

Multiple Sequence Alignment (MSA) is an essential tool in protein structure modeling, gene and protein function prediction, DNA motif recognition, phylogenetic analysis, and many other bioinformatics tasks. Therefore, improving the accuracy of multiple sequence alignment is an important long-term objective in bioinformatics. We designed and developed a new method MSACompro to incorporate predicted secondary structure, relative solvent accessibility, and residue-residue contact information into the currently most accurate posterior probability-based MSA methods to improve the accuracy of multiple sequence alignments. Different from the multiple sequence alignment methods that use the tertiary structure information of some sequences, our method uses the structural information purely predicted from sequences. In this chapter, we first introduce some background and related techniques in the field of multiple sequence alignment. Then, we describe the detailed algorithm of MSACompro. Finally, we show that integrating predicted protein structural information improved the multiple sequence alignment accuracy. PMID:24170409

Deng, Xin; Cheng, Jianlin

2014-01-01

 
 
 
 
81

Improving phonetic alignment by handling secondary sequence structures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this talk a modification of the traditional Needleman-Wunsch algorithm for pairwise sequence alignment is proposed which makes it possible to align sequences not only according to their primary but also to their secondary structure.

List, Johann-Mattis

82

IWS: Integrated web server for protein sequence and structure analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Rapid increase in protein sequence information from genome sequencing projects demand the intervention of bioinformatics tools to recognize interesting gene-products and associated function. Often, multiple algorithms need to be employed to improve accuracy in predictions and several structure...

Shameer, Khader; Sowdhamini, Ramanathan

83

Designing polymorphic ISSR primers in order to study gene sequences x and y types glutenin subunits in 1D locus controlling favourable baking quality in elite mutant lines of bread wheat  

International Nuclear Information System (INIS)

Baking quality is one of important traits in qualitative improvement of bread wheat. Gluten prolamins determine wheat flour quality for different technological process such as bread making. Between gluten proteins, High Molecular Glutenin (HMW) group and specially, d allele in 1D locus with x-type and y-type subunits are very valuable in baking quality. In this study, amino acid sequences of x-type subunits (2.1, 2.2, 2.2*, 5) and y-type subunits (10, 12) related to 1D locus were searched, found and compared together using Genedoc software. After amino acid sequences alignment of y-type subunits and x-type subunits, it was characterized that deletion, insertion (duplication) and point mutations in these subunits involved in biological function of proteins. most important insertion and deletion mutations were 185 amino acids sequence insertion of 2.2* subunit and 102 amino acids sequence insertion of x2.2 subunit in position 486 of amino acid sequence and six amino acid sequence deletion IGQGQQ in position 203 of y10 subunit. From important point mutations can be pointed to conversion of serine to cysteine in position 118 of x 5 subunit and substitution of glutamine to histidine in position 626 of x5 subunit. Finally, polymorph ISSR primers in repetitive domains were designed on similarities and differences in subunits of x and y-types. These primers show good banding polymorphisms in elite mutant lines, standard commercial cultivars and F2 populations from crosses. (author)

2008-01-01

84

Crystal Structure of Human Liver delta {4}-3-Ketosteroid 5 beta-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis  

Energy Technology Data Exchange (ETDEWEB)

AKR1D1 (steroid 5{beta}-reductase) reduces all 4-3-ketosteroids to form 5{beta}-dihydrosteroids, a first step in the clearance of steroid hormones and an essential step in the synthesis of all bile acids. The reduction of the carbon-carbon double bond in an a,{beta}-unsaturated ketone by 5{beta}-reductase is a unique reaction in steroid enzymology because hydride transfer from NADPH to the {beta}-face of a 4-3-ketosteroid yields a cis-A/B-ring configuration with an {approx}90 bend in steroid structure. Here, we report the first x-ray crystal structure of a mammalian steroid hormone carbon-carbon double bond reductase, human 4-3-ketosteroid 5{beta}-reductase (AKR1D1), and its complexes with intact substrates. We have determined the structures of AKR1D1 complexes with NADP+ at 1.79- and 1.35- Angstroms resolution (HEPES bound in the active site), NADP+ and cortisone at 1.90- Angstroms resolution, NADP+ and progesterone at 2.03- Angstroms resolution, and NADP+ and testosterone at 1.62- Angstroms resolution. Complexes with cortisone and progesterone reveal productive substrate binding orientations based on the proximity of each steroid carbon-carbon double bond to the re-face of the nicotinamide ring of NADP+. This orientation would permit 4-pro-(R)-hydride transfer from NADPH. Each steroid carbonyl accepts hydrogen bonds from catalytic residues Tyr58 and Glu120. The Y58F and E120A mutants are devoid of activity, supporting a role for this dyad in the catalytic mechanism. Intriguingly, testosterone binds nonproductively, thereby rationalizing the substrate inhibition observed with this particular steroid. The locations of disease-linked mutations thought to be responsible for bile acid deficiency are also revealed.

Di Costanzo,L.; Drury, J.; Penning, T.; Christianson, D.

2008-01-01

85

Crystal Structure of Human Liver ?4-3-Ketosteroid 5?-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis*S??  

Science.gov (United States)

AKR1D1 (steroid 5?-reductase) reduces all ?4-3-ketosteroids to form 5?-dihydrosteroids, a first step in the clearance of steroid hormones and an essential step in the synthesis of all bile acids. The reduction of the carbon-carbon double bond in an ?,?-unsaturated ketone by 5?-reductase is a unique reaction in steroid enzymology because hydride transfer from NADPH to the ?-face of a ?4-3-ketosteroid yields a cis-A/B-ring configuration with an ?90° bend in steroid structure. Here, we report the first x-ray crystal structure of a mammalian steroid hormone carbon-carbon double bond reductase, human ?4-3-ketosteroid 5?-reductase (AKR1D1), and its complexes with intact substrates. We have determined the structures of AKR1D1 complexes with NADP+ at 1.79- and 1.35-Å resolution (HEPES bound in the active site), NADP+ and cortisone at 1.90-Å resolution, NADP+ and progesterone at 2.03-Å resolution, and NADP+ and testosterone at 1.62-Å resolution. Complexes with cortisone and progesterone reveal productive substrate binding orientations based on the proximity of each steroid carbon-carbon double bond to the re-face of the nicotinamide ring of NADP+. This orientation would permit 4-pro-(R)-hydride transfer from NADPH. Each steroid carbonyl accepts hydrogen bonds from catalytic residues Tyr58 and Glu120. The Y58F and E120A mutants are devoid of activity, supporting a role for this dyad in the catalytic mechanism. Intriguingly, testosterone binds nonproductively, thereby rationalizing the substrate inhibition observed with this particular steroid. The locations of disease-linked mutations thought to be responsible for bile acid deficiency are also revealed.

Di Costanzo, Luigi; Drury, Jason E.; Penning, Trevor M.; Christianson, David W.

2008-01-01

86

Sequence analysis of the cDNA for the human casein kinase I {delta} (CSNK1D) gene and its chromosomal localization  

Energy Technology Data Exchange (ETDEWEB)

This article reports on the genetic mapping of a cDNA clone encoding human casein kinase I (CK1) using fluorescence in situ hybridization and polymerase chain reaction analysis of human-rodent hybrid cell panels. When compared to the amino acid sequence in the kinase domain of the rat, this cDNA seems to be a human homologue of the CK1 {delta} isoform. Sequence similarity to the kinase domains and function in DNA repair in Saccharomyces cerevisiae and Saccharomyces pombe are discussed. 14 refs., 2 figs.

Kusuda, Jun; Hidari, Nobuko; Hirai, Momoki; Hashimoto, Katsuyuki [Univ. of Tokyo (Japan)

1996-02-15

87

Structural elucidation of four new furostanol saponins from Tupistra chinensis by 1D and 2D NMR spectroscopy.  

UK PubMed Central (United Kingdom)

Four new furostanol saponins (1-4), two pairs of diastereoisomers, were isolated from methanolic extracts of Tupistra chinensis rhizomes and their structures were assigned from (1)H and (13)C NMR spectra, DEPT, and by 2D COSY, NOESY, HMQC, and HMBC experiments.

Zou K; Wang JZ; Guo ZY; Du M; Wu J; Zhou Y; Dan FJ; Liu C

2009-01-01

88

Structural elucidation of four new furostanol saponins from Tupistra chinensis by 1D and 2D NMR spectroscopy.  

Science.gov (United States)

Four new furostanol saponins (1-4), two pairs of diastereoisomers, were isolated from methanolic extracts of Tupistra chinensis rhizomes and their structures were assigned from (1)H and (13)C NMR spectra, DEPT, and by 2D COSY, NOESY, HMQC, and HMBC experiments. PMID:19003938

Zou, Kun; Wang, Jun-zhi; Guo, Zhi-yong; Du, Ming; Wu, Jun; Zhou, Yuan; Dan, Fei-jun; Liu, Chuang

2009-01-01

89

Two extensions of 1D Toda hierarchy  

International Nuclear Information System (INIS)

The extended Toda hierarchy of Carlet, Dubrovin and Zhang is reconsidered in light of a 2 + 1D extension of the 1D Toda hierarchy constructed by Ogawa. These two extensions of the 1D Toda hierarchy turn out to have a very similar structure, and the former may be thought of as a kind of dimensional reduction of the latter. In particular, this explains an origin of the mysterious structure of the bilinear formalism proposed by Milanov.

2010-10-29

90

Tails of the dynamical structure factor of 1D spinless fermions beyond the Tomonaga-Luttinger approximation  

International Nuclear Information System (INIS)

[en] We consider one-dimensional interacting spinless fermions with a non-linear spectrum in a clean quantum wire (non-linear bosonization). We compute diagrammatically the one-dimensional dynamical structure factor, S(?, q), beyond the Tomonaga-Luttinger approximation focusing on its tails, i.e. vertical bar ? vertical bar >> vq. We provide a re-derivation, through diagrammatics, of the result of Pustilnik, Mishchenko, Glazman, and Andreev. We also extend their results to finite temperatures and long-range interactions. As applications we determine curvature and interaction corrections to the small- momentum, high-frequency conductivity and the electron-electron scattering rate. (author)

2005-01-01

91

1D 13C-NMR Data as Molecular Descriptors in Spectra — Structure Relationship Analysis of Oligosaccharides  

Directory of Open Access Journals (Sweden)

Full Text Available Spectra-structure relationships were investigated for estimating the anomeric configuration, residues and type of linkages of linear and branched trisaccharides using 13C-NMR chemical shifts. For this study, 119 pyranosyl trisaccharides were used that are trimers of the ? or ? anomers of D-glucose, D-galactose, D-mannose, L-fucose or L-rhamnose residues bonded through a or b glycosidic linkages of types 1?2, 1?3, 1?4, or 1?6, as well as methoxylated and/or N-acetylated amino trisaccharides. Machine learning experiments were performed for: (1) classification of the anomeric configuration of the first unit, second unit and reducing end; (2) classification of the type of first and second linkages; (3) classification of the three residues: reducing end, middle and first residue; and (4) classification of the chain type. Our previously model for predicting the structure of disaccharides was incorporated in this new model with an improvement of the predictive power. The best results were achieved using Random Forests with 204 di- and trisaccharides for the training set—it could correctly classify 83%, 90%, 88%, 85%, 85%, 75%, 79%, 68% and 94% of the test set (69 compounds) for the nine tasks, respectively, on the basis of unassigned chemical shifts.

Florbela Pereira

2012-01-01

92

SAAS: Short Amino Acid Sequence - A Promising Protein Secondary Structure Prediction Method of Single Sequence  

Directory of Open Access Journals (Sweden)

Full Text Available In statistical methods of predicting protein secondary structure, many researchers focus on single amino acid frequencies in ?-helices, ?-sheets, and so on, or the impact near amino acids on an amino acid forming a secondary structure. But the paper considers a short sequence of amino acids (3, 4, 5 or 6 amino acids) as integer, and statistics short sequence's probability forming secondary structure. Also, many researchers select low homologous sequences as statistical database. But this paper select whole PDB database. In this paper we propose a strategy to predict protein secondary structure using simple statistical method. Numerical computation shows that, short amino acids sequence as integer to statistics, which can easy see trend of short sequence forming secondary structure, and it will work well to select large statistical database (whole PDB database) without considering homologous, and Q3 accuracy is ca. 74% using this paper proposed simple statistical method, but accuracy of others statistical methods is less than 70%.

Zhou Yuan Wu; Ray P. S. Han

2013-01-01

93

Prediction of RNA Secondary Structure from Random Sequences using ZEM  

Directory of Open Access Journals (Sweden)

Full Text Available The biological role of many RNA crucially depends on their structure. The in depth understanding of the secondary structure of RNA would provide a better insight in to their functionality. Predicting secondary structure of RNA is the most important factor in determining its 3d structure and functions. This work proposes a model for exploring the features of a number of RNA sequences simultaneously so that comparison of sequences can be made and relevant sequences can be identified. The proposed model accepts RNA sequences in any valid biological file format. For each given sequence, required number of random sequences are generated. The generated sequences should have the same base composition as that of original sequence. ZEM (Zuker?s Energy Minimization) Algorithm finds the biologically correct structure of each RNA sequence and its corresponding free energy value. The proposed prototype enables to experiment with a number of RNA sequences and to study their features so that biologically relevant inferences can be made. An important area where it finds application is in the design of pharmaceutical products.

Cinita Mary Mathew

2012-01-01

94

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

Daniels Noah M; Nadimpalli Shilpa; Cowen Lenore J

2012-01-01

95

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment.  

UK PubMed Central (United Kingdom)

BACKGROUND: The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. RESULTS: We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. CONCLUSIONS: Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

Daniels NM; Nadimpalli S; Cowen LJ

2012-01-01

96

Crystal Structure of Human Liver [delta][superscript 4]-3-Ketosteroid 5[beta]-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis  

Energy Technology Data Exchange (ETDEWEB)

AKR1D1 (steroid 5{beta}-reductase) reduces all {Delta}{sup 4}-3-ketosteroids to form 5{beta}-dihydrosteroids, a first step in the clearance of steroid hormones and an essential step in the synthesis of all bile acids. The reduction of the carbon-carbon double bond in an {alpha}{beta}-unsaturated ketone by 5{beta}-reductase is a unique reaction in steroid enzymology because hydride transfer from NADPH to the {beta}-face of a {Delta}{sup 4}-3-ketosteroid yields a cis-A/B-ring configuration with an {approx}90{sup o} bend in steroid structure. Here, we report the first x-ray crystal structure of a mammalian steroid hormone carbon-carbon double bond reductase, human {Delta}{sup 4}-3-ketosteroid 5{beta}-reductase (AKR1D1), and its complexes with intact substrates. We have determined the structures of AKR1D1 complexes with NADP{sup +} at 1.79- and 1.35-{angstrom} resolution (HEPES bound in the active site), NADP{sup +} and cortisone at 1.90-{angstrom} resolution, NADP{sup +} and progesterone at 2.03-{angstrom} resolution, and NADP{sup +} and testosterone at 1.62-{angstrom} resolution. Complexes with cortisone and progesterone reveal productive substrate binding orientations based on the proximity of each steroid carbon-carbon double bond to the re-face of the nicotinamide ring of NADP{sup +}. This orientation would permit 4-pro-(R)-hydride transfer from NADPH. Each steroid carbonyl accepts hydrogen bonds from catalytic residues Tyr{sup 58} and Glu{sup 120}. The Y58F and E120A mutants are devoid of activity, supporting a role for this dyad in the catalytic mechanism. Intriguingly, testosterone binds nonproductively, thereby rationalizing the substrate inhibition observed with this particular steroid. The locations of disease-linked mutations thought to be responsible for bile acid deficiency are also revealed.

Di Costanzo, Luigi; Drury, Jason E.; Penning, Trevor M.; Christianson, David W. (UPENN); (UPENN-MED)

2008-07-15

97

Evolutionary optimization of biopolymers and sequence structure maps  

Energy Technology Data Exchange (ETDEWEB)

Searching for biopolymers having a predefined function is a core problem of biotechnology, biochemistry and pharmacy. On the level of RNA sequences and their corresponding secondary structures we show that this problem can be analyzed mathematically. The strategy will be to study the properties of the RNA sequence to secondary structure mapping that is essential for the understanding of the search process. We show that to each secondary structure s there exists a neutral network consisting of all sequences folding into s. This network can be modeled as a random graph and has the following generic properties: it is dense and has a giant component within the graph of compatible sequences. The neutral network percolates sequence space and any two neutral nets come close in terms of Hamming distance. We investigate the distribution of the orders of neutral nets and show that above a certain threshold the topology of neutral nets allows to find practically all frequent secondary structures.

Reidys, C.M.; Kopp, S.; Schuster, P. [Institut fuer Molekulare Biotechnologie, Jena (Germany)

1996-06-01

98

DNA sequence and structure requirements for cleavage of V(D)J recombination signal sequences.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Purified RAG1 and RAG2 proteins can cleave DNA at V(D)J recombination signals. In dissecting the DNA sequence and structural requirements for cleavage, we find that the heptamer and nonamer motifs of the recombination signal sequence can independently direct both steps of the cleavage reaction. Prop...

Cuomo, C A; Mundy, C L; Oettinger, M A

99

Mononuclear, dinuclear and 1-D polymeric complexes of Cd(II) of a pyridyl pyrazole ligand: Syntheses, crystal structures and photoluminescence studies  

Science.gov (United States)

The syntheses, crystal structures and photoluminescence properties of four new Cd(II) complexes are reported using strongly coordinating ligand 3,5-dimethyl-1-(2?-pyridyl) pyrazole (L) in presence of anionic ancillary bridging ligands as nitrite, chloride and dicyanamide. Among the complexes two (1 and 2) are monomeric, 3 is ?2 - chloro bridged dimer and the last one (4) is a mixed alternate chloro - end to end (EE) dicyanamide bridged 1D polymer. All the four complexes have been X-ray crystallographically characterized. The ligand L behaves as a potent bidentate neutral N, N donor. Geometrical diversity of Cd(II) complexes is due to no loss or gain of crystal field stability with the variation of geometry. Consequently the stability of a structure depends on steric requirements. The ligand L shows considerable fluorescence and all four complexes in methanol exhibit interesting photoluminescence properties with different emission intensities. The band maxima and fluorescence efficiency (in methanol) are found to be dependent on the coordination chromophore and structural rigidity induced by the incorporated Cd(II) ion. Among the synthesized complexes 1 exhibits the highest fluorescence intensity in methanol.

Das, Kinsuk; Konar, Saugata; Jana, Atanu; Barik, Anil Kumar; Roy, Sangita; Kar, Susanta Kumar

2013-03-01

100

Lipophilic bismuth phosphates: a molecular tetradecanuclear cage and a 1D-coordination polymer. Synthesis, structure and conversion to BiPO4.  

Science.gov (United States)

The reaction of the phosphate monoester {(ArO)PO(OH)2} (Ar = 2,6-i-Pr2C6H3) with BiPh3 in a 1 : 1 ratio in refluxing toluene afforded a tetradecabismuth-oxo-phosphate cage [{(ArO)PO3}10{(ArO)PO2OH}2(Bi14O10)·2(CH3OH)]·3C6H12·3CH3OH·2H2O (Ar = 2,6-i-Pr2C6H3) (1). On the other hand the reaction of the phosphate diester {((t)BuO)2PO(OH)} with BiPh3 in a 1 : 1 ratio at room temperature in ethanol afforded the 1D-coordination polymer [Bi(C6H5)2((t)BuO)2PO2]n (2). The molecular structure of 1 reveals that the cage is comprised of a central planar Bi6 rim and two Bi4 poles. The entire aggregate is held together by multiple coordination of O(2-), [(ArO)P(O)(OH)](-), [(ArO)PO3](2-) and methanol ligands. 2 is a 1D-coordination polymer where adjacent bismuth is bridged by isobidentate [((t)BuO)2PO2](-) ligands. In solution, however, 2 decomposes into the monomeric repeat unit [Ph2Bi{((t)BuO)2PO2}] which is indicated by ESI-MS studies. Thermolysis of 1 and 2 at 700 °C affords a pure phase of BiPO4. PMID:23632600

Chandrasekhar, Vadapalli; Metre, Ramesh K; Suriya Narayanan, Ramakirushnan

2013-04-30

 
 
 
 
101

Lipophilic bismuth phosphates: a molecular tetradecanuclear cage and a 1D-coordination polymer. Synthesis, structure and conversion to BiPO4.  

UK PubMed Central (United Kingdom)

The reaction of the phosphate monoester {(ArO)PO(OH)2} (Ar = 2,6-i-Pr2C6H3) with BiPh3 in a 1 : 1 ratio in refluxing toluene afforded a tetradecabismuth-oxo-phosphate cage [{(ArO)PO3}10{(ArO)PO2OH}2(Bi14O10)·2(CH3OH)]·3C6H12·3CH3OH·2H2O (Ar = 2,6-i-Pr2C6H3) (1). On the other hand the reaction of the phosphate diester {((t)BuO)2PO(OH)} with BiPh3 in a 1 : 1 ratio at room temperature in ethanol afforded the 1D-coordination polymer [Bi(C6H5)2((t)BuO)2PO2]n (2). The molecular structure of 1 reveals that the cage is comprised of a central planar Bi6 rim and two Bi4 poles. The entire aggregate is held together by multiple coordination of O(2-), [(ArO)P(O)(OH)](-), [(ArO)PO3](2-) and methanol ligands. 2 is a 1D-coordination polymer where adjacent bismuth is bridged by isobidentate [((t)BuO)2PO2](-) ligands. In solution, however, 2 decomposes into the monomeric repeat unit [Ph2Bi{((t)BuO)2PO2}] which is indicated by ESI-MS studies. Thermolysis of 1 and 2 at 700 °C affords a pure phase of BiPO4.

Chandrasekhar V; Metre RK; Suriya Narayanan R

2013-06-01

102

Scaling and hierarchical structures in DNA sequences.  

UK PubMed Central (United Kingdom)

A method of analyzing DNA correlation structure is introduced. Density fluctuations of nucleotides are shown to display an extended self-similarity scaling when the scale varies between 100 and 8000 base pairs. The scaling is accurately described by a hierarchical structure model of She and Leveque [Phys. Rev. Lett. 72, 336 (1994)

Ouyang Z; Wang C; She ZS

2004-08-01

103

Scaling and hierarchical structures in DNA sequences.  

Science.gov (United States)

A method of analyzing DNA correlation structure is introduced. Density fluctuations of nucleotides are shown to display an extended self-similarity scaling when the scale varies between 100 and 8000 base pairs. The scaling is accurately described by a hierarchical structure model of She and Leveque [Phys. Rev. Lett. 72, 336 (1994)

Ouyang, Zhengqing; Wang, Chao; She, Zhen-Su

2004-08-13

104

Better 1D predictions by experts with machines.  

UK PubMed Central (United Kingdom)

Accuracy of predicting protein secondary structure and solvent accessibility has been improved significantly by using evolutionary information contained in multiple sequence alignments. For the second Asilomar meeting, predictions were made automatically for all targets using the publicly available prediction service PredictProtein. Additionally, a semiautomatic procedure for generating more informative alignments was used in combination with the PHD prediction methods. Results confirmed the estimates for prediction accuracy. Furthermore, the more informative alignments yielded better predictions. The fairly accurate predictions of 1D structure were successfully used by various groups for the Asilomar meeting as first step toward predicting higher dimensions of protein structure.

Rost B

1997-01-01

105

Glass transition in secondary structures formed by random RNA sequences  

CERN Multimedia

Formation of RNA secondary structures is an example of the sequence-structure problem omnipresent in biopolymers. A theoretical question of recent interest is whether a random RNA sequence undergoes a finite temperature glass transition. We answer this question affirmatively by first establishing the perturbative stability of the high temperature phase via a two replica calculation. Subsequently, we show that this phase cannot persist down to zero temperature by considering energetic contributions due to rare regions of complementary subsequences.

Bundschuh, R

2001-01-01

106

De novo design of sequences for nucleic acid structural engineering.  

UK PubMed Central (United Kingdom)

An interactive procedure has been developed to assign sequences for the design of nucleic acid secondary structure. The primary goal of the procedure is to facilitate macromolecular architecture studies through the design of branched nucleic acid mono- and oligo-junction constructs in a convenient fashion. The essential feature of the sequence-symmetry minimization algorithm employed is the treatment of short sequences as vocabulary elements whose repetition decreases control over the resulting secondary structure. Both manual and semi-automatic application of this approach are available. The design of linear nucleic acid molecules or molecules containing single-stranded loops or connectors is also possible through application of the procedure.

Seeman NC

1990-12-01

107

Relation between sequence and structure in membrane proteins.  

UK PubMed Central (United Kingdom)

MOTIVATION: Integral polytopic membrane proteins contain only two types of folds in their transmembrane domains: ?-helix bundles and ?-barrels. The increasing number of available crystal structures of these proteins permits an initial estimation of how sequence variability affects the structure conservation in their transmembrane domains. We, thus, aim to determine the pairwise sequence identity necessary to maintain the transmembrane molecular architectures compatible with the hydrophobic nature of the lipid bilayer. RESULTS: Root-mean-square deviation (rmsd) and sequence identity were calculated from the structural alignments of pairs of homologous polytopic membrane proteins sharing the same fold. Analysis of these data reveals that transmembrane segment pairs with sequence identity in the so-called 'twilight zone' (20-35%) display high-structural similarity (rmsd < 1.5 Å). Moreover, a large group of ?-barrel pairs with low-sequence identity (<20%) still maintain a close structural similarity (rmsd < 2.5 Å). Thus, we conclude that fold preservation in transmembrane regions requires less sequence conservation than for globular proteins. These findings have direct implications in homology modeling of evolutionary-related membrane proteins. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Olivella M; Gonzalez A; Pardo L; Deupi X

2013-07-01

108

Structured Estolides: Control of Length and Sequence  

UK PubMed Central (United Kingdom)

Using ester-forming reactions such as carbodiimide coupling and a modified Yamaguchi symmetrical anhydride method, a variety of estolides based on 17-hydroxy oleic and 17-hydroxy stearic acid have been prepared. These hydroxy fatty acids are produced in good yields from hydrolysis of sophorolipids, which are in turn derived from fermentation of fats and oils. Since the estolides are formed one unit, or ester bond, at a time, their length and sequence can be precisely controlled. The key to this control is the use of protecting groups at either the carboxylic or hydroxy end of the starting hydroxy fatty acids. Two mono-protected dimers, for example, when combined in a fragment-condensation approach, give a tetramer with no “contamination” from estolides of other lengths. This methodology opens the way to functionalized estolides, and several variants were prepared: hybrid estolides, containing non-fatty acid moieties such as amino acids; polymerizable estolides, containing a norbornene unit; and non-linear estolides that extend from a branched core such as glycerol or pentaerythritol. With the benzoyl chloride-mediated symmetrical anhydride method, yields for individual coupling steps ranged from 75 to 93%.

Zerkowski JonathanA; Nun?ez Alberto; Solaiman DanielKY

2008-03-01

109

1D to 2D Na+ ion diffusion inherently linked to structural transitions in Na0.7CoO2.  

Science.gov (United States)

We report the observation of a stepwise "melting" of the low-temperature Na-vacancy order in the layered transition-metal oxide Na0.7CoO2. High-resolution neutron powder diffraction analysis indicates the existence of two first-order structural transitions, one at T1?290??K followed by a second at T2?400??K. Detailed analysis strongly suggests that both transitions are linked to changes in the Na mobility. Our data are consistent with a two-step disappearance of Na-vacancy order through the successive opening of first quasi-1D (T1>T>T2) and then 2D (T>T2) Na diffusion paths. These results shed new light on previous, seemingly incompatible, experimental interpretations regarding the relationship between Na-vacancy order and Na dynamics in this material. They also represent an important step towards the tuning of physical properties and the design of tailored functional materials through an improved control and understanding of ionic diffusion. PMID:23848903

Medarde, M; Mena, M; Gavilano, J L; Pomjakushina, E; Sugiyama, J; Kamazawa, K; Pomjakushin, V Yu; Sheptyakov, D; Batlogg, B; Ott, H R; Månsson, M; Juranyi, F

2013-06-26

110

Dinuclear and 1D iron(III) Schiff base complexes bridged by 4-salicylideneamino-1,2,4-triazolate: X-ray structures and magnetic properties.  

Science.gov (United States)

Four new iron(III) complexes were obtained by the reaction of 4-salicylideneamino-1,2,4-triazole (Hsaltrz) and selected dinuclear ?-oxo-bridged iron(III) Schiff base complexes [{FeL(4)}(2)(?-O)], where L(4) represents a terminal tetradentate dianionic Schiff-base ligand. X-ray structural analysis revealed a novel bridging mode of ?N,?O of the saltrz ligand to form dinuclear complexes [{Fe(salen)(?-saltrz)}(2)]·CH(3)OH (1) (H(2)salen = N,N'-ethylenebis(salicylimine)) and [{Fe(salpn)(?-saltrz)}(2)] (2) (H(2)salpn = N,N'-1,2-propylenbis(salicylimine)), whereas one-dimensional (1D) zig-zag chains were formed in the case of [{Fe(salch)(?-saltrz)}·0.5CH(3)OH](n) (3) (H(2)salch = N,N'-cyclohexanebis(salicylimine)) and [Fe(salophen)(?-saltrz)](n) (4) (H(2)salophen = N,N'-o-phenylenebis(salicylimine)). It was also shown that the rigidity of the terminal ligand L(4) can be considered as the key factor for the molecular dimensionality of the products. The thorough magnetic analysis based on SQUID experiments, including the isotropic exchange and the zero-field splitting of both temperature and field dependent data, was performed for dimeric (1 and 2) and also for polymeric compounds (3 and 4) and revealed weak antiferromagnetic exchange mediated by the saltrz anions with much larger D-parameter (|D|?|J|). PMID:21968851

Herchel, Radovan; Pavelek, Lubomír; Trávní?ek, Zden?k

2011-10-04

111

Dinuclear and 1D iron(III) Schiff base complexes bridged by 4-salicylideneamino-1,2,4-triazolate: X-ray structures and magnetic properties.  

UK PubMed Central (United Kingdom)

Four new iron(III) complexes were obtained by the reaction of 4-salicylideneamino-1,2,4-triazole (Hsaltrz) and selected dinuclear ?-oxo-bridged iron(III) Schiff base complexes [{FeL(4)}(2)(?-O)], where L(4) represents a terminal tetradentate dianionic Schiff-base ligand. X-ray structural analysis revealed a novel bridging mode of ?N,?O of the saltrz ligand to form dinuclear complexes [{Fe(salen)(?-saltrz)}(2)]·CH(3)OH (1) (H(2)salen = N,N'-ethylenebis(salicylimine)) and [{Fe(salpn)(?-saltrz)}(2)] (2) (H(2)salpn = N,N'-1,2-propylenbis(salicylimine)), whereas one-dimensional (1D) zig-zag chains were formed in the case of [{Fe(salch)(?-saltrz)}·0.5CH(3)OH](n) (3) (H(2)salch = N,N'-cyclohexanebis(salicylimine)) and [Fe(salophen)(?-saltrz)](n) (4) (H(2)salophen = N,N'-o-phenylenebis(salicylimine)). It was also shown that the rigidity of the terminal ligand L(4) can be considered as the key factor for the molecular dimensionality of the products. The thorough magnetic analysis based on SQUID experiments, including the isotropic exchange and the zero-field splitting of both temperature and field dependent data, was performed for dimeric (1 and 2) and also for polymeric compounds (3 and 4) and revealed weak antiferromagnetic exchange mediated by the saltrz anions with much larger D-parameter (|D|?|J|).

Herchel R; Pavelek L; Trávní?ek Z

2011-11-01

112

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%  

DEFF Research Database (Denmark)

Motivation: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding todya as these often are conserved in structure rather than in sequence. Even though the number of available methods is growing, it is still of interest to pairwise detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on FILDALIGN and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy as well as for substitution matrices similar to RIBOSUM. The new FOLDALIGN implementation is tested on a dataset where the ncRNAs and eleRNAs have sequence similarity <40% and where the ncRNAs and eleRNAs are energetically indistinguishable from the surrounding genomic sequence context. The method is tested in two ways: (1) its ability to find the common structure between the genes only and (2) its ability to locate ncRNAs and eleRNAs in a genomic context. In case (1), it makes sense to compare with methods like Dynalign, and the performances are very similar, but FOLDALIGN is substantially faster. The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. Availability: The program is available online at http://foldalign.kvl.dk Contact: gorodkin@bioinf.kvl.dk

Havgaard, Jakob Hull; LyngsØ, Rune B.

2005-01-01

113

The genome sequence and structure of rice chromosome 1.  

UK PubMed Central (United Kingdom)

The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequence indicates the importance of a high-quality finished sequence.

Sasaki T; Matsumoto T; Yamamoto K; Sakata K; Baba T; Katayose Y; Wu J; Niimura Y; Cheng Z; Nagamura Y; Antonio BA; Kanamori H; Hosokawa S; Masukawa M; Arikawa K; Chiden Y; Hayashi M; Okamoto M; Ando T; Aoki H; Arita K; Hamada M; Harada C; Hijishita S; Honda M; Ichikawa Y; Idonuma A; Iijima M; Ikeda M; Ikeno M; Ito S; Ito T; Ito Y; Ito Y; Iwabuchi A; Kamiya K; Karasawa W; Katagiri S; Kikuta A; Kobayashi N; Kono I; Machita K; Maehara T; Mizuno H; Mizubayashi T; Mukai Y; Nagasaki H; Nakashima M; Nakama Y; Nakamichi Y; Nakamura M; Namiki N; Negishi M; Ohta I; Ono N; Saji S; Sakai K; Shibata M; Shimokawa T; Shomura A; Song J; Takazaki Y; Terasawa K; Tsuji K; Waki K; Yamagata H; Yamane H; Yoshiki S; Yoshihara R; Yukawa K; Zhong H; Iwama H; Endo T; Ito H; Hahn JH; Kim HI; Eun MY; Yano M; Jiang J; Gojobori T

2002-11-01

114

Data structures and compression algorithms for genomic sequence data.  

UK PubMed Central (United Kingdom)

MOTIVATION: The continuing exponential accumulation of full genome data, including full diploid human genomes, creates new challenges not only for understanding genomic structure, function and evolution, but also for the storage, navigation and privacy of genomic data. Here, we develop data structures and algorithms for the efficient storage of genomic and other sequence data that may also facilitate querying and protecting the data. RESULTS: The general idea is to encode only the differences between a genome sequence and a reference sequence, using absolute or relative coordinates for the location of the differences. These locations and the corresponding differential variants can be encoded into binary strings using various entropy coding methods, from fixed codes such as Golomb and Elias codes, to variables codes, such as Huffman codes. We demonstrate the approach and various tradeoffs using highly variables human mitochondrial genome sequences as a testbed. With only a partial level of optimization, 3615 genome sequences occupying 56 MB in GenBank are compressed down to only 167 KB, achieving a 345-fold compression rate, using the revised Cambridge Reference Sequence as the reference sequence. Using the consensus sequence as the reference sequence, the data can be stored using only 133 KB, corresponding to a 433-fold level of compression, roughly a 23% improvement. Extensions to nuclear genomes and high-throughput sequencing data are discussed. AVAILABILITY: Data are publicly available from GenBank, the HapMap web site, and the MITOMAP database. Supplementary materials with additional results, statistics, and software implementations are available from http://mammag.web.uci.edu/bin/view/Mitowiki/ProjectDNACompression.

Brandon MC; Wallace DC; Baldi P

2009-07-01

115

PCR-introduced loop structure as primer in DNA sequencing.  

UK PubMed Central (United Kingdom)

The need for a primer hybridization step before sequencing has been eliminated using a stem-loop structure generated by PCR. The loop structure is obtained by careful design of the PCR primer or by cloning the target DNA into a dedicated vector (pRIT 28HP). After solid-phase capture of the PCR product, the loop is formed by elution of the non-bound strand. Here, we show that both the immobilized and the eluted strand can be analyzed using conventional Sanger DNA sequencing and the novel pyrosequencing method as described previously. By using a stem-loop structure as a primer for DNA sequencing, the risk for mispriming is minimized.

Ronaghi M; Pettersson B; Uhlén M; Nyrén P

1998-11-01

116

Music and language perception: expectations, structural integration, and cognitive sequencing.  

UK PubMed Central (United Kingdom)

Music can be described as sequences of events that are structured in pitch and time. Studying music processing provides insight into how complex event sequences are learned, perceived, and represented by the brain. Given the temporal nature of sound, expectations, structural integration, and cognitive sequencing are central in music perception (i.e., which sounds are most likely to come next and at what moment should they occur?). This paper focuses on similarities in music and language cognition research, showing that music cognition research provides insight into the understanding of not only music processing but also language processing and the processing of other structured stimuli. The hypothesis of shared resources between music and language processing and of domain-general dynamic attention has motivated the development of research to test music as a means to stimulate sensory, cognitive, and motor processes.

Tillmann B

2012-10-01

117

COMPARATIVE SEQUENCE AND STRUCTURAL CONFORMATION ANALYSIS OF RECA PROTEIN  

Directory of Open Access Journals (Sweden)

Full Text Available Water molecules are very important for stabilizing the protein structures. The influence of hydration (or) dehydration on protein structures leads to the changes in the activity of proteins as well their conformation. In our present study, we madde an attempt to understand the various RecA protein sequence similarity with respect to E. coli RecA Protein and comparative structure and functional conformation studies between MsRecA protein (dehydrated state) and EcRecA + DNA bound structures (active state) as well ATP-complexed DrRecA protein structure. From the sequence similarity studies, it was identified that the E.coli RecA protein exhibits the highest sequence similarity (100%) with the Shigella dysenteriae serotype 1 (strain Sd197), Shigella flexneri and the lowest sequence similarity (46%) with the Mycoplasma genitalium. From the structural alignment & superposition studies, it can be inferred that the low hydrated MsRecA protein conformation is very closely similar to the active conformation of the EcRecA protein. This confers that the lower less water molecules favors the active conformational state of the RecA protein in both M. smegmatis & E. coli whereas the ATP-bound complex of RecA protein of D. radiodurans is exhibiting different conformation from the active state conformation.

Amajala Krishna Chaitanya; DSVGK. Kaladhar; S. Suresh; Bhaskar Reddy

2013-01-01

118

A series of silver(I) pyridone-sulfonates with 1-D "butterfly" chain, 2-D lamellar network and 3-D pillared layered frameworks: syntheses, structures and characterizations.  

Science.gov (United States)

A series of silver(I) pyridone-sulfonates, namely [Ag5(HL1)3(NO3)2(H2O)]n (1) [Ag2(HL1)2]n.2nH2O (2), [Ag2(HL1)(NO3)]n (3), and [Ag3(HL2)2(NO3)(H2O)]n (4) (HL1 = 4(1H)-pyridone-3-sulfonate monoanion, HL2 = 2(1H)-pyridone-5-sulfonate monoanion), have been synthesized and characterized by elemental analyses, IR, TG, PL and X-ray analyses. Complex 1, which exhibits a novel continuous silver polyhedral framework containing four kinds of coordination spheres, has been recently reported. Complex 2 presents the first one-dimensional (1-D) "butterfly" array composed of SO3-bridged columns of Ag(I) ions and symmetric pendant organic groups in silver(I) sulfonates, while complex 3 possesses a two-dimensional (2-D) layer structure in which the inorganic network substructure consists of helical chains of edge-sharing Ag1 distorted octahedra linked through dimers of edge-sharing Ag2 distorted anti-trigonal prisms by sharing two corners and two edges. Replacing H2L1 by H2L2 leads to the formation of complex 4, a three-dimensional (3-D) pillared layered framework, which is also extended by the rare mu4 nitrate anion. In complexes 1-4, all the inorganic parts can be considered as being built up from versatile polyhedra of silver(I) centers by sharing corners, edges or faces. The sulfonic group shows some novel coordination modes, which is first reported here. Solid-state fluorescence quenching and thermal stability are discussed for all of these complexes. PMID:19672500

Deng, Zhao-Peng; Zhu, Zhi-Biao; Gao, Shan; Huo, Li-Hua; Zhao, Hui; Ng, Seik Weng

2009-07-06

119

A series of silver(I) pyridone-sulfonates with 1-D "butterfly" chain, 2-D lamellar network and 3-D pillared layered frameworks: syntheses, structures and characterizations.  

