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1

Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core  

SciTech Connect

Protein design tests our understanding of protein stability and structure. Successful design methods should allow the exploration of sequence space not found in nature. However, when redesigning naturally occurring protein structures, most fixed backbone design algorithms return amino acid sequences that share strong sequence identity with wild-type sequences, especially in the protein core. This behavior places a restriction on functional space that can be explored and is not consistent with observations from nature, where sequences of low identity have similar structures. Here, we allow backbone flexibility during design to mutate every position in the core (38 residues) of a four-helix bundle protein. Only small perturbations to the backbone, 12 {angstrom}, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 {angstrom}).

Murphy, Grant S.; Mills, Jeffrey L.; Miley, Michael J.; Machius, Mischa; Szyperski, Thomas; Kuhlman, Brian (UNC); (SUNYB)

2012-08-10

2

Measurement and Classification of Out-of-Sequence Packets in a Tier1 IP Backbone  

Microsoft Academic Search

We present a measurement study and classification methodology for out-of-sequence packets in TCP connections observed within the Sprint IP backbone. Such out-of-sequence packets can result from many causes including loss, looping, reordering, or duplication in the network. It is important to quantify and understand the causes of such out-of-sequence packets since they are one indication of the \\

Sharad Jaiswal; Gianluca Iannaccone; Christophe Diot; James F. Kurose; Donald F. Towsley

2003-01-01

3

Measurement and classification of out-of-sequence packets in a tier-1 IP backbone  

Microsoft Academic Search

We present a measurement study and classification methodology for out-of-sequence packets in TCP connections observed within the Sprint IP backbone. Such out-of-sequence packets can result from many causes including loss, looping, reordering, or duplication in the network. It is important to quantify and understand the causes of such out-of-sequence packets since they are one indication of the \\

Sharad Jaiswalt; Gianluca Iannaccone; Christophe Diot; James F. Kurose; Donald F. Towsley

2002-01-01

4

Investigations into Sequence and Conformational Dependence of Backbone Entropy, Inter-basin  

E-print Network

Investigations into Sequence and Conformational Dependence of Backbone Entropy, Inter-basin The populations and transitions between Ramachandran basins are stu- died for combinations of the standard 20 and employing seven commonly used force-fields. Both the basin populations and inter-conversion rates

Berry, R. Stephen

5

Sequence-dependent backbone dynamics of a viral fusogen transmembrane helix.  

PubMed

The transmembrane domains of membrane fusogenic proteins are known to contribute to lipid bilayer mixing as indicated by mutational studies and functional reconstitution of peptide mimics. Here, we demonstrate that mutations of a GxxxG motif or of Ile residues, that were previously shown to compromise the fusogenicity of the Vesicular Stomatitis virus G-protein transmembrane helix, reduce its backbone dynamics as determined by deuterium/hydrogen-exchange kinetics. Thus, the backbone dynamics of these helices may be linked to their fusogenicity which is consistent with the known over-representation of Gly and Ile in viral fusogen transmembrane helices. The transmembrane domains of membrane fusogenic proteins are known to contribute to lipid bilayer mixing. Our present results demonstrate that mutations of certain residues, that were previously shown to compromise the fusogenicity of the Vesicular Stomatitis virus G-protein transmembrane helix, reduce its backbone dynamics. Thus, the data suggest a relationship between sequence, backbone dynamics, and fusogenicity of transmembrane segments of viral fusogenic proteins. PMID:22593029

Stelzer, Walter; Langosch, Dieter

2012-07-01

6

Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design  

PubMed Central

Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface), interactions between and within parts of the structure (e.g. domains) can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others. PMID:21789164

Smith, Colin A.; Kortemme, Tanja

2011-01-01

7

Comparative experimental investigation on the actuation mechanisms of ionic polymer–metal composites with different backbones and water contents  

SciTech Connect

Water-based ionic polymer–metal composites (IPMCs) exhibit complex deformation properties, especially when the water content changes. To explore the general actuation mechanisms, both Nafion and Flemion membranes are used as the polymer backbones. IPMC deformation includes three stages: fast anode deformation, relaxation deformation, and slow anode deformation, which is mainly dependent on the water content and the backbone. When the water content decreases from 21 to 14?wt.?%, Nafion–IPMC exhibits a large negative relaxation deformation, zero deformation, a positive relaxation deformation, and a positive steady deformation without relaxation in sequence. Despite the slow anode deformation, Flemion–IPMC also shows a slight relaxation deformation, which disappears when the water content is less than 13?wt.?%. The different water states are investigated at different water contents using nuclear magnetic resonance spectroscopy. The free water, which decreases rapidly at the beginning through evaporation, is proven to be critical for relaxation deformation. For the backbone, indirect evidence from the steady current response is correlated with the slow anode deformation of Flemion-IPMC. The latter is explained by the secondary dissociation of the weak acid group –COOH. Finally, we thoroughly explain not only the three deformations by swelling but also their evolvement with decreasing water content. A fitting model is also presented based on a multi-diffusion equation to reveal the deformation processes more clearly, the results from which are in good agreement with the experimental results.

Zhu, Zicai; Chang, Longfei; Wang, Yanjie; Chen, Hualing, E-mail: hlchen@mail.xjtu.edu.cn [State Key Laboratory of Mechanical Structure Strength and Vibration, Xi'an Jiaotong University, Xi'an 710049 (China); School of Mechanical Engineering, Xi'an Jiaotong University, Xi'an 710049 (China); Asaka, Kinji [Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka 563-8577 (Japan); Zhao, Hongxia [Niumag Corporation, Shanghai 200333 (China); Li, Dichen [School of Mechanical Engineering, Xi'an Jiaotong University, Xi'an 710049 (China); State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an 710049 (China)

2014-03-28

8

Comparative experimental investigation on the actuation mechanisms of ionic polymer-metal composites with different backbones and water contents  

NASA Astrophysics Data System (ADS)

Water-based ionic polymer-metal composites (IPMCs) exhibit complex deformation properties, especially when the water content changes. To explore the general actuation mechanisms, both Nafion and Flemion membranes are used as the polymer backbones. IPMC deformation includes three stages: fast anode deformation, relaxation deformation, and slow anode deformation, which is mainly dependent on the water content and the backbone. When the water content decreases from 21 to 14 wt. %, Nafion-IPMC exhibits a large negative relaxation deformation, zero deformation, a positive relaxation deformation, and a positive steady deformation without relaxation in sequence. Despite the slow anode deformation, Flemion-IPMC also shows a slight relaxation deformation, which disappears when the water content is less than 13 wt. %. The different water states are investigated at different water contents using nuclear magnetic resonance spectroscopy. The free water, which decreases rapidly at the beginning through evaporation, is proven to be critical for relaxation deformation. For the backbone, indirect evidence from the steady current response is correlated with the slow anode deformation of Flemion-IPMC. The latter is explained by the secondary dissociation of the weak acid group -COOH. Finally, we thoroughly explain not only the three deformations by swelling but also their evolvement with decreasing water content. A fitting model is also presented based on a multi-diffusion equation to reveal the deformation processes more clearly, the results from which are in good agreement with the experimental results.

Zhu, Zicai; Chang, Longfei; Asaka, Kinji; Wang, Yanjie; Chen, Hualing; Zhao, Hongxia; Li, Dichen

2014-03-01

9

[Cotransformation of rice by bar and cecropin B gene expression cassettes lacking vector backbone sequences].  

PubMed

Whole plasmids are used in both Agrobacterium-mediated transformation and direct DNA transfer, generally leading to the integration of vector backbone sequences into the host genome along with the transgene(s). The undesirable vector backbone sequences may not only promote transgene rearrangements and affect transgene or endogenous gene expression negatively, but have disadvantage on the safe assessment of the transformants as "desert DNA". The direct DNA transforming systems can transfer minimal gene expression cassettes (promoter, open reading frame, terminator) into plant genome and generate "safer" transformants, also it can delivery multiple genes of agronomic relevance to economically-important crop plants. But there is seldom researching reports on the topic till now. The present paper studied some factors that affecting the transforming efficiency of liner gene expression cassettes to rice varieties by particle bombardment, and the integration patterns of the gene expression cassettes in rice genome were compared with that of the whole plasmids. The results showed: (1) The transforming frequency of gene expression cassettes to rice via particle bombardment is 0.1%-0.5%, the cotransforming frequency of non-selectable gene is about 50%-60% when two separate gene expression cassettes were used for transformation. Increasing the DNA mole content can increase the transforming frequency and the beside sequences of gene constructs may play an important role on the variation of transforming efficiency between different rice varieties. (2) It's reported that the selectable and non-selectable transgene expression cassettes generated low-copy-number transgenic plants with simple integration patterns. While our results showed that the non-selectable cecropin B gene cassette generated simple integration patterns with 1-3 copies in the rice genome, but the selectable bar gene cassette which got 4-14 copies had much more complex integration patterns than that of the whole plasmids which got 1-3 copies only. As the bar gene is promoted by the CaMV35 promoter, in which there is a 19 bp palindromic sequence could act as recombination hot spot and lead to DNA rearrangement, we presumed that the transgene recombination events happened during the integration course have generated the complex Southern patterns of bar gene expression cassette. The recombination character, the heredity behavior and the expression law of gene expression cassettes in the rice genomes will be reported in our future papers. PMID:12776601

Zhao, Yan; Yu, Yan-Chun; Qian, Qian; Yan, Mei-Xian; Huang, Da-Nian

2003-02-01

10

DNA Sequence Analysis of Regions Surrounding blaCMY-2 from Multiple Salmonella Plasmid Backbones  

PubMed Central

The emergence in the United States of resistance to expanded-spectrum cephalosporin (e.g., ceftriaxone) within the salmonellae has been associated primarily with three large (>100-kb) plasmids (designated types A, B, and C) and one 10.1-kb plasmid (type D) that carry the blaCMY-2 gene. In the present study, the distribution of these four known blaCMY-2-carrying plasmids among 35 ceftriaxone-resistant Salmonella isolates obtained from 1998 to 2001 was examined. Twenty-three of these isolates were Salmonella enterica serotype Newport, 10 were Salmonella enterica serotype Typhimurium, 1 was Salmonella enterica serotype Agona, and 1 was Salmonella enterica serotype Reading. All 23 serotype Newport isolates carried a type C plasmid, and 5, 4, and 1 serovar Typhimurium isolate carried type B, A, and C plasmids, respectively. Both the serotype Agona and serotype Reading isolates carried type A plasmids. None of the isolates carried a type D plasmid. Hybridization data suggested that plasmid types A and C were highly related replicons. DNA sequencing revealed that the region surrounding blaCMY-2 was highly conserved in all three plasmid types analyzed (types B, C, and D) and was related to a region surrounding blaCMY-5 from the Klebsiella oxytoca plasmid pTKH11. These findings are consistent with a model in which blaCMY-2 has been disseminated primarily through plasmid transfer, and not by mobilization of the gene itself, to multiple Salmonella chromosomal backbones. PMID:15273090

Giles, W. P.; Benson, A. K.; Olson, M. E.; Hutkins, R. W.; Whichard, J. M.; Winokur, P. L.; Fey, P. D.

2004-01-01

11

TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences.  

PubMed

Protein backbone torsion angles (Phi) and (Psi) involve two rotation angles rotating around the C(?)-N bond (Phi) and the C(?)-C bond (Psi). Due to the planarity of the linked rigid peptide bonds, these two angles can essentially determine the backbone geometry of proteins. Accordingly, the accurate prediction of protein backbone torsion angle from sequence information can assist the prediction of protein structures. In this study, we develop a new approach called TANGLE (Torsion ANGLE predictor) to predict the protein backbone torsion angles from amino acid sequences. TANGLE uses a two-level support vector regression approach to perform real-value torsion angle prediction using a variety of features derived from amino acid sequences, including the evolutionary profiles in the form of position-specific scoring matrices, predicted secondary structure, solvent accessibility and natively disordered region as well as other global sequence features. When evaluated based on a large benchmark dataset of 1,526 non-homologous proteins, the mean absolute errors (MAEs) of the Phi and Psi angle prediction are 27.8° and 44.6°, respectively, which are 1% and 3% respectively lower than that using one of the state-of-the-art prediction tools ANGLOR. Moreover, the prediction of TANGLE is significantly better than a random predictor that was built on the amino acid-specific basis, with the p-value<1.46e-147 and 7.97e-150, respectively by the Wilcoxon signed rank test. As a complementary approach to the current torsion angle prediction algorithms, TANGLE should prove useful in predicting protein structural properties and assisting protein fold recognition by applying the predicted torsion angles as useful restraints. TANGLE is freely accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/TANGLE/. PMID:22319565

Song, Jiangning; Tan, Hao; Wang, Mingjun; Webb, Geoffrey I; Akutsu, Tatsuya

2012-01-01

12

Sequence-dependent DNA structure: the role of the sugar-phosphate backbone 1 1 Edited by T. Richmond  

Microsoft Academic Search

A detailed analysis of the coupling between the conformational properties of the sugar-phosphate backbone and the base stacking interactions in dinucleotide steps of double helical DNA is described. In X-ray crystal structures of oligonucleotides, the backbone shows one major degree of freedom, consisting of the torsion angles ?, ?, ? and the pseudorotation phase angle, P. The remaining torsion angles

Martin J. Packer; Christopher A. Hunter

1998-01-01

13

Loss of Internal Backbone Carbonyls: Additional Evidence for Sequence-Scrambling in Collision-Induced Dissociation of y-Type Ions  

NASA Astrophysics Data System (ADS)

It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAH AA-NH2 heptapeptide and des-acetylated-?-melanocyte-stimulating hormone (d?-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MSn), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/ z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/ z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-"like" ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.

Harper, Brett; Miladi, Mahsan; Solouki, Touradj

2014-10-01

14

Comparative experimental study of ionic polymer-metal composites with different backbone ionomers and in various cation forms  

NASA Astrophysics Data System (ADS)

An ionic polymer-metal composite (IPMC) consisting of a thin perfluorinated ionomer (usually, Nafion or Flemion) strip, platinum, and/or gold plated on both faces and neutralized by a certain amount of appropriate cations undergoes large bending motion when, in a hydrated state, a small electric field is applied across its thickness. When the same membrane is suddenly bent, a small voltage of the order of millivolts is produced across its surfaces. Hence IPMCs can serve as soft bending actuators and sensors. This coupled electrical-chemical-mechanical response of IPMCs depends on the structure of the backbone ionic polymer, the morphology and conductivity of the metal electrodes, the nature of the cations, and the level of hydration (or other solvent uptake). We have carried out extensive experimental studies on both Nafion- and Flemion-based IPMCs in various cation forms, seeking to understand the fundamental properties of these composites, to explore the mechanism of their actuation, and finally, to optimize their performance for various potential applications. The results of some of these tests on both Nafion- and Flemion-based IPMCs with alkali-metal or alkyl-ammonium cations are reported here. Compared with Nafion-based IPMCs, Flemion-based IPMCs with fine dendritic gold electrodes have higher ion-exchange capacity, better surface conductivity, higher hydration capacity, and higher longitudinal stiffness. They also display greater bending actuation under the same applied voltage. In addition, they do not display a reverse relaxation under a sustained dc voltage, which is typical of Nafion-based IPMCs in alkali-metal form. Flemion IPMCs thus are promising composites for application as bending actuators.

Nemat-Nasser, Sia; Wu, Yongxian

2003-05-01

15

Composition for nucleic acid sequencing  

DOEpatents

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

Korlach, Jonas (Ithaca, NY); Webb, Watt W. (Ithaca, NY); Levene, Michael (Ithaca, NY); Turner, Stephen (Ithaca, NY); Craighead, Harold G. (Ithaca, NY); Foquet, Mathieu (Ithaca, NY)

2008-08-26

16

Sequence-specific backbone (1)H, (13)C, and (15)N resonance assignments of human ribonuclease 4.  

PubMed

Human ribonuclease 4 (RNase 4) is the most evolutionarily conserved member of the 8 canonical human pancreatic-like RNases, showing more than 90 % identity with bovine and porcine homologues. The enzyme displays ribonucleolytic activity with a strong preference for uracil-containing RNA substrates, a feature only shared with human eosinophil derived-neurotoxin (EDN, or RNase 2) and eosinophil cationic protein (ECP, or RNase 3). It is also the shortest member of the human family, with a significantly truncated C-terminal tail. Its unique active-site pocket and high degree of conservation among vertebrates suggest that the enzyme plays a crucial biological function. Here, we report on the (1)H, (13)C and (15)N backbone resonance assignments of RNase 4, providing means to characterize its molecular function at the atomic level by NMR. PMID:25030111

Gagné, Donald; Doucet, Nicolas

2015-04-01

17

Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship  

PubMed Central

Protein Blocks (PBs) comprise a structural alphabet of 16 protein fragments, each 5 C? long. They make it possible to approximate and correctly predict local protein three-dimensional (3D) structures. We have selected the 72 most frequent sequences of five PBs, which we call Structural Words (SWs). Analysis of four different protein data banks shows that SWs cover 92% of the amino acids in them and provide a good structural approximation for residues (i.e., sequences) 9 C? long. We present most of them in a simple network that describes 90% of the overall residues and, interestingly, includes more than 80% of the amino acids present in coils. Analysis of the network shows the specificity and quality of the 3D descriptions as well as a new type of relation between local folds and amino acid distribution. The results show that the 3D structure of these protein data banks can be easily described by a combination of subgraphs included in the network. Finally, a Bayesian probabilistic approach improved the prediction rate by 4%. PMID:12441385

de Brevern, Alexandre G.; Valadié, Hélène; Hazout, Serge; Etchebest, Catherine

2002-01-01

18

N-terminal peptide sequence repetition influences the kinetics of backbone fragmentation: a manifestation of the Jahn-Teller effect?  

PubMed

Analysis of large (>10,000 entries) databases consisting of high-resolution tandem mass spectra of peptide dications revealed with high statistical significance (P?sequences composed of the same amino acids (i.e., in general AB- and BA- bonds cleave more often than AA- and BB- bonds). This effect seems to depend upon the collisional energy, being stronger at lower energies. The phenomenon is likely to indicate the presence of the diketopiperazine structure for at least some b2 (+) ions. When consisting of two identical amino acids, these species should form through intermediates that have a symmetric geometry and, thus, must be subject to the Jahn-Teller effect that reduces the stability of such systems. PMID:23633015

Good, David M; Yang, Hongqian; Zubarev, Roman A

2013-11-01

19

N-Terminal Peptide Sequence Repetition Influences the Kinetics of Backbone Fragmentation: A Manifestation of the Jahn-Teller Effect?  

NASA Astrophysics Data System (ADS)

Analysis of large (>10,000 entries) databases consisting of high-resolution tandem mass spectra of peptide dications revealed with high statistical significance ( P < 1?10-3) that peptides with non-identical first two N-terminal amino acids undergo cleavages of the second peptide bond at higher rates than repetitive sequences composed of the same amino acids (i.e., in general AB- and BA- bonds cleave more often than AA- and BB- bonds). This effect seems to depend upon the collisional energy, being stronger at lower energies. The phenomenon is likely to indicate the presence of the diketopiperazine structure for at least some b2 + ions. When consisting of two identical amino acids, these species should form through intermediates that have a symmetric geometry and, thus, must be subject to the Jahn-Teller effect that reduces the stability of such systems.

Good, David M.; Yang, Hongqian; Zubarev, Roman A.

2013-11-01

20

Comparative experimental study of ionic polymer-metal composites with different backbone ionomers and in various cation forms  

Microsoft Academic Search

An ionic polymer-metal composite (IPMC) consisting of a thin perfluorinated ionomer (usually, Nafion or Flemion) strip, platinum, and\\/or gold plated on both faces and neutralized by a certain amount of appropriate cations undergoes large bending motion when, in a hydrated state, a small electric field is applied across its thickness. When the same membrane is suddenly bent, a small voltage

Sia Nemat-Nasser; Yongxian Wu

2003-01-01

21

Sea Lion Skeleton - Backbone  

NSDL National Science Digital Library

Sea lions are vertebrates with both backbones and ribs. The backbone is a gliding joint, allowing the animal to be flexible, while the ribs main function is to protect it's inner organs. The short tail helps to balance the animal while walking on land.

Ketan Patel (California State University, Fullerton; Student, Biological Sciences)

2007-07-27

22

Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences  

E-print Network

Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences of life, the biological information of nucleic acid polymers must have increased to encode functional work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization

Nowak, Martin A.

23

Automatically Compositing Still Images and Landscape Video Sequences  

Microsoft Academic Search

We present an approach to deliver high-quality composites of panned, tilted, and zoomed landscape video sequences with computer-generated still images, targeted at large-scale construction projects. We propose a fully automatic camera-tracking algorithm to accurately composite computer-generated still images into panned, tilted, and zoomed video-sequence frames taken by hand or from a tripod. It provides an excellent means for a visual

Xueying Qin; Eihachiro Nakamae; Katsumi Tadamura

2002-01-01

24

Nucleotide sequence composition and method for detection of neisseria gonorrhoeae  

SciTech Connect

This patent describes a composition of matter that is specific for {ital Neisseria gonorrhoeae}. It comprises: at least one nucleotide sequence for which the ratio of the amount of the sequence which hybridizes to chromosomal DNA of {ital Neisseria gonorrhoeae} to the amount of the sequence which hybridizes to chromosomal DNA of {ital Neisseria meningitidis} is greater than about five. The ratio being obtained by a method described.

Lo, A.; Yang, H.L.

1990-02-13

25

Spines, backbones and orthopedic surgery. Spines, backbones and orthopedic surgery.  

E-print Network

1/ 17 Spines, backbones and orthopedic surgery. Spines, backbones and orthopedic surgery. Simon;2/ 17 Spines, backbones and orthopedic surgery. Motivation #12;2/ 17 Spines, backbones and orthopedic surgery. Motivation Recent work (B-boys & Schweinsberg, Aidekon-Harris) considers branching Brownian

26

Methods and compositions for efficient nucleic acid sequencing  

DOEpatents

Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

Drmanac, Radoje

2006-07-04

27

Methods and compositions for efficient nucleic acid sequencing  

DOEpatents

Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

Drmanac, Radoje (850 E. Greenwich Pl., Palo Alto, CA 94303)

2002-01-01

28

Crocodile Skeleton - Backbone  

NSDL National Science Digital Library

The crocodile is a reptile that has a long and narrow skeleton. The backbone (a gliding joint) of this animal extends into a powerful tail, allowing it to swim through water. The ribs of the crocodile are small and serve to protect its inner organs.

Ketan Patel (California State University, Fullerton; Student, Biological Sciences)

2007-07-27

29

Dolphin Skeleton - Backbone  

NSDL National Science Digital Library

The dolphin is built to be sleek. Its body is made of almost entirely backbone (a gliding joint) which makes it very flexible under water. The ribs protect the inner organs of the dolphin and the tail beats from side to side, thrusting the animal forward.

Ketan Patel (California State University, Fullerton; Student, Biological Sciences)

2007-07-27

30

Recombinant chimeric virus with wild-type dengue 4 virus premembrane and envelope and virulent yellow fever virus Asibi backbone sequences is dramatically attenuated in nonhuman primates.  

PubMed

Candidate vaccine ChimeriVax viruses are attenuated, efficacious, safe, and highly unlikely to be transmitted by arthropod vectors. Nevertheless, concerns have been raised about the use of these vaccines because of the potential for recombination between vaccine and wild-type (WT) strains. To evaluate the vertebrate pathogenicity of such a worst-case recombinant, ChimeriVax-dengue (DEN) 4 virus was chimerized with the WT Asibi yellow fever virus. In this worst-case scenario, chimeric viruses remained fully attenuated in nonhuman primates. We therefore conclude that, even in the highly unlikely event of "virulent" backbone reversion, the safety of ChimeriVax-DEN vaccines would not be compromised. PMID:18266603

McGee, Charles E; Lewis, Mark G; Claire, Marisa St; Wagner, Wendeline; Lang, Jean; Guy, Bruno; Tsetsarkin, Konstantin; Higgs, Stephen; Decelle, Thierry

2008-03-01

31

Structural requirements for the biosynthesis of backbone cyclic peptide libraries  

E-print Network

Structural requirements for the biosynthesis of backbone cyclic peptide libraries Charles P. Scott to biosynthesis of backbone cyclic peptide libraries that combines the strengths of synthetic and genetic methods is very promiscuous with respect to peptide substrate composition, and can generate cyclic products

Ahmad, Sajjad

32

Soil amino acid composition across a boreal forest successional sequence  

Microsoft Academic Search

Soil amino acids are important sources of organic nitrogen for plant nutrition, yet few studies have examined which amino acids are most prevalent in the soil. In this study, we examined the composition, concentration, and seasonal patterns of soil amino acids across a primary successional sequence encompassing a natural gradient of plant productivity and soil physicochemical characteristics. Soil was collected

Nancy R. Werdin-Pfisterer; Knut Kielland; Richard D. Boone

2009-01-01

33

Monomer composition and sequence of alginates from Pseudomonas aeruginosa  

Microsoft Academic Search

Alginates from four strains of Pseudomonas aeruginosa, one mucoid strain isolated from a technical water system, one strain isolated from a patient with cystic fibrosis and two mutants of this strain with a defect which affects the O-acetylation of the extracellular alginate, have been isolated and analysed for monomer composition and sequence by 13C-nuclear magnetic resonance (NMR) spectroscopy. The detected

N. Schürks; J. Wingender; H.-C. Flemming; C. Mayer

2002-01-01

34

Load sequence effects on the fatigue of unnotched composite materials  

NASA Technical Reports Server (NTRS)

A more comprehensive version of an earlier fatigue and residual strength degradation model is proposed to predict the effect of load sequence on the statistical fatigue behavior of composite laminates. The model, which reduces to various fatigue models proposed in the literature by means of approximations, is verified by a survey of experiments on glass/epoxy laminates. It is shown that the correlation between the model and the test results under dual stress levels is reasonable, and that a simplified version of the model is verified by experiments on graphite/epoxy laminates in which the correlation between theoretical predictions and results under dual stress levels is satisfactory. The model is also shown capable of predicting the effect of proof loads on the fatigue behavior of composite materials.

Yang, J. N.; Jones, D. L.

1981-01-01

35

Throughput Optimization in Mobile Backbone Networks  

E-print Network

This paper describes new algorithms for throughput optimization in a mobile backbone network. This hierarchical communication framework combines mobile backbone nodes, which have superior mobility and communication capability, ...

Craparo, Emily M.

36

Ancestral Sequence Reconstruction in Primate Mitochondrial DNA: Compositional Bias and Effect on Functional Inference  

E-print Network

Ancestral Sequence Reconstruction in Primate Mitochondrial DNA: Compositional Bias and Effect, Louisiana State University; and Department of Biological Sciences, University at Albany Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past

Pollock, David

37

Sequence of the 68,869 bp IncP-1alpha plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements.  

PubMed

To analyse the significance of conjugative broad-host-range IncP-1alpha plasmids for the spread of antibiotic resistance determinants in waste-water treatment plants we isolated and characterised five different IncP-1alpha plasmids from bacteria of activated sludge and the final effluents of a municipal waste-water treatment plant. These plasmids mediate resistance to ampicillin, cefaclor, cefuroxime, gentamicin, kanamycin, spectinomycin, streptomycin, tetracycline, tobramycin, and trimethoprim. The complete 68,869 bp DNA-sequence of the IncP-1alpha plasmid pTB11 was determined. The pTB11 backbone modules for replication (Rep), mating pair formation (Trb), multimer resolution (Mrs), post-segregational killing (Psk), conjugative DNA-transfer (Tra), plasmid control (Ctl), and stable maintenance and inheritance (KilA, KilE, and KilC) are highly conserved as compared to the 'Birmingham' IncP-1alpha plasmids. In contrast to the 'Birmingham' plasmids pTB11 carries an insert of a Tn402-derivative integrating a class 1 integron in the intergenic region between the multimer resolution operon parCBA and the post-segregational killing operon parDE. The integron comprises the resistance gene cassettes oxa2 (beta-lactamase), aacA4 (aminoglycoside-6'N-acetyltransferase), and aadA1 (aminoglycoside-3'-adenylyltransferase) and a complete tniABQR transposition module. Integron-specific sequences were also identified on other IncP-1alpha plasmids analysed in this work. In contrast to the 'Birmingham' plasmids the pTB11 tetracycline resistance module carries a pecM- and a pncA-like gene downstream of the tetracycline resistance gene tetA and contains an insertion of the new insertion sequence element ISTB11. The transposable elements IS21 and Tn1 which disrupted, respectively, orf7 and klcB on the 'Birmingham' plasmids are not present on pTB11. Identification of IncP-1alpha plasmids in bacteria of the waste-water treatment plant's final effluents indicates that bacteria carrying these kind of plasmids are released into the environment. PMID:15848226

Tennstedt, Thomas; Szczepanowski, Rafael; Krahn, Irene; Pühler, Alfred; Schlüter, Andreas

2005-05-01

38

Modeling compositional dynamics based on GC and purine contents of protein-coding sequences  

PubMed Central

Background Understanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge. Results To model the compositional dynamics of protein-coding sequences, we propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, with no prerequisite of homologous sequences or their alignments. We evaluated the two models by quantifying theoretical compositions of a large collection of protein-coding sequences (including 46 of Archaea, 686 of Bacteria, and 826 of Eukarya), yielding consistent theoretical compositions across all the collected sequences. Conclusions We show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms. Reviewers This article was reviewed by Zhaolei Zhang (nominated by Mark Gerstein), Guruprasad Ananda (nominated by Kateryna Makova), and Daniel Haft. PMID:21059261

2010-01-01

39

Chemical characteristics and antithrombotic effect of chondroitin sulfates from sturgeon skull and sturgeon backbone.  

PubMed

Chondroitin sulfates (CSs) were extracted from sturgeon skull and backbone, and their chemical composition, anticoagulant, anti-platelet and thrombolysis activities were evaluated. The average molecular weights of CS from sturgeon skull and backbone were 38.5kDa and 49.2kDa, respectively. Disaccharide analysis indicated that the sturgeon backbone CS was primarily composed of disaccharide monosulfated in position four of the GalNAc (37.8%) and disaccharide monosulfated in position six of the GalNAc (59.6%) while sturgeon skull CS was primarily composed of nonsulfated disaccharide (74.2%). Sturgeon backbone CS showed stronger antithrombotic effect than sturgeon skull CS. Sturgeon backbone CS could significantly prolong activated partial thromboplastin time (APTT) and thrombin time (TT), inhibited ADP-induced platelet aggregation and dissolved platelet plasma clots in vitro. The results suggested that sturgeon backbone CS can be explored as a functional food with antithrombotic function. PMID:25843879

Gui, Meng; Song, Juyi; Zhang, Lu; Wang, Shun; Wu, Ruiyun; Ma, Changwei; Li, Pinglan

2015-06-01

40

Diverse nucleotide compositions and sequence fluctuation in Rubisco protein genes  

NASA Astrophysics Data System (ADS)

The Rubisco protein-enzyme is arguably the most abundance protein on Earth. The biology dogma of transcription and translation necessitates the study of the Rubisco genes and Rubisco-like genes in various species. Stronger correlation of fractal dimension of the atomic number fluctuation along a DNA sequence with Shannon entropy has been observed in the studied Rubisco-like gene sequences, suggesting a more diverse evolutionary pressure and constraints in the Rubisco sequences. The strategy of using metal for structural stabilization appears to be an ancient mechanism, with data from the porphobilinogen deaminase gene in Capsaspora owczarzaki and Monosiga brevicollis. Using the chi-square distance probability, our analysis supports the conjecture that the more ancient Rubisco-like sequence in Microcystis aeruginosa would have experienced very different evolutionary pressure and bio-chemical constraint as compared to Bordetella bronchiseptica, the two microbes occupying either end of the correlation graph. Our exploratory study would indicate that high fractal dimension Rubisco sequence would support high carbon dioxide rate via the Michaelis- Menten coefficient; with implication for the control of the whooping cough pathogen Bordetella bronchiseptica, a microbe containing a high fractal dimension Rubisco-like sequence (2.07). Using the internal comparison of chi-square distance probability for 16S rRNA (~ E-22) versus radiation repair Rec-A gene (~ E-05) in high GC content Deinococcus radiodurans, our analysis supports the conjecture that high GC content microbes containing Rubisco-like sequence are likely to include an extra-terrestrial origin, relative to Deinococcus radiodurans. Similar photosynthesis process that could utilize host star radiation would not compete with radiation resistant process from the biology dogma perspective in environments such as Mars and exoplanets.

Holden, Todd; Dehipawala, S.; Cheung, E.; Bienaime, R.; Ye, J.; Tremberger, G., Jr.; Schneider, P.; Lieberman, D.; Cheung, T.

2011-10-01

41

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design  

PubMed Central

Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones), oligooxopiperazines, oligo-peptoids, -peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org). This work helps address the peptidomimetic community's need for an automated and expandable modeling tool for noncanonical backbones. PMID:23869206

Craven, Timothy W.; Butterfoss, Glenn L.; Chou, Fang-Chieh; Lyskov, Sergey; Bullock, Brooke N.; Watkins, Andrew; Labonte, Jason W.; Pacella, Michael; Kilambi, Krishna Praneeth; Leaver-Fay, Andrew; Kuhlman, Brian; Gray, Jeffrey J.; Bradley, Philip; Kirshenbaum, Kent; Arora, Paramjit S.; Das, Rhiju; Bonneau, Richard

2013-01-01

42

Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain  

PubMed Central

Understanding of the effects of the backbone cyclization on the structure and dynamics of a protein is essential for using protein topology engineering to alter protein stability and function. Here we have determined, for the first time, the structure and dynamics of the linear and various circular constructs of the N-SH3 domain from protein c-Crk. These constructs differ in the length and amino acid composition of the cyclization region. The backbone cyclization was carried out using intein-mediated intramolecular chemical ligation between the juxtaposed N- and the C-termini. The structure and backbone dynamics studies were performed using solution NMR. Our data suggest that the backbone cyclization has little effect on the overall three-dimensional structure of the SH3 domain: besides the termini, only minor structural changes were found in the proximity of the cyclization region. In contrast to the structure, backbone dynamics are significantly affected by the cyclization. On the subnanosecond time scale, the backbone of all circular constructs on average appears more rigid than that of the linear SH3 domain; this effect is observed over the entire backbone and is not limited to the cyclization site. The backbone mobility of the circular constructs becomes less restricted with increasing length of the circularization loop. In addition, significant conformational exchange motions (on the sub-millisecond time scale) were found in the N-Src loop and in the adjacent ?-strands in all circular constructs studied in this work. These effects of backbone cyclization on protein dynamics have potential implications for the stability of the protein fold and for ligand binding. PMID:25905098

Schumann, Frank H.; Varadan, Ranjani; Tayakuniyil, Praveen P.; Grossman, Jennifer H.; Camarero, Julio A.; Fushman, David

2015-01-01

43

Epoxy\\/Polyurethane\\/Clay Ternary Nanocomposites – Effect of Components Mixing Sequence on the Composites Properties  

Microsoft Academic Search

The present work investigates the mixing sequence of montmorillonite (MMT) and polyurethane (PUR) on epoxy resin (EP) properties. Mechanical properties were evaluated and structures analyzed by means of infrared spectroscopy (FTIR), X-ray diffraction (XRD) and transmission electron microscopy (TEM). The measured properties of all tested compositions were improved in comparison with unmodified epoxy resin. The best mechanical properties were exhibited

M. Bakar; M. Lavorgna; J. Szyma?ska; A. D?tkowska

2012-01-01

44

ON DEGENERATION OF THE SPECTRAL SEQUENCE FOR THE COMPOSITION OF ZUCKERMAN FUNCTORS  

E-print Network

ON DEGENERATION OF THE SPECTRAL SEQUENCE FOR THE COMPOSITION OF ZUCKERMAN FUNCTORS Dragan Milici(g) - M(g, K) and K,T : M(g, T) - M(g, K). These adjoints are called the Zuckerman functors. Clearly, K = K,T T . Zuckerman functors are left exact and have finite right cohomological dimension. There

Milicic, Dragan

45

Protein location prediction using atomic composition and global features of the amino acid sequence  

SciTech Connect

Subcellular location of protein is constructive information in determining its function, screening for drug candidates, vaccine design, annotation of gene products and in selecting relevant proteins for further studies. Computational prediction of subcellular localization deals with predicting the location of a protein from its amino acid sequence. For a computational localization prediction method to be more accurate, it should exploit all possible relevant biological features that contribute to the subcellular localization. In this work, we extracted the biological features from the full length protein sequence to incorporate more biological information. A new biological feature, distribution of atomic composition is effectively used with, multiple physiochemical properties, amino acid composition, three part amino acid composition, and sequence similarity for predicting the subcellular location of the protein. Support Vector Machines are designed for four modules and prediction is made by a weighted voting system. Our system makes prediction with an accuracy of 100, 82.47, 88.81 for self-consistency test, jackknife test and independent data test respectively. Our results provide evidence that the prediction based on the biological features derived from the full length amino acid sequence gives better accuracy than those derived from N-terminal alone. Considering the features as a distribution within the entire sequence will bring out underlying property distribution to a greater detail to enhance the prediction accuracy.

Cherian, Betsy Sheena, E-mail: betsy.skb@gmail.com [Centre for Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram, Kerala (India); Nair, Achuthsankar S. [Centre for Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram, Kerala (India)] [Centre for Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram, Kerala (India)

2010-01-22

46

2005 Special Issue A novel approach to extracting features from motif content and protein composition for protein sequence classification  

Microsoft Academic Search

This paper presents a novel approach to extracting features from motif content and protein composition for protein sequence classification. First, we formulate a protein sequence as a fixed-dimensional vector using the motif content and protein composition. Then, we further project the vectors into a low-dimensional space by the Principal Component Analysis (PCA) so that they can be represented by a

Xing-Ming Zhao; Yiu-Ming Cheung; De-Shuang Huang

47

Optimum stacking sequence design of composite sandwich panel using genetic algorithms  

NASA Astrophysics Data System (ADS)

Composite sandwich structures recently gained preference for various structural components over conventional metals and simple composite laminates in the aerospace industries. For most widely used composite sandwich structures, the optimization problems only requires the determination of the best stacking sequence and the number of laminae with different fiber orientations. Genetic algorithm optimization technique based on Darwin's theory of survival of the fittest and evolution is most suitable for solving such optimization problems. The present research work focuses on the stacking sequence optimization of composite sandwich panels with laminated face-sheets for both critical buckling load maximization and thickness minimization problems, subjected to bi-axial compressive loading. In the previous studies, only balanced and even-numbered simple composite laminate panels have been investigated ignoring the effects of bending-twisting coupling terms. The current work broadens the application of genetic algorithms to more complex composite sandwich panels with balanced, unbalanced, even and odd-numbered face-sheet laminates including the effects of bending-twisting coupling terms.

Bir, Amarpreet Singh

48

Polyolefin backbone substitution in binders for low temperature powder injection moulding feedstocks.  

PubMed

This paper reports the substitution of polyolefin backbone binder components with low melting temperature carnauba wax for powder injection moulding applications. The effect of various binder compositions of Al?O? feedstock on thermal degradation parameters is investigated by thermogravimetric analysis. Within the experimental framework 29 original feedstock compositions were prepared and the superiority of carnauba wax over the polyethylene binder backbone was demonstrated in compositions containing polyethylene glycol as the initial opening agent and governing the proper mechanism of the degradation process. Moreover, the replacement of synthetic polymer by the natural wax contributes to an increase of environmental sustainability of modern industrial technologies. PMID:24583880

Hausnerova, Berenika; Kuritka, Ivo; Bleyan, Davit

2014-01-01

49

Cervical Exercise: The Backbone of Spine Treatment  

MedlinePLUS

North American Spine Society Public Education Series Cervical Exercise: The Backbone of Spine Treatment How important is it? What can be ... exercises. The Importance of Exercise for the Neck Spine experts agree that physical activity is important for ...

50

A Global Compositional Complexity Measure for Biological Sequences: AT-rich and GC-rich Genomes Encode Less Complex Proteins  

Microsoft Academic Search

Different local regions of natural amino acid or nucleotide sequences show remarkable heterogeneity in residue composition, reflecting diversity in evolutionary history and physicochemical constraints. Compositional complexity measures are helpful for describing and understanding this variegation. Motivated by some open problems in comparative genomics and protein folding, we have developed a new 'global' compositional complexity measure, G1, which overcomes a crucial

Honghui Wan; John C. Wootton

2000-01-01

51

Determination of load sequence effects on the degradation and failure of composite materials. [Graphite-epoxy composites  

NASA Technical Reports Server (NTRS)

A theoretical model was established to predict the fatigue behavior of composite materials, with emphasis placed on predictions of the degradation of residual strength and residual stiffness during fatigue cycling. The model parameters were evaluated from three test series including static strength fatigue life and residual strength tests. The tests were applied to two graphite/epoxy laminates. Load sequence effects were emphasized for both laminates and the predicted results agreed quite well with subsequent verification tests. Dynamic as well as static stiffness reduction data were collected by use of a PDP11-03 computer, which performed quite satisfactorily and permitted the recording of a substantial amount of dynamic stiffness reduction data.

Yang, J. N.; Jones, D. L.

1981-01-01

52

External Tank - The Structure Backbone  

NASA Technical Reports Server (NTRS)

The External Tank forms the structural backbone of the Space Shuttle in the launch configuration. Because the tank flies to orbital velocity with the Space Shuttle Orbiter, minimization of weight is mandatory, to maximize payload performance. Choice of lightweight materials both for structure and thermal conditioning was necessary. The tank is large, and unique manufacturing facilities, tooling, handling, and transportation operations were required. Weld processes and tooling evolved with the design as it matured through several block changes, to reduce weight. Non Destructive Evaluation methods were used to assure integrity of welds and thermal protection system materials. The aluminum-lithium alloy was used near the end of the program and weld processes and weld repair techniques had to be refined. Development and implementation of friction stir welding was a substantial technology development incorporated during the Program. Automated thermal protection system application processes were developed for the majority of the tank surface. Material obsolescence was an issue throughout the 40 year program. The final configuration and tank weight enabled international space station assembly in a high inclination orbit allowing international cooperation with the Russian Federal Space Agency. Numerous process controls were implemented to assure product quality, and innovative proof testing was accomplished prior to delivery. Process controls were implemented to assure cleanliness in the production environment, to control contaminants, and to preclude corrosion. Each tank was accepted via rigorous inspections, including non-destructive evaluation techniques, proof testing, and all systems testing. In the post STS-107 era, the project focused on ascent debris risk reduction. This was accomplished via stringent process controls, post flight assessment using substantially improved imagery, and selective redesigns. These efforts were supported with a number of test programs to simulate combined environments. Processing improvements included development and use of low spray guns for foam application, additional human factors considerations for production, use of high fidelity mockups during hardware processing with video review, improved tank access, extensive use of non destructive evaluation, and producibility enhancements. Design improvements included redesigned bipod fittings, a bellows heater, a feedline camera active during ascent flight, removal of the protuberance airload ramps, redesigned ice frost ramps, and titanium brackets replaced aluminum brackets on the liquid oxygen feedline. Post flight assessment improved due to significant addition of imagery assets, greatly improving situational awareness. The debris risk was reduced by two orders of magnitude. During this time a major natural disaster was overcome when Katrina damaged the manufacturing facility. Numerous lessons from these efforts are documented within the paper.

Welzyn, Kenneth; Pilet, Jeffrey C.; Diecidue-Conners, Dawn; Worden, Michelle; Guillot, Michelle

2011-01-01

53

Effects of material and stacking sequence on behavior of composite plates with holes  

Microsoft Academic Search

Strain distributions to failure, tensile and compressive strain-concentration factors, and strength-reduction factors were determined for glass-, boron-, and graphite-epoxy plates with holes loaded in tension. Strain gages, photoelastic coatings and moiré techniques were used. Ten variations of layup and stacking sequence were studied.The boron-epoxy composite was found to be the stiffest and strongest of the three. The graphite laminate with

I. M. Daniel; R. E. Rowlands; J. B. Whiteside

1974-01-01

54

A view of an elemental naturalist at the DNA world (Base composition, sequences, methylation)  

Microsoft Academic Search

The pioneering data on base composition and pyrimidine sequences in DNA of pro-and eukaryotes are considered, and their significance\\u000a for the origin of genosystematics is discussed. The modern views on specificity and functional role of enzymatic DNA methylation\\u000a in eukaryotes are described. DNA methylation controls all genetic functions and is a mechanism of cellular differentiation\\u000a and gene silencing. A model

B. F. Vanyushin

2007-01-01

55

Bias explorer: measurements of compositional bias in EMBL and GenBank sequence files  

Microsoft Academic Search

A Windows application for compositional analysis of sequenced genomes (EMBL or GenBank flat files) is available as freeware.\\u000a The application allows the user to quantify word bias using Markov chain analysis and it allows the user to generate sliding\\u000a window data for GC-skew, AT-skew, purine excess, keto excess and discrete word counts. The mathematical routines reside in\\u000a a dynamic link

Anders Fuglsang

2004-01-01

56

Low-biodegradable composite chemical wastewater treatment by biofilm configured sequencing batch reactor (SBBR)  

Microsoft Academic Search

Biofilm configured system with sequencing\\/periodic discontinuous batch mode operation was evaluated for the treatment of low-biodegradable composite chemical wastewater (low BOD\\/COD ratio ?0.3, high sulfate content: 1.75g\\/l) in aerobic metabolic function. Reactor was operated under anoxic–aerobic–anoxic microenvironment conditions with a total cycle period of 24h [fill: 15min; reaction: 23h (aeration along with recirculation); settle: 30min; decant: 15min] and the performance

S. Venkata Mohan; N. Chandrasekhara Rao; P. N. Sarma

2007-01-01

57

Indian Railways Backbone of Information Transport in India  

E-print Network

1 Indian Railways ­ Backbone of Information Transport in India Santosh Kumar, Ohio State University: Indian Railways is the backbone of public transport in India. With ever- increasing number of people to be the backbone of any country's economy. Indian Railways undoubtedly is the backbone of public transport in India

Kumar, Santosh

58

Conformation Dependence of Backbone Geometry in Proteins  

PubMed Central

Summary Protein structure determination and predictive modeling have long been guided by the paradigm that the peptide backbone has a single, context-independent ideal geometry. Both quantum-mechanics calculations and empirical analyses have shown this is an incorrect simplification in that backbone covalent geometry actually varies systematically as a function of the ? and ? backbone dihedral angles. Here, we use a nonredundant set of ultrahigh-resolution protein structures to define these conformation-dependent variations. The trends have a rational, structural basis that can be explained by avoidance of atomic clashes or optimization of favorable electrostatic interactions. To facilitate adoption of this new paradigm, we have created a conformation-dependent library of covalent bond lengths and bond angles and shown that it has improved accuracy over existing methods without any additional variables to optimize. Protein structures derived both from crystallographic refinement and predictive modeling both stand to benefit from incorporation of the new paradigm. PMID:19836332

Berkholz, Donald S.; Shapovalov, Maxim V.; Dunbrack, Roland L.; Karplus, P. Andrew

2009-01-01

59

Sequence composition and environment effects on residue fluctuations in protein structures  

E-print Network

The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per residue elastic network model accounting for the nonhomogeneous protein mass distribution and the inter-atomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues, showing agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups. The structural instability in proteins possibly relates to the high content of the highly fluctuating residues and a deficiency of the weakly fluctuating residues in irregular secondary structure elements (loops), chameleon sequences and disordered proteins. Strong correlation between residue fluctuations and the sequence composition of protein loops supports this hypothesis. Comparing fluctuations of binding site residues (interface residues) with other surface residues shows that, on average, the interface is more rigid than the rest of the protein surface and Gly, Ala, Ser, Cys, Leu and Trp have a propensity to form more stable docking patches on the interface. The findings have broad implications for understanding mechanisms of protein association and stability of protein structures.

Anatoly M. Ruvinsky; Ilya A. Vakser

2009-07-28

60

Changing protein backbone topology: Structural and dynamic consequences of the backbone cyclization in SH3 domain  

NASA Astrophysics Data System (ADS)

Changing the topology of the normal linear backbone architecture of the polypeptide chain could provide a powerful tool for understanding and manipulating protein structure and function. In particular, backbone circularization (i.e. formation of a peptide bond between the N- and C- termini) is of considerable interest for understanding of the mechanisms underlying protein folding and stability. Here we describe the effect of the backbone circularization on the structure and backbone dynamics of the N-terminal SH3 domain from the murine c-Crk adapter protein. Several circular constructs of various lengths were obtained using intein-based chemical ligation (Camarero et al. J. Mol. Biol. 308, 1045 (2001)). We applied NMR to determine and compare the solution structure and backbone dynamics of the linear and circular forms of the protein. Our data indicate that the circularization does not significantly alter the structure of the protein core. The analysis of the backbone mobility in the sub-nanosecond time range suggests a slight rigidification of the entire backbone upon cyclization. Significant contributions from conformational exchange motions are observed in the region between beta-strands 2 and 3 in the circular constructs, probably caused by the circularization-induced strain in the protein structure.