UK PubMed Central (United Kingdom)

A series of silver(I) pyridone-sulfonates, namely [Ag5(HL1)3(NO3)2(H2O)]n (1) [Ag2(HL1)2]n.2nH2O (2), [Ag2(HL1)(NO3)]n (3), and [Ag3(HL2)2(NO3)(H2O)]n (4) (HL1 = 4(1H)-pyridone-3-sulfonate monoanion, HL2 = 2(1H)-pyridone-5-sulfonate monoanion), have been synthesized and characterized by elemental analyses, IR, TG, PL and X-ray analyses. Complex 1, which exhibits a novel continuous silver polyhedral framework containing four kinds of coordination spheres, has been recently reported. Complex 2 presents the first one-dimensional (1-D) "butterfly" array composed of SO3-bridged columns of Ag(I) ions and symmetric pendant organic groups in silver(I) sulfonates, while complex 3 possesses a two-dimensional (2-D) layer structure in which the inorganic network substructure consists of helical chains of edge-sharing Ag1 distorted octahedra linked through dimers of edge-sharing Ag2 distorted anti-trigonal prisms by sharing two corners and two edges. Replacing H2L1 by H2L2 leads to the formation of complex 4, a three-dimensional (3-D) pillared layered framework, which is also extended by the rare mu4 nitrate anion. In complexes 1-4, all the inorganic parts can be considered as being built up from versatile polyhedra of silver(I) centers by sharing corners, edges or faces. The sulfonic group shows some novel coordination modes, which is first reported here. Solid-state fluorescence quenching and thermal stability are discussed for all of these complexes.

Deng ZP; Zhu ZB; Gao S; Huo LH; Zhao H; Ng SW

2009-09-01

120

Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences, we predict seven classes from sequences that share twilight-zone identity with the training sequences. Results The proposed MODular Approach to Structural class prediction (MODAS) method is unique as it allows for selection of any subset of the classes. MODAS is also the first to utilize a novel, custom-built feature-based sequence representation that combines evolutionary profiles and predicted secondary structure. The features quantify information relevant to the definition of the classes including conservation of residues and arrangement and number of helix/strand segments. Our comprehensive design considers 8 feature selection methods and 4 classifiers to develop Support Vector Machine-based classifiers that are tailored for each of the seven classes. Tests on 5 twilight-zone and 1 high-similarity benchmark datasets and comparison with over two dozens of modern competing predictors show that MODAS provides the best overall accuracy that ranges between 80% and 96.7% (83.5% for the twilight-zone datasets), depending on the dataset. This translates into 19% and 8% error rate reduction when compared against the best performing competing method on two largest datasets. The proposed predictor provides accurate predictions at 58% accuracy for membrane proteins class, which is not considered by majority of existing methods, in spite that this class accounts for only 2% of the data. Our predictive model is analyzed to demonstrate how and why the input features are associated with the corresponding classes. Conclusions The improved predictions stem from the novel features that express collocation of the secondary structure segments in the protein sequence and that combine evolutionary and secondary structure information. Our work demonstrates that conservation and arrangement of the secondary structure segments predicted along the protein chain can successfully predict structural classes which are defined based on the spatial arrangement of the secondary structures. A web server is available at http://biomine.ece.ualberta.ca/MODAS/.

Mizianty Marcin J; Kurgan Lukasz

2009-01-01

 
 
 
 
121

Occurrence probability of structured motifs in random sequences.  

UK PubMed Central (United Kingdom)

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.

Robin S; Daudin JJ; Richard H; Sagot MF; Schbath S

2002-01-01

122

Identifying the mechanisms underpinning recognition of structured sequences of action.  

UK PubMed Central (United Kingdom)

We present three experiments to identify the specific information sources that skilled participants use to make recognition judgements when presented with dynamic, structured stimuli. A group of less skilled participants acted as controls. In all experiments, participants were presented with filmed stimuli containing structured action sequences. In a subsequent recognition phase, participants were presented with new and previously seen stimuli and were required to make judgements as to whether or not each sequence had been presented earlier (or were edited versions of earlier sequences). In experiment 1, skilled participants demonstrated superior sensitivity in recognition when viewing dynamic clips compared with static images and clips where the frames were presented in a nonsequential, randomized manner, implicating the importance of motion information when identifying familiar or unfamiliar sequences. In experiment 2, we presented normal and mirror-reversed sequences in order to distort access to absolute motion information. Skilled participants demonstrated superior recognition sensitivity, but no significant differences were observed across viewing conditions, leading to the suggestion that skilled participants are more likely to extract relative rather than absolute motion when making such judgements. In experiment 3, we manipulated relative motion information by occluding several display features for the duration of each film sequence. A significant decrement in performance was reported when centrally located features were occluded compared to those located in more peripheral positions. Findings indicate that skilled participants are particularly sensitive to relative motion information when attempting to identify familiarity in dynamic, visual displays involving interaction between numerous features.

Williams AM; North JS; Hope ER

2012-01-01

123

Massively Parallel Interrogation of Aptamer Sequence, Structure and Function  

Energy Technology Data Exchange (ETDEWEB)

Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. Methodology/Principal Findings. High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and interchip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

Fischer, N O; Tok, J B; Tarasow, T M

2008-02-08

124

Predicting local quality of a sequence-structure alignment.  

UK PubMed Central (United Kingdom)

Although protein structure prediction has made great progress in recent years, a protein model derived from automated prediction methods is subject to various errors. As methods for structure prediction develop, a continuing problem is how to evaluate the quality of a protein model, especially to identify some well-predicted regions of the model, so that the structural biology community can benefit from the automated structure prediction. It is also important to identify badly-predicted regions in a model so that some refinement measurements can be applied to it. We present two complementary techniques, FragQA and PosQA, to accurately predict local quality of a sequence-structure (i.e. sequence-template) alignment generated by comparative modeling (i.e. homology modeling and threading). FragQA and PosQA predict local quality from two different perspectives. Different from existing methods, FragQA directly predicts cRMSD between a continuously aligned fragment determined by an alignment and the corresponding fragment in the native structure, while PosQA predicts the quality of an individual aligned position. Both FragQA and PosQA use an SVM (Support Vector Machine) regression method to perform prediction using similar information extracted from a single given alignment. Experimental results demonstrate that FragQA performs well on predicting local fragment quality, and PosQA outperforms two top-notch methods, ProQres and ProQprof. Our results indicate that (1) local quality can be predicted well; (2) local sequence evolutionary information (i.e. sequence similarity) is the major factor in predicting local quality; and (3) structural information such as solvent accessibility and secondary structure helps to improve the prediction performance.

Gao X; Xu J; Li SC; Li M

2009-10-01

125

Structural evidence for a new IgG1 antibody sequence allele of cattle.  

UK PubMed Central (United Kingdom)

Analysis of the heavy-chain gene (pTGHC9907) encoding a bovine IgG1 antibody against bovine herpes virus type 1 (BHV-1) isolated from a Holstein cow has led to the identification of a new IgG1 sequence allele. A comparison of nucleotide sequence of pTGHC9907 with the IgG1(a) (clone 2) and IgG1(b) (clone 8.10) sequence variants and unclassified IgG1 cDNA sequence (clone 8.75) has revealed significant differences in the hinge region spanning codons 216-230. The Thr224 and Thr226 of IgG1(a) were replaced with Arg224 and Pro226, while both Thr218 and Pro224 of IgG1(b) were substituted with Arg with deletion of Ser225 in HB9907 antibody. Additional amino acid substitutions were noted in the CH1 (positions 190, 192), CH2 (position 281) and CH3 (position 402) exons. Thus, the polymorphic sites occurred in all constant domains, but were clustered in the hinge region of IgG1. Examination of a three-dimensional model of the HB9907 heavy chain revealed that all sequence variations were on the surface of the IgG and are possible targets for recognition by antisera and effector molecules such as cellular adhesion molecules. The presence in the CH1 domain of a repeating motif of Pro-Ala-Ser-Ser indicated a potential structure-enhancing function and a role in cellular adhesion and migration. Replacement of Thr with Arg residues within the hinge was predicted to have a dual effect of reducing the number of O-linked glycosylation sites and increasing the susceptibility to degradation by protease-secreting bacteria of the hinge region. As unclassified IgG1 cDNA sequence (clone 8.75) is structurally distinct from other variants, it is also classified as IgG1(d). Collectively, these observations support the identification of a new allotypic variant of bovine IgG1, designated as IgG1(c) that is distinct in both sequence and structure from the known sequence variants.

Saini SS; Farrugia W; Muthusamy N; Ramsland PA; Kaushik AK

2007-01-01

126

PredyFlexy: flexibility and local structure prediction from sequence.  

UK PubMed Central (United Kingdom)

Protein structures are necessary for understanding protein function at a molecular level. Dynamics and flexibility of protein structures are also key elements of protein function. So, we have proposed to look at protein flexibility using novel methods: (i) using a structural alphabet and (ii) combining classical X-ray B-factor data and molecular dynamics simulations. First, we established a library composed of structural prototypes (LSPs) to describe protein structure by a limited set of recurring local structures. We developed a prediction method that proposes structural candidates in terms of LSPs and predict protein flexibility along a given sequence. Second, we examine flexibility according to two different descriptors: X-ray B-factors considered as good indicators of flexibility and the root mean square fluctuations, based on molecular dynamics simulations. We then define three flexibility classes and propose a method based on the LSP prediction method for predicting flexibility along the sequence. This method does not resort to sophisticate learning of flexibility but predicts flexibility from average flexibility of predicted local structures. The method is implemented in PredyFlexy web server. Results are similar to those obtained with the most recent, cutting-edge methods based on direct learning of flexibility data conducted with sophisticated algorithms. PredyFlexy can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/predyflexy/.

de Brevern AG; Bornot A; Craveur P; Etchebest C; Gelly JC

2012-07-01

127

Molecular and Supramolecular Structural Studies on Human Tropoelastin Sequences  

Science.gov (United States)

One of the unusual properties of elastin is its ability to coacervate, which has been proposed to play an important role in the alignment of monomeric elastin for cross-linking into the polymeric elastin matrix. The temperature at which this transition takes place depends on several factors including protein concentration, ionic strength, and pH. Previously, polypeptide sequences encoded by different exons of the human tropoelastin gene have been analyzed for their ability to coacervate and to self-assemble. Few of them were indeed able to coacervate and only one, that encoded by exon 30 (EX30), gave amyloid fibers. In this article, we report on two chemically synthesized peptides—a decapeptide and an octadecapeptide—whose sequences are contained in the longer EX30 peptide and on a polypeptide (EX1–7) of 125 amino-acid residues corresponding to the sequence coded by the exons 1–7 and on a polypeptide (EX2–7) of 99 amino-acid residues encoded by exons 2–7 of human tropoelastin obtained by recombinant DNA techniques. Molecular and supramolecular structural characterization of these peptides showed that a minimum sequence of ?20 amino acids is needed to form amyloid fibers in the exon 30-derived peptides. The N-terminal region of mature tropoelastin (EX2–7) gives rise to a coacervate and forms elastinlike fibers, whereas the polypeptide sequence containing the signal peptide (EX1–7) forms mainly amyloid fibers. Circular dichroism spectra show that ?-structure is ubiquitous in all the sequences studied, suggesting that the presence of a ?-structure is a necessary, although not sufficient, requirement for the appearance of amyloid fibers.

Ostuni, Angela; Bochicchio, Brigida; Armentano, Maria F.; Bisaccia, Faustino; Tamburro, Antonio M.

2007-01-01

128

SBSPKS: structure based sequence analysis of polyketide synthases.  

UK PubMed Central (United Kingdom)

Polyketide synthases (PKSs) catalyze biosynthesis of a diverse family of pharmaceutically important secondary metabolites. Bioinformatics analysis of sequence and structural features of PKS proteins plays a crucial role in discovery of new natural products by genome mining, as well as in design of novel secondary metabolites by biosynthetic engineering. The availability of the crystal structures of various PKS catalytic and docking domains, and mammalian fatty acid synthase module prompted us to develop SBSPKS software which consists of three major components. Model_3D_PKS can be used for modeling, visualization and analysis of 3D structure of individual PKS catalytic domains, dimeric structures for complete PKS modules and prediction of substrate specificity. Dock_Dom_Anal identifies the key interacting residue pairs in inter-subunit interfaces based on alignment of inter-polypeptide linker sequences to the docking domain structure. In case of modular PKS with multiple open reading frames (ORFs), it can predict the cognate order of substrate channeling based on combinatorial evaluation of all possible interface contacts. NRPS-PKS provides user friendly tools for identifying various catalytic domains in the sequence of a Type I PKS protein and comparing them with experimentally characterized PKS/NRPS clusters cataloged in the backend databases of SBSPKS. SBSPKS is available at http://www.nii.ac.in/sbspks.html.

Anand S; Prasad MV; Yadav G; Kumar N; Shehara J; Ansari MZ; Mohanty D

2010-07-01

129

HSP: evolved and conserved proteins, structure and sequence studies  

Directory of Open Access Journals (Sweden)

Full Text Available Heat shock proteins (HSPs) are the proteins which are present normally in the cell but theirexpression level increases under stress condition and are mainly divided into five groups, low molecularweight HSP (LMW HSP), HSP 60, HSP 70, HSP 90 and high molecular weight HSP (HMW HSP). All theseclasses of HSPs are highly conserved and ubiquitous in nature and hence serve as a good model forphylogenetic analysis. For the first time in this study,the sequence and structural analysis has been carriedout to predict evolution of HSPs. The results obtained clearly show higher degree of sequence and structuralconservation. HSP 60 and HSP 70 are highly conserved in terms of both sequence and structure alignmentin comparison to HSP 90. The minimum amino acid identity that has been observed between all thehomologous sequences is 32.46%, 38%, 23.60% for HSP 60, HSP 70 and HSP 90 respectively, indicatingHSP 70 as the most conserved protein family followed by HSP 60 and HSP 90 family. The structuralanalysis of these proteins showed dominance of beta sheets in HSP70 and helices in HSP 90. The detailedanalysis of all the HSP homologues revealed high conservation of glycine residues and ATP binding pockets.Thus this study has revealed that HSPs are highly structurally and functionally conserved proteins andwarrants further detailed analysis at organism level.

Desai N.S.; Agarwal A.A.; Uplap S.S.

2010-01-01

130

Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags  

Energy Technology Data Exchange (ETDEWEB)

Computational methods for gene identification in genomic sequences typically have two phases: coding region prediction and gene parsing. While there are many effective methods for predicting coding regions (exons), parsing the predicted exons into proper gene structures, to a large extent, remains an unsolved problem. This paper presents an algorithm for inferring gene structures from predicted exon candidates, based on Expressed Sequence Tags (ESTs) and biological intuition/rules. The algorithm first finds all the related ESTs in the EST database (dbEST) for each predicted exon, and infers the boundaries of one or a series of genes based on the available EST information and biological rules. Then it constructs gene models within each pair of gene boundaries, that are most consistent with the EST information. By exploiting EST information and biological rules, the algorithm can (1) model complicated multiple gene structures, including embedded genes, (2) identify falsely-predicted exons and locate missed exons, and (3) make more accurate exon boundary predictions. The algorithm has been implemented and tested on long genomic sequences with a number of genes. Test results show that very accurate (predicted) gene models can be expected when related ESTs exist for the predicted exons.

Xu, Y.; Mural, R.; Uberbacher, E.

1997-02-01

131

Evaluation of nucleic acid sequencing of the D1/D2 region of the large subunit of the 28S rDNA and the internal transcribed spacer region using SmartGene IDNS [corrected] software for identification of filamentous fungi in a clinical laboratory.  

UK PubMed Central (United Kingdom)

Filamentous fungal infections have recently increased because of the increasing numbers of immunocompromised hosts. In this study, we evaluated DNA sequencing of the D1/D2 region of the large subunit of the 28S ribosomal RNA gene and the internal transcribed spacer (ITS) region using SmartGene (SG; SmartGene Inc., Raleigh, NC) for the identification of a broad range of commonly encountered filamentous fungi. The SG proofreaders were used to upload, align, and edit fragments, and the resultant sequences were interpreted using the quality-controlled SG database. The results were compared with reference identifications using conventional phenotypic methods or ITS DNA sequences obtained from GenBank if phenotypic identifications were inconclusive. A total of 146 clinical isolates were included in this study, representing 49 different genera. The overall agreements of the D1/D2 and the ITS sequencing methods to reference identification were 97.2% (95% CI, 93.1% to 98.9%) and 97.7% (95% CI, 92.8% to 99.4%), respectively. Of the 146 isolates, 18 (12.3%) did not amplify using the ITS universal primers after repeated attempts and, therefore, could not be sequenced using this target. Correct identification was achieved for 100% (95% CI, 97.4% to 100%) of the isolates when applying both the D1/D2 and ITS targets. In summary, DNA sequencing using SG software provides a rapid, accurate, and reliable tool for the identification of filamentous fungi in a clinical laboratory.

Kwiatkowski NP; Babiker WM; Merz WG; Carroll KC; Zhang SX

2012-07-01

132

Inferring social network structure from bacterial sequence data.  

Science.gov (United States)

Using DNA sequence data from pathogens to infer transmission networks has traditionally been done in the context of epidemics and outbreaks. Sequence data could analogously be applied to cases of ubiquitous commensal bacteria; however, instead of inferring chains of transmission to track the spread of a pathogen, sequence data for bacteria circulating in an endemic equilibrium could be used to infer information about host contact networks. Here, we show--using simulated data--that multilocus DNA sequence data, based on multilocus sequence typing schemes (MLST), from isolates of commensal bacteria can be used to infer both local and global properties of the contact networks of the populations being sampled. Specifically, for MLST data simulated from small-world networks, the small world parameter controlling the degree of structure in the contact network can robustly be estimated. Moreover, we show that pairwise distances in the network--degrees of separation--correlate with genetic distances between isolates, so that how far apart two individuals in the network are can be inferred from MLST analysis of their commensal bacteria. This result has important consequences, and we show an example from epidemiology: how this result could be used to test for infectious origins of diseases of unknown etiology. PMID:21829645

Pluci?ski, Mateusz M; Starfield, Richard; Almeida, Rodrigo P P

2011-08-01

133

Inferring Social Network Structure from Bacterial Sequence Data  

Science.gov (United States)

Using DNA sequence data from pathogens to infer transmission networks has traditionally been done in the context of epidemics and outbreaks. Sequence data could analogously be applied to cases of ubiquitous commensal bacteria; however, instead of inferring chains of transmission to track the spread of a pathogen, sequence data for bacteria circulating in an endemic equilibrium could be used to infer information about host contact networks. Here, we show—using simulated data—that multilocus DNA sequence data, based on multilocus sequence typing schemes (MLST), from isolates of commensal bacteria can be used to infer both local and global properties of the contact networks of the populations being sampled. Specifically, for MLST data simulated from small-world networks, the small world parameter controlling the degree of structure in the contact network can robustly be estimated. Moreover, we show that pairwise distances in the network—degrees of separation—correlate with genetic distances between isolates, so that how far apart two individuals in the network are can be inferred from MLST analysis of their commensal bacteria. This result has important consequences, and we show an example from epidemiology: how this result could be used to test for infectious origins of diseases of unknown etiology.

Plucinski, Mateusz M.; Starfield, Richard; Almeida, Rodrigo P. P.

2011-01-01

134

Early-Stage Folding in Proteins (In Silico) Sequence-to-Structure Relation  

Directory of Open Access Journals (Sweden)

Full Text Available A sequence-to-structure library has been created based on the complete PDB database. The tetrapeptide was selected as a unit representing a well-defined structural motif. Seven structural forms were introduced for structure classification. The early-stage folding conformations were used as the objects for structure analysis and classification. The degree of determinability was estimated for the sequence-to-structure and structure-to-sequence relations. Probability calculus and informational entropy were applied for quantitative estimation of the mutual relation between them. The structural motifs representing different forms of loops and bends were found to favor particular sequences in structure-to-sequence analysis.

Brylinski Micha?; Konieczny Leszek; Czerwonko Patryk; Jurkowski Wiktor; Roterman Irena

2005-01-01

135

Sequence, structure, and function of peptide self-assembled monolayers.  

Science.gov (United States)

Cysteine is commonly used to attach peptides onto gold surfaces. Here we show that the inclusion of an additional linker with a length of four residues (-PPPPC) and a rigid, hydrophobic nature is a better choice for forming peptide self-assembled monolayers (SAMs) with a well-ordered structure and high surface density. We compared the structure and function of the nonfouling peptide EKEKEKE-PPPPC-Am with EKEKEKE-C-Am. Circular dichroism, attenuated total internal reflection Fourier transform IR spectroscopy, and molecular dynamics results showed that EKEKEKE-PPPPC-Am forms a secondary structure while EKEKEKE-C-Am has a random structure. Surface plasmon resonance sensor results showed that protein adsorption on EKEKEKE-PPPPC-Am/gold is very low with small variation while protein adsorption on EKEKEKE-C-Am/gold is high with large variation. X-ray photoelectron spectroscopy results showed that both peptides have strong gold-thiol binding with the gold surface, indicating that their difference in protein adsorption is due to their assembled structures. Further experimental and simulation studies were performed to show that -PPPPC is a better linker than -PC, -PPC, and -PPPC. Finally, we extended EKEKEKE-PPPPC-Am with the cell-binding sequence RGD and demonstrated control over specific versus nonspecific cell adhesion without using poly(ethylene glycol). Adding a functional peptide to the nonfouling EK sequence avoids complex chemistries that are used for its connection to synthetic materials. PMID:22401132

Nowinski, Ann K; Sun, Fang; White, Andrew D; Keefe, Andrew J; Jiang, Shaoyi

2012-03-22

136

Sequence, structure, and function of peptide self-assembled monolayers.  

UK PubMed Central (United Kingdom)

Cysteine is commonly used to attach peptides onto gold surfaces. Here we show that the inclusion of an additional linker with a length of four residues (-PPPPC) and a rigid, hydrophobic nature is a better choice for forming peptide self-assembled monolayers (SAMs) with a well-ordered structure and high surface density. We compared the structure and function of the nonfouling peptide EKEKEKE-PPPPC-Am with EKEKEKE-C-Am. Circular dichroism, attenuated total internal reflection Fourier transform IR spectroscopy, and molecular dynamics results showed that EKEKEKE-PPPPC-Am forms a secondary structure while EKEKEKE-C-Am has a random structure. Surface plasmon resonance sensor results showed that protein adsorption on EKEKEKE-PPPPC-Am/gold is very low with small variation while protein adsorption on EKEKEKE-C-Am/gold is high with large variation. X-ray photoelectron spectroscopy results showed that both peptides have strong gold-thiol binding with the gold surface, indicating that their difference in protein adsorption is due to their assembled structures. Further experimental and simulation studies were performed to show that -PPPPC is a better linker than -PC, -PPC, and -PPPC. Finally, we extended EKEKEKE-PPPPC-Am with the cell-binding sequence RGD and demonstrated control over specific versus nonspecific cell adhesion without using poly(ethylene glycol). Adding a functional peptide to the nonfouling EK sequence avoids complex chemistries that are used for its connection to synthetic materials.

Nowinski AK; Sun F; White AD; Keefe AJ; Jiang S

2012-04-01

137

RNAstrand: reading direction of structured RNAs in multiple sequence alignments.  

UK PubMed Central (United Kingdom)

MOTIVATION: Genome-wide screens for structured ncRNA genes in mammals, urochordates, and nematodes have predicted thousands of putative ncRNA genes and other structured RNA motifs. A prerequisite for their functional annotation is to determine the reading direction with high precision. RESULTS: While folding energies of an RNA and its reverse complement are similar, the differences are sufficient at least in conjunction with substitution patterns to discriminate between structured RNAs and their complements. We present here a support vector machine that reliably classifies the reading direction of a structured RNA from a multiple sequence alignment and provides a considerable improvement in classification accuracy over previous approaches. SOFTWARE: RNAstrand is freely available as a stand-alone tool from http://www.bioinf.uni-leipzig.de/Software/RNAstrand and is also included in the latest release of RNAz, a part of the Vienna RNA Package.

Reiche K; Stadler PF

2007-01-01

138

RNAstrand: reading direction of structured RNAs in multiple sequence alignments  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Motivation Genome-wide screens for structured ncRNA genes in mammals, urochordates, and nematodes have predicted thousands of putative ncRNA genes and other structured RNA motifs. A prerequisite for their functional annotation is to determine the reading direction with high precision. Results While folding energies of an RNA and its reverse complement are similar, the differences are sufficient at least in conjunction with substitution patterns to discriminate between structured RNAs and their complements. We present here a support vector machine that reliably classifies the reading direction of a structured RNA from a multiple sequence alignment and provides a considerable improvement in classification accuracy over previous approaches. Software RNAstrand is freely available as a stand-alone tool from http://www.bioinf.uni-leipzig.de/Software/RNAstrand and is also included in the latest release of RNAz, a part of the Vienna RNA Package.

Reiche Kristin; Stadler Peter F

2007-01-01

139

Sequence, genomic structure, and chromosomal assignment of human DOC-2  

Energy Technology Data Exchange (ETDEWEB)

DOC-2 is a human gene originally identified as a 767-bp cDNA fragment isolated from normal ovarian epithelial cells by differential display against ovarian carcinoma cells. We have now determined the complete cDNA sequence of the 3.2-kb DOC-2 transcript and localized the gene to chromosome 5. A 12.5-kb genomic fragment at the 5{prime}-end of DOC-2 has also been sequenced, revealing the intron-exon structure of the first eight exons (788 bases) of the DOC-2 gene. Translation of the DOC-2 cDNA predicts a hydrophobic protein of 770 amino acid residues with a molecular weight of 82.5 kDa. Comparison of the DNA and amino acid sequences of DOC-2 to publicly accessible sequence data-bases revealed 83% identity to p96, a murine-responsive phosphoprotein. In addition, about 45% identity was observed between the first 140 N-terminal residues of DOC-2 and the Caenorhabditas elegans M110.5 and Drosophila melanoaster Dab genes. 14 refs., 3 figs.

Albertsen, H.M.; Williams, B.; Smith, S.A. [Univ. of Utah, Salt Lake City, UT (United States)] [and others

1996-04-15

140

Topological characterization of crystalline ice structures from coordination sequences.  

Science.gov (United States)

Topological properties of crystalline ice structures are studied by considering ring statistics, coordination sequences, and topological density of different ice phases. The coordination sequences (number of sites at topological distance k from a reference site) have been obtained by direct enumeration until at least 40 coordination spheres for different ice polymorphs. This allows us to study the asymptotic behavior of the mean number of sites in the k-th shell, Mk, for high values of k: Mk?ak(2), a being a structure-dependent parameter. Small departures from a strict parabolic dependence have been studied by considering first and second differences of the series {Mk} for each structure. The parameter a ranges from 2.00 for ice VI to 4.27 for ice XII, and is used to define a topological density for these solid phases of water. Correlations between such topological density and the actual volume of ice phases are discussed. Ices Ih and Ic are found to depart from the general trend in this correlation due to the large void space in their structures. PMID:23986009

Herrero, Carlos P; Ramírez, Rafael

2013-08-28

 
 
 
 
141

Recursive dynamic programming for adaptive sequence and structure alignment  

Energy Technology Data Exchange (ETDEWEB)

We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost parameters is circumvented. In order to evaluate the RDP approach we analyse whether known and accepted multiple alignments based on structural information can be reproduced with the RDP method.

Thiele, R.; Zimmer, R.; Lengauer, T. [GMD SCAI, Sankt Augustin (Germany)

1995-12-31

142

Topological characterization of crystalline ice structures from coordination sequences.  

UK PubMed Central (United Kingdom)

Topological properties of crystalline ice structures are studied by considering ring statistics, coordination sequences, and topological density of different ice phases. The coordination sequences (number of sites at topological distance k from a reference site) have been obtained by direct enumeration until at least 40 coordination spheres for different ice polymorphs. This allows us to study the asymptotic behavior of the mean number of sites in the k-th shell, Mk, for high values of k: Mk?ak(2), a being a structure-dependent parameter. Small departures from a strict parabolic dependence have been studied by considering first and second differences of the series {Mk} for each structure. The parameter a ranges from 2.00 for ice VI to 4.27 for ice XII, and is used to define a topological density for these solid phases of water. Correlations between such topological density and the actual volume of ice phases are discussed. Ices Ih and Ic are found to depart from the general trend in this correlation due to the large void space in their structures.

Herrero CP; Ramírez R

2013-10-01

143

Data Structures: Sequence Problems, Range Queries, and Fault Tolerance  

DEFF Research Database (Denmark)

The focus of this dissertation is on algorithms, in particular data structures that give provably ecient solutions for sequence analysis problems, range queries, and fault tolerant computing. The work presented in this dissertation is divided into three parts. In Part I we consider algorithms for a range of sequence analysis problems that have risen from applications in pattern matching, bioinformatics, and data mining. On a high level, each problem is dened by a function and some constraints and the job at hand is to locate subsequences that score high with this function and are not invalidated by the constraints. Many variants and similar problems have been proposed leading to several dierent approaches and algorithms. We consider problems where the function is the sum of the elements in the sequence and the constraints only bound the length of the subsequences considered. We give optimal algorithms for several variants of the problem based on a simple idea and classic algorithms and data structures. In Part II we consider range query data structures. This a category of problems where the task is to preprocess an input sequence using as little time and space as possible such that one can eciently compute a certain function on the elements in a given query subsequence. There are many types of functions that has been considered in connection with input from dierent sources. The input could be ip-data sorted by ip-address, real estate prices sorted by zip code, advertising cost sorted by time etc. We consider data structures for two classic statistics functions, namely median and mode. Finally, Part III investigates fault tolerant algorithms and data structures. This deals with the trend of avoiding elaborate error checking and correction circuitry that would impose non-negligible costs in terms of hardware performance and money in the design of todays high speed memory technologies. Hardware, power failures, and environmental conditions such as cosmic rays and alpha particles can all alter the memory in unpredictable ways. In applications where large memory capacities are needed at low cost, it makes sense to assume that the algorithms themselves are in charge for dealing with memory faults. We investigate searching, sorting and counting algorithms and data structures that provably returns sensible information in spite of memory corruptions.

JØrgensen, Allan GrØnlund

2010-01-01

144

Structure and sequence determinants of aggregation investigated with molecular dynamics.  

UK PubMed Central (United Kingdom)

Spontaneous self-assembly and amyloid formation are a general property of many polypeptides and the information controlling these processes is encoded in the sequence. This determines the form and structural features of the interacting partners that regulate the properties of the final aggregates. Understanding the correlations between sequence, structure and dynamics in peptides and proteins at an atomistic level of resolution still represents one of the grand challenges of modern biological chemistry. In this context, computer simulations represent a valuable approach to understand recognition and spontaneous self-organization, processes that cannot be directly observed experimentally. Herein, we will discuss cases illustrating the extent to which simulations can be used to understand the self-organization properties of natural and designed amyloidogenic peptide sequences. The simulations provide evidence for the influence of specific interactions with well defined stereochemical constraints on fibril formation. The results from our and other groups suggest that simulations can be applied to detect the critical physico-chemical determinants of a certain process and can be helpful in the design of new chemical systems and experiments.

Moroni E; Scarabelli G; Colombo G

2009-01-01

145

The sequence, structure and evolutionary features of HOTAIR in mammals.  

UK PubMed Central (United Kingdom)

BACKGROUND: An increasing number of long noncoding RNAs (lncRNAs) have been identified recently. Different from all the others that function in cis to regulate local gene expression, the newly identified HOTAIR is located between HoxC11 and HoxC12 in the human genome and regulates HoxD expression in multiple tissues. Like the well-characterised lncRNA Xist, HOTAIR binds to polycomb proteins to methylate histones at multiple HoxD loci, but unlike Xist, many details of its structure and function, as well as the trans regulation, remain unclear. Moreover, HOTAIR is involved in the aberrant regulation of gene expression in cancer. RESULTS: To identify conserved domains in HOTAIR and study the phylogenetic distribution of this lncRNA, we searched the genomes of 10 mammalian and 3 non-mammalian vertebrates for matches to its 6 exons and the two conserved domains within the 1800 bp exon6 using Infernal. There was just one high-scoring hit for each mammal, but many low-scoring hits were found in both mammals and non-mammalian vertebrates. These hits and their flanking genes in four placental mammals and platypus were examined to determine whether HOTAIR contained elements shared by other lncRNAs. Several of the hits were within unknown transcripts or ncRNAs, many were within introns of, or antisense to, protein-coding genes, and conservation of the flanking genes was observed only between human and chimpanzee. Phylogenetic analysis revealed discrete evolutionary dynamics for orthologous sequences of HOTAIR exons. Exon1 at the 5' end and a domain in exon6 near the 3' end, which contain domains that bind to multiple proteins, have evolved faster in primates than in other mammals. Structures were predicted for exon1, two domains of exon6 and the full HOTAIR sequence. The sequence and structure of two fragments, in exon1 and the domain B of exon6 respectively, were identified to robustly occur in predicted structures of exon1, domain B of exon6 and the full HOTAIR in mammals. CONCLUSIONS: HOTAIR exists in mammals, has poorly conserved sequences and considerably conserved structures, and has evolved faster than nearby HoxC genes. Exons of HOTAIR show distinct evolutionary features, and a 239 bp domain in the 1804 bp exon6 is especially conserved. These features, together with the absence of some exons and sequences in mouse, rat and kangaroo, suggest ab initio generation of HOTAIR in marsupials. Structure prediction identifies two fragments in the 5' end exon1 and the 3' end domain B of exon6, with sequence and structure invariably occurring in various predicted structures of exon1, the domain B of exon6 and the full HOTAIR.

He S; Liu S; Zhu H

2011-01-01

146

The sequence, structure and evolutionary features of HOTAIR in mammals  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background An increasing number of long noncoding RNAs (lncRNAs) have been identified recently. Different from all the others that function in cis to regulate local gene expression, the newly identified HOTAIR is located between HoxC11 and HoxC12 in the human genome and regulates HoxD expression in multiple tissues. Like the well-characterised lncRNA Xist, HOTAIR binds to polycomb proteins to methylate histones at multiple HoxD loci, but unlike Xist, many details of its structure and function, as well as the trans regulation, remain unclear. Moreover, HOTAIR is involved in the aberrant regulation of gene expression in cancer. Results To identify conserved domains in HOTAIR and study the phylogenetic distribution of this lncRNA, we searched the genomes of 10 mammalian and 3 non-mammalian vertebrates for matches to its 6 exons and the two conserved domains within the 1800 bp exon6 using Infernal. There was just one high-scoring hit for each mammal, but many low-scoring hits were found in both mammals and non-mammalian vertebrates. These hits and their flanking genes in four placental mammals and platypus were examined to determine whether HOTAIR contained elements shared by other lncRNAs. Several of the hits were within unknown transcripts or ncRNAs, many were within introns of, or antisense to, protein-coding genes, and conservation of the flanking genes was observed only between human and chimpanzee. Phylogenetic analysis revealed discrete evolutionary dynamics for orthologous sequences of HOTAIR exons. Exon1 at the 5' end and a domain in exon6 near the 3' end, which contain domains that bind to multiple proteins, have evolved faster in primates than in other mammals. Structures were predicted for exon1, two domains of exon6 and the full HOTAIR sequence. The sequence and structure of two fragments, in exon1 and the domain B of exon6 respectively, were identified to robustly occur in predicted structures of exon1, domain B of exon6 and the full HOTAIR in mammals. Conclusions HOTAIR exists in mammals, has poorly conserved sequences and considerably conserved structures, and has evolved faster than nearby HoxC genes. Exons of HOTAIR show distinct evolutionary features, and a 239 bp domain in the 1804 bp exon6 is especially conserved. These features, together with the absence of some exons and sequences in mouse, rat and kangaroo, suggest ab initio generation of HOTAIR in marsupials. Structure prediction identifies two fragments in the 5' end exon1 and the 3' end domain B of exon6, with sequence and structure invariably occurring in various predicted structures of exon1, the domain B of exon6 and the full HOTAIR.

He Sha; Liu Shiping; Zhu Hao

2011-01-01

147

Evolution of planetary nebulae. I. Structures, ionizations, and morphological sequences  

International Nuclear Information System (INIS)

[en] An atlas of CCD pictures of fifty-one planetary nebulae (PNs) taken in the light of low-, moderate-, and high-ionization emission lines is presented. The shapes of many of the PNs can be organized into an empirical morphological sequence of round, elliptical, bipolar, and butterfly classes. Many PNs, especially the ones of high surface brightness such as NGC 2392, 3242, 6543, 6826, and 7662, show evidence for thin inclusions of anomalously low ionization in a high-ionization substrate. The morphological sequence of PNs is shown to be consistent with the precepts of the shaping of PNs by interacting winds. This consistency places the concepts of ongoing hydrodynamic shaping of PNs on firm grounds, and justifies further observations that can lead to a better understanding of the physical processes. PNs are proposed as an ideal astrophysical laboratory for studying the interactions of winds on a structured environment. 39 references

1987-01-01

148

X-ray structure of 1D-coordination polymer of copperII bearing 1,4-pyrazine-2,3-dicarboxylic acid and 2-aminopyrimidine  

Directory of Open Access Journals (Sweden)

Full Text Available The new 1D-coordination polymer of CuII ion, {(2- apymH)2[Cu(pyzdc)2] .6H2O}n, (2-apym = 2-aminopyrimidine, pyzdcH2 = 1,4- pyrazine-2,3-dicarboxylic acid), was synthesized based on proton transfer mechanism and characterized by elemental analysis, infrared spectroscopy, and single crystal X-ray diffraction. The coordination polymer consists of infinite anionic chains of [Cu(pyzdc)2]2- anion bridged crossing double chain running along a-axis and discrete (2-apymH)+ fragment. The CuII ion is located on inversion centre in the basal plane of an elongated octahedron and two oxygen atoms from adjacent (pyzdc)2-ligands occupy axial position. The interaction between oxygen atoms of water molecules along with the dicarboxylic acid play an important role in the overall supramolecular assembly.

Mirzaei Masoud; Eshtiagh-Hosseini Hossein; Hassanpoor Azam; Barba Victor

2012-01-01

149

Modulation of DNA radiolysis by sequence, structure and ligands  

International Nuclear Information System (INIS)

DNA structure, topology and interactions with ligands are continuously changing during the cell cycle, through phenomena such as replication or transcription. Until recently, it was considered that ionizing radiations break DNA strands with the same probability at all nucleotide sites. Using restriction fragments and synthetic oligonucleotides, we have shown that DNA is heterogeneously radiosensitive. The breakage probability at a given nucleotide site depends on nucleotide type and sequence, presence of ligands (metal ions, proteins, polyamines) and structural parameters (strandedness, handedness, minor groove depth, topological stress). We have observed that in 'naked'(without ligands) dna, the bent 5'-AATT regions that present a narrow minor groove are less sensitive than 'random DNA'. In a (GC)n sequence, all G sites are more radiosensitive, and all C sites are more radioresistant in a negatively super-coiling-induced left-handed Z-DNA than in the right-handed B-DNA. Some G's located in particular regions of single stranded DNA are more radiosensitive than in double stranded DNA. We have also shown that several natural ligands, such as Cu2+, polyamines or DNA-binding proteins modify DNA radiosensitivity directly of via the structural modifications that they induce in DNA. (authors)

1997-01-01

150

Structure and sequence of the human sulphamidase gene.  

Science.gov (United States)

Sanfilippo A syndrome (MPS-IIIA) is a mucopolysaccharide lysosomal storage disorder caused by a deficiency in the lysosomal enzyme, sulphamidase (EC 3.10.1.1), which is required for the degradation of heparan sulphate. A genomic clone containing the entire sulphamidase gene was isolated from a chromosome 17-specific gridded cosmid library. The structure of the gene and the sequence of the exon/intron boundaries and the 5' promoter region were determined. The sulphamidase gene is split into 8 exons spanning approximately 11 kb. PMID:8946167

Karageorgos, L E; Guo, X H; Blanch, L; Weber, B; Anson, D S; Scott, H S; Hopwood, J J

1996-08-31

151

Structure and sequence of the human sulphamidase gene.  

UK PubMed Central (United Kingdom)

Sanfilippo A syndrome (MPS-IIIA) is a mucopolysaccharide lysosomal storage disorder caused by a deficiency in the lysosomal enzyme, sulphamidase (EC 3.10.1.1), which is required for the degradation of heparan sulphate. A genomic clone containing the entire sulphamidase gene was isolated from a chromosome 17-specific gridded cosmid library. The structure of the gene and the sequence of the exon/intron boundaries and the 5' promoter region were determined. The sulphamidase gene is split into 8 exons spanning approximately 11 kb.