Schumann, Frank; Varadan, Ranjani; Pudiavettil, Praveen; Camarero, Julio; Fushman, David

2002-03-01

61

SEQUENCE  

E-print Network

The Fibonacci sequence {Fn: n _> 0} is defined as F0 = l, Fx = 1, Fn =Fn.1 +Fn_z for n> 2. Let ^i,j- Fi/Fj • Alladi [1] defined a Farey-Fibonacci sequence fn of order n as the sequence obtained by arranging the terms of the set

K. C. Prasad

1980-01-01

62

Photopolymerization of aromatic acrylate containing phosphine oxide backbone and its application to holographic recording  

Microsoft Academic Search

Photopolymer compositions for holographic recording were prepared from aromatic diacrylate having phosphine oxide backbone, a hybrid sol gel, and photoinitiator. The physical and holographic properties of photopolymer were controlled by the ratio of precursor triethoxysilylpropyl polyethyleneglycol carbamate (TSPEG) in a hybrid sol gel binder and the content of monomer. The photopolymerization rate and conversion of monomer were monitored by photo-differential

Yu Mi Chang; Sung Cheol Yoon; Mijeong Han

2007-01-01

63

Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence.  

PubMed

The role of base pair composition and stacking sequence in the optical properties and electronic transitions of DNA is of fundamental interest. We present and compare the optical properties of DNA oligonucleotides (AT)10, (AT)5(GC)5, and (AT-GC)5 using both ab initio methods and UV-vis molar absorbance measurements. Our data indicate a strong dependence of both the position and intensity of UV absorbance features on oligonucleotide composition and stacking sequence. The partial densities of states for each oligonucleotide indicate that the valence band edge arises from a feature associated with the PO4(3-) complex anion, and the conduction band edge arises from anti-bonding states in DNA base pairs. The results show a strong correspondence between the ab initio and experimentally determined optical properties. These results highlight the benefit of full spectral analysis of DNA, as opposed to reductive methods that consider only the 260 nm absorbance (A260) or simple purity ratios, such as A260/A230 or A260/A280, and suggest that the slope of the absorption edge onset may provide a useful metric for the degree of base pair stacking in DNA. These insights may prove useful for applications in biology, bioelectronics, and mesoscale self-assembly. PMID:25584920

Schimelman, Jacob B; Dryden, Daniel M; Poudel, Lokendra; Krawiec, Katherine E; Ma, Yingfang; Podgornik, Rudolf; Parsegian, V Adrian; Denoyer, Linda K; Ching, Wai-Yim; Steinmetz, Nicole F; French, Roger H

2015-01-28

64

[PSI+] Maintenance Is Dependent on the Composition, Not Primary Sequence, of the Oligopeptide Repeat Domain  

PubMed Central

[PSI+], the prion form of the yeast Sup35 protein, results from the structural conversion of Sup35 from a soluble form into an infectious amyloid form. The infectivity of prions is thought to result from chaperone-dependent fiber cleavage that breaks large prion fibers into smaller, inheritable propagons. Like the mammalian prion protein PrP, Sup35 contains an oligopeptide repeat domain. Deletion analysis indicates that the oligopeptide repeat domain is critical for [PSI+] propagation, while a distinct region of the prion domain is responsible for prion nucleation. The PrP oligopeptide repeat domain can substitute for the Sup35 oligopeptide repeat domain in supporting [PSI+] propagation, suggesting a common role for repeats in supporting prion maintenance. However, randomizing the order of the amino acids in the Sup35 prion domain does not block prion formation or propagation, suggesting that amino acid composition is the primary determinant of Sup35's prion propensity. Thus, it is unclear what role the oligopeptide repeats play in [PSI+] propagation: the repeats could simply act as a non-specific spacer separating the prion nucleation domain from the rest of the protein; the repeats could contain specific compositional elements that promote prion propagation; or the repeats, while not essential for prion propagation, might explain some unique features of [PSI+]. Here, we test these three hypotheses and show that the ability of the Sup35 and PrP repeats to support [PSI+] propagation stems from their amino acid composition, not their primary sequences. Furthermore, we demonstrate that compositional requirements for the repeat domain are distinct from those of the nucleation domain, indicating that prion nucleation and propagation are driven by distinct compositional features. PMID:21760933

Toombs, James A.; Liss, Nathan M.; Cobble, Kacy R.; Ben-Musa, Zobaida; Ross, Eric D.

2011-01-01

65

Sequence composition and environment effects on residue fluctuations in protein structures  

NASA Astrophysics Data System (ADS)

Structure fluctuations in proteins affect a broad range of cell phenomena, including stability of proteins and their fragments, allosteric transitions, and energy transfer. This study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per-residue elastic network model accounting for the nonhomogeneous protein mass distribution and the interatomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues in agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups: (i) highly fluctuating-Gly, Ala, Ser, Pro, and Asp, (ii) moderately fluctuating-Thr, Asn, Gln, Lys, Glu, Arg, Val, and Cys, and (iii) weakly fluctuating-Ile, Leu, Met, Phe, Tyr, Trp, and His. The structural instability in proteins possibly relates to the high content of the highly fluctuating residues and a deficiency of the weakly fluctuating residues in irregular secondary structure elements (loops), chameleon sequences, and disordered proteins. Strong correlation between residue fluctuations and the sequence composition of protein loops supports this hypothesis. Comparing fluctuations of binding site residues (interface residues) with other surface residues shows that, on average, the interface is more rigid than the rest of the protein surface and Gly, Ala, Ser, Cys, Leu, and Trp have a propensity to form more stable docking patches on the interface. The findings have broad implications for understanding mechanisms of protein association and stability of protein structures.

Ruvinsky, Anatoly M.; Vakser, Ilya A.

2010-10-01

66

Chou's pseudo amino acid composition improves sequence-based antifreeze protein prediction.  

PubMed

Antifreeze proteins (AFP) in living organisms play a key role in their tolerance to extremely cold temperatures and have a wide range of biotechnological applications. But on account of diversity, their identification has been challenging to biologists. Earlier work explored in this area has yet to cover introduction of sequence order information which is known to represent important properties of various proteins and protein systems for prediction purposes. In this study, the effect of Chou's pseudo amino acid composition that presents sequence order of proteins was systematically explored using support vector machines for AFP prediction. Our findings suggest that introduction of sequence order information helps identify AFPs with an accuracy of 84.75% on independent test dataset, outperforming approaches such as AFP-Pred and iAFP. The relative performance calculated using Youden's Index (Sensitivity+Specificity-1) was found to be 0.71 for our predictor (AFP-PseAAC), 0.48 for AFP-Pred and 0.05 for iAFP. We hope this novel prediction approach will aid in AFP based research for biotechnological applications. PMID:24732262

Mondal, Sukanta; Pai, Priyadarshini P

2014-09-01

67

Quantum chemical studies of peptide nucleic acid monomers and role of cyclohexyl modification on backbone flexibility  

NASA Astrophysics Data System (ADS)

Peptide nucleic acids (PNA) bind sequence specifically to DNA/RNA and are of major interest for all fields of molecular biology and could form the basis for gene-targeted drugs. Modifications are introduced in PNA to overcome problems associated with orientational selectivity in binding, to restrict conformational flexibility of backbone, and to discriminate binding for either DNA or RNA. The addition of geometrical isomers (1R,2S and 1S,2R) of cyclohexyl ring in the backbone of PNA could bring rigidification to PNA backbone and may impart specificity toward RNA. Therefore, quantum chemical studies are aimed to explore the conformational space, to find out preferred stable conformations of PNA and modified (1R,2S and 1S,2R) cyclohexyl PNA monomer. Content:text/plain; charset="UTF-8"

Sharma, Smriti; Sonavane, Uddhavesh B.; Joshi, Rajendra R.

68

Backbone-free transformation of barrel medic (Medicago truncatula) with a Medicago-derived transfer DNA.  

PubMed

In the present work, Agrobacterium tumefaciens-mediated genetic transformation of the model legume Medicago truncatula Gaertn. (barrel medic) was carried out using the pSIM843 vector that contains a Medicago-derived transfer DNA, delineated by a 25-bp sequence homologous to bacterial T-DNA borders. The transfer DNA contains an expression cassette for the nptII (neomycin phosphotransferase) gene and is flanked by an expression cassette for the backbone integration marker gene ipt (isopentenyl transferase). Our results demonstrate that the Medicago-derived RB-like elements efficiently support DNA mobilization from A. tumefaciens to M. truncatula. Kanamycin-resistant shoots with normal phenotype and ipt-shooty lines were recovered at a frequency of 11.7 and 7.8%, respectively. Polymerase chain reaction (PCR) analyses demonstrated that 44.4% of the independent transgenic lines were backbone-free and evidenced the occurrence of backbone-transfer events. PMID:20571798

Confalonieri, Massimo; Borghetti, Roberto; Macovei, Anca; Testoni, Claudia; Carbonera, Daniela; Fevereiro, Manuel Pedro Salema; Rommens, Caius; Swords, Kathy; Piano, Efisio; Balestrazzi, Alma

2010-09-01

69

Construction and Maintenance of Wireless Mobile Backbone Networks  

E-print Network

We study a novel hierarchical wireless networking approach in which some of the nodes are more capable than others. In such networks, the more capable nodes can serve as mobile backbone nodes and provide a backbone over ...

Srinivas, Anand

70

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis  

PubMed Central

Background Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. In each case the underlying data are similar and are composed of counts of sequencing reads mapped to a large number of features in each sample. Despite this underlying similarity, the data analysis methods used for these experimental designs are all different, and do not translate across experiments. Alternative methods have been developed in the physical and geological sciences that treat similar data as compositions. Compositional data analysis methods transform the data to relative abundances with the result that the analyses are more robust and reproducible. Results Data from an in vitro selective growth experiment, an RNA-seq experiment and the Human Microbiome Project 16S rRNA gene abundance dataset were examined by ALDEx2, a compositional data analysis tool that uses Bayesian methods to infer technical and statistical error. The ALDEx2 approach is shown to be suitable for all three types of data: it correctly identifies both the direction and differential abundance of features in the differential growth experiment, it identifies a substantially similar set of differentially expressed genes in the RNA-seq dataset as the leading tools and it identifies as differential the taxa that distinguish the tongue dorsum and buccal mucosa in the Human Microbiome Project dataset. The design of ALDEx2 reduces the number of false positive identifications that result from datasets composed of many features in few samples. Conclusion Statistical analysis of high-throughput sequencing datasets composed of per feature counts showed that the ALDEx2 R package is a simple and robust tool, which can be applied to RNA-seq, 16S rRNA gene sequencing and differential growth datasets, and by extension to other techniques that use a similar approach. PMID:24910773

2014-01-01

71

Large-scale Measurement and Modeling of Backbone Internet Trac  

E-print Network

findings that suggest that backbone traffic is smooth. The traffic analysis work to date has focused­range correlations. Section 3 presents empirical results on a large volume of Tier 1 backbone traffic. The resultsLarge-scale Measurement and Modeling of Backbone Internet TraÆc Matthew Roughan and Joel Gottlieb

Roughan, Matthew

72

Sequence-specific 1 N backbone assignment of Psb27  

E-print Network

(PSII) catalyzes the first step of the pho- tosynthetic light reaction of cyanobacteria, algae as a side product. All animal life depends on this important reaction because it sustains the oxygenic--especially of the D1 core subunit. This unique repair cycle (Mulo et al. 2008) includes (1) at least partial dis

Roegner, Matthias

73

Sequencer  

NSDL National Science Digital Library

In this activity, students enter the starting number, multiplier, and add-on for a sequence to be graphed. This activity allows students to explore arithmetic and geometric sequences as well as combinations of the two. This activity can also be used to introduce the concepts surrounding limits and infinity. This activity includes supplemental materials, including background information about the topics covered, a description of how to use the application, and exploration questions for use with the java applet.

2010-01-01

74

Use of Composite Protein Database including Search Result Sequences for Mass Spectrometric Analysis of Cell Secretome  

PubMed Central

Mass spectrometric (MS) data of human cell secretomes are usually run through the conventional human database for identification. However, the search may result in false identifications due to contamination of the secretome with fetal bovine serum (FBS) proteins. To overcome this challenge, here we provide a composite protein database including human as well as 199 FBS protein sequences for MS data search of human cell secretomes. Searching against the human-FBS database returned more reliable results with fewer false-positive and false-negative identifications compared to using either a human only database or a human-bovine database. Furthermore, the improved results validated our strategy without complex experiments like SILAC. We expect our strategy to improve the accuracy of human secreted protein identification and to also add value for general use. PMID:25822838

Shin, Jihye; Kim, Gamin; Kabir, Mohammad Humayun; Park, Seong Jun; Lee, Seoung Taek; Lee, Cheolju

2015-01-01

75

Sequence composition and environment effects on residue fluctuations in protein structures  

E-print Network

The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per residue elastic network model accounting for the nonhomogeneous protein mass distribution and the inter-atomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues, showing agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups. The structural instability in proteins possibly relates to the high con...

Ruvinsky, Anatoly M

2009-01-01

76

Role of sequence and membrane composition in structure of transmembrane domain of Amyloid Precursor Protein  

NASA Astrophysics Data System (ADS)

Aggregation of proteins of known sequence is linked to a variety of neurodegenerative disorders. The amyloid ? (A?) protein associated with Alzheimer's Disease (AD) is derived from cleavage of the 99 amino acid C-terminal fragment of Amyloid Precursor Protein (APP-C99) by ?-secretase. Certain familial mutations of APP-C99 have been shown to lead to altered production of A? protein and the early onset of AD. We describe simulation studies exploring the structure of APP-C99 in micelle and membrane environments. Our studies explore how changes in sequence and membrane composition influence (1) the structure of monomeric APP-C99 and (2) APP-C99 homodimer structure and stability. Comparison of simulation results with recent NMR studies of APP-C99 monomers and dimers in micelle and bicelle environments provide insight into how critical aspects of APP-C99 structure and dimerization correlate with secretase processing, an essential component of the A? protein aggregation pathway and AD.

Straub, John

2013-03-01

77

SEQUENCING  

NSDL National Science Digital Library

DESK Standard: Summarize important ideas/events; summarize supporting details in sequence. . DATES: You can begin this activity on January 22. You should complete it by January 26. OBJECTIVE: It is important to remember the events of a story in the order they happen. You wouldn\\'t want to know how a good story ends before reading all of the ...

Mr. Hughes

2006-02-24

78

Telephone wire is backbone of security system  

SciTech Connect

Video provides a variety of low-cost, high-quality solutions in today`s security environment. Cost-conscious managers of power generation stations, casinos, prison facilities, military bases and office buildings are considering using regular telephone wire (unshielded twisted pair-UTP) within their existing systems as the backbone of a video to the PC, personal and video-conferencing and training are other areas where phone wire in a building can save money and provide an alternative to coax or fiber for video. More and more, businesses and government agencies are meeting their needs efficiently by using telephone wires for more than just telephones.

Brede, K.; Rackson, L.T.

1995-09-01

79

A backbone-based theory of protein folding  

PubMed Central

Under physiological conditions, a protein undergoes a spontaneous disorder ? order transition called “folding.” The protein polymer is highly flexible when unfolded but adopts its unique native, three-dimensional structure when folded. Current experimental knowledge comes primarily from thermodynamic measurements in solution or the structures of individual molecules, elucidated by either x-ray crystallography or NMR spectroscopy. From the former, we know the enthalpy, entropy, and free energy differences between the folded and unfolded forms of hundreds of proteins under a variety of solvent/cosolvent conditions. From the latter, we know the structures of ?35,000 proteins, which are built on scaffolds of hydrogen-bonded structural elements, ?-helix and ?-sheet. Anfinsen showed that the amino acid sequence alone is sufficient to determine a protein's structure, but the molecular mechanism responsible for self-assembly remains an open question, probably the most fundamental open question in biochemistry. This perspective is a hybrid: partly review, partly proposal. First, we summarize key ideas regarding protein folding developed over the past half-century and culminating in the current mindset. In this view, the energetics of side-chain interactions dominate the folding process, driving the chain to self-organize under folding conditions. Next, having taken stock, we propose an alternative model that inverts the prevailing side-chain/backbone paradigm. Here, the energetics of backbone hydrogen bonds dominate the folding process, with preorganization in the unfolded state. Then, under folding conditions, the resultant fold is selected from a limited repertoire of structural possibilities, each corresponding to a distinct hydrogen-bonded arrangement of ?-helices and/or strands of ?-sheet. PMID:17075053

Rose, George D.; Fleming, Patrick J.; Banavar, Jayanth R.; Maritan, Amos

2006-01-01

80

Large-scale measurement and modeling of backbone Internet traffic  

Microsoft Academic Search

There is a brewing controversy in the traffic modeling community concerning how to model backbone traffic. The fundamental work on self-similarity in data traffic appears to be contradicted by recent findings that suggest that backbone traffic is smooth. The traffic analysis work to date has focused on high-quality but limited-scope packet trace measurements; this limits its applicability to high-speed backbone

Matthew Roughan; Joel Gottlieb

2002-01-01

81

Side chain chemistry mediates backbone fragmentation in hydrogen deficient peptide radicals.  

PubMed

A crown ether based, photolabile radical precursor which forms noncovalent complexes with peptides has been prepared. The peptide/precursor complexes can be electrosprayed, isolated in an ion trap, and then subjected to laser photolysis and collision induced dissociation to generate hydrogen deficient peptide radicals. It is demonstrated that these peptide radicals behave very differently from the hydrogen rich peptide radicals generated by electron capture methods. In fact, it is shown that side chain chemistry dictates both the occurrence and relative abundance of backbone fragments that are observed. Fragmentation at aromatic residues occurs preferentially over most other amino acids. The origin of this selectivity relates to the mechanism by which backbone dissociation is initiated. The first step is abstraction of a beta-hydrogen from the side chain, followed by beta-elimination to yield primarily a-type fragment ions. Calculations reveal that those side chains which can easily lose a beta-hydrogen correlate well with experimentally favored sites for backbone fragmentation. In addition, radical mediated side chain losses from the parent peptide are frequently observed. Eleven amino acids exhibit unique mass losses from side chains which positively identify that particular amino acid as part of the parent peptide. Therefore, side chain losses allow one to unambiguously narrow the possible sequences for a parent peptide, which when combined with predictable backbone fragmentation should lead to greatly increased confidence in peptide identification. PMID:19113886

Sun, Qingyu; Nelson, Hosea; Ly, Tony; Stoltz, Brian M; Julian, Ryan R

2009-02-01

82

Backbone hydration determines the folding signature of amino Acid residues.  

PubMed

The relation between the sequence of a protein and its three-dimensional structure remains largely unknown. A lasting dream is to elucidate the side-chain-dependent driving forces that govern the folding process. Different structural data suggest that aromatic amino acids play a particular role in the stabilization of protein structures. To better understand the underlying mechanism, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC data for aromatic substitutions provide evidence for a kink in the peptide backbone. Analysis of the MD simulations shows that the formation of internal hydrogen bonds underlying a helical turn is key to reproduce the experimental RDC values. The simulations further reveal that the driving force leading to such helical-turn conformations arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process. PMID:25794270

Bignucolo, Olivier; Leung, Hoi Tik Alvin; Grzesiek, Stephan; Bernèche, Simon

2015-04-01

83

Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages  

PubMed Central

Background It has been hypothesized that rapid divergence in centromere sequences accompanies rapid karyotypic change during speciation. However, the reuse of breakpoints coincident with centromeres in the evolution of divergent karyotypes poses a potential paradox. In distantly related species where the same centromere breakpoints are used in the independent derivation of karyotypes, centromere-specific sequences may undergo convergent evolution rather than rapid sequence divergence. To determine whether centromere sequence composition follows the phylogenetic history of species evolution or patterns of convergent breakpoint reuse through chromosome evolution, we examined the phylogenetic trajectory of centromere sequences within a group of karyotypically diverse mammals, macropodine marsupials (wallabies, wallaroos and kangaroos). Results The evolution of three classes of centromere sequences across nine species within the genus Macropus (including Wallabia) were compared with the phylogenetic history of a mitochondrial gene, Cytochrome b (Cyt b), a nuclear gene, selenocysteine tRNA (TRSP), and the chromosomal histories of the syntenic blocks that define the different karyotype arrangements. Convergent contraction or expansion of predominant satellites is found to accompany specific karyotype rearrangements. The phylogenetic history of these centromere sequences includes the convergence of centromere composition in divergent species through convergent breakpoint reuse between syntenic blocks. Conclusion These data support the 'library hypothesis' of centromere evolution within this genus as each species possesses all three satellites yet each species has experienced differential expansion and contraction of individual classes. Thus, we have identified a correlation between the evolution of centromere satellite sequences, the reuse of syntenic breakpoints, and karyotype convergence in the context of a gene-based phylogeny. PMID:17708770

Bulazel, Kira V; Ferreri, Gianni C; Eldridge, Mark DB; O'Neill, Rachel J

2007-01-01

84

Photopolymerization of aromatic acrylate containing phosphine oxide backbone and its application to holographic recording  

Microsoft Academic Search

Photopolymer compositions for holographic recording were prepared from aromatic diacrylate having phosphine oxide backbone, a hybrid sol–gel, and photoinitiator. The physical and holographic properties of photopolymer were controlled by the ratio of precursor triethoxysilylpropyl polyethyleneglycol carbamate (TSPEG) in a hybrid sol–gel binder and the content of monomer.The photopolymerization rate and conversion of monomer were monitored by photo-differential scanning calorimetry (photo-DSC).

Yu Mi Chang; Sung Cheol Yoon; Mijeong Han

2007-01-01

85

N-terminal amino acid sequences and amino acid compositions of the Spirochaeta aurantia flagellar filament polypeptides.  

PubMed

The amino-terminal sequences and amino acid compositions of the three major and two minor polypeptides constituting the filaments of Spirochaeta aurantia periplasmic flagella were determined. The amino-terminal sequence of the major 37.5-kDa outer layer polypeptide is identical to the sequence downstream of the proposed signal peptide of the protein encoded by the S. aurantia flaA gene. However, the amino acid composition of the 37.5-kDa polypeptide is not in agreement with that inferred from the sequence of flaA. The 34- and 31.5-kDa major filament core polypeptides and the 33- and 32-kDa minor core polypeptides show a striking similarity to each other, and the amino-terminal sequences of these core polypeptides show extensive identity with homologous proteins from members of other genera of spirochetes. An additional 36-kDa minor polypeptide that occurs occasionally in preparations of S. aurantia periplasmic flagella appears to be mixed with the 37.5-kDa outer layer polypeptide or a degradation product of this polypeptide. PMID:1991729

Parales, J; Greenberg, E P

1991-02-01

86

Sofosbuvir as backbone of interferon free treatments.  

PubMed

Sofosbuvir is the first-in-class NS5B nucleotide analogues to be launched for hepatitis C virus (HCV) treatment. Its viral potency, pangenotypic activity and high barrier to resistance make it the ideal candidate to become a backbone for several IFN-free regimens. Recent data demonstrated that sofosbuvir either with ribavirin alone or in combination with other direct-acting antivirals (DAAs) as daclatasvir, ledipasvir or simeprevir are able to cure HCV in at least 90% or over of patients. Treatment experienced genotype 3 population may remain the most difficult to treat population, but ongoing DAA combination studies will help to fill this gap. Safety profile of sofosbuvir or combination with other DAAs is good. Resistance to sofosbuvir did not appear as a significant issue. The rationale for using this class of drug and the available clinical data are reviewed. PMID:25453869

Bourlière, Marc; Oules, Valèrie; Ansaldi, Christelle; Adhoute, Xavier; Castellani, Paul

2014-12-15

87

RosettaDesign-Plastic: designing a moving target using backbone and rotamer ensembles. Christian D. Schenkelberg1, Derek J. Pitman1, Alisa Neeman2, Yao-ming Huang3, Christopher  

E-print Network

RosettaDesign-Plastic: designing a moving target using backbone and rotamer ensembles. Christian D computational design, we have implemented a design scheme termed "plastic" design which incorporates elements of these existing backbone flexibility models. Plastic design involves designing a protein primary sequence

Bystroff, Chris

88

-Backbone Colorings Along Pairwise Disjoint Stars and Matchings  

E-print Network

number, star, matching. 2000 Mathematics Subject Classification: 05C15, 05C85, 05C17 Preprint submitted-Backbone Colorings Along Pairwise Disjoint Stars and Matchings H.J. Broersma a J. Fujisawa b L where the backbone is either a collection of pairwise disjoint stars or a matching. We show

Paulusma, Daniel

89

Polyarylether composition and membrane  

DOEpatents

A composition including a polyarylether copolymer is provided. The copolymer includes a polyarylether backbone; and a sulfonated oligomeric group bonded to the polyarylether suitable for use as a cation conducting membrane. Method of bonding a sulfonated oligomeric group to the polyarylether backbone to form a polyarylether copolymer. The membrane may be formed from the polyarylether copolymer composition. The chain length of the sulfonated oligomeric group may be controlled to affect or control the ion conductivity of the membrane.

Hung, Joyce (Auburn, AL); Brunelle, Daniel Joseph (Burnt Hills, NY); Harmon, Marianne Elisabeth (Redondo Beach, CA); Moore, David Roger (Albany, NY); Stone, Joshua James (Worcester, NY); Zhou, Hongyi (Niskayuna, NY); Suriano, Joseph Anthony (Clifton Park, NY)

2010-11-09

90

A mapping of an ensemble of mitochondrial sequences for various organisms into 3D space based on the word composition.  

PubMed

To visualize a bird's-eye view of an ensemble of mitochondrial genome sequences for various species, we recently developed a novel method of mapping a biological sequence ensemble into Three-Dimensional (3D) vector space. First, we represented a biological sequence of a species s by a word-composition vector x(s), where its length [absolute value]x(s)[absolute value] represents the sequence length, and its unit vector x(s)/[absolute value]x(s)[absolute value] represents the relative composition of the K-tuple words through the sequence and the size of the dimension, N=4(K), is the number of all possible words with the length of K. Second, we mapped the vector x(s) to the 3D position vector y(s), based on the two following simple principles: (1) [absolute value]y(s)[absolute value]=[absolute value]x(s)[absolute value] and (2) the angle between y(s) and y(t) maximally correlates with the angle between x(s) and x(t). The mitochondrial genome sequences for 311 species, including 177 Animalia, 85 Fungi and 49 Green plants, were mapped into 3D space by using K=7. The mapping was successful because the angles between vectors before and after the mapping highly correlated with each other (correlation coefficients were 0.92-0.97). Interestingly, the Animalia kingdom is distributed along a single arc belt (just like the Milky Way on a Celestial Globe), and the Fungi and Green plant kingdoms are distributed in a similar arc belt. These two arc belts intersect at their respective middle regions and form a cross structure just like a jet aircraft fuselage and its wings. This new mapping method will allow researchers to intuitively interpret the visual information presented in the maps in a highly effective manner. PMID:22776549

Aita, Takuyo; Nishigaki, Koichi

2012-11-01

91

Site-specific oligodeoxynucleotide backbone modification for the covalent incorporation of reporter groups  

SciTech Connect

A protocol has been developed to enable the site-specific incorporation of reporter groups to the oligodeoxynucleotide backbone. The introduction of a reactive center within the oligonucleotide sequence was accomplished using relatively standard procedures and was compatible with automated DNA synthesis techniques. The site-specific introduction of a phosphorothioate diester was achieved by substitution of a nonbridging oxygen in an internucleotidic phosphodiester by sulfur. Phosphorothioate diester-containing oligodeoxynucleotides were amenable to alkylation with reporter groups containing haloacetamides, aziridine sulfonamides, or [gamma]-bromo-[alpha], [beta]-unsaturated carbonyls. Labeling reactions proceeded most efficiently after incubation for 24 h at 50[degrees]C in the pH range of 5-8. A thiol tether has been incorporated into the oligodeoxynucleotide backbone by oxidizing a specifically placed internucleotidic hydrogen-phosphonate in the presence of cystamine. The thiol is deprotected by treatment with dithiothreitol. The tethered sulfhydryl reacts with a large variety of functional groups, and may be used to extend reporter groups at a distance from the backbone. The phosphoramidate linkage is stable over a very large range of pH. The alkylation of oligodeoxynucleotides occurred solely at the phosphorothioate diester or at the tethered sulfhydryl. Duplex structures containing either a labeled phosphorothioate or thiol tether had thermal stabilities generally similar to those of the unlabeled sequence. Labeling of an internucleotidic phosphorothioate diester or a tethered thiol provides a rapid and simple method for the site-specific covalent attachment of fluorophores, spin labels, drug derivatives or prosthetic groups to the oligonucleotide backbone. The introduction of more than one reactive center may be accomplished without necessarily increasing the complexity of the overall procedure.

Fidanza, J.A.

1992-01-01

92

Ancestral Sequence Reconstruction in Primate Mitochondrial DNA: Compositional Bias and Effect on Functional Inference  

Microsoft Academic Search

Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood (ML) is generally thought to provide relatively accurate reconstructed sequences compared to parsimony, but both methods

Neeraja M. Krishnan; Caro-Beth Stewart; A. P. Jason de Koning; David D. Pollock

2004-01-01

93

Radiation Safety System (RSS) backbones: Design, engineering, fabrication, and installation  

SciTech Connect

The Radiation Safety System (RSS) backbones are part of an electrical/electronic/mechanical system ensuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS backbones control the safety-fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low-energy beam transport. The backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two linac backbone segments and the experimental area segments form a continuous cable plant over 3500 feet from the beam plugs to the tip on the longest tail. The backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely. {copyright} {ital 1998 American Institute of Physics.}

Wilmarth, J.E.; Sturrock, J.C.; Gallegos, F.R. [Los Alamos Neutron Scattering Center, LANSCE Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

1998-12-01

94

Radiation Safety System (RSS) backbones: Design, engineering, fabrication, and installation  

SciTech Connect

The Radiation Safety System (RSS) backbones are part of an electrical/electronic/mechanical system ensuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS backbones control the safety-fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low-energy beam transport. The backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two linac backbone segments and the experimental area segments form a continuous cable plant over 3500 feet from the beam plugs to the tip on the longest tail. The backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

Wilmarth, J. E.; Sturrock, J. C.; Gallegos, F. R. [Los Alamos Neutron Scattering Center, LANSCE Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

1998-12-10

95

Radiation safety system (RSS) backbones: Design, engineering, fabrication and installation  

SciTech Connect

The Radiation Safety System (RSS) Backbones are part of an electrical/electronic/mechanical system insuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS Backbones control the safety fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low energy beam transport. The Backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the Backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two Linac Backbone segments and experimental area segments form a continuous cable plant over 3,500 feet from beam plugs to the tip on the longest tail. The Backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

Wilmarth, J.E.; Sturrock, J.C.; Gallegos, F.R.

1998-12-01

96

Radiation Safety System (RSS) backbones: Design, engineering, fabrication, and installation  

NASA Astrophysics Data System (ADS)

The Radiation Safety System (RSS) backbones are part of an electrical/electronic/mechanical system ensuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS backbones control the safety-fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low-energy beam transport. The backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two linac backbone segments and the experimental area segments form a continuous cable plant over 3500 feet from the beam plugs to the tip on the longest tail. The backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

Wilmarth, J. E.; Sturrock, J. C.; Gallegos, F. R.

1998-12-01

97

Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location  

PubMed Central

Background The observation that specific members of the microbial intestinal community can be shared among vertebrate hosts has promoted the concept of a core microbiota whose composition is determined by host-specific selection. Most studies investigating this concept in individual hosts have focused on mammals, yet the diversity of fish lineages provides unique comparative opportunities from an evolutionary, immunological and environmental perspective. Here we describe microbial intestinal communities of eleven individual Atlantic cod (Gadus morhua) caught at a single location based on an extensively 454 sequenced 16S rRNA library of the V3 region. Results We obtained a total of 280447 sequences and identify 573 Operational Taxonomic Units (OTUs) at 97% sequence similarity level, ranging from 40 to 228 OTUs per individual. We find that ten OTUs are shared, though the number of reads of these OTUs is highly variable. This variation is further illustrated by community diversity estimates that fluctuate several orders of magnitude among specimens. The shared OTUs belong to the orders of Vibrionales, which quantitatively dominate the Atlantic cod intestinal microbiota, followed by variable numbers of Bacteroidales, Erysipelotrichales, Clostridiales, Alteromonadales and Deferribacterales. Conclusions The microbial intestinal community composition varies significantly in individual Atlantic cod specimens caught at a single location. This high variation among specimens suggests that a complex combination of factors influence the species distribution of these intestinal communities. PMID:24206635

2013-01-01

98

Essential oil composition and internal transcribed spacer (ITS) sequence variability of four South-Croatian Satureja species (Lamiaceae).  

PubMed

The purpose of this study was to compare the essential oil profiles of four South-Croatian Satureja species, as determined by GC/FID and GC/MS, with their DNA sequences for an internal transcribed spacer (ITS1-5.8S-ITS2) of the nuclear ribosomal DNA. A phylogenetic analysis showed that S. montana and S. cuneifolia, characterized by a similar essential oil composition, rich in the monoterpene hydrocarbon carvacrol, clustered together with high and moderate bootstrap support. On the contrary, S. subspicata and S. visianii, characterized by quite unique essential oil compositions, clustered together with the moderate bootstrap support. All four Croatian Satureja species clustered in one clade, separately from Macaronesian S. hortensis,although it had essential oil composition similar to that of S. montana and S. cuneifolia. This is the first report on the comparison between the phytochemical and DNA sequence data in Satureja species and useful contribution to the better understanding of interspecies relationships in this genus. PMID:19255551

Bezi?, Nada; Samani?, Ivica; Dunki?, Valerija; Besendorfer, Visnja; Puizina, Jasna

2009-01-01

99

The venom composition of the parasitic wasp Chelonus inanitus resolved by combined expressed sequence tags analysis and proteomic approach  

PubMed Central

Background Parasitic wasps constitute one of the largest group of venomous animals. Although some physiological effects of their venoms are well documented, relatively little is known at the molecular level on the protein composition of these secretions. To identify the majority of the venom proteins of the endoparasitoid wasp Chelonus inanitus (Hymenoptera: Braconidae), we have randomly sequenced 2111 expressed sequence tags (ESTs) from a cDNA library of venom gland. In parallel, proteins from pure venom were separated by gel electrophoresis and individually submitted to a nano-LC-MS/MS analysis allowing comparison of peptides and ESTs sequences. Results About 60% of sequenced ESTs encoded proteins whose presence in venom was attested by mass spectrometry. Most of the remaining ESTs corresponded to gene products likely involved in the transcriptional and translational machinery of venom gland cells. In addition, a small number of transcripts were found to encode proteins that share sequence similarity with well-known venom constituents of social hymenopteran species, such as hyaluronidase-like proteins and an Allergen-5 protein. An overall number of 29 venom proteins could be identified through the combination of ESTs sequencing and proteomic analyses. The most highly redundant set of ESTs encoded a protein that shared sequence similarity with a venom protein of unknown function potentially specific of the Chelonus lineage. Venom components specific to C. inanitus included a C-type lectin domain containing protein, a chemosensory protein-like protein, a protein related to yellow-e3 and ten new proteins which shared no significant sequence similarity with known sequences. In addition, several venom proteins potentially able to interact with chitin were also identified including a chitinase, an imaginal disc growth factor-like protein and two putative mucin-like peritrophins. Conclusions The use of the combined approaches has allowed to discriminate between cellular and truly venom proteins. The venom of C. inanitus appears as a mixture of conserved venom components and of potentially lineage-specific proteins. These new molecular data enrich our knowledge on parasitoid venoms and more generally, might contribute to a better understanding of the evolution and functional diversity of venom proteins within Hymenoptera. PMID:21138570

2010-01-01

100

Palynological composition of a Lower Cretaceous South American tropical sequence: Climatic implications and diversity comparisons with other latitudes.  

USGS Publications Warehouse

Premise of the study: Reconstruction of floristic patterns during the early diversification of angiosperms is impeded by the scarce fossil record, especially in tropical latitudes. Here we collected quantitative palynological data from a stratigraphic sequence in tropical South America to provide floristic and climatic insights into such tropical environments during the Early Cretaceous. Methods: We reconstructed the floristic composition of an Aptian-Albian tropical sequence from central Colombia using quantitative palynology (rarefied species richness and abundance) and used it to infer its predominant climatic conditions. Additionally, we compared our results with available quantitative data from three other sequences encompassing 70 floristic assemblages to determine latitudinal diversity patterns. Key results: Abundance of humidity indicators was higher than that of aridity indicators (61% vs. 10%). Additionally, we found an angiosperm latitudinal diversity gradient (LDG) for the Aptian, but not for the Albian, and an inverted LDG of the overall diversity for the Albian. Angiosperm species turnover during the Albian, however, was higher in humid tropics. Conclusions: There were humid climates in northwestern South America during the Aptian-Albian interval contrary to the widespread aridity expected for the tropical belt. The Albian inverted overall LDG is produced by a faster increase in per-sample angiosperm and pteridophyte diversity in temperate latitudes. However, humid tropical sequences had higher rates of floristic turnover suggesting a higher degree of morphological variation than in temperate regions.

Mejia-Velasquez, Paula J.; Dilcher, David L.; Jaramillo, Carlos A.; Fortini, Lucas B.; Manchester, Steven R.

2012-01-01

101

A backbone lever-arm effect enhances polymer mechanochemistry  

NASA Astrophysics Data System (ADS)

Mechanical forces along a polymer backbone can be used to bring about remarkable reactivity in embedded mechanically active functional groups, but little attention has been paid to how a given polymer backbone delivers that force to the reactant. Here, single-molecule force spectroscopy was used to directly quantify and compare the forces associated with the ring opening of gem-dibromo and gem-dichlorocyclopropanes affixed along the backbone of cis-polynorbornene and cis-polybutadiene. The critical force for isomerization drops by about one-third in the polynorbornene scaffold relative to polybutadiene. The root of the effect lies in more efficient chemomechanical coupling through the polynorbornene backbone, which acts as a phenomenological lever with greater mechanical advantage than polybutadiene. The experimental results are supported computationally and provide the foundation for a new strategy by which to engineer mechanochemical reactivity.

Klukovich, Hope M.; Kouznetsova, Tatiana B.; Kean, Zachary S.; Lenhardt, Jeremy M.; Craig, Stephen L.

2013-02-01

102

Apollo 17 petrology and experimental determination of differentiation sequences in model moon compositions  

NASA Technical Reports Server (NTRS)

Experimental studies of model moon compositions are discussed, taking into account questions related to the differentiation of the outer layer of the moon. Phase relations for a series of proposed lunar compositions have been determined and a petrographic and electron microprobe study was conducted on four Apollo 17 samples. Two of the samples consist of high-titanium mare basalts, one includes crushed anorthosite and gabbro, and another contains blue-gray breccia.

Hodges, F. N.; Kushiro, I.

1974-01-01

103

Estimating the composition of species in metagenomes by clustering of next-generation read sequences.  

PubMed

Faster and cheaper sequencing technologies together with the ability to sequence uncultured microbes collected from any environment present us an opportunity to distill meaningful information from the millions of new genomic sequences from environmental samples, called metagenome. Contrary to conventional cultured microbes, however, the metagenomic data is extremely heterogeneous and noisy. Therefore the separation of the sets of sequenced genomic fragments that belong to different microbes is essential for successful assembly of microbial genomes. In this paper, we present a novel clustering method for a given metagenomic dataset. The metagenomic dataset has some distinguished features because (i) it is possible that similar sequence patterns may exist in different species and (ii) each species has different number of individuals in the given metagenomic dataset. Our method overcomes these obstacles by using the Gaussian mixture model and analysis of mixture profiles, and taking advantage of genomic signatures extracted from the metagenomic dataset. Unlike conventional clustering methods where clusters are discovered through global similarities of data instances, our method builds clusters by combining the data instances sharing local similarities captured by mixture analysis. By considering shared mixture components, our method is able to create clusters of genomic sequences although they are globally distinct each other. We applied our method to an artificial metagenomic dataset comprised of simulated 47 million reads from 25 real microbial genomes, and analyzed the resulting clusters in terms of the number of clusters, the number of participating species and dominant species in each cluster. Even though our approach cannot address all challenges in the field of metagenome sequence clustering, we believe that out method can contribute to take a step forward to achieve the goals. PMID:25072168

Seok, Ho-Sik; Hong, Woonyoung; Kim, Jaebum

2014-10-01

104

Three-Dimensional Solutions for Contact Area in Laminated Composite Pinned Joints with Symmetric and Non-Symmetric Stacking Sequences  

NASA Astrophysics Data System (ADS)

The aim of this study is computing and evaluating the behavior of the laminated composite plate at the contact area in single lap, mechanically fastened joints. The analyses involve three dimensional finite element models performed by ABAQUS 6.4-PR11 code to evaluate the stress distribution in contact surface, separation angle, the magnitude and location of maximum radial stress. Results are determined for composite laminates with different layer configurations and attempts are made to validate the models with previous works. For cross ply and angle ply configurations only symmetric stacking sequences are used while for quasi-isotropic laminate both symmetric and non-symmetric models are generated. In cross-ply laminate symmetric separation about bearing plane could be found while in quasi-isotropic and angle-ply laminates non-symmetric separation occurs. Also, the separation angle is less than 90° in symmetric laminates and greater than 90° in some plies of non-symmetric laminates.

Javadi, H.; Rajabi, I.; Yavari, V.; Kadivar, M. H.

105

Large-scale measurement and modeling of backbone Internet traffic  

NASA Astrophysics Data System (ADS)

There is a brewing controversy in the traffic modeling community concerning how to model backbone traffic. The fundamental work on self-similarity in data traffic appears to be contradicted by recent findings that suggest that backbone traffic is smooth. The traffic analysis work to date has focused on high-quality but limited-scope packet trace measurements; this limits its applicability to high-speed backbone traffic. This paper uses more than one year's worth of SNMP traffic data covering an entire Tier 1 ISP backbone to address the question of how backbone network traffic should be modeled. Although the limitations of SNMP measurements do not permit us to comment on the fine timescale behavior of the traffic, careful analysis of the data suggests that irrespective of the variation at fine timescales, we can construct a simple traffic model that captures key features of the observed traffic. Furthermore, the model's parameters are measurable using existing network infrastructure, making this model practical in a present-day operational network. In addition to its practicality, the model verifies basic statistical multiplexing results, and thus sheds deep insight into how smooth backbone traffic really is.

Roughan, Matthew; Gottlieb, Joel

2002-07-01

106

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.  

PubMed

It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. This study developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for classifying incomplete transcripts and sense-antisense pairs. The implementation of CNCI offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolutionary divergence between vertebrates, and invertebrates, or between plants, and provided a long non-coding RNA catalog of orangutan. CNCI software is available at http://www.bioinfo.org/software/cnci. PMID:23892401

Sun, Liang; Luo, Haitao; Bu, Dechao; Zhao, Guoguang; Yu, Kuntao; Zhang, Changhai; Liu, Yuanning; Chen, Runsheng; Zhao, Yi

2013-09-01

107

The effect of load sequence on the statistical fatigue of composites  

NASA Technical Reports Server (NTRS)

A theoretical model to predict the effect of loading sequence on the statistical distributions of the fatigue life and the residual strength under n-stress levels of cyclic loading is derived on the basis of a three-parameter model. In particular, the dual stress fatigue cumulative damage is studied, showing that the Miner's sum (the cumulative damage sum at fatigue failure) is a statistical variable. It is proved theoretically that the Miner's sum is always greater than or equal to unity for the high-low load sequence, while it is always smaller than or equal to unity for the low-high load sequence, with the deviation from unity increasing as the difference between the high and the low stress levels increases. An experimental test program using graphite/epoxy angle-ply laminates, carried out to generate statistically meaningful data for verifying the proposed model, is discussed.

Yang, J. N.; Jones, D. L.

1979-01-01

108

CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition  

PubMed Central

The analysis of DNA composition and codon usage reveals many factors that influence the evolution of genes and genomes. In this chapter, we show how to use CodonExplorer, a web tool and interactive database that contains millions of genes, to better understand the principles governing evolution at the single gene and whole-genome level. We present principles and practical procedures for using analyses of GC content and codon usage frequency to identify highly expressed or horizontally transferred genes and to study the relative contribution of different types of mutation to gene and genome composition. CodonExplorer’s combination of a user-friendly web interface and a comprehensive genomic database makes these diverse analyses fast and straightforward to perform. CodonExplorer is thus a powerful tool that facilitates and automates a wide range of compositional analyses. PMID:19378146

Zaneveld, Jesse; Hamady, Micah; Sueoka, Noboru; Knight, Rob

2010-01-01

109

Radical-driven peptide backbone dissociation tandem mass spectrometry.  

PubMed

In recent years, a number of novel tandem mass spectrometry approaches utilizing radical-driven peptide gas-phase fragmentation chemistry have been developed. These approaches show a peptide fragmentation pattern quite different from that of collision-induced dissociation (CID). The peptide fragmentation features of these approaches share some in common with electron capture dissociation (ECD) or electron transfer dissociation (ETD) without the use of sophisticated equipment such as a Fourier-transform mass spectrometer. For example, Siu and coworkers showed that CID of transition metal (ligand)-peptide ternary complexes led to the formation of peptide radical ions through dissociative electron transfer (Chu et al., 2000. J Phys Chem B 104:3393-3397). The subsequent collisional activation of the generated radical ions resulted in a number of characteristic product ions, including a, c, x, z-type fragments and notable side-chain losses. Another example is the free radical initiated peptide sequencing (FRIPS) approach, in which Porter et al. and Beauchamp et al. independently introduced a free radical initiator to the primary amine group of the lysine side chain or N-terminus of peptides (Masterson et al., 2004. J Am Chem Soc 126:720-721; Hodyss et al., 2005 J Am Chem Soc 127: 12436-12437). Photodetachment of gaseous multiply charged peptide anions (Joly et al., 2008. J Am Chem Soc 130:13832-13833) and UV photodissociation of photolabile radical precursors including a C-I bond (Ly & Julian, 2008. J Am Chem Soc 130:351-358; Ly & Julian, 2009. J Am Soc Mass Spectrom 20:1148-1158) also provide another route to generate radical ions. In this review, we provide a brief summary of recent results obtained through the radical-driven peptide backbone dissociation tandem mass spectrometry approach. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 34: 116-132, 2015. PMID:24863492

Oh, Han Bin; Moon, Bongjin

2015-04-01

110

Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol.  

PubMed

The precise appraisal of the composition of the human gut microbiota still represents a challenging task. The advent of next generation sequencing approaches has opened new ways to dissect the microbial biodiversity of this ecosystem through the use of 16S rRNA gene-based microbiota analysis approaches. However, the detailed representation of specific groups or members of the human gut microbiota, for example Bifidobacteria, may be skewed by the PCR primers employed in the amplification step of the 16S rRNA gene-based microbial profiling pipeline and by the limited resolution of the 16S rRNA gene variable regions. Here, we define the internal transcribed spacer (ITS) sequences of all currently known Bifidobacterium taxa, providing a Bifidobacterium-specific primer pair that targets a hypervariable region within the ITS suitable for precise taxonomic identification of all 48 so far recognized members of the Bifidobacterium genus. In addition, we present an optimized protocol for ITS-based profiling utilizing qiime software, allowing accurate and subspecies-specific compositional reconstruction of the bifidobacterial community in the human gut. PMID:25117972

Milani, Christian; Lugli, Gabriele A; Turroni, Francesca; Mancabelli, Leonardo; Duranti, Sabrina; Viappiani, Alice; Mangifesta, Marta; Segata, Nicola; van Sinderen, Douwe; Ventura, Marco

2014-11-01

111

MIT/LIDS Technical Report #2676, Oct. 2005 Construction and Maintenance of a Mobile Backbone  

E-print Network

-to-end communication can take place. A novel hierarchical approach for a Mobile Backbone Network operating (RN) can directly communicate with at least one Mobile Backbone Node (MBN). All communication a backbone for reliable communication. A Mobile Backbone Network is composed of two types of nodes. The first

Zussman, Gil

112

Fragmentation Characteristics of Deprotonated N-linked Glycopeptides: Influences of Amino Acid Composition and Sequence  

NASA Astrophysics Data System (ADS)

Glycopeptide structural analysis using tandem mass spectrometry is becoming a common approach for elucidating site-specific N-glycosylation. The analysis is generally performed in positive-ion mode. Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. The fragment ion species were found to be significantly variable depending on their amino acid sequence and could be classified into three types: (i) glycan fragment ions, (ii) glycan-lost fragment ions and their secondary cleavage products, and (iii) fragment ions with intact glycan moiety. The CID spectra of glycopeptides having a short peptide sequence were dominated by type (i) glycan fragments (e.g., 2,4AR, 2,4AR-1, D, and E ions). These fragments define detailed structural features of the glycan moiety such as branching. For glycopeptides with medium or long peptide sequences, the major fragments were type (ii) ions (e.g., [peptide + 0,2X0-H]- and [peptide-NH3-H]-). The appearance of type (iii) ions strongly depended on the peptide sequence, and especially on the presence of Asp, Asn, and Glu. When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36]-, was abundantly formed. Observed fragments are reasonably explained by a combination of existing fragmentation rules suggested for N-glycans and peptides.

Nishikaze, Takashi; Kawabata, Shin-ichirou; Tanaka, Koichi

2014-06-01

113

The correlation of protein hydropathy with the base composition of coding sequences  

Microsoft Academic Search

The “universal correlation” (D'Onofrio, G., Bernardi, G., 1992. A universal compositionalcorrelation amomg codon positions. Gene 110, 81–88.) that holds between ?GC3? and ?GC1? or ?GC2? (?GC? values are the average values of the coding sequences of each genome analyzed) at both the inter- and intra-genomic level, was re-analyzed on a vastly larger dataset. The results showed a slight, but significant,

Giuseppe D'Onofrio; Kamel Jabbari; Hector Musto; Giorgio Bernardi

1999-01-01

114

PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors.  

PubMed

Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, which can be applied to whole-genome sequencing data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations. We introduce a principled phylogenic correction for VAFs in loci affected by copy number alterations and we show that this correction greatly improves subclonal reconstruction compared to existing methods. PhyloWGS is free, open-source software, available at https://github.com/morrislab/phylowgs. PMID:25786235

Deshwar, Amit G; Vembu, Shankar; Yung, Christina K; Jang, Gun Ho; Stein, Lincoln; Morris, Quaid

2015-01-01

115

Sequence-based analysis of the microbial composition of water kefir from multiple sources.  

PubMed

Water kefir is a water-sucrose-based beverage, fermented by a symbiosis of bacteria and yeast to produce a final product that is lightly carbonated, acidic and that has a low alcohol percentage. The microorganisms present in water kefir are introduced via water kefir grains, which consist of a polysaccharide matrix in which the microorganisms are embedded. We aimed to provide a comprehensive sequencing-based analysis of the bacterial population of water kefir beverages and grains, while providing an initial insight into the corresponding fungal population. To facilitate this objective, four water kefirs were sourced from the UK, Canada and the United States. Culture-independent, high-throughput, sequencing-based analyses revealed that the bacterial fraction of each water kefir and grain was dominated by Zymomonas, an ethanol-producing bacterium, which has not previously been detected at such a scale. The other genera detected were representatives of the lactic acid bacteria and acetic acid bacteria. Our analysis of the fungal component established that it was comprised of the genera Dekkera, Hanseniaspora, Saccharomyces, Zygosaccharomyces, Torulaspora and Lachancea. This information will assist in the ultimate identification of the microorganisms responsible for the potentially health-promoting attributes of these beverages. PMID:24004255

Marsh, Alan J; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D

2013-11-01

116

Composites  

NSDL National Science Digital Library

In this activity, learners explore how composites work by creating and testing their own composite for an imaginary company. This activity shows learners that composites are simply materials that are made up of two or more visibly distinct substances. Use this activity to talk about how composites are everywhere in our lives.

Cornell Center for Materials Research

2003-01-01

117

First Survey of the Wheat Chromosome 5A Composition through a Next Generation Sequencing Approach  

PubMed Central

Wheat is one of the world's most important crops and is characterized by a large polyploid genome. One way to reduce genome complexity is to isolate single chromosomes using flow cytometry. Low coverage DNA sequencing can provide a snapshot of individual chromosomes, allowing a fast characterization of their main features and comparison with other genomes. We used massively parallel 454 pyrosequencing to obtain a 2x coverage of wheat chromosome 5A. The resulting sequence assembly was used to identify TEs, genes and miRNAs, as well as to infer a virtual gene order based on the synteny with other grass genomes. Repetitive elements account for more than 75% of the genome. Gene content was estimated considering non-redundant reads showing at least one match to ESTs or proteins. The results indicate that the coding fraction represents 1.08% and 1.3% of the short and long arm respectively, projecting the number of genes of the whole chromosome to approximately 5,000. 195 candidate miRNA precursors belonging to 16 miRNA families were identified. The 5A genes were used to search for syntenic relationships between grass genomes. The short arm is closely related to Brachypodium chromosome 4, sorghum chromosome 8 and rice chromosome 12; the long arm to regions of Brachypodium chromosomes 4 and 1, sorghum chromosomes 1 and 2 and rice chromosomes 9 and 3. From these similarities it was possible to infer the virtual gene order of 392 (5AS) and 1,480 (5AL) genes of chromosome 5A, which was compared to, and found to be largely congruent with the available physical map of this chromosome. PMID:22028874

Vitulo, Nicola; Albiero, Alessandro; Forcato, Claudio; Campagna, Davide; Dal Pero, Francesca; Bagnaresi, Paolo; Colaiacovo, Moreno; Faccioli, Primetta; Lamontanara, Antonella; Šimková, Hana; Kubaláková, Marie; Perrotta, Gaetano; Facella, Paolo; Lopez, Loredana; Pietrella, Marco; Gianese, Giulio; Doležel, Jaroslav; Giuliano, Giovanni; Cattivelli, Luigi; Valle, Giorgio; Stanca, A. Michele

2011-01-01

118

Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing.  

PubMed

In this study, Illumina high-throughput sequencing was used to reveal the community structures of nine coking wastewater treatment plants (CWWTPs) in China for the first time. The sludge systems exhibited a similar community composition at each taxonomic level. Compared to previous studies, some of the core genera in municipal wastewater treatment plants such as Zoogloea, Prosthecobacter and Gp6 were detected as minor species. Thiobacillus (20.83%), Comamonas (6.58%), Thauera (4.02%), Azoarcus (7.78%) and Rhodoplanes (1.42%) were the dominant genera shared by at least six CWWTPs. The percentages of autotrophic ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were unexpectedly low, which were verified by both real-time PCR and fluorescence in situ hybridization analyses. Hierarchical clustering and canonical correspondence analysis indicated that operation mode, flow rate and temperature might be the key factors in community formation. This study provides new insights into our understanding of microbial community compositions and structures of CWWTPs. PMID:25569032

Ma, Qiao; Qu, Yuanyuan; Shen, Wenli; Zhang, Zhaojing; Wang, Jingwei; Liu, Ziyan; Li, Duanxing; Li, Huijie; Zhou, Jiti

2015-03-01

119

Triazole linkages and backbone branches in nucleic acids for biological and extra-biological applications  

NASA Astrophysics Data System (ADS)

The recently increasing evidence of nucleic acids' alternative roles in biology and potential as useful nanomaterials and therapeutic agents has enabled the development of useful probes, elaborate nanostructures and therapeutic effectors based on nucleic acids. The study of alternative nucleic acid structure and function, particularly RNA, hinges on the ability to introduce site-specific modifications that either provide clues to the nucleic acid structure function relationship or alter the nucleic acid's function. Although the available chemistries allow for the conjugation of useful labels and molecules, their limitations lie in their tedious conjugation conditions or the lability of the installed probes. The development and optimization of click chemistry with RNA now provides the access to a robust and orthogonal conjugation methodology while providing stable conjugates. Our ability to introduce click reactive groups enzymatically, rather than only in the solid-phase, allows for the modification of larger, more cell relevant RNAs. Additionally, ligation of modified RNAs with larger RNA constructs through click chemistry represents an improvement over traditional ligation techniques. We determined that the triazole linkage generated through click chemistry is compatible in diverse nucleic acid based biological systems. Click chemistry has also been developed for extra-biological applications, particularly with DNA. We have expanded its use to generate useful polymer-DNA conjugates which can form controllable soft nanoparticles which take advantage of DNA's properties, i.e. DNA hybridization and computing. Additionally, we have generated protein-DNA conjugates and assembled protein-polymer hybrids mediated by DNA hybridization. The use of click chemistry in these reactions allows for the facile synthesis of these unnatural conjugates. We have also developed backbone branched DNA through click chemistry and showed that these branched DNAs are useful in generating well-defined architectures based solely on DNA. While backbone branched DNAs are useful for nanotechnological applications, backbone branches in RNA occur in nature and are involved in the distinct but related processes of splicing, debranching and RNAi. Therefore we have developed protocols for the synthesis of backbone branched nucleic acids in the solid-phase using photoprotecting groups. Using the synthesized backbone branched RNAs we have uncovered a specific substrate requirement of debranching enzyme which distinguishes it from other homologous proteins with alternative functions. Finally, through the marriage of click chemistry and backbone branches, we have produced useful progeny in the synthesis of lariat RNAs. We investigated the potential of these lariats as therapeutic agents by synthesizing siRNA sequences as lariats. We showed that these lariats are efficiently debranched by debranching enzyme and are able to induce an RNAi response in vivo. Altogether, the development of click chemistry and backbone branched nucleic acids represents a significant advantage in the ability to modify nucleic acid structure and affect its function. I envision that these methods can become generally useful to probe nucleic acid systems, useful nanomaterials and functional effectors in nucleic acid based therapies.

Paredes, Eduardo

120

LARC-IA: A flexible backbone polyimide  

NASA Technical Reports Server (NTRS)

A new linear, aromatic, thermoplastic polyimide, prepared from oxydiphthalic anhydride (ODPA) and 3,4'-oxydianiline (ODA) in diglyme and identified as LARC-IA, was synthesized and evaluated. The monomers are relatively inexpensive and physiologically safe. Molecular weight was controlled by use of a monofunctional anhydride, phthalic anhydride (PA), in order to promote controlled flow and wetting properties. The polymer is considered a safe alternative to commercially available LARC-TPI which is prepared with an expensive diamine of uncertain carcinogenicity. The evaluation was based primarily on the polymer's adhesive properties as determined by thermal and water boil exposure of lap shear specimens. Strengths were determined at room temperature, 177, 204 and 232 C before and after exposure to determine the adhesive system's durability to adverse environments over a period of time. Other properties (FWT, G(1c), film and composite properties) were examined which were determined to be typical of a high temperature polyimide. Results of the study show a favorable comparison to LARC-TPI, a commercially available polyimide.

Progar, Donald J.; Stclair, Terry L.

1990-01-01

121

Sequences of Mixed Ions in Polypeptoid Surfaces  

NASA Astrophysics Data System (ADS)

Polypeptoids, a unique, sequence specific class of polymers, are used to investigate the influence of charge spacing, grouping, and chemistry on the surface properties of polymer coatings. Short peptoid oligomers composed of cationic and anionic groups, and superhydrophobic (fluorinated) functionalities were attached to a synthetic backbone to form comb-shaped molecules. These molecules display different surface chemistry as a function of side chain composition, as indicated by near edge X-ray absorption fine structure spectroscopy (NEXAFS). A 50:50 ratio of peptoid:fluorinated functionality resulted in optimal surface segregation of the comb block while preventing surface reconstruction upon immersing the polymer films in water. Antifouling experiments with the green algae Ulva showed that polymers with non-ionic peptoid functional groups resulted in superior antifouling coatings compared to polymers with charged peptoids. The effects of decreasing the peptoid charge spacing even further (zwitterionic side chains) and exploring stronger ionic moieties, such as phosphate groups, will also be discussed.

Buss, Hilda; van Zoelen, Wendy; Ellebracht, Nathan; Zuckermann, Ronald; Segalman, Rachel

2013-03-01

122

Automated assignment of backbone NMR peaks using constrained bipartite matching  

Microsoft Academic Search

Peak assignment is a key step in solving protein structures using nuclear magnetic resonance. The authors present a new computational framework for automating this process, particularly for backbone resonance peak assignment, as a constrained weighted bipartite matching problem. Although it's NP-hard, they have developed a rigorous algorithm to solve the problem

Ying Xu; Dong Xu; Dongsup Kai; VICTOR OLMAN; JANE RAZUMOVSKAYA; Tao Jiang

2002-01-01

123

Provisioning IP Backbone Networks to Support Latency Sensitive Traffic  

Microsoft Academic Search

To support latency sensitive traffic such as voice, network providers can either use service differentiation to prioritize such traffic or provision their network with enough bandwidth so that all traffic meets the most stringent delay requirements. In the context of wide- area Internet backbones, two factors make overprovisioning an attractive approach. First, the high link speeds and large volumes of

Chuck Fraleigh; Fouad A. Tobagi; Christophe Diot

2003-01-01

124

Monitoring the backbone conformation of valinomycin by Raman optical activity.  

PubMed

Raman optical activity (ROA) spectroscopy is used to investigate the backbone conformation of valinomycin in methanol and dioxane solution. Experimental Raman and ROA spectral differences are interpreted by using density functional calculations, molecular dynamics, and Cartesian tensor transfer. Of the several conformers with different numbers of intramolecular hydrogen bonds which were preselected by calculations of relative energies, the dominant ones are identified on the basis of ROA. To separate the backbone signal from that of the side chains, conformational search for the isopropyl residues is performed for each backbone conformer. In dioxane, the most populated conformer does not exhibit C(3) symmetry, but adopts a distorted "bracelet" structure, similar to a crystal structure. This complements previous NMR spectroscopic results that could not distinguish the nonsymmetric structures. In methanol, a different, "propeller" conformer is indicated by ROA, which has three loops resembling a standard ?-turn peptide motif. Molecular dynamics simulations suggest that the propeller structure is very flexible in methanol. Spectra simulated for geometries not having the ?-turn do not agree with experiment. On the basis of these results, a distinct +/- ROA couplet at ?1335/1317 cm(-1) observed in the extended amide III region is assigned to a turn in the valinomycin backbone. PMID:21384485

Yamamoto, Shigeki; Watarai, Hitoshi; Bou?, Petr

2011-06-01

125

A proposed architecture for the GENI backbone platform  

Microsoft Academic Search

The GENI Project (Global Environment for Network Innovation) is a major NSF-sponsored initiative that seeks to create a national research facility to enable experimental deployment of innovative new network archi- tectures on a sufficient scale to enable realistic evaluation. One key component of the GENI system will be the GENI Backbone Platform (GBP) that provides the resources needed to allow

Jonathan S. Turner

2006-01-01

126

Impact of template backbone heterogeneity on RNA polymerase II transcription  

PubMed Central

Variations in the sugar component (ribose or deoxyribose) and the nature of the phosphodiester linkage (3?-5? or 2?-5? orientation) have been a challenge for genetic information transfer from the very beginning of evolution. RNA polymerase II (pol II) governs the transcription of DNA into precursor mRNA in all eukaryotic cells. How pol II recognizes DNA template backbone (phosphodiester linkage and sugar) and whether it tolerates the backbone heterogeneity remain elusive. Such knowledge is not only important for elucidating the chemical basis of transcriptional fidelity but also provides new insights into molecular evolution. In this study, we systematically and quantitatively investigated pol II transcriptional behaviors through different template backbone variants. We revealed that pol II can well tolerate and bypass sugar heterogeneity sites at the template but stalls at phosphodiester linkage heterogeneity sites. The distinct impacts of these two backbone components on pol II transcription reveal the molecular basis of template recognition during pol II transcription and provide the evolutionary insight from the RNA world to the contemporary ‘imperfect’ DNA world. In addition, our results also reveal the transcriptional consequences from ribose-containing genomic DNA. PMID:25662224

Xu, Liang; Wang, Wei; Zhang, Lu; Chong, Jenny; Huang, Xuhui; Wang, Dong

2015-01-01

127

Ethernet VPN (EVPN) & Provider Backbone Bridging Ethernet VPN  

E-print Network

Ethernet VPN (EVPN) & Provider Backbone Bridging Ethernet VPN (PBBEVPN) MS Scholarly Paper:003:00 PM Location: Engineering building, Room 3202 Abstract-- In the current VPN infrastructure, MultiProtocol Label Switching (MPLS) based Layer 2 VPN (L2VPN) is highly deployed by enterprises

128

The Graphical Representation of the Digital Astronaut Physiology Backbone  

NASA Technical Reports Server (NTRS)

This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

Briers, Demarcus

2010-01-01

129

Increasing protein production by directed vector backbone evolution  

PubMed Central

Recombinant protein production in prokaryotic and eukaryotic organisms was a key enabling technology for the rapid development of industrial and molecular biotechnology. However, despite all progress the improvement of protein production is an ongoing challenge and of high importance for cost-effective enzyme production. With the epMEGAWHOP mutagenesis protocol for vector backbone optimization we report a novel directed evolution based approach to increase protein production levels by randomly introducing mutations in the vector backbone. In the current study we validate the epMEGAWHOP mutagenesis protocol for three different expression systems. The latter demonstrated the general applicability of the epMEGAWHOP method. Cellulase and lipase production was doubled in one round of directed evolution by random mutagenesis of pET28a(+) and pET22b(+) vector backbones. Protease production using the vector pHY300PLK was increased ~4-times with an average of ~1.25 mutations per kb vector backbone. The epMEGAWHOP does not require any rational understanding of the expression machinery and can generally be applied to enzymes, expression vectors and related hosts. epMEGAWHOP is therefore from our point of view a robust, rapid and straight forward alternative for increasing protein production in general and for biotechnological applications. PMID:23890095

2013-01-01

130

Relay Placement for Minimizing Congestion in Wireless Backbone Networks*  

E-print Network

networks than RF and wireline optical links, as RF links do not offer the high bandwidth required Park MD 20742 Email: {kashyap, ftsun, shayman}@glue.umd.edu Abstract-- Wireless optical networks of minimizing the congestion in wireless optical (FSO) backbone networks by placing controllable relay nodes. We

Shayman, Mark A.

131

Impact of template backbone heterogeneity on RNA polymerase II transcription.  

PubMed

Variations in the sugar component (ribose or deoxyribose) and the nature of the phosphodiester linkage (3'-5' or 2'-5' orientation) have been a challenge for genetic information transfer from the very beginning of evolution. RNA polymerase II (pol II) governs the transcription of DNA into precursor mRNA in all eukaryotic cells. How pol II recognizes DNA template backbone (phosphodiester linkage and sugar) and whether it tolerates the backbone heterogeneity remain elusive. Such knowledge is not only important for elucidating the chemical basis of transcriptional fidelity but also provides new insights into molecular evolution. In this study, we systematically and quantitatively investigated pol II transcriptional behaviors through different template backbone variants. We revealed that pol II can well tolerate and bypass sugar heterogeneity sites at the template but stalls at phosphodiester linkage heterogeneity sites. The distinct impacts of these two backbone components on pol II transcription reveal the molecular basis of template recognition during pol II transcription and provide the evolutionary insight from the RNA world to the contemporary 'imperfect' DNA world. In addition, our results also reveal the transcriptional consequences from ribose-containing genomic DNA. PMID:25662224

Xu, Liang; Wang, Wei; Zhang, Lu; Chong, Jenny; Huang, Xuhui; Wang, Dong

2015-02-27

132

Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples.  

PubMed

Kombucha is a sweetened tea beverage that, as a consequence of fermentation, contains ethanol, carbon dioxide, a high concentration of acid (gluconic, acetic and lactic) as well as a number of other metabolites and is thought to contain a number of health-promoting components. The sucrose-tea solution is fermented by a symbiosis of bacteria and yeast embedded within a cellulosic pellicle, which forms a floating mat in the tea, and generates a new layer with each successful fermentation. The specific identity of the microbial populations present has been the focus of attention but, to date, the majority of studies have relied on culture-based analyses. To gain a more comprehensive insight into the kombucha microbiota we have carried out the first culture-independent, high-throughput sequencing analysis of the bacterial and fungal populations of 5 distinct pellicles as well as the resultant fermented kombucha at two time points. Following the analysis it was established that the major bacterial genus present was Gluconacetobacter, present at >85% in most samples, with only trace populations of Acetobacter detected (<2%). A prominent Lactobacillus population was also identified (up to 30%), with a number of sub-dominant genera, not previously associated with kombucha, also being revealed. The yeast populations were found to be dominated by Zygosaccharomyces at >95% in the fermented beverage, with a greater fungal diversity present in the cellulosic pellicle, including numerous species not identified in kombucha previously. Ultimately, this study represents the most accurate description of the microbiology of kombucha to date. PMID:24290641

Marsh, Alan J; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D

2014-04-01

133

Novel Variants of AbaR Resistance Islands with a Common Backbone in Acinetobacter baumannii Isolates of European Clone II  

PubMed Central

In this study, the genetic organization of three novel genomic antibiotic resistance islands (AbaRs) in Acinetobacter baumannii isolates belonging to group of European clone II (EC II) comM integrated sequences of 18-, 21-, and 23-kb resistance islands were determined. These resistance islands carry the backbone of AbaR-type transposon structures, which are composed of the transposition module coding for potential transposition proteins and other genes coding for the intact universal stress protein (uspA), sulfate permease (sul), and proteins of unknown function. The antibiotic resistance genes strA, strB, tetB, and tetR and insertion sequence CR2 element were found to be inserted into the AbaR transposons. GenBank homology searches indicated that they are closely related to the AbaR sequences found integrated in comM in strains of EC II (A. baumannii strains 1656-2 and TCDC-AB0715) and AbaR4 integrated in another location of A. baumannii AB0057 (EC I). All of the AbaRs showed structural similarity to the previously described AbaR4 island and share a 12,008-bp backbone. AbaRs contain Tn1213, Tn2006, and the multiple fragments which could be derived from transposons Tn3, Tn10, Tn21, Tn1000, Tn5393, and Tn6020, the insertion sequences IS26, ISAba1, ISAba14, and ISCR2, and the class 1 integron. Moreover, chromosomal DNA was inserted into distinct regions of the AbaR backbone. Sequence analysis suggested that the AbaR-type transposons have evolved through insertions, deletions, and homologous recombination. AbaR islands, sharing the core structure similar to AbaR4, appeared to be distributed in isolates of EC I and EC II via integration into distinct genomic sites, i.e., pho and comM, respectively. PMID:22290980

Povilonis, Justas; Sužied?lien?, Edita

2012-01-01

134

The composition of coding joints formed in V(D)J recombination is strongly affected by the nucleotide sequence of the coding ends and their relationship to the recombination signal sequences.  

PubMed Central

V(D)J recombination proceeds in two stages. Precise cleavage at the border of the conserved recombination signal sequences (RSSs) and the coding ends results in flush double-stranded signal ends and coding ends terminating in hairpins. In the second stage, the signal and coding ends are processed into signal and coding joints. Coding ends containing certain nucleotide homopolymers affect the efficiency of V(D)J recombination. In this study, we have tested the effect of small changes in coding-end nucleotide composition on the frequency of coding- and signal joint formation. Furthermore, we have determined the sequences of coding joints resulting from recombination of coding ends with different compositions. We found that the presence of two T nucleotides 5' of both RSSs, but not a single T, reduces the frequency of signal joint formation, i.e., interferes with the cleavage stage of V(D)J recombination. However, coding-joint processing is sensitive even to a single T. Both the sequence of the coding ends and the particular RSS (12-mer or 23-mer) with which the coding end is associated affect the final composition of the coding joints. Thus, the presence of P nucleotides, the conservation of one undeleted coding end, the formation of joints without any deletions, and the template-dependent insertion of nucleotides are strongly influenced by the coding-end nucleotide composition and/or RSS association. The implications of these results with respect to the processing of coding ends are discussed. PMID:9199354

Ezekiel, U R; Sun, T; Bozek, G; Storb, U

1997-01-01

135

Efficiency of high molecular weight backbone degradable HPMA copolymer-prostaglandin E1 conjugate in promotion of bone formation in ovariectomized rats.  

PubMed

Multiblock, high molecular weight, linear, backbone degradable HPMA copolymer-prostaglandin E1 (PGE1) conjugate has been synthesized by RAFT polymerization mediated by a new bifunctional chain transfer agent (CTA), which contains an enzymatically degradable oligopeptide sequence flanked by two dithiobenzoate groups, followed by postpolymerization aminolysis and thiol-ene chain extension. The multiblock conjugate contains Asp8 as the bone targeting moiety and enzymatically degradable bonds in the polymer backbone; in vivo degradation produces cleavage products that are below the renal threshold. Using an ovariectomized (OVX) rat model, the accumulation in bone and efficacy to promote bone formation was evaluated; low molecular weight conjugates served as control. The results indicated a higher accumulation in bone, greater enhancement of bone density, and higher plasma osteocalcin levels for the backbone degradable conjugate. PMID:23731780

Pan, Huaizhong; Sima, Monika; Miller, Scott C; Kope?ková, Pavla; Yang, Jiyuan; Kope?ek, Jind?ich

2013-09-01

136

Efficiency of High Molecular Weight Backbone Degradable HPMA Copolymer – Prostaglandin E1 Conjugate in Promotion of Bone Formation in Ovariectomized Rats  

PubMed Central

Multiblock, high molecular weight, linear, backbone degradable HPMA copolymer-prostaglandin E1 (PGE1) conjugate has been synthesized by RAFT polymerization mediated by a new bifunctional chain transfer agent (CTA), which contains an enzymatically degradable oligopeptide sequence flanked by two dithiobenzoate groups, followed by post-polymerization aminolysis and thiol-ene chain extension. The multiblock conjugate contains Asp8 as the bone-targeting moiety and enzymatically degradable bonds in the polymer backbone; in vivo degradation produces cleavage products that are below the renal threshold. Using an ovariectomized (OVX) rat model, the accumulation in bone and efficacy to promote bone formation was evaluated; low molecular weight conjugates served as control. The results indicated a higher accumulation in bone, greater enhancement of bone density, and higher plasma osteocalcin levels for the backbone degradable conjugate. PMID:23731780

Pan, Huaizhong; Sima, Monika; Miller, Scott C.; Kope?ková, Pavla; Yang, Jiyuan; Kope?ek, Jind?ich

2013-01-01

137

Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. PROTEIN BACKBONES: AQUEOUS STAUDINGER LIGATIONS  

E-print Network

permission. PROTEIN BACKBONES: AQUEOUS STAUDINGER LIGATIONS AND SYNTHETIC ISOSTERES by Annie Tam permission. PROTEIN BACKBONES: AQUEOUS STAUDINGER LIGATIONS AND SYNTHETIC ISOSTERES Annie Tam Under. Further reproduction prohibited without permission. A dissertation entitled PROTEIN BACKBONES: AQUEOUS

Raines, Ronald T.

138

Snake-Like Units Using Flexible Backbones and Actuation Redundancy for Enhanced Miniaturization  

E-print Network

Snake-Like Units Using Flexible Backbones and Actuation Redundancy for Enhanced Miniaturization-backbone snake-like unit with actuation redundancy and push-pull actuation. The design of this snake-like unit kinematic and virtual work model is used to perform this comparison between a multi-backbone snake like unit

Simaan, Nabil

139

Distributed QoS Routing for Backbone Overlay , Swapna S. Gokhale2  

E-print Network

Distributed QoS Routing for Backbone Overlay Networks Li Lao1 , Swapna S. Gokhale2 , and Jun-added services. Due to the difficulty of supporting end-to-end QoS purely in end-user overlays, backbone over- lays for QoS support have been proposed. In this paper, we describe a backbone QoS overlay network

Cui, Jun-Hong

140

RDC derived protein backbone resonance assignment using fragment assembly  

Microsoft Academic Search

Experimental residual dipolar couplings (RDCs) in combination with structural models have the potential for accelerating the\\u000a protein backbone resonance assignment process because RDCs can be measured accurately and interpreted quantitatively. However,\\u000a this application has been limited due to the need for very high-resolution structural templates. Here, we introduce a new\\u000a approach to resonance assignment based on optimal agreement between the

Xingsheng Wang; Brian Tash; John M. Flanagan; Fang Tian

2011-01-01

141

Packet-level traffic measurements from the Sprint IP backbone  

Microsoft Academic Search

Network traffic measurements provide essential data for networking research and network management. In this article we describe a passive monitoring system designed to capture GPS synchronized packet-level traffic measurements on OC-3, OC-12, and OC-48 links. Our system is deployed in four POP in the Sprint IP backbone. Measurement data is stored on a 10 Tbyte storage area network and analyzed

Chuck Fraleigh; Sue Moon; Bryan Lyles; Chase Cotton; Mujahid Khan; Deb Moll; Rob Rockell; Ted Seely; S. C. Diot

2003-01-01

142

Extracting the Globally and Locally Adaptive Backbone of Complex Networks  

PubMed Central

A complex network is a useful tool for representing and analyzing complex systems, such as the world-wide web and transportation systems. However, the growing size of complex networks is becoming an obstacle to the understanding of the topological structure and their characteristics. In this study, a globally and locally adaptive network backbone (GLANB) extraction method is proposed. The GLANB method uses the involvement of links in shortest paths and a statistical hypothesis to evaluate the statistical importance of the links; then it extracts the backbone, based on the statistical importance, from the network by filtering the less important links and preserving the more important links; the result is an extracted subnetwork with fewer links and nodes. The GLANB determines the importance of the links by synthetically considering the topological structure, the weights of the links and the degrees of the nodes. The links that have a small weight but are important from the view of topological structure are not belittled. The GLANB method can be applied to all types of networks regardless of whether they are weighted or unweighted and regardless of whether they are directed or undirected. The experiments on four real networks show that the link importance distribution given by the GLANB method has a bimodal shape, which gives a robust classification of the links; moreover, the GLANB method tends to put the nodes that are identified as the core of the network by the k-shell algorithm into the backbone. This method can help us to understand the structure of the networks better, to determine what links are important for transferring information, and to express the network by a backbone easily. PMID:24936975

Zhang, Xiaohang; Zhang, Zecong; Zhao, Han; Wang, Qi; Zhu, Ji

2014-01-01

143

Extracting the multiscale backbone of complex weighted networks  

PubMed Central

A large number of complex systems find a natural abstraction in the form of weighted networks whose nodes represent the elements of the system and the weighted edges identify the presence of an interaction and its relative strength. In recent years, the study of an increasing number of large-scale networks has highlighted the statistical heterogeneity of their interaction pattern, with degree and weight distributions that vary over many orders of magnitude. These features, along with the large number of elements and links, make the extraction of the truly relevant connections forming the network's backbone a very challenging problem. More specifically, coarse-graining approaches and filtering techniques come into conflict with the multiscale nature of large-scale systems. Here, we define a filtering method that offers a practical procedure to extract the relevant connection backbone in complex multiscale networks, preserving the edges that represent statistically significant deviations with respect to a null model for the local assignment of weights to edges. An important aspect of the method is that it does not belittle small-scale interactions and operates at all scales defined by the weight distribution. We apply our method to real-world network instances and compare the obtained results with alternative backbone extraction techniques. PMID:19357301

Serrano, M. Ángeles; Boguñá, Marián; Vespignani, Alessandro

2009-01-01

144

Strong liquid-crystalline polymeric compositions  

DOEpatents

Strong liquid-crystalline polymeric (LCP) compositions of matter are described. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment. 27 figures.

Dowell, F.

1993-12-07

145

Strong liquid-crystalline polymeric compositions  

DOEpatents

Strong liquid-crystalline polymeric (LCP) compositions of matter. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment.

Dowell, Flonnie (Los Alamos, NM)

1993-01-01

146

VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences  

Microsoft Academic Search

BACKGROUND: Understanding the community structure of microbes is typically accomplished by sequencing 16S ribosomal RNA (16S rRNA) genes. These community data can be represented by constructing a phylogenetic tree and comparing it with other samples using statistical methods. However, owing to high computational complexity, these methods are insufficient to effectively analyze the millions of sequences produced by new sequencing technologies

Hiroshi Mori; Fumito Maruyama; Ken Kurokawa

2010-01-01

147

Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources  

PubMed Central

Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists. PMID:23894461

Marsh, Alan J.; O’Sullivan, Orla; Hill, Colin; Ross, R. Paul; Cotter, Paul D.

2013-01-01

148

Coarse-grained models of the proteins backbone conformational dynamics.  

PubMed

Coarse-grained models are more and more frequently used in the studies of the proteins structural and dynamic properties, since the reduced number of degrees of freedom allows to enhance the conformational space exploration. This chapter attempts to provide an overview of the various coarse-grained models that were applied to study the functional conformational changes of the polypeptides main chain around their native state. It will more specifically discuss the methods used to represent the protein backbone flexibility and to account for the physico-chemical interactions that stabilize the secondary structure elements. PMID:24446361

Ha-Duong, Tap

2014-01-01

149

Paleoproterozoic sequences and magmatic complexes of the Losevo suture zone of the Voronezh crystalline massif: Geological position, material composition, geochemistry, and paleogeodynamics  

NASA Astrophysics Data System (ADS)

In order to resolve the contradictions associated with uncertainty in the identification of the material composition, subdivision, and conditions of formation of the Paleoproterozoic intrusive, metavolcanogenic, and metasedimentary sequences of the Losevo suture zone of the Voronezh crystalline massif, this work presents geological, petrographic, petrochemical, and geochemical features of these sequences. The stratigraphic and magmatic scheme of the central part of the Losevo suture zone is clarified. In particular, the Paleoproterozoic Losevo Series is divided into two sequences: Strelitsa (marginal sea) and Podgornoe (island arc). A new hypabyssal Novo-Voronezh metagabbro-diabase complex, comagmatic to metatholeiites of the Podgornoe sequence, is distinguished. The isotope age of the Strelitsa sequence is assumed to be 2172 ± 17 Ma on the basis of the results of age dating of zircon cores from the Usman plagiogranites, intruding this sequence. The upper age boundary of the Strelitsa sequence corresponds to the age of premetamorphic gabbro of the Rozhdestvenskoe complex, comagmatic to metavolcanites (2120 ± 11-2158 ± 43 Ma). The age of the Usman plagiogranite complex is clarified. On the basis of geological-structural and petrographic-mineralogical analyses of metavolcanogenic rocks, lithological analysis of metasedimentary formations, and new geochemical data obtained from metavolcanites and metamorphosed deposits, the pattern of paleogeodynamic evolution of the Losevo suture zone in the first half of the Paleoproterozoic is proposed. The next stages are distinguished: (1) intrusion of tholeiites of transition T-MORB type in spreading zones and deposition of terrigenous strata in the marginal sea basins; (2) intrusion of Nb-depleted tholeiites and plagiorhyolites, the geochemical characteristics indicating their formation in the subduction setting; (3) intrusion of gabbroids of the Rozhdestvenskoe complex; (4) formation of an island arc synchronously with stage 2, tholeiitic and calc-alkaline (Podgornoe sequence) volcanism; (5) intrusions of gabbro-diabases, subsynchronous to volcanism, of the Novovoronezh complex and diorite-granitoides, crystallization of granitoides of the Usman complex; (6) a break in sedimentation and formation of molasses of the Voronezh (Somovo) Formation.

Terentiev, R. A.

2014-03-01

150

Phosphorylation alters backbone conformational preferences of serine and threonine peptides.  

PubMed

Despite the notion that a control of protein function by phosphorylation works mainly by inducing its conformational changes, the phosphorylation effects on even small peptide conformation have not been fully understood yet. To study its possible effects on serine and threonine peptide conformations, we recently carried out pH- and temperature-dependent circular dichroism (CD) as well as (1)H NMR studies of the phosphorylated serine and threonine peptides and compared them with their unphosphorylated analogs. In the present article, by performing the self-consistent singular value decomposition analysis of the temperature-dependent CD spectra and by analyzing the (3)J(H(N),H(?)) coupling constants extracted from the NMR spectra, the populations of the polyproline II (PPII) and ?-strand conformers of the phosphorylated Ser and Thr peptides are determined. As temperature is increased, the ?-strand populations of both phosphorylated serine and threonine peptides increase. However, the dependences of PPII/?-strand population ratio on pH are different for these two cases. The phosphorylation of the serine peptide enhances the PPII propensity, whereas that of the threonine peptide has the opposite effect. This suggests that the serine and threonine phosphorylations can alter the backbone conformational propensity via direct but selective intramolecular hydrogen-bonding interactions with the peptide N--H groups. This clearly indicates that the phosphoryl group actively participates in modulating the peptide backbone conformations. PMID:21989936

Kim, Su-Yeon; Jung, Youngae; Hwang, Geum-Sook; Han, Hogyu; Cho, Minhaeng

2011-11-01

151

A phylogenetic backbone for Bivalvia: an RNA-seq approach  

PubMed Central

Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000–20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the monophyly of Protobranchia and Heterodonta, and resolving the position of particular groups such as Palaeoheterodonta, Archiheterodonta and Anomalodesmata. This now fully resolved backbone demonstrates that genomic approaches using hundreds of genes are feasible for resolving phylogenetic questions in bivalves and other animals. PMID:25589608

González, Vanessa L.; Andrade, Sónia C. S.; Bieler, Rüdiger; Collins, Timothy M.; Dunn, Casey W.; Mikkelsen, Paula M.; Taylor, John D.; Giribet, Gonzalo

2015-01-01

152

A phylogenetic backbone for Bivalvia: an RNA-seq approach.  

PubMed

Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000-20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the monophyly of Protobranchia and Heterodonta, and resolving the position of particular groups such as Palaeoheterodonta, Archiheterodonta and Anomalodesmata. This now fully resolved backbone demonstrates that genomic approaches using hundreds of genes are feasible for resolving phylogenetic questions in bivalves and other animals. PMID:25589608

González, Vanessa L; Andrade, Sónia C S; Bieler, Rüdiger; Collins, Timothy M; Dunn, Casey W; Mikkelsen, Paula M; Taylor, John D; Giribet, Gonzalo

2015-02-22

153

Bacterial Community Composition in Central European Running Waters Examined by Temperature Gradient Gel Electrophoresis and Sequence Analysis of 16S rRNA Genes? †  

PubMed Central

The bacterial community composition in small streams and a river in central Germany was examined by temperature gradient gel electrophoresis (TGGE) with PCR products of 16S rRNA gene fragments and sequence analysis. Complex TGGE band patterns suggested high levels of diversity of bacterial species in all habitats of these environments. Cluster analyses demonstrated distinct differences among the communities in stream and spring water, sandy sediments, biofilms on stones, degrading leaves, and soil. The differences between stream water and sediment were more significant than those between sites within the same habitat along the stretch from the stream source to the mouth. TGGE data from an entire stream course suggest that, in the upper reach of the stream, a special suspended bacterial community is already established and changes only slightly downstream. The bacterial communities in water and sediment in an acidic headwater with a pH below 5 were highly similar to each other but deviated distinctly from the communities at the other sites. As ascertained by nucleotide sequence analysis, stream water communities were dominated by Betaproteobacteria (one-third of the total bacteria), whereas sediment communities were composed mainly of Betaproteobacteria and members of the Fibrobacteres/Acidobacteria group (each accounting for about 25% of bacteria). Sequences obtained from bacteria from water samples indicated the presence of typical cosmopolitan freshwater organisms. TGGE bands shared between stream and soil samples, as well as sequences found in bacteria from stream samples that were related to those of soil bacteria, demonstrated the occurrence of some species in both stream and soil habitats. Changes in bacterial community composition were correlated with geographic distance along a stream, but in comparisons of different streams and rivers, community composition was correlated only with environmental conditions. PMID:18024682

Beier, Sara; Witzel, Karl-Paul; Marxsen, Jürgen

2008-01-01

154

Bacterial community composition in Central European running waters examined by temperature gradient gel electrophoresis and sequence analysis of 16S rRNA genes.  

PubMed

The bacterial community composition in small streams and a river in central Germany was examined by temperature gradient gel electrophoresis (TGGE) with PCR products of 16S rRNA gene fragments and sequence analysis. Complex TGGE band patterns suggested high levels of diversity of bacterial species in all habitats of these environments. Cluster analyses demonstrated distinct differences among the communities in stream and spring water, sandy sediments, biofilms on stones, degrading leaves, and soil. The differences between stream water and sediment were more significant than those between sites within the same habitat along the stretch from the stream source to the mouth. TGGE data from an entire stream course suggest that, in the upper reach of the stream, a special suspended bacterial community is already established and changes only slightly downstream. The bacterial communities in water and sediment in an acidic headwater with a pH below 5 were highly similar to each other but deviated distinctly from the communities at the other sites. As ascertained by nucleotide sequence analysis, stream water communities were dominated by Betaproteobacteria (one-third of the total bacteria), whereas sediment communities were composed mainly of Betaproteobacteria and members of the Fibrobacteres/Acidobacteria group (each accounting for about 25% of bacteria). Sequences obtained from bacteria from water samples indicated the presence of typical cosmopolitan freshwater organisms. TGGE bands shared between stream and soil samples, as well as sequences found in bacteria from stream samples that were related to those of soil bacteria, demonstrated the occurrence of some species in both stream and soil habitats. Changes in bacterial community composition were correlated with geographic distance along a stream, but in comparisons of different streams and rivers, community composition was correlated only with environmental conditions. PMID:18024682

Beier, Sara; Witzel, Karl-Paul; Marxsen, Jürgen

2008-01-01

155

Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes  

PubMed Central

Background In mammals, splice-regulatory domains impose marked trends on the relative abundance of certain amino acids near exon-intron boundaries. Is this a mammalian particularity or symptomatic of exonic splicing regulation across taxa? Are such trends more common in species that a priori have a harder time identifying exon ends, that is, those with pre-mRNA rich in intronic sequence? We address these questions surveying exon composition in a sample of phylogenetically diverse genomes. Results Biased amino acid usage near exon-intron boundaries is common throughout the metazoa but not restricted to the metazoa. There is extensive cross-species concordance as to which amino acids are affected, and reduced/elevated abundances are well predicted by knowledge of splice enhancers. Species expected to rely on exon definition for splicing, that is, those with a higher ratio of intronic to coding sequence, more introns per gene and longer introns, exhibit more amino acid skews. Notably, this includes the intron-rich basidiomycete Cryptococcus neoformans, which, unlike intron-poor ascomycetes (Schizosaccharomyces pombe, Saccharomyces cerevisiae), exhibits compositional biases reminiscent of the metazoa. Strikingly, 5 prime ends of nematode exons deviate radically from normality: amino acids strongly preferred near boundaries are strongly avoided in other species, and vice versa. This we suggest is a measure to avoid attracting trans-splicing machinery. Conclusion Constraints on amino acid composition near exon-intron boundaries are phylogenetically widespread and characteristic of species where exon localization should be problematic. That compositional biases accord with sequence preferences of splice-regulatory proteins and are absent in ascomycetes is consistent with selection on exonic splicing regulation. PMID:18257921

Warnecke, Tobias; Parmley, Joanna L; Hurst, Laurence D

2008-01-01

156

Composites  

NASA Astrophysics Data System (ADS)

The Composites market is arguably the most challenging and profitable market for phenolic resins aside from electronics. The variety of products and processes encountered creates the challenges, and the demand for high performance in critical operations brings value. Phenolic composite materials are rendered into a wide range of components to supply a diverse and fragmented commercial base that includes customers in aerospace (Space Shuttle), aircraft (interiors and brakes), mass transit (interiors), defense (blast protection), marine, mine ducting, off-shore (ducts and grating) and infrastructure (architectural) to name a few. For example, phenolic resin is a critical adhesive in the manufacture of honeycomb sandwich panels. Various solvent and water based resins are described along with resin characteristics and the role of metal ions for enhanced thermal stability of the resin used to coat the honeycomb. Featured new developments include pultrusion of phenolic grating, success in RTM/VARTM fabricated parts, new ballistic developments for military vehicles and high char yield carbon-carbon composites along with many others. Additionally, global regional market resin volumes and sales are presented and compared with other thermosetting resin systems.

Taylor, John G.

157

Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment  

PubMed Central

Obtaining NMR assignments for slowly tumbling molecules such as detergent-solubilized membrane proteins is often compromised by low sensitivity as well as spectral overlap. Both problems can be addressed by amino-acid specific isotope labeling in conjunction with 15N–1H correlation experiments. In this work an extended combinatorial selective in vitro labeling scheme is proposed that seeks to reduce the number of samples required for assignment. Including three different species of amino acids in each sample, 15N, 1- 13C, and fully 13C/15 N labeled, permits identification of more amino acid types and sequential pairs than would be possible with previously published combinatorial methods. The new protocol involves recording of up to five 2D triple-resonance experiments to distinguish the various isotopomeric dipeptide species. The pattern of backbone NH cross peaks in this series of spectra adds a new dimension to the combinatorial grid, which otherwise mostly relies on comparison of [15N, 1H]–HSQC and possibly 2D HN(CO) spectra of samples with different labeled amino acid compositions. Application to two ?-helical membrane proteins shows that using no more than three samples information can be accumulated such that backbone assignments can be completed solely based on 3D HNCA/ HN(CO)CA experiments. Alternatively, in the case of severe signal overlap in certain regions of the standard suite of triple-resonance spectra acquired on uniformly labeled protein, or missing signals due to a lack of efficiency of 3D experiments, the remaining gaps can be filled. PMID:22252484

Löhr, Frank; Reckel, Sina; Karbyshev, Mikhail; Connolly, Peter J.; Abdul-Manan, Norzehan; Bernhard, Frank; Moore, Jonathan M.

2013-01-01

158

Polypeptide backbone, C(?) and methyl group resonance assignments of the 24 kDa plectin repeat domain 6 from human protein plectin.  

PubMed

The 500 kDa protein plectin is essential for the cytoskeletal organization of most mammalian cells and it is up-regulated in some types of cancer. Here, we report nearly complete sequence-specific polypeptide backbone, (13)C(?) and methyl group resonance assignments for 24 kDa human plectin(4403-4606) containing the C-terminal plectin repeat domain 6. PMID:24722902

Pulavarti, Surya V S R K; Eletsky, Alexander; Huang, Yuanpeng J; Acton, Thomas B; Xiao, Rong; Everett, John K; Montelione, Gaetano T; Szyperski, Thomas

2015-04-01

159

Animal Protection and Structural Studies of a Consensus Sequence Vaccine Targeting the Receptor Binding Domain of the Type IV Pilus of Pseudomonas aeruginosa  

SciTech Connect

One of the main obstacles in the development of a vaccine against Pseudomonas aeruginosa is the requirement that it is protective against a wide range of virulent strains. We have developed a synthetic-peptide consensus-sequence vaccine (Cs1) that targets the host receptor-binding domain (RBD) of the type IV pilus of P. aeruginosa. Here, we show that this vaccine provides increased protection against challenge by the four piliated strains that we have examined (PAK, PAO, KB7 and P1) in the A.BY/SnJ mouse model of acute P. aeruginosa infection. To further characterize the consensus sequence, we engineered Cs1 into the PAK monomeric pilin protein and determined the crystal structure of the chimeric Cs1 pilin to 1.35 {angstrom} resolution. The substitutions (T130K and E135P) used to create Cs1 do not disrupt the conserved backbone conformation of the pilin RBD. In fact, based on the Cs1 pilin structure, we hypothesize that the E135P substitution bolsters the conserved backbone conformation and may partially explain the immunological activity of Cs1. Structural analysis of Cs1, PAK and K122-4 pilins reveal substitutions of non-conserved residues in the RBD are compensated for by complementary changes in the rest of the pilin monomer. Thus, the interactions between the RBD and the rest of the pilin can either be mediated by polar interactions of a hydrogen bond network in some strains or by hydrophobic interactions in others. Both configurations maintain a conserved backbone conformation of the RBD. Thus, the backbone conformation is critical in our consensus-sequence vaccine design and that cross-reactivity of the antibody response may be modulated by the composition of exposed side-chains on the surface of the RBD. This structure will guide our future vaccine design by focusing our investigation on the four variable residue positions that are exposed on the RBD surface.

Kao, Daniel J.; Churchill, Mair E.A.; Irvin, Randall T.; Hodges, Robert S. (Alberta); (Colorado)

2008-09-23

160

Automatic and Reliable Extraction of Dendrite Backbone from Optical Microscopy Images  

Microsoft Academic Search

\\u000a The morphology and structure of 3D dendritic backbones are the essential to understand the neuronal circuitry and behaviors\\u000a in the neurodegenerative diseases. As a big challenge, the research of extraction of dendritic backbones using image processing\\u000a and analysis technology has attracted many computational scientists. This paper proposes a reliable and robust approach for\\u000a automatically extract dendritic backbones in 3D optical

Liang Xiao; Xiaosong Yuan; Zack Galbreath; Badrinath Roysam

2010-01-01

161

A Native to Amyloidogenic Transition Regulated by a Backbone Trigger  

SciTech Connect

Many polypeptides can self-associate into linear, aggregated assemblies termed amyloid fibers. High-resolution structural insights into the mechanism of fibrillogenesis are elusive owing to the transient and mixed oligomeric nature of assembly intermediates. Here, we report the conformational changes that initiate fiber formation by beta-2-microglobulin (beta2m) in dialysis-related amyloidosis. Access of beta2m to amyloidogenic conformations is catalyzed by selective binding of divalent cations. The chemical basis of this process was determined to be backbone isomerization of a conserved proline. On the basis of this finding, we designed a beta2m variant that closely adopts this intermediate state. The variant has kinetic, thermodynamic and catalytic properties consistent with its being a fibrillogenic intermediate of wild-type beta2m. Furthermore, it is stable and folded, enabling us to unambiguously determine the initiating conformational changes for amyloid assembly at atomic resolution.

Eakin,C.; Berman, A.; Miranker, A.

2006-01-01

162

Transforming plastic surfaces with electrophilic backbones from hydrophobic to hydrophilic.  