Karageorgos LE; Guo XH; Blanch L; Weber B; Anson DS; Scott HS; Hopwood JJ

1996-08-01

152

Age-structured Trait Substitution Sequence Process and Canonical Equation  

CERN Multimedia

We are interested in a stochastic model of trait and age-structured population undergoing mutation and selection. We start with a continuous time, discrete individual-centered population process. Taking the large population and rare mutations limits under a well-chosen time-scale separation condition, we obtain a jump process that generalizes the Trait Substitution Sequence process describing Adaptive Dynamics for populations without age structure. Under the additional assumption of small mutations, we derive an age-dependent ordinary differential equation that extends the Canonical Equation. These evolutionary approximations have never been introduced to our knowledge. They are based on ecological phenomena represented by PDEs that generalize the Gurtin-McCamy equation in Demography. Another particularity is that they involve a fitness function, describing the probability of invasion of the resident population by the mutant one, that can not always be computed explicitly. Examples illustrate how adding an ag...

Méléard, Sylvie

2007-01-01

153

PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users. Results A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models. Conclusions PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures. The ease of use, integration with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, are the key features of this tool. Source code, installation instructions, video tutorials and a user's guide are freely available at the URL http://schubert.bio.uniroma1.it/pymod/index.html

Bramucci Emanuele; Paiardini Alessandro; Bossa Francesco; Pascarella Stefano

2012-01-01

154

Structure and magnetism of the quasi-1-d K4Cu(MoO4)3 and the structure of K4Zn(MoO4)3.  

UK PubMed Central (United Kingdom)

Single crystals of K(4)Cu(MoO(4))(3) and nonmagnetic K(4)Zn(MoO(4))(3) have been grown by the flux-growth method. K(4)Cu(MoO(4))(3) can be described as a quantum quasi-1-d antiferromagnet with correlations between neighboring Cu(2+) ions but no magnetic long-range ordering down to 0.4 K. Comparison of the structure and magnetic properties of isostructural A(4)Cu(MoO(4))(3) (A = K, Rb) allows the isolation of the effects of low dimensionality from structural distortion along the Cu-O-Mo chains. The characteristic one-dimensional behavior is hence suppressed to lower the temperature in K(4)Cu(MoO(4))(3) in comparison with that of the Rb analogue. For example, a broad peak in the specific heat is observed ~2.3 K at 0 T, which is consistent with the onset of the quantum spin liquid state.

Menard MC; Ishii R; Nakatsuji S; Chan JY

2011-09-01

155

Structure and magnetism of the quasi-1-d K4Cu(MoO4)3 and the structure of K4Zn(MoO4)3.  

Science.gov (United States)

Single crystals of K(4)Cu(MoO(4))(3) and nonmagnetic K(4)Zn(MoO(4))(3) have been grown by the flux-growth method. K(4)Cu(MoO(4))(3) can be described as a quantum quasi-1-d antiferromagnet with correlations between neighboring Cu(2+) ions but no magnetic long-range ordering down to 0.4 K. Comparison of the structure and magnetic properties of isostructural A(4)Cu(MoO(4))(3) (A = K, Rb) allows the isolation of the effects of low dimensionality from structural distortion along the Cu-O-Mo chains. The characteristic one-dimensional behavior is hence suppressed to lower the temperature in K(4)Cu(MoO(4))(3) in comparison with that of the Rb analogue. For example, a broad peak in the specific heat is observed ~2.3 K at 0 T, which is consistent with the onset of the quantum spin liquid state. PMID:21853975

Menard, Melissa C; Ishii, Rieko; Nakatsuji, Satoru; Chan, Julia Y

2011-08-18

156

Deletion of the Phytophthora sojae avirulence gene Avr1d causes gain of virulence on Rps1d.  

UK PubMed Central (United Kingdom)

Phytophthora sojae is an oomycete and a pathogen of soybean that causes root rot. During infection P. sojae delivers effector proteins into host cells to foster disease. However, effector-triggered immunity (ETI) results when pathogen factors are recognized by host resistance (R) proteins. We have now identified the P. sojae Avr1d gene, which encodes a predicted effector protein with the amino acid motif Arg-X-Leu-Arg (RXLR). Genetic mapping of 16 different P. sojae isolates and of a segregating F2 population of 40 individuals shows that the predicted RXLR effector gene Avh6 precisely cosegregates with the Avr1d phenotype. Transient expression assays confirm that Avr1d triggers cell death specifically in Rps1d soybean plants. The Avr1d gene is present in P. sojae strains that are avirulent on Rps1d, whereas the gene is deleted from the genome of virulent strains. Two sequence variants of the Avr1d gene encoding different protein products occur in P. sojae strains, but both are recognized by Rps1d and cause ETI. Liposome binding assays show that Avr1d has affinity for phosphatidylinositol 4-phosphate and that binding can be disrupted by mutation of lysine residues in the carboxy-terminal effector domain of the protein. The identification of Avr1d aids pathogen diagnostics and soybean cultivar development.

Na R; Yu D; Qutob D; Zhao J; Gijzen M

2013-08-01

157

On Cognition, Structured Sequence Processing, and Adaptive Dynamical Systems  

Science.gov (United States)

Cognitive neuroscience approaches the brain as a cognitive system: a system that functionally is conceptualized in terms of information processing. We outline some aspects of this concept and consider a physical system to be an information processing device when a subclass of its physical states can be viewed as representational/cognitive and transitions between these can be conceptualized as a process operating on these states by implementing operations on the corresponding representational structures. We identify a generic and fundamental problem in cognition: sequentially organized structured processing. Structured sequence processing provides the brain, in an essential sense, with its processing logic. In an approach addressing this problem, we illustrate how to integrate levels of analysis within a framework of adaptive dynamical systems. We note that the dynamical system framework lends itself to a description of asynchronous event-driven devices, which is likely to be important in cognition because the brain appears to be an asynchronous processing system. We use the human language faculty and natural language processing as a concrete example through out.

Petersson, Karl Magnus

2008-11-01

158

Infinite sequence of Poincare group extensions: structure and dynamics  

International Nuclear Information System (INIS)

We study the structure and dynamics of the infinite sequence of extensions of the Poincare algebra whose method of construction was described in a previous paper (Bonanos and Gomis J. Phys. A: Math. Theor. 42 (2009) 145206 (arXiv:hep-th/0808.2243)). We give explicitly the Maurer-Cartan (MC) 1-forms of the extended Lie algebras up to level 3. Using these forms and introducing a corresponding set of new dynamical couplings, we construct an invariant Lagrangian, which describes the dynamics of a distribution of charged particles in an external electromagnetic field. At each extension, the distribution is approximated by a set of moments about the world line of its center of mass and the field by its Taylor series expansion about the same line. The equations of motion after the second extensions contain back-reaction terms of the moments on the world line.

2010-01-08

159

Performance of secondary structure prediction methods on proteins containing structurally ambivalent sequence fragments.  

Science.gov (United States)

Several approaches for predicting secondary structures from sequences have been developed and reached a fair accuracy. One of the most rigorous tests for these prediction methods is their ability to correctly predict identical fragments of protein sequences adopting different secondary structures in unrelated proteins. In our previous work, we obtained 30 identical octapeptide sequence fragments adopting different backbone conformations. It is of interest to find whether the presence of structurally ambivalent fragments in proteins will affect the accuracy of secondary structure prediction methods or not. Hence, in this work, we have made a systematic comparative analysis on secondary structure prediction results of 30 identical octapeptide pairs and 52 identical heptapeptide pairs adopting different conformations with the aid of segment overlap measure. The results reveal the better performance of profile-based methods such as PSIpred and JPred and misprediction by classical rule-based methods such as Garnier Osguthorpe Robson Method and Double Prediction Method. The results discussed here insist that modern secondary structure prediction methods are able to better discriminate conformationally ambivalent peptide fragments. © 2012 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 148-153, 2013. PMID:23616098

Saravanan, K Mani; Selvaraj, Samuel

2013-04-01

160

SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. Results SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. Conclusion The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are capable of separating the structural classes in spite of their low dimensionality. We also demonstrate that the SCPRED's predictions can be successfully used as a post-processing filter to improve performance of modern fold classification methods.

Kurgan Lukasz; Cios Krzysztof; Chen Ke

2008-01-01

 
 
 
 
161

Predicting a set of minimal free energy RNA secondary structures common to two sequences.  

UK PubMed Central (United Kingdom)

MOTIVATION: Function derives from structure, therefore, there is need for methods to predict functional RNA structures. RESULTS: The Dynalign algorithm, which predicts the lowest free energy secondary structure common to two unaligned RNA sequences, is extended to the prediction of a set of low-energy structures. Dot plots can be drawn to show all base pairs in structures within an energy increment. Dynalign predicts more well-defined structures than structure prediction using a single sequence; in 5S rRNA sequences, the average number of base pairs in structures with energy within 20% of the lowest energy structure is 317 using Dynalign, but 569 using a single sequence. Structure prediction with Dynalign can also be constrained according to experiment or comparative analysis. The accuracy, measured as sensitivity and positive predictive value, of Dynalign is greater than predictions with a single sequence. AVAILABILITY: Dynalign can be downloaded at http://rna.urmc.rochester.edu

Mathews DH

2005-05-01

162

Structural properties of replication origins in yeast DNA sequences  

International Nuclear Information System (INIS)

[en] Sequence-dependent DNA flexibility is an important structural property originating from the DNA 3D structure. In this paper, we investigate the DNA flexibility of the budding yeast (S. Cerevisiae) replication origins on a genome-wide scale using flexibility parameters from two different models, the trinucleotide and the tetranucleotide models. Based on analyzing average flexibility profiles of 270 replication origins, we find that yeast replication origins are significantly rigid compared with their surrounding genomic regions. To further understand the highly distinctive property of replication origins, we compare the flexibility patterns between yeast replication origins and promoters, and find that they both contain significantly rigid DNAs. Our results suggest that DNA flexibility is an important factor that helps proteins recognize and bind the target sites in order to initiate DNA replication. Inspired by the role of the rigid region in promoters, we speculate that the rigid replication origins may facilitate binding of proteins, including the origin recognition complex (ORC), Cdc6, Cdt1 and the MCM2-7 complex

2008-09-10

163

Beyond supersecondary structure: the global properties of protein sequences.  

UK PubMed Central (United Kingdom)

Analysis of the global properties of protein sequences, rather than single-site or local properties, has been shown to lead to new understanding of folding and function. Here we describe the use of software which can describe sequences numerically in an orthonormal fashion, Fourier-analyze those sequences, and verify the statistical significance of the resulting Fourier coefficients. The resulting parameters can be used to study problems involving sequences from a unique perspective.

Rackovsky S

2013-01-01

164

Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The secondary structure of an RNA must be known before the relationship between its structure and function can be determined. One way to predict the secondary structure of an RNA is to identify covarying residues that maintain the pairings (Watson-Crick, Wobble and non-canonical pairings). This "comparative approach" consists of identifying mutations from homologous sequence alignments. The sequences must covary enough for compensatory mutations to be revealed, but comparison is difficult if they are too different. Thus the choice of homologous sequences is critical. While many possible combinations of homologous sequences may be used for prediction, only a few will give good structure predictions. This can be due to poor quality alignment in stems or to the variability of certain sequences. This problem of sequence selection is currently unsolved. Results This paper describes an algorithm, SSCA, which measures the suitability of sequences for the comparative approach. It is based on evolutionary models with structure constraints, particularly those on sequence variations and stem alignment. We propose three models, based on different constraints on sequence alignments. We show the results of the SSCA algorithm for predicting the secondary structure of several RNAs. SSCA enabled us to choose sets of homologous sequences that gave better predictions than arbitrarily chosen sets of homologous sequences. Conclusion SSCA is an algorithm for selecting combinations of RNA homologous sequences suitable for secondary structure predictions with the comparative approach.

Engelen Stéfan; Tahi Fariza

2007-01-01

165

Structural characterization of genomes by large scale sequence-structure threading  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Using sequence-structure threading we have conducted structural characterization of complete proteomes of 37 archaeal, bacterial and eukaryotic organisms (including worm, fly, mouse and human) totaling 167,888 genes. Results The reported data represent first rather general evaluation of performance of full sequence-structure threading on multiple genomes providing opportunity to evaluate its general applicability for large scale studies. According to the estimated results the sequence-structure threading has assigned protein folds to more then 60% of eukaryotic, 68% of archaeal and 70% of bacterial proteomes. The repertoires of protein classes, architectures, topologies and homologous superfamilies (according to the CATH 2.4 classification) have been established for distant organisms and superkingdoms. It has been found that the average abundance of CATH classes decreases from "alpha and beta" to "mainly beta", followed by "mainly alpha" and "few secondary structures". 3-Layer (aba) Sandwich has been characterized as the most abundant protein architecture and Rossman fold as the most common topology. Conclusion The analysis of genomic occurrences of CATH 2.4 protein homologous superfamilies and topologies has revealed the power-law character of their distributions. The corresponding double logarithmic "frequency – genomic occurrence" dependences characteristic of scale-free systems have been established for individual organisms and for three superkingdoms. Supplementary materials to this works are available at 1.

Cherkasov Artem; Jones Steven JM

2004-01-01

166

Sublocalization of seven human simple sequence repeat polymorphic markers: D5S349, D5S351, and D5S355 to 5q11. 2-q13. 1, D5S350 to 5p13. 1-p14, D5S35s to 5q31. 2-q33. 1, D5S353 to 5q33. 2-qter, and D5S354 to 5q13. 2-q15  

Energy Technology Data Exchange (ETDEWEB)

Seven highly informative human simple sequence repeat polymorphisms that map to human chromosome 5 have been sublocalized using a panel of somatic cell hybrids that retain naturally occurring deletions (4, 7). Simple sequence repeats are useful in the construction of high-resolution maps of the human genome because they are highly polymorphic and easily typed by the polymerase chain reaction (2, 9, 10, 11). The presence or absence of each of the seven simple sequence repeats, D5S349, D5S350, D5S351, D5S352, D5S353, D5S354, and D5S355, in a panel of somatic cell hybrids was determined using the polymerase chain reaction. The sequence of the PCR primer sets was previously reported by Hudson et al. Each PCR was carried out in a total volume of 25 PI using 0.2 pg DNA in 67 mM Tris-HCI (pH 8.3),6.7 mM MgCl[sub 2], 16.6 mM ammonium sulfate, 10 mM [beta]-mercaptoethanol, 1.25 mM each dNTP, 25 pmol each primer, and I unit of Thermos aquaticus DNA polymerase. The initial denaturation was at 94[degrees]R C for 1.5 min and the annealing temperatures ranged from 57 to 67[degrees]R C. Figure 1 depicts the chromosome 5 natural deletion mapping panel and the location of the markers. D5S350 was present in all hybrid cell lines except HHW1124 and HHW764 (SRO p13.1-p14). D5S349, D5S351, and D5S355 were absent in HHW1064 and HHW1124 and present in all other cell lines (SROq11.2-q13.1).D5S354 was absent in HHW1124 and present in all other cell lines (SRO q13.2-q15). D5S352 was present in all cell lines (SRO q31.2-q33.1), and D5S353 was present in all cell lines except HHW1138 (SRO q33.2-qter). 11 refs., 1 fig.

Warrington, J.A.; Wasmuth, J.J. (Univ. of California, Irvine (United States))

1993-01-01

167

Evidence for 5-HT1D beta but not 5-HT1D alpha receptor subtype expression in canine large coronary arteries and saphenous vein.  

UK PubMed Central (United Kingdom)

OBJECTIVE: 5-Hydroxytryptamine1D (5-HT1D) receptors are believed to play a major role in the vasoconstriction of vascular smooth muscle in human coronary arteries. However, unequivocal evidence as to which subtype of this receptor (5-HT1D alpha or 5-HT1D beta) is involved in these vasoconstrictory effects is lacking. The aim of this study was to identify in the dog the 5-HT1D receptor subtype encoding mRNAs expressed in several large coronary arteries and in the saphenous vein. METHODS: Degenerate oligonucleotide primers that selectively recognized only mammalian 5-HT1D alpha and 5-HT1D beta receptor sequences were used in RT-PCR experiments to study 5-HT1D receptor subtype expression in endothelium-denuded saphenous vein and large coronary arteries from beagle and alsatian dogs. Resulting PCR products were analysed and identified by Southern blots and sequencing. RESULTS: An identical PCR product whose sequence closely resembles that of the human 5-HT1D beta receptor (98% amino acid identity) was obtained from reverse-transcribed RNA isolated from either saphenous vein or coronary arteries, irrespective of dog race. Absence of 5-HT1D alpha expression was confirmed by Southern blot analysis. Control experiments using canine genomic DNA as template illustrated, nonetheless, that the primers chosen could amplify both 5-HT1D alpha and 5-HT1D beta sequences. CONCLUSION: Using RT-PCR, we isolated from dog vascular smooth muscle a cDNA fragment whose nucleotide sequence would encode a previously-unreported canine homologue of the 5-HT1D beta receptor. We illustrated that this subtype is the only 5-HT1D receptor subtype expressed in dog saphenous vein and large coronary arteries. The implications of these findings are discussed in light of results from functional studies of 5-HT1-like receptor-mediated effects in these canine blood vessels.

Sgard F; Faure C; Graham D

1996-05-01

168

STP Ising 1D Program  

Science.gov (United States)

The STP 1DIsing program is a Monte Carlo simulation of a one-dimensional Ising model in equilibrium with a heat bath at temperature T using the Metropolis algorithm. The default is N=64 spins up (s = 1) with no external field with heat bath temperature T=1. STP Ising1D is part of a suite of Open Source Physics programs that model aspects of Statistical and Thermal Physics (STP). The program is distributed as a ready-to-run (compiled) Java archive. Double clicking the stp_Ising1D.jar file will run the program if Java is installed on your computer. Additional programs can be found by searching ComPADRE for Open Source Physics, STP, or Statistical and Thermal Physics.

Gould, Harvey; Tobochnik, Jan; Christian, Wolfgang; Cox, Anne

2008-05-28

169

1D Quantum States Applet  

Science.gov (United States)

This simulation shows time-dependent 1D quantum bound state wavefunctions for a number of different wells. Position, momentum, parity, energy, and current can all be viewed, with phase shown with color. Eigentstates can be selected using the energy level diagram. Multiple-energy-eigenstate wavefunctions can be created through changes in the amplitude and phase of the basis states using spinors. Postion and energy measurements can be taken, resulting in new states of the system.

Falstad, Paul

2004-05-17

170

Three new 2-D metal-organic frameworks containing 1-D metal chains bridged by N-benzesulfonyl-glutamic acid: Syntheses, crystal structures and properties  

International Nuclear Information System (INIS)

[en] To explore the possibility of obtaining the metal-organic frameworks (MOFs) bearing the bsgluH2 ligand, two new Cd(II) and one Cu(II) coordination polymers, [Cd(bsglu)(bipy)] n (1), [Cd(bsglu).(H2O)] n (2) and {[Cu2(bsglu)2(bipy)2].4H2O} n (3) (bsglu=N-benzesulfonyl-glutamic acid bianion, bipy=2,2'-bipyridine) were synthesized and characterized by IR, elemental analysis and X-ray diffraction analysis. Compounds 1 and 3 exhibit one-dimensional coordination chains, which are further connected to form two-dimensional supramolecular networks through ?-? aromatic stacking interactions in a novel zipper-like way. Compound 2 presents a two-dimensional layer structure. To the best of our knowledge, 2 is the first two-dimensional complex formed from transition metal and bsgluH2 ligand. Interestingly, the bsglu anion exhibits remarkable versatile coordination modes in these complexes. Fluorescent analyses show that 1 exhibits photoluminescence in the solid state. Magnetic measurements for 3 revealed that the Cu(II) chain exhibit a weak antiferromagnetic behavior with a J value of -0.606 cm-1. - Graphical abstract: Three new complexes, [Cd(bsglu)(bipy)] n (1), [Cd(bsglu).(H2O)] n (2) and {[Cu2(bsglu)2(bipy)2].4H2O} n (3), constructed from Cd(II) or Cu(II) salt with N-benzesulfonyl-glutamic acid were synthesized and characterized. Compounds 1 and 3 exhibit one-dimensional chains which are further connected to form two-dimensional supramolecular networks through ?-? aromatic stacking interactions in a novel zipper-like way. Compound 2 presents a two-dimensional layer structure. Luminescence of 1 and magnetic properties of 3 are also investigated

2007-01-01

171

Structure and neural expression of a zebrafish homeobox sequence.  

Science.gov (United States)

A genomic library of zebrafish was constructed and screened with homeobox-containing probes. One of the positive clones contains a transcribed region which shares extensive sequence homology with the murine Hox-1.4 and Hox-2.6 genes and the human HHO.c13 gene. Characterization of this zebrafish homologue (ZF-13) with respect to expression demonstrated that it is transcribed during embryogenesis where a major RNA species of 2.5 kb and a minor transcript of 4.6 kb are detected. The highest concentration of both transcripts was found in embryos at the stage of somite formation. By in situ hybridization the spatial localization of expression was analysed in hatching embryos. Hybridization signals were mainly detected throughout the neural tube and in the brain. A small amount of RNA derived from ZF-13 was localized in differentiated muscle cells. Our results suggest that homeobox genes of distantly related vertebrate species are very similar with respect to structure and function. PMID:2468579

Njølstad, P R; Molven, A; Eiken, H G; Fjose, A

1988-12-15

172

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource.  

UK PubMed Central (United Kingdom)

The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS database. The SIFTS process includes cross-references to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The information is exported in XML format, one file for each PDB entry, and is made available by FTP. Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information.

Velankar S; Dana JM; Jacobsen J; van Ginkel G; Gane PJ; Luo J; Oldfield TJ; O'Donovan C; Martin MJ; Kleywegt GJ

2013-01-01

173

Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.  

UK PubMed Central (United Kingdom)

MOTIVATION: With recent advances in sequencing, structural and functional studies of RNA lag behind the discovery of sequences. Computational analysis of RNA is increasingly important to reveal structure-function relationships with low cost and speed. The purpose of this study is to use multiple homologous sequences to infer a conserved RNA structure. RESULTS: A new algorithm, called Multilign, is presented to find the lowest free energy RNA secondary structure common to multiple sequences. Multilign is based on Dynalign, which is a program that simultaneously aligns and folds two sequences to find the lowest free energy conserved structure. For Multilign, Dynalign is used to progressively construct a conserved structure from multiple pairwise calculations, with one sequence used in all pairwise calculations. A base pair is predicted only if it is contained in the set of low free energy structures predicted by all Dynalign calculations. In this way, Multilign improves prediction accuracy by keeping the genuine base pairs and excluding competing false base pairs. Multilign has computational complexity that scales linearly in the number of sequences. Multilign was tested on extensive datasets of sequences with known structure and its prediction accuracy is among the best of available algorithms. Multilign can run on long sequences (> 1500 nt) and an arbitrarily large number of sequences. AVAILABILITY: The algorithm is implemented in ANSI C++ and can be downloaded as part of the RNAstructure package at: http://rna.urmc.rochester.edu.

Xu Z; Mathews DH

2011-03-01

174

Moments of the Spin Structure Functions g1p and g1d for 0.05 < Q2 < 3.0 GeV2  

Energy Technology Data Exchange (ETDEWEB)

The spin structure functions $g_1$ for the proton and the deuteron have been measured over a wide kinematic range in $x$ and \\Q2 using 1.6 and 5.7 GeV longitudinally polarized electrons incident upon polarized NH$_3$ and ND$_3$ targets at Jefferson Lab. Scattered electrons were detected in the CEBAF Large Acceptance Spectrometer, for $0.05 < Q^2 < 5 $\\ GeV$^2$ and $W < 3$ GeV. The first moments of $g_1$ for the proton and deuteron are presented -- both have a negative slope at low \\Q2, as predicted by the extended Gerasimov-Drell-Hearn sum rule. The first result for the generalized forward spin polarizability of the proton $\\gamma_0^p$ is also reported, and shows evidence of scaling above $Q^2$ = 1.5 GeV$^2$. Although the first moments of $g_1$ are consistent with Chiral Perturbation Theory (\\ChPT) calculations up to approximately $Q^2 = 0.06$ GeV$^2$, a significant discrepancy is observed between the $\\gamma_0^p$ data and \\ChPT\\ for $\\gamma_0^p$,even at the lowest \\Q2.

Prok, Yelena; Bosted, Peter; Burkert, Volker; Deur, Alexandre; Dharmawardane, Kahanawita; Dodge, Gail; Griffioen, Keith; Kuhn, Sebastian; Minehart, Ralph; Adams, Gary; Amaryan, Moscov; Amaryan, Moskov; Anghinolfi, Marco; Asryan, G.; Audit, Gerard; Avagyan, Harutyun; Baghdasaryan, Hovhannes; Baillie, Nathan; Ball, J.P.; Ball, Jacques; Baltzell, Nathan; Barrow, Steve; Battaglieri, Marco; Beard, Kevin; Bedlinskiy, Ivan; Bektasoglu, Mehmet; Bellis, Matthew; Benmouna, Nawal; Berman, Barry; Biselli, Angela; Blaszczyk, Lukasz; Boyarinov, Sergey; Bonner, Billy; Bouchigny, Sylvain; Bradford, Robert; Branford, Derek; Briscoe, William; Brooks, William; Bultmann, S.; Bueltmann, Stephen; Butuceanu, Cornel; Calarco, John; Careccia, Sharon; Carman, Daniel; Casey, Liam; Cazes, Antoine; Chen, Shifeng; Cheng, Lu; Cole, Philip; Collins, Patrick; Coltharp, Philip; Cords, Dieter; Corvisiero, Pietro; Crabb, Donald; Crede, Volker; Cummings, John; Dale, Daniel; Dashyan, Natalya; De Masi, Rita; De Vita, Raffaella; De Sanctis, Enzo; Degtiarenko, Pavel; Denizli, Haluk; Dennis, Lawrence; Dhuga, Kalvir; Dickson, Richard; Djalali, Chaden; Doughty, David; Dugger, Michael; Dytman, Steven; Dzyubak, Oleksandr; Egiyan, Hovanes; Egiyan, Kim; Elfassi, Lamiaa; Elouadrhiri, Latifa; Eugenio, Paul; Fatemi, Renee; Fedotov, Gleb; Feldman, Gerald; Fersch, Robert; Feuerbach, Robert; Forest, Tony; Fradi, Ahmed; Funsten, Herbert; Garcon, Michel; Gavalian, Gagik; Gevorgyan, Nerses; Gilfoyle, Gerard; Giovanetti, Kevin; Girod, Francois-Xavier; Goetz, John; Golovach, Evgeny; Gothe, Ralf; Guidal, Michel; Guillo, Matthieu; Guler, Nevzat; Guo, Lei; Gyurjyan, Vardan; Hadjidakis, Cynthia; Hafidi, Kawtar; Hakobyan, Hayk; Hanretty, Charles; Hardie, John; Hassall, Neil; Heddle, David; Hersman, F.; Hicks, Kenneth; Hleiqawi, Ishaq; Holtrop, Maurik; Huertas, Marco; Hyde, Charles; Ilieva, Yordanka; Ireland, David; Ishkhanov, Boris; Isupov, Evgeny; Ito, Mark; Jenkins, David; Jo, Hyon-Suk; Johnstone, John; Joo, Kyungseon; Juengst, Henry; Kalantarians, Narbe; Keith, Christopher; Kellie, James; Khandaker, Mahbubul; Kim, Kui; Kim, Kyungmo; Kim, Wooyoung; Klein, Andreas; Klein, Franz; Klusman, Mike; Kossov, Mikhail; Krahn, Zebulun; Kramer, Laird; Kubarovsky, Valery; Kuhn, Joachim; Kuleshov, Sergey; Kuznetsov, Viacheslav; Lachniet, Jeff; Laget, Jean; Langheinrich, Jorn; Lawrence, Dave; Lima, Ana; Livingston, Kenneth; Lu, Haiyun; Lukashin, K.; MacCormick, Marion; Marchand, Claude; Markov, Nikolai; Mattione, Paul; McAleer, Simeon; McKinnon, Bryan; McNabb, John; Mecking, Bernhard; Mestayer, Mac; Meyer, Curtis; Mibe, Tsutomu; Mikhaylov, Konstantin; Mirazita, Marco; Miskimen, Rory; Mokeev, Viktor; Morand, Ludyvine; Moreno, Brahim; Moriya, Kei; Morrow, Steven; Moteabbed, Maryam; Mueller, James; Munevar Espitia, Edwin; Mutchler, Gordon; Nadel-Turonski, Pawel; Nasseripour, Rakhsha; Niccolai, Silvia; Niculescu, Gabriel; Niculescu, Maria-Ioana; Niczyporuk, Bogdan; Niroula, Megh; Niyazov, Rustam; Nozar, Mina; O' Rielly, Grant; Osipenko, Mikhail; Ostrovidov, Alexander; Park, Kijun; Pasyuk, Evgueni; Paterson, Craig; Anefalos Pereira, S.; Philips, Sasha; Pierce, J.; Pivnyuk, Nikolay; Pocanic, Dinko; Pogorelko, Oleg; Popa, Iulian; Pozdnyakov, Sergey; Preedom, Barry; Price, John; Procureur, Sebastien; Protopopescu, Dan; Qin, Liming; Raue, Brian; Riccardi, Gregory; Ricco, Giovanni; Ripani, Marco; Ritchie, Barry; Rosner, Guenther; Rossi, Patrizia; Rowntree, David; Rubin, Philip; Sabatie, Franck; Salamanca, Julian; Salgado, Carlos; Santoro, Joseph; Sapunenko, Vladimir; Schumacher, Reinhard; Seely, Mikell; Serov, Vladimir; Sharabian, Youri; Sharov, Dmitri; Shaw, Jeffrey; Shvedunov, Nikolay; Skabelin, Alexander; Smith, Elton; Smith, Lee; Sober, Daniel; Sokhan, Daria; Stavinskiy, Aleksey; Stepanyan, Samuel; Stepanyan, Stepan; Stokes, Burnham; Stoler, Paul; Strakovski, Igor; Strauch, Steffen; Suleiman, Riad; Taiuti, Mauro; Tedeschi, David; Tkabladze, Avtandil; Tkachenko, Svyatoslav; Todor, Luminita; Ungaro, Maurizio; V

2009-02-01

175

Moments of the Spin Structure Functions g_1^p and g_1^d for 0.05 < Q^2 < 3.0 GeV^2  

CERN Multimedia

The spin structure functions g_1 for the proton and the deuteron have been measured over a wide kinematic range in x and Q2 using 1.6 and 5.7 GeV longitudinally polarized electrons incident upon polarized NH_3 and ND_3 targets at Jefferson Lab. Scattered electrons were detected in the CEBAF Large Acceptance Spectrometer, for 0.05 < Q^2 < 5 GeV^2 and W < 3 GeV. The first moments of g_1 for the proton and deuteron are presented -- both have a negative slope at low Q2, as predicted by the extended Gerasimov-Drell-Hearn sum rule. The first result for the generalized forward spin polarizability of the proton gamma_0^p is also reported, and shows evidence of scaling above Q^2 = 1.5 GeV^2. Although the first moments of g_1 are consistent with Chiral Perturbation Theory (ChPT) calculations up to approximately Q^2 = 0.06 GeV^2, a significant discrepancy is observed between the \\gamma_0^p data and ChPT for gamma_0^p,even at the lowest Q2.

Prok, Y; Burkert, V D; Deur, A; Dharmawardane, K V; Dodge, G E; Griffioen, K A; Kuhn, S E; Minehart, R; Adams, G; Amaryan, M J; Anghinolfi, M; Asryan, G; Audit, G; Avakian, H; Bagdasaryan, H; Baillie, N; Ball, J P; Baltzell, N A; Barrow, S; Battaglieri, M; Beard, K; Bedlinskiy, I; Bektasoglu, M; Bellis, M; Benmouna, N; Berman, B L; Biselli, A S; Blaszczyk, L; Boiarinov, S; Bonner, B E; Bouchigny, S; Bradford, R; Branford, D; Briscoe, W J; Brooks, W K; Bültmann, S; Butuceanu, C; Calarco, J R; Careccia, S L; Carman, D S; Casey, L; Cazes, A; Chen, S; Cheng, L; Cole, P L; Collins, P; Coltharp, P; Cords, D; Corvisiero, P; Crabb, D; Credé, V; Cummings, J P; Dale, D; Dashyan, N; De Masi, R; De Vita, R; De Sanctis, E; Degtyarenko, P V; Denizli, H; Dennis, L; Dhuga, K S; Dickson, R; Djalali, C; Doughty, D; Dugger, M; Dytman, S; Dzyubak, O P; Egiyan, H; Egiyan, K S; El Fassi, L; Elouadrhiri, L; Eugenio, P; Fatemi, R; Fedotov, G; Feldman, G; Fersh, R G; Feuerbach, R J; Forest, T A; Fradi, A; Funsten, H; Garçon, M; Gavalian, G; Gevorgyan, N; Gilfoyle, G P; Giovanetti, K L; Girod, F X; Goetz, J T; Golovatch, E; Gothe, R W; Guidal, M; Guillo, M; Guler, N; Guo, L; Gyurjyan, V; Hadjidakis, C; Hafidi, K; Hakobyan, H; Hanretty, C; Hardie, J; Hassall, N; Heddle, D; Hersman, F W; Hicks, K; Hleiqawi, I; Holtrop, M; Huertas, M; Hyde-Wright, C E; Ilieva, Y; Ireland, D G; Ishkhanov, B S; Isupov, E L; Ito, M M; Jenkins, D; Jo, H S; Johnstone, J R; Joo, K; Jüngst, H G; Kalantarians, N; Keith, C D; Kellie, J D; Khandaker, M; Kim, K Y; Kim, K; Kim, W; Klein, A; Klein, F J; Klusman, M; Kossov, M; Krahn, Z; Kramer, L H; Kubarovski, V; Kühn, J; Kuleshov, S V; Kuznetsov, V; Lachniet, J; Laget, J M; Langheinrich, J; Lawrence, D; Ji Li; Lima, A C S; Livingston, K; Lu, H Y; Lukashin, K; MacCormick, M; Marchand, C; Markov, N; Mattione, P; McAleer, S; McKinnon, B; McNabb, J W C; Mecking, B A; Mestayer, M D; Meyer, C A; Mibe, T; Mikhailov, K; Mirazita, M; Miskimen, R; Mokeev, V; Morand, L; Moreno, B; Moriya, K; Morrow, S A; Moteabbed, M; Müller, J; Munevar, E; Mutchler, G S; Nadel-Turonski, P; Nasseripour, R; Niccolai, S; Niculescu, G; Niculescu, I; Niczyporuk, B B; Niroula, M R; Niyazov, R A; Nozar, M; O'Rielly, G V; Osipenko, M; Ostrovidov, A I; Park, K; Pasyuk, E; Paterson, C; Anefalos Pereira, S; Philips, S A; Pierce, J; Pivnyuk, N; Pocanic, D; Pogorelko, O; Popa, I; Pozdniakov, S; Preedom, B M; Price, J W; Procureur, S; Protopopescu, D; Qin, L M; Raue, B A; Riccardi, G; Ricco, G; Ripani, M; Ritchie, B G; Rosner, G; Rossi, P; Rowntree, D; Rubin, P D; Sabati, F; Salamanca, J; Salgado, C; Santoro, e J P; Sapunenko, V; Schumacher, R A; Seely, M L; Serov, V S; Sharabyan, Yu G; Sharov, D; Shaw, J; Shvedunov, N V; Skabelin, A V; Smith, E S; Smith, L C; Sober, D I; Sokhan, D; Stavinsky, A; Stepanyan, S S; Stepanyan, S; Stokes, B E; Stoler, P; Strakovsky, I I; Strauch, S; Suleiman, R; Taiuti, M; Tedeschi, D J; Tkabladze, A; Tkachenko, S; Todor, L; Ungaro, M; Vineyard, M F; Vlassov, A V; Watts, D P; Weinstein, L B; Weygand, D P; Williams, M; Wolin, E; Wood, M H; Yegneswaran, A; Yun, J; Zana, L; Zhang, J; Zhao, B; Zhao, Z W

2008-01-01

176

Crystal Structures of Mouse CD1d-IGb3 Complex And Its Cognate Valpha14 T Cell Receptor Suggest a Model for Dual Recognition of Foreign And Self Glycolipids  

Energy Technology Data Exchange (ETDEWEB)

The semi-invariant Valpha14Jalpha18 T cell receptor (TCR) is expressed by regulatory NKT cells and has the unique ability to recognize chemically diverse ligands presented by CD1d. The crystal structure of CD1d complexed to a natural, endogenous ligand, isoglobotrihexosylceramide (iGb3), illustrates the extent of this diversity when compared to the binding of potent, exogenous ligands, such as alpha-galactosylceramide (alpha-GalCer). A single mode of recognition for these two classes of ligands would then appear problematic for a single T cell receptor. However, the Valpha14 TCR adopts two different conformations in the crystal where, in one configuration, the presence of a larger cavity between the two CDR3 regions could accommodate iGb3 and, in the other, a smaller cavity fits alpha-GalCer more snugly. Alternatively, the extended iGb3 headgroup could be 'squashed' upon docking of the TCR and accommodated between the CD1 and TCR surfaces. Thus, the same TCR may adopt alternative modes of recognition for these foreign and self-ligands for NKT cell activation.

Zajonc, D.M.; Saveage, P.B.; Bendelac, A.; Wilson, I.A.; Teyton, L.

2009-05-28

177

1D helix, 2D brick-wall and herringbone, and 3D interpenetration d10 metal-organic framework structures assembled from pyridine-2,6-dicarboxylic acid N-oxide.  

UK PubMed Central (United Kingdom)

Five novel interesting d(10) metal coordination polymers, [Zn(PDCO)(H2O)2]n (PDCO = pyridine-2,6-dicarboxylic acid N-oxide) (1), [Zn2(PDCO)2(4,4'-bpy)2(H2O)2.3H2O]n (bpy = bipyridine) (2), [Zn(PDCO)(bix)]n (bix = 1,4-bis(imidazol-1-ylmethyl)benzene) (3), [Zn(PDCO)(bbi).0.5H2O]n (bbi = 1,1'-(1,4-butanediyl)bis(imidazole)) (4), and [Cd(PDCO)(bix)(1.5).1.5H2O]n (5), have been synthesized under hydrothermal conditions and structurally characterized. Polymer 1 possesses a one-dimensional (1D) helical chainlike structure with 4(1) helices running along the c-axis with a pitch of 10.090 Angstroms. Polymer 2 has an infinite chiral two-dimensional (2D) brick-wall-like layer structure in the ac plane built from achiral components, while both 3 and 4 exhibit an infinite 2D herringbone architecture, respectively extended in the ac and ab plane. Polymer 5 features a most remarkable and unique three-dimensional (3D) porous framework with 2-fold interpenetration related by symmetry, which contains channels in the b and c directions, both distributed in a rectangular grid fashion. Compounds 1-5, with systematic variation in dimensionality from 1D to 2D to 3D, are the first examples of d(10) metal coordination polymers into which pyridinedicarboxylic acid N-oxide has been introduced. In addition, polymers 1, 4, and 5 display strong blue fluorescent emissions in the solid state. Polymer 3 exhibits a strong SHG response, estimated to be approximately 0.9 times that of urea.

Wen LL; Dang DB; Duan CY; Li YZ; Tian ZF; Meng QJ

2005-10-01

178

The internal structure of fault zones in basaltic sequences  

Science.gov (United States)

In contrary to most sedimentary rocks that need burial for consolidation, effusive basalts solidify quickly thus imposing a different mechanical behavior at the surface. Extensional stresses due to gravitational failure, caldera collapse or general tectonic forces generate prominent morphologies and large dilatant structures with impacts for hydraulic, mechanical and also bionomic aspects. In this study we present insights of field work on the Koa`e fault zone on Kilauea volcano/Hawai`i combined with the analysis of a scaled analogue model of normal faults in cohesive sequences. The Koa`e fault zone is a 12 km long normal fault zone connecting sections of the two rift zones. Unlike the predominantly mode-I cracks of the rift zones, the Koa`e faults show up to 20 m high sub-vertical fault scarps accompanied with footwall fissures. Open fractures, broken or buckled ramp structures and sub-vertical walls are the key elements in what is considered to be a volcanic growth fault system. Our analogue model visualizes the deformation of brittle flow units on top of a buried fault. The model uses dry hemihydrate powder with a tensional strength of 33 Pa, and a curved yield envelope. Depending on the rock prototype a scaling relationship of 1:5000-40000 is apparent. The faults initiate as sub-vertical mode-I fissuring at the surface propagating downward. Some of the open fissures on the footwall are deactivated; others evolve into faults producing the morphological scarps. A shallow antithetic fracture decouples a surface slap on the hanging wall producing the morphological ramps seen in the field. Its rotation is responsible for cavities and buckling. The internal structure of the shallow faults is open and filled partly with collapsing wall fragments that are progressively milled down at deeper levels. The model implies that normal faults in basalt are largely dilatant systems with a prominent mode-I component up to several meters magnitude. If the insights of the work are not only applicable to rift zones but also to normal faulting at Mid Oceanic Ridges, local hydrothermal systems could be focused to the open voids. Mineral precipitation as well as the formation of habitats within the faults is imaginable.

Holland, M.; Urai, J. L.; Martel, S.

2005-12-01

179

Homoleptic 1-D iron selenolate complexes-synthesis, structure, magnetic and thermal behaviour of (1)(?)[Fe(SeR)2] (R=Ph, Mes).  

UK PubMed Central (United Kingdom)

The first examples of polymeric homoleptic iron chalcogenolato complexes (1)(?)[Fe(SePh)(2)] and (1)(?)[Fe(SeMes)(2)] (Ph = phenyl = C(6)H(5), Mes = mesityl = C(6)H(2)-2,4,6-(CH(3))(3)) have been both prepared by reaction of [Fe(N(SiMe(3))(2))(2)] with two equivalents of HSeR (R = Ph, Mes) while (1)(?)[Fe(SePh)(2)] was found to be also easily accessible through reactions of either FeCl(2), Fe(OOCCH(3))(2) or FeCl(3) with PhSeSiMe(3) in THF. In the crystal, the two compounds form one-dimensional chains with bridging selenolate ligands comprising distinctly different Fe-Se-Fe bridging angles, namely 71.15-72.57° in (1)(?)[Fe(SePh)(2)] and 91.80° in (1)(?)[Fe(SeMes)(2)]. Magnetic measurements supported by DFT calculations reveal that this geometrical change has a pronounced influence on the antiferromagnetic exchange interactions of the unpaired electrons along the chains in the two different compounds with a calculated magnetic exchange coupling constant of J = -137 cm(-1) in (1)(?)[Fe(SePh)(2)] and J = -20 cm(-1) in (1)(?)[Fe(SeMes)(2)]. In addition we were able to show that the ring molecule [Fe(SePh)(2)](12) which is a structural isomer of (1)(?)[Fe(SePh)(2)] behaves magnetically similar to the latter one. Investigations by powder XRD reveal that the ring molecule is only a metastable intermediate which converts in THF completely to form (1)(?)[Fe(SePh)(2)]. Thermal gravimetric analysis of (1)(?)[Fe(SePh)(2)] under vacuum conditions shows that the compound is thermally labile and already starts to decompose above 30 °C in a two step process under cleavage of SePh(2) to finally form at 250 °C tetragonal PbO-type FeSe. The reaction of (1)(?)[Fe(SePh)(2)] with the Lewis base 1,10-phenanthroline yielded, depending on the conditions, the octahedral monomeric complexes [Fe(SePh)(2)(1,10-phen)(2)] and [Fe(1,10-phen)(3)][Fe(SePh)(4)].

Eichhöfer A; Buth G; Dolci F; Fink K; Mole RA; Wood PT

2011-07-01

180

Syntheses, structures, and IR spectroscopic characterization of new uranyl sulfate/selenate 1D-chain, 2D-sheet and 3D-framework  

International Nuclear Information System (INIS)

Three uranyl sulfates, (C6H20N4)[(UO2)2 . (SO4)4(H2O)2](H2O)6 (TETAUS), (C15H14N3)[(UO2) . (SO4)2](NO3)(H2O)2 (TPUS), and K2[(UO2)(SO4)2(H2O)] . H2O (KUS), and two uranyl selenates, K(H3O)[(UO2)2 . (SeO4)3(H2O)](H2O)6 (KUSe) and (H3O)2[(UO2)2(SeO4)3 . (H2O)] (USe), were synthesized by slow evaporation of aqueous solutions at room temperature. TETAUS crystallizes in space group P anti 1, a = 6.7186(5) A, b = 9.2625(7) A, c = 13.1078(9) A, ? = 72.337(2) , ? = 89.198(2) , ? = 70.037(1) , V = 726.89(9) A3, Z = 1. TPUS is triclinic, P anti 1, a = 6.9732(7) A, b = 13.569(1) A, c = 13.641(1) A, ? = 111.809(2) , ? = 102.386(2) , ? = 93.833(2) , V = 1150.0(2) A3, Z = 2. KUS is orthorhombic, Cmca, a = 12.171(2) A, b = 16.689(3) A, c = 10.997(2) A, V = 2233.8(6) A3, Z = 8. These uranyl sulfates are built from infinite one-dimensional uranyl sulfate chains with different topologies. KUSe is monoclinic, P21/n, a = 14.715(1) A, b = 10.1557(7) A, c = 15.833(1) A, ? = 114.415(1) , V = 2154.5(3) A3, Z = 4. Its structure is based on a two-dimensional uranyl selenate sheet. USe crystallizes in space group P21/c, a = 10.6124(2) A, b = 14.7717(3) A, c = 13.7139(3) A, ? = 96.989(1) , V = 2133.86(8) A3, Z = 4, with a complex three-dimensional uranyl selenate framework containing channels extending in three directions. (orig.)

2010-01-01

 
 
 
 
181

Sequences  

UK PubMed Central (United Kingdom)

The present invention discloses sequence information relating to pyranosone dehydratase. The invention further relates to the use of pyranosone dehydratase in the conversion of AF to APP and microthecin and the conversion of glucosone to cortalcerone.

INGE WEIERGANG; SHUKUN YU

182

Resolution-optimized NMR measurement of {sup 1}D{sub CH}, {sup 1}D{sub CC} and {sup 2}D{sub CH} residual dipolar couplings in nucleic acid bases  

Energy Technology Data Exchange (ETDEWEB)

New methods are described for accurate measurement of multiple residual dipolar couplings in nucleic acid bases. The methods use TROSY-type pulse sequences for optimizing resolution and sensitivity, and rely on the E.COSY principle to measure the relatively small two-bond {sup 2}D{sub CH} couplings at high precision. Measurements are demonstrated for a 24-nt stem-loop RNA sequence, uniformly enriched in {sup 13}C, and aligned in Pf1. The recently described pseudo-3D method is used to provide homonuclear {sup 1}H-{sup 1}H decoupling, which minimizes cross-correlation effects and optimizes resolution. Up to seven {sup 1}H-{sup 13}C and {sup 13}C-{sup 13}C couplings are measured for pyrimidines (U and C), including {sup 1}D{sub C5H5}, {sup 1}D{sub C6H6}, {sup 2}D{sub C5H6}, {sup 2}D{sub C6H5}, {sup 1}D{sub C5C4}, {sup 1}D{sub C5C6}, and {sup 2}D{sub C4H5}. For adenine, four base couplings ({sup 1}D{sub C2H2}, {sup 1}D{sub C8H8}, {sup 1}D{sub C4C5}, and {sup 1}D{sub C5C6}) are readily measured whereas for guanine only three couplings are accessible at high relative accuracy ({sup 1}D{sub C8H8}, {sup 1}D{sub C4C5}, and {sup 1}D{sub C5C6}). Only three dipolar couplings are linearly independent in planar structures such as nucleic acid bases, permitting cross validation of the data and evaluation of their accuracies. For the vast majority of dipolar couplings, the error is found to be less than {+-}3% of their possible range, indicating that the measurement accuracy is not limiting when using these couplings as restraints in structure calculations. Reported isotropic values of the one- and two-bond J couplings cluster very tightly for each type of nucleotide.

Boisbouvier, Jerome; Bryce, David L.; O' Neil-Cabello, Erin [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (United States); Nikonowicz, Edward P. [Rice University, Department of Biochemistry and Cell Biology (United States); Bax, Ad [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (United States)], E-mail: bax@nih.gov

2004-11-15

183

SuGra on G2 Structure Backgrounds that Asymptote to AdS4 and Holographic Duals of Confining 2+1d Gauge Theories with N=1 SUSY  

CERN Multimedia

In this work the solution generated by performing a U-duality on a deformation of the Maldacena-Nastase solution is studied. This is a solution of type-IIA with a metric that is asymptotically AdS4 and supports a G2 structure. It is believed to be dual to a 2+1d, N=1 gauge theory similar to the baryonic branch of Klebanov-Strassler with an additional intermediate scale. An improved radial coordinate is used allowing the derivation of UV series solutions to the BPS equation that persist to all orders. A study of the properties of the dual field theory is performed which includes an operator analysis, Wilson loops and a proposal for gauge couplings. The gauge theory dual appears to be a confining Chern-Simons quiver with gauge couplings that become constant at high energies.

Macpherson, Niall T

2013-01-01

184

SuGra on G 2 structure backgrounds that asymptote to AdS4 and holographic duals of confining 2 + 1 d gauge theories with mathcal{N}=1 SUSY  

Science.gov (United States)

In this work the solution generated by performing a U-duality on a deformation of the Maldacena-Nastase solution is studied. This is a solution of type-IIA with a metric that is asymptotically AdS4 and supports a G 2 structure. It is believed to be dual to a 2+1 d, {N}=1 gaugetheorysimilartothebaryonicbranchofKlebanov-Strasslerwithanadditional intermediate scale. An improved radial coordinate is used allowing the derivation of UV series solutions to the BPS equation that persist to all orders. A study of the properties of the dual field theory is performed which includes an operator analysis, Wilson loops and a proposal for gauge couplings. The gauge theory dual appears to be a confining Chern-Simons quiver with gauge couplings that become constant at high energies.

Macpherson, Niall T.

2013-04-01

185

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis  

Directory of Open Access Journals (Sweden)

Full Text Available RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available.

Muhammad Afzal; Ahmad Ali Shahid; Abida Shehzadi; Shahid Nadeem; Tayyab Husnain

2012-01-01

186

4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database), we are faced with the problem to handle sequences and their associated secondary structures synchronously. Results 4SALE fills this gap. The application allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis. Conclusion 4SALE, which provides an user-friendly and intuitive interface, is a comprehensive toolbox for RNA analysis based on sequence and secondary structure information. The program connects sequence and structure databases like the ITS2 Database to phylogeny programs as for example the CBCAnalyzer. 4SALE is written in JAVA and therefore platform independent. The software is freely available and distributed from the website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de

Seibel Philipp N; Müller Tobias; Dandekar Thomas; Schultz Jörg; Wolf Matthias

2006-01-01

187

Primary and secondary structure of hamster vimentin predicted from the nucleotide sequence.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The nucleotide sequence of two recombinant plasmids containing hamster vimentin cDNA was determined. The sequence comprises 1,640 base pairs and reveals virtually the total primary structure of vimentin and a large part of the 3' noncoding region. Secondary structure prediction methods allow the cha...

Quax-Jeuken, Y E; Quax, W J; Bloemendal, H

188

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.  

UK PubMed Central (United Kingdom)

With the rapid increase in the size of the genome sequence database, computational analysis of RNA will become increasingly important in revealing structure-function relationships and potential drug targets. RNA secondary structure prediction for a single sequence is 73 % accurate on average for a large database of known secondary structures. This level of accuracy provides a good starting point for determining a secondary structure either by comparative sequence analysis or by the interpretation of experimental studies. Dynalign is a new computer algorithm that improves the accuracy of structure prediction by combining free energy minimization and comparative sequence analysis to find a low free energy structure common to two sequences without requiring any sequence identity. It uses a dynamic programming construct suggested by Sankoff. Dynalign, however, restricts the maximum distance, M, allowed between aligned nucleotides in the two sequences. This makes the calculation tractable because the complexity is simplified to O(M(3)N(3)), where N is the length of the shorter sequence. The accuracy of Dynalign was tested with sets of 13 tRNAs, seven 5 S rRNAs, and two R2 3' UTR sequences. On average, Dynalign predicted 86.1 % of known base-pairs in the tRNAs, as compared to 59.7 % for free energy minimization alone. For the 5 S rRNAs, the average accuracy improves from 47.8 % to 86.4 %. The secondary structure of the R2 3' UTR from Drosophila takahashii is poorly predicted by standard free energy minimization. With Dynalign, however, the structure predicted in tandem with the sequence from Drosophila melanogaster nearly matches the structure determined by comparative sequence analysis.

Mathews DH; Turner DH

2002-03-01

189

ZnO1-x nanorod arrays/ZnO thin film bilayer structure: from homojunction diode and high-performance memristor to complementary 1D1R application.  

UK PubMed Central (United Kingdom)

We present a ZnO(1-x) nanorod array (NR)/ZnO thin film (TF) bilayer structure synthesized at a low temperature, exhibiting a uniquely rectifying characteristic as a homojunction diode and a resistive switching behavior as memory at different biases. The homojunction diode is due to asymmetric Schottky barriers at interfaces of the Pt/ZnO NRs and the ZnO TF/Pt, respectively. The ZnO(1-x) NRs/ZnO TF bilayer structure also shows an excellent resistive switching behavior, including a reduced operation power and enhanced performances resulting from supplements of confined oxygen vacancies by the ZnO(1-x) NRs for rupture and recovery of conducting filaments inside the ZnO TF layer. A hydrophobic behavior with a contact angle of ~125° can be found on the ZnO(1-x) NRs/ZnO TF bilayer structure, demonstrating a self-cleaning effect. Finally, a successful demonstration of complementary 1D1R configurations can be achieved by simply connecting two identical devices back to back in series, realizing the possibility of a low-temperature all-ZnO-based memory system.

Huang CH; Huang JS; Lin SM; Chang WY; He JH; Chueh YL

2012-09-01

190

ZnO1-x nanorod arrays/ZnO thin film bilayer structure: from homojunction diode and high-performance memristor to complementary 1D1R application.  

Science.gov (United States)

We present a ZnO(1-x) nanorod array (NR)/ZnO thin film (TF) bilayer structure synthesized at a low temperature, exhibiting a uniquely rectifying characteristic as a homojunction diode and a resistive switching behavior as memory at different biases. The homojunction diode is due to asymmetric Schottky barriers at interfaces of the Pt/ZnO NRs and the ZnO TF/Pt, respectively. The ZnO(1-x) NRs/ZnO TF bilayer structure also shows an excellent resistive switching behavior, including a reduced operation power and enhanced performances resulting from supplements of confined oxygen vacancies by the ZnO(1-x) NRs for rupture and recovery of conducting filaments inside the ZnO TF layer. A hydrophobic behavior with a contact angle of ~125° can be found on the ZnO(1-x) NRs/ZnO TF bilayer structure, demonstrating a self-cleaning effect. Finally, a successful demonstration of complementary 1D1R configurations can be achieved by simply connecting two identical devices back to back in series, realizing the possibility of a low-temperature all-ZnO-based memory system. PMID:22900519

Huang, Chi-Hsin; Huang, Jian-Shiou; Lin, Shih-Ming; Chang, Wen-Yuan; He, Jr-Hau; Chueh, Yu-Lun

2012-09-06

191

1D Signal Phase Unwrapper  

International Nuclear Information System (INIS)

Signal phase values are crucial in seismic data interpretation to enhance the analysis of amplitudes, bright spots, dim spots etc. Phase values can be zeroed in a section to enhance signal comparison which can be related to velocities and other petro-physical properties. Homomorphic signal processing and deconvolution both require exact phase value estimates. Consequently, in-depth investigations are necessary to solve problems of phase estimation in various wave propagation situations. Meanwhile, phase values are often measured modulo-2 called principal values and the amount of phase estimation in various wave propagation situations. Meanwhile, values are often measured modulo-2 called principal values and the amount of phase information is independent of any integer multiple of 2 added to the principal value phase. However, to be useful for linear processing, this principal value phase has to be unwrapped. This will result in a continuous function, the 2 discontinuities being eliminated, or at least reduced. Operations like deconvolution and homomorphic signal processing require unwrapped phase values. Phase unwrapping is applied to pre-stack data for the computation of PVA phase variation with angle of incidence attribute used to improve processing and interpretation.Conventional 1D phase unwrapping algorithms integrate the wrapped phase difference between two contiguous points. This was later improved to use adaptive integration of phase differences. Alternatively, phase difference ambiguity due to sparse sampling can be overcome by taking samples at progressively closer intervals. These methods are often inadequate due to problems of aliasing caused by rapid phase value variations. We develop a 1D phase unwrapping technique using the amplitude of a complex trace and discrete Fourier transforms. This technique is simple, very reliable and less sensitive to aliasing. It exploits the periodicity of Fourier transform to unwind wrapped phase values. We demonstrate this technique using synthetic and real data.

2002-01-01

192

Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl- 8-(1'-D-ribityl) lumazine, and its analogues, riboflavin and flavin mononucleotide, at high resolution.  

UK PubMed Central (United Kingdom)

Lumazine protein (LumP) is a fluorescent accessory protein having 6,7-dimethyl-8-(1'-d-ribityl) lumazine (DMRL) as its authentic chromophore. It modulates the emission of bacterial luciferase to shorter wavelengths with increasing luminous strength. To obtain structural information on the native structure as well as the interaction with bacterial luciferase, we have determined the crystal structures of LumP from Photobacterium kishitanii in complexes with DMRL and its analogues, riboflavin (RBF) and flavin mononucleotide (FMN), at resolutions of 2.00, 1.42, and 2.00 A. LumP consists of two beta barrels that have nearly identical folds, the N-terminal and C-terminal barrels. The structures of LumP in complex with all of the chromophores studied are all essentially identical, except around the chromophores. In all of the structures, the chromophore is tethered to the narrow cavity via many hydrogen bonds in the N-terminal domain. These are absent in the C-terminal domain. Hydrogen bonding in LumP-FMN is decreased in comparison with that in LumP-RBF because the phosphate moiety of FMN protrudes out of the narrow cavity. In LumP-DMRL, the side chain of Gln65 is close to the ring system, and a new water molecule that stabilizes the ligand is observed near Ser48. Therefore, DMRL packs more tightly in the ligand-binding site than RBF or FMN. A docking simulation of bacterial luciferase and LumP suggests that the chromophore is located close enough for direct energy transfer to occur. Moreover, the surface potentials around the ligand-binding sites of LumP and bacterial luciferase exhibit complementary charge distributions, which would have a significant effect on the interaction between LumP and luciferase.

Sato Y; Shimizu S; Ohtaki A; Noguchi K; Miyatake H; Dohmae N; Sasaki S; Odaka M; Yohda M

2010-01-01

193

NKT TCR recognition of CD1d-?-C-galactosylceramide.  

Science.gov (United States)

NKT cells respond to a variety of CD1d-restricted glycolipid Ags that are structurally related to the prototypic Ag ?-galactosylceramide (?-GalCer). A modified analog of ?-GalCer with a carbon-based glycosidic linkage (?-C-GalCer) has generated great interest because of its apparent ability to promote prolonged, Th1-biased immune responses. In this study, we report the activation of spleen NKT cells to ?-C-GalCer, and related C-glycoside ligands, is weaker than that of ?-GalCer. Furthermore, the V?8.2 and V?7 NKT TCR affinity for CD1d-?-C-GalCer, and some related analogs, is ?10-fold lower than that for the NKT TCR-CD1d-?-GalCer interaction. Nevertheless, the crystal structure of the V?8.2 NKT TCR-CD1d-?-C-GalCer complex is similar to that of the corresponding NKT TCR-CD1d-?-GalCer complex, although subtle differences at the interface provide a basis for understanding the lower affinity of the NKT TCR-CD1d-?-C-GalCer interaction. Our findings support the concept that for CD1d-restricted NKT cells, altered glycolipid ligands can promote markedly different responses while adopting similar TCR-docking topologies. PMID:21964029

Patel, Onisha; Cameron, Garth; Pellicci, Daniel G; Liu, Zheng; Byun, Hoe-Sup; Beddoe, Travis; McCluskey, James; Franck, Richard W; Castaño, A Raúl; Harrak, Youssef; Llebaria, Amadeu; Bittman, Robert; Porcelli, Steven A; Godfrey, Dale I; Rossjohn, Jamie

2011-09-30

194

NKT TCR recognition of CD1d-?-C-galactosylceramide.  

UK PubMed Central (United Kingdom)

NKT cells respond to a variety of CD1d-restricted glycolipid Ags that are structurally related to the prototypic Ag ?-galactosylceramide (?-GalCer). A modified analog of ?-GalCer with a carbon-based glycosidic linkage (?-C-GalCer) has generated great interest because of its apparent ability to promote prolonged, Th1-biased immune responses. In this study, we report the activation of spleen NKT cells to ?-C-GalCer, and related C-glycoside ligands, is weaker than that of ?-GalCer. Furthermore, the V?8.2 and V?7 NKT TCR affinity for CD1d-?-C-GalCer, and some related analogs, is ?10-fold lower than that for the NKT TCR-CD1d-?-GalCer interaction. Nevertheless, the crystal structure of the V?8.2 NKT TCR-CD1d-?-C-GalCer complex is similar to that of the corresponding NKT TCR-CD1d-?-GalCer complex, although subtle differences at the interface provide a basis for understanding the lower affinity of the NKT TCR-CD1d-?-C-GalCer interaction. Our findings support the concept that for CD1d-restricted NKT cells, altered glycolipid ligands can promote markedly different responses while adopting similar TCR-docking topologies.

Patel O; Cameron G; Pellicci DG; Liu Z; Byun HS; Beddoe T; McCluskey J; Franck RW; Castaño AR; Harrak Y; Llebaria A; Bittman R; Porcelli SA; Godfrey DI; Rossjohn J

2011-11-01

195

Structural Electronic and Magnetic Properties of Quasi-1D Quantum Magnets [Ni(HF2)(pyz)2]X (pyz = pyrazine; X = PF6- SbF6-) Exhibiting Ni-FHF-Ni and Ni-pyz-Ni Spin Interactions  

Energy Technology Data Exchange (ETDEWEB)

[Ni(HF{sub 2})(pyz){sub 2}]X {l_brace}pyz = pyrazine; X = PF{sub 6}{sup -} (1), SbF{sub 6}{sup -} (2){r_brace} were structurally characterized by synchrotron X-ray powder diffraction and found to possess axially compressed NiN{sub 4}F{sub 2} octahedra. At 298 K, 1 is monoclinic (C2/c) with unit cell parameters, a = 9.9481(3), b = 9.9421(3), c = 12.5953(4) {angstrom}, and {beta} = 81.610(3){sup o} while 2 is tetragonal (P4/nmm) with a = b = 9.9359(3) and c = 6.4471(2) {angstrom} and is isomorphic with the Cu-analogue. Infinite one-dimensional (1D) Ni-FHF-Ni chains propagate along the c-axis which are linked via {mu}-pyz bridges in the ab-plane to afford three-dimensional polymeric frameworks with PF{sub 6}{sup -} and SbF{sub 6}{sup -} counterions occupying the interior sites. A major difference between 1 and 2 is that the Ni-F-H bonds are bent (157{sup o}) in 1 but are linear in 2. Ligand field calculations (LFT) based on an angular overlap model (AOM), with comparison to the electronic absorption spectra, indicate greater {pi}-donation of the HF{sub 2}{sup -} ligand in 1 owing to the bent Ni-F-H bonds. Magnetic susceptibility data for 1 and 2 exhibit broad maxima at 7.4 and 15 K, respectively, and {lambda}-like peaks in dxT/dT at 6.2 and 12.2 K that are ascribed to transitions to long-range antiferromagnetic order (TN). Muon-spin relaxation and specific heat studies confirm these TN's. A comparative analysis of x vs T to various 1D Heisenberg/Ising models suggests moderate antiferromagnetic interactions, with the primary interaction strength determined to be 3.05/3.42 K (1) and 5.65/6.37 K (2). However, high critical fields of 19 and 37.4 T obtained from low temperature pulsed-field magnetization data indicate that a single exchange constant (J1D) alone is insufficient to explain the data and that residual terms in the spin Hamiltonian, which could include interchain magnetic couplings (J), as mediated by Ni-pyz-Ni, and single-ion anisotropy (D), must be considered. While it is difficult to draw absolute conclusions regarding the magnitude (and sign) of J and D based solely on powder data, further support offered by related Ni(II)-pyz compounds and our LFT and density-functional theory (DFT) results lead us to a consistent quasi-1D magnetic description for 1 and 2.

J Manson; S Lapidus; P Stephens; P Peterson; K Carreiro; H Southerland; T Lancaster; S Blundell; A Steele; et al.

2011-12-31

196

Structure is three to ten times more conserved than sequence--a study of structural response in protein cores.  

UK PubMed Central (United Kingdom)

Protein structures change during evolution in response to mutations. Here, we analyze the mapping between sequence and structure in a set of structurally aligned protein domains. To avoid artifacts, we restricted our attention only to the core components of these structures. We found that on average, using different measures of structural change, protein cores evolve linearly with evolutionary distance (amino acid substitutions per site). This is true irrespective of which measure of structural change we used, whether RMSD or discrete structural descriptors for secondary structure, accessibility, or contacts. This linear response allows us to quantify the claim that structure is more conserved than sequence. Using structural alphabets of similar cardinality to the sequence alphabet, structural cores evolve three to ten times slower than sequences. Although we observed an average linear response, we found a wide variance. Different domain families varied fivefold in structural response to evolution. An attempt to categorically analyze this variance among subgroups by structural and functional category revealed only one statistically significant trend. This trend can be explained by the fact that beta-sheets change faster than alpha-helices, most likely due to that they are shorter and that change occurs at the ends of the secondary structure elements.

Illergård K; Ardell DH; Elofsson A

2009-11-01

197

Identifying time-clustering structures in lightning sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Two years of lightning data, measured during 2002 and 2003 in an area of southern Italy, have been analyzed in order to reveal scaling behaviour in their time dynamics. We used the Allan Factor method to evidence the presence of time-clustering in the lightning data. We found that i) the sequence of...

Telesca, L; Bernardi, M; Rovelli, C

198

Analysis of the Rotational Structure in the High-Resolution Infrared Spectra of cis,cis- and trans,trans-1,4-DIFLUOROBUTADIENE-1-d_{1} and trans,trans-1,4-DIFLUOROBUTADIENE-1,4-d_{2}  

Science.gov (United States)

Samples of cis,cis- and trans,trans-1,4-difluorobutadiene-1-d_{1} (DFBD) and trans,trans-DFBD-1,4-d_{2} have been synthesized and investigated with high-resolution (0.0015 cm^{-1}) infrared spectroscopy. For the first two species the rotational structure in more than one band has been analyzed. For the 1,4-d_{2} species the spectrum of only one C-type band was available in an isotopic mixture. Ground state rotational constants are reported for all three molecules. It is proposed that quartic centrifugal distortion constants computed with a B3LYP/cc-pVTZ model can be used to assess the quality of observed rotational constants. The favorable comparison of predicted and observed ground state rotational constants for all four ^{13}C species of cis,trans-DFBD, which is MW active, demonstrates that the ground state rotational constants for the ^{13}C species of the cis,cis and trans,trans isomers can be successfully predicted with high accuracy. Rotational constants for a full set of isotopologues will be used to determine accurate semiexperimental equilibrium structures of the cis,cis and trans,trans species of DFBD. N. C. Craig, C. M. Oertel, D. C. Oertel, M. J. Tubergen, R. J. Lavrich, A. M Chaka J. Phys. Chem. A 106, 4230-4235 (2002).

Craig, Norman C.; Chen, Yihui; Lu, Yuhua; Neese, Christopher F.; Nemchick, Deacon J.; Blake, Thomas A.

2013-06-01

199

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA. Results Here we introduce an all-against-all sequence- and three-dimensional (3D) structure-based comparison of a representative set of RNA structures, which have allowed us to quantitatively confirm that: (i) there is a measurable relationship between sequence and structure conservation that weakens for alignments resulting in below 60% sequence identity, (ii) evolution tends to conserve more RNA structure than sequence, and (iii) there is a twilight zone for RNA homology detection. Discussion The computational analysis here presented quantitatively describes the relationship between sequence and structure for RNA molecules and defines a twilight zone region for detecting RNA homology. Our work could represent the theoretical basis and limitations for future developments in comparative RNA 3D structure prediction.

Capriotti Emidio; Marti-Renom Marc A

2010-01-01

200

Structure and Evolution of Pre-Main Sequence Stars  

CERN Document Server

Low-mass pre-main sequence (PMS) stars are strong and variable X-ray emitters, as has been well established by EINSTEIN and ROSAT observatories. It was originally believed that this emission was of thermal nature and primarily originated from coronal activity (magnetically confined loops, in analogy with Solar activity) on contracting young stars. Broadband spectral analysis showed that the emission was not isothermal and that elemental abundances were non-Solar. The resolving power of the Chandra and XMM X-ray gratings spectrometers have provided the first, tantalizing details concerning the physical conditions such as temperatures, densities, and abundances that characterize the X-ray emitting regions of young star. These existing high resolution spectrometers, however, simply do not have the effective area to measure diagnostic lines for a large number of PMS stars over required to answer global questions such as: how does magnetic activity in PMS stars differ from that of main sequence stars, how do they ...

Schulz, Norbert S; Bautz, Mark W; Canizares, Claude C; Davis, John; Dewey, Dan; Huenemoerder, David P; Heilmann, Ralf; Houck, John; Marshall, Herman L; Nowak, Mike; Schattenburg, Mark; Audard, Marc; Drake, Jeremy; Gagne, Marc; Kastner, Joel; Kallman, Tim; Lautenegger, Maurice; Lee, Julia; Miller, Jon; Montmerle, Thierry; Mukai, Koji; Osten, Rachel; Parerels, Frits; Pollock, Andy; Preibisch, Thomas; Raymond, John; Reale, Fabio; Smith, Randall; Testa, Paola; Weintraub, David

2009-01-01

 
 
 
 
201

Sequence and secondary structure variation in the Gyrodactylus (Platyhelminthes: Monogenea) ribosomal RNA gene array.  

Science.gov (United States)

Nucleotide sequences were determined for the rRNA internal transcribed spacers 1 and 2 (ITS1 and 2) and the 5' terminus of the large subunit rRNA in selected Gyrodactylus species. Examination of primary sequence variation and secondary structure models in ITS2 and variable region V4 of the small subunit rRNA revealed that structure was largely conserved despite significant variation in sequence. ITS1 sequences were highly variable, and models of structure were unreliable but, despite this, show some resemblance to structures predicted in Digenea. ITS2 models demonstrated binding of the 3' end of 5.8S rRNA to the 5' end of the large subunit rRNA and enabled the termini of these genes to be defined with greater confidence than previously. The structure model shown here may prove useful in future phylogenetic analyses. PMID:10864256

Cunningham, C O; Aliesky, H; Collins, C M

2000-06-01

202

Sequence and secondary structure variation in the Gyrodactylus (Platyhelminthes: Monogenea) ribosomal RNA gene array.  

UK PubMed Central (United Kingdom)

Nucleotide sequences were determined for the rRNA internal transcribed spacers 1 and 2 (ITS1 and 2) and the 5' terminus of the large subunit rRNA in selected Gyrodactylus species. Examination of primary sequence variation and secondary structure models in ITS2 and variable region V4 of the small subunit rRNA revealed that structure was largely conserved despite significant variation in sequence. ITS1 sequences were highly variable, and models of structure were unreliable but, despite this, show some resemblance to structures predicted in Digenea. ITS2 models demonstrated binding of the 3' end of 5.8S rRNA to the 5' end of the large subunit rRNA and enabled the termini of these genes to be defined with greater confidence than previously. The structure model shown here may prove useful in future phylogenetic analyses.

Cunningham CO; Aliesky H; Collins CM

2000-06-01

203

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.  

Science.gov (United States)

BACKGROUND: The search for distant homologs has become an import issue in genome annotation. A particular difficulty is posed by divergent homologs that have lost recognizable sequence similarity. This same problem also arises in the recognition of novel members of large classes of RNAs such as snoRNAsor microRNAs that consist of families unrelated by common descent. Current homology search tools for structured RNAs are either based entirely on sequence similarity (such as blast or hmmer) or combine sequence and secondary structure. The most prominent example of the latter class of tools is Infernal. Alternatives are descriptor-based methods. In most practical applications published to-date, however, the information contained in covariance models or manually prescribed search patterns is dominated by sequence information. Here we ask two related questions: (1) Is secondary structure alone informative for homology search and the detection of novel members of RNA classes? (2) To what extent is the thermodynamic propensity of the target sequence to fold into the correct secondary structure helpful for this task? RESULTS: Sequence-structure alignment can be used as an alternative search strategy. In this scenario, the query consists of a base pairing probability matrix, which can be derived either from a single sequence or from a multiple alignment representing a set of known representatives. Sequence information can be optionally added to the query. The target sequence is pre-processed to obtain local base pairing probabilities. As a search engine we devised a semi-global scanning variant of LocARNA's algorithm for sequence-structure alignment. The LocARNAscan tool is optimized for speed and low memory consumption. In benchmarking experiments on artificial data we observe that the inclusion of thermodynamic stability is helpful, albeit only in a regime of extremely low sequence information in the query. We observe, furthermore, that the sensitivity is bounded in particular by the limited accuracy of the predicted local structures of the target sequence. CONCLUSIONS: Although we demonstrate that a purely structure-based homology search is feasible in principle, it is unlikely to outperform tools such as Infernal in most application scenarios, where a substantial amount of sequence information is typically available. The LocARNAscan approach will profit, however, from high throughput methods to determine RNA secondary structure. In transcriptomewide applications, such methods will provide accurate structure annotations on the target side. AVAILABILITY: Source code of the free software LocARNAscan 1.0 and supplementary data are available at http://www.bioinf.uni-leipzig.de/Software/LocARNAscan. PMID:23601347

Will, Sebastian; Siebauer, Michael F; Heyne, Steffen; Engelhardt, Jan; Stadler, Peter F; Reiche, Kristin; Backofen, Rolf

2013-04-20

204

Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima  

DEFF Research Database (Denmark)

The recently published complete DNA sequence of the bacterium Thermotoga maritima provides evidence, based on protein sequence conservation, for lateral gene transfer between Archaea and Bacteria. We introduce a new method of periodicity analysis of DNA sequences, based on structural parameters, which brings independent evidence for the lateral gene transfer in the genome of T.maritima, The structural analysis relates the Archaea-like DNA sequences to the genome of Pyrococcus horikoshii. Analysis of 24 complete genomic DNA sequences shows different periodicity patterns for organisms of different origin, The typical genomic periodicity for Bacteria is 11 bp whilst it is 10 bp for Archaea, Eukaryotes have more complex spectra but the dominant period in the yeast Saccharomyces cerevisiae is 10.2 bp. These periodicities are most likely reflective of differences in chromatin structure.

Worning, Peder; Jensen, Lars Juhl

2000-01-01

205

Unraveling the sequence and structure of the protein osteocalcin from a 42 ka fossil horse  

Science.gov (United States)

We report the first complete amino acid sequence and evidence of secondary structure for osteocalcin from a temperate fossil. The osteocalcin derives from a 42 ka equid bone excavated from Juniper Cave, Wyoming. Results were determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-MS) and Edman sequencing with independent confirmation of the sequence in two laboratories. The ancient sequence was compared to that of three modern taxa: horse (Equus caballus), zebra (Equus grevyi), and donkey (Equus asinus). Although there was no difference in sequence among modern taxa, MALDI-MS and Edman sequencing show that residues 48 and 49 of our modern horse are Thr, Ala rather than Pro, Val as previously reported (Carstanjen B., Wattiez, R., Armory, H., Lepage, O.M., Remy, B., 2002. Isolation and characterization of equine osteocalcin. Ann. Med. Vet.146(1), 31 38). MALDI-MS and Edman sequencing data indicate that the osteocalcin sequence of the 42 ka fossil is similar to that of modern horse. Previously inaccessible structural attributes for ancient osteocalcin were observed. Glu39 rather than Gln39 is consistent with deamidation, a process known to occur during fossilization and aging. Two post-translational modifications were documented: Hyp9 and a disulfide bridge. The latter suggests at least partial retention of secondary structure. As has been done for ancient DNA research, we recommend standards for preparation and criteria for authenticating results of ancient protein sequencing.

Ostrom, Peggy H.; Gandhi, Hasand; Strahler, John R.; Walker, Angela K.; Andrews, Philip C.; Leykam, Joseph; Stafford, Thomas W.; Kelly, Robert L.; Walker, Danny N.; Buckley, Mike; Humpula, James

2006-04-01

206

Dissect: detection and characterization of novel structural alterations in transcribed sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Motivation: Computational identification of genomic structural variants via high-throughput sequencing is an important problem for which a number of highly sophisticated solutions have been recently developed. With the advent of high-throughput transcriptome sequencing (RNA-Seq), the problem of iden...

Yorukoglu, Deniz; Hach, Faraz; Swanson, Lucas; Collins, Colin C.; Birol, Inanc; Sahinalp, S. Cenk

207

PDBpaint, a visualization webservice to tag protein structures with sequence annotations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

SUMMARY: Protein features are often displayed along the linear sequence of amino acids that make up that protein, but in reality these features occupy a position in the folded protein's three-dimensional space. Mapping sequence features to known or predicted protein structures is useful when trying ...

Fournier, D.; Andrade-Navarro, M.A.

208

Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Wurst is a protein threading program with an emphasis on high quality sequence to structure alignments (http://www.zbh.uni-hamburg.de/wurst). Submitted sequences are aligned to each of about 3000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticat...

Torda, Andrew E.; Procter, James B.; Huber, Thomas

209

The sexual inducer of Volvox carteri. Primary structure deduced from cDNA sequence.  

UK PubMed Central (United Kingdom)

The primary structure of the sexual inducer of Volvox carteri f. nagariensis has been deduced by cloning and sequence analysis of cDNA. The sexual inducer contains 208 amino acids including a signal sequence. A total of six potential N-glycosylation sites are found within the polypeptide chain. At the genomic level, the sexual inducer protein is encoded in five exons.

Mages HW; Tschochner H; Sumper M

1988-07-01

210

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns  

Science.gov (United States)

Background It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enough for searching large sequence databases because of the high computational costs of the underlying sequence-structure alignment problem. Results We present new fast index-based and online algorithms for approximate matching of RNA sequence-structure patterns supporting a full set of edit operations on single bases and base pairs. Our methods efficiently compute semi-global alignments of structural RNA patterns and substrings of the target sequence whose costs satisfy a user-defined sequence-structure edit distance threshold. For this purpose, we introduce a new computing scheme to optimally reuse the entries of the required dynamic programming matrices for all substrings and combine it with a technique for avoiding the alignment computation of non-matching substrings. Our new index-based methods exploit suffix arrays preprocessed from the target database and achieve running times that are sublinear in the size of the searched sequences. To support the description of RNA molecules that fold into complex secondary structures with multiple ordered sequence-structure patterns, we use fast algorithms for the local or global chaining of approximate sequence-structure pattern matches. The chaining step removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our improved online algorithm is faster than the best previous method by up to factor 45. Our best new index-based algorithm achieves a speedup of factor 560. Conclusions The presented methods achieve considerable speedups compared to the best previous method. This, together with the expected sublinear running time of the presented index-based algorithms, allows for the first time approximate matching of RNA sequence-structure patterns in large sequence databases. Beyond the algorithmic contributions, we provide with RaligNAtor a robust and well documented open-source software package implementing the algorithms presented in this manuscript. The RaligNAtor software is available at http://www.zbh.uni-hamburg.de/ralignator.

2013-01-01

211

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns.  

UK PubMed Central (United Kingdom)

BACKGROUND: It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enough for searching large sequence databases because of the high computational costs of the underlying sequence-structure alignment problem. RESULTS: We present new fast index-based and online algorithms for approximate matching of RNA sequence-structure patterns supporting a full set of edit operations on single bases and base pairs. Our methods efficiently compute semi-global alignments of structural RNA patterns and substrings of the target sequence whose costs satisfy a user-defined sequence-structure edit distance threshold. For this purpose, we introduce a new computing scheme to optimally reuse the entries of the required dynamic programming matrices for all substrings and combine it with a technique for avoiding the alignment computation of non-matching substrings. Our new index-based methods exploit suffix arrays preprocessed from the target database and achieve running times that are sublinear in the size of the searched sequences. To support the description of RNA molecules that fold into complex secondary structures with multiple ordered sequence-structure patterns, we use fast algorithms for the local or global chaining of approximate sequence-structure pattern matches. The chaining step removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our improved online algorithm is faster than the best previous method by up to factor 45. Our best new index-based algorithm achieves a speedup of factor 560. CONCLUSIONS: The presented methods achieve considerable speedups compared to the best previous method. This, together with the expected sublinear running time of the presented index-based algorithms, allows for the first time approximate matching of RNA sequence-structure patterns in large sequence databases. Beyond the algorithmic contributions, we provide with RaligNAtor a robust and well documented open-source software package implementing the algorithms presented in this manuscript. The RaligNAtor software is available at http://www.zbh.uni-hamburg.de/ralignator.

Meyer F; Kurtz S; Beckstette M

2013-01-01

212

Balloon Rockets in 1D  

Science.gov (United States)

In this structured inquiry activity students will work in groups/ teams to build a balloon rocket of their own design. The rocket will race in one dimension and require that they apply their knowledge of position, time, and velocity.