PubMed

We demonstrate a simple nonaqueous reaction scheme for transforming the surface of plastics from hydrophobic to hydrophilic. The chemical modification is achieved by base-catalyzed trans-esterification with polyols. It is permanent, does not release contaminants, and causes no optical or mechanical distortion of the plastic. We present contact angle measurements to show successful modification of several types of plastics including poly(ethylene terephthalate) (PET) and polycarbonate (PC). Its applicability to blood analysis is explored using chemically modified PET blood collection tubes and found to be quite satisfactory. We expect this approach will reduce the cost of manufacturing plastic devices with optimized wettability and can be generalized to other types of plastic materials having an electrophilic linkage as its backbone. PMID:25565370

Kim, Samuel; Bowen, Raffick A R; Zare, Richard N

2015-01-28

163

Compositional variations across a dunite - harzburgite - lherzolite - plagioclase lherzolite sequence at the Trinity ophiolite: Evidence for multiple episodes of melt flow and melt-rock reaction in the mantle  

Microsoft Academic Search

In the preceding report we showed experimentally that the dunite-harzburgite-lherzolite (DHL) sequence found in the mantle sections of ophiolite could be formed by reactive dissolution of lherzolite in a basaltic liquid. The most striking results of our lherzolite dissolution experiments are the sharp mineralogical boundaries between adjacent lithologies and simple monotonic composition variations in minerals across the DHL sequence. Here

Z. T. Morgan; Y. Liang; P. Kelemen

2004-01-01

164

DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure.  

PubMed

The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied. PMID:25257543

Rubin, Benjamin E R; Sanders, Jon G; Hampton-Marcell, Jarrad; Owens, Sarah M; Gilbert, Jack A; Moreau, Corrie S

2014-12-01

165

DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure  

PubMed Central

The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied. PMID:25257543

Rubin, Benjamin E R; Sanders, Jon G; Hampton-Marcell, Jarrad; Owens, Sarah M; Gilbert, Jack A; Moreau, Corrie S

2014-01-01

166

The Contributions of Replication Orientation, Gene Direction, and Signal Sequences to Base-Composition Asymmetries in Bacterial Genomes  

Microsoft Academic Search

.   Asymmetries in base composition between the leading and the lagging strands have been observed previously in many prokaryotic\\u000a genomes. Since a majority of genes is encoded on the leading strand in these genomes, previous analyses have not been able\\u000a to determine the relative contribution to the base composition skews of replication processes and transcriptional and\\/or translational\\u000a forces. Using qualitative

Elisabeth R. M. Tillier; Richard A. Collins

2000-01-01

167

High-cost, high-capacity backbone for global brain communication  

E-print Network

-capacity backbone for global brain communication. connectome | graph | tractography Integrative brain functionHigh-cost, high-capacity backbone for global brain communication Martijn P. van den Heuvela,1 of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405 Edited by Terrence J. Sejnowski

Pillow, Jonathan

168

Live-attenuated influenza A virus vaccines using a B virus backbone  

Technology Transfer Automated Retrieval System (TEKTRAN)

The currently FDA-licensed live attenuated influenza virus vaccine contains a trivalent mixture of types A (H1N1 and H3N2) and B vaccine viruses. The two A virus vaccines have the backbone of a cold-adapted influenza A virus and the B virus vaccine has the six backbone segments derived from a cold-...

169

The phosphate clamp: a small and independent motif for nucleic acid backbone recognition  

E-print Network

The phosphate clamp: a small and independent motif for nucleic acid backbone recognition Seiji extended along the phosphate backbone and bridging the minor groove. The square planar tetra-am(m)ine Pt(II) units form bidentate N-O-N complexes with OP atoms, in a Phosphate Clamp motif. The geometry

Williams, Loren

170

Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity  

E-print Network

Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity Simon of alternative nucleotides would support the assembly of nucleic acid polymers containing nonheritable backbone of heterogeneous nucleic acid molecules could evolve reproducible function. For such evolution to be possible

Heller, Eric

171

Flooding Attacks Detection in Traffic of Backbone Osman Salem, Ali Makke, Jean Tajer, Ahmed Mehaoua  

E-print Network

Flooding Attacks Detection in Traffic of Backbone Networks Osman Salem, Ali Makke, Jean Tajer to flooding attacks that lead to denial of service. This paper proposes a new framework to detect anomalies and to provide early alerts for flooding attacks in backbone networks. Thus allow to quickly react in order

Boyer, Edmond

172

Consequences of binding an S-adenosylmethionine analogue on the structure and dynamics of the thiopurine methyltransferase protein backbone.  

PubMed

In humans, the enzyme thiopurine methyltransferase (TPMT) metabolizes 6-thiopurine (6-TP) medications, commonly used for immune suppression and for the treatment of hematopoietic malignancies. Genetic polymorphisms in the TPMT protein sequence accelerate intracellular degradation of the enzyme through an ubiquitylation and proteasomal-dependent pathway. Research has led to the hypothesis that these polymorphisms destabilize the native structure of TPMT, resulting in the formation of misfolded or partially unfolded states, which are subsequently recognized for intracellular degradation. Addition of the cosubstrate, S-adenosylmethionine (SAM), prevents degradation of the TPMT polymorphs in experimental assays, presumably by stabilizing the native structure. Using a bacterial orthologue of TPMT from Pseudomonas syringae, we have used NMR spectroscopy to describe the consequences of binding sinefungin, a SAM analogue, on the structure and dynamics of the TPMT protein backbone. NMR chemical shift mapping experiments localize sinefungin to a highly conserved site in classical methyltransferases. Distal chemical shift changes involving the presumed active site cover imply indirect conformational changes induced by sinefungin, which may play a role in substrate recognition or the catalytic mechanism. Analysis of protein backbone dynamics based on NMR relaxation reveals a combination of complementary effects. Whereas the peripheral, inserted structural elements of the TPMT topology are conformationally stabilized by the presence of sinefungin, a consistent increase in backbone mobility is observed for the central, conserved structural elements. The potential implications for the structural and dynamic effects of binding sinefungin for the catalytic mechanism of the enzyme and the stabilization of the degradation-susceptible TPMT polymorphs are discussed. PMID:15379558

Scheuermann, Thomas H; Keeler, Camille; Hodsdon, Michael E

2004-09-28

173

iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition.  

PubMed

Translation is a key process for gene expression. Timely identification of the translation initiation site (TIS) is very important for conducting in-depth genome analysis. With the avalanche of genome sequences generated in the postgenomic age, it is highly desirable to develop automated methods for rapidly and effectively identifying TIS. Although some computational methods were proposed in this regard, none of them considered the global or long-range sequence-order effects of DNA, and hence their prediction quality was limited. To count this kind of effects, a new predictor, called "iTIS-PseTNC," was developed by incorporating the physicochemical properties into the pseudo trinucleotide composition, quite similar to the PseAAC (pseudo amino acid composition) approach widely used in computational proteomics. It was observed by the rigorous cross-validation test on the benchmark dataset that the overall success rate achieved by the new predictor in identifying TIS locations was over 97%. As a web server, iTIS-PseTNC is freely accessible at http://lin.uestc.edu.cn/server/iTIS-PseTNC. To maximize the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web server to obtain the desired results without the need to go through detailed mathematical equations, which are presented in this paper just for the integrity of the new prection method. PMID:25016190

Chen, Wei; Feng, Peng-Mian; Deng, En-Ze; Lin, Hao; Chou, Kuo-Chen

2014-10-01

174

Measurement and Classification of OutofSequence Packets in a Tier1 IP Backbone  

E-print Network

, Gianluca Iannaccone, Christophe Diot, Jim Kurose, Don Towsley Abstract--- We present a classification is with Thomson, Boulogne, France; email: christophe.diot@thomson.net. J. Kurose and D. Towsley are with the Computer Science Depart­ ment at the University of Massachusetts, Amherst, MA, USA; email: {kurose

Massachusetts at Amherst, University of

175

Measurement and Classi cation of Out-of-Sequence Packets in a Tier-1 IP Backbone  

E-print Network

, Gianluca Iannaccone, Christophe Diot, Jim Kurose, Don Towsley Abstract We present a classi cation is with Thomson, Boulogne, France; email: christophe.diot@thomson.net. J. Kurose and D. Towsley are with the Computer Science Depart- ment at the University of Massachusetts, Amherst, MA, USA; email: {kurose

Massachusetts at Amherst, University of

176

Whole-rock geochemistry and Sr-Nd isotopic composition of the pre-rift sequence of the Camamu Basin, northeastern Brazil  

NASA Astrophysics Data System (ADS)

Whole-rock geochemistry, combined with Sr-Nd isotopic composition of pelitic sedimentary rocks, have been considered to be useful parameters to estimate not only their provenance but also to make inferences about their depositional environment as well as the weathering processes they have been through. The basal sedimentary units of the basins of the northeastern Brazilian continental margin, particularly those of the pre-rift sequence, have been subject of interest of studies based on chemical and isotopic data, since they lack fossil content to establish their age and, therefore, stratigraphic correlations are difficult. The major and trace element contents as well as Sr-Nd isotopic compositions of whole-rock shale samples from five outcrops attributed to the pre-rift supersequence of the Camamu Basin were analyzed with the purpose of characterizing and obtaining further information that would allow a better correlation between the sites studied. The geochemical data suggest that the rocks exposed in the studied outcrops are part of the same sedimentary unit and that they might be correlated to the Capianga Member of the Aliança Formation of the Recôncavo Basin, exposed to the north of the Camamu Basin. The chemical index of alteration (CIA) suggests conditions associated with a humid tropical/subtropical climate at the time of deposition. Nd isotopic compositions indicate provenance from the Paleoproterozoic rocks of the Sao Francisco craton. The results presented here, therefore, show that the combined use of chemical and isotopic analyses may be of great interest to characterize and correlate lithologically homogeneous clastic sedimentary sequences.

Silva, D. R. A.; Mizusaki, A. M. P.; Milani, E. J.; Pimentel, M.; Kawashita, K.

2012-11-01

177

Methods in Enzymology: “Flexible backbone sampling methods to model and design protein alternative conformations”  

PubMed Central

Sampling alternative conformations is key to understanding how proteins work and engineering them for new functions. However, accurately characterizing and modeling protein conformational ensembles remains experimentally and computationally challenging. These challenges must be met before protein conformational heterogeneity can be exploited in protein engineering and design. Here, as a stepping stone, we describe methods to detect alternative conformations in proteins and strategies to model these near-native conformational changes based on backrub-type Monte Carlo moves in Rosetta. We illustrate how Rosetta simulations that apply backrub moves improve modeling of point mutant side chain conformations, native side chain conformational heterogeneity, functional conformational changes, tolerated sequence space, protein interaction specificity, and amino acid co-variation across protein-protein interfaces. We include relevant Rosetta command lines and RosettaScripts to encourage the application of these types of simulations to other systems. Our work highlights that critical scoring and sampling improvements will be necessary to approximate conformational landscapes. Challenges for the future development of these methods include modeling conformational changes that propagate away from designed mutation sites and modulating backbone flexibility to predictively design functionally important conformational heterogeneity. PMID:23422426

Ollikainen, Noah; Smith, Colin A.; Fraser, James S.; Kortemme, Tanja

2013-01-01

178

Thermogelling Biodegradable Polymers with Hydrophilic Backbones: PEG-g-PLGA  

SciTech Connect

The aqueous solutions of poly(ethylene glycol)grafted with poly(lactic acid-co-glycolic acid) flow freely at room temperature but form gels at higher temperature. The existence of micelles in water at low polymer concentration was confirmed by Cro-transmission electron microscopy and dye solubilization studies. The micellar diameter and critical micelle concentration are about 9 nm and 0.47 wt.% respectively. The critical gel concentration, above which a gel phase appears was 16 wt.% and sol-to-gel transition temperature was slightly affected by the concentration in the range of 16 {approx} 25 wt.%. At sol-to-gel transition, viscosity increased abruptly and C-NMR showed molecular motion of hydrophilic poly(lactic acid-co-glycolic acid) side-chains increased. The hydrogel of PEG-g-PLGA with hydrophilic backbones was transparent during degradation and remained a gel for one week, suggesting a promising material for short-term drug delivery.

Jeong, Byeongmoon; Kibbey, Merinda R.; Birnbaum, Jerome C.; Won, You-Yeong; Gutowska, Anna

2000-10-31

179

Backbone of complex networks of corporations: The flow of control  

NASA Astrophysics Data System (ADS)

We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

Glattfelder, J. B.; Battiston, S.

2009-09-01

180

Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures  

PubMed Central

Background Protein phosphorylation catalyzed by kinases plays crucial regulatory roles in cellular processes. Given the high-throughput mass spectrometry-based experiments, the desire to annotate the catalytic kinases for in vivo phosphorylation sites has motivated. Thus, a variety of computational methods have been developed for performing a large-scale prediction of kinase-specific phosphorylation sites. However, most of the proposed methods solely rely on the local amino acid sequences surrounding the phosphorylation sites. An increasing number of three-dimensional structures make it possible to physically investigate the structural environment of phosphorylation sites. Results In this work, all of the experimental phosphorylation sites are mapped to the protein entries of Protein Data Bank by sequence identity. It resulted in a total of 4508 phosphorylation sites containing the protein three-dimensional (3D) structures. To identify phosphorylation sites on protein 3D structures, this work incorporates support vector machines (SVMs) with the information of linear motifs and spatial amino acid composition, which is determined for each kinase group by calculating the relative frequencies of 20 amino acid types within a specific radial distance from central phosphorylated amino acid residue. After the cross-validation evaluation, most of the kinase-specific models trained with the consideration of structural information outperform the models considering only the sequence information. Furthermore, the independent testing set which is not included in training set has demonstrated that the proposed method could provide a comparable performance to other popular tools. Conclusion The proposed method is shown to be capable of predicting kinase-specific phosphorylation sites on 3D structures and has been implemented as a web server which is freely accessible at http://csb.cse.yzu.edu.tw/PhosK3D/. Due to the difficulty of identifying the kinase-specific phosphorylation sites with similar sequenced motifs, this work also integrates the 3D structural information to improve the cross classifying specificity. PMID:24564522

2013-01-01

181

Distributed QoS Routing for Backbone Overlay Jun-Hong Cui, Swapna S. Gokhale, Li Lao and Jijun Lu  

E-print Network

1 Distributed QoS Routing for Backbone Overlay Networks Jun-Hong Cui, Swapna S. Gokhale, Li Lao, but due to the difficulty of supporting end-to-end QoS purely in end-user overlays, backbone overlays for QoS support have been proposed. In this paper, we describe a backbone QoS overlay network

Cui, Jun-Hong

182

Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones under poor solvent conditions  

E-print Network

Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones.1088/0953-8984/25/28/285105 Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones under poor/285105 Abstract Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor

Theodorakis, Panagiotis E.

183

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold  

SciTech Connect

The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.

Azoitei, Mihai L.; Correia, Bruno E.; Ban, Yih-En Andrew; Carrico, Chris; Kalyuzhniy, Oleksandr; Chen, Lei; Schroeter, Alexandria; Huang, Po-Ssu; McLellan, Jason S.; Kwong, Peter D.; Baker, David; Strong, Roland K.; Schief, William R. (UWASH); (FHCRC); (NIAID)

2012-02-07

184

Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont.  

PubMed

Comparative genomics of closely related bacterial strains can clarify mutational processes and selective forces that impact genetic variation. Among primary bacterial endosymbionts of insects, such analyses have revealed ongoing genome reduction, raising questions about the ultimate evolutionary fate of these partnerships. Here, we explored genomic variation within Blochmannia vafer, an obligate mutualist of the ant Camponotus vafer. Polymorphism analysis of the Illumina data set used previously for de novo assembly revealed a second Bl. vafer genotype. To determine why a single ant colony contained two symbiont genotypes, we examined polymorphisms in 12 C. vafer mitochondrial sequences assembled from the Illumina data; the spectrum of variants suggests that the colony contained two maternal lineages, each harboring a distinct Bl. vafer genotype. Comparing the two Bl. vafer genotypes revealed that purifying selection purged most indels and nonsynonymous differences from protein-coding genes. We also discovered that indels occur frequently in multimeric simple sequence repeats, which are relatively abundant in Bl. vafer and may play a more substantial role in generating variation in this ant mutualist than in the aphid endosymbiont Buchnera. Finally, we explored how an apparent relocation of the origin of replication in Bl. vafer and the resulting shift in strand-associated mutational pressures may have caused accelerated gene loss and an elevated rate of indel polymorphisms in the region spanning the origin relocation. Combined, these results point to significant impacts of purifying selection on genomic polymorphisms as well as distinct patterns of indels associated with unusual genomic features of Blochmannia. PMID:22117087

Williams, Laura E; Wernegreen, Jennifer J

2012-01-01

185

Time between collection and storage significantly influences bacterial sequence composition in sputum samples from cystic fibrosis respiratory infections.  

PubMed

Spontaneously expectorated sputum is traditionally used as the sampling method for the investigation of lower airway infections. While guidelines exist for the handling of these samples for culture-based diagnostic microbiology, there is no comparable consensus on their handling prior to culture-independent analysis. The increasing incorporation of culture-independent approaches in diagnostic microbiology means that it is of critical importance to assess potential biases. The aim of this study was to assess the impact of delayed freezing on culture-independent microbiological analyses and to identify acceptable parameters for sample handling. Sputum samples from eight adult cystic fibrosis (CF) patients were collected and aliquoted into sterile Bijou bottles. Aliquots were stored at room temperature before being frozen at -80 °C for increasing intervals, up to a 72-h period. Samples were treated with propidium monoazide to distinguish live from dead cells prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterize their bacterial compositions. Substantial variation was observed in samples with high-diversity bacterial communities over time, whereas little variation was observed in low-diversity communities dominated by recognized CF pathogens, regardless of time to freezing. Partitioning into common and rare species demonstrated that the rare species drove changes in similarity. The percentage abundance of anaerobes over the study significantly decreased after 12 h at room temperature (P = 0.008). Failure to stabilize samples at -80 °C within 12 h of collection results in significant changes in the detected community composition. PMID:24920767

Cuthbertson, Leah; Rogers, Geraint B; Walker, Alan W; Oliver, Anna; Hafiz, Tarana; Hoffman, Lucas R; Carroll, Mary P; Parkhill, Julian; Bruce, Kenneth D; van der Gast, Christopher J

2014-08-01

186

A Synthetic HIV-1 Subtype C Backbone Generates Comparable PR and RT Resistance Profiles to a Subtype B Backbone in a Recombinant Virus Assay  

PubMed Central

In order to determine phenotypic protease and reverse transcriptase inhibitor-associated resistance in HIV subtype C virus, we have synthetically constructed an HIV-1 subtype C (HIV-1-C) viral backbone for use in a recombinant virus assay. The in silico designed viral genome was divided into 4 fragments, which were chemically synthesized and joined together by conventional subcloning. Subsequently, gag-protease-reverse-transcriptase (GPRT) fragments from 8 HIV-1 subtype C-infected patient samples were RT-PCR-amplified and cloned into the HIV-1-C backbone (deleted for GPRT) using In-Fusion reagents. Recombinant viruses (1 to 5 per patient sample) were produced in MT4-eGFP cells where cyto-pathogenic effect (CPE), p24 and Viral Load (VL) were monitored. The resulting HIV-1-C recombinant virus stocks (RVS) were added to MT4-eGFP cells in the presence of serial dilutions of antiretroviral drugs (PI, NNRTI, NRTI) to determine the fold-change in IC50 compared to the IC50 of wild-type HIV-1 virus. Additionally, viral RNA was extracted from the HIV-1-C RVS and the amplified GPRT products were used to generate recombinant virus in a subtype B backbone. Phenotypic resistance profiles in a subtype B and subtype C backbone were compared. The following observations were made: i) functional, infectious HIV-1 subtype C viruses were generated, confirmed by VL and p24 measurements; ii) their rate of infection was slower than viruses generated in the subtype B backbone; iii) they did not produce clear CPE in MT4 cells; and iv) drug resistance profiles generated in both backbones were very similar, including re-sensitizing effects like M184V on AZT. PMID:21629677

Nauwelaers, David; Van Houtte, Margriet; Winters, Bart; Steegen, Kim; Van Baelen, Kurt; Chi, Ellen; Zhou, Mimi; Steiner, Derek; Bonesteel, Rachelle; Aston, Colin; Stuyver, Lieven J.

2011-01-01

187

Detection of induced mutations in CaFAD2 genes by next-generation sequencing leading to the production of improved oil composition in Crambe abyssinica.  

PubMed

Crambe abyssinica is a hexaploid oil crop for industrial applications. An increase of erucic acid (C22:1) and reduction of polyunsaturated fatty acid (PUFA) contents in crambe oil is a valuable improvement. An increase in oleic acid (C18:1), a reduction in PUFA and possibly an increase in C22:1 can be obtained by down-regulating the expression of fatty acid desaturase2 genes (CaFAD2), which code for the enzyme that converts C18:1 into C18:2. We conducted EMS-mutagenesis in crambe, followed by Illumina sequencing, to screen mutations in three expressed CaFAD2 genes. Two novel analysis strategies were used to detect mutation sites. In the first strategy, mutation detection targeted specific sequence motifs. In the second strategy, every nucleotide position in a CaFAD2 fragment was tested for the presence of mutations. Seventeen novel mutations were detected in 1100 one-dimensional pools (11 000 individuals) in three expressed CaFAD2 genes, including non-sense mutations and mis-sense mutations in CaFAD2-C1, -C2 and -C3. The homozygous non-sense mutants for CaFAD2-C3 resulted in a 25% higher content of C18:1 and 25% lower content of PUFA compared to the wild type. The mis-sense mutations only led to small changes in oil composition. Concluding, targeted mutation detection using NGS in a polyploid was successfully applied and it was found that a non-sense mutation in even a single CaFAD2 gene can lead to changes in crambe oil composition. Stacking the mutations in different CaFAD2 may gain additional changes in C18:1 and PUFA contents. PMID:25393152

Cheng, Jihua; Salentijn, Elma M J; Huang, Bangquan; Denneboom, Christel; Qi, Weicong; Dechesne, Annemarie C; Krens, Frans A; Visser, Richard G F; van Loo, Eibertus N

2014-11-13

188

Sequence analysis of styrenic copolymers by tandem mass spectrometry.  

PubMed

Styrene and smaller molar amounts of either m-dimethylsilylstyrene (m-DMSS) or p-dimethylsilylstyrene (p-DMSS) were copolymerized under living anionic polymerization conditions, and the compositions, architectures, and sequences of the resulting copolymers were characterized by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and tandem mass spectrometry (MS(2)). MS analysis revealed that linear copolymer chains containing phenyl-Si(CH3)2H pendants were the major product for both DMSS comonomers. In addition, two-armed architectures with phenyl-Si(CH3)2-benzyl branches were detected as minor products. The comonomer sequence in the linear chains was established by MS(2) experiments on lithiated oligomers, based on the DMSS content of fragments generated by backbone C-C bond scissions and with the help of reference MS(2) spectra obtained from a polystyrene homopolymer and polystyrene end-capped with a p-DMSS block. The MS(2) data provided conclusive evidence that copolymerization of styrene/DMSS mixtures leads to chains with a rather random distribution of the silylated comonomer when m-DMSS is used, but to chains with tapered block structures, with the silylated units near the initiator, when p-DMSS is used. Hence, MS(2) fragmentation patterns permit not only differentiation of the sequences generated in the synthesis, but also the determination of specific comonomer locations along the polymer chain. PMID:25181590

Yol, Aleer M; Janoski, Jonathan; Quirk, Roderic P; Wesdemiotis, Chrys

2014-10-01

189

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition.  

PubMed

The ?(54) promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the ?(54) promoters. Here, a predictor called 'iPro54-PseKNC' was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called 'pseudo k-tuple nucleotide composition', which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the ?(54) promoters. PMID:25361964

Lin, Hao; Deng, En-Ze; Ding, Hui; Chen, Wei; Chou, Kuo-Chen

2014-12-01

190

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition  

PubMed Central

The ?54 promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the ?54 promoters. Here, a predictor called ‘iPro54-PseKNC’ was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called ‘pseudo k-tuple nucleotide composition’, which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the ?54 promoters. PMID:25361964

Lin, Hao; Deng, En-Ze; Ding, Hui; Chen, Wei; Chou, Kuo-Chen

2014-01-01

191

Concordance of HIV Type 1 Tropism Phenotype to Predictions Using Web-Based Analysis of V3 Sequences: Composite Algorithms May Be Needed to Properly Assess Viral Tropism  

PubMed Central

Abstract Genotypic prediction of HIV-1 tropism has been considered a practical surrogate for phenotypic tests and recently an European Consensus has set up recommendations for its use in clinical practice. Twenty-five antiretroviral-experienced patients, all heavily treated cases with a median of 16 years of antiretroviral therapy, had viral tropism determined by the Trofile assay and predicted by HIV-1 sequencing of partial env, followed by interpretation using web-based tools. Trofile determined 17/24 (71%) as X4 tropic or dual/mixed viruses, with one nonreportable result. The use of European consensus recommendations for single sequences (geno2pheno false-positive rates 20% cutoff) would lead to 4/24 (16.7%) misclassifications, whereas a composite algorithm misclassified 1/24 (4%). The use of the geno2pheno clinical option using CD4 T cell counts at collection was useful in resolving some discrepancies. Applying the European recommendations followed by additional web-based tools for cases around the recommended cutoff would resolve most misclassifications. PMID:21919801

Cabral, Gabriela Bastos; Ferreira, João Leandro de Paula; Coelho, Luana Portes Osório; Fonsi, Mylva; Estevam, Denise Lotufo; Cavalcanti, Jaqueline Souza

2012-01-01

192

Concordance of HIV type 1 tropism phenotype to predictions using web-based analysis of V3 sequences: composite algorithms may be needed to properly assess viral tropism.  

PubMed

Genotypic prediction of HIV-1 tropism has been considered a practical surrogate for phenotypic tests and recently an European Consensus has set up recommendations for its use in clinical practice. Twenty-five antiretroviral-experienced patients, all heavily treated cases with a median of 16 years of antiretroviral therapy, had viral tropism determined by the Trofile assay and predicted by HIV-1 sequencing of partial env, followed by interpretation using web-based tools. Trofile determined 17/24 (71%) as X4 tropic or dual/mixed viruses, with one nonreportable result. The use of European consensus recommendations for single sequences (geno2pheno false-positive rates 20% cutoff) would lead to 4/24 (16.7%) misclassifications, whereas a composite algorithm misclassified 1/24 (4%). The use of the geno2pheno clinical option using CD4 T cell counts at collection was useful in resolving some discrepancies. Applying the European recommendations followed by additional web-based tools for cases around the recommended cutoff would resolve most misclassifications. PMID:21919801

Cabral, Gabriela Bastos; Ferreira, João Leandro de Paula; Coelho, Luana Portes Osório; Fonsi, Mylva; Estevam, Denise Lotufo; Cavalcanti, Jaqueline Souza; Brígido, Luis Fernando de Macedo

2012-07-01

193

In a changing environment, network backbone upgrades emerge as a wise investment.  

PubMed

The numbers, locations and needs of users change constantly, but they'll always want more bandwidth. Many experts say that upgrading to higher-speed backbones seems to be the smart investment for unsettled times. PMID:10167513

Cupito, M C

1997-05-01

194

RNA Structure and Function 485 RNA backbone rotamers finding your way in  

E-print Network

University, Durham, NC 27710-3711, U.S.A. Abstract Despite the importance of local structural detail for nucleic acid bases: the backbone has a high number of degrees of freedom, frequently underdetermined

Richardson, David

195

Internet Traffic Measurements over the Spanish R&D IP\\/ATM Network Backbone  

Microsoft Academic Search

Abstract The increasing adoption of ATM technology in the main Internet backbones,is introducing new factors of complexity in the network dimensioning, management, and operation fields. On the one hand, the behavior of the IP\\/ATM protocol stack is still not well understood. On the other hand, the aggregated traffic supported by high-speed Internet backbones responds to complex patterns which are highly

M. Alvarez-Campana; A. Azcorra; J. Berrocal; J. R. Pérez; Area de Ingeniería Telemática

196

'Genome order index' should not be used for defining compositional constraints in nucleotide sequences - a case study of the Z-curve  

PubMed Central

Background The Z-curve is a three dimensional representation of DNA sequences proposed over a decade ago and has been extensively applied to sequence segmentation, horizontal gene transfer detection, and sequence analysis. Based on the Z-curve, a "genome order index," was proposed, which is defined as S = a2+ c2+t2+g2, where a, c, t, and g are the nucleotide frequencies of A, C, T, and G, respectively. This index was found to be smaller than 1/3 for almost all tested genomes, which was taken as support for the existence of a constraint on genome composition. A geometric explanation for this constraint has been suggested. Each genome was represented by a point P whose distance from the four faces of a regular tetrahedron was given by the frequencies a, c, t, and g. They claimed that an inscribed sphere of radius r = 1/ contains almost all points corresponding to various genomes, implying that S composition. Moreover, S can be easily computed from the Gini-Simpson index and be directly derived from entropy and is redundant. Overall, the Z-curve and S are over-complicated measures to GC content and Shannon H index, respectively. Reviewers This article was reviewed by Claus Wilke, Joel Bader, Marek Kimmel and Uladzislau Hryshkevich (nominated by Itai Yanai). PMID:20158921

2010-01-01

197

In search of true reads: A classification approach to next generation sequencing data selection  

Microsoft Academic Search

Next generation sequencing (NGS) technology has increasingly become the backbone of transcriptomics analysis, but sequencer error causes biases in the read counts. In this paper we establish a framework for predicting true sequences from NGS data. We formulate this task as a classification problem. We define several features, such as log likelihood ratio of estimated true counts, error probability and

Edward Wijaya; J.-F. Pessiot; M. C. Frith; W. Fujibuchi; K. Asai; P. Horton

2010-01-01

198

Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass (Lolium perenne (L.)).  

PubMed

Perennial ryegrass (Lolium perenne L.) is the most important forage crop in temperate livestock agriculture. Its nutritional quality has significant impact on the quality of meat and milk for human consumption. Evidence suggests that higher energy content in forage can assist in reducing greenhouse gas emissions from ruminants. Increasing the fatty acid content (especially ?-linolenic acid, an omega-3 fatty acid) may thus contribute to better forage, but little is known about the genetic basis of variation for this trait. To this end, quantitative trait loci (QTLs) were identified associated with major fatty acid content in perennial ryegrass using a population derived from a cross between the heterozygous and outbreeding high-sugar grass variety AberMagic and an older variety, Aurora. A genetic map with 434 restriction-associated DNA (RAD) and SSR markers was generated. Significant QTLs for the content of palmitic (C16:0) on linkage groups (LGs) 2 and 7; stearic (C18:0) on LGs 3, 4 and 7; linoleic (C18:2n-6) on LGs 2 and 5; and ?-linolenic acids (C18:3n-3) on LG 1 were identified. Two candidate genes (a lipase and a beta-ketoacyl CoA synthase), both associated with C16:0, and separately with C18:2n-6 and C18:0 contents, were identified. The physical positions of these genes in rice and their genetic positions in perennial ryegrass were consistent with established syntenic relationships between these two species. Validation of these associations is required, but the utility of RAD markers for rapid generation of genetic maps and QTL analysis has been demonstrated for fatty acid composition in a global forage crop. PMID:23331642

Hegarty, Matthew; Yadav, Rattan; Lee, Michael; Armstead, Ian; Sanderson, Ruth; Scollan, Nigel; Powell, Wayne; Skøt, Leif

2013-06-01

199

A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits  

Microsoft Academic Search

BACKGROUND: A number of different quantitative trait loci (QTL) for various phenotypic traits, including milk production, functional, and conformation traits in dairy cattle as well as growth and body composition traits in meat cattle, have been mapped consistently in the middle region of bovine chromosome 6 (BTA6). Dense genetic and physical maps and, ultimately, a fully annotated genome sequence as

Rosemarie Weikard; Tom Goldammer; Pascal Laurent; James E Womack; Christa Kuehn

2006-01-01

200

ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction  

E-print Network

) histogram of Y from B. doi:10.1371/journal.pone.0003400.g002 Torsion Angle Prediction PLoS ONE | www.plosone.org 3 October 2008 | Volume 3 | Issue 10 | e3400 Y ~ {0:8z rand, 0ƒ X v 5 {0:2z rand, 5ƒ X v 15 0:8z rand, 15ƒ X v 26 0:2z rand, 26ƒ X v 30 8... >>>: , ð3Þ where rand is a random number uniformly distributed in [20.15, 0.15]. In Figure 2B, the Y values are generated with random fluctuations around two sine waves, i.e. Y ~ sin (X )z rand, 0ƒ X v 15 sin (2X )z rand, 15ƒ X v30 #2; , ð4Þ where rand...

Wu, Sitao; Zhang, Yang

2008-10-15

201

Solution rheology of hydrophobically modified associative polymers: Effects of backbone composition  

E-print Network

of applications including cosmetic and personal care products, paints, paper coating, and anti-icing fluids Company, UCAR Emulsion Systems, 410 Gregson Drive, Cary, North Carolina 27511 Alan E. Tonelli Fiber

Khan, Saad A.

202

Acute Effects of TiO2 Nanomaterials on the Viability and Taxonomic Composition of Aquatic Bacterial Communities Assessed via High-Throughput Screening and Next Generation Sequencing  

PubMed Central

The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of complex microbial communities. In this study toxicity screening via a HTS platform was used in combination with next generation sequencing (NGS) to assess responses of bacterial communities from two aquatic habitats, Lake Michigan (LM) and the Chicago River (CR), to short-term exposure in their native waters to several commercial TiO2 nanomaterials under simulated solar irradiation. Results demonstrate that bacterial communities from LM and CR differed in their sensitivity to nano-TiO2, with the community from CR being more resistant. NGS analysis revealed that the composition of the bacterial communities from LM and CR were significantly altered by exposure to nano-TiO2, including decreases in overall bacterial diversity, decreases in the relative abundance of Actinomycetales, Sphingobacteriales, Limnohabitans, and Flavobacterium, and a significant increase in Limnobacter. These results suggest that the release of nano-TiO2 to the environment has the potential to alter the composition of aquatic bacterial communities, which could have implications for the stability and function of aquatic ecosystems. The novel combination of HTS and NGS described in this study represents a major advance over current methods for assessing ENM ecotoxicity because the relative toxicities of multiple ENMs to thousands of naturally occurring bacterial species can be assessed simultaneously under environmentally relevant conditions. PMID:25162615

Binh, Chu Thi Thanh; Tong, Tiezheng; Gaillard, Jean-François; Gray, Kimberly A.; Kelly, John J.

2014-01-01

203

The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog  

PubMed Central

Background Comparison of experimentally determined mesophilic and thermophilic homologous protein structures is an important tool for understanding the mechanisms that contribute to thermal stability. Of particular interest are pairs of homologous structures that are structurally very similar, but differ significantly in thermal stability. Results We report the X-ray crystal structure of a Thermoanaerobacter tengcongensis ribose binding protein (tteRBP) determined to 1.9 Å resolution. We find that tteRBP is significantly more stable (appTm value ~102°C) than the mesophilic Escherichia coli ribose binding protein (ecRBP) (appTm value ~56°C). The tteRBP has essentially the identical backbone conformation (0.41 Å RMSD of 235/271 C? positions and 0.65 Å RMSD of 270/271 C? positions) as ecRBP. Classification of the amino acid substitutions as a function of structure therefore allows the identification of amino acids which potentially contribute to the observed thermal stability of tteRBP in the absence of large structural heterogeneities. Conclusion The near identity of backbone structures of this pair of proteins entails that the significant differences in their thermal stabilities are encoded exclusively by the identity of the amino acid side-chains. Furthermore, the degree of sequence divergence is strongly correlated with structure; with a high degree of conservation in the core progressing to increased diversity in the boundary and surface regions. Different factors that may possibly contribute to thermal stability appear to be differentially encoded in each of these regions of the protein. The tteRBP/ecRBP pair therefore offers an opportunity to dissect contributions to thermal stability by side-chains alone in the absence of large structural differences. PMID:18373848

Cuneo, Matthew J; Tian, Yaji; Allert, Malin; Hellinga, Homme W

2008-01-01

204

Subgraph “Backbone” Analysis of Dynamic Brain Networks during Consciousness and Anesthesia  

PubMed Central

General anesthesia significantly alters brain network connectivity. Graph-theoretical analysis has been used extensively to study static brain networks but may be limited in the study of rapidly changing brain connectivity during induction of or recovery from general anesthesia. Here we introduce a novel method to study the temporal evolution of network modules in the brain. We recorded multichannel electroencephalograms (EEG) from 18 surgical patients who underwent general anesthesia with either propofol (n?=?9) or sevoflurane (n?=?9). Time series data were used to reconstruct networks; each electroencephalographic channel was defined as a node and correlated activity between the channels was defined as a link. We analyzed the frequency of subgraphs in the network with a defined number of links; subgraphs with a high probability of occurrence were deemed network “backbones.” We analyzed the behavior of network backbones across consciousness, anesthetic induction, anesthetic maintenance, and two points of recovery. Constitutive, variable and state-specific backbones were identified across anesthetic state transitions. Brain networks derived from neurophysiologic data can be deconstructed into network backbones that change rapidly across states of consciousness. This technique enabled a granular description of network evolution over time. The concept of network backbones may facilitate graph-theoretical analysis of dynamically changing networks. PMID:23967131

Shin, Jeongkyu; Mashour, George A.; Ku, Seungwoo; Kim, Seunghwan; Lee, Uncheol

2013-01-01

205

Subgraph "backbone" analysis of dynamic brain networks during consciousness and anesthesia.  

PubMed

General anesthesia significantly alters brain network connectivity. Graph-theoretical analysis has been used extensively to study static brain networks but may be limited in the study of rapidly changing brain connectivity during induction of or recovery from general anesthesia. Here we introduce a novel method to study the temporal evolution of network modules in the brain. We recorded multichannel electroencephalograms (EEG) from 18 surgical patients who underwent general anesthesia with either propofol (n?=?9) or sevoflurane (n?=?9). Time series data were used to reconstruct networks; each electroencephalographic channel was defined as a node and correlated activity between the channels was defined as a link. We analyzed the frequency of subgraphs in the network with a defined number of links; subgraphs with a high probability of occurrence were deemed network "backbones." We analyzed the behavior of network backbones across consciousness, anesthetic induction, anesthetic maintenance, and two points of recovery. Constitutive, variable and state-specific backbones were identified across anesthetic state transitions. Brain networks derived from neurophysiologic data can be deconstructed into network backbones that change rapidly across states of consciousness. This technique enabled a granular description of network evolution over time. The concept of network backbones may facilitate graph-theoretical analysis of dynamically changing networks. PMID:23967131

Shin, Jeongkyu; Mashour, George A; Ku, Seungwoo; Kim, Seunghwan; Lee, Uncheol

2013-01-01

206

Understanding GFP posttranslational chemistry: structures of designed variants that achieve backbone fragmentation, hydrolysis, and decarboxylation.  

PubMed

The green fluorescent protein (GFP) creates a fluorophore out of three sequential amino acids by promoting spontaneous posttranslational modifications. Here, we use high-resolution crystallography to characterize GFP variants that not only undergo peptide backbone cyclization but additional denaturation-induced peptide backbone fragmentation, native peptide hydrolysis, and decarboxylation reactions. Our analyses indicate that architectural features that favor GFP peptide cyclization also drive peptide hydrolysis. These results are relevant for the maturation pathways of GFP homologues, such as the kindling fluorescent protein and the Kaede protein, which use backbone cleavage to red-shift the spectral properties of their chromophores. We further propose a photochemical mechanism for the decarboxylation reaction, supporting a role for the GFP protein environment in facilitating radical formation and one-electron chemistry, which may be important in activating oxygen for the oxidation step of chromophore biosynthesis. Together, our results characterize GFP posttranslational modification chemistry with implications for the energetic landscape of backbone cyclization and subsequent reactions, and for the rational design of predetermined spontaneous backbone cyclization and cleavage reactions. PMID:16594705

Barondeau, David P; Kassmann, Carey J; Tainer, John A; Getzoff, Elizabeth D

2006-04-12

207

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking  

PubMed Central

Protein–protein docking algorithms aim to predict the structure of a complex given the atomic structures of the proteins that assemble it. The docking procedure usually consists of two main steps: docking candidate generation and their refinement. The refinement stage aims to improve the accuracy of the candidate solutions and to identify near-native solutions among them. During protein–protein interaction, both side chains and backbone change their conformation. Refinement methods should model these conformational changes in order to obtain a more accurate model of the complex. Handling protein backbone flexibility is a major challenge for docking methodologies, since backbone flexibility adds a huge number of degrees of freedom to the search space. FiberDock is the first docking refinement web server, which accounts for both backbone and side-chain flexibility. Given a set of up to 100 potential docking candidates, FiberDock models the backbone and side-chain movements that occur during the interaction, refines the structures and scores them according to an energy function. The FiberDock web server is free and available with no login requirement at http://bioinfo3d.cs.tau.ac.il/FiberDock/. PMID:20460459

Mashiach, Efrat; Nussinov, Ruth; Wolfson, Haim J.

2010-01-01

208

Backbone dipoles generate positive potentials in all proteins: origins and implications of the effect.  

PubMed Central

Asymmetry in packing the peptide amide dipole results in larger positive than negative regions in proteins of all folding motifs. The average side chain potential in 305 proteins is 109 +/- 30 mV (2. 5 +/- 0.7 kcal/mol/e). Because the backbone has zero net charge, the non-zero potential is unexpected. The larger oxygen at the negative and smaller proton at the positive end of the amide dipole yield positive potentials because: 1) at allowed phi and psi angles residues come off the backbone into the positive end of their own amide dipole, avoiding the large oxygen; and 2) amide dipoles with their carbonyl oxygen surface exposed and amine proton buried make the protein interior more positive. Twice as many amides have their oxygens exposed than their amine protons. The distribution of acidic and basic residues shows the importance of the bias toward positive backbone potentials. Thirty percent of the Asp, Glu, Lys, and Arg are buried. Sixty percent of buried residues are acids, only 40% bases. The positive backbone potential stabilizes ionization of 20% of the acids by >3 pH units (-4.1 kcal/mol). Only 6.5% of the bases are equivalently stabilized by negative regions. The backbone stabilizes bound anions such as phosphates and rarely stabilizes bound cations. PMID:10692303

Gunner, M R; Saleh, M A; Cross, E; ud-Doula, A; Wise, M

2000-01-01

209

Lactobacillus rhamnosus Accelerates Zebrafish Backbone Calcification and Gonadal Differentiation through Effects on the GnRH and IGF Systems  

PubMed Central

Endogenous microbiota play essential roles in the host’s immune system, physiology, reproduction and nutrient metabolism. We hypothesized that a continuous administration of an exogenous probiotic might also influence the host’s development. Thus, we treated zebrafish from birth to sexual maturation (2-months treatment) with Lactobacillus rhamnosus, a probiotic species intended for human use. We monitored for the presence of L. rhamnosus during the entire treatment. Zebrafish at 6 days post fertilization (dpf) exhibited elevated gene expression levels for Insulin-like growth factors -I and -II, Peroxisome proliferator activated receptors -? and -?, VDR-? and RAR-? when compared to untreated-10 days old zebrafish. Using a gonadotropin-releasing hormone 3 GFP transgenic zebrafish (GnRH3-GFP), higher GnRH3 expression was found at 6, 8 and 10 dpf upon L. rhamnosus treatment. The same larvae exhibited earlier backbone calcification and gonad maturation. Noteworthy in the gonad development was the presence of first testes differentiation at 3 weeks post fertilization in the treated zebrafish population -which normally occurs at 8 weeks- and a dramatic sex ratio modulation (93% females, 7% males in control vs. 55% females, 45% males in the treated group). We infer that administration of L. rhamnosus stimulated the IGF system, leading to a faster backbone calcification. Moreover we hypothesize a role for administration of L. rhamnosus on GnRH3 modulation during early larval development, which in turn affects gonadal development and sex differentiation. These findings suggest a significant role of the microbiota composition on the host organism development profile and open new perspectives in the study of probiotics usage and application. PMID:23029107

Avella, Matteo A.; Place, Allen; Du, Shao-Jun; Williams, Ernest; Silvi, Stefania; Zohar, Yonathan; Carnevali, Oliana

2012-01-01

210

Persistence and Epidemic Propagation of a Pseudomonas aeruginosa Sequence Type 235 Clone Harboring an IS26 Composite Transposon Carrying the blaIMP-1 Integron in Hiroshima, Japan, 2005 to 2012.  

PubMed

A 9-year surveillance for multidrug-resistant (MDR) Pseudomonas aeruginosa in the Hiroshima region showed that the number of isolates harboring the metallo-?-lactamase gene blaIMP-1 abruptly increased after 2004, recorded the highest peak in 2006, and showed a tendency to decline afterwards, indicating a history of an epidemic. PCR mapping of the variable regions of the integrons showed that this epidemic was caused by the clonal persistence and propagation of an MDR P. aeruginosa strain harboring the blaIMP-1 gene and an aminoglycoside 6'-N-acetyltransferase gene, aac(6')-Iae in a class I integron (In113), whose integrase gene intl1 was disrupted by an IS26 insertion. Sequence analysis of the representative strain PA058447 resistance element containing the In113-derived gene cassette array showed that the element forms an IS26 transposon embedded in the chromosome. It has a Tn21 backbone and is composed of two segments sandwiched by three IS26s. In Japan, clonal nationwide expansion of an MDR P. aeruginosa NCGM2.S1 harboring chromosomally encoded In113 with intact intl1 is reported. Multilocus sequence typing and genomic comparison strongly suggest that PA058447 and NCGM2.S1 belong to the same clonal lineage. Moreover, the structures of the resistance element in the two strains are very similar, but the sites of insertion into the chromosome are different. Based on tagging information of the IS26 present in both resistance elements, we suggest that the MDR P. aeruginosa clone causing the epidemic in Hiroshima for the past 9 years originated from a common ancestor genome of PA058447 and NCGM2.S1 through an IS26 insertion into intl1 of In113 and through IS26-mediated genomic rearrangements. PMID:25712351

Shimizu, Wataru; Kayama, Shizuo; Kouda, Shuntaro; Ogura, Yoshitoshi; Kobayashi, Kanao; Shigemoto, Norifumi; Shimada, Norimitsu; Yano, Raita; Hisatsune, Junzo; Kato, Fuminori; Hayashi, Tetsuya; Sueda, Taijiro; Ohge, Hiroki; Sugai, Motoyuki

2015-05-01

211

Nonparametric Combinatorial Sequence Models  

NASA Astrophysics Data System (ADS)

This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This paper presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three sequence datasets which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution induced by the prior. By integrating out the posterior our method compares favorably to leading binding predictors.

Wauthier, Fabian L.; Jordan, Michael I.; Jojic, Nebojsa

212

Anion-Conducting Polymer, Composition, and Membrane  

DOEpatents

Anion-conducing polymers and membranes with enhanced stability to aqueous alkali include a polymer backbone with attached sulfonium, phosphazenium, phosphazene, and guanidinium residues. Compositions also with enhanced stability to aqueous alkali include a support embedded with sulfonium, phosphazenium, and guanidinium salts.

Pivovar, Bryan S. (Los Alamos, NM); Thorn, David L. (Los Alamos, NM)

2008-10-21

213

Anion-conducting polymer, composition, and membrane  

DOEpatents

Anion-conducing polymers and membranes with enhanced stability to aqueous alkali include a polymer backbone with attached sulfonium, phosphazenium, phosphazene, and guanidinium residues. Compositions also with enhanced stability to aqueous alkali include a support embedded with sulfonium, phosphazenium, and guanidinium salts.

Pivovar, Bryan S. (Los Alamos, NM); Thorn, David L. (Los Alamos, NM)

2010-12-07

214

Anion-conducting polymer, composition, and membrane  

DOEpatents

Anion-conducing polymers and membranes with enhanced stability to aqueous alkali include a polymer backbone with attached sulfonium, phosphazenium, phosphazene, and guanidinium residues. Compositions also with enhanced stability to aqueous alkali include a support embedded with sulfonium, phosphazenium, and guanidinium salts.

Pivovar, Bryan S. (Los Alamos, NM); Thorn, David L. (Los Alamos, NM)

2011-11-22

215

Remote Enantioselection Transmitted by an Achiral Peptide Nucleic Acid Backbone  

NASA Technical Reports Server (NTRS)

short homochiral segment of DNA into a PNA helix could have guaranteed that the next short segment of DNA to be incorporated would have the same handedness as the first. Once two segments of the same handedness were present, the probability that a third segment would have the same handedness would increase, and so on. Evolution could then slowly dilute out the PNA part. This scenario would ultimately allow the formation of a chiral oligonucleotide by processes that are largely resistant to enantiomeric crossinhibition. It is important to note that the ligation of homochiral dinucleotides on a nucleic acid template would probably be at least as enantiospecific as the reaction that we have studied. The disadvantage of using chiral monomers as components of a replicating system arises from the difficulty of generating a first long homochiral template from a racemic mixture of monomers, although results of experiments designed to overcome this difficulty by employing homochiral tetramers have been reported.l l The probability of obtaining a homochiral n-mer from achiral substrates is approximately 1P-I if the nontemplate-directed extension of the primer is not enantioselective. Hence, it would be very hard to get started with a homochiral 40-mer, for example. No such difficulty exists in a scenario that originates with an achiral genetic material and in which the incorporation of very few chiral monomers in this achiral background gradually progresses towards homochirality. It seems possible that some PNA sequences could act as catalysts, analogous to ribozymes, even though PNA lacks clear metal binding sites. Although such catalysts could not be enantioselective, the incorporation of as few as two chiral nucleotides could then impose chiral specificity on the system. Furthermore, such patch chimeras could help to bridge the gap in catalytic potential between PNA and RNA, while guaranteeing enantioselectivity.