213

3-D simulation of nanopore structure for DNA sequencing.  

Science.gov (United States)

In this paper, we propose a method for simulating nanopore structure by using conventional 3-D simulation tool to mimic the I-V behavior of the nanopore structure. In the simulation, we use lightly doped silicon for ionic solution where some parameters like electron affinity and dielectric constant are fitted to consider the ionic solution. By using this method, we can simulate the I-V behavior of nanopore structure depending on the location and the size of the sphere shaped silicon oxide which is considered to be an indicator of a DNA base. In addition, we simulate an Ionic Field Effect Transistor (IFET) which has basically the nanopore structure, and show that the simulated curves follow sufficiently the I-V behavior of the measurement data. Therefore, we think it is reasonable to apply parameter modeling mentioned above to simulate nanopore structure. The key idea is to modify electron affinity of silicon which is used to mimic the KCl solution to avoid band bending and depletion inside the nanopore. We could efficiently utilize conventional 3-D simulation tool to simulate the I-V behavior of nanopore structures. PMID:22966538

Park, Jun-Mo; Pak, Y Eugene; Chun, Honggu; Lee, Jong-Ho

2012-07-01

214

3-D simulation of nanopore structure for DNA sequencing.  

UK PubMed Central (United Kingdom)

In this paper, we propose a method for simulating nanopore structure by using conventional 3-D simulation tool to mimic the I-V behavior of the nanopore structure. In the simulation, we use lightly doped silicon for ionic solution where some parameters like electron affinity and dielectric constant are fitted to consider the ionic solution. By using this method, we can simulate the I-V behavior of nanopore structure depending on the location and the size of the sphere shaped silicon oxide which is considered to be an indicator of a DNA base. In addition, we simulate an Ionic Field Effect Transistor (IFET) which has basically the nanopore structure, and show that the simulated curves follow sufficiently the I-V behavior of the measurement data. Therefore, we think it is reasonable to apply parameter modeling mentioned above to simulate nanopore structure. The key idea is to modify electron affinity of silicon which is used to mimic the KCl solution to avoid band bending and depletion inside the nanopore. We could efficiently utilize conventional 3-D simulation tool to simulate the I-V behavior of nanopore structures.

Park JM; Pak YE; Chun H; Lee JH

2012-07-01

215

Sequence and structure space model of protein divergence driven by point mutations.  

UK PubMed Central (United Kingdom)

New folds of protein structures emerge in evolution as a result of insertions, deletions or shuffling of fragments of underlying gene sequences, and from aggregated effects of point mutations. The result of these evolutionary processes is a rich and complex universe of protein sequences and structures, with characteristic features such as heavy-tailed distribution of fold occurrences, and a distinct shape of relationship between sequence identity and structure similarity. Better understanding of how the protein universe evolved to its present form can be achieved by creating models of protein structure evolution. Here we introduce a stochastic model of evolution that involves residue substitutions as the sole source of structure innovation, and is nonetheless able to reproduce the diversity of the protein domains repertoire, its cluster structure with heavy-tailed distribution of family sizes, and presence of the twilight zone populated with remote homologs.

Arod? T; P?onka PM

2013-08-01

216

Sequence- and structure-based prediction of eukaryotic proteinphosphorylation sites  

DEFF Research Database (Denmark)

Protein phosphorylation at serine, threonine or tyrosine residues affects a multitude of cellular signaling processes. Howis specificity in substrate recognition and phosphorylation by protein kinases achieved? Here, we present an artificialneural network method that predicts phosphorylation sites in independent sequences with a sensitivity in the range from69 % to 96 %. As an example, we predict novel phosphorylation sites in the p300/CBP protein that may regulateinteraction with transcription factors and histone acetyltransferase activity. In addition, serine and threonine residues inp300/CBP that can be modified by O-linked glycosylation with N-acetylglucosamine are identified. Glycosylation mayprevent phosphorylation at these sites, a mechanism named yin-yang regulation. The prediction server is available on theInternet at http://www.cbs.dtu.dk/services/NetPhos/or via e-mail to NetPhos@cbs. dtu.dk. Copyright 1999 AcademicPress.

Blom, Nikolaj; Gammeltoft, Steen

1999-01-01

217

TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.  

UK PubMed Central (United Kingdom)

BACKGROUND: The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. RESULTS: TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold.TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a significance threshold are shown to be more accurate for TurboFold than for alternative methods that estimate base pairing probabilities. TurboFold-MEA, which uses base pairing probabilities from TurboFold in a maximum expected accuracy algorithm for secondary structure prediction, has accuracy comparable to the best performing secondary structure prediction methods. The computational and memory requirements for TurboFold are modest and, in terms of sequence length and number of sequences, scale much more favorably than joint alignment and folding algorithms. CONCLUSIONS: TurboFold is an iterative probabilistic method for predicting secondary structures for multiple RNA sequences that efficiently and accurately combines the information from the comparative analysis between sequences with the thermodynamic folding model. Unlike most other multi-sequence structure prediction methods, TurboFold does not enforce strict commonality of structures and is therefore useful for predicting structures for homologous sequences that have diverged significantly. TurboFold can be downloaded as part of the RNAstructure package at http://rna.urmc.rochester.edu.

Harmanci AO; Sharma G; Mathews DH

2011-01-01

218

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. Results TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold. TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a significance threshold are shown to be more accurate for TurboFold than for alternative methods that estimate base pairing probabilities. TurboFold-MEA, which uses base pairing probabilities from TurboFold in a maximum expected accuracy algorithm for secondary structure prediction, has accuracy comparable to the best performing secondary structure prediction methods. The computational and memory requirements for TurboFold are modest and, in terms of sequence length and number of sequences, scale much more favorably than joint alignment and folding algorithms. Conclusions TurboFold is an iterative probabilistic method for predicting secondary structures for multiple RNA sequences that efficiently and accurately combines the information from the comparative analysis between sequences with the thermodynamic folding model. Unlike most other multi-sequence structure prediction methods, TurboFold does not enforce strict commonality of structures and is therefore useful for predicting structures for homologous sequences that have diverged significantly. TurboFold can be downloaded as part of the RNAstructure package at http://rna.urmc.rochester.edu.

Harmanci Arif O; Sharma Gaurav; Mathews David H

2011-01-01

219

Hydrophobic cluster analysis of G protein-coupled receptors: a powerful tool to derive structural and functional information from 2D-representation of protein sequences.  

UK PubMed Central (United Kingdom)

Current methods for comparative analyses of protein sequences are 1D-alignments of amino acid sequences based on the maximization of amino acid identity (homology) and the prediction of secondary structure elements. This method has a major drawback once the amino acid identity drops below 20-25%, since maximization of a homology score does not take into account any structural information. A new technique called Hydrophobic Cluster Analysis (HCA) has been developed by Lemesle-Varloot et al. (Biochimie 72, 555-574), 1990). This consists of comparing several sequences simultaneously and combining homology detection with secondary structure analysis. HCA is primarily based on the detection and comparison of structural segments constituting the hydrophobic core of globular protein domains, with or without transmembrane domains. We have applied HCA to the analysis of different families of G-protein coupled receptors, such as catecholamine receptors as well as peptide hormone receptors. Utilizing HCA the thrombin receptor, a new and as yet unique member of the family of G-protein coupled receptors, can be clearly classified as being closely related to the family of neuropeptide receptors rather than to the catecholamine receptors for which the shape of the hydrophobic clusters and the length of their third cytoplasmic loop are very different. Furthermore, the potential of HCA to predict relationships between new putative and already characterized members of this family of receptors will be presented.

Lentes KU; Mathieu E; Bischoff R; Rasmussen UB; Pavirani A

1993-01-01

220

Identification of two forebrain structures that mediate execution of memorized sequences in the pigeon.  

UK PubMed Central (United Kingdom)

The execution of action sequences is the basis of most behavior. However, little is known about the neural foundation of visuomotor sequence execution in birds, although pigeons are a classic model animal to study sequence learning and production. Recently, we identified two structures in the pigeon brain, the nidopallium intermedium medialis pars laterale (NIML) and the nidopallium caudolaterale (NCL), that are involved in the execution of a serial reaction time task (SRTT). In the SRTT sequence execution is always cue guided. Thus the previous study could not unambiguously clarify whether NCL and NIML contribute to a memory-based execution of sequential behavior. In addition, a possibly differential role of these two structures could not be identified. Therefore, the present study was conducted to further elucidate the role of NCL and NIML in sequence execution in a task where pigeons performed a memorized four-item sequence. Transient inactivation of each NIML and NCL severely impaired sequence execution. The results confirm and extend our previous findings. NIML and NCL seem to store sequence information in parallel. However, the results support the hypothesis that NCL, in contrast to NIML, is especially required for sequence initiation.

Helduser S; Cheng S; Güntürkün O

2013-02-01

 
 
 
 
221

Predicting the secondary structure common to two RNA sequences with Dynalign.  

UK PubMed Central (United Kingdom)

Dynalign is a dynamic programming algorithm for the simultaneous prediction of the lowest-free-energy secondary structure common to two RNA sequences and the alignment of the two sequences. It has been shown that the average accuracy of secondary structure prediction is improved using Dynalign, as compared to free-energy minimization of a single sequence. This unit provides protocols for using Dynalign on a Microsoft Windows platform as part of the RNAstructure package, and for compiling and using Dynalign on Unix/Linux computers.

Mathews D

2004-12-01

222

Hydrothermal syntheses, crystal structures and properties of 0-D, 1-D and 2-D organic-inorganic hybrid borotungstates constructed from Keggin-type heteropolyanion [?-BW12O40]5- and transition-metal complexes  

International Nuclear Information System (INIS)

Three novel organic-inorganic hybrid borotungstates {[Ni(phen)2(H2O)]2H(?-BW12O40)}.4H2O (1), [CuI(2,2'-bipy)(4,4'-bipy)0.5]2{[CuI(2,2'-bipy)]2CuI(4,4'-bipy)2 (?-BW12O40)} (2) and {[CuI(4,4'-bipy)]3H2(?-BW12O40)}.3.5H2O (3) (phen=1,10-phenanthroline, 2,2'-bipy=2,2'-bipyridine, 4,4'-bipy=4,4'-bipyridine) have been hydrothermally synthesized and structurally characterized by elemental analyses, IR, UV spectra, powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), single-crystal X-ray diffraction, X-ray photoelectron spectroscopy (XPS) and photoluminescence. The structural analysis reveals that 1 consists of a 0-D bisupporting polyoxometalate cluster where two [Ni(phen)2(H2O)]2+ cations are grafted on the polyoxoanion [?-BW12O40]5- through two terminal oxygen atoms, 2 shows a 1-D infinite chain constructed from [?-BW12O40]5- polyoxoanions and {[CuI(2,2'-bipy)]2CuI(4,4'-bipy)2}3+ cations by means of alternating fashion, and 3 displays an unprecedented 2D extended structure built by [?-BW12O40]5- polyoxoanions and -CuI-4,4'-bipy- linear chains, in which each [?-BW12O40]5- polyoxoanion acts as a tetradentate inorganic ligand and provides three terminal oxygen atom and one two-bridging oxygen atom. The presence of NiII and WVI in 1, CuI ions and WVI in 2 and 3 are identified by XPS spectra. The photoluminescence of 2 and 3 are also investigated. - Graphical abstract: Three novel organic-inorganic hybrid borotungstates {[Ni(phen)2(H2O)]2H(?-BW12O40)}.4H2O (1), [CuI(2,2'-bipy) (4,4'-bipy)0.5]2{[CuI(2,2'-bipy)]2CuI(4,4'-bipy)2(?-BW12O40)} (2) and {[CuI(4,4'-bipy)]3H2(?-BW12O40)}.3.5H2O (3) have been hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction, thermogravimetric analyses, X-ray photoelectron spectroscopy and photoluminescence.

2009-01-01

223

MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.  

UK PubMed Central (United Kingdom)

SUMMARY: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model. Availability and implementation: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Kosinski J; Barbato A; Tramontano A

2013-04-01

224

Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA.  

Science.gov (United States)

Using a combination of RNA sequencing and construction of cDNA clones followed by DNA sequencing, we have determined the primary nucleotide sequence of U3 snRNA in Xenopus laevis and Xenopus borealis. This molecule has a length of 219 nucleotides. Alignment of the Xenopus sequences with U3 snRNA sequences from other organisms reveals three evolutionarily conserved blocks. We have probed the secondary structure of U3 snRNA in intact Xenopus laevis nuclei using single-strand specific chemical reagents; primer extension was used to map the positions of chemical modification. The three blocks of conserved sequences fall within single-stranded regions, and are therefore accessible for interaction with other molecules. Models of U3 snRNA function are discussed in light of these data. PMID:3357768

Jeppesen, C; Stebbins-Boaz, B; Gerbi, S A

1988-03-25

225

Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA.  

UK PubMed Central (United Kingdom)

Using a combination of RNA sequencing and construction of cDNA clones followed by DNA sequencing, we have determined the primary nucleotide sequence of U3 snRNA in Xenopus laevis and Xenopus borealis. This molecule has a length of 219 nucleotides. Alignment of the Xenopus sequences with U3 snRNA sequences from other organisms reveals three evolutionarily conserved blocks. We have probed the secondary structure of U3 snRNA in intact Xenopus laevis nuclei using single-strand specific chemical reagents; primer extension was used to map the positions of chemical modification. The three blocks of conserved sequences fall within single-stranded regions, and are therefore accessible for interaction with other molecules. Models of U3 snRNA function are discussed in light of these data.

Jeppesen C; Stebbins-Boaz B; Gerbi SA

1988-03-01

226

NMR and macromolecules: Sequence, dynamic, and domain structure  

Energy Technology Data Exchange (ETDEWEB)

This book reports on recent innovations and developments in the use of nuclear magnetic resonance spectroscopy for characterizing polymers. Includes introductory information for those becoming familiar with NMR of polymers as well as gives detailed descriptions of how this analytical technique provides useful structural data. Covers NMR studies of both solid and liquid polymers.

Randall, J.C.

1984-01-01

227

A Minimal Avian Retroviral Packaging Sequence Has a Complex Structure  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have defined a 160-nucleotide region, M?, from the 5? leader region of the Rous sarcoma virus genome that is sufficient to direct the packaging of a heterologous RNA. M? contains the putative O3 stem structure that has previously been shown, and that has been confirmed in this study, to be import...

Banks, Jennifer D.; Yeo, Ashly; Green, Kristen; Cepeda, Franzmarie; Linial, Maxine L.

228

Relaxation of a 1-D gravitational system  

CERN Document Server

We study the relaxation towards thermodynamical equilibrium of a 1-D gravitational system. This OSC model shows a series of critical energies $E_{cn}$ where new equilibria appear and we focus on the homogeneous ($n=0$), one-peak ($n=\\pm 1$) and two-peak ($n=2$) states. Using numerical simulations we investigate the relaxation to the stable equilibrium $n=\\pm 1$ of this $N-$body system starting from initial conditions defined by equilibria $n=0$ and $n=2$. We find that in a fashion similar to other long-range systems the relaxation involves a fast violent relaxation phase followed by a slow collisional phase as the system goes through a series of quasi-stationary states. Moreover, in cases where this slow second stage leads to a dynamically unstable configuration (two peaks with a high mass ratio) it is followed by a new sequence ``violent relaxation/slow collisional relaxation''. We obtain an analytical estimate of the relaxation time $t_{2\\to \\pm 1}$ through the mean escape time of a particle from its potent...

Valageas, P

2006-01-01

229

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences  

Science.gov (United States)

More than a simple carrier of the genetic information, messenger RNA (mRNA) coding regions can also harbor functional elements that evolved to control different post-transcriptional processes, such as mRNA splicing, localization and translation. Functional elements in RNA molecules are often encoded by secondary structure elements. In this aticle, we introduce Structural Profile Assignment of RNA Coding Sequences (SPARCS), an efficient method to analyze the (secondary) structure profile of protein-coding regions in mRNAs. First, we develop a novel algorithm that enables us to sample uniformly the sequence landscape preserving the dinucleotide frequency and the encoded amino acid sequence of the input mRNA. Then, we use this algorithm to generate a set of artificial sequences that is used to estimate the Z-score of classical structural metrics such as the sum of base pairing probabilities and the base pairing entropy. Finally, we use these metrics to predict structured and unstructured regions in the input mRNA sequence. We applied our methods to study the structural profile of the ASH1 genes and recovered key structural elements. A web server implementing this discovery pipeline is available at http://csb.cs.mcgill.ca/sparcs together with the source code of the sampling algorithm.

Zhang, Yang; Ponty, Yann; Blanchette, Mathieu; Lecuyer, Eric; Waldispuhl, Jerome

2013-01-01

230

Sequence and secondary structure of the 5' external transcribed spacer of mouse pre-rRNA.  

UK PubMed Central (United Kingdom)

We report the sequence of the 4006-nucleotide 5' external transcribed spacer (5'ETS) of the mouse ribosomal primary transcript. These data complete the sequence of the 13.4-kb mouse rRNA gene, thus providing a mammalian rRNA gene structure, in addition to yeast and Xenopus. The mouse 5'ETS displays a highly biased base content (very high in GC and particularly low in A), closely similar to the other transcribed spacers of the mouse ribosomal gene. This region seems to have accumulated sequence variation relatively rapidly during vertebrate evolution, with the possible insertion in rodents of sequences structurally similar to retroposons. About half the length of the mouse 5'ETS can fold into a giant and highly stable secondary structure, which is probably evolutionarily conserved in mammals and which could play an important role in the higher-order organization of mammalian pre-ribosomes.

Bourbon H; Michot B; Hassouna N; Feliu J; Bachellerie JP

1988-04-01

231

Energies, fine structure, hyperfine structure and Auger widths of the core-excited states for the Li isoelectronic sequence  

International Nuclear Information System (INIS)

The relativistic energies, fine structures, hyperfine structures, Auger rates and widths of the core-excited states for the Li isoelectronic sequence (Z = 10-20) are studied using the saddle-point variational method and the saddle-point complex-rotation method. The oscillator strengths, radiative rates, wavelengths and lifetimes are also reported. Properties such as fine-structure splitting, radiative and Auger rate regularly change along the Li isoelectronic sequence are discussed. The results are compared with other theoretical and experimental data in the literature

2008-03-28

232

The Sequence Structures of Human MicroRNA Molecules and Their Implications  

Science.gov (United States)

The count of the nucleotides in a cloned, short genomic sequence has become an important criterion to annotate such a sequence as a miRNA molecule. While the majority of human mature miRNA sequences consist of 22 nucleotides, there exists discrepancy in the characteristic lengths of the miRNA sequences. There is also a lack of systematic studies on such length distribution and on the biological factors that are related to or may affect this length. In this paper, we intend to fill this gap by investigating the sequence structure of human miRNA molecules using statistics tools. We demonstrate that the traditional discrete probability distributions do not model the length distribution of the human mature miRNAs well, and we obtain the statistical distribution model with a decent fit. We observe that the four nucleotide bases in a miRNA sequence are not randomly distributed, implying that possible structural patterns such as dinucleotide (trinucleotide or higher order) may exist. Furthermore, we study the relationships of this length distribution to multiple important factors such as evolutionary conservation, tumorigenesis, the length of precursor loop structures, and the number of predicted targets. The association between the miRNA sequence length and the distributions of target site counts in corresponding predicted genes is also presented. This study results in several novel findings worthy of further investigation that include: (1) rapid evolution introduces variation to the miRNA sequence length distribution; (2) miRNAs with extreme sequence lengths are unlikely to be cancer-related; and (3) the miRNA sequence length is positively correlated to the precursor length and the number of predicted target genes.

Fang, Zhide; Du, Ruofei; Edwards, Andrea; Flemington, Erik K.; Zhang, Kun

2013-01-01

233

Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing.  

UK PubMed Central (United Kingdom)

RNA structure is important for RNA function and regulation, and there is growing interest in determining the RNA structure of many transcripts. Here we provide a detailed protocol for the parallel analysis of RNA structure (PARS) for probing RNA secondary structures genome-wide. In this method, enzymatic footprinting is coupled to high-throughput sequencing to provide secondary structure data for thousands of RNAs simultaneously. The entire experimental protocol takes ?5 d to complete, and sequencing and data analysis take an additional 6-8 d. PARS was developed using the yeast genome as proof of principle, but its approach should be applicable to probing RNA structures from different transcriptomes and structural dynamics under diverse solution conditions.

Wan Y; Qu K; Ouyang Z; Chang HY

2013-05-01

234

Comparative sequence analysis and patterns of covariation in RNA secondary structures.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small sub...

Parsch, J; Braverman, J M; Stephan, W

235

Quantitative 1D saturation profiles on chalk by NMR.  

DEFF Research Database (Denmark)

Quantitative one-dimensional saturation profiles showing the distribution of water and oil in chalk core samples are calculated from NMR measurements utilizing a 1D CSI spectroscopy pulse sequence. Saturation profiles may be acquired under conditions of fluid flow through the sample. Results reveal that strong saturation gradients exist in chalk core samples after core floods, due to capillary effects. The method is useful in analysis of corefloods, e.g., for determination of capillary pressure functions

Olsen, Dan; Topp, Simon

1996-01-01

236

A coleopteran triosephosphate isomerase: X-ray structure and phylogenetic impact of insect sequences.  

Science.gov (United States)

A coleopteran triosephosphate isomerase (TIM) from Tenebrio molitor (yellow mealworm beetle) was recombinantly expressed in Escherichia coli and characterized with respect to thermal stability, kinetic parameters and oligomeric state. The enzyme was successfully crystallized and the structure determined by X-ray analysis to 2.0 A resolution. This is the first example of an invertebrate TIM. We compare structural features with known structures of TIMs from microorganisms, plants and vertebrates, and discuss the utility of the Tenebrio TIM sequence, together with several newly sequenced insect TIMs, for molecular phylogenetic analysis. PMID:19849721

Knobeloch, D; Schmidt, A; Scheerer, P; Krauss, N; Wessner, H; Scholz, Ch; Küttner, G; von Rintelen, T; Wessel, A; Höhne, W

2009-10-22

237

A coleopteran triosephosphate isomerase: X-ray structure and phylogenetic impact of insect sequences.  

UK PubMed Central (United Kingdom)

A coleopteran triosephosphate isomerase (TIM) from Tenebrio molitor (yellow mealworm beetle) was recombinantly expressed in Escherichia coli and characterized with respect to thermal stability, kinetic parameters and oligomeric state. The enzyme was successfully crystallized and the structure determined by X-ray analysis to 2.0 A resolution. This is the first example of an invertebrate TIM. We compare structural features with known structures of TIMs from microorganisms, plants and vertebrates, and discuss the utility of the Tenebrio TIM sequence, together with several newly sequenced insect TIMs, for molecular phylogenetic analysis.

Knobeloch D; Schmidt A; Scheerer P; Krauss N; Wessner H; Scholz Ch; Küttner G; von Rintelen T; Wessel A; Höhne W

2010-02-01

238

Implications of some flow sedimentary structures within Miocene evaporitic sequence, Red Sea, Egypt  

Energy Technology Data Exchange (ETDEWEB)

Some typical flow sedimentary structures were clearly detected within the middle Miocene alternating gypsiferous and anhydritic clays of the evaporitic sequence in Ras Gemsa and Um El-Huweitat localities. Sedimentologic analyses of the different structural forms revealed that they were originally formed from unlithified sediments and due to submarine flowage. These structures were formed as a result of stress-load, compression, and rotation. Such a genetic approach is helpful in deducing the environmental conditions within which these sediments accumulated. Degrees of flowage and affected stresses on similar lithologic associations could be considered strong evidence for correlation within the extended Miocene evaporitic sequence along the Red Sea coast.

Wali, A.

1984-09-01

239

Sequence Analysis of the Protein Structure Homology Modeling of Growth Hormone Gene from Salmo trutta caspius  

Directory of Open Access Journals (Sweden)

Full Text Available In view of the growth hormone protein investigated and characterized from Salmo trutta caspius. Growth hormone gene in the Salmo trutta caspius have six exons in the full length that is translated into a Molecular Weight (kDa): ssDNA: 64.98 and dsDNA: 129.6. There are also 210 amino acid residue. The assembled full length of DNA contains open reading frame of growth hormone gene that contains 15 sequences in the full length. The average GC content is 47% and AT content is 53%. This protein multiple alignment has shown that this peptide is 100% identical to the corresponding homologous protein in the growth hormone protein which including Salmo salar (Accession number: AAA49558.1) and Rainbow trout (Salmo trutta) (Accession number: AAA49555.1") sequences. The sequence of protein had deposited in Gene Bank, Accession number: AEK70940. Also we were analyzed second and third structure between sequences reported in Gene Bank Network system. The results are shown, there are homology between second structure in three sequences including: Salmo trutta caspius, Salmo salar and Rainbow trout. Regarding third structure, Salmo trutta caspius and Salmo salar are same type, but Rainbow trout has different homology with Salmo trutta caspius and Salmo salar. However, the sequences were observed three parallel " helix and in second structure there were almost same percent ? sheet.

Abolhasan Rezaei; Sheyda Akhshabi

2012-01-01

240

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure  

DEFF Research Database (Denmark)

Human and mouse genome sequences contain roughly 100,000 regions that are unalignable in primary sequence and neighbor corresponding alignable regions between both organisms. These pairs are generally assumed to be nonconserved, although the level of structural conservation between these has never been investigated. Owing to the limitations in computational methods, comparative genomics has been lacking the ability to compare such nonconserved sequence regions for conserved structural RNA elements. We have investigated the presence of structural RNA elements by conducting a local structural alignment, using FOLDALIGN, on a subset of these 100,000 corresponding regions and estimate that 1800 contain common RNA structures. Comparing our results with the recent mapping of transcribed fragments (transfrags) in human, we find that high-scoring candidates are twice as likely to be found in regions overlapped by transfrags than regions that are not overlapped by transfrags. To verify the coexpression between predicted candidates in human and mouse, we conducted expression studies by RT-PCR and Northern blotting on mouse candidates, which overlap with transfrags on human chromosome 20. RT-PCR results confirmed expression of 32 out of 36 candidates, whereas Northern blots confirmed four out of 12 candidates. Furthermore, many RT-PCR results indicate differential expression in different tissues. Hence, our findings suggest that there are corresponding regions between human and mouse, which contain expressed non-coding RNA sequences not alignable in primary sequence.

Torarinsson, Elfar; Sawera, Milena

2006-01-01

 
 
 
 
241

A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures.  

UK PubMed Central (United Kingdom)

BACKGROUND: Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. DESCRIPTION: We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. CONCLUSION: We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.

Popadin KY; Mamirova LA; Kondrashov FA

2007-01-01

242

Bi3+/M2+ oxyphosphate: a continuous series of polycationic species from the 1D single chain to the 2D planes. Part 2: Crystal structure of three original structural types showing a combination of new ribbonlike polycations.  

Science.gov (United States)

With the assistance of structural models deduced from the high-resolution electron microscope (HREM) investigation presented in Part 1 of this work, three new structural types were pointed out in Bi2O3-MO-P2O5 ternary systems. Their crystal structures are built on the arrangement of 2D polycationic ribbons formed of edge-sharing O(Bi,M)4 tetrahedra and isolated by PO4 groups. Prior to this study, materials with ribbons up to n = 3 tetrahedra wide have been discovered. The original structures presented here display longer n = 4-6 cases, which suggests a possible continuous series of polycationic entities that range from the single chain (one tetrahedron wide) to the infinite [Bi2O2]2+ Aurivillius layer. The ribbons with n > 3 show strong structural modifications that are able to bring a good ribbon-phosphate cohesion. In addition to these fascinating structural results, this work fully confirms the validity of the decoding established from HREM images of a single crystallite in inhomogeneous mixtures. PMID:16903715

Colmont, Marie; Huvé, Marielle; Mentré, Olivier

2006-08-21

243

Overview of PSB track on gene structure identification in large-scale genomic sequence  

Energy Technology Data Exchange (ETDEWEB)

The recent funding of more than a dozen major genome centers to begin community-wide high-throughput sequencing of the human genome has created a significant new challenge for the computational analysis of DNA sequence and the prediction of gene structure and function. It has been estimated that on average from 1996 to 2003, approximately 2 million bases of newly finished DNA sequence will be produced every day and be made available on the Internet and in central databases. The finished (fully assembled) sequence generated each day will represent approximately 75 new genes (and their respective proteins), and many times this number will be represented in partially completed sequences. The information contained in these is of immeasurable value to medical research, biotechnology, the pharmaceutical industry and researchers in a host of fields ranging from microorganism metabolism, to structural biology, to bioremediation. Sequencing of microorganisms and other model organisms is also ramping up at a very rapid rate. The genomes for yeast and several microorganisms such as H. influenza have recently been fully sequenced, although the significance of many genes remains to be determined.

Uberbacher, E.C.; Xu, Y.

1998-12-31

244

How does sequence structure affect the judgment of time? Exploring a weighted sum of segments model.  

UK PubMed Central (United Kingdom)

This paper examines the judgment of segmented temporal intervals, using short tone sequences as a convenient test case. In four experiments, we investigate how the relative lengths, arrangement, and pitches of the tones in a sequence affect judgments of sequence duration, and ask whether the data can be described by a simple weighted sum of segments model. The model incorporates three basic assumptions: (i) the judgment of each segment is a negatively accelerated function of its duration, (ii) the judgment of the overall interval is produced by summing the judgments of each segment, and (iii) more recent segments are weighted more heavily. We also assume that higher-pitched tones are judged to last longer. Empirically, sequences with equal-sized segments were consistently judged longer than those with accelerating or decelerating structures. Furthermore, temporal structure interacted with duration, such that accelerating sequences were judged longer than decelerating ones at short durations but the effect reversed at longer durations. These effects were modulated by the number of tones in the sequence, the rate of acceleration/deceleration, and whether the sequence had ascending or descending pitch, and were well-described by the weighted sum model. The data provide strong constraints on theories of temporal judgment, and the weighted sum of segments model offers a useful basis for future theoretical and empirical investigation.

Matthews WJ

2013-05-01

245

Structure elucidation of beta-mannanase: from the electron-density map to the DNA sequence.  

Science.gov (United States)

The crystal structure of affinity-purified Thermomonospora fusca beta-mannanase has been solved despite the lack of the major part of the amino-acid sequence. A high-quality electron-density map allowed the identification of a stretch of eight amino acids close to the C-terminus which was used to design a degenerate downstream PCR primer. Together with a specific primer previously derived from the N-terminus, 95.7% of the mannanase gene sequence was obtained from genomic T. fusca DNA by PCR. The structure-derived sequence was then compared with the DNA-derived sequence and corrected when necessary. Applying the presented protocol, there was no need to manually build a model at an early stage of structure determination, an erroneous and tedious process, especially in the absence of the amino-acid sequence. Using the DNA sequence information and the current version of ARP/wARP, 281 residues, or 93% of the polypeptide chain (including side chains), were built and refined to an R factor of 16.5% without any manual intervention. PMID:11134925

Hilge, M; Perrakis, A; Abrahams, J P; Winterhalter, K; Piontek, K; Gloor, S M

2001-01-01

246

Simulation of Organic Solar Cells Using AMPS-1D Program  

Directory of Open Access Journals (Sweden)

Full Text Available The analysis of microelectronic and photonic structure in one dimension program [AMPS-1D] program has been successfully used to study inorganic solar cells. In this work the program has been used to optimize the performance of the organic solar cells. The cells considered consist of poly(2-methoxy-5-(3,7- dimethyloctyloxy)-1,4-phenylenevinylene) [MDMO-PPV

Samah G. Babiker; Yong Shuai

2012-01-01

247

The Anticarsia gemmatalis nuclear polyhedrosis virus polyhedrin gene region: sequence analysis, gene product and structural comparisons.  

UK PubMed Central (United Kingdom)

The genomic region of the Anticarsia gemmatalis multiple nucleocapsid nuclear polyhedrosis virus (AgMNPV) strain 2D encoding the polyhedrin gene was cloned and mapped, and a 2085 bp SphI-PstI fragment containing the gene was sequenced. The polyhedrin polypeptide of the parental isolate AgMNPV was manually sequenced, and the amino acid sequence obtained agreed with that deduced from the DNA coding region sequence. AgMNPV and Orgyia pseudotsugata MNPV (OpMNPV) are similar in terms of promoter structure and polyhedrin primary sequence, and the polyhedrin gene of both viruses is transcribed in the anti-clockwise direction in relation to their physical maps. The region upstream from the polyhedrin gene of AgMNPV, OpMNPV, Bombyx mori NPV and Autographa californica MNPV (AcMNPV) was compared and this showed that the open reading frame (ORF) common to all four viruses (ORF 5) has sequence homology with the AcMNPV 25K gene. The sequences between ORF 5 and the polyhedrin gene were found to be variable among the polyhedrin gene loci compared. Additionally, conserved elements in the promoters of the very late genes encoding polyhedrin and granulin, and those encoding two p10 proteins were found to share sequence homology and positional similarity with consensus regions in the conserved boxes A and C, responsible for binding transcription factors to eukaryotic 5S ribosomal RNA genes, and to box C of tRNA genes.

Zanotto PM; Sampaio MJ; Johnson DW; Rocha TL; Maruniak JE

1992-05-01

248

RNA-Pareto: Interactive Analysis of Pareto-optimal RNA Sequence-Structure Alignments.  

UK PubMed Central (United Kingdom)

SUMMARY: Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions which all represent different possible weighting parameters. We now provide the interactive graphical software tool RNA-Pareto which allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set.Availability and Implementation: The software is written in Java 6 (graphical user interface) and C++ (dynamic programming algorithms). The source code and binaries for Linux, Windows and Mac OS are freely available at http://sysbio.uni-ulm.de and are licensed under the GNU GPLv3. CONTACT: hans.kestler@uni-ulm.de.

Schnattinger T; Schöning U; Marchfelder A; Kestler HA

2013-09-01

249

libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny  

Directory of Open Access Journals (Sweden)

Full Text Available Background An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task. Results The bioinformatics library libcov is a collection of C++ classes that provides a high and low-level interface to maximum likelihood phylogenetics, sequence analysis and a data structure for structural biological methods. libcov can be used to compute likelihoods, search tree topologies, estimate site rates, cluster sequences, manipulate tree structures and compare phylogenies for a broad selection of applications. Conclusion Using this library, it is possible to rapidly prototype applications that use the sophistication of phylogenetic likelihoods without getting involved in a major software engineering project. libcov is thus a potentially valuable building block to develop in-house methodologies in the field of protein phylogenetics.

Butt Davin; Roger Andrew J; Blouin Christian

2005-01-01

250

Biological Sequence Analysis with Multivariate String Kernels.  

UK PubMed Central (United Kingdom)

String kernel-based machine learning methods have yielded great success in practical tasks of structured/sequential data analysis. They often exhibit state-of-the-art performance on many practical tasks of sequence analysis such as biological sequence classification, remote homology detection, or protein superfamily and fold prediction. However, typical string kernel methods rely on analysis of discrete one-dimensional (1D) string data (e.g., DNA or amino acid sequences). In this work we address the multi-class biological sequence classification problems using multivariate representations in the form of sequences of features vectors (as in biological sequence profiles, or sequences of individual amino acid physico-chemical descriptors) and a class of multivariate string kernels that exploit these representations. On a number of protein sequence classification tasks proposed multivariate representations and kernels show significant 15-20\\% improvements compared to existing state-of-the-art sequence classification methods.

Kuksa PP

2013-03-01

251

Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Automatic identification of structure fingerprints from a group of diverse protein structures is challenging, especially for proteins whose divergent amino acid sequences may fall into the "twilight-" or "midnight-" zones where pair-wise sequence identities to known sequences fall below 25% and sequence-based functional annotations often fail. Results Here we report a novel graph database mining method and demonstrate its application to protein structure pattern identification and structure classification. The biologic motivation of our study is to recognize common structure patterns in "immunoevasins", proteins mediating virus evasion of host immune defense. Our experimental study, using both viral and non-viral proteins, demonstrates the efficiency and efficacy of the proposed method. Conclusion We present a theoretic framework, offer a practical software implementation for incorporating prior domain knowledge, such as substitution matrices as studied here, and devise an efficient algorithm to identify approximate matched frequent subgraphs. By doing so, we significantly expanded the analytical power of sophisticated data mining algorithms in dealing with large volume of complicated and noisy protein structure data. And without loss of generality, choice of appropriate compatibility matrices allows our method to be easily employed in domains where subgraph labels have some uncertainty.

Jia Yi; Huan Jun; Buhr Vincent; Zhang Jintao; Carayannopoulos Leonidas N

2009-01-01

252

Comparative genomics beyond sequence-based alignments : RNA structures in the ENCODE regions  

DEFF Research Database (Denmark)

Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment methods to misalign, or even refuse to align, homologous ncRNAs, consequently obscuring that structural signal. We have used CMfinder, a structure-oriented local alignment tool, to search the ENCODE regions of vertebrate multiple alignments. In agreement with other studies, we find a large number of potential RNA structures in the ENCODE regions. We report 6587 candidate regions with an estimated false-positive rate of 50%. More intriguingly, many of these candidates may be better represented by alignments taking the RNA secondary structure into account than those based on primary sequence alone, often quite dramatically. For example, approximately one-quarter of our predicted motifs show revisions in >50% of their aligned positions. Furthermore, our results are strongly complementary to those discovered by sequence-alignment-based approaches--84% of our candidates are not covered by Washietl et al., increasing the number of ncRNA candidates in the ENCODE region by 32%. In a group of 11 ncRNA candidates that were tested by RT-PCR, 10 were confirmed to be present as RNA transcripts in human tissue, and most show evidence of significant differential expression across tissues. Our results broadly suggest caution in any analysis relying on multiple sequence alignments in less well-conserved regions, clearly support growing appreciation for the biological significance of ncRNAs, and strongly support the argument for considering RNA structure directly in any searches for these elements.

Torarinsson, Elfar; Yao, Zizhen

2008-01-01

253

Characterization of the sequence spectrum of DNA based on the appearance frequency of the nucleotide sequences of the genome——A new method for analysis of genome structure  

Directory of Open Access Journals (Sweden)

Full Text Available The nucleotide (base) sequence of the genome might reflect biological information beyond the coding sequences. The appearance frequencies of successive base sequences (key sequences) were calculated for entire genomes. Based on the appearance frequency of the key sequences of the genome, any DNA sequences on the genome could be expressed as a sequence spectrum with the adjoining base sequences, which could be used to study the corresponding biological phenomena. In this paper, we used 64 successive three- base sequences (triplets) as the key sequences, and determined and compared the spectra of specific genes to the chromosome, or specific genes to tRNA genes in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Escherichia coli. Based on these analyses, a gene and its corresponding position on the chromosome showed highly similar spectra with the same fold enlargement (approximately 400-fold) in the S. cerevisiae, S. pombe and E. coli genomes. In addition, the homologous structure of genes that encode proteins was also observed with appropriate tRNA gene(s) in the genome. This analytical method might faithfully reflect the encoded biological information, that is, the conservation of the base sequences was to make sense the conservation of the translated amino acids sequence in the coding region, and might be universally applicable to other genomes, even those that consisted of multiple chromosomes.

Masatoshi Nakahara; Masaharu Takeda

2010-01-01

254

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.  

UK PubMed Central (United Kingdom)

Classical approaches to determine structures of noncoding RNA (ncRNA) probed only one RNA at a time with enzymes and chemicals, using gel electrophoresis to identify reactive positions. To accelerate RNA structure inference, we developed fragmentation sequencing (FragSeq), a high-throughput RNA structure probing method that uses high-throughput RNA sequencing of fragments generated by digestion with nuclease P1, which specifically cleaves single-stranded nucleic acids. In experiments probing the entire mouse nuclear transcriptome, we accurately and simultaneously mapped single-stranded RNA regions in multiple ncRNAs with known structure. We probed in two cell types to verify reproducibility. We also identified and experimentally validated structured regions in ncRNAs with, to our knowledge, no previously reported probing data.

Underwood JG; Uzilov AV; Katzman S; Onodera CS; Mainzer JE; Mathews DH; Lowe TM; Salama SR; Haussler D

2010-12-01

255

Consequences of domain insertion on sequence-structure divergence in a superfold.  

UK PubMed Central (United Kingdom)

Although the universe of protein structures is vast, these innumerable structures can be categorized into a finite number of folds. New functions commonly evolve by elaboration of existing scaffolds, for example, via domain insertions. Thus, understanding structural diversity of a protein fold evolving via domain insertions is a fundamental challenge. The haloalkanoic dehalogenase superfamily serves as an excellent model system wherein a variable cap domain accessorizes the ubiquitous Rossmann-fold core domain. Here, we determine the impact of the cap-domain insertion on the sequence and structure divergence of the core domain. Through quantitative analysis on a unique dataset of 154 core-domain-only and cap-domain-only structures, basic principles of their evolution have been uncovered. The relationship between sequence and structure divergence of the core domain is shown to be monotonic and independent of the corresponding type of domain insert, reflecting the robustness of the Rossmann fold to mutation. However, core domains with the same cap type share greater similarity at the sequence and structure levels, suggesting interplay between the cap and core domains. Notably, results reveal that the variance in structure maps to ?-helices flanking the central ?-sheet and not to the domain-domain interface. Collectively, these results hint at intramolecular coevolution where the fold diverges differentially in the context of an accessory domain, a feature that might also apply to other multidomain superfamilies.

Pandya C; Brown S; Pieper U; Sali A; Dunaway-Mariano D; Babbitt PC; Xia Y; Allen KN

2013-09-01

256

Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device.  

UK PubMed Central (United Kingdom)

We show how a bird's-eye view of genomic structure can be obtained at ?1-kb resolution from long (?2 Mb) DNA molecules extracted from whole chromosomes in a nanofluidic laboratory-on-a-chip. We use an improved single-molecule denaturation mapping approach to detect repetitive elements and known as well as unique structural variation. Following its mapping, a molecule of interest was rescued from the chip; amplified and localized to a chromosome by FISH; and interrogated down to 1-bp resolution with a commercial sequencer, thereby reconciling haplotype-phased chromosome substructure with sequence.

Marie R; Pedersen JN; Bauer DL; Rasmussen KH; Yusuf M; Volpi E; Flyvbjerg H; Kristensen A; Mir KU

2013-03-01

257

Sequence and structural analyses of nuclear export signals in the NESdb database.  

Science.gov (United States)

We compiled >200 nuclear export signal (NES)-containing CRM1 cargoes in a database named NESdb. We analyzed the sequences and three-dimensional structures of natural, experimentally identified NESs and of false-positive NESs that were generated from the database in order to identify properties that might distinguish the two groups of sequences. Analyses of amino acid frequencies, sequence logos, and agreement with existing NES consensus sequences revealed strong preferences for the ?1-X(3)-?2-X(2)-?3-X-?4 pattern and for negatively charged amino acids in the nonhydrophobic positions of experimentally identified NESs but not of false positives. Strong preferences against certain hydrophobic amino acids in the hydrophobic positions were also revealed. These findings led to a new and more precise NES consensus. More important, three-dimensional structures are now available for 68 NESs within 56 different cargo proteins. Analyses of these structures showed that experimentally identified NESs are more likely than the false positives to adopt ?-helical conformations that transition to loops at their C-termini and more likely to be surface accessible within their protein domains or be present in disordered or unobserved parts of the structures. Such distinguishing features for real NESs might be useful in future NES prediction efforts. Finally, we also tested CRM1-binding of 40 NESs that were found in the 56 structures. We found that 16 of the NES peptides did not bind CRM1, hence illustrating how NESs are easily misidentified. PMID:22833565

Xu, Darui; Farmer, Alicia; Collett, Garen; Grishin, Nick V; Chook, Yuh Min

2012-07-25

258

Sequence and structural analyses of nuclear export signals in the NESdb database.  

UK PubMed Central (United Kingdom)

We compiled >200 nuclear export signal (NES)-containing CRM1 cargoes in a database named NESdb. We analyzed the sequences and three-dimensional structures of natural, experimentally identified NESs and of false-positive NESs that were generated from the database in order to identify properties that might distinguish the two groups of sequences. Analyses of amino acid frequencies, sequence logos, and agreement with existing NES consensus sequences revealed strong preferences for the ?1-X(3)-?2-X(2)-?3-X-?4 pattern and for negatively charged amino acids in the nonhydrophobic positions of experimentally identified NESs but not of false positives. Strong preferences against certain hydrophobic amino acids in the hydrophobic positions were also revealed. These findings led to a new and more precise NES consensus. More important, three-dimensional structures are now available for 68 NESs within 56 different cargo proteins. Analyses of these structures showed that experimentally identified NESs are more likely than the false positives to adopt ?-helical conformations that transition to loops at their C-termini and more likely to be surface accessible within their protein domains or be present in disordered or unobserved parts of the structures. Such distinguishing features for real NESs might be useful in future NES prediction efforts. Finally, we also tested CRM1-binding of 40 NESs that were found in the 56 structures. We found that 16 of the NES peptides did not bind CRM1, hence illustrating how NESs are easily misidentified.

Xu D; Farmer A; Collett G; Grishin NV; Chook YM

2012-09-01

259

A multilocus sequence typing scheme implies population structure and reveals several putative novel Achromobacter species.  

Science.gov (United States)

The genus Achromobacter currently is comprised of seven species, including Achromobacter xylosoxidans, an opportunistic and nosocomial pathogen that displays broad-spectrum antimicrobial resistance and is recognized as causing chronic respiratory tract infection in persons with cystic fibrosis (CF). To enable strain typing for global epidemiologic investigations, to clarify the taxonomy of "Achromobacter-like" strains, and to elucidate the population structure of this genus, we developed a genus-level multilocus sequence typing (MLST) scheme. We employed in silico analyses of whole-genome sequences of several phylogenetically related genera, including Bordetella, Burkholderia, Cupriavidus, Herminiimonas, Janthinobacterium, Methylibium, and Ralstonia, for selecting loci and designing PCR primers. Using this MLST scheme, we analyzed 107 genetically diverse Achromobacter isolates cultured from biologic specimens from CF and non-CF patients, 1 isolate recovered from sludge, and an additional 39 strains obtained from culture collections. Sequence data from these 147 strains, plus three recently genome-sequenced Achromobacter strains, were assigned to 129 sequence types based on seven loci. Calculation of the nucleotide divergence of concatenated locus sequences within and between MLST clusters confirmed the seven previously named Achromobacter species and revealed 14 additional genogroups. Indices of association showed significant linkage disequilibrium in all of the species/genogroups able to be tested, indicating that each group has a clonal population structure. No clear segregation of species/genogroups between CF and non-CF sources was found. PMID:22785192

Spilker, Theodore; Vandamme, Peter; Lipuma, John J

2012-07-11

260

A multilocus sequence typing scheme implies population structure and reveals several putative novel Achromobacter species.  

UK PubMed Central (United Kingdom)

The genus Achromobacter currently is comprised of seven species, including Achromobacter xylosoxidans, an opportunistic and nosocomial pathogen that displays broad-spectrum antimicrobial resistance and is recognized as causing chronic respiratory tract infection in persons with cystic fibrosis (CF). To enable strain typing for global epidemiologic investigations, to clarify the taxonomy of "Achromobacter-like" strains, and to elucidate the population structure of this genus, we developed a genus-level multilocus sequence typing (MLST) scheme. We employed in silico analyses of whole-genome sequences of several phylogenetically related genera, including Bordetella, Burkholderia, Cupriavidus, Herminiimonas, Janthinobacterium, Methylibium, and Ralstonia, for selecting loci and designing PCR primers. Using this MLST scheme, we analyzed 107 genetically diverse Achromobacter isolates cultured from biologic specimens from CF and non-CF patients, 1 isolate recovered from sludge, and an additional 39 strains obtained from culture collections. Sequence data from these 147 strains, plus three recently genome-sequenced Achromobacter strains, were assigned to 129 sequence types based on seven loci. Calculation of the nucleotide divergence of concatenated locus sequences within and between MLST clusters confirmed the seven previously named Achromobacter species and revealed 14 additional genogroups. Indices of association showed significant linkage disequilibrium in all of the species/genogroups able to be tested, indicating that each group has a clonal population structure. No clear segregation of species/genogroups between CF and non-CF sources was found.

Spilker T; Vandamme P; Lipuma JJ

2012-09-01

 
 
 
 
261

Structural characterization of HDPE/LLDPE blend-based nano composites obtained by different blending sequence  

International Nuclear Information System (INIS)

The blending sequence affects the morphology formation of the nanocomposites. In this work, the blending sequences were explored to determine its influence in the rheological behavior of HDPE/LLDPE/OMMT nanocomposites. The nanocomposites were obtained by melt-intercalation using a mixture of LLDPE-g-MA and HDPE-g-MA as compatibilizer system in a torque rheometer at 180 deg C and five blending sequences were studied. The materials structures were characterized by wide angle X-ray diffraction (WAXD) and by rheological properties. The nanoclay's addition increased the shear viscosity at low shear rates, changing the behavior of HDPE/LLDPE matrix to a Bingham model behavior with an apparent yield stress. Intense interactions were obtained for the blending sequence where LLDPE and/or LLDPE-g-MA were first reinforced with organoclay since the intercalation process occurs preferentially in the amorphous phase. (author)

2011-01-01

262

The Escherichia coli rna gene encoding RNase I: sequence and unusual promoter structure.  

UK PubMed Central (United Kingdom)

A clone containing the Escherichia coli rna gene encoding the nonspecific endoribonuclease, RNase I, was isolated and sequenced. The sequence of the 1070-nucleotide (nt) fragment agreed completely with that of a rna clone recently reported by Meador and Kennell [Gene 95 (1990) 1-7]. The transcription start point (tsp) of rna was identified using primer extension analysis, and its promoter sequence was established by comparison of RNase I expression levels in various deletion mutants. Our results indicate that the rna promoter is highly unusual. Its -35 region shows a poor match to the consensus sequence, and moreover, it is located within a stem-loop structure that apparently is a Rho-independent transcription termination site for an upstream gene.

Zhu L; Deutscher MP

1992-09-01

263

Comparative analysis of MR sequences to detect structural brain lesions in tuberous sclerosis  

International Nuclear Information System (INIS)

Tuberous sclerosis (TS) is a neurocutaneous genetically inherited disease with variable penetrance characterized by dysplasias and hamartomas affecting multiple organs. MR is the imaging method of choice to demonstrate structural brain lesions in TS. To compare MR sequences and determine which is most useful for the demonstration of each type of brain lesion in TS patients. We reviewed MR scans of 18 TS patients for the presence of cortical tubers, white matter lesions (radial bands), subependymal nodules, and subependymal giant cell astrocytoma (SGCA) on the following sequences: (1) T1-weighted spin-echo (T1 SE) images before and after gadolinium (Gd) injection; (2) nonenhanced T1 SE sequence with an additional magnetization transfer contrast medium pulse on resonance (T1 SE/MTC); and (3) fluid-attenuated inversion recovery (FLAIR) sequence. Cortical tubers were found in significantly (P

2006-01-01

264

Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background RNA-binding proteins (RBPs) play diverse roles in eukaryotic RNA processing. Despite their pervasive functions in coding and noncoding RNA biogenesis and regulation, elucidating the sequence specificities that define protein-RNA interactions remains a major challenge. Recently, CLIP-seq (Cross-linking immunoprecipitation followed by high-throughput sequencing) has been successfully implemented to study the transcriptome-wide binding patterns of SRSF1, PTBP1, NOVA and fox2 proteins. These studies either adopted traditional methods like Multiple EM for Motif Elicitation (MEME) to discover the sequence consensus of RBP's binding sites or used Z-score statistics to search for the overrepresented nucleotides of a certain size. We argue that most of these methods are not well-suited for RNA motif identification, as they are unable to incorporate the RNA structural context of protein-RNA interactions, which may affect to binding specificity. Here, we describe a novel model-based approach--RNAMotifModeler to identify the consensus of protein-RNA binding regions by integrating sequence features and RNA secondary structures. Results As an example, we implemented RNAMotifModeler on SRSF1 (SF2/ASF) CLIP-seq data. The sequence-structural consensus we identified is a purine-rich octamer 'AGAAGAAG' in a highly single-stranded RNA context. The unpaired probabilities, the probabilities of not forming pairs, are significantly higher than negative controls and the flanking sequence surrounding the binding site, indicating that SRSF1 proteins tend to bind on single-stranded RNA. Further statistical evaluations revealed that the second and fifth bases of SRSF1octamer motif have much stronger sequence specificities, but weaker single-strandedness, while the third, fourth, sixth and seventh bases are far more likely to be single-stranded, but have more degenerate sequence specificities. Therefore, we hypothesize that nucleotide specificity and secondary structure play complementary roles during binding site recognition by SRSF1. Conclusion In this study, we presented a computational model to predict the sequence consensus and optimal RNA secondary structure for protein-RNA binding regions. The successful implementation on SRSF1 CLIP-seq data demonstrates great potential to improve our understanding on the binding specificity of RNA binding proteins.

Wang Xin; Juan Liran; Lv Junjie; Wang Kejun; Sanford Jeremy R; Liu Yunlong

2011-01-01

265

The T1D Exchange clinic registry.  

UK PubMed Central (United Kingdom)

CONTEXT: The T1D Exchange includes a clinic-based registry, a patient-centric web site called Glu, and a biobank. OBJECTIVE: The aim of the study was to describe the T1D Exchange clinic registry and provide an overview of participant characteristics. DESIGN: Data obtained through participant completion of a questionnaire and chart extraction include diabetes history, management, and monitoring; general health; lifestyle; family history; socioeconomic factors; medications; acute and chronic diabetic complications; other medical conditions; and laboratory results. SETTING: Data were collected from 67 endocrinology centers throughout the United States. PATIENTS: We studied 25,833 adults and children with presumed autoimmune type 1 diabetes (T1D). RESULTS: Participants ranged in age from less than 1 to 93 yr, 50% were female, 82% were Caucasian, 50% used an insulin pump, 6% used continuous glucose monitoring, and 16% had a first-degree family member with T1D. Glycosylated hemoglobin at enrollment averaged 8.3% and was highest in 13 to 25 yr olds. The prevalence of renal disease was ?4% until T1D was present for at least 10 yr, and retinopathy treatment was ?2% until T1D was present for at least 20 yr. A severe hypoglycemic event (seizure or coma) in the prior 12 months was reported by 7% of participants and diabetic ketoacidosis in the prior 12 months by 8%. CONCLUSIONS: The T1D Exchange clinic registry provides a database of important information on individuals with T1D in the United States. The rich dataset of the registry provides an opportunity to address numerous issues of relevance to clinicians and patients, including assessments of associations between patient characteristics and diabetes management factors with outcomes.

Beck RW; Tamborlane WV; Bergenstal RM; Miller KM; DuBose SN; Hall CA

2012-12-01

266

Social exploration of 1D games.  

DEFF Research Database (Denmark)

In this paper the apparently meaningless concept of a 1 dimensional computer game is explored, via netnography. A small number of games was designed and implemented, in close contact with online communities of players and developers, providing evidence that 1 dimension is enough to produce interesting gameplay, to allow for level design and even to leave room for artistic considerations on 1D rendering. General techniques to re-design classic 2D games into 1D are also emerging from this exploration.

Valente, Andrea; Marchetti, Emanuela

2013-01-01

267

Social exploration of 1D games  

DEFF Research Database (Denmark)

In this paper the apparently meaningless concept of a 1 dimensional computer game is explored, via netnography. A small number of games was designed and implemented, in close contact with online communities of players and developers, providing evidence that 1 dimension is enough to produce interesting gameplay, to allow for level design and even to leave room for artistic considerations on 1D rendering. General techniques to re-design classic 2D games into 1D are also emerging from this exploration.

Valente, Andrea; Marchetti, Emanuela

2013-01-01

268

SEQUENCE AND STRUCTURAL ANALYSIS OF ?-CARRAGEENAN-DERIVED OLIGOSACCHARIDES BY TWO-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE  

UK PubMed Central (United Kingdom)

?-Carrageenan was hydrolyzed with mild hydrochloric acid and separated into a series of oligosaccharides, the sequences and structures of which were investigated by double-quantum filtered correlation spectroscopy (DQF-COSY), total correlation spectroscopy (TOCSY), heteronuclear multiple-quantum coherence (HMQC), and heteronuclear multiple-bond correlation (HMBC) techniques, respectively. The chemical structures and conformations of the individual sugar residues were identified, as well as the sequential connectivity of the oligosaccharides. The interresidue nuclear Overhauser effects (NOEs)/rotating frame Overhauser effects (ROEs) revealed an ordered helical structure of the carrageenan oligosaccharide chains. Therefore, a general two-dimensional (2-D) NMR methodology for the unambiguous sequence and structure analysis of ?-carrageenan-derived oligosaccharides was established in this study.

Zhang Wei; Liu Ming; Hansen PoulErik; Yu Guangli; Yang Bo; Zhao Xia

2010-08-01

269

Sequence-based identification of 3D structural modules in RNA with RMDetect.  

UK PubMed Central (United Kingdom)

Structural RNA modules, sets of ordered non-Watson-Crick base pairs embedded between Watson-Crick pairs, have central roles as architectural organizers and sites of ligand binding in RNA molecules, and are recurrently observed in RNA families throughout the phylogeny. Here we describe a computational tool, RNA three-dimensional (3D) modules detection, or RMDetect, for identifying known 3D structural modules in single and multiple RNA sequences in the absence of any other information. Currently, four modules can be searched for: G-bulge loop, kink-turn, C-loop and tandem-GA loop. In control test sequences we found all of the known modules with a false discovery rate of 0.23. Scanning through 1,444 publicly available alignments, we identified 21 yet unreported modules and 141 known modules. RMDetect can be used to refine RNA 2D structure, assemble RNA 3D models, and search and annotate structured RNAs in genomic data.

Cruz JA; Westhof E

2011-06-01

270

Structural and Sequence Stratigraphic Analysis of the Onshore Nile Delta, Egypt.  

Science.gov (United States)

The Nile Delta is considered the earliest known delta in the world. It was already described by Herodotus in the 5th Century AC. Nowadays; the Nile Delta is an emerging giant gas province in the Middle East with proven gas reserves which have more than doubled in size in the last years. The Nile Delta basin contains a thick sedimentary sequence inferred to extend from Jurassic to recent time. Structural styles and depositional environments varied during this period. Facies architecture and sequence stratigraphy of the Nile Delta are resolved using seismic stratigraphy based on (2D seismic lines) including synthetic seismograms and tying in well log data. Synthetic seismograms were constructed using sonic and density logs. The combination of structural interpretation and sequence stratigraphy of the development of the basin was resolved. Seven chrono-stratigraphic boundaries have been identified and correlated on seismic and well log data. Several unconformity boundaries also identified on seismic lines range from angular to disconformity type. Furthermore, time structure maps, velocity maps, depth structure maps as well as Isopach maps were constructed using seismic lines and log data. Several structural features were identified: normal faults, growth faults, listric faults, secondary antithetic faults and large rotated fault blocks of manly Miocene age. In some cases minor rollover structures could be identified. Sedimentary features such as paleo-channels were distinctively recognized. Typical Sequence stratigraphic features such as incised valley, clinoforms, topsets, offlaps and onlaps are identified and traced on the seismic lines allowing a good insight into sequence stratigraphic history of the Nile Delta most especially in the Miocene to Pliocene clastic sedimentary succession.

Barakat, Moataz; Dominik, Wilhelm

2010-05-01

271

Reading the three-dimensional structure of a protein from its amino acid sequence  

CERN Multimedia

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of a protein whose sequence is known. This situation is not particularly satisfactory, in keeping with the fact that while linear sequencing of the amino acids specifying a protein is relatively simple to carry out, the determination of the folded-native-conformation can only be done by an elaborate X-ray diffraction analysis performed on crystals of the protein or, if the protein is very small, by nuclear magnetic resonance techniques. Using insight obtained from lattice model simulations of the folding of small proteins (fewer than 100 residues), in particular of the fact that this phenomenon is essentially controlled by conserved contacts among strongly interacting amino acids, which also stabilize local elementary structures formed early in the folding process and leading...

Broglia, R A

2000-01-01

272

The Structure of a Bernoulli Process Variation of the Fibonacci Sequence  

CERN Multimedia

We consider the structure of a variation of the Fibonacci sequence which is determined by a Bernoulli process. The associated structure of all Bernoulli variations of the Fibonacci sequence can be represented by a directed binary tree, which we denote X, with vertex labels representing the specific state of the recurrence variation. Since X is a binary tree, we can consider the term of a sequence variation given by a finite traversal of X represented by a binary code t. We then prove that the traversal of X that is the reflection of the digits of t gives exactly the integer term corresponding to t. We consider how to further this result with the statement of an additional conjecture. Finally, we give connections to Fibonacci expansions, the Stern-Brocot tree, and we apply our methods to the Three Hat Problem as seen in ``Puzzle Corner'' of the ``Technology Review'' magazine.

Benson, Brian A

2007-01-01

273

Examining protein surface structure in highly conserved sequence variants with mass spectrometry.  

UK PubMed Central (United Kingdom)

A simple mass spectrometry-based method capable of examining protein structure called SNAPP (selective noncovalent adduct protein probing) is used to evaluate the structural consequences of point mutations in naturally occurring sequence variants from different species. SNAPP monitors changes in the attachment of noncovalent adducts to proteins as a function of structural state. Mutations that lead to perturbations to the electrostatic surface structure of a protein affect noncovalent attachment and are easily observed with SNAPP. Mutations that do not alter the tertiary structure or electrostatic surface structure yield similar results by SNAPP. For example, bovine, porcine, and human insulin all have very similar backbone structures and no basic or acidic residue mutations, and the SNAPP distributions for all three proteins are very similar. In contrast, four variants of cytochrome c (cytc) have varying degrees of sequence homology, which are reflected in the observed SNAPP distributions. Bovine and pigeon cytc have several basic or acidic residue substitutions relative to horse cytc, but the SNAPP distributions for all three proteins are similar. This suggests that these mutations do not significantly influence the protein surface structure. On the other hand, yeast cytc has the least sequence homology and exhibits a unique, though related, SNAPP distribution. Even greater differences are observed for lysozyme. Hen and human lysozyme have identical tertiary structures but significant variations in the locations of numerous basic and acidic residues. The SNAPP distributions are quite distinct for the two forms of lysozyme, suggesting significant differences in the surface structures. In summary, SNAPP experiments are relatively easy to perform, require minimal sample consumption, and provide a facile route for comparison of protein surface structure between highly homologous proteins.

Tao Y; Julian RR

2012-02-01

274

The effect of disease associated point mutations on 5?-reductase (AKR1D1) enzyme function  

Science.gov (United States)

The stereospecific 5?-reduction of ?4-3-ketosterols is very difficult to achieve chemically and introduces a 90° bend between ring A and B of the planar steroid. In mammals, the reaction is catalyzed by steroid 5?-reductase, a member of the aldo-keto reductase (AKR) family. The human enzyme, AKR1D1, plays an essential role in bile-acid biosynthesis since the 5?-configuration is required for the emulsifying properties of bile. Deficient 5?-reductase activity can lead to cholestasis and neo-natal liver failure and is often lethal if it remains untreated. In five patients with 5?-reductase deficiency, sequencing revealed individual, non-synonymous point mutations in the AKR1D1 gene: L106F, P133R, G223E, P198L and R261C. However, mapping these mutations to the AKR1D1 crystal structure failed to reveal any obvious involvement in substrate or cofactor binding or catalytic mechanism, and it remained unclear whether these mutations could be causal for the observed disease. We analyzed the positions of the reported mutations and found that they reside in highly conserved portions of AKR1D1 and hypothesized that they would likely lead to changes in protein folding, and hence enzyme activity. Attempts to purify the mutant enzymes for further characterization by over-expression in E.coli yielded sufficient amounts of only one mutant (P133R). This enzyme exhibited reduced Km and kcat with the bile acid intermediate ?4-cholesten-7?-ol-3-one as substrate reminiscent of uncompetitive inhibition. In addition, P133R displayed no change in cofactor affinity but was more thermolabile as judged by CD-spectroscopy. When all AKR1D1 mutants were expressed in HEK 293 cells, protein expression levels and enzyme activity were dramatically reduced. Furthermore, cycloheximide treatment revealed decreased stability of several of the mutants compared to wild type. Our data show, that all five mutations identified in patients with functional bile acid deficiency strongly affected AKR1D1 enzyme functionality and therefore may be causal for this disease.

Mindnich, Rebekka; Drury, Jason E.; Penning, Trevor M.

2011-01-01

275

Cover sequence stratigraphy and structure of the Corbin basement culmination, Georgia Blue Ridge  

Energy Technology Data Exchange (ETDEWEB)

Southernmost Greenville basement (Corbin Gneiss (CG)) exposed in the western Blue Ridge occurs in two axial culminations of an isoclinal NW overturned anticlinorium. The anticlinorium lies west of the Murphy Syncline and the two structures appear to be genetically related. In the Lake Arrowhead area west of Waleska, the CG is directly overlain by a thin metapelitic unit containing coarse clasts derived from the CG. This is overlain by arkosic metaconglomerates, coarse arkoses and sandstones interlayered with metapellites. Cross-beddings in metasandstones face away from the CG contact indicating that the eastern limb is upright. A distinctive siliceous marble unit approximately 20 m thick occurs above the lower meta-clastic sequence. Lack of detrital texture, highly irregular shape of quartz grains and thin layers of meta-chert above the marble suggest that the original rock was siliceous limestone. Above the marble is a thick sequence of highly carbonaceous metapelite interlayered with coarse clast bearing, muddy matrix supported diamictites. The upper part of the cover sequences consists of highly carbonaceous pelites interlayered with thin layers of carbonaceous limestone. East of the anticlinorium cored by CG west of Lake Arrowhead, the structure of the cover sequences is dominated by two parallel isoclinal synclines trending approximately N-S. The western syncline consists of the lower coarse meta-clastic rocks in both limbs and graphitic metapelite in the core. However the east limb is considerably thinned by a tectonic slide or thrust fault. This fault brings a very thin, discontinuous band of highly sheared gneissic basement rock structurally above the syncline and reduces the width of the anticline between the two cover sequence synclines significantly. The eastern syncline is cut obliquely NE-SW by a second fault along the Shoal Creek NW of Waleska which brings the Great Smoky Group structurally above the CG cover sequences.

Li, Li; Tull, J.F. (Florida State Univ., Tallahassee, FL (United States). Dept. of Geology)

1993-03-01

276

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Motivation: Predicting RNA–RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods for the prediction of interactions are all based on single sequences. Since comparative methods have already been useful in RNA structure determination, we assume that ...

Seemann, Stefan E.; Richter, Andreas S.; Gesell, Tanja; Backofen, Rolf; Gorodkin, Jan

277

Characterization of the Bacillus anthracis S-layer: cloning and sequencing of the structural gene.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Bacillus anthracis, a gram-positive, spore-forming bacterium, is the etiological agent of anthrax. The gene coding for the S-layer protein (sap) was cloned on two contiguous fragments in Escherichia coli, and the complete sequence of the structural gene was determined. The protein, Sap, is composed ...

Etienne-Toumelin, I; Sirard, J C; Duflot, E; Mock, M; Fouet, A

278

Predicting Function of Genes and Proteins from Sequence, Structure and Expression Data  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Functional genomics refers to the task of determining gene and protein function for whole genomes, and requires computational analysis of large amounts of biological data including DNA and protein sequences, protein structures and gene expressions. Machine learning methods provide a powerful tool...

Hvidsten, Torgeir R.

279

Estimating the Repeat Structure and Length of DNA Sequences Using ?-Tuples  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In shotgun sequencing projects, the genome or BAC length is not always known. We approach estimating genome length by first estimating the repeat structure of the genome or BAC, sometimes of interest in its own right, on the basis of a set of random reads from a genome project. Moreover, we can f...

Li, Xiaoman; Waterman, Michael S.

280

Genomic structure and possible retroviral origin of the chicken CR1 repetitive DNA sequence family.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have analyzed the sequence and structure of three CR1 family repetitive elements found in the region adjoining the 3' end of a chicken calmodulin gene. Members of this family are approximately equal to 300 base pairs long and are dispersed throughout the chicken genome. The present data, when tak...

Stumph, W E; Hodgson, C P; Tsai, M J; O'Malley, B W

 
 
 
 
281

High evolutionary conservation of the secondary structure and of certain nucleotide sequences of U5 RNA.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The nucleotide sequence of chicken, pheasant, duck and Tetrahymena pyriformis U5 RNAs as well as that of new mammalian variant U5 RNAs was determined and compared to that of rat and HeLa cells U5 RNAs. Primary structure conservation is about 95% between rat and human cells, 82% between mammals and b...

Branlant, C; Krol, A; Lazar, E; Haendler, B; Jacob, M; Galego-Dias, L; Pousada, C

282

Recognition of a sequence as a structure containing series of recurring vectors from an alphabet  

Science.gov (United States)

A polynomial-time algorithm is designed for finding an optimal solution of a discrete optimization problem to which a pattern recognition problem is reduced, namely, the noise-proof recognition of a sequence as a structure consisting of contiguous subsequences in the form of series of identical nonzero vectors from an alphabet of vectors in the Euclidean space that alternate with zero vectors.

Kel'manov, A. V.; Mikhailova, L. V.

2013-07-01

283

Sequence Diversity, Predicted Two-Dimensional Protein Structure, and Epitope Mapping of Neisserial Opa Proteins  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The sequence diversity of 45 Opa outer membrane proteins from Neisseria meningitidis, Neisseria gonorrhoeae, Neisseria sicca, and Neisseria flava indicates that horizontal genetic exchange of opa alleles has been rare between these species. A two-dimensional structural model containing four surface-...

Malorny, Burkhard; Morelli, Giovanna; Kusecek, Barica; Kolberg, Jan; Achtman, Mark

284

WebScipio: An online tool for the determination of gene structures using protein sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Obtaining the gene structure for a given protein encoding gene is an important step in many analyses. A software suited for this task should be readily accessible, accurate, easy to handle and should provide the user with a coherent representation of the most probable gene structure. It should be rigorous enough to optimise features on the level of single bases and at the same time flexible enough to allow for cross-species searches. Results WebScipio, a web interface to the Scipio software, allows a user to obtain the corresponding coding sequence structure of a here given a query protein sequence that belongs to an already assembled eukaryotic genome. The resulting gene structure is presented in various human readable formats like a schematic representation, and a detailed alignment of the query and the target sequence highlighting any discrepancies. WebScipio can also be used to identify and characterise the gene structures of homologs in related organisms. In addition, it offers a web service for integration with other programs. Conclusion WebScipio is a tool that allows users to get a high-quality gene structure prediction from a protein query. It offers more than 250 eukaryotic genomes that can be searched and produces predictions that are close to what can be achieved by manual annotation, for in-species and cross-species searches alike. WebScipio is freely accessible at http://www.webscipio.org.

Odronitz Florian; Pillmann Holger; Keller Oliver; Waack Stephan; Kollmar Martin

2008-01-01

285

Trinucleotide repeat system for sequence specificity analysis of RNA structure probing reagents.  

Science.gov (United States)

Chemical and enzymatic structural probes have been used for decades to obtain rapid and comprehensive information regarding the molecular architecture of various RNAs. Despite their widespread use, the sequence specificity of these RNA structural probing reagents has not yet been thoroughly characterized. In this study, we revisited the properties of commonly used structural probes such as Pb(II) ions, ribonuclease V1, ribonuclease T2, and the S1 and mung bean nucleases by testing them on highly regular triplet repeat sequences representing phosphodiester bonds with every possible combination of 3' and 5' adjacent nucleotides. We show that Pb(II) ions preferentially cleave after pyrimidines and that S1 nuclease possesses a previously overlooked specificity toward phosphodiester bonds following G residues. We also observed that mung bean nuclease shows a preference for cleaving ApN bonds and that RNase V1 mainly recognizes U residues in both single- and double-stranded RNAs. These data are important for accurate interpretation of the results of structure probing experiments and for assignment of the correct structure to individual RNA molecules. The triplet repeat transcript system described here may be considered as a reliable platform for determining the sequence specificity of other reagents used to probe RNA structure. PMID:20302838

Sobczak, Krzysztof; Michlewski, Gracjan; de Mezer, Mateusz; Krol, Jacek; Krzyzosiak, Wlodzimierz J

2010-03-17

286

Trinucleotide repeat system for sequence specificity analysis of RNA structure probing reagents.  

UK PubMed Central (United Kingdom)

Chemical and enzymatic structural probes have been used for decades to obtain rapid and comprehensive information regarding the molecular architecture of various RNAs. Despite their widespread use, the sequence specificity of these RNA structural probing reagents has not yet been thoroughly characterized. In this study, we revisited the properties of commonly used structural probes such as Pb(II) ions, ribonuclease V1, ribonuclease T2, and the S1 and mung bean nucleases by testing them on highly regular triplet repeat sequences representing phosphodiester bonds with every possible combination of 3' and 5' adjacent nucleotides. We show that Pb(II) ions preferentially cleave after pyrimidines and that S1 nuclease possesses a previously overlooked specificity toward phosphodiester bonds following G residues. We also observed that mung bean nuclease shows a preference for cleaving ApN bonds and that RNase V1 mainly recognizes U residues in both single- and double-stranded RNAs. These data are important for accurate interpretation of the results of structure probing experiments and for assignment of the correct structure to individual RNA molecules. The triplet repeat transcript system described here may be considered as a reliable platform for determining the sequence specificity of other reagents used to probe RNA structure.

Sobczak K; Michlewski G; de Mezer M; Krol J; Krzyzosiak WJ

2010-07-01

287

Sequence of the human 40-kDa keratin reveals an unusual structure with very high sequence identity to the corresponding bovine keratin  

International Nuclear Information System (INIS)

[en] The complete amino acid and DNA sequences of the human 40-kDa keratin are reported. The DNA sequence encodes a protein of 44,098 Da, which is unique in that it lacks the terminal non-?-helical tail segment found in all other keratins. When the human 40-kDa keratin amino acid sequence is compared to the corresponding bovine keratin, the overall identity is 89%. The coil-forming regions are 89% identical and the head regions are 88% identical. This similarity is also evident in the DNA sequence of the coding region, the 5' upstream sequences, and the 3' noncoding sequences. The high degree of cross-species identity between bovine and human 40-kDa keratins suggests that there is strong evolutionary pressure to conserve the structure of this keratin. This in turn suggests an important and universal role for this intermediate filament subunit in all species

1988-01-01

288

Polaron in a quasi 1D cylindrical quantum wire  

Directory of Open Access Journals (Sweden)

Full Text Available Polaron states in a quasi 1D cylindrical quantum wire with a parabolic confinement potential are investigated applying the Feynman variational principle. The effect of the wire radius on the polaron ground state energy level, the mass and the Fröhlich electron-phonon-coupling constant are obtained for the case of a quasi 1D cylindrical quantum wire. The effect of anisotropy of the structure on the polaron ground state energy level and the mass are also investigated. It is observed that as the wire radius tends to zero, the polaron mass and energy diverge logarithmically. The polaron mass and energy differ from the canonical strong-coupling behavior by the Fröhlich electron-phonon coupling constant and the radius of the quasi 1D cylindrical quantum wire that are expressed through a logarithmic function. Moreover, it is observed that the polaron energy and mass for strong coupling for the case of the quasi 1D cylindrical quantum wire are greater than those for bulk crystals. It is also observed that the anisotropy of the structure considerably affects both the polaron ground state energy level and the mass. It is found that as the radius of the cylindrical wire reduces, the regimes of the weak and intermediate coupling polaron shorten while the region of the strong coupling polaron broadens and extends into those of the weak and intermediate ones. Analytic expressions for the polaron ground state energy level and mass are derived for the case of strong coupling polarons.

L.C.Fai; V.Teboul; A.Monteil; S.Maabou; I.Nsangou

2005-01-01

289

A sequence-based survey of the complex structural organization of tumor genomes  

Energy Technology Data Exchange (ETDEWEB)

The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using End Sequencing Profiling (ESP), which relies on paired-end sequencing of cloned tumor genomes. In this study, brain, breast, ovary and prostate tumors along with three breast cancer cell lines were surveyed with ESP yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization (FISH) confirmed translocations and complex tumor genome structures that include coamplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison of the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms (SNPs) revealed candidate somatic mutations and an elevated rate of novel SNPs in an ovarian tumor. These results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than previously appreciated and that genomic fusions including fusion transcripts and proteins may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.

Collins, Colin; Raphael, Benjamin J.; Volik, Stanislav; Yu, Peng; Wu, Chunxiao; Huang, Guiqing; Linardopoulou, Elena V.; Trask, Barbara J.; Waldman, Frederic; Costello, Joseph; Pienta, Kenneth J.; Mills, Gordon B.; Bajsarowicz, Krystyna; Kobayashi, Yasuko; Sridharan, Shivaranjani; Paris, Pamela; Tao, Quanzhou; Aerni, Sarah J.; Brown, Raymond P.; Bashir, Ali; Gray, Joe W.; Cheng, Jan-Fang; de Jong, Pieter; Nefedov, Mikhail; Ried, Thomas; Padilla-Nash, Hesed M.; Collins, Colin C.

2008-04-03

290

Microbial structures, functions, and metabolic pathways in wastewater treatment bioreactors revealed using high-throughput sequencing.  

UK PubMed Central (United Kingdom)

The objective of this study was to explore microbial community structures, functional profiles, and metabolic pathways in a lab-scale and a full-scale wastewater treatment bioreactors. In order to do this, over 12 gigabases of metagenomic sequence data and 600,000 paired-end sequences of bacterial 16S rRNA gene were generated with the Illumina HiSeq 2000 platform, using DNA extracted from activated sludge in the two bioreactors. Three kinds of sequences (16S rRNA gene amplicons, 16S rRNA gene sequences obtained from metagenomic sequencing, and predicted proteins) were used to conduct taxonomic assignments. Specially, relative abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were analyzed. Compared with quantitative real-time PCR (qPCR), metagenomic sequencing was demonstrated to be a better approach to quantify AOA and AOB in activated sludge samples. It was found that AOB were more abundant than AOA in both reactors. Furthermore, the analysis of the metabolic profiles indicated that the overall patterns of metabolic pathways in the two reactors were quite similar (73.3% of functions shared). However, for some pathways (such as carbohydrate metabolism and membrane transport), the two reactors differed in the number of pathway-specific genes.

Ye L; Zhang T; Wang T; Fang Z

2012-12-01

291

Dissect: detection and characterization of novel structural alterations in transcribed sequences.  

UK PubMed Central (United Kingdom)

MOTIVATION: Computational identification of genomic structural variants via high-throughput sequencing is an important problem for which a number of highly sophisticated solutions have been recently developed. With the advent of high-throughput transcriptome sequencing (RNA-Seq), the problem of identifying structural alterations in the transcriptome is now attracting significant attention. In this article, we introduce two novel algorithmic formulations for identifying transcriptomic structural variants through aligning transcripts to the reference genome under the consideration of such variation. The first formulation is based on a nucleotide-level alignment model; a second, potentially faster formulation is based on chaining fragments shared between each transcript and the reference genome. Based on these formulations, we introduce a novel transcriptome-to-genome alignment tool, Dissect (DIScovery of Structural Alteration Event Containing Transcripts), which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. Dissect is suitable for whole transcriptome structural variation discovery problems involving sufficiently long reads or accurately assembled contigs. RESULTS: We tested Dissect on simulated transcripts altered via structural events, as well as assembled RNA-Seq contigs from human prostate cancer cell line C4-2. Our results indicate that Dissect has high sensitivity and specificity in identifying structural alteration events in simulated transcripts as well as uncovering novel structural alterations in cancer transcriptomes. AVAILABILITY: Dissect is available for public use at: http://dissect-trans.sourceforge.net.

Yorukoglu D; Hach F; Swanson L; Collins CC; Birol I; Sahinalp SC

2012-06-01

292

GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences.  

UK PubMed Central (United Kingdom)

The widespread use of the original version of GRASP revealed the importance of the visualization of physicochemical and structural properties on the molecular surface. This chapter describes a new version of GRASP that contains many new capabilities. In terms of analysis tools, the most notable new features are sequence and structure analysis and alignment tools and the graphical integration of sequence and structural information. Not all the new GRASP2 could be described here and more capabilities are continually being added. An on-line manual, details on obtaining the software, and technical notes about the program and the Troll software library can be found at the Honig laboratory Web site (http://trantor.bioc.columbia.edu).

Petrey D; Honig B

2003-01-01

293

Tick-borne encephalitis virus genome. The nucleotide sequence coding for virion structural proteins.  

UK PubMed Central (United Kingdom)

RNA of a flavivirus, tick-borne encephalitis virus (TBEV; strain Sofjin), was subjected to reverse transcription and the DNA copy was transformed into double-stranded DNA by the action of E. coli DNA-polymerase I (Klenow fragment). This DNA was annealed with plasmid pBR322. The recombinant plasmids were cloned in E. coli K802. The nucleotide sequence of the inserts of the clones, coding for region structural proteins C, M, E and nonstructural protein NS1, was determined by the Maxam-Gilbert method. The genes of structural proteins form a compact cluster. Homology has been studied of the TBEV sequences found with the structures of proteins and RNAs of other flaviviruses, yellow fever virus and West Nile virus, and a high degree of homology was found.