Kozlov, Igor A.; Orgel, Leslie E.; Nielsen, Peter E.

2000-01-01

216

A Polynomial-Time Algorithm for de novo Protein Backbone Structure Determination from NMR Data  

E-print Network

-hard [53], and rigorous approaches to structure determination based on solving this problemA Polynomial-Time Algorithm for de novo Protein Backbone Structure Determination from NMR Data algorithmic formulations of this problem focused on using local distance restraints from NMR (e.g., nuclear

Donald, Bruce Randall

217

EUCLIDEAN NETWORKS WITH A BACKBONE AND A LIMIT THEOREM FOR MINIMUM SPANNING CATERPILLARS  

E-print Network

EUCLIDEAN NETWORKS WITH A BACKBONE AND A LIMIT THEOREM FOR MINIMUM SPANNING CATERPILLARS PETAR JEVTI´C AND J. MICHAEL STEELE Abstract. A caterpillar network (or graph) G is a tree with the property caterpillars (MSCs) where the vertices are points in the Euclidean plane and the costs of the path edges

Steele, J. Michael

218

A mechanism for admission control of the input traffic to the UMTS backbone network  

Microsoft Academic Search

As the demand for multimedia applications on the Internet grows, it is hoped that UMTS backbones supports different applications with QoS, mainly those that are sensitive to delay and jitter. In this paper, we propose a mechanism that makes the admission control of the ingress edge routers. Such a mechanism provides a differentiated treatment to the traffic of several flows

P. D. de Alecrim; P. R. Guardieiro

2005-01-01

219

Graduate Education in Kinesiology: Are We Part of "America's Backbone for Competitiveness and Innovation"?  

ERIC Educational Resources Information Center

Graduate education in the United States has been identified as being the backbone of American competitiveness and innovation in a recent report by the Council of Graduate Schools. The report provides a framework for examining the role of graduate education in partnership with business and government to advance an action agenda for achieving…

DePauw, Karen P.

2008-01-01

220

Energy Sensing and Monitoring Framework with an Integrated Communication Backbone in Energy Efficient Intelligent Buildings  

E-print Network

Efficient Intelligent Buildings Jianli Pan1, 3, a , Shanzhi Chen2, b , Raj Jain3, c , Subharthi Paul3, d 1 framework with integrated communication backbone in the intelligent building environments. Specifically in the intelligent buildings to realize the goals of coordination, integration, and energy efficiency. Also, we

Jain, Raj

221

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.  

PubMed

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH ?backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. Proteins 2015; 83:922-930. © 2015 Wiley Periodicals, Inc. PMID:25739366

Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

2015-05-01

222

Distributed Mobile Disk Cover A Building Block for Mobile Backbone Networks  

E-print Network

type includes mobile nodes with superior communication, mobility, and computation capabilities as well-wide communication. Fig. 1 illustrates an example of the architecture of a Mobile Backbone Network. The set of MBNs has to be placed and mobilized such that (i) every RN can directly communicate MBN RN Fig. 1. A Mobile

Zussman, Gil

223

A Proposed Architecture for the GENI Backbone Platform Jonathan S. Turner  

E-print Network

A Proposed Architecture for the GENI Backbone Platform Jonathan S. Turner Applied Research Laboratory Washington University in St. Louis jon.turner@wustl.edu Abstract. The GENI Project (Global on a sufficient scale to enable realistic evaluation. One key component of the GENI system will be the GENI

Turner, Jonathan S.

224

Backbone Dipoles Generate Positive Potentials in all Proteins: Origins and Implications of the Effect  

E-print Network

40% bases. The positive backbone potential stabilizes ionization of 20% of the acids by 3 pH units stabilizes bound anions such as phosphates and rarely stabilizes bound cations. INTRODUCTION The amide group and CAO groups in the protein interior find hydrogen bonds to replace those made to water in the unfolded

Gunner, Marilyn

225

The BVID Allocation Problem in 802.1Qay Provider Backbone Bridged Traffic Engineered Networks  

Microsoft Academic Search

Carrier Ethernet has rapidly advanced itself to become an important technology for metro transport. PBB-TE or Provider Backbone Bridging -Traffic Engineering is one of the mechanisms being considered for the deployment of Carrier Ethernet. PBB-TE relies on the assignment of a network- specific VLAN tag, called the BVID, which is further dependent on customer and service provider VLAN tags, service

Deval Bhamare; Ashutosh Upadhyaya; Saurabh Mehta; Ashwin Kshirasagar; Ashwin Gumaste

2011-01-01

226

A Formula for the Intersection Angle of Backbone Arcs with the Bounding Circle for  

E-print Network

creates Circle Limit III. · 1979: In a Leonardo article, Coxeter uses hyperbolic trigonometry to calculate trigonometry to determine that the angle that the backbone arcs make with the bounding circle is given by: cos, using hyperbolic trigonometry to derive the more general formula that applied to (p,3,3) patterns: cos

Dunham, Doug

227

A facile route to flavone and neoflavone backbones via a regioselective palladium catalyzed oxidative Heck reaction.  

PubMed

A straightforward and atom-economical base-free palladium-catalyzed regioselective direct arylation of coumarins and chromenones is devised. This protocol is compatible with a wide variety of electron-donating and -withdrawing substituents and allows construction of various biologically important flavone and neoflavone backbones. PMID:22318701

Khoobi, Mehdi; Alipour, Masoumeh; Zarei, Samaneh; Jafarpour, Farnaz; Shafiee, Abbas

2012-03-21

228

Backbone Ordering in Amphiphile Monolayers Jeremy Schofield and Stuart A. Rice,  

E-print Network

Backbone Ordering in Amphiphile Monolayers Jeremy Schofield and Stuart A. Rice, Department. An alternative to the Landau theory of the phase transitions in amphiphile monolayers, namely density functional­chain amphiphile monolayers, correctly predicting the direction, magnitude and the dependence on surface area per

Schofield, Jeremy

229

TRACKING ELEPHANT FLOWS IN INTERNET BACKBONE TRAFFIC WITH AN FPGA-BASED CACHE  

E-print Network

TRACKING ELEPHANT FLOWS IN INTERNET BACKBONE TRAFFIC WITH AN FPGA-BASED CACHE Martin Zadnik an FPGA-friendly approach to track- ing elephant flows in network traffic. Our approach, Single Step elephant flows: con- servatively promoting potential elephants and evicting low- rate flows in LRU manner

Haddadi, Hamed

230

Understanding VoIP from Backbone Measurements Robert Birke, Marco Mellia, Michele Petracca  

E-print Network

Understanding VoIP from Backbone Measurements Robert Birke, Marco Mellia, Michele Petracca´el´ecom Paris - GET/ENST/INFRES/RMS dario.rossi@enst.fr Abstract-- VoIP has widely been addressed VoIP and high-speed data access to the end-user. Traffic characterization will focus on several

Mellia, Marco

231

Computer simulation of bottle brush polymers with flexible backbone: Good solvent versus Theta solvent conditions  

E-print Network

By Molecular Dynamics simulation of a coarse-grained bead-spring type model for a cylindrical molecular brush with a backbone chain of $N_b$ effective monomers to which with grafting density $\\sigma$ side chains with $N$ effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side chain lengths are in the range $5 \\le N \\le 40$, backbone chain lengths are in the range $50 \\le N_b \\le 200$, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer chains are accessible, $N_b \\le 1027$, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of side chains and the backbone chain and discuss their $N$-dependence in terms of power laws and the associated effective exponents. We show that even at the Theta point the side chains are considerably stretched, their linear dimension depending on the solvent quality only weakly. Effective persistence lengths are extracted both from the orientational correlations and from the backbone end-to-end distance; it is shown that different measures of the persistence length (which would all agree for Gaussian chains) are not mutually consistent with each other, and depend distinctly both on $N_b$ and the solvent quality. A brief discussion of pertinent experiments is given.

Panagiotis E. Theodorakis; Hsiao-Ping Hsu; Wolfgang Paul; Kurt Binder

2011-11-02

232

An Adaptive Broadband Mobile Ad-Hoc Radio Backbone System; DARPA NetCentric Demonstration - Ft. Benning, GA, January 2006  

Microsoft Academic Search

This paper describes a novel autonomously adaptive networked radio system that provides a broadband tactical mobile backbone to enable netcentric warfare. The system was successfully demonstrated to seamlessly interconnect multiple heterogeneous networked radio systems during the DARPA NetCentric (NC) demonstration at Ft. Benning, GA in January 2006, serving as the high availability terrestrial backbone link between dismount units that were

Scott Seidel; Tim Krout; Larry Stotts

2006-01-01

233

Phase behaviour of two-component bottle-brush polymers with flexible backbones under poor solvent conditions  

E-print Network

The phase behaviour of two-component bottle-brush polymers with fully flexible backbones under poor solvent conditions is studied via molecular-dynamics simulations, using a coarse-grained bead-spring model and side chains of up to $N=40$ effective monomers. We consider a symmetric model where side chains of type A and B are grafted alternately onto a flexible backbone. The aim of this study to explore the phase behaviour of two-component bottle-brushes depending on parameters, such as as the grafting density $\\sigma$, the backbone length $N_b$, the side-chain length $N$, and the temperature $T$. Based on a cluster analysis, we identify for our range of parameters the regimes of fully phase separated systems, i.e., A-type side chains form one cluster and B-type chains another, while the interface that separates these two clusters contains the backbone monomers. We find that pearl-necklace or Janus-like structures, which normally occur for bottle-brush polymers with rigid backbones under poor solvent conditions, are fully attributed to the backbone rigidity, and, therefore, such structures are unlikely in the case of bottle brushes with fully flexible backbones. Also, a comparative discussion with earlier work on the phase behaviour of single-component bottle-brush polymers with flexible backbones is performed.

Nikolaos G. Fytas; Panagiotis E. Theodorakis

2014-04-16

234

Backbone and Side-Chain Cleavages in Electron Detachment Dissociation (EDD) Iwona Anusiewicz,, Marek Jasionowski, Piotr Skurski,, and Jack Simons*,  

E-print Network

Backbone and Side-Chain Cleavages in Electron Detachment Dissociation (EDD) Iwona Anusiewicz are computed for the observed CR-C backbone bond cleavage as well as for side-chain loss for a variety of side chains (valine, arginine, glutamic acid, and tyrosine). It is found that CR-C bond cleavage is favored

Simons, Jack

235

Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene Trees  

PubMed Central

Plasmids of the incompatibility group IncP-1 can transfer and replicate in many genera of the Proteobacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. Although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of IncP-1 plasmids. As a consequence, phylogeny estimation based on backbone genes is expected to produce conflicting gene tree topologies. The main goal of this study was therefore to infer the evolutionary history of IncP-1 plasmids in the presence of both vertical and horizontal gene transfer. This was achieved by quantifying the incongruence among gene trees and attributing it to known causes such as 1) phylogenetic uncertainty, 2) coalescent stochasticity, and 3) horizontal inheritance. Topologies of gene trees exhibited more incongruence than could be attributed to phylogenetic uncertainty alone. Species-tree estimation using a Bayesian framework that takes coalescent stochasticity into account was well supported, but it differed slightly from the maximum-likelihood tree estimated by concatenation of backbone genes. After removal of the gene that demonstrated a signal of intergroup recombination, the concatenated tree was congruent with the species-tree estimate, which itself was robust to inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene exchange both within and among IncP-1 subgroups, the backbone genome of these IncP-1 plasmids retains a detectable vertical evolutionary history. PMID:22936717

Sen, Diya; Brown, Celeste J.; Top, Eva M.; Sullivan, Jack

2013-01-01

236

Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees.  

PubMed

Plasmids of the incompatibility group IncP-1 can transfer and replicate in many genera of the Proteobacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. Although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of IncP-1 plasmids. As a consequence, phylogeny estimation based on backbone genes is expected to produce conflicting gene tree topologies. The main goal of this study was therefore to infer the evolutionary history of IncP-1 plasmids in the presence of both vertical and horizontal gene transfer. This was achieved by quantifying the incongruence among gene trees and attributing it to known causes such as 1) phylogenetic uncertainty, 2) coalescent stochasticity, and 3) horizontal inheritance. Topologies of gene trees exhibited more incongruence than could be attributed to phylogenetic uncertainty alone. Species-tree estimation using a Bayesian framework that takes coalescent stochasticity into account was well supported, but it differed slightly from the maximum-likelihood tree estimated by concatenation of backbone genes. After removal of the gene that demonstrated a signal of intergroup recombination, the concatenated tree was congruent with the species-tree estimate, which itself was robust to inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene exchange both within and among IncP-1 subgroups, the backbone genome of these IncP-1 plasmids retains a detectable vertical evolutionary history. PMID:22936717

Sen, Diya; Brown, Celeste J; Top, Eva M; Sullivan, Jack

2013-01-01

237

pH dependence of conformational fluctuations of the protein backbone.  

PubMed

Proton binding equilibria (pK(a) values) of ionizable groups in proteins are exquisitely sensitive to their microenvironments. Apparent pK(a) values measured for individual ionizable residues with NMR spectroscopy are actually population-weighted averages of the pK(a) in different conformational microstates. NMR spectroscopy experiments with staphylococcal nuclease were used to test the hypothesis that pK(a) values of surface Glu and Asp residues are affected by pH-sensitive fluctuations of the backbone between folded and locally unfolded conformations. (15)N spin relaxation studies showed that as the pH decreases from the neutral into the acidic range the amplitudes of backbone fluctuations in the ps-ns timescale increase near carboxylic residues. Hydrogen exchange experiments suggested that backbone conformational fluctuations promoted by decreasing pH also reflect slower local or sub-global unfolding near carboxylic groups. This study has implications for structure-based pKa calculations: (1) The timescale of the backbone's response to ionization events in proteins can range from ps to ms, and even longer; (2) pH-sensitive fluctuations of the backbone can be localized to both the segment the ionizable residue is attached to or the one that occludes the ionizable group; (3) Structural perturbations are not necessarily propagated through Coulomb interactions; instead, local fluctuations appear to be coupled through the co-operativity inherent to elements of secondary structure and to networks of hydrogen bonds. These results are consistent with the idea that local conformational fluctuations and stabilities are important determinants of apparent pK(a) values of ionizable residues in proteins. PMID:25137073

Richman, Daniel E; Majumdar, Ananya; García-Moreno E, Bertrand

2014-11-01

238

Characterization of the binding properties of SIRT2 inhibitors with a N-(3-phenylpropenoyl)-glycine tryptamide backbone.  

PubMed

SIRT2 inhibitors with a N-(3-phenylpropenoyl)-glycine tryptamide backbone were studied. This backbone has been developed in our group, and it is derived from a compound originally found by virtual screening. In addition, compounds with a smaller 3-phenylpropenoic acid tryptamide backbone were also included in the study. Binding modes for the new compounds and the previously reported compounds were analyzed with molecular modelling methods. The approach, which included a combination of molecular dynamics, molecular docking and cluster analysis, showed that certain docking poses were favourable despite the conformational variation in the target protein. The N-(3-phenylpropenoyl)-glycine tryptamide backbone is also a good backbone for SIRT2 inhibitors, and the series of compounds includes several potent SIRT2 inhibitors. PMID:18701307

Kiviranta, Päivi H; Salo, Heikki S; Leppänen, Jukka; Rinne, Valtteri M; Kyrylenko, Sergiy; Kuusisto, Erkki; Suuronen, Tiina; Salminen, Antero; Poso, Antti; Lahtela-Kakkonen, Maija; Wallén, Erik A A

2008-09-01

239

Structural Conservation, Variability, and Immunogenicity of the T6 Backbone Pilin of Serotype M6 Streptococcus pyogenes  

PubMed Central

Group A streptococcus (GAS; Streptococcus pyogenes) is a Gram-positive human pathogen that causes a broad range of diseases ranging from acute pharyngitis to the poststreptococcal sequelae of acute rheumatic fever. GAS pili are highly diverse, long protein polymers that extend from the cell surface. They have multiple roles in infection and are promising candidates for vaccine development. This study describes the structure of the T6 backbone pilin (BP; Lancefield T-antigen) from the important M6 serotype. The structure reveals a modular arrangement of three tandem immunoglobulin-like domains, two with internal isopeptide bonds. The T6 pilin lysine, essential for polymerization, is located in a novel VAKS motif that is structurally homologous to the canonical YPKN pilin lysine in other three- and four-domain Gram-positive pilins. The T6 structure also highlights a conserved pilin core whose surface is decorated with highly variable loops and extensions. Comparison to other Gram-positive BPs shows that many of the largest variable extensions are found in conserved locations. Studies with sera from patients diagnosed with GAS-associated acute rheumatic fever showed that each of the three T6 domains, and the largest of the variable extensions (V8), are targeted by IgG during infection in vivo. Although the GAS BP show large variations in size and sequence, the modular nature of the pilus proteins revealed by the T6 structure may aid the future design of a pilus-based vaccine. PMID:24778112

Moreland, Nicole J.; Loh, Jacelyn M.; Bell, Anita; Atatoa Carr, Polly; Proft, Thomas; Baker, Edward N.

2014-01-01

240

Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus  

PubMed Central

The pilus 2a backbone protein (BP-2a) is one of the most structurally and functionally characterized components of a potential vaccine formulation against Group B Streptococcus. It is characterized by six main immunologically distinct allelic variants, each inducing variant-specific protection. To investigate the molecular determinants driving the variant immunogenic specificity of BP-2a, in terms of single residue contributions, we generated six monoclonal antibodies against a specific protein variant based on their capability to recognize the polymerized pili structure on the bacterial surface. Three mAbs were also able to induce complement-dependent opsonophagocytosis killing of live GBS and target the same linear epitope present in the structurally defined and immunodominant domain D3 of the protein. Molecular docking between the modelled scFv antibody sequences and the BP-2a crystal structure revealed the potential role at the binding interface of some non-conserved antigen residues. Mutagenesis analysis confirmed the necessity of a perfect balance between charges, size and polarity at the binding interface to obtain specific binding of mAbs to the protein antigen for a neutralizing response. PMID:23825940

Nuccitelli, Annalisa; Rinaudo, C. Daniela; Brogioni, Barbara; Cozzi, Roberta; Ferrer-Navarro, Mario; Yero, Daniel; Telford, John L.; Grandi, Guido; Daura, Xavier; Zacharias, Martin; Maione, Domenico

2013-01-01

241

Facile backbone (1H, 15N, 13Ca, and 13C') assignment of 13C/15N-labeled proteins using orthogonal projection planes of HNN and HN(C)N experiments and its automation.  

PubMed

Recently, we introduced an efficient high-throughput protocol for backbone assignment of small folded proteins based on two-dimensional (2D) projections of HN(C)N suite of experiments and its automation [Borkar et al., J. Biomol. NMR 2011, 50(3), 285-297]. This strategy provides complete sequence-specific assignment of backbone ((1)H, (15)N, (13)C(?), and (13)C') resonances in less than a day; thus, it has great implications for high-throughput structural proteomics. However, in cases when such small folded protein exhibits substantial amide (1)H shift degeneracy (typically seen in alpha-helical proteins), the strategy may fail or lead to ambiguities. Another limitation is with respect to the identification of checkpoints from the variants of 2D-hncNH spectrum. For example, a protein with many GG, GA, AA, SS, TS, TT, and TS types of dipeptide stretches along its sequence, thus the identification of NH cross-peak corresponding to second G, A, S, or T becomes difficult. In this backdrop, we present here two improvements to enhance the utility of the proposed high-throughput AUTOmatic Backbone Assignment protocol: (i) use of 2D-hNnH spectrum and its variants that display additional (1)H-(15)N correlations and thus help to resolve ambiguities arising because of amide (1)H shift degeneracy and (ii) optimization of the ?(CN) delay in the 2D-hncNH experiment that, when properly adjusted, is observed to help remove ambiguities in the identification of the checkpoints. These improvements have also been incorporated in the automation program AUTOmatic Backbone Assignment. Finally, the performance of the strategy and the automation has been demonstrated using the chicken SH3 domain protein. PMID:22508472

Kumar, Dinesh; Borkar, Aditi; Hosur, Ramakrishna V

2012-05-01

242

Transcriptome Sequencing and Expression Analysis of Terpenoid Biosynthesis Genes in Litsea cubeba  

PubMed Central

Background Aromatic essential oils extracted from fresh fruits of Litsea cubeba (Lour.) Pers., have diverse medical and economic values. The dominant components in these essential oils are monoterpenes and sesquiterpenes. Understanding the molecular mechanisms of terpenoid biosynthesis is essential for improving the yield and quality of terpenes. However, the 40 available L. cubeba nucleotide sequences in the public databases are insufficient for studying the molecular mechanisms. Thus, high-throughput transcriptome sequencing of L. cubeba is necessary to generate large quantities of transcript sequences for the purpose of gene discovery, especially terpenoid biosynthesis related genes. Results Using Illumina paired-end sequencing, approximately 23.5 million high-quality reads were generated. De novo assembly yielded 68,648 unigenes with an average length of 834 bp. A total of 38,439 (56%) unigenes were annotated for their functions, and 35,732 and 25,806 unigenes could be aligned to the GO and COG database, respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 16,130 unigenes were assigned to 297 KEGG pathways, and 61 unigenes, which contained the mevalonate and 2-C-methyl-D-erythritol 4-phosphate pathways, could be related to terpenoid backbone biosynthesis. Of the 12,963 unigenes, 285 were annotated to the terpenoid pathways using the PlantCyc database. Additionally, 14 terpene synthase genes were identified from the transcriptome. The expression patterns of the 16 genes related to terpenoid biosynthesis were analyzed by RT-qPCR to explore their putative functions. Conclusion RNA sequencing was effective in identifying a large quantity of sequence information. To our knowledge, this study is the first exploration of the L. cubeba transcriptome, and the substantial amount of transcripts obtained will accelerate the understanding of the molecular mechanisms of essential oils biosynthesis. The results may help improve future genetic and genomics studies on the molecular mechanisms behind the chemical composition of essential oils in L. cubeba fruits. PMID:24130803

Han, Xiao-Jiao; Wang, Yang-Dong; Chen, Yi-Cun; Lin, Li-Yuan; Wu, Qing-Ke

2013-01-01

243

Backbone cyclization of a recombinant cystine-knot peptide by engineered Sortase A.  

PubMed

Cyclotides belong to the family of cyclic cystine-knot peptides and have shown promise as scaffolds for protein engineering and pharmacological modulation of cellular protein activity. Cyclotides are characterized by a cystine-knotted topology and a head-to-tail cyclic polypeptide backbone. While they are primarily produced in plants, cyclotides have also been obtained by chemical synthesis. However, there is still a need for methods to generate cyclotides in high yields to near homogeneity. Here, we report a biomimetic approach which utilizes an engineered version of the enzyme Sortase A to catalyze amide backbone cyclization of the recombinant cyclotide MCoTI-II, thereby allowing the efficient production of active homogenous species in high yields. Our results provide proof of concept for using engineered Sortase A to produce cyclic MCoTI-II and should be generally applicable to generating other cyclic cystine-knot peptides. PMID:25448598

Stanger, Karen; Maurer, Till; Kaluarachchi, Harini; Coons, Mary; Franke, Yvonne; Hannoush, Rami N

2014-11-28

244

An experimental teleradiology transmission system using a high-speed ATM backbone network.  

PubMed

We evaluated the performance of an experimental teleradiology system based on a high-speed ATM backbone network. Image acquisition, transmission and the disk-to-display processing times were measured. Computerized tomography (CT) scans printed on 14 inch x 17 inch (36 cm x 43 cm) films were digitized and transferred over the network. The average time for the entire process was 1 min 30 s. Three radiologists interpreted 20 cases. For CT image interpretation, the reading time for one case ranged from 2 to 12 min (mean 6 min 46 s) on a monitor, and from 1 to 3 min (mean 1 min 31 s) with the original film. The ATM backbone network operating at 156 Mbit/s provided sufficient speed for remote consultation. However, further improvements in the operability of the system, especially the image viewing station, are necessary before it will be satisfactory for clinical use. PMID:10824380

Kato, K; Shimamoto, K; Ishigaki, T; Niimi, R; Ishiguchi, T; Mimura, T; Yamauchi, K; Ikeda, M; Iwata, A

2000-01-01

245

The molecular structure of spider dragline silk: Folding and orientation of the protein backbone  

PubMed Central

The design principles of spider dragline silk, nature's high-performance fiber, are still largely unknown, in particular for the noncrystalline glycine-rich domains, which form the bulk of the material. Here we apply two-dimensional solid-state NMR to determine the distribution of the backbone torsion angles (?,?) as well as the orientation of the polypeptide backbone toward the fiber at both the glycine and alanine residues. Instead of an “amorphous matrix,” suggested earlier for the glycine-rich domains, these new data indicate that all domains in dragline silk have a preferred secondary structure and are strongly oriented, with the chains predominantly parallel to the fiber. As proposed previously, the alanine residues are predominantly found in a ? sheet conformation. The glycine residues are partly incorporated into the ? sheets and otherwise form helical structures with an approximate 3-fold symmetry. PMID:12149440

van Beek, J. D.; Hess, S.; Vollrath, F.; Meier, B. H.

2002-01-01

246

Protein Backbone Torsion Angle-Based Structure Comparison and Secondary Structure Database Web Server  

PubMed Central

Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses. PMID:24124412

Jung, Sunghoon; Bae, Se-Eun; Ahn, Insung

2013-01-01

247

Protonation-deprotonation of the glycine backbone as followed by Raman scattering and multiconformational analysis  

NASA Astrophysics Data System (ADS)

Because of the absence of the side chain in its chemical structure and its well defined Raman spectra, glycine was selected here to follow its backbone protonation-deprotonation. The scan of the recorded spectra in the 1800-300 cm-1 region led us to assign those obtained at pH 1, 6 and 12 to the cationic, zwitterionic and anionic species, respectively. These data complete well those previously published by Bykov et al. (2008) [16] devoted to the high wavenumber Raman spectra (>2500 cm-1). To reinforce our discussion, DFT calculations were carried out on the clusters of glycine + 5H2O, mimicking reasonably the first hydration shell of the amino acid. Geometry optimization of 141 initial clusters, reflecting plausible combinations of the backbone torsion angles, allowed exploration of the conformational features, as well as construction of the theoretical Raman spectra by considering the most stable clusters containing each glycine species.

Hernández, Belén; Pflüger, Fernando; Kruglik, Sergei G.; Ghomi, Mahmoud

2013-11-01

248

Branching of the galacturonan backbone of comaruman, a pectin from the marsh cinquefoil Comarum palustre L.  

PubMed

Galacturonan, the main constituent of the backbone (core) of the comaruman macromolecule, a pectin from the marsh cinquefoil Comarum palustre L., was obtained on partial acid hydrolysis of the pectin. Using atomic force microscopy and methylation analysis of the galacturonan, the backbone of the comaruman macromolecule was shown to contain branches as side chains consisting of alpha-1,4-linked residues of D-galactopyranosyl uronic acid attached to the 2- and 3-positions of the galacturonic acid residues of the core, in addition to linear regions of alpha-1,4-D-galacturonan. A few side chains appear to attach to 2,3-positions of the D-galacturonic acid residues. PMID:16732733

Ovodova, R G; Popov, S V; Bushneva, O A; Golovchenko, V V; Chizhov, A O; Klinov, D V; Ovodov, Yu S

2006-05-01

249

Repeat Motions and Backbone Flexibility in Designed Proteins with Different Numbers of Identical Consensus Tetratricopeptide Repeats †  

Microsoft Academic Search

The tetratricopeptide repeat (TPR) is a 34-residue helix-turn-helix motif that occurs as three or more tandem repeats in a wide variety of proteins. We have determined the repeat motions and backbone fluctuations of proteins containing two or three consensus TPR repeats (CTPR2 and CPTR3, respectively) using 15N NMR relaxation measurements. Rotational diffusion tensors calculated from these data for each repeat

Cecilia Y. Cheng; Virginia A. Jarymowycz; Aitziber L. Cortajarena; Lynne Regan; Martin J. Stone

2006-01-01

250

Potent inhibition of HIV1 replication by backbone cyclic peptides bearing the Rev arginine rich motif  

Microsoft Academic Search

Summary  Due to its essential role in the virus life cycle, the viral regulatory protein Rev constitutes an attractive target for the\\u000a development of new antiviral molecules. In this work, a series of Backbone Cyclic Peptide (BCP) analogs that bear a conformationally\\u000a constrained arginine rich motif (ARM) of Rev were tested for in vitro inhibition of HIV-1 replication. We observed a potent

Laurent Chaloin; Fatima Smagulova; Elana Hariton-Gazal; Laurence Briant; Abraham Loyter; Christian Devaux

2007-01-01

251

Tritium containing polymers having a polymer backbone substantially void of tritium  

DOEpatents

A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium. 2 figs.

Jensen, G.A.; Nelson, D.A.; Molton, P.M.

1992-03-31

252

Backbone and side chain NMR assignments for the ribosome assembly factor Nop6 from Saccharomyces cerevisiae.  

PubMed

The Saccharomyces cerevisiae Nop6 protein is involved in the maturation of the small ribosomal subunit. It contains a central RNA binding domain and a predicted C-terminal coiled-coil domain. Here we report the almost complete (>90%) (1)H,(13)C,(15)N backbone and side chain NMR assignment of a 15 kDa Nop6 construct comprising the RNA binding and coiled-coil domains. PMID:23921755

Wurm, Jan Philip; Lioutikov, Anatoli; Kötter, Peter; Entian, Karl-Dieter; Wöhnert, Jens

2014-10-01

253

Rerouting for handover in mobile networks with connection-oriented backbones: an experimental testbed  

Microsoft Academic Search

The rerouting of connections for handover in a broadband mobile cellular network is investigated. We address networks with a connection-oriented backbone, which supports quality-of-service (QoS). Moreover it is assumed an IP-style multicast on top of the connection-oriented network. We advocate to utilize the IP-style multicast in order to reroute connections for handover. Three rerouting schemes are proposed, which are based

Andreas Festag; T. Assimakopulos; Lars Westerhoff; Adam Wolisz

2000-01-01

254

Analysis of Measured Single-Hop Delay from an Operational Backbone Network  

Microsoft Academic Search

We measure and analyze the single-hop packet delay through op- erational routers in a backbone IP network. First we present our delay measurements through a single router. Then we identify step- by-step the factors contributing to single-hop delay. In addition to packet processing, transmission, and queueing delays, we iden- tify the presence of very large delays due to non-work-conserving router

Konstantina Papagiannaki; Sue B. Moon; Chuck Fraleigh; Patrick Thiran; Fouad A. Tobagi; Christophe Diot

2002-01-01

255

Structural studies of a protein using the assigned back-bone carbonyl carbon-13 NMR resonances  

NASA Astrophysics Data System (ADS)

Several new methods to observe and assign the back-bone peptide carbonyl carbon NMR resonances of a protein have been developed and applied for Streptomyces subtilisin inhibitor. With the assigned carbonyl resonances various site-specific structural information can be obtained for virtually any site of the peptide chain. By putting those site-specific NMR parameters, including chemical shifts, rotational structures around peptide bond, and solvent accessibilities, together a new algorithm to predict the protein structures in solution has emerged.

Kainosho, M.; Nagao, H.; Imamura, Y.; Uchida, K.; Tomonaga, N.; Nakamura, Y.; Tsuji, T.

1985-01-01

256

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data.  

PubMed

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly. PMID:12794897

Perczel, András; Jákli, Imre; McAllister, Michael A; Csizmadia, Imre G

2003-06-01

257

Computational Design of the Sequence and Structure of a Protein-Binding Peptide  

SciTech Connect

The de novo design of protein-binding peptides is challenging because it requires the identification of both a sequence and a backbone conformation favorable for binding. We used a computational strategy that iterates between structure and sequence optimization to redesign the C-terminal portion of the RGS14 GoLoco motif peptide so that it adopts a new conformation when bound to G{alpha}{sub i1}. An X-ray crystal structure of the redesigned complex closely matches the computational model, with a backbone root-mean-square deviation of 1.1 {angstrom}.

Sammond, Deanne W.; Bosch, Dustin E.; Butterfoss, Glenn L.; Purbeck, Carrie; Machius, Mischa; Siderovski, David P.; Kuhlman, Brian (UNC)

2012-08-10

258

Molecular phylogenetics before sequences  

PubMed Central

From 1971 to 1985, Carl Woese and colleagues generated oligonucleotide catalogs of 16S/18S rRNAs from more than 400 organisms. Using these incomplete and imperfect data, Carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large RNA components of the translational apparatus. They recognized a third domain of life, revealed the phylogenetic backbone of bacteria (and its limitations), delineated taxa, and explored the tempo and mode of microbial evolution. For these discoveries to have stood the test of time, oligonucleotide catalogs must carry significant phylogenetic signal; they thus bear re-examination in view of the current interest in alignment-free phylogenetics based on k-mers. Here we consider the aims, successes, and limitations of this early phase of molecular phylogenetics. We computationally generate oligonucleotide sets (e-catalogs) from 16S/18S rRNA sequences, calculate pairwise distances between them based on D2 statistics, compute distance trees, and compare their performance against alignment-based and k-mer trees. Although the catalogs themselves were superseded by full-length sequences, this stage in the development of computational molecular biology remains instructive for us today. PMID:24572375

Ragan, Mark A; Bernard, Guillaume; Chan, Cheong Xin

2014-01-01

259

Biocleavable comb-shaped gene carriers from dextran backbones with bioreducible ATRP initiation sites.  

PubMed

It is of crucial importance to design reduction-sensitive polysaccharide-based copolymers for intracellular triggered gene and drug delivery. In this work, a simple two-step method involving the reaction of hydroxyl groups of dextran with cystamine was first developed to introduce reduction-sensitive disulfide linked initiation sites of atom transfer radical polymerization (ATRP) onto dextran. Well-defined biocleavable comb-shaped vectors consisting of nonionic dextran backbones and disulfide-linked cationic P(DMAEMA) side chains were subsequently prepared via ATRP for highly efficient gene delivery. The P(DMAEMA) side chains can be readily cleavable from the dextran backbones under reducible conditions. Moreover, the bioreducible P(DMAEMA) side chains can be functionalized by poly(poly(ethylene glycol)ethyl ether methacrylate) (P(PEGEEMA)) end blocks to reduce the cytotoxicity and further enhance the gene transfection efficiency. This present study demonstrated that properly grafting short bioreducible polycation side chains from a nonionic polysaccharide backbone with biocleavable ATRP initiation sites is an effective means to produce a class of polysaccharide-based gene delivery vectors. PMID:22136712

Wang, Zeng-Hui; Zhu, Yun; Chai, Ming-Ying; Yang, Wan-Tai; Xu, Fu-Jian

2012-02-01

260

Conjugated backbone orientation variation in high mobility regioregular PT based copolymers  

NASA Astrophysics Data System (ADS)

The synthesis of novel solution processable conjugated polymers is an active field of study due to the potential to fabricate low cost, high though-put electronic devices such as organic field effect transistors (OFET). A regioregular copolymer based on cyclopenta[2,1-b:3,4-b']dithiophene (CDT) and pyridal[2,1,3]thiadiazole (PT) structural units has been prepared by using polymerization reactions involving reactants specifically designed to avoid random orientation of the asymmetric PT heterocycle. Compared to it's regiorandom counterpart, the regioregular polymer exhibits a two orders of magnitude increase in hole mobility from 0.005 to 0.6 cm^2V-1 s-1. A combination of X-ray scattering techniques were employed to quantitatively access the degree of orientation and crystallinity in thin films (15-20 nm) that matched device architecture. We examined the backbone orientation dependence as a function of depth via grazing incidence wide angle X-ray scattering (GIWAXS) and found significant differences in the backbone stacking orientation between the regiorandom and regioregular copolymers. These experiments suggest the backbone regularity leads to significant differences in the structural arrangement and it is another important design criteria to consider in the design of new conjugated copolymers with asymmetric structural units.

Perez, Louis; Ying, Lei; Bazan, Guillermo; Kramer, Edward

2013-03-01

261

Relationships between 31P chemical shift tensors and conformation of nucleic acid backbone: a DFT study.  

PubMed

Density functional theory (DFT) has been applied to study the conformational dependence of 31P chemical shift tensors in B-DNA. The gg and gt conformations of backbone phosphate groups representing BI- and BII-DNA have been examined. Calculations have been carried out on static models of dimethyl phosphate (dmp) and dinucleoside-3',5'-monophosphate with bases replaced by hydrogen atoms in vacuo as well as in an explicit solvent. Trends in 31P chemical shift anisotropy (CSA) tensors with respect to the backbone torsion angles alpha, zeta, beta, and epsilon are presented. Although these trends do not change qualitatively upon solvation, quantitative changes result in the reduction of the chemical shift anisotropy. For alpha and zeta in the range from 270 degrees to 330 degrees and from 240 degrees to 300 degrees , respectively, the delta22 and delta33 principal components vary within as much as 30 ppm, showing a marked dependence on backbone conformation. The calculated 31P chemical shift tensor principal axes deviate from the axes of O-P-O bond angles by at most 5 degrees . For solvent models, our results are in a good agreement with experimental estimates of relative gg and gt isotropic chemical shifts. Solvation also brings the theoretical deltaiso of the gg conformation closer to the experimental gg data of barium diethyl phosphate. PMID:17315915

Precechtelová, Jana; Munzarová, Markéta L; Novák, Petr; Sklenár, Vladimír

2007-03-15

262

NMR Studies of Localized Water and Protein Backbone Dynamics in Mechanically Strained Elastin  

PubMed Central

We report on measurements of the dynamics of localized waters of hydration and the protein backbone of elastin, a remarkable resilient protein found in vertebrate tissues, as a function of the applied external strain. Using deuterium 2D T1–T2 NMR, we separate four reservoirs in the elastin–water system characterized by water with distinguishable mobilities. The measured correlation times corresponding to random tumbling of water localized to the protein is observed to decrease with increasing strain and is interpreted as an increase in its orientational entropy. The NMR T1 and T1? relaxation times of the carbonyl and aliphatic carbons of the protein backbone are measured and indicate a reduction in the correlation time as the elastomer strain is increased. It is argued, and supported by MD simulation of a short model elastin peptide [VPGVG]3, that the observed changes in the backbone dynamics give rise to the development of an entropic elastomeric force that is responsible for elastins’ remarkable elasticity. PMID:22017547

Sun, Cheng; Mitchell, Odingo; Huang, Jiaxin; Boutis, Gregory S.

2013-01-01

263

The Manufacturing Process for the NASA Composite Crew Module Demonstration Structure  

NASA Technical Reports Server (NTRS)

This paper will describe the approaches and methods selected in fabrication of a carbon composite demonstration structure for the Composite Crew Module (CCM) Program. The program is managed by the NASA Safety and Engineering Center with participants from ten NASA Centers and AFRL. Multiple aerospace contractors are participating in the design development, tooling and fabrication effort as well. The goal of the program is to develop an agency wide design team for composite habitable spacecraft. The specific goals for this development project are: a).To gain hands on experience in design, building and testing a composite crew module. b) To validate key assumptions by resolving composite spacecraft design details through fabrication and testing of hardware. This abstract is based on Preliminary Design data..The final design will continue to evolve through the fall of 2007 with fabrication mostly completed by conference date. From a structures perspective, the.CCM can be viewed as a pressure module with variable pressure time histories and a series of both impact and quasi-static, high intensity point, line, and area distributed loads. The portion of the overall space vehicle being designed and. fabricated by the CCM team is just the pressure module and primary loading points. The heaviest point loads are applied and distributed to the pressure module at.an aluminum Service Module/Alternate Launch Abort System (SM/ALAS) fittings and at Main and Drogue Chute fittings. Significant line loads with metal to metal impact is applied at.the Lids ring. These major external point and line loads as well as pressure impact loads (blast and water landing) are applied to the lobed floor though the reentry shield and crushable materials. The pressure module is divided into upper and lower. shells that mate together with a bonded belly band splice joint to create the completed structural assembly. The benefits of a split CCM far outweigh the risks of a joint. These benefits include lower tooling cost and less manufacturing risk. Assembly of the top and bottom halves of the pressure shell will allow access to the interior of the shell throughout remaining fabrication sequence and can also potentially permit extensive installation of equipment and .crew facilities prior to final assembly of the two shell halves. A Pi pre-form is a woven carbon composite material which is provided in pre-impregnated form and frozen for long term storage. The cross-section shape allows the top of the pi to be bonded to a flat or curved surface with a second flat plate composite section bonded between two upstanding legs of the Pi. One of the regions relying on the merits of the Pi pre-form is the backbone. All connections among plates of the backbone structure, including the upper flanges, and to the lobe base of the pressure shell are currently joined by Pi pre-forms. The intersection of backbone composite plates is formed by application of two Pi pre-forms, top flanges and lobed surfaces are bonded with one Pi pre-form. The process of applying the pre-impregnated pi-preform will be demonstrated to include important steps like surface preparation, forming, application of pressure dams, vacuum bagging for consolidation, and curing techniques. Chopped carbon fiber tooling was selected over other traditional metallic and carbon fiber tooling. The requirement of schedule and cost economy for a moderate reuse cure tool warranted composite tooling options. Composite tooling schedule duration of 18 weeks compared favorably against other metallic tooling including invar tooling. Composite tooling also shows significant cost savings over low CTE metallic options. The composite tooling options were divided into two groups and the final decision was based on the cost, schedule, tolerance, temperature, and reuse requirements.

Pelham, Larry; Higgins, John E.

2008-01-01

264

``TBONE''--A HIGHSPEED (ATM) BACKBONE FOR TEXAS Richard Ewing 1 2 3 , Jane Armstrong 1 , Leland Ellis 2 ,  

E-print Network

``TBONE''--A HIGH­SPEED (ATM) BACKBONE FOR TEXAS Richard Ewing 1 2 3 , Jane Armstrong 1 , Leland of urban and rural geography---linking Houston, San Antonio, Austin, College Station, Dallas/Ft. Worth

Ewing, Richard E.

265

Effect of laminate stacking sequence on the high frequency fatigue behavior of SCS-6 fiber-reinforced Si{sub 3}N{sub 4} matrix composites  

SciTech Connect

In many potential applications, continuous fiber-reinforced ceramic matrix composites (CFCMCs) will encounter cyclic fatigue loadings at high frequencies (25 Hz or higher). While most of the work in the area of fatigue of CFCMCs, stress-strain hysteresis occurs during fatigue and is associated with energy dissipation in the composite. In addition to this, the repeated friction and sliding between fiber and matrix are responsible for a substantial temperature rise at the fiber/matrix interface. In this study, [0/90] and [{+-}45] SCS-6 (silicon carbide)/Si{sub 3}N{sub 4} composites made by hot pressing were investigated under high frequency fatigue loadings. The angle-ply laminate showed the same extent of heating as cross-ply laminates, but at much lower stress levels. Frictional heating was caused by sliding at the fiber/matrix interface. Temperature rise due to heat generation in the specimens correlated very well with damage in modulus as a function of fatigue cycles in the composites. Matrix microcracking was more predominant in the angle ply than in the cross-ply composite, due to the much lower stiffness of the angle-ply composite in the longitudinal loading direction.

Chawla, N. [Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Materials Science and Engineering

1997-11-01

266

Preparation of Er3+:Y3Al5O12/TiO2 composite film and influence of layer number and layer sequence on the visible-light photocatalytic activity  

NASA Astrophysics Data System (ADS)

In this work, the Er3+:Y3Al5O12 as up-conversion luminescence agent was mixed with TiO2 and the corresponding Er3+:Y3Al5O12/TiO2 composite films were prepared on the one-sided surface of treated sheet glass through sol-gel dip-coating method. The prepared Er3+:Y3Al5O12/TiO2 composite films were characterized by X-ray diffraction (XRD) and scanning electron microscope (SEM). Their photocatalytic activities were examined through the degradation of some organic dyes under visible-light irradiation. The degradation process of organic dyes was monitored by UV-Vis spectrophotometer. Furthermore, some main influence factors on the visible-light photocatalytic activity of Er3+:Y3Al5O12/TiO2 composite film such as heat-treatment temperature and heat-treatment time were studied. The results indicate that three layer Er3+:Y3Al5O12/TiO2 composite films with one Er3+:Y3Al5O12/TiO2 composite film (as first layer close to sheet glass) and two pure TiO2 film (as second and third layers) display a higher visible-light photocatalytic activity during photocatalytic degradation of Azo Fuchsine. In addition, the results showed that the visible-light photocatalytic activity of Er3+:Y3Al5O12/TiO2 composite film related to the layer number and layer sequence on the sheet glass. Perhaps, the research results may offer some meaningful references for developing solar energy continuous flow wastewater treatment reactor.

Zhang, L.; Ma, C. H.; Wang, J.; Li, S. G.; Li, Y.; Wang, B. X.

2014-12-01

267

Capacity analysis for WDM fiber-radio backbones with star-tree and ring architecture incorporating wavelength interleaving  

Microsoft Academic Search

We present a model based on link budget calculations to investigate the capacity of a wavelength-division-multiplexed (WDM) fiber-radio backbone incorporating a wavelength-interleaving technique. The wavelength-interleaving technique improves the optical spectral efficiency of the millimeter-wave fiber-radio systems incorporating optical single sideband with carrier modulation. In this paper, we investigate the capacity limitations of WDM fiber-radio backbones incorporating both wavelength interleaving and

Christina Lim; Ampalavanapillai Nirmalathas; Dalma Novak; Rodney Waterhouse

2003-01-01

268

Global transcriptional regulator KorC coordinates expression of three backbone modules of the broad-host-range RA3 plasmid from IncU incompatibility group.  

PubMed

The broad-host-range conjugative RA3 plasmid from IncU incompatibility group has been isolated from the fish pathogen Aeromonas hydrophila. DNA sequencing has revealed a mosaic modular structure of RA3 with the stabilization module showing some similarity to IncP-1 genes and the conjugative transfer module highly similar to that from PromA plasmids. The integrity of the mosaic plasmid genome seems to be specified by its regulatory network. In this paper the transcriptional regulator KorC was analyzed. KorCRA3 (98 amino acids) is encoded in the stabilization region and represses four strong promoters by binding to a conserved palindrome sequence, designated OC on the basis of homology to the KorC operator sequences in IncP-1 plasmids. Two of the KorCRA3-regulated promoters precede the first two cistrons in the stabilization module, one fires towards replication module, remaining one controls a tricistronic operon, whose products are involved in the conjugative transfer process. Despite the similarity between the binding sites in IncU and IncP-1 plasmids, no cross-reactivity between their KorC proteins has been detected. KorC emerges as a global regulator of RA3, coordinating all its backbone functions: replication, stable maintenance and conjugative transfer. PMID:23583562

Ludwiczak, M; Dolowy, P; Markowska, A; Szarlak, J; Kulinska, A; Jagura-Burdzy, G

2013-07-01

269

Understanding the Sequence-Dependence of DNA Groove Dimensions: Implications for DNA Interactions  

PubMed Central

Background The B-DNA major and minor groove dimensions are crucial for DNA-protein interactions. It has long been thought that the groove dimensions depend on the DNA sequence, however this relationship has remained elusive. Here, our aim is to elucidate how the DNA sequence intrinsically shapes the grooves. Methodology/Principal Findings The present study is based on the analysis of datasets of free and protein-bound DNA crystal structures, and from a compilation of NMR 31P chemical shifts measured on free DNA in solution on a broad range of representative sequences. The 31P chemical shifts can be interpreted in terms of the BI?BII backbone conformations and dynamics. The grooves width and depth of free and protein-bound DNA are found to be clearly related to the BI/BII backbone conformational states. The DNA propensity to undergo BI?BII backbone transitions is highly sequence-dependent and can be quantified at the dinucleotide level. This dual relationship, between DNA sequence and backbone behavior on one hand, and backbone behavior and groove dimensions on the other hand, allows to decipher the link between DNA sequence and groove dimensions. It also firmly establishes that proteins take advantage of the intrinsic DNA groove properties. Conclusions/Significance The study provides a general framework explaining how the DNA sequence shapes the groove dimensions in free and protein-bound DNA, with far-reaching implications for DNA-protein indirect readout in both specific and non specific interactions. PMID:21209967

Oguey, Christophe; Foloppe, Nicolas; Hartmann, Brigitte

2010-01-01

270

Backbone 1H, 15N, 13C and Ile, Leu, Val methyl chemical shift assignments for the 33.5 kDa N-terminal domain of Candida albicans ALS1.  