Pletnev AG; Yamshchikov VF; Blinov VM

1986-05-01

294

Conversion of Human Steroid 5?-Reductase (AKR1D1) into 3?-Hydroxysteroid Dehydrogenase by Single Point Mutation E120H  

Science.gov (United States)

Human aldo-keto reductase 1D1 (AKR1D1) and AKR1C enzymes are essential for bile acid biosynthesis and steroid hormone metabolism. AKR1D1 catalyzes the 5?-reduction of ?4-3-ketosteroids, whereas AKR1C enzymes are hydroxysteroid dehydrogenases (HSDs). These enzymes share high sequence identity and catalyze 4-pro-(R)-hydride transfer from NADPH to an electrophilic carbon but differ in that one residue in the conserved AKR catalytic tetrad, His120 (AKR1D1 numbering), is substituted by a glutamate in AKR1D1. We find that the AKR1D1 E120H mutant abolishes 5?-reductase activity and introduces HSD activity. However, the E120H mutant unexpectedly favors dihydrosteroids with the 5?-configuration and, unlike most of the AKR1C enzymes, shows a dominant stereochemical preference to act as a 3?-HSD as opposed to a 3?-HSD. The catalytic efficiency achieved for 3?-HSD activity is higher than that observed for any AKR to date. High resolution crystal structures of the E120H mutant in complex with epiandrosterone, 5?-dihydrotestosterone, and ?4-androstene-3,17-dione elucidated the structural basis for this functional change. The glutamate-histidine substitution prevents a 3-ketosteroid from penetrating the active site so that hydride transfer is directed toward the C3 carbonyl group rather than the ?4-double bond and confers 3?-HSD activity on the 5?-reductase. Structures indicate that stereospecificity of HSD activity is achieved because the steroid flips over to present its ?-face to the A-face of NADPH. This is in contrast to the AKR1C enzymes, which can invert stereochemistry when the steroid swings across the binding pocket. These studies show how a single point mutation in AKR1D1 can introduce HSD activity with unexpected configurational and stereochemical preference.

Chen, Mo; Drury, Jason E.; Christianson, David W.; Penning, Trevor M.

2012-01-01

295

Conversion of human steroid 5?-reductase (AKR1D1) into 3?-hydroxysteroid dehydrogenase by single point mutation E120H: example of perfect enzyme engineering.  

UK PubMed Central (United Kingdom)

Human aldo-keto reductase 1D1 (AKR1D1) and AKR1C enzymes are essential for bile acid biosynthesis and steroid hormone metabolism. AKR1D1 catalyzes the 5?-reduction of ?(4)-3-ketosteroids, whereas AKR1C enzymes are hydroxysteroid dehydrogenases (HSDs). These enzymes share high sequence identity and catalyze 4-pro-(R)-hydride transfer from NADPH to an electrophilic carbon but differ in that one residue in the conserved AKR catalytic tetrad, His(120) (AKR1D1 numbering), is substituted by a glutamate in AKR1D1. We find that the AKR1D1 E120H mutant abolishes 5?-reductase activity and introduces HSD activity. However, the E120H mutant unexpectedly favors dihydrosteroids with the 5?-configuration and, unlike most of the AKR1C enzymes, shows a dominant stereochemical preference to act as a 3?-HSD as opposed to a 3?-HSD. The catalytic efficiency achieved for 3?-HSD activity is higher than that observed for any AKR to date. High resolution crystal structures of the E120H mutant in complex with epiandrosterone, 5?-dihydrotestosterone, and ?(4)-androstene-3,17-dione elucidated the structural basis for this functional change. The glutamate-histidine substitution prevents a 3-ketosteroid from penetrating the active site so that hydride transfer is directed toward the C3 carbonyl group rather than the ?(4)-double bond and confers 3?-HSD activity on the 5?-reductase. Structures indicate that stereospecificity of HSD activity is achieved because the steroid flips over to present its ?-face to the A-face of NADPH. This is in contrast to the AKR1C enzymes, which can invert stereochemistry when the steroid swings across the binding pocket. These studies show how a single point mutation in AKR1D1 can introduce HSD activity with unexpected configurational and stereochemical preference.

Chen M; Drury JE; Christianson DW; Penning TM

2012-05-01

296

Sequence and structural analysis of two designed proteins with 88% identity adopting different folds.  

UK PubMed Central (United Kingdom)

Protein folding is a natural phenomenon by which a sequence of amino acids folds into a unique functional three-dimensional structure. Although the sequence code that governs folding remains a mystery, one can identify key inter-residue contacts responsible for a given topology. In nature, there are many pairs of proteins of a given length that share little or no sequence identity. Similarly, there are many proteins that share a common topology but lack significant evidence of homology. In order to tackle this problem, protein engineering studies have been used to determine the minimal number of amino acid residues that codes for a particular fold. In recent years, the coupling of theoretical models and experiments in the study of protein folding has resulted in providing some fruitful clues. He et al. have designed two proteins with 88% sequence identity, which adopt different folds and functions. In this work, we have systematically analysed these two proteins by performing pentapeptide search, secondary structure predictions, variation in inter-residue interactions and residue-residue pair preferences, surrounding hydrophobicity computations, conformational switching and energy computations. We conclude that the local secondary structural preference of the two designed proteins at the Nand C-terminal ends to adopt either coil or strand conformation may be a crucial factor in adopting the different folds. Early on during the process of folding, both proteins may choose different energetically favourable pathways to attain the different folds.

Saravanan KM; Balasubramanian H; Nallusamy S; Samuel S

2010-12-01

297

Group-specific structural features of the 5'-proximal sequences of coronavirus genomic RNAs.  

Science.gov (United States)

Global predictions of the secondary structure of coronavirus (CoV) 5' untranslated regions and adjacent coding sequences revealed the presence of conserved structural elements. Stem loops (SL) 1, 2, 4, and 5 were predicted in all CoVs, while the core leader transcription-regulating sequence (L-TRS) forms SL3 in only some CoVs. SL5 in group I and II CoVs, with the exception of group IIa CoVs, is characterized by the presence of a large sequence insertion capable of forming hairpins with the conserved 5'-UUYCGU-3' loop sequence. Structure probing confirmed the existence of these hairpins in the group I Human coronavirus-229E and the group II Severe acute respiratory syndrome coronavirus (SARS-CoV). In general, the pattern of the 5' cis-acting elements is highly related to the lineage of CoVs, including features of the conserved hairpins in SL5. The function of these conserved hairpins as a putative packaging signal is discussed. PMID:20202661

Chen, Shih-Cheng; Olsthoorn, René C L

2010-03-04

298

Bioinformatical approaches to RNA structure prediction & Sequencing of an ancient human genome  

DEFF Research Database (Denmark)

Stinus Lindgreen has been working in two different fields during his Ph.D. The first part has been focused on computational approaches to predict the structure of non-coding RNA molecules at the base pairing level. This has resulted in the analysis of various measures of the base pairing potential in families of related RNA sequences. Also, the program MASTR was developed to perform simultaneous alignment of multiple RNA sequences and prediction of a common secondary structure. The webserver WAR was developed to make it easy for non-computer savy researchers to use the many RNA structure prediction tools that exist. The second part has been focused on the mapping and genotyping of ancient genomic DNA. The development of next generation sequencing technologies combined with the use of ancient DNA material present the researchers with some special challenges in the analyses. This work resulted in the publication of the first genome of an ancient human individual, where close to the theoretical maximum of the genome sequence was recovered with high confidence. Part of the project was the development of the program SNPest for genotyping and SNP calling that models various sources of error and predicts genotypes with the highest posterior probability.

Lindgreen, Stinus

2010-01-01

299

Data structures and compression algorithms for high-throughput sequencing technologies.  

UK PubMed Central (United Kingdom)

BACKGROUND: High-throughput sequencing (HTS) technologies play important roles in the life sciences by allowing the rapid parallel sequencing of very large numbers of relatively short nucleotide sequences, in applications ranging from genome sequencing and resequencing to digital microarrays and ChIP-Seq experiments. As experiments scale up, HTS technologies create new bioinformatics challenges for the storage and sharing of HTS data. RESULTS: We develop data structures and compression algorithms for HTS data. A processing stage maps short sequences to a reference genome or a large table of sequences. Then the integers representing the short sequence absolute or relative addresses, their length, and the substitutions they may contain are compressed and stored using various entropy coding algorithms, including both old and new fixed codes (e.g Golomb, Elias Gamma, MOV) and variable codes (e.g. Huffman). The general methodology is illustrated and applied to several HTS data sets. Results show that the information contained in HTS files can be compressed by a factor of 10 or more, depending on the statistical properties of the data sets and various other choices and constraints. Our algorithms fair well against general purpose compression programs such as gzip, bzip2 and 7zip; timing results show that our algorithms are consistently faster than the best general purpose compression programs. CONCLUSIONS: It is not likely that exactly one encoding strategy will be optimal for all types of HTS data. Different experimental conditions are going to generate various data distributions whereby one encoding strategy can be more effective than another. We have implemented some of our encoding algorithms into the software package GenCompress which is available upon request from the authors. With the advent of HTS technology and increasingly new experimental protocols for using the technology, sequence databases are expected to continue rising in size. The methodology we have proposed is general, and these advanced compression techniques should allow researchers to manage and share their HTS data in a more timely fashion.

Daily K; Rigor P; Christley S; Xie X; Baldi P

2010-01-01

300

Systematic MCDF studies of isotope shifts, hyperfine structures and transition probabilities in the lithium isoelectronic sequence  

International Nuclear Information System (INIS)

Results from multiconfiguration Dirac-Fock calculations of isotope shifts, hyperfine structures and transition probabilites of the 1s22s 2S - 1s22p 2P transitions in the lithium isoelectronic sequence are reported. Using the active space method, the configuration space is systematically increased allowing the convergence of the calculated properties to be studied. The size and importance of the relativistic effects are investigated by comparing the calculated values with the corresponding values from non-relativistic multiconfiguration Hartree-Fock calculations. For the most highly ionized atoms in the sequence, the effects of the Breit interaction are investigated

1996-01-01

 
 
 
 
301

Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences.  

UK PubMed Central (United Kingdom)

N-SCAN is a gene-prediction system that combines the methods of ab initio predictors like GENSCAN with information derived from genome comparison. It is the latest in the TWINSCAN series of programs. This unit describes the use of N-SCAN to identify gene structures in eukaryotic genomic sequences. Protocols for using N-SCAN through its Web interface and from the command line in a Linux environment are provided. Detailed discussion about the appropriate parameter settings, input-sequence processing, and choice of genome for comparison are included.

van Baren MJ; Koebbe BC; Brent MR

2007-12-01

302

Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences.  

Science.gov (United States)

N-SCAN is a gene-prediction system that combines the methods of ab initio predictors like GENSCAN with information derived from genome comparison. It is the latest in the TWINSCAN series of programs. This unit describes the use of N-SCAN to identify gene structures in eukaryotic genomic sequences. Protocols for using N-SCAN through its Web interface and from the command line in a Linux environment are provided. Detailed discussion about the appropriate parameter settings, input-sequence processing, and choice of genome for comparison are included. PMID:18428682

van Baren, Marijke J; Koebbe, Brian C; Brent, Michael R

2007-12-01

303

Structure- and sequence-analysis inspired engineering of proteins for enhanced thermostability.  

UK PubMed Central (United Kingdom)

Protein engineering strategies for increasing stability can be improved by replacing random mutagenesis and high-throughput screening by approaches that include bioinformatics and computational design. Mutations can be focused on regions in the structure that are most flexible and involved in the early steps of thermal unfolding. Sequence analysis can often predict the position and nature of stabilizing mutations, and may allow the reconstruction of thermostable ancestral sequences. Various computational tools make it possible to design stabilizing features, such as hydrophobic clusters and surface charges. Different methods for designing chimeric enzymes can also support the engineering of more stable proteins without the need of high-throughput screening.

Wijma HJ; Floor RJ; Janssen DB

2013-08-01

304

Auslander-Reiten sequences and $t$-structures on the homotopy category of an abelian category  

CERN Multimedia

Let $\\Cab$ be an abelian category and let $\\KC$ be the bounded homotopy category of cochain complexes in $\\Cab$. We consider a $t$-structure on $\\KC$ that maps to the standard $t$-structure on the derived category $\\DC$ under the localization functor. Let $\\A$ be the heart of the $t$-structure. In the case when $\\Cab$ has finite length we show that objects of $\\Cab$ correspond to projective objects of $\\A$ and that simple objects of $\\A$ (if they exist) are given by Auslander's and Reiten's almost split sequences in $\\Cab$.

Backelin, Erik

2009-01-01

305

Stem-loop structures of the repetitive DNA sequences located at human centromeres  

Energy Technology Data Exchange (ETDEWEB)

The presence of the highly conserved repetitive DNA sequences in the human centromeres argues for a special role of these sequences in their biological functions - most likely achieved by the formation of unusual structures. This prompted us to carry out quantitative one- and two-dimensional nuclear magnetic resonance (lD/2D NMR) spectroscopy to determine the structural properties of the human centromeric repeats, d(AATGG){sub n.d}(CCATT){sub n}. The studies on centromeric DNAs reveal that the complementary sequence, d(AATGG){sub n.d}(CCATT){sub n}, adopts the usual Watson-Crick B-DNA duplex and the pyrimidine-rich d(CCATT){sub n} strand is essentially a random coil. However, the purine-rich d(AATGG){sub n} strand is shown to adopt unusual stem-loop structures for repeat lengths, n=2,3,4, and 6. In addition to normal Watson-Crick A{center_dot}T pairs, the stem-loop structures are stabilized by mismatch A{center_dot}G and G{center_dot}G pairs in the stem and G-G-A stacking in the loop. Stem-loop structures of d(AATGG)n are independently verified by gel electrophoresis and nuclease digestion studies. Thermal melting studies show that the DNA repeats, d(AATGG){sub n}, are as stable as the corresponding Watson-Crick duplex d(AATGG){sub n.d}(CCATT){sub n}. Therefore, the sequence d(AATGG){sub n} can, indeed, nucleate a stem-loop structure at little free-energy cost and if, during mitosis, they are located on the chromosome surface they can provide specific recognition sites for kinetochore function.

Gupta, G.; Garcia, A.E.; Ratliff, R.; Moyzis, R.K. [Los Alamos National Lab., NM (United States); Catasti, P.; Hong, Lin; Yau, P. [California Univ., Davis, CA (United States). Dept. of Biological Chemistry; Bradbury, E.M. [Los Alamos National Lab., NM (United States)]|[California Univ., Davis, CA (United States). Dept. of Biological Chemistry

1993-09-01

306

Data mining of sequences and 3D structures of allergenic proteins.  

UK PubMed Central (United Kingdom)

MOTIVATION: Many sequences, and in some cases structures, of proteins that induce an allergic response in atopic individuals have been determined in recent years. This data indicates that allergens, regardless of source, fall into discreet protein families. Similarities in the sequence may explain clinically observed cross-reactivities between different biological triggers. However, previously available allergy databases group allergens according to their biological sources, or observed clinical cross-reactivities, without providing data about the proteins. A computer-aided data mining system is needed to compare the sequential and structural details of known allergens. This information will aid in predicting allergenic cross-responses and eventually in determining possible common characteristics of IgE recognition. RESULTS: The new web-based Structural Database of Allergenic Proteins (SDAP) permits the user to quickly compare the sequence and structure of allergenic proteins. Data from literature sources and previously existing lists of allergens are combined in a MySQL interactive database with a wide selection of bioinformatics applications. SDAP can be used to rapidly determine the relationship between allergens and to screen novel proteins for the presence of IgE or T-cell epitopes they may share with known allergens. Further, our novel similarity search method, based on five dimensional descriptors of amino acid properties, can be used to scan the SDAP entries with a peptide sequence. For example, when a known IgE binding epitope from shrimp tropomyosin was used as a query, the method rapidly identified a similar sequence in known shellfish and insect allergens. This prediction of cross-reactivity between allergens is consistent with clinical observations. AVAILABILITY: SDAP is available on the web at http://fermi.utmb.edu/SDAP/index.html

Ivanciuc O; Schein CH; Braun W

2002-10-01

307

STP Random Walk 1D Program  

Science.gov (United States)

The RandomWalk1D program simulates a random walk in one dimension for steps of unit length and equal time intervals. The default number of steps is N = 16 and the probability of going right or left at any step is the same (the probability p of going to the right for a single step is 0.5). RandomWalk1D is part of a suite of Open Source Physics programs that model aspects of Statistical and Thermal Physics (STP). The program is distributed as a ready-to-run (compiled) Java archive. Double clicking the stp RandomWalk1D.jar file will run the program if Java is installed on your computer. Additional programs can be found by searching ComPADRE for Open Source Physics, STP, or Statistical and Thermal Physics.

Gould, Harvey; Tobochnik, Jan; Christian, Wolfgang; Cox, Anne

2008-10-10

308

Coupling method of 1-d/1-d and 1-d/3-d junctions for an implict WCOBRA/TRAC  

Energy Technology Data Exchange (ETDEWEB)

COBRA/TRAC is an advanced thermal-hydraulic computer code, originally developed by Battelle Pacific Northwest Laboratories. The code combines a two-fluid, three-dimensional (3-d) program, COBRA-TF, with a one-dimensional (1-d) drift flux program, TRAC-PD2. COBRA-TF is designed to be used to model the pressurized water reactor (PWR), and loop components are modeled with TRAC-PD2. An implicit method was proposed for the COBRA part of the code, and some success was achieved as demonstrated by an analysis of a film-boiling experiment for a steady-state and power ascension transient. On the other hand, TRAC-PD2 includes an option to choose a semi-implicit or an implicit method in solving component equations. This implicit option improves running time somewhat, but the junctions among the components are treated semi-implicitly. So, the time step is controlled by the Courant numbers at the 1-d/3-d and 1-d/1-d component junctions. In order to speed up the code further, the solution method for the junctions must be changed to implicit. An implicit method is introduced. It is evaluated by a COBRA/TRAC model of a less-of-fluid test (LOFT) and a two-loop PWR.

Takeuchi, K.; Young, M.Y.

1988-01-01

309

PALLAS-1D(V3): variable-dimension version of PALLAS-1D(VII)  

International Nuclear Information System (INIS)

[en] The PALLAS-1D(V3) program is a variable-dimension version of the PALLAS-1D(VII) code, which is the revised version of the PALLAS-PL, SP-Br code. The PALLAS-1D(VII) code could treat transport of both neutrons and gamma rays, in particular of secondary photons including the bremsstrahlung and annihilation photons. This document gives a full description of input and output data for PALLAS-1D(V3) code, also with the input description of several sample problems. (author)

1990-01-01

310

Genome sequence, comparative analysis and haplotype structure of the domestic dog.  

UK PubMed Central (United Kingdom)

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

Lindblad-Toh K; Wade CM; Mikkelsen TS; Karlsson EK; Jaffe DB; Kamal M; Clamp M; Chang JL; Kulbokas EJ 3rd; Zody MC; Mauceli E; Xie X; Breen M; Wayne RK; Ostrander EA; Ponting CP; Galibert F; Smith DR; DeJong PJ; Kirkness E; Alvarez P; Biagi T; Brockman W; Butler J; Chin CW; Cook A; Cuff J; Daly MJ; DeCaprio D; Gnerre S; Grabherr M; Kellis M; Kleber M; Bardeleben C; Goodstadt L; Heger A; Hitte C; Kim L; Koepfli KP; Parker HG; Pollinger JP; Searle SM; Sutter NB; Thomas R; Webber C; Baldwin J; Abebe A; Abouelleil A; Aftuck L; Ait-Zahra M; Aldredge T; Allen N; An P; Anderson S; Antoine C; Arachchi H; Aslam A; Ayotte L; Bachantsang P; Barry A; Bayul T; Benamara M; Berlin A; Bessette D; Blitshteyn B; Bloom T; Blye J; Boguslavskiy L; Bonnet C; Boukhgalter B; Brown A; Cahill P; Calixte N; Camarata J; Cheshatsang Y; Chu J; Citroen M; Collymore A; Cooke P; Dawoe T; Daza R; Decktor K; DeGray S; Dhargay N; Dooley K; Dooley K; Dorje P; Dorjee K; Dorris L; Duffey N; Dupes A; Egbiremolen O; Elong R; Falk J; Farina A; Faro S; Ferguson D; Ferreira P; Fisher S; FitzGerald M; Foley K; Foley C; Franke A; Friedrich D; Gage D; Garber M; Gearin G; Giannoukos G; Goode T; Goyette A; Graham J; Grandbois E; Gyaltsen K; Hafez N; Hagopian D; Hagos B; Hall J; Healy C; Hegarty R; Honan T; Horn A; Houde N; Hughes L; Hunnicutt L; Husby M; Jester B; Jones C; Kamat A; Kanga B; Kells C; Khazanovich D; Kieu AC; Kisner P; Kumar M; Lance K; Landers T; Lara M; Lee W; Leger JP; Lennon N; Leuper L; LeVine S; Liu J; Liu X; Lokyitsang Y; Lokyitsang T; Lui A; Macdonald J; Major J; Marabella R; Maru K; Matthews C; McDonough S; Mehta T; Meldrim J; Melnikov A; Meneus L; Mihalev A; Mihova T; Miller K; Mittelman R; Mlenga V; Mulrain L; Munson G; Navidi A; Naylor J; Nguyen T; Nguyen N; Nguyen C; Nguyen T; Nicol R; Norbu N; Norbu C; Novod N; Nyima T; Olandt P; O'Neill B; O'Neill K; Osman S; Oyono L; Patti C; Perrin D; Phunkhang P; Pierre F; Priest M; Rachupka A; Raghuraman S; Rameau R; Ray V; Raymond C; Rege F; Rise C; Rogers J; Rogov P; Sahalie J; Settipalli S; Sharpe T; Shea T; Sheehan M; Sherpa N; Shi J; Shih D; Sloan J; Smith C; Sparrow T; Stalker J; Stange-Thomann N; Stavropoulos S; Stone C; Stone S; Sykes S; Tchuinga P; Tenzing P; Tesfaye S; Thoulutsang D; Thoulutsang Y; Topham K; Topping I; Tsamla T; Vassiliev H; Venkataraman V; Vo A; Wangchuk T; Wangdi T; Weiand M; Wilkinson J; Wilson A; Yadav S; Yang S; Yang X; Young G; Yu Q; Zainoun J; Zembek L; Zimmer A; Lander ES

2005-12-01

311

Multi-scale coding of genomic information: From DNA sequence to genome structure and function  

International Nuclear Information System (INIS)

[en] Understanding how chromatin is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. Since the different orders of packaging in the hierarchical organization of DNA condition the accessibility of DNA sequence elements to trans-acting factors that control the transcription and replication processes, there is actually a wealth of structural and dynamical information to learn in the primary DNA sequence. In this review, we show that when using concepts, methodologies, numerical and experimental techniques coming from statistical mechanics and nonlinear physics combined with wavelet-based multi-scale signal processing, we are able to decipher the multi-scale sequence encoding of chromatin condensation-decondensation mechanisms that play a fundamental role in regulating many molecular processes involved in nuclear functions.

2011-01-01

312

Common nucleotide sequence of structural gene encoding fibroblast growth factor 4 in eight cattle derived from three breeds.  

UK PubMed Central (United Kingdom)

Fibroblast growth factor 4 (FGF4) is considered as a crucial gene for the proper development of bovine embryos. However, the complete nucleotide sequences of the structural genes encoding FGF4 in identified breeds are still unknown. In the present study, direct sequencing of PCR products derived from genomic DNA samples obtained from three Japanese Black, two Japanese Shorthorn and three Holstein cattle, revealed that the nucleotide sequences of the structural gene encoding FGF4 matched completely among these eight cattle. On the other hand, differences in the nucleotide sequences, leading to substitutions, insertions or deletions of amino acid residues were detected when compared with the already reported sequence from unidentified breeds. We cannot rule out a possibility that the structural gene elucidated in the present study is widely distributed in cattle. To the best of our knowledge, this is the first determination of the complete nucleotide sequence of the structural gene encoding bovine FGF4 in identified breeds.

Sato S; Takahashi T; Nishinomiya H; Katoh M; Itoh R; Yokoo M; Yokoo M; Iha M; Mori Y; Kasuga K; Kojima I; Kobayashi M

2012-03-01

313

Common nucleotide sequence of structural gene encoding fibroblast growth factor 4 in eight cattle derived from three breeds.  

Science.gov (United States)

Fibroblast growth factor 4 (FGF4) is considered as a crucial gene for the proper development of bovine embryos. However, the complete nucleotide sequences of the structural genes encoding FGF4 in identified breeds are still unknown. In the present study, direct sequencing of PCR products derived from genomic DNA samples obtained from three Japanese Black, two Japanese Shorthorn and three Holstein cattle, revealed that the nucleotide sequences of the structural gene encoding FGF4 matched completely among these eight cattle. On the other hand, differences in the nucleotide sequences, leading to substitutions, insertions or deletions of amino acid residues were detected when compared with the already reported sequence from unidentified breeds. We cannot rule out a possibility that the structural gene elucidated in the present study is widely distributed in cattle. To the best of our knowledge, this is the first determination of the complete nucleotide sequence of the structural gene encoding bovine FGF4 in identified breeds. PMID:22435631

Sato, Sho; Takahashi, Toshikiyo; Nishinomiya, Hiroshi; Katoh, Makiko; Itoh, Ryu; Yokoo, Masaki; Yokoo, Mari; Iha, Momoe; Mori, Yuki; Kasuga, Kano; Kojima, Ikuo; Kobayashi, Masayuki

2012-01-30

314

A structural study for the optimisation of functional motifs encoded in protein sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that – at least in some cases – the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure. Results Here we present a new procedure aimed at improving the sensitivity and/ or specificity of poorly-performing patterns. The procedure can be summarised as follows: 1. residues structurally conserved in different proteins, that are true positives for a pattern, are identified by means of a computational technique and by visual inspection. 2. the sequence positions of the structurally conserved residues falling outside the pattern are used to build extended sequence patterns. 3. the extended patterns are optimised on the SWISS-PROT database for their sensitivity and specificity. The method was applied to eight PROSITE patterns. Whenever structurally conserved residues are found in the surface region close to the pattern (seven out of eight cases), the addition of information inferred from structural analysis is shown to improve pattern selectivity and in some cases selectivity and sensitivity as well. In some of the cases considered the procedure allowed the identification of functionally interesting residues, whose biological role is also discussed. Conclusion Our method can be applied to any type of functional motif or pattern (not only PROSITE ones) which is not able to select all and only the true positive hits and for which at least two true positive structures are available. The computational technique for the identification of structurally conserved residues is already available on request and will be soon accessible on our web server. The procedure is intended for the use of pattern database curators and of scientists interested in a specific protein family for which no specific or selective patterns are yet available.

Via Allegra; Helmer-Citterich Manuela

2004-01-01

315

DNA sequences of the D-serine deaminase control region and N-terminal portion of the structural gene.  

UK PubMed Central (United Kingdom)

We determined the DNA sequence of the D-serine deaminase promoter region and of the N-terminal region of the structural gene. There are possibilities in the promoter for secondary structure and for initiation recognition sequences, and there is an open reading frame. The N-terminal sequence for the structural gene confirms that part of the amino acid sequence previously determined by E. Schlitz and W. Schmitt (FEBS Lett. 134:57-62, 1981), including the active site of the enzyme, and spans the two regions unresolved by their work.

McFall E; Runkel L

1983-06-01

316

DOE-2 Supplement, Version 2. 1D  

Energy Technology Data Exchange (ETDEWEB)

This package of updates to the DOE-2 documentation brings the previously published materials (with the exception of the Users Guide) up to Version 2.1D of the DOE-2 program. The user may verify that the program being used is 2.1D by checking the first page of the output and also the upper right hand heading of any output page of the computer printout. This document contains in concise form the basis information on all commands and keywords in the DOE-2 Building Description Language (BDL) as well as a number of supplementary tables and maps.

1989-06-01

317

Polydiacetylene-Peptide 1D Nanomaterials.  

Science.gov (United States)

Polydiacetylenes have received intense attention on account of their well-established chromic alterations that are detectable often by the naked eye, making them ideal for a variety of applications such as biosensory materials. These polymers have been fabricated in a variety of materials platforms including 3D crystals, 2D monolayers, and 0D spherical vesicles; however, 1D morphologies that might be useful for directional energy migration are less common. This article describes the development and current research efforts of protein-based 1D nanowire-like supramolecular assemblies with embedded polydiacetylenes. PMID:23922317

Diegelmann, Stephen R; Tovar, John D

2013-08-06

318

Polydiacetylene-Peptide 1D Nanomaterials.  

UK PubMed Central (United Kingdom)

Polydiacetylenes have received intense attention on account of their well-established chromic alterations that are detectable often by the naked eye, making them ideal for a variety of applications such as biosensory materials. These polymers have been fabricated in a variety of materials platforms including 3D crystals, 2D monolayers, and 0D spherical vesicles; however, 1D morphologies that might be useful for directional energy migration are less common. This article describes the development and current research efforts of protein-based 1D nanowire-like supramolecular assemblies with embedded polydiacetylenes.

Diegelmann SR; Tovar JD

2013-09-01

319

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.  

UK PubMed Central (United Kingdom)

BACKGROUND: We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. RESULTS: We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. CONCLUSION: Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm - this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN - have comparable overall performance with different strengths and weaknesses.

Dowell RD; Eddy SR

2006-01-01

320

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints  

Science.gov (United States)

Background We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. Results We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. Conclusion Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm – this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN – have comparable overall performance with different strengths and weaknesses.

Dowell, Robin D; Eddy, Sean R

2006-01-01

 
 
 
 
321

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. Results We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. Conclusion Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm – this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN – have comparable overall performance with different strengths and weaknesses.

Dowell Robin D; Eddy Sean R

2006-01-01

322

Structural divergence is more extensive than sequence divergence for a family of intrinsically disordered proteins.  

Science.gov (United States)

The p53 transactivation domain (p53TAD) is an intrinsically disordered protein (IDP) domain that undergoes coupled folding and binding when interacting with partner proteins like the E3 ligase, MDM2, and the 70 kDa subunit of replication protein A, RPA70. The secondary structure and dynamics of six closely related mammalian homologues of p53TAD were investigated using nuclear magnetic resonance (NMR) spectroscopy. Differences in both transient secondary structure and backbone dynamics were observed for the homologues. Many of these differences were localized to the binding sites for MDM2 and RPA70. The amount of transient helical secondary structure observed for the MDM2 binding site was lower for the dog and mouse homologues, compared with human, and the amount of transient helical secondary structure observed for the RPA70 binding site was higher for guinea pig and rabbit, compared with human. Differences in the amount of transient helical secondary structure observed for the MDM2 binding site were directly related to amino acid substitutions occurring on the solvent exposed side of the amphipathic helix that forms during the p53TAD/MDM2 interaction. Differences in the amount of transient helical secondary structure were not as easily explained for the RPA70 binding site because of its extensive sequence divergence. Clustering analysis shows that the divergence in the transient secondary structure of the p53TAD homologues exceeds the amino acid sequence divergence. In contrast, strong correlations were observed between the backbone dynamics of the homologues and the sequence identity matrix, suggesting that the dynamic behavior of IDPs is a conserved evolutionary feature. PMID:23606624

Borcherds, Wade; Kashtanov, Stepan; Wu, Hongwei; Daughdrill, Gary W

2013-07-23

323

Structural divergence is more extensive than sequence divergence for a family of intrinsically disordered proteins.  

UK PubMed Central (United Kingdom)

The p53 transactivation domain (p53TAD) is an intrinsically disordered protein (IDP) domain that undergoes coupled folding and binding when interacting with partner proteins like the E3 ligase, MDM2, and the 70 kDa subunit of replication protein A, RPA70. The secondary structure and dynamics of six closely related mammalian homologues of p53TAD were investigated using nuclear magnetic resonance (NMR) spectroscopy. Differences in both transient secondary structure and backbone dynamics were observed for the homologues. Many of these differences were localized to the binding sites for MDM2 and RPA70. The amount of transient helical secondary structure observed for the MDM2 binding site was lower for the dog and mouse homologues, compared with human, and the amount of transient helical secondary structure observed for the RPA70 binding site was higher for guinea pig and rabbit, compared with human. Differences in the amount of transient helical secondary structure observed for the MDM2 binding site were directly related to amino acid substitutions occurring on the solvent exposed side of the amphipathic helix that forms during the p53TAD/MDM2 interaction. Differences in the amount of transient helical secondary structure were not as easily explained for the RPA70 binding site because of its extensive sequence divergence. Clustering analysis shows that the divergence in the transient secondary structure of the p53TAD homologues exceeds the amino acid sequence divergence. In contrast, strong correlations were observed between the backbone dynamics of the homologues and the sequence identity matrix, suggesting that the dynamic behavior of IDPs is a conserved evolutionary feature.

Borcherds W; Kashtanov S; Wu H; Daughdrill GW

2013-10-01

324

Multiple amino Acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.  

UK PubMed Central (United Kingdom)

Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 ?- and ?-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as "core" for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf) yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification provides the bases for new analyses of the three-dimensional structure and for mutagenesis studies.

Howard JB; Kechris KJ; Rees DC; Glazer AN

2013-01-01

325

Multiple amino Acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.  

Science.gov (United States)

Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 ?- and ?-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as "core" for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf) yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification provides the bases for new analyses of the three-dimensional structure and for mutagenesis studies. PMID:24019874

Howard, James B; Kechris, Katerina J; Rees, Douglas C; Glazer, Alexander N

2013-09-03

326

High-resolution NMR structure of an AT-rich DNA sequence  

Energy Technology Data Exchange (ETDEWEB)

We have determined, by proton NMR and complete relaxation matrix methods, the high-resolution structure of a DNA oligonucleotide in solution with nine contiguous AT base pairs. The stretch of AT pairs, TAATTATAA.TTATAATTA, is imbedded in a 27-nucleotide stem-and-loop construct, which is stabilized by terminal GC base pairs and an extraordinarily stable DNA loop GAA (Hirao et al., 1994, Nucleic Acids Res.22, 576-582). The AT-rich sequence has three repeated TAA.TTA motifs, one in the reverse orientation. Comparison of the local conformations of the three motifs shows that the sequence context has a minor effect here: atomic RMSD between the three TAA.TTA fragments is 0.4-0.5 A, while each fragment is defined within the RMSD of 0.3-0.4 A. The AT-rich stem also contains a consensus sequence for the Pribnow box, TATAAT. The TpA, ApT, and TpT.ApA steps have characteristic local conformations, a combination of which determines a unique sequence-dependent pattern of minor groove width variation. All three TpA steps are locally bent in the direction compressing the major groove of DNA. These bends, however, compensate each other, because of their relative position in the sequence, so that the overall helical axis is essentially straight.

Ulyanov, Nikolai B. [University of California, Department of Pharmaceutical Chemistry (United States); Bauer, William R. [State University of New York, Department of Molecular Genetics and Microbiology, Health Sciences Center (United States); James, Thomas L. [University of California, Department of Pharmaceutical Chemistry (United States)], E-mail: james@picasso.ucsf.edu

2002-03-15

327

High-resolution NMR structure of an AT-rich DNA sequence  

International Nuclear Information System (INIS)

We have determined, by proton NMR and complete relaxation matrix methods, the high-resolution structure of a DNA oligonucleotide in solution with nine contiguous AT base pairs. The stretch of AT pairs, TAATTATAA.TTATAATTA, is imbedded in a 27-nucleotide stem-and-loop construct, which is stabilized by terminal GC base pairs and an extraordinarily stable DNA loop GAA (Hirao et al., 1994, Nucleic Acids Res.22, 576-582). The AT-rich sequence has three repeated TAA.TTA motifs, one in the reverse orientation. Comparison of the local conformations of the three motifs shows that the sequence context has a minor effect here: atomic RMSD between the three TAA.TTA fragments is 0.4-0.5 A, while each fragment is defined within the RMSD of 0.3-0.4 A. The AT-rich stem also contains a consensus sequence for the Pribnow box, TATAAT. The TpA, ApT, and TpT.ApA steps have characteristic local conformations, a combination of which determines a unique sequence-dependent pattern of minor groove width variation. All three TpA steps are locally bent in the direction compressing the major groove of DNA. These bends, however, compensate each other, because of their relative position in the sequence, so that the overall helical axis is essentially straight.

2002-01-01

328

Sequence similarity between xylose isomerase and replicase: another TIM-barrel in the replicase structure?  

UK PubMed Central (United Kingdom)

The BLAST search using the strand beta 2 (46_GAHGVTFHDDDLIP) of the (alpha/beta)8-barrel of xylose isomerase from Streptomyces olivochromogenes resulted in retrieving the sequentially similar segment of replicase from garlic latent virus (692_GGHGIGFHRDD). The detailed analysis of the entire amino acid sequences of both xylose isomerase and replicase suggested that the polypeptide segment 644-1046 of replicase (the entire length of this enzyme is 1924 residues) could share the structure of xylose isomerase (20.7% identity using the entire sequence of xylose isomerase). The relatedness of replicase and xylose isomerase is supported by the fact that the sequence similarity can be observed along the whole sequence of xylose isomerase (386 amino acid residues). The sequence of replicase exhibits moreover the similarity with that of lycopene cyclase, an enzyme implicated in the beta-carotene biosynthesis, that was previously found to share similarity with xylose isomerase. Thus the relevant segment of replicase is predicted to adopt an (alpha/beta)8-barrel topology similar to that of xylose isomerase.

Janecek S

1997-10-01

329

Multilocus Sequence Typing Analysis of Staphylococcus lugdunensis Implies a Clonal Population Structure  

Science.gov (United States)

Staphylococcus lugdunensis is recognized as one of the major pathogenic species within the genus Staphylococcus, even though it belongs to the coagulase-negative group. A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 87 S. lugdunensis isolates from various clinical and geographic sources by DNA sequence analysis of seven housekeeping genes (aroE, dat, ddl, gmk, ldh, recA, and yqiL). The number of alleles ranged from four (gmk and ldh) to nine (yqiL). Allelic profiles allowed the definition of 20 different sequence types (STs) and five clonal complexes. The 20 STs lacked correlation with geographic source. Isolates recovered from hematogenic infections (blood or osteoarticular isolates) or from skin and soft tissue infections did not cluster in separate lineages. Penicillin-resistant isolates clustered mainly in one clonal complex, unlike glycopeptide-tolerant isolates, which did not constitute a distinct subpopulation within S. lugdunensis. Phylogenies from the sequences of the seven individual housekeeping genes were congruent, indicating a predominantly mutational evolution of these genes. Quantitative analysis of the linkages between alleles from the seven loci revealed a significant linkage disequilibrium, thus confirming a clonal population structure for S. lugdunensis. This first MLST scheme for S. lugdunensis provides a new tool for investigating the macroepidemiology and phylogeny of this unusually virulent coagulase-negative Staphylococcus.

Chassain, Benoit; Lemee, Ludovic; Didi, Jennifer; Thiberge, Jean-Michel; Brisse, Sylvain; Pons, Jean-Louis

2012-01-01

330

Multilocus sequence typing analysis of Staphylococcus lugdunensis implies a clonal population structure.  

Science.gov (United States)

Staphylococcus lugdunensis is recognized as one of the major pathogenic species within the genus Staphylococcus, even though it belongs to the coagulase-negative group. A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 87 S. lugdunensis isolates from various clinical and geographic sources by DNA sequence analysis of seven housekeeping genes (aroE, dat, ddl, gmk, ldh, recA, and yqiL). The number of alleles ranged from four (gmk and ldh) to nine (yqiL). Allelic profiles allowed the definition of 20 different sequence types (STs) and five clonal complexes. The 20 STs lacked correlation with geographic source. Isolates recovered from hematogenic infections (blood or osteoarticular isolates) or from skin and soft tissue infections did not cluster in separate lineages. Penicillin-resistant isolates clustered mainly in one clonal complex, unlike glycopeptide-tolerant isolates, which did not constitute a distinct subpopulation within S. lugdunensis. Phylogenies from the sequences of the seven individual housekeeping genes were congruent, indicating a predominantly mutational evolution of these genes. Quantitative analysis of the linkages between alleles from the seven loci revealed a significant linkage disequilibrium, thus confirming a clonal population structure for S. lugdunensis. This first MLST scheme for S. lugdunensis provides a new tool for investigating the macroepidemiology and phylogeny of this unusually virulent coagulase-negative Staphylococcus. PMID:22785196

Chassain, Benoît; Lemée, Ludovic; Didi, Jennifer; Thiberge, Jean-Michel; Brisse, Sylvain; Pons, Jean-Louis; Pestel-Caron, Martine

2012-07-11

331

Multilocus sequence typing analysis of Staphylococcus lugdunensis implies a clonal population structure.  