PubMed

The agglutinin-like-sequence (ALS) family of adhesion proteins are a key virulence factor for C. albicans. These proteins have been implicated in several functions, notably adhesion and invasion of different cell types, as well as binding to peptides and proteins in the cell surface and extracellular matrix. In order to understand their binding mechanism and en route to a full structural determination by NMR, here we report the resonance assignments of backbone atoms plus Ile, Leu and Val methyls for residues 18-329 of ALS1, which comprises the 33.5 kDa binding domain. PMID:20556550

Yan, Robert; Simpson, Peter J; Matthews, Stephen J; Cota, Ernesto

2010-10-01

271

Oxygen and carbon stable isotope composition of authigenic carbonates in loess sequences from the Carpathian margin and Podolia, as a palaeoclimatic record  

Microsoft Academic Search

Samples were collected from the outcrops situated in the north and east of the Carpathian Margin, in the transition zone between the area of loess covers of Eastern and Western Europe. The chosen localities include two zones of temperate climate with slightly different prevailing wind directions. These loess–palaeosol sequences formed and develop in different time intervals: Early Quaternary Epoch (Podolia,

Bo?ena ??cka; Maria ?anczont; Teresa Madeyska

2009-01-01

272

Protein sequence randomness and sequence/structure correlations.  

PubMed Central

We investigated protein sequence/structure correlation by constructing a space of protein sequences, based on methods developed previously for constructing a space of protein structures. The space is constructed by using a representation of the amino acids as vectors of 10 property factors that encode almost all of their physical properties. Each sequence is represented by a distribution of overlapping sequence fragments. A distance between any two sequences can be calculated. By attaching a weight to each factor, intersequence distances can be varied. We optimize the correlation between corresponding distances in the sequence and structure spaces. The optimal correlation between the sequence and structure spaces is significantly better than that which results from correlating randomly generated sequences, having the overall composition of the data base, with the structure space. However, sets of randomly generated sequences, each of which approximates the composition of the real sequence it replaces, produce correlations with the structure space that are as good as that observed for the actual protein sequences. A connection is proposed with previous studies of the protein folding code. It is shown that the most important property factors for the correlation of the sequence and structure spaces are related to helix/bend preference, side chain bulk, and beta-structure preference. PMID:7787038

Rahman, R S; Rackovsky, S

1995-01-01

273

Self reinforcing polymer composites  

SciTech Connect

In the advent of liquid crystalline polymers (LCPs), self reinforcing polymer composites comprising a polymer matrix and an LCP reinforcement, have become a reality. The so called self reinforcement is due to the LCPs orientability characteristics resulting from their rigid molecular backbone and anisotropy structure in the fluid state. Orientation development takes place during melt processing of the LCP composite blends where shear as well as elongational flows occur prior to consolidation to the solid state. By proper flow control anisotropy develops and in-situ composites are obtained. Polymer composites comprising self-reinforcement by LCPs during processing induced flow, were analyzed and studied with respect to their orientation development and resultant mechanical properties. The analysis commenced with the hydrodynamics of immiscible fluids in shear and elongational flows. Based on the analysis, orientation and morphology development in capillary extrusion was studied, using a variety of thermoplastic polymer matrices like amorphous and crystalline polyamides, polycarbonate and polyester in conjunction of a naphthalene based thermotropic LCP. Based on the flow-morphology relationship the amorphous polyamide/LCP composite was further investigated as it exhibited enhanced properties. Laminated composites based on LCP/amorphous polyamide were developed composed of unidirectional extruded and drawn sheets that were subsequently compression molded. Unidirectional, +45/{minus}45 and quasi-isotropic laminates were prepared and analyzed as to their microstructure and mechanical properties.

Kenig, S. [Israel Plastics and Rubber Center, Haifa (Israel)

1993-12-31

274

On the structure of the inverse kinematics map of a fragment of protein backbone.  

PubMed

Loop closure in proteins requires computing the values of the inverse kinematics (IK) map for a backbone fragment with 2n > or = 6 torsional degrees of freedom (dofs). It occurs in a variety of contexts, e.g., structure determination from electron-density maps, loop insertion in homology-based structure prediction, backbone tweaking for protein energy minimization, and the study of protein mobility in folded states. The first part of this paper analyzes the global structure of the IK map for a fragment of protein backbone with 6 torsional dofs for a slightly idealized kinematic model, called the canonical model. This model, which assumes that every two consecutive torsional bonds C(alpha)--C and N--C(alpha) are exactly parallel, makes it possible to separately compute the inverse orientation map and the inverse position map. The singularities of both maps and their images, the critical sets, respectively, decompose SO(3) x R(3) into open regions where the number of IK solutions is constant. This decomposition leads to a constructive proof of the existence of a region in R(3) x SO(3) where the IK of the 6-dof fragment attains its theoretical maximum of 16 solutions. The second part of this paper extends this analysis to study fragments with more than 6 torsional dofs. It describes an efficient recursive algorithm to sample IK solutions for such fragments, by identifying the feasible range of each successive torsional dof. A numerical homotopy algorithm is then used to deform the IK solutions for a canonical fragment into solutions for a noncanonical fragment. Computational results for fragments ranging from 8 to 30 dofs are presented. PMID:17542001

Milgram, R J; Liu, Guanfeng; Latombe, J C

2008-01-15

275

Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces.  

PubMed

To improve our understanding of the organization and evolution of the wheat (Triticum aestivum) genome, we sequenced and annotated 13-Mb contigs (18.2 Mb) originating from different regions of its largest chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Illumina/Solexa sequencing. All regions carried genes irrespective of their chromosomal location. However, gene distribution was not random, with 75% of them clustered into small islands containing three genes on average. A twofold increase of gene density was observed toward the telomeres likely due to high tandem and interchromosomal duplication events. A total of 3222 transposable elements were identified, including 800 new families. Most of them are complete but showed a highly nested structure spread over distances as large as 200 kb. A succession of amplification waves involving different transposable element families led to contrasted sequence compositions between the proximal and distal regions. Finally, with an estimate of 50,000 genes per diploid genome, our data suggest that wheat may have a higher gene number than other cereals. Indeed, comparisons with rice (Oryza sativa) and Brachypodium revealed that a high number of additional noncollinear genes are interspersed within a highly conserved ancestral grass gene backbone, supporting the idea of an accelerated evolution in the Triticeae lineages. PMID:20581307

Choulet, Frédéric; Wicker, Thomas; Rustenholz, Camille; Paux, Etienne; Salse, Jérome; Leroy, Philippe; Schlub, Stéphane; Le Paslier, Marie-Christine; Magdelenat, Ghislaine; Gonthier, Catherine; Couloux, Arnaud; Budak, Hikmet; Breen, James; Pumphrey, Michael; Liu, Sixin; Kong, Xiuying; Jia, Jizeng; Gut, Marta; Brunel, Dominique; Anderson, James A; Gill, Bikram S; Appels, Rudi; Keller, Beat; Feuillet, Catherine

2010-06-01

276

Structural effects of DNQ-PAC backbone on resist lithographic properties  

NASA Astrophysics Data System (ADS)

Model backbones without hydroxyl groups and fully esterified diazonaphthoquinone PACs were studied to identify critical structural parameters for dissolution inhibition in conventional diazonaphthoquinone/novolac photoresist systems. Hydrophobicity, presence of a site interactive with novolac, and proximaity of DNQ groups were identified as critical parameters. In general, the inhibiting ability of model compounds or PACs were found to be correlated with their retention time on reverse phase HPLC, a measure of hydrophobicity. Evidence is shown there to support the suggestion that the DNQ group provides a strong hydrogen bonding site to enhance efficiency of inhibition. PACs having DNQ groups in close proximity had lower inhibition than PACs with DNQs far apart.

Uenishi, Kazuya; Kawabe, Yasumasa; Kokubo, Tadayoshi; Slater, Sydney G.; Blakeney, Andrew J.

1991-06-01

277

Synthesis and properties of carbohydrate-phosphate backbone-modified oligonucleotide analogues and nucleic acid mimetics  

NASA Astrophysics Data System (ADS)

Advances in the synthesis of oligo(deoxy)ribonucleotide analogues and nucleic acid mimetics made in the last decade are summarized. Attention is focused on new methods for the synthesis of derivatives with a modified ribose-phosphate backbone (phosphorothioate, boranophosphate, and nucleoside phosphonate derivatives) and derivatives devoid of the phosphate group. Among nucleic acid mimetics, conformationally restricted modified peptide nucleic acids, including those bearing a negative or positive charge, and morpholino oligomers are considered. Advantages and drawbacks of the main types of analogues as regards the complexity of the synthesis and the possibility of their application as antisense agents or reagents for hybridization analysis are compared.

Abramova, Tatyana V.; Silnikov, Vladimir N.

2011-05-01

278

Integrating the university medical center. Phase one: providing an information backbone.  

PubMed Central

UCLA School of Medicine represents a diverse computing community where the creation of each individual network has been driven by applications, price/performance and functionality. Indeed, the ability to connect to other computers has had no bearing on selection. Yet, there exists a need to seamlessly connect the individual networks to other minicomputers, mainframes and remote computers. We have created a school wide backbone network that will enable an individual from a single workstation to access a wide variety of services residing on any number of machines. PMID:1807658

Berry, S. J.; Reber, E.; Offeman, W. E.

1991-01-01

279

Sequence assembly  

E-print Network

nucleotide sequences • Most of what we have looked at so far has been related to amino acid sequencesSequence alignment works on nucleotide sequences, too, but if they are known coding sequences, using the translation works better for most tasks. • Other informatics tasks related to only nucleotide sequences: –Sequence assembly –Gene finding and genomic sequence annotation –Promoter recognition The sequence assembly problem • Sequencing machines are able to handle only 500-1000 base fragments at a time (a read) • These fragments must be assembled into a single continuous genomic sequence. • There are two broad approaches to this problem: –Use of a map, or ordered set of markers along a sequence –Use of many overlapping sequences (high coverage) to infer ordering directly from the sequences themselves. • Generally, used together in varying degrees The basic idea • Assembling fragments into contigs requires the detection of significant overlapping regions at the ends of each fragment: 2 contigs • How much overlap is required? –Assume long enough fragment end sequences appear exactly once in the genome. If we see such a sequence in two fragments, they overlap. –Assembly is then the “shortest common superstring” problem. A simple model • Imagine a sequence is random and drawn from an equiprobable distribution of nucleotides • P(seq) =.25 n, n is the length of the sequence. • P(seq occurs exactly once) =.25 n * (m-n) where m is length of genome, n of sequence. • How long does a sequence have to be to have p.25 n * (m-n), or n=12 for 100kb, 18 for

Lawrence Hunter Ph. D

280

Repeat Sequence Proteins as Matrices for Nanocomposites  

SciTech Connect

Recombinant protein-inorganic nanocomposites comprised of exfoliated Na+ montmorillonite (MMT) in a recombinant protein matrix based on silk-like and elastin-like amino acid motifs (silk elastin-like protein (SELP)) were formed via a solution blending process. Charged residues along the protein backbone are shown to dominate long-range interactions, whereas the SELP repeat sequence leads to local protein/MMT compatibility. Up to a 50% increase in room temperature modulus and a comparable decrease in high temperature coefficient of thermal expansion occur for cast films containing 2-10 wt.% MMT.

Drummy, L.; Koerner, H; Phillips, D; McAuliffe, J; Kumar, M; Farmer, B; Vaia, R; Naik, R

2009-01-01

281

The cellulose synthase superfamily in fully sequenced plants and algae  

Microsoft Academic Search

BACKGROUND: The cellulose synthase superfamily has been classified into nine cellulose synthase-like (Csl) families and one cellulose synthase (CesA) family. The Csl families have been proposed to be involved in the synthesis of the backbones of hemicelluloses of plant cell walls. With 17 plant and algal genomes fully sequenced, we sought to conduct a genome-wide and systematic investigation of this

Yanbin Yin; Jinling Huang; Ying Xu

2009-01-01

282

Phosphorothioate backbone modifications of nucleotide-based drugs are potent platelet activators.  

PubMed

Nucleotide-based drug candidates such as antisense oligonucleotides, aptamers, immunoreceptor-activating nucleotides, or (anti)microRNAs hold great therapeutic promise for many human diseases. Phosphorothioate (PS) backbone modification of nucleotide-based drugs is common practice to protect these promising drug candidates from rapid degradation by plasma and intracellular nucleases. Effects of the changes in physicochemical properties associated with PS modification on platelets have not been elucidated so far. Here we report the unexpected binding of PS-modified oligonucleotides to platelets eliciting strong platelet activation, signaling, reactive oxygen species generation, adhesion, spreading, aggregation, and thrombus formation in vitro and in vivo. Mechanistically, the platelet-specific receptor glycoprotein VI (GPVI) mediates these platelet-activating effects. Notably, platelets from GPVI function-deficient patients do not exhibit binding of PS-modified oligonucleotides, and platelet activation is fully abolished. Our data demonstrate a novel, unexpected, PS backbone-dependent, platelet-activating effect of nucleotide-based drug candidates mediated by GPVI. This unforeseen effect should be considered in the ongoing development programs for the broad range of upcoming and promising DNA/RNA therapeutics. PMID:25646267

Flierl, Ulrike; Nero, Tracy L; Lim, Bock; Arthur, Jane F; Yao, Yu; Jung, Stephanie M; Gitz, Eelo; Pollitt, Alice Y; Zaldivia, Maria T K; Jandrot-Perrus, Martine; Schäfer, Andreas; Nieswandt, Bernhard; Andrews, Robert K; Parker, Michael W; Gardiner, Elizabeth E; Peter, Karlheinz

2015-02-01

283

Di-Isocyanate Crosslinked Aerogels with 1, 6-Bis (Trimethoxysilyl) Hexane Incorporated in Silica Backbone  

NASA Technical Reports Server (NTRS)

Silica aerogels are desirable materials for many applications that take advantage of their light weight and low thermal conductivity. Addition of a conformal polymer coating which bonds with the amine decorated surface of the silica network improves the strength of the aerogels by as much as 200 times. Even with vast improvement in strength they still tend to undergo brittle failure due to the rigid silica backbone. We hope to increase the flexibility and elastic recovery of the silica based aerogel by altering the silica back-bone by incorporation of more flexible hexane links. To this end, we investigated the use of 1,6-bis(trimethoxysilyl)hexane (BTMSH), a polysilsesquioxane precursor3, as an additional co-reactant to prepare silica gels which were subsequently cross-linked with di-isocyanate. Previously, this approach of adding flexibility by BTMSH incorporation was demonstrated with styrene cross-linked aerogels. In our study, we varied silane concentration, mol % of silicon from BTMSH and di-isocyanate concentration by weight percent to attempt to optimize both the flexibility and the strength of the aerogels.

Vivod, Stephanie L.; Meador, Mary Ann B.; Nguyen, Baochau N.; Quade, Derek; Randall, Jason; Perry, Renee

2008-01-01

284

Efficient delivery of RNAi prodrugs containing reversible charge-neutralizing phosphotriester backbone modifications  

PubMed Central

RNA interference (RNAi) has great potential to treat human disease1–3. However, in vivo delivery of short interfering RNAs (siRNAs), which are negatively charged double-stranded RNA macromolecules, remains a major hurdle4–9. Current siRNA delivery has begun to move away from large lipid and synthetic nanoparticles to more defined molecular conjugates9. Here we address this issue by synthesis of short interfering ribonucleic neutrals (siRNNs) whose phosphate backbone contains neutral phosphotriester groups, allowing for delivery into cells. Once inside cells, siRNNs are converted by cytoplasmic thioesterases into native, charged phosphodiester-backbone siRNAs, which induce robust RNAi responses. siRNNs have favorable drug-like properties, including high synthetic yields, serum stability and absence of innate immune responses. Unlike siRNAs, siRNNs avidly bind serum albumin to positively influence pharmacokinetic properties. Systemic delivery of siRNNs conjugated to a hepatocyte-specific targeting domain induced extended dose-dependent in vivo RNAi responses in mice. We believe that siRNNs represent a technology that will open new avenues for development of RNAi therapeutics. PMID:25402614

Meade, Bryan R; Gogoi, Khirud; Hamil, Alexander S; Palm-Apergi, Caroline; van den Berg, Arjen; Hagopian, Jonathan C; Springer, Aaron D; Eguchi, Akiko; Kacsinta, Apollo D; Dowdy, Connor F; Presente, Asaf; Lönn, Peter; Kaulich, Manuel; Yoshioka, Naohisa; Gros, Edwige; Cui, Xian-Shu; Dowdy, Steven F

2015-01-01

285

Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement.  

PubMed

Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common use today have been designed on the assumption that each type of bond or angle has a single ideal value that is independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and, as a first step towards using such information to build more accurate models, ultra-high-resolution protein crystal structures have been used to derive a conformation-dependent library (CDL) of restraints for the protein backbone [Berkholz et al. (2009) Structure 17, 1316-1325]. Here, we report the introduction of this CDL into the phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the CDL yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In phenix, use of the CDL can be selected by simply specifying the cdl = True option. This successful implementation paves the way for further aspects of the context dependence of ideal geometry to be characterized and applied to improve experimental and predictive modeling accuracy. PMID:24890778

Moriarty, Nigel W; Tronrud, Dale E; Adams, Paul D; Karplus, P Andrew

2014-09-01

286

Generation of transgenic Drosophila expressing shRNAs in the miR-1 backbone.  

PubMed

In Drosophila, long-term effects of RNA interference (RNAi) must be achieved by integrating into the genome a template from which an RNAi trigger is transcribed by cellular RNA polymerases, generally RNA polymerase II or III. With encoded triggers, not only can essentially permanent silencing be achieved, but control can also be exerted over the level of trigger expression, with a resulting variation in the degree to which the target is silenced. Knockdown can also be controlled in a temporal and cell-type-dependent fashion through the use of well-established transgenic methodologies and well-tested promoters. The forms of encoded triggers vary. Long double-stranded RNAs can be expressed as extended inverted repeats. The nearest equivalent of a small interfering RNA is an artificial microRNA (miRNA) or short hairpin RNA (shRNA), where a natural miRNA backbone (also called a scaffold) is remodeled to produce a different small RNA or a small inverted repeat (<30 nucleotides) is simply expressed. This protocol describes creation of transgenic Drosophila carrying shRNA inserts in a remodeled endogenous miRNA backbone. The protocol applies to the use of miRNA-based shRNAs, but most of the vectors, principles of experimental design, and methods are also applicable to long inverted repeat transgenes. PMID:24786506

Chang, Kenneth; Marran, Krista; Valentine, Amy; Hannon, Gregory J

2014-05-01

287

Backbone-base interactions critical to quantum stabilization of transfer RNA anticodon structure.  

PubMed

Transfer RNA (tRNA) anticodons adopt a highly ordered 3'-stack without significant base overlap. Density functional theory at the M06-2X/6-31+G(d,p) level in combination with natural bond orbital analysis was utilized to calculate the intramolecular interactions within the tRNA anticodon that are responsible for stabilizing the stair-stepped conformation. Ten tRNA X-ray crystal structures were obtained from the PDB databank and were trimmed to include only the anticodon bases. Hydrogenic positions were added and optimized for the structures in the stair-stepped conformation. The sugar-phosphate backbone has been retained for these calculations, revealing the role it plays in RNA structural stability. It was found that electrostatic interactions between the sugar-phosphate backbone and the base provide the most stability, rather than the traditionally studied interbase stacking. Base-stacking interactions, though present, were weak and inconsistent. Aqueous solvation was found to have little effect on the intramolecular interactions. PMID:23742318

Witts, Rachel N; Hopson, Emily C; Koballa, Drew E; Van Boening, Thomas A; Hopkins, Nicholas H; Patterson, Eric V; Nagan, Maria C

2013-06-27

288

Secondary-Structure Design of Proteins by a Backbone Torsion Energy  

NASA Astrophysics Data System (ADS)

We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backbone dihedral angles ? and \\psi. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both ? and \\psi can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase/decrease the ?-helix-forming tendencies by lowering/raising the torsion-energy surface in the ?-helix region and likewise increase/decrease the ?-sheet-forming tendencies by lowering/raising the surface in the ?-sheet region in the Ramachandran space. We applied our approach to AMBER parm94 and AMBER parm96 force fields and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming tendencies by performing folding simulations of ?-helical and ?-hairpin peptides.

Sakae, Yoshitake; Okamoto, Yuko

2006-05-01

289

1H, 13C, and 15N backbone assignment and secondary structure of the receptor-binding domain of vascular endothelial growth factor.  

PubMed Central

Nearly complete sequence-specific 1H, 13C, and 15N resonance assignments are reported for the backbone atoms of the receptor-binding domain of vascular endothelial growth factor (VEGF), a 23-kDa homodimeric protein that is a major regulator of both normal and pathological angiogenesis. The assignment strategy relied on the use of seven 3D triple-resonance experiments [HN(CO)CA, HNCA, HNCO, (HCA)CONH, HN(COCA)HA, HN(CA)HA, and CBCA-(CO)NH] and a 3D 15N-TOCSY-HSQC experiment recorded on a 0.5 mM (12 mg/mL) sample at 500 MHz, pH 7.0, 45 degrees C. Under these conditions, 15N relaxation data show that the protein has a rotational correlation time of 15.0 ns. Despite this unusually long correlation time, assignments were obtained for 94 of the 99 residues; 8 residues lack amide 1H and 15N assignments, presumably due to rapid exchange of the amide 1H with solvent under the experimental conditions used. The secondary structure of the protein was deduced from the chemical shift indices of the 1H alpha, 13C alpha, 13C beta, and 13CO nuclei, and from analysis of backbone NOEs observed in a 3D 15N-NOESY-HSQC spectrum. Two helices and a significant amount of beta-sheet structure were identified, in general agreement with the secondary structure found in a recently determined crystal structure of a similar VEGF construct [Muller YA et al., 1997, Proc Natl Acad Sci USA 94:7192-7197]. PMID:9336848

Fairbrother, W. J.; Champe, M. A.; Christinger, H. W.; Keyt, B. A.; Starovasnik, M. A.

1997-01-01

290

Biosensors for DNA sequence detection  

NASA Technical Reports Server (NTRS)

DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

Vercoutere, Wenonah; Akeson, Mark

2002-01-01

291

Biosensors for DNA sequence detection.  

PubMed

DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores. PMID:12470736

Vercoutere, Wenonah; Akeson, Mark

2002-12-01

292

Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa  

Microsoft Academic Search

Background  Pollen development in flowering plants requires strict control of the gene expression program and genetic information stability\\u000a by mechanisms possibly including the miRNA pathway. However, our understanding of the miRNA pathway in pollen development\\u000a remains limited, and the dynamic profile of miRNAs in developing pollen is unknown.\\u000a \\u000a \\u000a \\u000a \\u000a Results  Using next-generation sequencing technology, we pyrosequenced small RNA populations from rice uninucleate microspores

Li Qin Wei; Long Feng Yan; Tai Wang

2011-01-01

293

Cycle Sequencing  

NSDL National Science Digital Library

This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents the cycle sequencing. The animation contains instructions on how to sequence a piece of DNA beginning with the raw materials needed, and details on the process: "Fluorescent dyes are added to the reactions, and a laser within an automated DNA sequencing machine is used to analyze the DNA fragments produced."

294

The chemical and hydrological evolution of an ancient potash-forming evaporite basin as constrained by mineral sequence, fluid inclusion composition, and numerical simulation  

NASA Astrophysics Data System (ADS)

The chemical evolution of the brine in a potash evaporite basin has been investigated by X-ray microanalysis of frozen primary inclusions trapped in halite. A Computer program based on thermodynamic equilibrium and mass balance principles has been used to simulate evaporation paths. The comparison between the results of calculations, the observed mineralogy and mineral sequence, and the solute content in fluid inclusions has placed constraints on the hydrological evolution of the basin. The upper Eocene basin of Navarra, southern Pyrenees, Spain, began as a marine basin, evolving from a moderate to a high degree of restriction, depositing first a basai anhydrite horizon, and then a thick sequence of massive halite. An additional inflow of CaCl 2 in the basin during seawater evaporation is proposed as the process responsible for the sulfate depletion required for sylvite instead of Mg-sulfates to form. Mixing of seawater with continental waters, bacterial sulfate reduction and "in situ" dolomitization are discarded. The basin subsequently closed to the sea and evolved with decreasing volume. Alternating bands of clays-halite-sylvite and then clays-halite-carnallite were deposited under the influence of seasonal continental recharge. Before reaching total desiccation the residual brine was diluted by continental water. The basin then evolved under an endoreic regime, where continental recharge and the recycling of previously-formed halite led to deposition of alternating beds of clays and halite.

Ayora, Carlos; Garcia-Veigas, Javier; Pueyo, Juan-Jose

1994-08-01

295

Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.  

PubMed

In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique adaptation may establish new paradigms for how receptor:ligand pairs co-evolve, in particular with respect to sexual conflict. PMID:24849290

Wilburn, Damien B; Bowen, Kathleen E; Doty, Kari A; Arumugam, Sengodagounder; Lane, Andrew N; Feldhoff, Pamela W; Feldhoff, Richard C

2014-01-01

296

An effective approach for alleviating cation-induced backbone degradation in aromatic ether-based alkaline polymer electrolytes.  

PubMed

Aromatic ether-based alkaline polymer electrolytes (APEs) are one of the most popular types of APEs being used in fuel cells. However, recent studies have demonstrated that upon being grafted by proximal cations some polar groups in the backbone of such APEs can be attacked by OH(-), leading to backbone degradation in an alkaline environment. To resolve this issue, we performed a systematic study on six APEs. We first replaced the polysulfone (PS) backbone with polyphenylsulfone (PPSU) and polyphenylether (PPO), whose molecular structures contain fewer polar groups. Although improved stability was seen after this change, cation-induced degradation was still obvious. Thus, our second move was to replace the ordinary quaternary ammonia (QA) cation, which had been closely attached to the polymer backbone, with a pendant-type QA (pQA), which was linked to the backbone through a long side chain. After a stability test in a 1 mol/L KOH solution at 80 °C for 30 days, all pQA-type APEs (pQAPS, pQAPPSU, and pQAPPO) exhibited as low as 8 wt % weight loss, which is close to the level of the bare backbone (5 wt %) and remarkably lower than those of the QA-type APEs (QAPS, QAPPSU, and QAPPO), whose weight losses under the same conditions were >30%. The pQA-type APEs also possessed clear microphase segregation morphology, which led to ionic conductivities that were higher, and water uptakes and degrees of membrane swelling that were lower, than those of the QA-type APEs. These observations unambiguously indicate that designing pendant-type cations is an effective approach to increasing the chemical stability of aromatic ether-based APEs. PMID:25594224

Han, Juanjuan; Liu, Qiong; Li, Xueqi; Pan, Jing; Wei, Ling; Wu, Ying; Peng, Hanqing; Wang, Ying; Li, Guangwei; Chen, Chen; Xiao, Li; Lu, Juntao; Zhuang, Lin

2015-02-01

297

The reference genetic linkage map for the multinational Brassica rapa genome sequencing project  

Microsoft Academic Search

We describe the construction of a reference genetic linkage map for the Brassica A genome, which will form the backbone for anchoring sequence contigs for the Multinational Brassica rapa Genome Sequencing Project. Seventy-eight doubled haploid lines derived from anther culture of the F1 of a cross between two diverse Chinese cabbage (B.\\u000a rapa ssp. pekinensis) inbred lines, ‘Chiifu-401-42’ (C) and

Su Ryun Choi; Graham R. Teakle; Prikshit Plaha; Jeong Hee Kim; Charlotte J. Allender; Elena Beynon; Zhong Yun Piao; Pilar Soengas; Tae Ho Han; Graham J. King; Guy C. Barker; Paul Hand; Derek J. Lydiate; Jacqueline Batley; David Edwards; Dal Hoe Koo; Jae Wook Bang; Beom-Seok Park; Yong Pyo Lim

2007-01-01

298

Magnetic and backbone exponents of the percolation and Ising models in three dimensions.  

PubMed

We investigate random-cluster representations of the q=1 - and 2-state Potts models in three dimensions, i.e., the bond-percolation and the Ising model, respectively. Using a recently developed sampling technique, we determine the probabilities C1 (r) and C2 (r) that a pair of lattice sites at a distance r are connected by at least one and two mutually independent paths, respectively. The scaling behavior of C1 and C2 at criticality is governed by the magnetic and the backbone scaling dimension X(h) and X(b) , respectively. From a finite-size analysis of the numerical data, we determine X(h) =0.4768 (7) and X(b) =1.125 (3) for the percolation and X(h) =0.5178 (7) and X(b) =0.829 (4) for the Ising model. PMID:15600459

Deng, Youjin; Blöte, Henk W J

2004-10-01

299

The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone.  

PubMed

Although protein folding is often described by motion on a funnel-shaped overall topology of the energy landscape, the many local interactions that can occur result in considerable landscape roughness which slows folding by increasing internal friction. Recent experimental results have brought to light that this roughness also causes unusual diffusional behaviour of the backbone of an unfolded protein, i.e. the relative motion of protein sections cannot be described by the normal diffusion equation, but shows strongly subdiffusional behaviour with a nonlinear time dependence of the mean square displacement, ?r(2)(t)??t(?) (?? 1). This results in significantly slower configurational equilibration than had been assumed hitherto. Analysis of the results also allows quantification of the energy landscape roughness, i.e. the root-mean-squared depth of local minima, yielding a value of 4-5kBT for a typical small protein. PMID:25412176

Volk, Martin; Milanesi, Lilia; Waltho, Jonathan P; Hunter, Christopher A; Beddard, Godfrey S

2015-01-14

300

Monolignol ferulate transferase introduces chemically labile linkages into the lignin backbone.  

PubMed

Redesigning lignin, the aromatic polymer fortifying plant cell walls, to be more amenable to chemical depolymerization can lower the energy required for industrial processing. We have engineered poplar trees to introduce ester linkages into the lignin polymer backbone by augmenting the monomer pool with monolignol ferulate conjugates. Herein, we describe the isolation of a transferase gene capable of forming these conjugates and its xylem-specific introduction into poplar. Enzyme kinetics, in planta expression, lignin structural analysis, and improved cell wall digestibility after mild alkaline pretreatment demonstrate that these trees produce the monolignol ferulate conjugates, export them to the wall, and use them during lignification. Tailoring plants to use such conjugates during cell wall biosynthesis is a promising way to produce plants that are designed for deconstruction. PMID:24700858

Wilkerson, C G; Mansfield, S D; Lu, F; Withers, S; Park, J-Y; Karlen, S D; Gonzales-Vigil, E; Padmakshan, D; Unda, F; Rencoret, J; Ralph, J

2014-04-01

301

Transistor Properties of Novel Organic Conducting Polymers Bearing Tetrathiafulvalene Units in the Backbone  

NASA Astrophysics Data System (ADS)

The organic field-effect transistor (OFET) properties of conducting polymers bearing a tetrathiafulvalene (TTF) unit in the backbone whose termini are capped with functional groups were investigated. The OFET devices were fabricated by a solution process under various fabrication conditions. All the devices showed typical p-type semiconducting behavior as expected from the electron-donating properties of TTF derivatives. Cast films exhibited higher field-effect mobilities than spin-coated films. Surface treatment with organic silane molecules produced no noticeable effects. When using thioacetyl-capped polymer, treatment of the OFET device in an ammonia atmosphere resulted in a field-effect mobility one order of magnitude higher than that of the pristine film. By contrast, there was no such enhancement with ethyl acetate-capped polymer. Atomic force microscopy observations revealed that the ammonia treatment promoted the ordering of the polymer chain, which resulted in improved electronic conduction.

Kashimura, Yoshiaki; Goto, Touichiro; Nakashima, Hiroshi; Furukawa, Kazuaki; Wang, Erjing; Li, Hongxiang; Hu, Wenping; Torimitsu, Keiichi

2010-01-01

302

Side chain and backbone contributions of Phe508 to CFTR folding  

SciTech Connect

Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

2010-12-07

303

Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants  

PubMed Central

Background Chaining is a major problem in constructing gene families. Results We define a new kind of cluster on graphs with strong and weak edges: soft cliques with backbones (SCWiB). This differs from other definitions in how it controls the "chaining effect", by ensuring clusters satisfy a tolerant edge density criterion that takes into account cluster size. We implement algorithms for decomposing a graph of similarities into SCWiBs. We compare examples of output from SCWiB and the Markov Cluster Algorithm (MCL), and also compare some curated Arabidopsis thaliana gene families with the results of automatic clustering. We apply our method to 44 published angiosperm genomes with annotation, and discover that Amborella trichopoda is distinct from all the others in having substantially and systematically smaller proportions of moderate- and large-size gene families. Conclusions We offer several possible evolutionary explanations for this result. PMID:25572777

2014-01-01

304

Synthesis and backbone conformations of cyclic hexapeptides cyclo-(Xxx-Pro-D-Gln)2.  

PubMed

The solution syntheses of cyclo-(Xxx-Pro-D-Gln)2, where Xxx = Gly, Ala, Leu, Phe and Val are described. Several routes were examined, the most successful involving the intermediate Z-Xxx-Pro-D-Gln-O-tBu and proceeding to cyclization of H-Xxx-Pro-D-Gln-Xxx-Pro-D-Gln-OH using diphenylphosphoryl azide. The N--H regions of the proton magnetic resonance spectra of aqueous solutions of these peptides were examined, and in the Xxx = Leu and Val peptides an unsymmetrical backbone, presumably with one cis Xxx-Pro peptide bond, was found to be important. Previous reports of cyclo-(Xxx-Pro-D-Yyy)2 peptides have shown only C2-symmetric forms. PMID:6853028

Kopple, K D; Parameswaran, K N

1983-03-01

305

[The simplest molecular model of 2'-deoxyribopolinucleotides sugar-phosphate backbone: quantum-chemical adequacy check].  

PubMed

The physical adequacy of the simplest molecular model "sugar residue (SR)--phosphate group (PG)--SR" of 2'-deoxyribopolinucleotides sugar-phosphate backbone is confirmed at DFT B3LYP/6-31++G(d,p) and DFT B3LYP/6-31G(d,p) of quantum-chemical methods. It is proved that complicacy of the model to the "SR-PG-SR-PG-SR" and higher levels does not noticeably change the numerical values of torsion angles. Also these angles depend negligibly on counterion nature (e.g. Na+ to Li+, K+ or Cs+ change) and transition from vacuum to continuum approximation with medium dielectrical values of 1.4, 24.9, and 78.4. It is shown that model loses its adequacy when PG is the end link. PMID:21888061

Vo?teshenko, I S; Zhurakivs'ky?, R O; Bulavin, L A; Govorun, D M

2011-01-01

306

Thermoplastic copolyimides and composites therefrom  

NASA Technical Reports Server (NTRS)

Copolyimide compositions and methods for their preparation which are melt-processible at relative low pressures, i.e. less than 1000 psi, and are suited for laminating and molding, are described. The invention additionally encompasses copolyimide precursors, reinforced polyimide composites and laminates made from said polyimides where the composite is reinforced by fibrous materials. This is achieved by reacting at least one aromatic dianhydride where each anhydride group is located on an aromatic ring with the carbonyl units in an ortho orientation relative to one another, with at least one diamine which is capable of a transmidization reaction upon incorporation into the polyimide backbone, and with at least one other diamine which is not capable of undergoing such reaction, the diamine which is capable of undergoing the transimidization reaction being present in an amount of from about 1-50 mole percent in relation to the diamine that is not susceptable to transimidization.

Harris, Frank (Inventor); Gabori, Patricia A. (Inventor)

1994-01-01

307

Statistical mechanics of protein allostery: Roles of backbone and side-chain structural fluctuations  

NASA Astrophysics Data System (ADS)

A statistical mechanical model of allosteric transition of proteins is developed by extending the structure-based model of protein folding to cases that a protein has two different native conformations. Partition function is calculated exactly within the model and free-energy surfaces associated with allostery are derived. In this paper, the model of allosteric transition proposed in a previous paper [Proc. Natl. Acad. Sci. U.S.A 134, 7775 (2010)] is reformulated to describe both fluctuation in side-chain configurations and that in backbone structures in a balanced way. The model is applied to example proteins, Ras, calmodulin, and CheY: Ras undergoes the allosteric transition between guanosine diphosphate (GDP)-bound and guanosine triphosphate (GTP)-bound forms, and the model results show that the GDP-bound form is stabilized enough to prevent unnecessary signal transmission, but the conformation in the GTP-bound state bears large fluctuation in side-chain configurations, which may help to bind multiple target proteins for multiple pathways of signaling. The calculated results of calmodulin show the scenario of sequential ordering in Ca2 + binding and the associated allosteric conformational change, which are realized though the sequential appearing of pre-existing structural fluctuations, i.e., fluctuations to show structures suitable to bind Ca2 + before its binding. Here, the pre-existing fluctuations to accept the second and third Ca2 + ions are dominated by the side-chain fluctuation. In CheY, the calculated side-chain fluctuation of Tyr106 is coordinated with the backbone structural change in the ?4-?4 loop, which explains the pre-existing Y-T coupling process in this protein. Ability of the model to explain allosteric transitions of example proteins supports the view that the large entropic effects lower the free-energy barrier of allosteric transition.

Itoh, Kazuhito; Sasai, Masaki

2011-03-01

308

40-Gbps optical backbone network deep packet inspection based on FPGA  

NASA Astrophysics Data System (ADS)

In the era of information, the big data, which contains huge information, brings about some problems, such as high speed transmission, storage and real-time analysis and process. As the important media for data transmission, the Internet is the significant part for big data processing research. With the large-scale usage of the Internet, the data streaming of network is increasing rapidly. The speed level in the main fiber optic communication of the present has reached 40Gbps, even 100Gbps, therefore data on the optical backbone network shows some features of massive data. Generally, data services are provided via IP packets on the optical backbone network, which is constituted with SDH (Synchronous Digital Hierarchy). Hence this method that IP packets are directly mapped into SDH payload is named POS (Packet over SDH) technology. Aiming at the problems of real time process of high speed massive data, this paper designs a process system platform based on ATCA for 40Gbps POS signal data stream recognition and packet content capture, which employs the FPGA as the CPU. This platform offers pre-processing of clustering algorithms, service traffic identification and data mining for the following big data storage and analysis with high efficiency. Also, the operational procedure is proposed in this paper. Four channels of 10Gbps POS signal decomposed by the analysis module, which chooses FPGA as the kernel, are inputted to the flow classification module and the pattern matching component based on TCAM. Based on the properties of the length of payload and net flows, buffer management is added to the platform to keep the key flow information. According to data stream analysis, DPI (deep packet inspection) and flow balance distribute, the signal is transmitted to the backend machine through the giga Ethernet ports on back board. Practice shows that the proposed platform is superior to the traditional applications based on ASIC and NP.

Zuo, Yuan; Huang, Zhiping; Su, Shaojing

2014-11-01

309

Short sequence motifs, overrepresented in mammalian conservednon-coding sequences  

SciTech Connect

Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by patterns in mutation, suggesting thatselection which causes their conservation is not always verystrong.

Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

2007-02-21

310

Helium-Abundance and Other Composition Effects on the Properties of Stellar Surface Convection in Solar-like Main-sequence Stars  

E-print Network

We investigate the effect of helium abundance and $\\alpha$-element enhancement on the properties of convection in envelopes of solar-like main-sequence stars stars using a grid of 3D radiation hydrodynamic simulations. Helium abundance increases the mean molecular weight of the gas, and alters opacity by displacing hydrogen. Since the scale of the effect of helium may depend on the metallicity, the grid consists of simulations with three helium abundances ($Y=0.1, 0.2, 0.3$), each with two metallicities ($Z=0.001, 0.020)$. We find that changing the helium mass fraction generally affects structure and convective dynamics in a way opposite to that of metallicity. Furthermore, the effect is considerably smaller than that of metallicity. The signature of helium differs from that of metallicity in the manner in which the photospheric velocity distribution is affected. \\rev{We also find that helium abundance and surface gravity behave largely in similar ways, but differ in the way they affect the mean molecular wei...

Tanner, Joel D; Demarque, Pierre

2013-01-01

311

Helium-abundance and Other Composition Effects on the Properties of Stellar Surface Convection in Solar-like Main-sequence Stars  

NASA Astrophysics Data System (ADS)

We investigate the effect of helium abundance and ?-element enhancement on the properties of convection in envelopes of solar-like main-sequence stars using a grid of three-dimensional radiation hydrodynamic simulations. Helium abundance increases the mean molecular weight of the gas and alters opacity by displacing hydrogen. Since the scale of the effect of helium may depend on the metallicity, the grid consists of simulations with three helium abundances (Y = 0.1, 0.2, 0.3), each with two metallicities (Z = 0.001, 0.020). We find that changing the helium mass fraction generally affects structure and convective dynamics in a way opposite to that of metallicity. Furthermore, the effect is considerably smaller than that of metallicity. The signature of helium differs from that of metallicity in the manner in which the photospheric velocity distribution is affected. We also find that helium abundance and surface gravity behave largely in similar ways, but differ in the way they affect the mean molecular weight. A simple model for spectral line formation suggests that the bisectors and absolute Doppler shifts of spectral lines depend on the helium abundance. We look at the effect of ?-element enhancement and find that it has a considerably smaller effect on the convective dynamics in the superadiabatic layer compared to that of helium abundance.

Tanner, Joel D.; Basu, Sarbani; Demarque, Pierre

2013-12-01

312

DNA Sequencing  

NSDL National Science Digital Library

Teachers' Domain presents this interactive, adapted from the Dolan DNA Learning Center, with reading material and animations to help students learn the basics of DNA sequencing. The lesson is divided two parts: Sanger Sequencing and Cycle Sequencing. The processes for both techniques are covered and animations help students visualize the material presented. On the site, visitors will also find a supplemental background essay, discussion questions, and standards alignment from Teachers' Domain.

313

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases.  

PubMed

• Compared with Sanger sequencing-based methods, pyrosequencing provides orders of magnitude more data on the diversity of organisms in their natural habitat, but its technological biases and relative accuracy remain poorly understood. • This study compares the performance of pyrosequencing and traditional sequencing for species' recovery of ectomycorrhizal fungi on root tips in a Cameroonian rain forest and addresses biases related to multi-template PCR and pyrosequencing analyses. • Pyrosequencing and the traditional method yielded qualitatively similar results, but there were slight, but significant, differences that affected the taxonomic view of the fungal community. We found that most pyrosequencing singletons were artifactual and contained a strongly elevated proportion of insertions compared with natural intra- and interspecific variation. The alternative primers, DNA extraction methods and PCR replicates strongly influenced the richness and community composition as recovered by pyrosequencing. • Pyrosequencing offers a powerful alternative for the identification of ectomycorrhizal fungi in pooled root samples, but requires careful selection of molecular tools. A well-populated backbone database facilitates the detection of biological and technical artifacts. The pyrosequencing pipeline is available at http://unite.ut.ee/454pipeline.tgz. PMID:20636324

Tedersoo, Leho; Nilsson, R Henrik; Abarenkov, Kessy; Jairus, Teele; Sadam, Ave; Saar, Irja; Bahram, Mohammad; Bechem, Eneke; Chuyong, George; Kõljalg, Urmas

2010-10-01

314

Pearl-necklace structures of molecular brushes with rigid backbone under poor solvent conditions: A simulation study  

E-print Network

Pearl-necklace structures of molecular brushes with rigid backbone under poor solvent conditions structure of "pearl-necklace" type is formed. The "pearls," however, have a strongly nonspherical ellipsoidal shape, due to the fact that several side chains cluster together in one pearl, qualitatively

Theodorakis, Panagiotis E.

315

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis  

SciTech Connect

We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 ?s, and the obtained trajectory of C{sub ?} atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

Naritomi, Yusuke [Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan)] [Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan); Fuchigami, Sotaro, E-mail: sotaro@tsurumi.yokohama-cu.ac.jp [Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan)] [Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan)

2013-12-07

316

A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data  

Microsoft Academic Search

We describe an efficient algorithm for protein backbone structure determination from solu- tion Nuclear Magnetic Resonance (NMR) data. A key feature of our algorithm is that it finds the conformation and orientation of secondary structure elements as well as the global fold in polynomial time. This is the first polynomial-time algorithm for de novo high-resolution biomacromolecular structure determination using experimentally

Lincong Wang; Ramgopal R. Mettu; Bruce Randall Donald

2006-01-01

317

Green Network Planning Model for Optical Backbones Jose Gutierrez, Tahir Riaz, Michael Jensen, Jens M. Pedersen and Ole B. Madsen  

E-print Network

. Unfortunately, the network planning tools have not followed energy efficiency criteria. There is a relationGreen Network Planning Model for Optical Backbones Jose Gutierrez, Tahir Riaz, Michael Jensen, Jens on the environment in general. In network planning there are existing planning models focused on QoS provisioning

Paris-Sud XI, Université de

318

Development of a poly(ortho ester) prototype with a latent acid in the polymer backbone for 5-fluorouracil delivery  

Microsoft Academic Search

A study has been carried out to determine whether the latest family of poly(ortho esters) can be converted into a practical delivery system. This polymer differs from the previously described polymers in that it incorporates a short segment of a latent acid in the polymer backbone. The following issues were specifically addressed: (a) can the erosion and drug release be

S. Y Ng; H. R Shen; E Lopez; Y Zherebin; J Barr; E Schacht; J Heller

2000-01-01

319

End-to-End QoS Architecture for VPNs: MPLS VPN Deployment in a Backbone Network  

Microsoft Academic Search

Virtual private networks (VPNs) enable companies to connect geographically dispersed offices and remote workers via secure links to the private company network, using the public Internet as a backbone. Specially, VPN service in the broadband data communication network is very important and necessary to take in users who want to specify group communication. VPN mechanisms are needed which work over

Haeryong Lee; Jeongyeon Hwang; Byungryong Kang; Kyoungpyo Jun

2000-01-01

320

Synergistic Inhibition of Human Cancer Cell Growth by Cytotoxic Drugs and Mixed Backbone Antisense Oligonucleotide Targeting Protein Kinase A  

Microsoft Academic Search

Protein kinase A type I plays a key role in neoplastic transformation, conveying mitogenic signals of different growth factors and oncogenes. Inhibition of protein kinase A type I by antisense oligonucleotides targeting its RIalpha regulatory subunit results in cancer cell growth inhibition in vitro and in vivo. A novel mixed backbone oligonucleotide HYB 190 and its mismatched control HYB 239

Giampaolo Tortora; Rosa Caputo; Vincenzo Damiano; Roberto Bianco; Stefano Pepe; A. Raffaele Bianco; Zhiwei Jiang; Sudhir Agrawal; Fortunato Ciardiello

1997-01-01

321

J. Chem. Soc., Perkin Trans. 1, 1997 1501 Building units for N-backbone cyclic peptides. Part 4.1  

E-print Network

J. Chem. Soc., Perkin Trans. 1, 1997 1501 Building units for N-backbone cyclic peptides. Part 4 by reductive alkylation of natural amino acids is reported. These new amino acids serve as building units or the chemical character of any amino acid residue required for bioactivity. This method also provides

Kasher, Roni

322

Simulation of large scale networks II: development of an internet backbone topology for large-scale network simulations  

Microsoft Academic Search

A number of network simulators are now capable of simulating systems with millions of devices, at the IP packet level. With this ability comes a need for realistic network descriptions of commensurate size. This paper describes our effort to build a detailed model of the U.S. Internet backbone based on measurements taken from a variety of mapping sources and tools.

Michael Liljenstam; Jason Liu; David M. Nicol

2003-01-01

323

Backbone Structure of the Amantadine-Blocked Trans-Membrane Domain M2 Proton Channel from Influenza A Virus  

E-print Network

Backbone Structure of the Amantadine-Blocked Trans-Membrane Domain M2 Proton Channel from Influenza proton channel of the Influenza A virus. Here, we present a structure of the M2 trans-membrane domain. INTRODUCTION Influenza is a worldwide epidemic that causes substantial morbidity and mortality. Of the three

Bertram, Richard

324

Empirical Study of a National-Scale Distributed Intrusion Detection System: Backbone-Level Filtering of HTML Responses in China  

Microsoft Academic Search

We present results from measurements of the filtering of HTTP HTML responses in China, which is based on string matching and TCP reset injection by backbone-level routers. This system, intended mainly for Internet censorship, is a national-scale filter based on intrusion detection system (IDS) technologies. Our results indicate that the Chinese censors discontinued this HTML response filtering for the majority

Jong Chun Park; Jedidiah R. Crandall

2010-01-01

325

Influence of the backbone structure on the release of bioactive volatiles from maleic acid-based polymer conjugates.  