UK PubMed Central (United Kingdom)

Staphylococcus lugdunensis is recognized as one of the major pathogenic species within the genus Staphylococcus, even though it belongs to the coagulase-negative group. A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 87 S. lugdunensis isolates from various clinical and geographic sources by DNA sequence analysis of seven housekeeping genes (aroE, dat, ddl, gmk, ldh, recA, and yqiL). The number of alleles ranged from four (gmk and ldh) to nine (yqiL). Allelic profiles allowed the definition of 20 different sequence types (STs) and five clonal complexes. The 20 STs lacked correlation with geographic source. Isolates recovered from hematogenic infections (blood or osteoarticular isolates) or from skin and soft tissue infections did not cluster in separate lineages. Penicillin-resistant isolates clustered mainly in one clonal complex, unlike glycopeptide-tolerant isolates, which did not constitute a distinct subpopulation within S. lugdunensis. Phylogenies from the sequences of the seven individual housekeeping genes were congruent, indicating a predominantly mutational evolution of these genes. Quantitative analysis of the linkages between alleles from the seven loci revealed a significant linkage disequilibrium, thus confirming a clonal population structure for S. lugdunensis. This first MLST scheme for S. lugdunensis provides a new tool for investigating the macroepidemiology and phylogeny of this unusually virulent coagulase-negative Staphylococcus.

Chassain B; Lemée L; Didi J; Thiberge JM; Brisse S; Pons JL; Pestel-Caron M

2012-09-01

332

Amino acid sequences and structures of chicken and turkey beta 2-microglobulin.  

DEFF Research Database (Denmark)

The complete amino acid sequences of chicken and turkey beta 2-microglobulins have been determined by analyses of tryptic, V8-proteolytic and cyanogen bromide fragments, and by N-terminal sequencing. Mass spectrometric analysis of chicken beta 2-microglobulin supports the sequence-derived Mr of 11,048. The higher apparent Mr obtained for the avian beta 2-microglobulins as compared to human beta 2-microglobulin by SDS-PAGE is not understood. Chicken and turkey beta 2-microglobulin consist of 98 residues and deviate at seven positions: 60, 66, 74-76, 78 and 82. The chicken and turkey sequences are identical to human beta 2-microglobulin at 46 and 47 positions, respectively, and to bovine beta 2-microglobulin at 47 positions, i.e. there is about 47% identity between avian and mammalian beta 2-microglobulins. The known X-ray crystallographic structures of bovine beta 2-microglobulin and human HLA-A2 complex suggest that the seven chicken to turkey differences are exposed to solvent in the avian MHC class I complex. The key residues of beta 2-microglobulin involved in alpha chain contacts within the MHC class I molecule are highly conserved between chicken and man. This explains that heterologous human beta 2-microglobulin can substitute the chicken beta 2-microglobulin in exchange studies with B-F (chicken MHC class I molecule), and suggests that the MHC class I structure is conserved over long evolutionary distances. Udgivelsesdato: null-null

Welinder, K G; Jespersen, H M

1991-01-01

333

Insights into the role of protein molecule size and structure on interfacial properties using designed sequences.  

UK PubMed Central (United Kingdom)

Mixtures of a large, structured protein with a smaller, unstructured component are inherently complex and hard to characterize at interfaces, leading to difficulties in understanding their interfacial behaviours and, therefore, formulation optimization. Here, we investigated interfacial properties of such a mixed system. Simplicity was achieved using designed sequences in which chemical differences had been eliminated to isolate the effect of molecular size and structure, namely a short unstructured peptide (DAMP1) and its longer structured protein concatamer (DAMP4). Interfacial tension measurements suggested that the size and bulk structuring of the larger molecule led to much slower adsorption kinetics. Neutron reflectometry at equilibrium revealed that both molecules adsorbed as a monolayer to the air-water interface (indicating unfolding of DAMP4 to give a chain of four connected DAMP1 molecules), with a concentration ratio equal to that in the bulk. This suggests the overall free energy of adsorption is equal despite differences in size and bulk structure. At small interfacial extensional strains, only molecule packing influenced the stress response. At larger strains, the effect of size became apparent, with DAMP4 registering a higher stress response and interfacial elasticity. When both components were present at the interface, most stress-dissipating movement was achieved by DAMP1. This work thus provides insights into the role of proteins' molecular size and structure on their interfacial properties, and the designed sequences introduced here can serve as effective tools for interfacial studies of proteins and polymers.

Dwyer MD; He L; James M; Nelson A; Middelberg AP

2013-03-01

334

Common recognition principles across diverse sequence and structural families of sialic acid binding proteins.  

UK PubMed Central (United Kingdom)

Sialic acids form a large family of 9-carbon monosaccharides and are integral components of glycoconjugates. They are known to bind to a wide range of receptors belonging to diverse sequence families and fold classes, and are key mediators in a plethora of cellular processes. Thus, it is of great interest to understand the features that give rise to such a recognition capability. Structural analyses using a non-redundant dataset of known sialic acid binding proteins was carried out, which included exhaustive binding site comparisons and site alignments using in-house algorithms, followed by clustering and tree computation, which has led to derivation of sialic acid recognition principles.Although the proteins in the dataset belong to several sequence and structure families, their binding sites could be grouped into only six types. Structural comparison of the binding sites indicate that all sites contain one or more different combinations of key structural features over a common scaffold. The six binding site types thus serve as structural motifs for recognising sialic acid. Scanning the motifs against a non-redundant set of binding sites from PDB indicated the motifs to be specific for sialic acid recognition. Knowledge of determinants obtained from this study will be useful for detecting function in unknown proteins. As an example analysis, a genome-wide scan for the motifs in structures of M.tuberculosis proteome, identified 17 hits that contain combinations of the features, suggesting a possible function of sialic acid binding by these proteins.

Bhagavat R; Chandra N

2013-09-01

335

Genetic structure of Marchalina hellenica (Hemiptera: Margarodidae) populations from Turkey: preliminary mtDNA sequencing data.  

UK PubMed Central (United Kingdom)

The scale insect Marchalina hellenica (Gennadius) (Hemiptera: Margarodidae) contributes to the production of pine honey in Turkey and Greece via the honeydew excreted when it feeds on pine trees. Although it is an insect of prime economic importance, there is no information on its genetic structure. Preliminary data were obtained based on sequencing analysis of 12s rDNA and COI mtDNA gene segments from samples from four areas of Turkey. Sequences of the 12s rDNA gene segment from Greek samples available in GenBank were also included. No variability was detected concerning the COI mtDNA gene segment analysis, although 13 haplotypes were revealed based on the 12s rDNA gene segment. The most distant population was from Mudanya-Bursa Province (Turkey). Further research is necessary on the genetic structure and variability of M. hellenica populations from the two neighboring countries.

Bouga M; Evangelou V; Lykoudis D; Cakmak I; Hatjina F

2011-12-01

336

Comparative mapping of sequence-based and structure-based protein domains  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Protein domains have long been an ill-defined concept in biology. They are generally described as autonomous folding units with evolutionary and functional independence. Both structure-based and sequence-based domain definitions have been widely used. But whether these types of models alone can capture all essential features of domains is still an open question. Methods Here we provide insight on domain definitions through comparative mapping of two domain classification databases, one sequence-based (Pfam) and the other structure-based (SCOP). A mapping score is defined to indicate the significance of the mapping, and the properties of the mapping matrices are studied. Results The mapping results show a general agreement between the two databases, as well as many interesting areas of disagreement. In the cases of disagreement, the functional and evolutionary characteristics of the domains are examined to determine which domain definition is biologically more informative.

Zhang Ya; Chandonia John-Marc; Ding Chris; Holbrook Stephen R

2005-01-01

337

Structure and Dynamics of DNA-dendrimer complexation: Role of counterions, water and base pair sequence  

CERN Multimedia

We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by free energy calculations and inherent structure determination. Simulations reveal formation of a stable complex and provide a detailed molecular level understanding of the structure and dynamics of such a complexation. The reaction free energy surface in the initial stage is found to be funnel-like with a significant barrier arising in the late stage due to the occurrence of misfolded states of DNA. Complexation shows surprisingly strong sensitivity to the ssDNA sequence which is found to arise from a competition between enthalpic versus entropic rigidity of ssDNA.

Maiti, P K; Maiti, Prabal K.; Bagchi, Biman

2006-01-01

338

Genetic structure of Marchalina hellenica (Hemiptera: Margarodidae) populations from Turkey: preliminary mtDNA sequencing data.  

Science.gov (United States)

The scale insect Marchalina hellenica (Gennadius) (Hemiptera: Margarodidae) contributes to the production of pine honey in Turkey and Greece via the honeydew excreted when it feeds on pine trees. Although it is an insect of prime economic importance, there is no information on its genetic structure. Preliminary data were obtained based on sequencing analysis of 12s rDNA and COI mtDNA gene segments from samples from four areas of Turkey. Sequences of the 12s rDNA gene segment from Greek samples available in GenBank were also included. No variability was detected concerning the COI mtDNA gene segment analysis, although 13 haplotypes were revealed based on the 12s rDNA gene segment. The most distant population was from Mudanya-Bursa Province (Turkey). Further research is necessary on the genetic structure and variability of M. hellenica populations from the two neighboring countries. PMID:21671122

Bouga, Maria; Evangelou, Vasiliki; Lykoudis, Dimitris; Cakmak, Ibrahim; Hatjina, Fani

2011-06-14

339

OUTLINE OF STRUCTURE OF MESOSOIC SEQUENCES OF THE HUMENSKÉ VRCHY MTS  

Directory of Open Access Journals (Sweden)

Full Text Available WNW - ESE horst of Mesozoic sequences of the Humenské vrchy Mts. forms NE margin of the East-ern Slovakian basin filled by Neogene vulcanosedimentary formations. They consist of Middle Triassic (Ani-sian) to Middle Cretaceous (Lower Cenomanian formations) belonging to Križna superficial nappe unit of the Western Carpathians. Structurally the sequence is composed of four directional sheets (i.e. Jasenovská, Klako-?iny, Kocovo, and Hôrka sheet) dipping to N - NNE. The sheet structure has been formed during Miocene back-ward thrust of the Paleogene flysch formations. Other dislocations of the same and N - S direction are of younger age. They are bound to final formation of Eastern Slovakian basin and they segment the horst to individual elevation and normal fault blocks.

Jacko Stanislav yun.

1997-01-01

340

A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Hypnales comprise over 50% of all pleurocarpous mosses. They provide a young radiation complicating phylogenetic analyses. To resolve the hypnalean phylogeny, it is necessary to use a phylogenetic marker providing highly variable features to resolve species on the one hand and conserved features enabling a backbone analysis on the other. Therefore we used highly variable internal transcribed spacer 2 (ITS2) sequences and conserved secondary structures, as deposited with the ITS2 Database, simultaneously. Findings We built an accurate and in parts robustly resolved large scale phylogeny for 1,634 currently available hypnalean ITS2 sequence-structure pairs. Conclusions Profile Neighbor-Joining revealed a possible hypnalean backbone, indicating that most of the hypnalean taxa classified as different moss families are polyphyletic assemblages awaiting taxonomic changes.

Merget Benjamin; Wolf Matthias

2010-01-01

 
 
 
 
341

Sequence and structure of a serine transfer RNA with GCU anticodon from mosquito mitochondria.  

UK PubMed Central (United Kingdom)

We have determined the primary sequence and modification status of a transfer RNA from mosquito mitochondria whose GCU anticodon indicates that it is a serine tRNA (tRNASerGCU), and have obtained information on higher order structure using partial digestion with nucleases S1 and T1 under non-denaturing conditions. Although its primary sequence homology to mammalian mitochondrial tRNASerGCU is modest (46%), the mosquito tRNA resembles its mammalian mitochondrial counterpart in that a plausible secondary structure configuration includes a drastically abbreviated D arm and a sex base-pair anticodon stem. Other unusual features include a ribose-methylated cytidine residue at the end of the anticodon stem, and the likely occurrence of a psi residue between the amino acid arm and arm IV.

Dubin DT; HsuChen CC; Cleaves GR; Timko KD

1984-06-01

342

De novo prediction of structured RNAs from genomic sequences  

DEFF Research Database (Denmark)

Growing recognition of the numerous, diverse and important roles played by non-coding RNA in all organisms motivates better elucidation of these cellular components. Comparative genomics is a powerful tool for this task and is arguably preferable to any high-throughput experimental technology currently available, because evolutionary conservation highlights functionally important regions. Conserved secondary structure, rather than primary sequence, is the hallmark of many functionally important RNAs, because compensatory substitutions in base-paired regions preserve structure. Unfortunately, such substitutions also obscure sequence identity and confound alignment algorithms, which complicates analysis greatly. This paper surveys recent computational advances in this difficult arena, which have enabled genome-scale prediction of cross-species conserved RNA elements. These predictions suggest that a wealth of these elements indeed exist

Gorodkin, Jan; Hofacker, Ivo L.

2010-01-01

343

First Observation of Upsilon(1D) States  

CERN Multimedia

The CLEO III experiment has recently accumulated a large statistics sample of 4.73 x 10^6 Upsilon(3S) decays. We present the first evidence for the production of the triplet Upsilon(1D) states in the four-photon cascade, Upslion(3S) -> gamma chi_b(2P), chi_b(2P) -> gamma Upsilon(1D), Upsilon(1D) -> gamma chi_b(1P), chi_b(1P) -> gamma Upsilon(1S), followed by the Upsilon(1S) annihilation to e+ e- or mu+ mu-. The signal has a significance of 9.7 standard deviations. The measured product branching ratio for these five decays, (3.3 +- 0.6 +- 0.5) x 10^{-5}, is consistent with the theoretical estimates. We see a 6.8 standard deviation signal for a state with a mass of 10162.2 +- 1.6 MeV/c^2, consistent with the Upsilon(1D_2) assignment. We also present improved measurements of the Upsilon(3S) -> pi0 pi0 Upsilon(1S) branching ratio and the associated di-pion mass distribution.

Csorna, S E; Bonvicini, G; Cinabro, D; Dubrovin, M; McGee, S; Bornheim, A; Lipeles, E; Pappas, S P; Shapiro, A; Sun, W M; Weinstein, A J; Mahapatra, R; Briere, R A; Chen, G P; Ferguson, T; Tatishvili, G T; Vogel, H; Adam, N E; Alexander, J P; Berkelman, K; Boisvert, V; Cassel, David G; Drell, P S; Duboscq, J E; Ecklund, K M; Ehrlich, R; Galik, R S; Gibbons, L; Gittelman, B; Gray, S W; Hartill, D L; Heltsley, B K; Hsu, L; Jones, C D; Kandaswamy, J; Kreinick, D L; Magerkurth, A; Mahlke-Krüger, H; Meyer, T O; Mistry, N B; Nordberg, E; Patterson, J R; Peterson, D; Pivarski, J; Riley, D; Sadoff, A J; Schwarthoff, H; Shepherd, M R; Thayer, J G; Urner, D; Viehhauser, G; Warburton, A; Weinberger, M; Athar, S B; Avery, P; Breva-Newell, L; Potlia, V; Stöck, H; Yelton, J; Brandenburg, G; Kim, D Y J; Wilson, R; Benslama, K; Eisenstein, B I; Ernst, J; Gollin, G D; Hans, R M; Karliner, I; Lowrey, N; Plager, C; Sedlack, C; Selen, M; Thaler, J J; Williams, J; Edwards, K W; Ammar, R; Besson, D; Zhao, X; Anderson, S; Frolov, V V; Kubota, Y; Lee, S J; Li, S Z; Poling, R A; Smith, A; Stepaniak, C J; Urheim, J; Metreveli, Z V; Seth, K K; Tomaradze, A G; Zweber, P; Ahmed, S; Alam, M S; Jian, L; Saleem, M; Wappler, F; Eckhart, E; Gan, K K; Gwon, C; Hart, T; Honscheid, K; Hufnagel, D; Kagan, H; Kass, R; Pedlar, T K; Thayer, J B; Von Törne, E; Wilksen, T; Zoeller, M M; Muramatsu, H; Richichi, S J; Severini, H; Skubic, P L; Dytman, S A; Müller, J A; Nam, S; Savinov, V; Chen, S; Hinson, J W; Lee, J; Miller, D H; Pavlunin, V; Shibata, E I; Shipsey, I P J; Cronin-Hennessy, D; Lyon, A L; Park, C S; Park, W; Thorndike, E H; Coan, T E; Gao, Y S; Liu, F; Maravin, Y; Stroynowski, R; Artuso, M; Boulahouache, C; Bukin, K; Dambasuren, E; Khroustalev, K; Mountain, R; Nandakumar, R; Skwarnicki, T; Stone, S; Wang, J C; Mahmood, A H

2002-01-01

344

1-D equations of radiation hydrodynamics  

International Nuclear Information System (INIS)

The radiation transfer equation is derived in the comoving frame, in curvilinear coordinates, to first order in u/c, no symmetry being assumed. This equation is then specialized to 1-D, and its moments are calculated for the limiting case of Thomson scattering. The equations of radiation hydrodynamics are also given

1985-01-01

345

Revised Mimivirus major capsid protein sequence reveals intron-containing gene structure and extra domain  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Acanthamoebae polyphaga Mimivirus (APM) is the largest known dsDNA virus. The viral particle has a nearly icosahedral structure with an internal capsid shell surrounded with a dense layer of fibrils. A Capsid protein sequence, D13L, was deduced from the APM L425 coding gene and was shown to be the most abundant protein found within the viral particle. However this protein remained poorly characterised until now. A revised protein sequence deposited in a database suggested an additional N-terminal stretch of 142 amino acids missing from the original deduced sequence. This result led us to investigate the L425 gene structure and the biochemical properties of the complete APM major Capsid protein. Results This study describes the full length 3430 bp Capsid coding gene and characterises the 593 amino acids long corresponding Capsid protein 1. The recombinant full length protein allowed the production of a specific monoclonal antibody able to detect the Capsid protein 1 within the viral particle. This protein appeared to be post-translationnally modified by glycosylation and phosphorylation. We proposed a secondary structure prediction of APM Capsid protein 1 compared to the Capsid protein structure of Paramecium Bursaria Chlorella Virus 1, another member of the Nucleo-Cytoplasmic Large DNA virus family. Conclusion The characterisation of the full length L425 Capsid coding gene of Acanthamoebae polyphaga Mimivirus provides new insights into the structure of the main Capsid protein. The production of a full length recombinant protein will be useful for further structural studies.

Azza Saïd; Cambillau Christian; Raoult Didier; Suzan-Monti Marie

2009-01-01

346

FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB  

DEFF Research Database (Denmark)

FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB) for structures of homologous proteins. The results are displayed both as an annotated sequence alignment, where the user-provided annotations as well as the sequence conservation between the query and the target sequence are displayed, and also as a publication-quality image of the 3D protein structure with the selected features and sequence conservation enhanced. The results are also returned in a readily parsable text format as well as a PyMol (http://pymol.sourceforge.net/) script file, which allows the user to easily modify the protein structure image to suit a specific purpose. FeatureMap3D can also be used without sequence annotation, to evaluate the quality of the alignment of the input sequences to the most homologous structures in the PDB, through the sequence conservation colored 3D structure visualization tool. FeatureMap3D is available at: http://www.cbs.dtu.dk/services/FeatureMap3D/.

Wernersson, Rasmus; Rapacki, Krzysztof

2006-01-01

347

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.  

UK PubMed Central (United Kingdom)

MOTIVATION: Predicting RNA-RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods for the prediction of interactions are all based on single sequences. Since comparative methods have already been useful in RNA structure determination, we assume that conserved RNA-RNA interactions also imply conserved function. Of these, we further assume that a non-negligible amount of the existing RNA-RNA interactions have also acquired compensating base changes throughout evolution. We implement a method, PETcofold, that can take covariance information in intra-molecular and inter-molecular base pairs into account to predict interactions and secondary structures of two multiple alignments of RNA sequences. RESULTS: PETcofold's ability to predict RNA-RNA interactions was evaluated on a carefully curated dataset of 32 bacterial small RNAs and their targets, which was manually extracted from the literature. For evaluation of both RNA-RNA interaction and structure prediction, we were able to extract only a few high-quality examples: one vertebrate small nucleolar RNA and four bacterial small RNAs. For these we show that the prediction can be improved by our comparative approach. Furthermore, PETcofold was evaluated on controlled data with phylogenetically simulated sequences enriched for covariance patterns at the interaction sites. We observed increased performance with increased amounts of covariance. AVAILABILITY: The program PETcofold is available as source code and can be downloaded from http://rth.dk/resources/petcofold.

Seemann SE; Richter AS; Gesell T; Backofen R; Gorodkin J

2011-01-01

348

PETcofold : predicting conserved interactions and structures of two multiple alignments of RNA sequences  

DEFF Research Database (Denmark)

MOTIVATION: Predicting RNA-RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods for the prediction of interactions are all based on single sequences. Since comparative methods have already been useful in RNA structure determination, we assume that conserved RNA-RNA interactions also imply conserved function. Of these, we further assume that a non-negligible amount of the existing RNA-RNA interactions have also acquired compensating base changes throughout evolution. We implement a method, PETcofold, that can take covariance information in intra-molecular and inter-molecular base pairs into account to predict interactions and secondary structures of two multiple alignments of RNA sequences. RESULTS: PETcofold's ability to predict RNA-RNA interactions was evaluated on a carefully curated dataset of 32 bacterial small RNAs and their targets, which was manually extracted from the literature. For evaluation of both RNA-RNA interaction and structure prediction, we were able to extract only a few high-quality examples: one vertebrate small nucleolar RNA and four bacterial small RNAs. For these we show that the prediction can be improved by our comparative approach. Furthermore, PETcofold was evaluated on controlled data with phylogenetically simulated sequences enriched for covariance patterns at the interaction sites. We observed increased performance with increased amounts of covariance. AVAILABILITY: The program PETcofold is available as source code and can be downloaded from http://rth.dk/resources/petcofold. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Seemann, Ernst Stefan; Richter, Andreas S.

2011-01-01

349

From sequence to structure and back again: approaches for predicting protein-DNA binding  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Gene regulation in higher organisms is achieved by a complex network of transcription factors (TFs). Modulating gene expression and exploring gene function are major aims in molecular biology. Furthermore, the identification of putative target genes for a certain TF serve as powerful tools for specific targeting of rational drugs. Detecting the short and variable transcription factor binding sites (TFBSs) in genomic DNA is an intriguing challenge for computational and structural biologists. Fast and reliable computational methods for predicting TFBSs on a whole-genome scale offer several advantages compared to the current experimental methods that are rather laborious and slow. Two main approaches are being explored, advanced sequence-based algorithms and structure-based methods. The aim of this review is to outline the computational and experimental methods currently being applied in the field of protein-DNA interactions. With a focus on the former, the current state of the art in modeling these interactions is discussed. Surveying sequence and structure-based methods for predicting TFBSs, we conclude that in order to achieve a sound and specific method applicable on genomic sequences it is desirable and important to bring these two approaches together.

Höglund Annette; Kohlbacher Oliver

2004-01-01

350

Phylogeny of Oedogoniales, Chaetophorales and Chaetopeltidales (Chlorophyceae): inferences from sequence-structure analysis of ITS2.  

UK PubMed Central (United Kingdom)

BACKGROUND AND AIMS: The green algal class Chlorophyceae comprises five orders (Chlamydomonadales, Sphaeropleales, Chaetophorales, Chaetopeltidales and Oedogoniales). Attempts to resolve the relationships among these groups have met with limited success. Studies of single genes (18S rRNA, 26S rRNA, rbcL or atpB) have largely failed to unambiguously resolve the relative positions of Oedogoniales, Chaetophorales and Chaetopeltidales (the OCC taxa). In contrast, recent genomics analyses of plastid data from OCC exemplars provided a robust phylogenetic analysis that supports a monophyletic OCC alliance. METHODS: An ITS2 data set was assembled to independently test the OCC hypothesis and to evaluate the performance of these data in assessing green algal phylogeny at the ordinal or class level. Sequence-structure analysis designed for use with ITS2 data was employed for phylogenetic reconstruction. KEY RESULTS: Results of this study yielded trees that were, in general, topologically congruent with the results from the genomic analyses, including support for the monophyly of the OCC alliance. CONCLUSIONS: Not all nodes from the ITS2 analyses exhibited robust support, but our investigation demonstrates that sequence-structure analyses of ITS2 provide a taxon-rich means of testing phylogenetic hypotheses at high taxonomic levels. Thus, the ITS2 data, in the context of sequence-structure analysis, provide an economical supplement or alternative to the single-marker approaches used in green algal phylogeny.

Buchheim MA; Sutherland DM; Schleicher T; Förster F; Wolf M

2012-01-01

351

Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing.  

UK PubMed Central (United Kingdom)

BACKGROUND: To understand the role of the community structure of microbes in the environment in the fermentation of Shaoxing rice wine, samples collected from a wine factory were subjected to Illumina-based metagenomic sequencing. RESULTS: De novo assembly of the sequencing reads allowed the characterisation of more than 23?thousand microbial genes derived from 1.7 and 1.88 Gbp of sequences from two samples fermented for 5 and 30 days respectively. The microbial community structure at different fermentation times of Shaoxing rice wine was revealed, showing the different roles of the microbiota in the fermentation process of Shaoxing rice wine. The gene function of both samples was also studied in the COG database, with most genes belonging to category S (function unknown), category E (amino acid transport and metabolism) and unclassified group. CONCLUSION: The results show that both the microbial community structure and gene function composition change greatly at different time points of Shaoxing rice wine fermentation. © 2013 Society of Chemical Industry.

Xie G; Wang L; Gao Q; Yu W; Hong X; Zhao L; Zou H

2013-09-01

352

SVM-PB-Pred: SVM based Protein Block prediction method using Sequence profiles and Secondary Structures.  

UK PubMed Central (United Kingdom)

We developed a support vector machine based web server called SVM-PB-Pred, to predict the Protein Block for any given amino acid sequence. The input features of SVM-PB-Pred include i) sequence profiles (PSSM) and ii) actual secondary structures (SS) from DSSP method or predicted secondary structures from NPS@ and GOR4 methods. There were three combined input features PSSM+SS(DSSP), PSSM+SS(NPS@) and PSSM+SS(GOR4) used to test and train the SVM models. Similarly, four datasets RS90, DB433, LI1264 and SP1577 were used to develop the SVM models. These four SVM models developed were tested using three different benchmarking tests namely; (i) self consistency, (ii) seven fold cross validation test and (iii) independent case test. The maximum possible prediction accuracy of ~70% was observed in self consistency test for the SVM models of both LI1264 and SP1577 datasets, where PSSM+SS(DSSP) input features was used to test. The prediction accuracies were reduced to ~53% for PSSM+SS(NPS@) and ~43% for PSSM+SS(GOR4) in independent case test, for the SVM models of above two same datasets. Using our method, it is possible to predict the protein block letters for any query protein sequence with ~53% accuracy, when the SP1577 dataset and predicted secondary structure from NPS@ server were used. The SVM-PB-Pred server can be freely accessed through http://bioinfo.bdu.ac.in/~svmpbpred.

Suresh V; Parthasarathy S

2013-07-01

353

Quantitative Correlation between the protein primary sequences and secondary structures in spider dragline silks.  

Science.gov (United States)

Synthetic spider silk holds great potential for use in various applications spanning medical uses to ultra lightweight armor; however, producing synthetic fibers with mechanical properties comparable to natural spider silk has eluded the scientific community. Natural dragline spider silks are commonly made from proteins that contain highly repetitive amino acid motifs, adopting an array of secondary structures. Before further advances can be made in the production of synthetic fibers based on spider silk proteins, it is imperative to know the percentage of each amino acid in the protein that forms a specific secondary structure. Linking these percentages to the primary amino acid sequence of the protein will establish a structural foundation for synthetic silk. In this study, nuclear magnetic resonance (NMR) techniques are used to quantify the percentage of Ala, Gly, and Ser that form both beta-sheet and helical secondary structures. The fraction of these three amino acids and their secondary structure are quantitatively correlated to the primary amino acid sequence for the proteins that comprise major and minor ampullate silk from the Nephila clavipes spider providing a blueprint for synthetic spider silks. PMID:20000730

Jenkins, Janelle E; Creager, Melinda S; Lewis, Randolph V; Holland, Gregory P; Yarger, Jeffery L

2010-01-11

354

Quantitative Correlation between the protein primary sequences and secondary structures in spider dragline silks.  

UK PubMed Central (United Kingdom)

Synthetic spider silk holds great potential for use in various applications spanning medical uses to ultra lightweight armor; however, producing synthetic fibers with mechanical properties comparable to natural spider silk has eluded the scientific community. Natural dragline spider silks are commonly made from proteins that contain highly repetitive amino acid motifs, adopting an array of secondary structures. Before further advances can be made in the production of synthetic fibers based on spider silk proteins, it is imperative to know the percentage of each amino acid in the protein that forms a specific secondary structure. Linking these percentages to the primary amino acid sequence of the protein will establish a structural foundation for synthetic silk. In this study, nuclear magnetic resonance (NMR) techniques are used to quantify the percentage of Ala, Gly, and Ser that form both beta-sheet and helical secondary structures. The fraction of these three amino acids and their secondary structure are quantitatively correlated to the primary amino acid sequence for the proteins that comprise major and minor ampullate silk from the Nephila clavipes spider providing a blueprint for synthetic spider silks.

Jenkins JE; Creager MS; Lewis RV; Holland GP; Yarger JL

2010-01-01

355

Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures.  

Science.gov (United States)

Mollusks are an extraordinarily diverse group of animals with an estimated 200,000 species, second only to the phylum Arthropoda. We conducted a comparative analysis of complete mitochondrial ribosomal large subunit sequences (LSU) of a chiton, two bivalves, six gastropods, and a cephalopod. In addition, we determined secondary structure models for each of them. Comparative analyses of nucleotide variation revealed substantial length variation among the taxa, with stylommatophoran gastropods possessing the shortest lengths. Phylogenetic analyses of the nucleotide sequence data supported the monophyly of Albinaria, Euhadra herklotsi + Cepaea nemoralis, Stylommatophora, Cerithioidea, and when only transversions are included, the Bivalvia. The phylogenetic limits of the mitochondrial LSU rRNA gene within mollusks appear to be up to 400 million years, although this estimate will have to be tested further with additional taxa. Our most novel finding was the discovery of phylogenetic signal in the secondary structure of rRNA of mollusks. The absence of entire stem/loop structures in Domains II, III, and V can be viewed as three shared derived characters uniting the stylommatophoran gastropods. The absence of the aforementioned stem/loop structure explains much of the observed length variation of the mitochondrial LSU rRNA found within mollusks. The distribution of these unique secondary structure characters within mollusks should be examined. PMID:10764537

Lydeard, C; Holznagel, W E; Schnare, M N; Gutell, R R

2000-04-01

356

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis.  

UK PubMed Central (United Kingdom)

BACKGROUND: Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2-L distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations. RESULTS: The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm. CONCLUSIONS: The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems.

Vinga S; Carvalho AM; Francisco AP; Russo LM; Almeida JS

2012-01-01

357

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2-L distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations. Results The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm. Conclusions The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems.

Vinga Susana; Carvalho Alexandra M; Francisco Alexandre P; Russo Luís MS; Almeida Jonas S

2012-01-01

358

RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins  

Science.gov (United States)

RBPmotif web server (http://www.rnamotif.org) implements tools to identify binding preferences of RNA-binding proteins (RBPs). Given a set of sequences that are known to be bound and unbound by the RBP of interest, RBPmotif provides two types of analysis: (i) de novo motif finding when there is no a priori knowledge on RBP’s binding preferences and (ii) analysis of structure preferences when there is a previously identified sequence motif for the RBP. De novo motif finding is performed with the previously published RNAcontext algorithm that learns discriminative motif models to identify both sequence and structure preferences. The results of this analysis include the inferred binding preferences of the RBP and the added predictive value of incorporating structure preferences. Second type of analysis investigates whether the instances of the previously identified sequence motif are enriched in a particular structure context in bound sequences, relative to its instances in unbound sequences. On completion, the results page shows the comparison of structure contexts of the motif instances between bound and unbound sequences and an assessment of statistical significance of detected preferences. In summary, RBPmotif web server enables the concurrent analysis of sequence and structure preferences of RBPs through a user-friendly interface.

Kazan, Hilal; Morris, Quaid

2013-01-01

359

RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins.  

UK PubMed Central (United Kingdom)

RBPmotif web server (http://www.rnamotif.org) implements tools to identify binding preferences of RNA-binding proteins (RBPs). Given a set of sequences that are known to be bound and unbound by the RBP of interest, RBPmotif provides two types of analysis: (i) de novo motif finding when there is no a priori knowledge on RBP's binding preferences and (ii) analysis of structure preferences when there is a previously identified sequence motif for the RBP. De novo motif finding is performed with the previously published RNAcontext algorithm that learns discriminative motif models to identify both sequence and structure preferences. The results of this analysis include the inferred binding preferences of the RBP and the added predictive value of incorporating structure preferences. Second type of analysis investigates whether the instances of the previously identified sequence motif are enriched in a particular structure context in bound sequences, relative to its instances in unbound sequences. On completion, the results page shows the comparison of structure contexts of the motif instances between bound and unbound sequences and an assessment of statistical significance of detected preferences. In summary, RBPmotif web server enables the concurrent analysis of sequence and structure preferences of RBPs through a user-friendly interface.

Kazan H; Morris Q

2013-07-01

360

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments.  

UK PubMed Central (United Kingdom)

MOTIVATION: The accurate prediction of residue-residue contacts, critical for maintaining the native fold of a protein, remains an open problem in the field of structural bioinformatics. Interest in this long-standing problem has increased recently with algorithmic improvements and the rapid growth in the sizes of sequence families. Progress could have major impacts in both structure and function prediction to name but two benefits. Sequence-based contact predictions are usually made by identifying correlated mutations within multiple sequence alignments (MSAs), most commonly through the information-theoretic approach of calculating mutual information between pairs of sites in proteins. These predictions are often inaccurate because the true covariation signal in the MSA is often masked by biases from many ancillary indirect-coupling or phylogenetic effects. Here we present a novel method, PSICOV, which introduces the use of sparse inverse covariance estimation to the problem of protein contact prediction. Our method builds on work which had previously demonstrated corrections for phylogenetic and entropic correlation noise and allows accurate discrimination of direct from indirectly coupled mutation correlations in the MSA. RESULTS: PSICOV displays a mean precision substantially better than the best performing normalized mutual information approach and Bayesian networks. For 118 out of 150 targets, the L/5 (i.e. top-L/5 predictions for a protein of length L) precision for long-range contacts (sequence separation >23) was ? 0.5, which represents an improvement sufficient to be of significant benefit in protein structure prediction or model quality assessment. AVAILABILITY: The PSICOV source code can be downloaded from http://bioinf.cs.ucl.ac.uk/downloads/PSICOV.

Jones DT; Buchan DW; Cozzetto D; Pontil M

2012-01-01

 
 
 
 
361

Correlations Between Amino Acids at Different Sites in Local Sequences of Protein Fragments with Given Structural Patterns  

Science.gov (United States)

Ample evidence suggests that the local structures of peptide fragments in native proteins are to some extent encoded by their local sequences. Detecting such local correlations is important but it is still an open question what would be the most appropriate method. This is partly because conventional sequence analyses treat amino acid preferences at each site of a protein sequence independently, while it is often the inter-site interactions that bring about local sequence-structure correlations. Here a new scheme is introduced to capture the correlation between amino acid preferences at different sites for different local structure types. A library of nine-residue fragments is constructed, and the fragments are divided into clusters based on their local structures. For each local structure cluster or type, chi-square tests are used to identify correlated preferences of amino acid combinations at pairs of sites. A score function is constructed including both the single site amino acid preferences and the dual-site amino acid combination preferences, which can be used to identify whether a sequence fragment would have a strong tendency to form a particular local structure in native proteins. The results show that, given a local structure pattern, dual-site amino acid combinations contain different information from single site amino acid preferences. Representative examples show that many of the statistically identified correlations agree with previously-proposed heuristic rules about local sequence-structure correlations, or are consistent with physical-chemical interactions required to stabilize particular local structures. Results also show that such dual-site correlations in the score function significantly improves the Z-score matching a sequence fragment to its native local structure relative to non-native local structures, and certain local structure types are highly predictable from the local sequence alone if inter-site correlations are considered.

Lu, Wen; Liu, Hai-yan

2007-02-01

362

The RNA component of the Bacillus subtilis RNase P. Sequence, activity, and partial secondary structure.  

UK PubMed Central (United Kingdom)

The gene defining the catalytic RNA component of RNase P in Bacillus subtilis 168 was cloned into bacteriophage lambda and plasmid vectors. The nucleotide sequence of the gene and its surroundings was determined from the cloned DNA and by directly sequencing or reverse transcribing the RNase P RNA. The B. subtilis RNase P RNA sequence (400-401 nucleotides) is remarkably different from that of Escherichia coli (377 nucleotides) (Reed, R. E., Baer, M. F., Guerrier-Takada, C., Donis-Keller, H., and Altman, S. (1982) Cell 30, 627-636; Sakamoto, H., Kimura, N., Nagawa, F., and Shimura, Y. (1983) Nucleic Acids Res. 11, 8237-8251). At best the two are less than 50% similar in sequence. To verify that the RNase P RNA gene was analyzed, a modified, putative gene was cloned adjacent to a bacteriophage T7 promoter and various transcripts were tested for RNase P activity. The intact gene transcript, but not fragments, showed full activity. Full catalytic activity was restored upon mixing the fragments. The extensive differences between the B. subtilis and E. coli RNase P RNAs precluded full covariance analysis of secondary structure, but phylogenetically consistent foldings for portions of both molecules could be derived.

Reich C; Gardiner KJ; Olsen GJ; Pace B; Marsh TL; Pace NR

1986-06-01

363

Structural analysis of a repetitive protein sequence motif in strepsirrhine primate amelogenin.  

UK PubMed Central (United Kingdom)

Strepsirrhines are members of a primate suborder that has a distinctive set of features associated with the development of the dentition. Amelogenin (AMEL), the better known of the enamel matrix proteins, forms 90% of the secreted organic matrix during amelogenesis. Although AMEL has been sequenced in numerous mammalian lineages, the only reported strepsirrhine AMEL sequences are those of the ring-tailed lemur and galago, which contain a set of additional proline-rich tandem repeats absent in all other primates species analyzed to date, but present in some non-primate mammals. Here, we first determined that these repeats are present in AMEL from three additional lemur species and thus are likely to be widespread throughout this group. To evaluate the functional relevance of these repeats in strepsirrhines, we engineered a mutated murine amelogenin sequence containing a similar proline-rich sequence to that of Lemur catta. In the monomeric form, the MQP insertions had no influence on the secondary structure or refolding properties, whereas in the assembled form, the insertions increased the hydrodynamic radii. We speculate that increased AMEL nanosphere size may influence enamel formation in strepsirrhine primates.

Lacruz RS; Lakshminarayanan R; Bromley KM; Hacia JG; Bromage TG; Snead ML; Moradian-Oldak J; Paine ML

2011-01-01

364

Structural Analysis of a Repetitive Protein Sequence Motif in Strepsirrhine Primate Amelogenin  

Science.gov (United States)

Strepsirrhines are members of a primate suborder that has a distinctive set of features associated with the development of the dentition. Amelogenin (AMEL), the better known of the enamel matrix proteins, forms 90% of the secreted organic matrix during amelogenesis. Although AMEL has been sequenced in numerous mammalian lineages, the only reported strepsirrhine AMEL sequences are those of the ring-tailed lemur and galago, which contain a set of additional proline-rich tandem repeats absent in all other primates species analyzed to date, but present in some non-primate mammals. Here, we first determined that these repeats are present in AMEL from three additional lemur species and thus are likely to be widespread throughout this group. To evaluate the functional relevance of these repeats in strepsirrhines, we engineered a mutated murine amelogenin sequence containing a similar proline-rich sequence to that of Lemur catta. In the monomeric form, the MQP insertions had no influence on the secondary structure or refolding properties, whereas in the assembled form, the insertions increased the hydrodynamic radii. We speculate that increased AMEL nanosphere size may influence enamel formation in strepsirrhine primates.

Bromley, Keith M.; Hacia, Joseph G.; Bromage, Timothy G.; Snead, Malcolm L.; Moradian-Oldak, Janet; Paine, Michael L.

2011-01-01