PubMed

Poly(maleic acid monoester)-based ?-mercapto ketones were synthesized and investigated as potential delivery systems for the controlled release of bioactive, volatile, ?,?-unsaturated enones (such as damascones and damascenones) by retro 1,4-addition. The bioconjugates were prepared in a one-pot synthesis using 2-mercaptoethanol as a linker. The thiol group of 2-mercaptoethanol adds to the double bond of the enone to form a ?-mercapto ketone, which was then grafted via nucleophilic ring-opening of the remaining alcohol function onto a series of alternating copolymers of maleic anhydride and 1-octadecene, ethylene, isobutylene, and methyl vinyl ether. The influence of copolymer backbones on the release of ?-damascone was investigated in buffered aqueous solution as a function of pH and time. In the presence of a cationic surfactant, the polymer conjugates were transferred from an aqueous medium to a cotton surface. The deposition and the release of ?-damascone from the cotton surface as a function of the polymer backbone structure were measured by fluorescence spectroscopy and dynamic headspace analysis, respectively. All polymer conjugates were found to deliver higher amounts of the volatile into the headspace than the reference consisting of unmodified ?-damascone. Polymers with a hydrophobic backbone were generally efficiently deposited on the cotton surface, but released ?-damascone only moderately in solution. Conjugates with a more hydrophilic backbone release the active compound more efficiently in water, but are deposited to a lower extent onto the target surface. A good balance of the hydrophobicity and hydrophilicity of the polymer backbone is the key factor to maximize the deposition of the conjugates on the target surface and to optimize the release of the bioactive volatiles. PMID:20936844

Berthier, Damien L; Paret, Nicolas; Trachsel, Alain; Herrmann, Andreas

2010-11-17

326

Sequencing technologies and genome sequencing  

Microsoft Academic Search

The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human\\u000a and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers\\u000a based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern\\u000a bioinformatics tools at unprecedented pace,

Chandra Shekhar Pareek; Rafal Smoczynski; Andrzej Tretyn

327

Sequence Bracelets  

NSDL National Science Digital Library

In this craft-based activity, learners make DNA sequence bracelets that carry the code of an organism such as a human, trout, chimpanzee or butterfly. This activity reinforces the principle of complementary base pairs as learners are given one strand of the sequence and they have to match up the other strand correctly.

Wellcome Trust Sanger Institute

2012-06-26

328

Sequence Nets  

E-print Network

We study a new class of networks, generated by sequences of letters taken from a finite alphabet consisting of $m$ letters (corresponding to $m$ types of nodes) and a fixed set of connectivity rules. Recently, it was shown how a binary alphabet might generate threshold nets in a similar fashion [Hagberg et al., Phys. Rev. E 74, 056116 (2006)]. Just like threshold nets, sequence nets in general possess a modular structure reminiscent of everyday life nets, and are easy to handle analytically (i.e., calculate degree distribution, shortest paths, betweenness centrality, etc.). Exploiting symmetry, we make a full classification of two- and three-letter sequence nets, discovering two new classes of two-letter sequence nets. The new sequence nets retain many of the desirable analytical properties of threshold nets while yielding richer possibilities for the modeling of everyday life complex networks more faithfully.

Jie Sun; Takashi Nishikawa; Daniel ben-Avraham

2008-04-23

329

(1, k)-Compositions Phyllis Chinn  

E-print Network

(1, k)-Compositions Phyllis Chinn Dept. of Mathematics, Humboldt State University phyllis@calstatela.edu Abstract A (1, k)-composition of a positive integer n consists of an ordered sequence of the integers 1 and k whose sum is n. A palindromic (1, k)-composition is one for which the sequence is the same from

Heubach, Silvia

330

sequence quality values Sanger sequencing  

E-print Network

phred sequence quality values #12;Sanger sequencing · DNA is fragmented · Cloned to a plasmid concept of phred quality values #12;Phred Qualities )(log10 10 pq -= · p=error probability for the base · if p=0.01 (1% chance of error), then q=20 · Phred quality values are rounded to the nearest integer #12

Borenstein, Elhanan

331

Recurrence Sequences  

NSDL National Science Digital Library

A book on recurrence sequences, an advanced topic in number theory, can be downloaded from this site. It deals mainly with linear recurrence sequences, and provides extensive theory, methods, and equations. While the material is quite complex, it has applications for various disciplines. The authors state, "these sequences appear almost everywhere in mathematics and computer science." The book is in draft form, and will be featured in the Surveys and Monographs series of the American Mathematical Society sometime in 2003. Until then, however, the book can be accessed here for the purpose of correcting any errors.

Everest, Graham.

332

Dna Sequencing  

DOEpatents

A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

1995-04-25

333

Solution studies of staphylococcal nuclease H124L. 1. Backbone sup 1 H and sup 15 N resonances and secondary structure of the unligated enzyme as identified by three-dimensional NMR spectroscopy  

SciTech Connect

The backbone {sup 1}H and {sup 15}N resonances of unligated staphylococcal nuclease H124L (recombinant protein produced in Escherichia coli whose sequence is identical to the nuclease produced by the V8 strain of Staphylococcus aureus) have been assigned by three-dimensional (3D) {sup 1}H-{sup 15}N NOESY-HMQC NMR spectroscopy at 14.1 tesla. The protein sample used in this study was labeled uniformly with {sup 15}N to a level greater than 95% by growing the E. coli host on a medium containing (99% {sup 15}N)ammonium sulfate as the sole nitrogen source. The assignments include 82% of the backbone {sup 1}H{sup N} and {sup 1}H{sup {alpha}} resonances as well as the {sup 15}N resonances of non-proline residues. Secondary structural elements ({alpha}-helices, {beta}-sheets, reverse turns, and loops) were determined by analysis of patterns of NOE connectivities present in the 3D spectrum.

Wang, Jinfeng; Mooberry, E.S.; Walkenhorst, W.F.; Markley, J.L. (Univ. of Wisconsin, Madison (United States))

1992-01-28

334

Antimicrobial activity of chitosan derivatives containing N-quaternized moieties in its backbone: a review.  

PubMed

Chitosan, which is derived from a deacetylation reaction of chitin, has attractive antimicrobial activity. However, chitosan applications as a biocide are only effective in acidic medium due to its low solubility in neutral and basic conditions. Also, the positive charges carried by the protonated amine groups of chitosan (in acidic conditions) that are the driving force for its solubilization are also associated with its antimicrobial activity. Therefore, chemical modifications of chitosan are required to enhance its solubility and broaden the spectrum of its applications, including as biocide. Quaternization on the nitrogen atom of chitosan is the most used route to render water-soluble chitosan-derivatives, especially at physiological pH conditions. Recent reports in the literature demonstrate that such chitosan-derivatives present excellent antimicrobial activity due to permanent positive charge on nitrogen atoms side-bonded to the polymer backbone. This review presents some relevant work regarding the use of quaternized chitosan-derivatives obtained by different synthetic paths in applications as antimicrobial agents. PMID:25402643

Martins, Alessandro F; Facchi, Suelen P; Follmann, Heveline D M; Pereira, Antonio G B; Rubira, Adley F; Muniz, Edvani C

2014-01-01

335

Mechanics and Chemistry: Sinle Molecule Bond Rupture Forces Correlate with Molecular Backbone Structure  

SciTech Connect

We simultaneously measure conductance and force across nanoscale junctions. A new, two-dimensional histogram technique is introduced to statistically extract bond rupture forces from a large data set of individual junction elongation traces. For the case of Au point contacts, we find a rupture force of 1.4 {+-} 0.2 nN, which is in good agreement with previous measurements. We then study systematic trends for single gold metal-molecule-metal junctions for a series of molecules terminated with amine and pyridine linkers. For all molecules studied, single molecule junctions rupture at the Au-N bond. Selective binding of the linker group allows us to correlate the N-Au bond-rupture force to the molecular backbone. We find that the rupture force ranges from 0.8 nN for 4,4' bipyridine to 0.5 nN in 1,4 diaminobenzene. These experimental results are in excellent quantitative agreement with density functional theory based adiabatic molecular junction elongation and rupture calculations.

Frei, M.; Hybertsen, M.; Aradhya, S.V.; Koentopp, M.; Venkataraman, L.

2011-03-02

336

APSY-NMR for protein backbone assignment in high-throughput structural biology.  

PubMed

A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [(1)H,(1)H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination. PMID:25428764

Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael; Pedrini, Bill; Herrmann, Torsten; Wüthrich, Kurt

2015-01-01

337

An Enhanced Backbone-Assisted Reliable Framework for Wireless Sensor Networks  

PubMed Central

An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs) encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR) scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability. PMID:22294890

Tufail, Ali; Khayam, Syed Ali; Raza, Muhammad Taqi; Ali, Amna; Kim, Ki-Hyung

2010-01-01

338

Participation of bacteriorhodopsin active-site lysine backbone in vibrations associated with retinal photochemistry.  

PubMed

Bacteriorhodopsin (bR) has been biosynthetically prepared with lysine deuterated at its alpha carbon (C alpha--H). The labeled membranes containing bR were investigated by difference Fourier transform infrared (FTIR) spectroscopy. It has been derived from K/bR and M/bR difference spectra (K and M are photocycle intermediates) that several bands previously assigned to the retinal chromophore are coupled to the C alpha--H. The vibrational modes that exhibit this coupling are principally associated with C15--H and N--H vibrations. [C alpha--2H]Lysine-labeled bR was fragmented enzymatically, and bR structures were regenerated with the C alpha--2H label either on lysine-216 and -172 or on the remaining five lysine residues of the protein. FTIR studies of the regenerated bR system, together with methylation of all lysines except the active-site lysine, reveal that the changes observed due to backbone labeling arise from the active-site lysine. The intensity of the C15--H out-of-plane wag is interpreted as a possible indication of a twist around the C15 = N bond. PMID:1549607

Gat, Y; Grossjean, M; Pinevsky, I; Takei, H; Rothman, Z; Sigrist, H; Lewis, A; Sheves, M

1992-03-15

339

Participation of bacteriorhodopsin active-site lysine backbone in vibrations associated with retinal photochemistry.  

PubMed Central

Bacteriorhodopsin (bR) has been biosynthetically prepared with lysine deuterated at its alpha carbon (C alpha--H). The labeled membranes containing bR were investigated by difference Fourier transform infrared (FTIR) spectroscopy. It has been derived from K/bR and M/bR difference spectra (K and M are photocycle intermediates) that several bands previously assigned to the retinal chromophore are coupled to the C alpha--H. The vibrational modes that exhibit this coupling are principally associated with C15--H and N--H vibrations. [C alpha--2H]Lysine-labeled bR was fragmented enzymatically, and bR structures were regenerated with the C alpha--2H label either on lysine-216 and -172 or on the remaining five lysine residues of the protein. FTIR studies of the regenerated bR system, together with methylation of all lysines except the active-site lysine, reveal that the changes observed due to backbone labeling arise from the active-site lysine. The intensity of the C15--H out-of-plane wag is interpreted as a possible indication of a twist around the C15 = N bond. PMID:1549607

Gat, Y; Grossjean, M; Pinevsky, I; Takei, H; Rothman, Z; Sigrist, H; Lewis, A; Sheves, M

1992-01-01

340

Antimicrobial Activity of Chitosan Derivatives Containing N-Quaternized Moieties in Its Backbone: A Review  

PubMed Central

Chitosan, which is derived from a deacetylation reaction of chitin, has attractive antimicrobial activity. However, chitosan applications as a biocide are only effective in acidic medium due to its low solubility in neutral and basic conditions. Also, the positive charges carried by the protonated amine groups of chitosan (in acidic conditions) that are the driving force for its solubilization are also associated with its antimicrobial activity. Therefore, chemical modifications of chitosan are required to enhance its solubility and broaden the spectrum of its applications, including as biocide. Quaternization on the nitrogen atom of chitosan is the most used route to render water-soluble chitosan-derivatives, especially at physiological pH conditions. Recent reports in the literature demonstrate that such chitosan-derivatives present excellent antimicrobial activity due to permanent positive charge on nitrogen atoms side-bonded to the polymer backbone. This review presents some relevant work regarding the use of quaternized chitosan-derivatives obtained by different synthetic paths in applications as antimicrobial agents. PMID:25402643

Martins, Alessandro F.; Facchi, Suelen P.; Follmann, Heveline D. M.; Pereira, Antonio G. B.; Rubira, Adley F.; Muniz, Edvani C.

2014-01-01

341

Ionization Cross Sections and Dissociation Channels of the DNA Sugar-Phosphate Backbone by Electron Collisions  

NASA Technical Reports Server (NTRS)

It has been suggested that the genotoxic effects of ionizing radiation in living cells are not caused by the highly energetic incident radiation, but rather are induced by less energetic secondary species generated, the most abundant of which are free electrons.' The secondary electrons will further react to cause DNA damage via indirect and direct mechanisms. Detailed knowledge of these mechanisms is ultimately important for the development of global models of cellular radiation damage. We are studying one possible mechanism for the formation cf DNA strand breaks involving dissociative ionization of the DNA sugar-phosphate backbone induced by secondary electron co!lisions. We will present ionization cross sections at electron collision energies between threshold and 10 KeV using the improved binary encounter dipole (iBED) formulation' Preliminary results of the possible dissociative ionization pathways will be presented. It is speculated that radical fragments produced from the dissociative ionization can further react, providing a possible mechanism for double strand breaks and base damage.

Dateo, Christopher; Huo, Winifred M.; Fletcher, Graham D.

2004-01-01

342

Quantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of 3J couplings  

PubMed Central

Three-bond 3JC?C? and 3JHNH? couplings in peptides and proteins both are functions of the intervening backbone torsion angle ?. In well ordered regions, 3JHNH? is tightly correlated with 3JC?C?, but the presence of large ? angle fluctuations differentially affects the two types of couplings. Assuming the ? angles to follow a Gaussian distribution, the width of this distribution can be extracted from 3JC?C? and 3JHNH?, as demonstrated for the folded proteins ubiquitin and GB3. In intrinsically disordered proteins, slow transverse relaxation permits measurement of 3JC?C? and 3JHNH couplings at very high precision, and impact of factors other than the intervening torsion angle on 3J will be minimal, making these couplings exceptionally valuable structural reporters. Analysis of ?-synuclein yields rather homogeneous widths of 69±6° for the ? angle distributions, and 3JC?C? values that agree well with those of a recent maximum entropy analysis of chemical shifts, J couplings, and 1H-1H NOEs. Data are consistent with a modest (? 30%) population of the polyproline II region. PMID:25590347

Lee, Jung Ho; Li, Fang; Grishaev, Alexander; Bax, Ad

2015-01-01

343

Quantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of (3)j couplings.  

PubMed

Three-bond (3)JC'C' and (3)JHNH? couplings in peptides and proteins are functions of the intervening backbone torsion angle ?. In well-ordered regions, (3)JHNH? is tightly correlated with (3)JC'C', but the presence of large ? angle fluctuations differentially affects the two types of couplings. Assuming the ? angles follow a Gaussian distribution, the width of this distribution can be extracted from (3)JC'C' and (3)JHNH?, as demonstrated for the folded proteins ubiquitin and GB3. In intrinsically disordered proteins, slow transverse relaxation permits measurement of (3)JC'C' and (3)JHNH couplings at very high precision, and impact of factors other than the intervening torsion angle on (3)J will be minimal, making these couplings exceptionally valuable structural reporters. Analysis of ?-synuclein yields rather homogeneous widths of 69 ± 6° for the ? angle distributions and (3)JC'C' values that agree well with those of a recent maximum entropy analysis of chemical shifts, J couplings, and (1)H-(1)H NOEs. Data are consistent with a modest (?30%) population of the polyproline II region. PMID:25590347

Lee, Jung Ho; Li, Fang; Grishaev, Alexander; Bax, Ad

2015-02-01

344

Sequence Data  

E-print Network

– Know how to access and read Genbank entries • Database Queries (BLASTing) – Know how to query database with BLAST (by web, command-line, & perl) – Know how to read BLAST reports No library is complete without a sequence database

Embl Genbank; At Ebi

345

Sequence Matching  

E-print Network

The vast increase of genomic sequence data reveals the limitation of single computer systems in terms of both processing and storage capacity. The only realistic way to cope with this growth in the near future will consist in using several computers rather than a single one. Catching up with the steady growth of genomic sequence data is likely to require systems with an increasingly large number of nodes.

Human Genome; Yoshiyuki Tanaka; Takeshi Nagashima; Akihiko Konagaya

346

Comparison of DNA Sequences with Protein Sequences  

Microsoft Academic Search

The FASTA package of sequence comparison programs has been expanded to include FASTX and FASTY, which compare a DNA sequence to a protein sequence database, translating the DNA sequence in three frames and aligning the translated DNA sequence to each sequence in the protein database, allowing gaps and frameshifts. Also new are TFASTX and TFASTY, which compare a protein sequence

William R. Pearson; Todd Wood; Zheng Zhang; Webb Miller

1997-01-01

347

Composition of the summer photosynthetic pico and nanoplankton communities in the Beaufort Sea assessed by T-RFLP and sequences of the 18S rRNA gene from flow cytometry sorted samples.  

PubMed

The composition of photosynthetic pico and nanoeukaryotes was investigated in the North East Pacific and the Arctic Ocean with special emphasis on the Beaufort Sea during the MALINA cruise in summer 2009. Photosynthetic populations were sorted using flow cytometry based on their size and pigment fluorescence. Diversity of the sorted photosynthetic eukaryotes was determined using terminal-restriction fragment length polymorphism analysis and cloning/sequencing of the 18S ribosomal RNA gene. Picoplankton was dominated by Mamiellophyceae, a class of small green algae previously included in the prasinophytes: in the North East Pacific, the contribution of an Arctic Micromonas ecotype increased steadily northward becoming the only taxon occurring at most stations throughout the Beaufort Sea. In contrast, nanoplankton was more diverse: North Pacific stations were dominated by Pseudo-nitzschia sp. whereas those in the Beaufort Sea were dominated by two distinct Chaetoceros species as well as by Chrysophyceae, Pelagophyceae and Chrysochromulina spp.. This study confirms the importance of Arctic Micromonas within picoplankton throughout the Beaufort Sea and demonstrates that the photosynthetic picoeukaryote community in the Arctic is much less diverse than at lower latitudes. Moreover, in contrast to what occurs in warmer waters, most of the key pico- and nanoplankton species found in the Beaufort Sea could be successfully established in culture. PMID:22278671

Balzano, Sergio; Marie, Dominique; Gourvil, Priscillia; Vaulot, Daniel

2012-08-01

348

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence  

E-print Network

plants have large and complex genomes with an abundance of repeated sequences.plants have large and complex genomes with a great abundance of repeated sequences.Sequence composition, organization, and evolution of the core Triticeae genome. Plant

2011-01-01

349

Progress in palladium-based catalytic systems for the sustainable synthesis of annulated heterocycles: a focus on indole backbones.  

PubMed

A survey highlighting the most recent palladium catalytic systems produced and their performances for progress in direct synthesis of indole backbones by heterocarbocyclization of reactive substrates is provided. The discussion is developed in relation with the principles of sustainable chemistry concerning atom and mass economy. In this respect, the general convergent character of the syntheses is of particular interest (one-pot, domino, cascade or tandem reactions), and the substrates accessibility and reactivity, together with the final waste production, are also important. This critical review clearly indicates that the development of ligand chemistry, mainly phosphines and carbenes, in the last few decades gave a significant impetus to powerful functionalization of indoles at virtually all positions of this ubiquitous backbone (118 references). PMID:22447100

Platon, Mélanie; Amardeil, Régine; Djakovitch, Laurent; Hierso, Jean-Cyrille

2012-05-21

350

Photoinduced bending behavior of cross-linked azobenzene liquid-crystalline polymer films with a poly(oxyethylene) backbone.  

PubMed

Cross-linked azobenzene liquid-crystalline polymer films with a poly(oxyethylene) backbone are synthesized by photoinitiated cationic copolymerization. Azobenzene moieties in the film surface toward the light source are simultaneously photoaligned during photopolymerization with unpolarized 436 nm light and thus form a splayed alignment in the whole film. The prepared films show reversible photoinduced bending behavior with opposite bending directions when different surfaces of one film face to ultraviolet light irradiation. PMID:24771514

Lv, Jiu-an; Wang, Weiru; Xu, Jixiang; Ikeda, Tomiki; Yu, Yanlei

2014-07-01

351

Liquid crystalline side chain polymer with a poly (Geraniol-co-MMA) backbone and phenylbenzoate mesogenic group: synthesis and characterization  

Microsoft Academic Search

A new side chain liquid crystalline polymers have been synthesized and characterized in which [geraniol-co-MMA] polymer are\\u000a used as a backbone linked via polymethylene spacer to phenyl benzoate mesogenic group. The polymer exhibits enantiotropic\\u000a liquid crystallinity with nematic phase and does not exhibit side chain crystallization .A clear difference between the nature\\u000a of the mesophase is evidenced between [Geraniol-co-MMA] main

Garima Misra; A. K. Srivastava

2008-01-01

352

Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones under poor solvent conditions  

NASA Astrophysics Data System (ADS)

Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N = 40 effective monomers. By variation of the solvent quality and the grafting density ? with which side chains are grafted onto the flexible backbone, we study for backbone lengths of up to Nb = 100 the crossover from the brush/coil regime to the dense collapsed state. At lower temperatures, where collapsed chains with a constant monomer density are observed, the choice of the above parameters does not play any role and it is the total number of monomers that defines the dimensions of the chains. Furthermore, bottle-brush polymers with longer side chains possess higher spherical symmetry compared to polymers with lower side-chain lengths in contrast to what one may intuitively expect, as the stretching of the side chains is less important than the increase of their length. At higher temperatures, always below the Theta (?) temperature, coil-like configurations, similar to a single polymer chain, or brush-like configurations, similar to a homogeneous cylindrical bottle-brush polymer with a rigid backbone, are observed, depending on the choice of the particular parameters N and ?. In the crossover regime between the collapsed state (globule) and the coil/brush regime the acylindricity increases, whereas for temperatures outside of this range, bottle-brush polymers maintain a highly cylindrical symmetry in all configurational states.

Fytas, Nikolaos G.; Theodorakis, Panagiotis E.

2013-07-01

353

Molecular dynamics simulations of single-component bottle-brush polymers with a flexible backbone under poor solvent conditions  

E-print Network

Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40 effective monomers. By variation of the solvent quality and the grafting density $\\sigma$ with which side chains are grafted onto the flexible backbone, we study for backbone lengths of up to $N_b=100$ the crossover from the brush/coil regime to the dense collapsed state. At lower temperatures, where collapsed chains with a constant monomer density are observed, the choice of the above parameters does not play any role and it is the total number of monomers that defines the dimensions of the chains. Furthermore, bottle-brush polymers with longer side chains possess higher spherical symmetry compared to chains with lower side-chain lengths in contrast to what one may intuitively expect, as the stretching of the side chains is less important than the increase of their length. At higher temperatures, always below the Theta ($\\Theta$) temperature, coil-like configurations, similar to a single polymer chain, or brush-like configurations, similar to a homogeneous cylindrical bottle-brush polymer with a rigid backbone, are observed, depending on the choice of the particular parameters $N$ and $\\sigma$. In the crossover regime between the collapsed state (globule) and the coil/brush regime the acylindricity increases, whereas for temperatures outside of this range, bottle-brush polymers maintain a highly cylindrical symmetry in all configurational states.

Nikolaos G. Fytas; Panagiotis E. Theodorakis

2013-06-04

354

Modeling of electrochemomechanical response of ionic polymer-metal composites with various solvents  

Microsoft Academic Search

Ionic polymer-metal composites (IPMCs) consist of a perfluorinated ionomer membrane (usually Nafion® or Flemion®) plated on both faces with a noble metal such as gold or platinum and neutralized with the necessary amount of counterions that balance the electrical charge of anions that are covalently fixed to the backbone ionomer. IPMCs are electroactive materials with potential applications as soft actuators

Sia Nemat-Nasser; Shahram Zamani

2006-01-01

355

Experimental study of Nafion-based ionic polymer-metal composites (IPMCs) with glycerol as solvent  

Microsoft Academic Search

Ionic polymer-metal composites (IPMCs) consist of a perfluorinated ionomer membrane (usually Nafion or Flemion) plated on both faces with a noble metal such as gold or platinum and neutralized with a certain amount of counterions that balance the electrical charge of anions covalently fixed to the membrane backbone. IPMCs are electroactive materials that can be used as actuators and sensors.

Shahram Zamani; Siavouche Nemat-Nasser

2005-01-01

356

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks  

PubMed Central

Summary Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T–T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X–T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A–T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues. PMID:25670992

Schmidtgall, Boris; Höbartner, Claudia

2015-01-01

357

A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13–19  

PubMed Central

In CAPRI rounds 13–19, the most native-like structure predicted by RosettaDock resulted in two high, one medium and one acceptable accuracy model out of 13 targets. The current rounds of CAPRI were especially challenging with many unbound and homology modeled starting structures. Novel docking methods, including EnsembleDock and SnugDock, allowed backbone conformational sampling during docking and enabled the creation of more accurate models. For Target 32, ?-amylase/subtilisin inhibitor-subtilisin savinase, we sampled different backbone conformations at an interfacial loop to produce five high-quality models including the most accurate structure submitted in the challenge (2.1 Å ligand rmsd, 0.52 Å interface rmsd). For Target 41, colicin-immunity protein, we used EnsembleDock to sample the ensemble of nuclear magnetic resonance (NMR) models of the immunity protein to generate a medium accuracy structure. Experimental data identifying the catalytic residues at the binding interface for Target 40 (trypsin-inhibitor) were used to filter RosettaDock global rigid body docking decoys to determine high accuracy predictions for the two distinct binding sites in which the inhibitor interacts with trypsin. We discuss our generalized approach to selecting appropriate methods for different types of docking problems. The current toolset provides some robustness to errors in homology models, but significant challenges remain in accommodating larger backbone uncertainties and in sampling adequately for global searches. PMID:20535822

Sircar, Aroop; Chaudhury, Sidhartha; Kilambi, Krishna Praneeth; Berrondo, Monica; Gray, Jeffrey J.

2010-01-01

358

Direct measurement of the correlated dynamics of the protein-backbone and proximal waters of hydration in mechanically strained elastin  

E-print Network

We report on the direct measurement of the correlation times of the protein backbone carbons and proximal waters of hydration in mechanically strained elastin by nuclear magnetic resonance methods. The experimental data indicate a decrease in the correlation times of the carbonyl carbons as the strain on the biopolymer is increased. These observations are in good agreement with short 4ns molecular dynamics simulations of (VPGVG)3, a well studied mimetic peptide of elastin. The experimental results also indicate a reduction in the correlation time of proximal waters of hydration with increasing strain applied to the elastomer. A simple model is suggested that correlates the increase in the motion of proximal waters of hydration to the increase in frequency of libration of the protein backbone that develops with increasing strain. Together, the reduction in the protein entropy accompanied with the increase in entropy of the proximal waters of hydration with increasing strain, support the notion that the source of elasticity is driven by an entropic mechanism arising from the change in entropy of the protein backbone.

Cheng Sun; Odingo Mitchell; Jiaxin Huang; Gregory S. Boutis

2011-04-05

359

Electron-impact total ionization cross sections of DNA sugar-phosphate backbone and an additivity principle  

NASA Technical Reports Server (NTRS)

The improved binary-encounter dipole (iBED) model [W.M. Huo, Phys. Rev. A64, 042719-1 (2001)l is used to study the total ionization cross sections of the DNA sugar-phosphate backbone by electron impact. Calculations using neutral fragments found that the total ionization cross sections of C3' - and C5', -deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3' - and C5" -deoxyribose-phospate cross sections, differing by less than 10%. The result implies that certain properties of the-DNA, like the total singly ionization cross section, are localized properties and a building-up or additivity principle may apply. This allows us to obtain accurate properties of larger molecular systems built up from the results of smaller subsystem fragments. Calculations are underway using a negatively charged sugar-phosphate backbone with a metal counter-ion.

Huo, Winifred M.; Dateo, Christopher E.

2005-01-01

360

Pressure response of protein backbone structure. Pressure-induced amide 15N chemical shifts in BPTI.  

PubMed Central

The effect of pressure on amide 15N chemical shifts was studied in uniformly 15N-labeled basic pancreatic trypsin inhibitor (BPTI) in 90%1H2O/10%2H2O, pH 4.6, by 1H-15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 +/- 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0-1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three-dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 A/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site-specific changes in phi, psi angles. For beta-sheet residues, a decrease in psi angles by 1-2 degrees/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 +/- 0.343 and 0.519 +/- 0.261 ppm/2 kbar, respectively) than for beta-sheet (0.295 +/- 0.195 ppm/2 kbar), suggesting that the pressure-induced structural changes (local compressibilities) are larger in helical and loop regions than in beta-sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in beta-sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place. PMID:10548039

Akasaka, K.; Li, H.; Yamada, H.; Li, R.; Thoresen, T.; Woodward, C. K.

1999-01-01

361

Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.  

PubMed

We use quantum mechanics/molecular mechanics simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA-cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ?15 kcal mol(-1), encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ?1-100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The nonmonotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton-transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA-cleavage reaction. PMID:21539371

Rosta, Edina; Nowotny, Marcin; Yang, Wei; Hummer, Gerhard

2011-06-15

362

Phosphorus chemical shifts in a nucleic acid backbone from combined molecular dynamics and density functional calculations.  

PubMed

A comprehensive quantum chemical analysis of the influence of backbone torsion angles on (31)P chemical shifts in DNAs has been carried out. An extensive DFT study employed snapshots obtained from the molecular dynamics simulation of [d(CGCGAATTCGCG)]2 to construct geometries of a hydrated dimethyl phosphate, which was used as a model for the phosphodiester linkage. Our calculations provided differences of 2.1 ± 0.3 and 1.6 ± 0.3 ppm between the B(I) and B(II) chemical shifts in two B-DNA residues of interest, which is in a very good agreement with the difference of 1.6 ppm inferred from experimental data. A more negative (31)P chemical shift for a residue in pure BI conformation compared to residues in mixed B(I)/B(II) conformation states is provided by DFT, in agreement with the NMR experiment. Statistical analysis of the MD/DFT data revealed a large dispersion of chemical shifts in both B(I) and B(II) regions of DNA structures. ?P ranges within 3.5 ± 0.8 ppm in the B(I) region and within 4.5 ± 1.5 ppm in the B(II) region. While the (31)P chemical shift becomes more negative with increasing ? in B(I)-DNA, it has the opposite trend in B(II)-DNA when both ? and ? increase simultaneously. The (31)P chemical shift is dominated by the torsion angles ? and ?, while an implicit treatment of ? and ? is sufficient. The presence of an explicit solvent leads to a damping and a 2-3 ppm upfield shift of the torsion angle dependences. PMID:21073198

P?ececht?lová, Jana; Novák, Petr; Munzarová, Markéta L; Kaupp, Martin; Sklená?, Vladimír

2010-12-01

363

The multiscale backbone of the human phenotype network based on biological pathways  

PubMed Central

Background Networks are commonly used to represent and analyze large and complex systems of interacting elements. In systems biology, human disease networks show interactions between disorders sharing common genetic background. We built pathway-based human phenotype network (PHPN) of over 800 physical attributes, diseases, and behavioral traits; based on about 2,300 genes and 1,200 biological pathways. Using GWAS phenotype-to-genes associations, and pathway data from Reactome, we connect human traits based on the common patterns of human biological pathways, detecting more pleiotropic effects, and expanding previous studies from a gene-centric approach to that of shared cell-processes. Results The resulting network has a heavily right-skewed degree distribution, placing it in the scale-free region of the network topologies spectrum. We extract the multi-scale information backbone of the PHPN based on the local densities of the network and discarding weak connection. Using a standard community detection algorithm, we construct phenotype modules of similar traits without applying expert biological knowledge. These modules can be assimilated to the disease classes. However, we are able to classify phenotypes according to shared biology, and not arbitrary disease classes. We present examples of expected clinical connections identified by PHPN as proof of principle. Conclusions We unveil a previously uncharacterized connection between phenotype modules and discuss potential mechanistic connections that are obvious only in retrospect. The PHPN shows tremendous potential to become a useful tool both in the unveiling of the diseases’ common biology, and in the elaboration of diagnosis and treatments. PMID:24460644

2014-01-01

364

Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities  

E-print Network

We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van der Waals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel $r^{-5}$ scaling behavior of the van der Waals interaction energy for small inter-polymer separation $r$, in contradistinction to the $r^{-4}$ scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently aligned identical polymers. Such behavior can assist the molecular recognition between polymers.

Bing-Sui Lu; Ali Naji; Rudolf Podgornik

2015-03-18

365

The reducing end sequence of wheat endosperm cell wall arabinoxylans.  

PubMed

Walls from wheat (Triticum aestivum L.) endosperm are composed primarily of hetero-(arabino)xylans (AXs) (70%) and (1?3)(1?4)-?-D-glucans (20%) with minor amounts of cellulose and heteromannans (2% each). To understand the differential solubility properties of the AXs, as well as aspects of their biosynthesis, we are sequencing the xylan backbone and examining the reducing end (RE) sequence(s) of wheat (monocot) AXs. A previous study of grass AXs (switchgrass, rice, Brachypodium, Miscanthus and foxtail millet) concluded that grasses lacked the comparable RE glycosyl sequence (4-?-D-Xylp-(1?4)-?-D-Xylp-(1?3)-?-L-Rhap-(1?2)-?-D-GalpA-(1?4)-D-Xylp) found in dicots and gymnosperms but the actual RE sequence was not determined. Here we report the isolation and structural characterisation of the RE oligosaccharide sequence(s) of wheat endosperm cell wall AXs. Walls were isolated as an alcohol-insoluble residue (AIR) and sequentially extracted with hot water (W-sol Fr) and 1M KOH containing 1% NaBH4 (KOH-sol Fr). Detailed structural analysis of the RE oligosaccharides was performed using a combination of methylation analysis, MALDI-TOF-MS, ESI-QTOF-MS, ESI-MS(n) and enzymic analysis. Analysis of RE oligosaccharides, both 2AB labelled (from W-sol Fr) and glycosyl-alditol (from KOH-sol Fr), revealed that the RE glycosyl sequence of wheat endosperm AX comprises a linear (1?4)-?-D-Xylp backbone which may be mono-substituted with either an ?-L-Araf residue at the reducing end ?-D-Xylp residue and/or penultimate RE ?-D-Xyl residue; ?-D-Xylp-(1?4)-[?-L-Araf-(1?3)](+/-)-?-D-Xylp-(1?4)-[?-L-Araf-(1?3)](+/-)-?-D-Xylp and/or an ?-D-GlcpA residue at the reducing end ?-D-Xylp residue; ?-D-Xylp-(1?4)-[?-L-Araf-(1?3)](+/-)-?-D-Xylp-(1?4)-[?-D-GlcAp-(1?2)]-?-D-Xylp. Thus, wheat endosperm AX backbones lacks the RE sequence found in dicot and gymnosperm xylans; a finding consistent with previous reports from other grass species. PMID:24462668

Ratnayake, Sunil; Beahan, Cherie T; Callahan, Damien L; Bacic, Antony

2014-03-11

366

Proteomics-grade de novo sequencing approach.  

PubMed

The conventional approach in modern proteomics to identify proteins from limited information provided by molecular and fragment masses of their enzymatic degradation products carries an inherent risk of both false positive and false negative identifications. For reliable identification of even known proteins, complete de novo sequencing of their peptides is desired. The main problems of conventional sequencing based on tandem mass spectrometry are incomplete backbone fragmentation and the frequent overlap of fragment masses. In this work, the first proteomics-grade de novo approach is presented, where the above problems are alleviated by the use of complementary fragmentation techniques CAD and ECD. Implementation of a high-current, large-area dispenser cathode as a source of low-energy electrons provided efficient ECD of doubly charged peptides, the most abundant species (65-80%), in a typical trypsin-based proteomics experiment. A new linear de novo algorithm is developed combining efficiency and speed, processing on a conventional 3 GHz PC, 1000 MS/MS data sets in 60 s. More than 6% of all MS/MS data for doubly charged peptides yielded complete sequences, and another 13% gave nearly complete sequences with a maximum gap of two amino acid residues. These figures are comparable with the typical success rates (5-15%) of database identification. For peptides reliably found in the database (Mowse score > or = 34), the agreement with de novo-derived full sequences was >95%. Full sequences were derived in 67% of the cases when full sequence information was present in MS/MS spectra. Thus the new de novo sequencing approach reached the same level of efficiency and reliability as conventional database-identification strategies. PMID:16335984

Savitski, Mikhail M; Nielsen, Michael L; Kjeldsen, Frank; Zubarev, Roman A

2005-01-01

367

Sequence Quantification  

E-print Network

Abstract. Several earlier papers have shown that bounded quantification is an expressive and comfortable addition to logic programming languages. One shortcoming of bounded quantification, however, is that it does not allow easy and efficient relation of corresponding elements of aggregations being quantified over (lockstep iteration). Bounded quantification also does not allow easy quantification over part of an aggregation, nor does it make it easy to accumulate a result over an aggregation. We generalize the concept of bounded quantification to quantification over any finite sequence, as we can use a rich family of operations on sequences to create a language facility that avoids the weaknesses mentioned above. We also propose a concrete syntax for sequence quantification in Prolog programs, which we have implemented as a source-to-source transformation.

unknown authors

368

Methods and compositions for chromosome-specific staining  

DOEpatents

Methods and compositions for chromosome-specific staining are provided. Compositions comprise heterogenous mixtures of labeled nucleic acid fragments having substantially complementary base sequences to unique sequence regions of the chromosomal DNA for which their associated staining reagent is specific. Methods include methods for making the chromosome-specific staining compositions of the invention, and methods for applying the staining compositions to chromosomes.

Gray, Joe W.; Pinkel, Daniel

2003-07-22

369

Backbone 1H, 15N, and 13C resonance assignments and secondary structure of a novel protein OGL-20P(T)-358 from hyperthermophile Thermococcus thioreducens sp. nov.  

PubMed

OGL-20P(T)-358 is a novel 66 amino acid residue protein from the hyperthermophile Thermococcus thioreducens sp. nov., strain OGL-20PT, which was collected from the wall of the hydrothermal black smoker in the Rainbow Vent along the mid-Atlantic ridge. This protein, which has no detectable sequence homology with proteins or domains of known function, has a calculated pI of 4.76 and a molecular mass of 8.2 kDa. We report here the backbone 1H, 15N, and 13C resonance assignments of OGL-20PT-358. Assignments are 97.5% (316/324) complete. Chemical shift index was used to determine the secondary structure of the protein, which appears to consist of primarily alpha-helical regions. This work is the foundation for future studies to determine the three-dimensional solution structure of the protein. PMID:18182861

Wilson, Randall; Hughes, Ronny; Curto, Ernest; Ng, Joseph; Twigg, Pamela

2007-12-31

370

Whole-Genome Sequence Variation among Multiple Isolates of Pseudomonas aeruginosa  

PubMed Central

Whole-genome shotgun sequencing was used to study the sequence variation of three Pseudomonas aeruginosa isolates, two from clonal infections of cystic fibrosis patients and one from an aquatic environment, relative to the genomic sequence of reference strain PAO1. The majority of the PAO1 genome is represented in these strains; however, at least three prominent islands of PAO1-specific sequence are apparent. Conversely, ?10% of the sequencing reads derived from each isolate fail to align with the PAO1 backbone. While average sequence variation among all strains is roughly 0.5%, regions of pronounced differences were evident in whole-genome scans of nucleotide diversity. We analyzed two such divergent loci, the pyoverdine and O-antigen biosynthesis regions, by complete resequencing. A thorough analysis of isolates collected over time from one of the cystic fibrosis patients revealed independent mutations resulting in the loss of O-antigen synthesis alternating with a mucoid phenotype. Overall, we conclude that most of the PAO1 genome represents a core P. aeruginosa backbone sequence while the strains addressed in this study possess additional genetic material that accounts for at least 10% of their genomes. Approximately half of these additional sequences are novel. PMID:12562802

Spencer, David H.; Kas, Arnold; Smith, Eric E.; Raymond, Christopher K.; Sims, Elizabeth H.; Hastings, Michele; Burns, Jane L.; Kaul, Rajinder; Olson, Maynard V.

2003-01-01

371

NMR structure determination of the Escherichia coli DnaJ molecular chaperone: secondary structure and backbone fold of the N-terminal region (residues 2-108) containing the highly conserved J domain.  

PubMed Central

DnaJ from Escherichia coli is a 376-amino acid protein that functions in conjunction with DnaK and GrpE as a chaperone machine. The N-terminal fragment of residues 2-108, DnaJ-(2-108), retains many of the activities of the full-length protein and contains a structural motif, the J domain of residues 2-72, which is highly conserved in a superfamily of proteins. In this paper, NMR spectroscopy was used to determine the secondary structure and the three-dimensional polypeptide backbone fold of DnaJ-(2-108). By using 13C/15N doubly labeled DnaJ-(2-108), nearly complete sequence-specific assignments were obtained for 1H, 15N, 13C alpha, and 13C beta, and about 40% of the peripheral aliphatic carbon resonances were also assigned. Four alpha-helices in polypeptide segments of residues 6-11, 18-31, 41-55, and 61-68 in the J domain were identified by sequential and medium-range nuclear Overhauser effects. For the J domain, the three-dimensional structure was calculated with the program DIANA from an input of 536 nuclear Overhauser effect upper-distance constraints and 52 spin-spin coupling constants. The polypeptide backbone fold is characterized by the formation of an antiparallel bundle of two long helices, residues 18-31 and 41-55, which is stabilized by a hydrophobic core of side chains that are highly conserved in homologous J domain sequences. The Gly/Phe-rich region from residues 77 to 108 is flexibly disordered in solution. Images PMID:7972061

Szyperski, T; Pellecchia, M; Wall, D; Georgopoulos, C; Wüthrich, K

1994-01-01

372

Small Angle Neutron Scattering Study of Conformation of Oligo(ethylene glycol)-Grafted Polystyrene in Dilute Solutions: Effect of the Backbone Length  

E-print Network

in Dilute Solutions: Effect of the Backbone Length Gang Cheng,1 Yuri B. Melnichenko,1 George D. Wignall,1. · The influence of the hydrophobic phenyl end groups on polymer-polymer interactions becomes especially pronounced

373

Chemical composition of a lipopolysaccharide from Legionella pneumophila  

Microsoft Academic Search

Lipopolysaccharide isolated from Legionella pneumophila (Phil. 1) was examined for chemical composition. The polysaccharide split off by mild acid hydrolysis contained rhamnose, mannose, glucose, quinovosamine, glucosamine and 2-keto-3-deoxyoctonate, in molar proportions 1.6:1.8:1.0:1.5:4.1:2.7. Heptoses were absent and glucose was probably mainly phosphorylated. The carbohydrate backbone of the lipid A part consisted of glucosamine, quinovosamine and glycerol, in the molar ratios 3.9:1.0:3.4,

Anders Sonesson; Erik Jantzen; Klaus Bryn; Lennart Larsson; Jan Eng

1989-01-01

374

Sequencing Time  

NSDL National Science Digital Library

In this activity, students gain an understanding of relative and numerical time by placing events in sequence and assigning relative times to the events. This will familarize them with the methods used by scientists to develop the geologic time scale. This activity contains objectives, materials, procedure, and extensions.

2007-12-12

375

Molecular basis for nanoscopic membrane curvature generation from quantum mechanical models and synthetic transporter sequences  

PubMed Central

We investigate the physical origin of peptide-induced membrane curvature by contrasting differences between H-bonding interactions of prototypical cationic amino acids, arginine (Arg) and lysine (Lys), with phosphate groups of phospholipid heads using quantum mechanical (QM) calculations of a minimum model, and test the results via synthetic oxaorbornene-based transporter sequences without the geometric constraints of polypeptide backbones. QM calculations suggest that although individual Lys can in principle coordinate two phosphates, they are not able to do so at small inter-Lys distances without drastic energetic penalties. In contrast, Arg can coordinate two phosphates down to less than 5 Å, where guanidinium groups can stack ‘face to face’. In agreement with these observations, poly-Lys cannot generate the nanoscale positive curvature necessary for inducing negative Gaussian membrane curvature, in contrast to poly-Arg. Also consistent with QM calculations, polyguanidine-oxanorbornene homopolymers (PGONs) showed that curvature generation is exquisitely sensitive to the guanidinium group spacing when the phosphate groups are near close packing. Addition of phenyl or butyl hydrophobic groups into guanidine-oxanorbornene polymers increased the amount of induced saddle-splay membrane curvature, and broadened the range of lipid compositions where saddle-splay curvature was induced. The enhancement of saddle-splay curvature generation and relaxation of lipid composition requirements via addition of hydrophobicity is consistent with activity profiles. While PGON polymers displayed selective antimicrobial activity against prototypical (Gram positive and negative) bacteria, polymers with phenyl and butyl groups were also active against red blood cells. Our results suggest that it is possible to achieve deterministic molecular design of pore forming peptides. PMID:23061419

Schmidt, Nathan W.; Lis, Michael; Zhao, Kun; Lai, Ghee Hwee; Alexandrova, Anastassia; Tew, Gregory N.; Wong, Gerard C. L.

2013-01-01

376

Effects of Peptide Backbone Amide-to-Ester Bond Substitution on the Cleavage Frequency in Electron Capture Dissociation and Collision-Activated Dissociation  

Microsoft Academic Search

Probing the mechanism of electron capture dissociation on variously modified model peptide polycations has resulted in discovering\\u000a many ways to prevent or reduce $$ {\\\\text{N}} - {{\\\\text{C}}_? } $$ bond fragmentation. Here we report on a rare finding of how to increase the backbone bond dissociation rate. In a number\\u000a of model peptides, amide-to-ester backbone bond substitution increased the frequency

Frank Kjeldsen; Roman A. Zubarev

2011-01-01

377

Bond dissociation energies and radical stabilization energies associated with model peptide-backbone radicals.  

PubMed

Bond dissociation energies (BDEs) and radical stabilization energies (RSEs) have been calculated for a series of models that represent a glycine-containing peptide-backbone. High-level methods that have been used include W1, CBS-QB3, U-CBS-QB3, and G3X(MP2)-RAD. Simpler methods used include MP2, B3-LYP, BMK, and MPWB1K in association with the 6-311+G(3df,2p) basis set. We find that the high-level methods produce BDEs and RSEs that are in good agreement with one another. Of the simpler methods, RBMK and RMPWB1K achieve good accuracy for BDEs and RSEs for all the species that were examined. For monosubstituted carbon-centered radicals, we find that the stabilizing effect (as measured by RSEs) of carbonyl substituents (CX=O) ranges from 24.7 to 36.9 kJ mol(-1), with the largest stabilization occurring for the CH=O group. Amino groups (NHY) also stabilize a monosubstituted alpha-carbon radical, with the calculated RSEs ranging from 44.5 to 49.5 kJ mol(-1), the largest stabilization occurring for the NH2 group. In combination, NHY and CX=O substituents on a disubstituted carbon-centered radical produce a large stabilizing effect ranging from 82.0 to 125.8 kJ mol(-1). This translates to a captodative (synergistic) stabilization of 12.8 to 39.4 kJ mol(-1). For monosubstituted nitrogen-centered radicals, we find that the stabilizing effect of methyl and related (CH2Z) substituents ranges from 25.9 to 31.7 kJ mol(-1), the largest stabilization occurring for the CH3 group. Carbonyl substituents (CX=O) destabilize a nitrogen-centered radical relative to the corresponding closed-shell molecule, with the calculated RSEs ranging from -30.8 to -22.3 kJ mol(-1), the largest destabilization occurring for the CH=O group. In combination, CH2Z and CX=O substituents at a nitrogen radical center produce a destabilizing effect ranging from -19.0 to -0.2 kJ mol(-1). This translates to an additional destabilization associated with disubstitution of -18.6 to -7.8 kJ mol(-1). PMID:16833974

Wood, Geoffrey P F; Moran, Damian; Jacob, Rebecca; Radom, Leo

2005-07-21

378

Next Generation DNA sequencing  

E-print Network

Next Generation DNA sequencing #12;#12;DNA sequencing throughput 1996 1998 2001 2009 100's 1,000's 1,000,000's 1,000,000,000's nucleotides sequenced per day per instrument #12;Alternative Sequencing Paradigms Real-time sequencing- by-synthesis Massively parallel sequencing Nanopore sequencing Sequencing

Borenstein, Elhanan

379

MSLICE Sequencing  

NASA Technical Reports Server (NTRS)

MSLICE Sequencing is a graphical tool for writing sequences and integrating them into RML files, as well as for producing SCMF files for uplink. When operated in a testbed environment, it also supports uplinking these SCMF files to the testbed via Chill. This software features a free-form textural sequence editor featuring syntax coloring, automatic content assistance (including command and argument completion proposals), complete with types, value ranges, unites, and descriptions from the command dictionary that appear as they are typed. The sequence editor also has a "field mode" that allows tabbing between arguments and displays type/range/units/description for each argument as it is edited. Color-coded error and warning annotations on problematic tokens are included, as well as indications of problems that are not visible in the current scroll range. "Quick Fix" suggestions are made for resolving problems, and all the features afforded by modern source editors are also included such as copy/cut/paste, undo/redo, and a sophisticated find-and-replace system optionally using regular expressions. The software offers a full XML editor for RML files, which features syntax coloring, content assistance and problem annotations as above. There is a form-based, "detail view" that allows structured editing of command arguments and sequence parameters when preferred. The "project view" shows the user s "workspace" as a tree of "resources" (projects, folders, and files) that can subsequently be opened in editors by double-clicking. Files can be added, deleted, dragged-dropped/copied-pasted between folders or projects, and these operations are undoable and redoable. A "problems view" contains a tabular list of all problems in the current workspace. Double-clicking on any row in the table opens an editor for the appropriate sequence, scrolling to the specific line with the problem, and highlighting the problematic characters. From there, one can invoke "quick fix" as described above to resolve the issue. Once resolved, saving the file causes the problem to be removed from the problem view.

Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

2011-01-01

380

Periodic sequence distribution of product ion abundances in electron capture dissociation of amphipathic peptides and proteins  

Microsoft Academic Search

The rules for product ion formation in electron capture dissociation (ECD) mass spectrometry of peptides and proteins remain\\u000a unclear. Random backbone cleavage probability and the nonspecific nature of ECD toward amino acid sequence have been reported,\\u000a contrary to preferential channels of fragmentation in slow heating-based tandem mass spectrometry. Here we demonstrate that\\u000a for amphipathic peptides and proteins, modulation of ECD

Hisham Ben Hamidane; Huan He; Oleg Yu. Tsybin; Mark R. Emmett; Christopher L. Hendrickson; Alan G. Marshall; Yury O. Tsybin

2009-01-01

381

Importance of phosphate contacts for sequence recognition by EcoRI restriction enzyme  

Microsoft Academic Search

We have studied the importance of charge and hydrogen-bonding potential of the phosphodiester backbone for binding and cleavage by EcoRI restriction endonuclease. We used 12-mer oligodeoxynucleotide substrates with single substitutions of phosphates by chiral methylphosphonates at each position of the recognition sequence –pGpApApTpTpCp–. Binding was moderately reduced between 4- and 400-fold more or less equally for the RP and SP-analogues

Olaf Rosati; Tushar K. Srivastava; Seturam B. Katti; Jürgen Alves

2002-01-01

382

Identifying the Tertiary Fold of Small Proteins with Different Topologies from Sequence and Secondary Structure using the Genetic Algorithm and Extended Criteria Specific for Strand Regions  

Microsoft Academic Search

Grid-free protein folding simulations based on sequence and secondary structure knowledge (using mostly experimentally determined secondary structure information but also analysing results from secondary structure predictions) were investigated using the genetic algorithm, a backbone representation, and standard dihedral angular conformations. Optimal structures are selected according to basic protein building principles. Having previously applied this approach to proteins with helical topology,

Thomas Dandekar; Patrick Argos

1996-01-01

383

HASH: a program to accurately predict protein Ha from neighboring backbone shifts  

E-print Network

atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical has a wide rage of potential NMR applications in structural and biological studies of proteins

Richardson, David

384

Insertion Sequences  

PubMed Central

Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

Mahillon, Jacques; Chandler, Michael

1998-01-01

385

Complete DNA sequence of yeast chromosome XI  

Microsoft Academic Search

The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map

B. Dujon; D. Alexandraki; B. André; W. Ansorge; V. Baladron; J. P. G. Ballesta; A. Banrevi; P. A. Bolle; M. Bolotin-Fukuhara; P. Bossier; G. Bou; J. Boyer; M. J. Buitrago; G. Cherét; L. Colleaux; B. Dalgnan-Fornier; F. Del Rey; C. Dion; H. Domdey; A. Düsterhöft; S. Düsterhus; K.-D. Entian; H. Erfle; P. F. Esteban; H. Feldmann; L. Fernandes; G. M. Fobo; C. Fritz; H. Fukuhara; C. Gabel; L. Gaillon; J. M. Carcia-Cantalejo; J. J. Garcia-Ramirez; M. E. Gent; M. Ghazvini; A. Goffeau; A. Gonzaléz; D. Grothues; P. Guerreiro; J. Hegemann; N. Hewitt; F. Hilger; C. P. Hollenberg; O. Horaitis; K. J. Indge; A. Jacquier; C. M. James; J. C. Jauniaux; A. Jimenez; H. Keuchel; L. Kirchrath; K. Kleine; P. Kötter; P. Legrain; S. Liebl; E. J. Louis; A. Maia E Silva; C. Marck; A.-L. Monnier; D. Möstl; S. Müller; B. Obermaier; S. G. Oliver; C. Pallier; S. Pascolo; F. Pfeiffer; P. Philippsen; R. J. Planta; F. M. Pohl; T. M. Pohl; R. Pöhlmann; D. Portetelle; B. Purnelle; V. Puzos; M. Ramezani Rad; S. W. Rasmussen; M. Remacha; J. L. Revuelta; G.-F. Richard; M. Rieger; C. Rodrigues-Pousada; M. Rose; T. Rupp; M. A. Santos; C. Schwager; C. Sensen; J. Skala; H. Soares; F. Sor; J. Stegemann; H. Tettelin; A. Thierry; M. Tzermia; L. A. Urrestarazu; L. van Dyck; J. C. van Vliet-Reedijk; M. Valens; M. Vandenbo; C. Vilela; S. Vissers; D. von Wettstein; H. Voss; S. Wiemann; G. Xu; J. Zimmermann; M. Haasemann; I. Becker; H. W. Mewes

1994-01-01

386

Direct Damage to the Backbone of DNA Oligomers Is Influenced by the OH Moiety at Strand Ends, by the Type of Base, and by Context  

PubMed Central

Previous studies on high molecular weight DNA found that backbone damage, as monitored by free base release, is relatively independent of the type of base; i.e., the yields of all four bases were nearly equal. This could be due to a lack of influence of any given base over damage to its own deoxyribose or it could be a consequence of averaging out disparities due to each base sampling a wide range of base contexts. This study is aimed at distinguishing between these two possibilities. Transparent films, prepared from palindromic oligodeoxynucleotides of d(CTCTCGAGAG), d(CTCTCGAGAGp), d(pCTCTCGAGAGp), d(GAGAGCTCTC), d(ACGCGCGCGT), d(AACGCGCGCGTT), d(CTCTCTTAATAATTATAATTATTAAGAGAG), and d(CTCTCTTAATATTAAGAGAG), were used for this investigation. The DNA films, hydrated to ~2.5 waters per nucleotide, were irradiated at RT under air using X-rays generated by a tungsten tube, immediately dissolved in nuclease-free water, and stored at 277 K for 24 h, and then unaltered free base release was measured using HPLC. Yields of free base release were based on a target mass consisting of the DNA and one counterion + 2.5 H2O/nucleotide. The yields of each base, G(C), G(G), G(T), and G(A) were determined for each of the above sequences. The observed yields lead to the following conclusions: (i) base release at the oligomer ends is favored over release at internal positions (called the end effect), (ii) phosphorylation of the OH moiety at the oligomer ends quenches the end effect, (iii) the magnitude of the end effect is influenced by the base at the end and the bases proximal to it, and (iv) the release of base is influenced by the base and its context. PMID:19722540

Sharma, Kiran Kumar K.; Bernhard, William A.

2009-01-01

387

Backbone Dynamics of the 18.5 kDa Isoform of Myelin Basic Protein Reveals Transient ?-Helices and a Calmodulin-Binding Site  

PubMed Central

The 18.5 kDa isoform of myelin basic protein (MBP) is the predominant form in adult human central nervous system myelin. It is an intrinsically disordered protein that functions both in membrane adhesion, and as a linker connecting the oligodendrocyte membrane to the underlying cytoskeleton; its specific interactions with calmodulin and SH3-domain containing proteins suggest further multifunctionality in signaling. Here, we have used multidimensional heteronuclear nuclear magnetic resonance spectroscopy to study the conformational dependence on environment of the protein in aqueous solution (100 mM KCl) and in a membrane-mimetic solvent (30% TFE-d2), particularly to analyze its secondary structure using chemical shift indexing, and to investigate its backbone dynamics using 15N spin relaxation measurements. Collectively, the data revealed three major segments of the protein with a propensity toward ?-helicity that was stabilized by membrane-mimetic conditions: T33-D46, V83-T92, and T142-L154 (murine 18.5 kDa sequence numbering). All of these regions corresponded with bioinformatics predictions of ordered secondary structure. The V83-T92 region comprises a primary immunodominant epitope that had previously been shown by site-directed spin labeling and electron paramagnetic resonance spectroscopy to be ?-helical in membrane-reconstituted systems. The T142-L154 segment overlapped with a predicted calmodulin-binding site. Chemical shift perturbation experiments using labeled MBP and unlabeled calmodulin demonstrated a dramatic conformational change in MBP upon association of the two proteins, and were consistent with the C-terminal segment of MBP being the primary binding site for calmodulin. PMID:18326633

Libich, David S.; Harauz, George

2008-01-01

388

{{text{C}}_{? }} - {text{C}} Bond Cleavage of the Peptide Backbone in MALDI In-Source Decay Using Salicylic Acid Derivative Matrices  

NASA Astrophysics Data System (ADS)

The use of 5-formylsalicylic acid (5-FSA) and 5-nitrosalicylic acid (5-NSA) as novel matrices for in-source decay (ISD) of peptides in matrix-assisted laser desorption/ionization (MALDI) is described. The use of 5-FSA and 5-NSA generated a- and x-series ions accompanied by oxidized peptides [M - 2 H + H]+. The preferential formation of a- and x-series ions was found to be dependent on the hydrogen-accepting ability of matrix. The hydrogen-accepting ability estimated from the ratio of signal intensity of oxidized product [M - 2 H + H]+ to that of non-oxidized protonated molecule [M + H]+ of peptide was of the order 5-NSA > 5-FSA > 5-aminosalicylic acid (5-ASA) ? 2,5-dihydroxyl benzoic acid (2,5-DHB) ? 0. The results suggest that the hydrogen transfer reaction from peptide to 5-FSA and 5-NSA occurs during the MALDI-ISD processes. The hydrogen abstraction from peptides results in the formation of oxidized peptides containing a radical site on the amide nitrogen with subsequent radical-induced cleavage at the {{{C}}_{? }} - {{C}} bond, leading to the formation of a- and x-series ions. The most significant feature of MALDI-ISD with 5-FSA and 5-NSA is the specific cleavage of the {{{C}}_{? }} - {{C}} bond of the peptide backbone without degradation of side-chain and post-translational modifications (PTM). The matrix provides a useful complementary method to conventional MALDI-ISD for amino acid sequencing and site localization of PTMs in peptides.

Asakawa, Daiki; Takayama, Mitsuo

2011-07-01

389

Fold versus Sequence Effects on the Driving Force for Protein Mediated Electron Transfer  

PubMed Central

Electron transport chains composed of electron transfer reactions mainly between proteins provide fast, efficient flow of energy in a variety of metabolic pathways. Reduction potentials are essential characteristics of the proteins because they determine the driving forces for the electron transfers. Since both polar and charged groups from the backbone and side chains define the electrostatic environment, both the fold and the sequence will contribute. However, while the role of a specific sequence may be determined by experimental mutagenesis studies of reduction potentials, understanding the role of the fold by experiment is much more difficult. Here, continuum electrostatics and density functional theory calculations are used to analyze reduction potentials in [4Fe-4S] proteins. A key feature is that multiple homologous proteins in three different folds are compared: six high potential iron-sulfur proteins, four bacterial ferredoxins, and four nitrogenase iron proteins. Calculated absolute reduction potentials are shown to be in quantitative agreement with electrochemical reduction potentials. Calculations further demonstrate that the contribution of the backbone is larger than that of the side chains and is consistent for homologous proteins but differs for non-homologous proteins, indicating that the fold is the major protein factor determining the reduction potential while the specific amino acid sequence tunes the reduction potential for a given fold. Moreover, the fold contribution is determined mainly by the proximity of the redox site to the protein surface and the orientation of the dipoles of backbone near the redox site. PMID:20635418

Perrin, Bradley Scott; Ichiye, Toshiko

2010-01-01

390

Using protein backbone mutagenesis to dissect the link between ion occupancy and C-type inactivation in K+ channels  

PubMed Central

K+ channels distinguish K+ from Na+ in the selectivity filter, which consists of four ion-binding sites (S1–S4, extracellular to intracellular) that are built mainly using the carbonyl oxygens from the protein backbone. In addition to ionic discrimination, the selectivity filter regulates the flow of ions across the membrane in a gating process referred to as C-type inactivation. A characteristic of C-type inactivation is a dependence on the permeant ion, but the mechanism by which permeant ions modulate C-type inactivation is not known. To investigate, we used amide-to-ester substitutions in the protein backbone of the selectivity filter to alter ion binding at specific sites and determined the effects on inactivation. The amide-to-ester substitutions in the protein backbone were introduced using protein semisynthesis or in vivo nonsense suppression approaches. We show that an ester substitution at the S1 site in the KcsA channel does not affect inactivation whereas ester substitutions at the S2 and S3 sites dramatically reduce inactivation. We determined the structure of the KcsA S2 ester mutant and found that the ester substitution eliminates K+ binding at the S2 site. We also show that an ester substitution at the S2 site in the KvAP channel has a similar effect of slowing inactivation. Our results link C-type inactivation to ion occupancy at the S2 site. Furthermore, they suggest that the differences in inactivation of K+ channels in K+ compared with Rb+ are due to different ion occupancies at the S2 site. PMID:24128761

Matulef, Kimberly; Komarov, Alexander G.; Costantino, Corey A.; Valiyaveetil, Francis I.

2013-01-01

391

Dimerization behavior of cinnamate group attached to flexible polymer backbone and its effect on the molecular orientation  

NASA Astrophysics Data System (ADS)

Cinnamate group is well-known for the dimerization reaction by ultraviolet irradiation and their anisotropic dimerization are used for aligning liquid crystals. In this work, we found that cinnamate groups attached to the flexible polymer backbone could be reacted by thermal energy as well as UV irradiation. Cinnamate group of flexible polymers shows different molecular orientation of cycloadducts, comparing with conventional polymers, and it also participates in insolubilization reaction by additional thermal treatment. The thermal insolubilization reaction of flexible cinnamate polymer might be appropriate for the enhancement of molecular orientation.

Sung, Shi-Joon; Cho, Ki-Yun; Yoo, Ji-Heum; Kim, Won Sun; Chang, Hyung-Seok; Cho, Iwhan; Park, Jung-Ki

2004-08-01

392

Characteristics of novel di-?-fluoroacrylate derivatives with polyfluoroalkyl aromatic backbone as a binder resin of direct filling materials.  

PubMed

To realize good mechanical properties and water resistance of a dental resin, novel di-?-fluoroacrylates with polyfluoroalkyl aromatic backbone were studied. The monomers were 2,2-bis(4-?-fluoroacryloxy phenyl)propane, 2,2-bis(4-?-fluoroacryloxy phenyl) hexafluoropropane, and 1,3-bis(2-?-fluoroacryloxy-2-hexafluoropropyl)benzene. The copolymers of the monomers and methyl methacrylate (MMA) were excellent in hardness, Izod impact strength, abrasion resistance, and water resistance, and showed similar values of compressive, diametral tensile, tensile, and bending strength compared with copolymers prepared from the corresponding dimethacrylate derivatives and MMA. PMID:21597214

Kurata, Shigeaki; Yamazaki, Noboru

2011-01-01

393

Self-Assembled Peptide Amphiphile Nanofibers and PEG Composite Hydrogels as Tunable ECM Mimetic Microenvironment.  

PubMed

Natural extracellular matrix (ECM) consists of complex signals interacting with each other to organize cellular behavior and responses. This sophisticated microenvironment can be mimicked by advanced materials presenting essential biochemical and physical properties in a synergistic manner. In this work, we developed a facile fabrication method for a novel nanofibrous self-assembled peptide amphiphile (PA) and poly(ethylene glycol) (PEG) composite hydrogel system with independently tunable biochemical, mechanical, and physical cues without any chemical modification of polymer backbone or additional polymer processing techniques to create synthetic ECM analogues. This approach allows noninteracting modification of multiple niche properties (e.g., bioactive ligands, stiffness, porosity), since no covalent conjugation method was used to modify PEG monomers for incorporation of bioactivity and porosity. Combining the self-assembled PA nanofibers with a chemically cross-linked polymer network simply by facile mixing followed by photopolymerization resulted in the formation of porous bioactive hydrogel systems. The resulting porous network can be functionalized with desired bioactive signaling epitopes by simply altering the amino acid sequence of the self-assembling PA molecule. In addition, the mechanical properties of the composite system can be precisely controlled by changing the PEG concentration. Therefore, nanofibrous self-assembled PA/PEG composite hydrogels reported in this work can provide new opportunities as versatile synthetic mimics of ECM with independently tunable biological and mechanical properties for tissue engineering and regenerative medicine applications. In addition, such systems could provide useful tools for investigation of how complex niche cues influence cellular behavior and tissue formation both in two-dimensional and three-dimensional platforms. PMID:25751623

Goktas, Melis; Cinar, Goksu; Orujalipoor, Ilghar; Ide, Semra; Tekinay, Ayse B; Guler, Mustafa O

2015-04-13

394

Controlled actuation of Nafion-based ionic polymer-metal composites (IPMCs)with ethylene glycol as solvent  

Microsoft Academic Search

Ionic polymer-metal composites (IPMCs) consist of a perfluorinated ionomer membrane (usually Nafion or Flemion). The ionomer is plated on both faces with a noble metal such as gold or platinum. It is neutralized with a certain amount of counterions that balance the electrical charge of anions covalently fixed to the backbone membrane. IPMCs are electroactive materials that can be used

Shahram Zamani; Sia Nemat-Nasser

2004-01-01

395

Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field  

PubMed Central

Continuing our effort to introduce d-amino-acid residues in the united residue (UNRES) force field developed in our laboratory, in this work the C? ··· C? ··· C? backbone-virtual-bond-valence-angle (?) potentials for systems containing d-amino-acid residues have been developed. The potentials were determined by integrating the combined energy surfaces of all possible triplets of terminally blocked glycine, alanine, and proline obtained with ab initio molecular quantum mechanics at the MP2/6-31G(d,p) level to calculate the corresponding potentials of mean force (PMFs). Subsequently, analytical expressions were fitted to the PMFs to give the virtual-bond-valence potentials to be used in UNRES. Alanine represented all types of amino-acid residues except glycine and proline. The blocking groups were either the N-acetyl and N?,N?-dimethyl or N-acetyl and pyrrolidyl group, depending on whether the residue next in sequence was an alanine-type or a proline residue. A total of 126 potentials (63 symmetry-unrelated potentials for each set of terminally blocking groups) were determined. Together with the torsional, double-torsional, and side-chain-rotamer potentials for polypeptide chains containing d-amino-acid residues determined in our earlier work (Sieradzan et al. J. Chem. Theory Comput., 2012, 8, 4746), the new virtual-bond-angle (?) potentials now constitute the complete set of physics-based potentials with which to run coarse-grained simulations of systems containing d-amino-acid residues. The ability of the extended UNRES force field to reproduce thermodynamics of polypeptide systems with d-amino-acid residues was tested by comparing the experimentally measured and the calculated free energies of helix formation of model KLALKLALxxLKLALKLA peptides, where x denotes any d- or l- amino-acid residue. The obtained results demonstrate that the UNRES force field with the new potentials reproduce the changes of free energies of helix formation upon d-substitution but overestimate the free energies of helix formation. To test the ability of UNRES with the new potentials to reproduce the structures of polypeptides with d-amino-acid residues, an ab initio replica-exchange folding simulation of thurincin H from Bacillus thuringiensis, which has d-amino-acid residues in the sequence, was carried out. UNRES was able to locate the native ?-helical hairpin structure as the dominant structure even though no native sulfide–carbon bonds were present in the simulation. PMID:24839411

2015-01-01

396

Solubility of polyethers in hydrocarbons at low temperatures. A model for potential genetic backbones on warm titans.  

PubMed

Ethers are proposed here as the repeating backbone linking units in linear genetic biopolymers that might support Darwinian evolution in hydrocarbon oceans. Hydrocarbon oceans are found in our own solar system as methane mixtures on Titan. They may be found as mixtures of higher alkanes (propane, for example) on warmer hydrocarbon-rich planets in exosolar systems ("warm Titans"). We report studies on the solubility of several short polyethers in propane over its liquid range (from 85 to 231 K, or -188°C to -42°C). These show that polyethers are reasonably soluble in propane at temperatures down to ca. 200 K. However, their solubilities drop dramatically at still lower temperatures and become immeasurably low below 170 K, still well above the ?95 K in Titan's oceans. Assuming that a liquid phase is essential for any living system, and genetic biopolymers must dissolve in that biosolvent to support Darwinism, these data suggest that we must look elsewhere to identify linear biopolymers that might support genetics in Titan's surface oceans. However, genetic molecules with polyether backbones may be suitable to support life in hydrocarbon oceans on warm Titans, where abundant organics and environments lacking corrosive water might make it easier for life to originate. Key Words: Titan-Extraterrestrial life-Extreme environments-Biopolymers-Biosensor. Astrobiology 15, 200-206. PMID:25761113

McLendon, Christopher; Opalko, F Jeffrey; Illangkoon, Heshan I; Benner, Steven A

2015-03-01

397

Synthesis of graft polyrotaxane by simultaneous capping of backbone and grafting from rings of pseudo-polyrotaxane  

PubMed Central

Summary Graft polyrotaxanes, with poly(?-caprolactone) (PCL) graft chains on the ring components were synthesized by the simultaneous ring-opening polymerization of ?-caprolactone from both ends of the backbone polymer, an end-functionalized polyethylene glycol (PEG) and the formation of inclusion complexes with ?-cyclodextrin (?-CD). PEG with multiple functional groups at each end was prepared by the condensation of PEG-amine and D-gluconic acid; the PEG derivative formed an inclusion complex with ?-CD. The polymerization of multiple hydroxy groups at the backbone ends resulted in a star-shaped end group, which served as a bulky capping group to prevent dethreading. In contrast, PEG with only one hydroxy group at each end did not produce polyrotaxanes, indicating that single PCL chains were too thin to confine ?-CDs to the complex. In addition, the grafting polymerization proceeded properly only when robust hydrogen bonds formed between ?-CDs were dissociated using a basic catalyst. Since the dissociation also induced dethreading, kinetic control of the polymerization and dissociation were crucial for producing graft polyrotaxanes. Consequently, this three-step reaction yielded graft polyrotaxanes in a good yield, demonstrating a significant simplification of the synthesis of graft polyrotaxanes. PMID:25383129

Inoue, Katsunari; Kudo, Masabumi

2014-01-01

398

Dynamics of ultraviolet-induced DNA lesions: Dewar formation guided by pre-tension induced by the backbone  

NASA Astrophysics Data System (ADS)

The photophysical and photochemical processes driving the formation of the ultraviolet (UV)-induced DNA Dewar lesion from the T(6-4)T dimer are investigated by time-resolved spectroscopy and quantum chemical modelling. Time-resolved absorption and emission spectroscopy in the UV revealed a biexponential decay of the electronically excited state (S1) with time constants in the 100 ps and 1 ns range. From the S1 state the system forms the Dewar lesion (proven by time-resolved infrared spectroscopy), the triplet state of the T(6-4)T dimer and the ground state of the original T(6-4)T dimer. The decay process from the excited singlet is activated and thus temperature dependent. Quantum chemical modelling is used to describe the reaction path via a minimum on the excited electronic potential energy surface in close proximity to a triplet state. The transition to the Dewar isomer competes with internal conversion and with triplet formation. Only if the backbone between the two thymines is closed, is the Dewar isomer formed with a significant yield. The simulations reveal that the tension built up by the backbone is required for guiding the reaction to the conical intersection leading to the Dewar isomer.

Fingerhut, B. P.; Herzog, T. T.; Ryseck, G.; Haiser, K.; Graupner, F. F.; Heil, K.; Gilch, P.; Schreier, W. J.; Carell, T.; de Vivie-Riedle, R.; Zinth, W.

2012-06-01

399

Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid  

PubMed Central

While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (?GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an ‘accessory’ during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context. PMID:25200075

Babbitt, Gregory A.; Alawad, Mohammed A.; Schulze, Katharina V.; Hudson, André O.

2014-01-01

400

Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: 2H NMR studies on perdeuterated C-phycocyanin.  

PubMed

Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high. PMID:24730877

Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

2014-03-01

401

Synthesis of graft polyrotaxane by simultaneous capping of backbone and grafting from rings of pseudo-polyrotaxane.  

PubMed

Graft polyrotaxanes, with poly(?-caprolactone) (PCL) graft chains on the ring components were synthesized by the simultaneous ring-opening polymerization of ?-caprolactone from both ends of the backbone polymer, an end-functionalized polyethylene glycol (PEG) and the formation of inclusion complexes with ?-cyclodextrin (?-CD). PEG with multiple functional groups at each end was prepared by the condensation of PEG-amine and D-gluconic acid; the PEG derivative formed an inclusion complex with ?-CD. The polymerization of multiple hydroxy groups at the backbone ends resulted in a star-shaped end group, which served as a bulky capping group to prevent dethreading. In contrast, PEG with only one hydroxy group at each end did not produce polyrotaxanes, indicating that single PCL chains were too thin to confine ?-CDs to the complex. In addition, the grafting polymerization proceeded properly only when robust hydrogen bonds formed between ?-CDs were dissociated using a basic catalyst. Since the dissociation also induced dethreading, kinetic control of the polymerization and dissociation were crucial for producing graft polyrotaxanes. Consequently, this three-step reaction yielded graft polyrotaxanes in a good yield, demonstrating a significant simplification of the synthesis of graft polyrotaxanes. PMID:25383129

Kato, Kazuaki; Inoue, Katsunari; Kudo, Masabumi; Ito, Kohzo

2014-01-01

402

Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin  

NASA Astrophysics Data System (ADS)

Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

2014-03-01

403

Effects of Phosphorylation on the Structure and Backbone Dynamics of the Intrinsically Disordered Connexin43 C-terminal Domain*  

PubMed Central

Phosphorylation of the connexin43 C-terminal (Cx43CT) domain regulates gap junction intercellular communication. However, an understanding of the mechanisms by which phosphorylation exerts its effects is lacking. Here, we test the hypothesis that phosphorylation regulates Cx43 gap junction intercellular communication by mediating structural changes in the C-terminal domain. Circular dichroism and nuclear magnetic resonance were used to characterize the effects of phosphorylation on the secondary structure and backbone dynamics of soluble and membrane-tethered Cx43CT domains. Cx43CT phospho-mimetic isoforms, which have Asp substitutions at specific Ser/Tyr sites, revealed phosphorylation alters the ?-helical content of the Cx43CT domain only when attached to the membrane. The changes in secondary structure are due to variations in the conformational preference and backbone flexibility of residues adjacent and distal to the site(s) of modification. In addition to the known direct effects of phosphorylation on molecular partner interactions, the data presented here suggest phosphorylation may also indirectly regulate binding affinity by altering the conformational preference of the Cx43CT domain. PMID:23828237

Grosely, Rosslyn; Kopanic, Jennifer L.; Nabors, Sarah; Kieken, Fabien; Spagnol, Gaëlle; Al-Mugotir, Mona; Zach, Sydney; Sorgen, Paul L.

2013-01-01

404

Improved site-specific recombinase-based method to produce selectable marker- and vector-backbone-free transgenic cells  

NASA Astrophysics Data System (ADS)

PhiC31 integrase-mediated gene delivery has been extensively used in gene therapy and animal transgenesis. However, random integration events are observed in phiC31-mediated integration in different types of mammalian cells; as a result, the efficiencies of pseudo attP site integration and evaluation of site-specific integration are compromised. To improve this system, we used an attB-TK fusion gene as a negative selection marker, thereby eliminating random integration during phiC31-mediated transfection. We also excised the selection system and plasmid bacterial backbone by using two other site-specific recombinases, Cre and Dre. Thus, we generated clean transgenic bovine fetal fibroblast cells free of selectable marker and plasmid bacterial backbone. These clean cells were used as donor nuclei for somatic cell nuclear transfer (SCNT), indicating a similar developmental competence of SCNT embryos to that of non-transgenic cells. Therefore, the present gene delivery system facilitated the development of gene therapy and agricultural biotechnology.

Yu, Yuan; Tong, Qi; Li, Zhongxia; Tian, Jinhai; Wang, Yizhi; Su, Feng; Wang, Yongsheng; Liu, Jun; Zhang, Yong

2014-02-01

405

Improved site-specific recombinase-based method to produce selectable marker- and vector-backbone-free transgenic cells  

PubMed Central

PhiC31 integrase-mediated gene delivery has been extensively used in gene therapy and animal transgenesis. However, random integration events are observed in phiC31-mediated integration in different types of mammalian cells; as a result, the efficiencies of pseudo attP site integration and evaluation of site-specific integration are compromised. To improve this system, we used an attB-TK fusion gene as a negative selection marker, thereby eliminating random integration during phiC31-mediated transfection. We also excised the selection system and plasmid bacterial backbone by using two other site-specific recombinases, Cre and Dre. Thus, we generated clean transgenic bovine fetal fibroblast cells free of selectable marker and plasmid bacterial backbone. These clean cells were used as donor nuclei for somatic cell nuclear transfer (SCNT), indicating a similar developmental competence of SCNT embryos to that of non-transgenic cells. Therefore, the present gene delivery system facilitated the development of gene therapy and agricultural biotechnology. PMID:24577484

Yu, Yuan; Tong, Qi; Li, Zhongxia; Tian, Jinhai; Wang, Yizhi; Su, Feng; Wang, Yongsheng; Liu, Jun; Zhang, Yong

2014-01-01

406

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations.  

PubMed

Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of (15)N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S(2)) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S(2)) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S(2) values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S(2) parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S(2) calculated from the experimental NMR relaxation measurements, in a site-specific manner. PMID:25600810

Liu, Qing; Shi, Chaowei; Yu, Lu; Zhang, Longhua; Xiong, Ying; Tian, Changlin

2015-02-13

407

Molecular Characterization of Transgene Integration by Next-Generation Sequencing in Transgenic Cattle  

PubMed Central

As the number of transgenic livestock increases, reliable detection and molecular characterization of transgene integration sites and copy number are crucial not only for interpreting the relationship between the integration site and the specific phenotype but also for commercial and economic demands. However, the ability of conventional PCR techniques to detect incomplete and multiple integration events is limited, making it technically challenging to characterize transgenes. Next-generation sequencing has enabled cost-effective, routine and widespread high-throughput genomic analysis. Here, we demonstrate the use of next-generation sequencing to extensively characterize cattle harboring a 150-kb human lactoferrin transgene that was initially analyzed by chromosome walking without success. Using this approach, the sites upstream and downstream of the target gene integration site in the host genome were identified at the single nucleotide level. The sequencing result was verified by event-specific PCR for the integration sites and FISH for the chromosomal location. Sequencing depth analysis revealed that multiple copies of the incomplete target gene and the vector backbone were present in the host genome. Upon integration, complex recombination was also observed between the target gene and the vector backbone. These findings indicate that next-generation sequencing is a reliable and accurate approach for the molecular characterization of the transgene sequence, integration sites and copy number in transgenic species. PMID:23185606

Zhang, Ran; Yin, Yinliang; Zhang, Yujun; Li, Kexin; Zhu, Hongxia; Gong, Qin; Wang, Jianwu; Hu, Xiaoxiang; Li, Ning

2012-01-01

408

Solid state nuclear magnetic resonance investigation of polymer backbone dynamics in poly(ethylene oxide) based lithium and sodium polyether-ester-sulfonate ionomers  

NASA Astrophysics Data System (ADS)

Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (Tg) have been investigated using solid-state nuclear magnetic resonance. Experiments detecting 13C with 1H decoupling under magic angle spinning (MAS) conditions identified the different components of the polymer backbone (PEO spacer and isophthalate groups) and their relative mobilities for a suite of lithium- and sodium-containing ionomer samples with varying cation contents. Variable temperature (203-373 K) 1H-13C cross-polarization MAS (CP-MAS) experiments also provided qualitative assessment of the differences in the motions of the polymer backbone components as a function of cation content and identity. Each of the main backbone components exhibit distinct motions, following the trends expected for motional characteristics based on earlier Quasi Elastic Neutron Scattering and 1H spin-lattice relaxation rate measurements. Previous 1H and 7Li spin-lattice relaxation measurements focused on both the polymer backbone and cation motion on the nanosecond timescale. The studies presented here assess the slower timescale motion of the polymer backbone allowing for a more comprehensive understanding of the polymer dynamics. The temperature dependences of 13C linewidths were used to both qualitatively and quantitatively examine the effects of cation content and identity on PEO spacer mobility. Variable contact time 1H-13C CP-MAS experiments were used to further assess the motions of the polymer backbone on the microsecond timescale. The motion of the PEO spacer, reported via the rate of magnetization transfer from 1H to 13C nuclei, becomes similar for T ˜x 1{.1} Tg in all ionic samples, indicating that at similar elevated reduced temperatures the motions of the polymer backbones on the microsecond timescale become insensitive to ion interactions. These results present an improved picture, beyond those of previous findings, for the dependence of backbone dynamics on cation density (and here, cation identity as well) in these amorphous PEO-based ionomer systems.

Roach, David J.; Dou, Shichen; Colby, Ralph H.; Mueller, Karl T.

2013-05-01

409

Solid State Nuclear Magnetic Resonance Investigation of Polymer Backbone Dynamics in Poly(Ethylene Oxide) Based Lithium and Sodium Polyether-ester-sulfonate Ionomers  

SciTech Connect

Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (Tg) have been investigated using solid-state nuclear magnetic resonance (NMR). Experiments detecting 13C with 1H decoupling under magic angle spinning (MAS) conditions identified the different components of the polymer backbone (PEO spacer and isophthalate groups) and their relative mobilities for a suite of lithium- and sodium-containing ionomer samples with varying cation contents. Variable temperature (203-373 K) 1H-13C cross-polarization MAS (CP-MAS) experiments also provided qualitative assessment of the differences in the motions of the polymer backbone components as a function of cation content and identity. Each of the main backbone components exhibit distinct motions, following the trends expected for motional characteristics based on earlier Quasi Elastic Neutron Scattering and 1H spin-lattice relaxation rate measurements. Previous 1H and 7Li spin-lattice relaxation measurements focused on both the polymer backbone and cation motion on the nanosecond timescale. The studies presented here assess the slower timescale motion of the polymer backbone allowing for a more comprehensive understanding of the polymer dynamics. The temperature dependences of 13C linewidths were used to both qualitatively and quantitatively examine the effects of cation content and identity on PEO spacer mobility. Variable contact time 1H-13C CP-MAS experiments were used to further assess the motions of the polymer backbone on the microsecond timescale. The motion of the PEO spacer, reported via the rate of magnetization transfer from 1H to 13C nuclei, becomes similar for T ? 1.1 Tg in all ionic samples, indicating that at similar elevated reduced temperatures the motions of the polymer backbones on the microsecond timescale become insensitive to ion interactions. These results present an improved picture, beyond those of previous findings, for the dependence of backbone dynamics on cation density (and here, cation identity as well) in these amorphous PEO-based ionomer systems.

Roach, David J. [Penn State Univ., State College, PA (United States). Dept. of Chemistry; Dou, Shichen [Penn State Univ., State College, PA (United States). Dept. of Materials Science and Engineering; Colby, Ralph H. [Penn State Univ., State College, PA (United States). Dept. of Materials Science and Engineering; Mueller, Karl T. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Penn State Univ., State College, PA (United States). Dept. of Chemistry

2013-05-21

410

Statistical linguistic study of DNA sequences  

E-print Network

A new family of compound Poisson distribution functions from statistical linguistic is used to study the n-tuples and nucleotide composition features of DNA sequences. The relative frequency distribution of the 6-tuples and 7- tuples occurrence studies suggest that most of the DNA sequences follow the general shape of the compound Poisson distribution. It is also noted that the $\\chi$-square test indicated that some of the sequences follow this distribution with a reasonable level of goodness of fit. The compositional segmentation study fits quite well using this new family of distribution functions. Furthermore, the absolute values of the relative frequency come out naturally from the linguistic model without ambiguity. It is suggesting that DNA sequences are not random sequences and they could possibly have subsequence structures.

K. L. Ng; S. P. Li

2003-08-07

411

Inferring phylogenies of evolving sequences without multiple sequence alignment  

PubMed Central

Alignment-free methods, in which shared properties of sub-sequences (e.g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference. However, the scalability and robustness of these methods to key evolutionary processes remain to be investigated. Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, D2 methods are more robust against among-site rate heterogeneity, compositional biases, genetic rearrangements and insertions/deletions, but are more sensitive to recent sequence divergence and sequence truncation. Across diverse empirical datasets, the alignment-free methods perform well for sequences sharing low divergence, at greater computation speed. Our findings provide strong evidence for the scalability and the potential use of alignment-free methods in large-scale phylogenomics. PMID:25266120

Chan, Cheong Xin; Bernard, Guillaume; Poirion, Olivier; Hogan, James M.; Ragan, Mark A.

2014-01-01

412

Phylogeny of Cephalopods Inferred from Mitochondrial DNA Sequences  

Microsoft Academic Search

Sequences of partial mitochondrial cytochrome oxidase III gene (533 bp) were obtained for 17 species of cephalopods, 14 decapods, 2 octopods, and 1 vampyromorph. This study aimed to: (1) compare partial COII and COIII amino acid sequences of three species of cephalopods with other invertebrates in terms of base composition and phylogenetic relationships. Cephalopod sequences are closer toKatharina tunicatasequences than

Laure Bonnaud; Renata Boucher-Rodoni; Monique Monnerot

1997-01-01

413

Simulations Using Random-Generated DNA and RNA Sequences  

ERIC Educational Resources Information Center

Using a very simple computer program written in BASIC, a very large number of random-generated DNA or RNA sequences are obtained. Students use these sequences to predict complementary sequences and translational products, evaluate base compositions, determine frequencies of particular triplet codons, and suggest possible secondary structures.…

Bryce, C. F. A.

1977-01-01

414

Biological Sequence Analysis 1 Biological Sequence Analysis  

E-print Network

Biological Sequence Analysis 1 Biological Sequence Analysis and Motif Discovery Introductory University http://www.fas.harvard.edu/~junliu jliu@stat.harvard.edu #12;Biological Sequence Analysis 2 Topics to be covered · Basic Biology: DNA, RNA, Protein; genetic code. · Biological Sequence Analysis ­ Pairwise

Liu, Jun

415

?ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA  

PubMed Central

We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters. PMID:25260586

Pasi, Marco; Maddocks, John H.; Beveridge, David; Bishop, Thomas C.; Case, David A.; Cheatham, Thomas; Dans, Pablo D.; Jayaram, B.; Lankas, Filip; Laughton, Charles; Mitchell, Jonathan; Osman, Roman; Orozco, Modesto; Pérez, Alberto; Petkevi?i?t?, Daiva; Spackova, Nada; Sponer, Jiri; Zakrzewska, Krystyna; Lavery, Richard

2014-01-01

416

Original stimuli-sensitive polysaccharide derivatives/N-isopropylacrylamide hydrogels. Role of polysaccharide backbone.  

PubMed

This article compares the properties of a novel class of unsaturated Xanthan and Gellan derivatives/N-isopropylacrylamide stimuli-responsive hydrogels synthesized by free radical polymerization. Xanthan and Gellan Gum were partially functionalized by esterification with maleic anhydride under various conditions. By copolymerization of these maleate polysaccharides with a N-isopropylacrylamide known temperature sensitive precursor, water-swollen hydrogels with interpenetrating polymer networks (IPN) were obtained. The hydrogels were characterized for their temperature and pH-responsive behaviour by equilibrium swelling experiments and differential scanning calorimetry. The investigation of these materials also includes solid-state (13)CP/MAS NMR and elemental analysis of the nitrogen content. Morphology was visualized by scanning electron microscopy. Depending upon composition and the nature of the base-polysaccharide, the hydrogels showed different response rates to the external changes of temperature as well as pH. By changing the feed composition ratio of precursors and crosslinking agent (?-cyclodextrin acrylate or N,N'-methylenebisacrylamide respectively) the phase transition temperature (lower critical solution temperature) could also be adjusted near to the body temperature for biomedical and biotechnological applications. The role of the rigidity and the charge density of the polysaccharide chain, its ability to form hydrogen bonding on these properties are more particularly considered. PMID:24750741

Hamcerencu, Mihaela; Desbrieres, Jacques; Popa, Marcel; Riess, Gérard

2012-06-20

417

Investigations of the water clusters of the protected amino acid Ac-Phe-OMe by applying IR/UV double resonance spectroscopy: microsolvation of the backbone.  

PubMed

In order to investigate the influence of hydration on the backbone of a peptide or protected amino acid, the successive aggregation of water to Ac-Phe-OMe is analysed by means of IR/UV double resonance spectroscopy. To achieve meaningful results the spectra have been recorded in the region of the amide A and OH stretching vibrations as well as the amide I/II modes. Comparison with ab initio and DFT calculations leads to size-selective structural assignments. Two isomers of the mono- and dihydrated clusters and one isomer of the trihydrated cluster are observed in the molecular beam leading to a formation of the first solvation shell of the backbone. In case of the trihydrated cluster the backbone geometry is remarkably changed compared to the structure of the monomer since a network of water molecules can be formed. PMID:20336250

Fricke, Holger; Schwing, Kirsten; Gerlach, Andreas; Unterberg, Claus; Gerhards, Markus

2010-04-14

418

Pentopyranosyl Oligonucleotide Systems. Part 11: Systems with Shortened Backbones: D)-beta-Ribopyranosyl-(4 yields 3 )- and (L)-alpha - Lyxopyranosyl-(4 yields 3 )-oligonucleotides  

NASA Technical Reports Server (NTRS)

The (L)-a-lyxopyranosyl-(4'yields 3')-oligonucleotide system-a member of a pentopyranosyl oligonucleotide family containing a shortened backbone-is capable of cooperative base-pairing and of cross-pairing with DNA and RNA. In contrast, corresponding (D)-beta-ribopyransoyl-(4' yields 3')-oligonucleotides do not show base-pairing under similar conditions. We conclude that oligonucleotide systems can violate the six-bonds-per-backbone-unit rule by having five bonds instead, if their vicinally bound phosphodiester bridges can assume an antiperiplanar conformation. An additional structural feature that seems relevant to the cross-pairing capability of the (L)-a-lyxopyranosyl-(4' yields 3')-oligonucleotide system is its (small) backbone/basepair axes inclination. An inclination which is similar to that in B-DNA seems to be a prerequisite for an oligonucleotide system s capability to cross-pair with DNA.

Wippo, Harald; Reck, Folkert; Kudick, Rene; Ramaseshan, Mahesh; Ceulemans, Griet; Bolli, Martin; Krishnamurthy, Ramanarayanan; Eschenmoser, Albert

2001-01-01

419

Bromine isotopic signature facilitates de novo sequencing of peptides in free-radical-initiated peptide sequencing (FRIPS) mass spectrometry.  

PubMed

We recently showed that free-radical-initiated peptide sequencing mass spectrometry (FRIPS MS) assisted by the remarkable thermochemical stability of (2,2,6,6-tetramethyl-piperidin-1-yl)oxyl (TEMPO) is another attractive radical-driven peptide fragmentation MS tool. Facile homolytic cleavage of the bond between the benzylic carbon and the oxygen of the TEMPO moiety in o-TEMPO-Bz-C(O)-peptide and the high reactivity of the benzylic radical species generated in •Bz-C(O)-peptide are key elements leading to extensive radical-driven peptide backbone fragmentation. In the present study, we demonstrate that the incorporation of bromine into the benzene ring, i.e. o-TEMPO-Bz(Br)-C(O)-peptide, allows unambiguous distinction of the N-terminal peptide fragments from the C-terminal fragments through the unique bromine doublet isotopic signature. Furthermore, bromine substitution does not alter the overall radical-driven peptide backbone dissociation pathways of o-TEMPO-Bz-C(O)-peptide. From a practical perspective, the presence of the bromine isotopic signature in the N-terminal peptide fragments in TEMPO-assisted FRIPS MS represents a useful and cost-effective opportunity for de novo peptide sequencing. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25800020

Nam, Jungjoo; Kwon, Hyuksu; Jang, Inae; Jeon, Aeran; Moon, Jingyu; Lee, Sun Young; Kang, Dukjin; Han, Sang Yun; Moon, Bongjin; Oh, Han Bin

2015-02-01

420

Marburg Virus VP35 Can Both Fully Coat the Backbone and Cap the Ends of dsRNA for Interferon Antagonism  

PubMed Central

Filoviruses, including Marburg virus (MARV) and Ebola virus (EBOV), cause fatal hemorrhagic fever in humans and non-human primates. All filoviruses encode a unique multi-functional protein termed VP35. The C-terminal double-stranded (ds)RNA-binding domain (RBD) of VP35 has been implicated in interferon antagonism and immune evasion. Crystal structures of the VP35 RBD from two ebolaviruses have previously demonstrated that the viral protein caps the ends of dsRNA. However, it is not yet understood how the expanses of dsRNA backbone, between the ends, are masked from immune surveillance during filovirus infection. Here, we report the crystal structure of MARV VP35 RBD bound to dsRNA. In the crystal structure, molecules of dsRNA stack end-to-end to form a pseudo-continuous oligonucleotide. This oligonucleotide is continuously and completely coated along its sugar-phosphate backbone by the MARV VP35 RBD. Analysis of dsRNA binding by dot-blot and isothermal titration calorimetry reveals that multiple copies of MARV VP35 RBD can indeed bind the dsRNA sugar-phosphate backbone in a cooperative manner in solution. Further, MARV VP35 RBD can also cap the ends of the dsRNA in solution, although this arrangement was not captured in crystals. Together, these studies suggest that MARV VP35 can both coat the backbone and cap the ends, and that for MARV, coating of the dsRNA backbone may be an essential mechanism by which dsRNA is masked from backbone-sensing immune surveillance molecules. PMID:23028316

Bale, Shridhar; Halfmann, Peter; Zandonatti, Michelle A.; Kunert, John; Kroon, Gerard J. A.; Kawaoka, Yoshihiro; MacRae, Ian J.; Wilson, Ian A.; Saphire, Erica Ollmann

2012-01-01

421

Protein structure quality assessment based on the distance profiles of consecutive backbone C? atoms  

PubMed Central

Predicting the three dimensional native state structure of a protein from its primary sequence is an unsolved grand challenge in molecular biology. Two main computational approaches have evolved to obtain the structure from the protein sequence - ab initio/de novo methods and template-based modeling - both of which typically generate multiple possible native state structures. Model quality assessment programs (MQAP) validate these predicted structures in order to identify the correct native state structure. Here, we propose a MQAP for assessing the quality of protein structures based on the distances of consecutive C? atoms. We hypothesize that the root-mean-square deviation of the distance of consecutive C? (RDCC) atoms from the ideal value of 3.8 Å, derived from a statistical analysis of high quality protein structures (top100H database), is minimized in native structures. Based on tests with the top100H set, we propose a RDCC cutoff value of 0.012 Å, above which a structure can be filtered out as a non-native structure. We applied the RDCC discriminator on decoy sets from the Decoys 'R' Us database to show that the native structures in all decoy sets tested have RDCC below the 0.012 Å cutoff. While most decoy sets were either indistinguishable using this discriminator or had very few violations, all the decoy structures in the fisa decoy set were discriminated by applying the RDCC criterion. This highlights the physical non-viability of the fisa decoy set, and possible issues in benchmarking other methods using this set. The source code and manual is made available at https://github.com/sanchak/mqap and permanently available on 10.5281/zenodo.7134. PMID:24555103

Chakraborty, Sandeep

2013-01-01

422

Interfacial Properties of Two-Carbon Fiber Reinforced Polycarbonate Composites Using Two-Synthesized Graft Copolymers as Coupling Agents  

Microsoft Academic Search

Two model coupling agents, water-dispersible (WDGP) and tetrahydrofuran (THF)-soluble graft copolymers (TSGP), were synthesized for carbon fiber\\/polycarbonate (PC) composites. WDGP contains a long polyacrylamide (PAAm) chain grafted on a PC backbone, whereas TSGP contains a short grafted PAAm chain. Measurements of the interfacial shear strength (IFSS) and other interfacial properties were evaluated using a fragmentation test for two-fiber composites (TFC)

Joung-Man Park

2000-01-01

423

From protein sequence to dynamics and disorder with DynaMine  

NASA Astrophysics Data System (ADS)

Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine—a fast, high-quality predictor of protein backbone dynamics. DynaMine uses only protein sequence information as input and shows great potential in distinguishing regions of different structural organization, such as folded domains, disordered linkers, molten globules and pre-structured binding motifs of different sizes. It also identifies disordered regions within proteins with an accuracy comparable to the most sophisticated existing predictors, without depending on prior disorder knowledge or three-dimensional structural information. DynaMine provides molecular biologists with an important new method that grasps the dynamical characteristics of any protein of interest, as we show here for human p53 and E1A from human adenovirus 5.

Cilia, Elisa; Pancsa, Rita; Tompa, Peter; Lenaerts, Tom; Vranken, Wim F.

2013-11-01

424

Backbone and partial side chain assignment of the microtubule binding domain of the MAP1B light chain.  

PubMed

Microtubule-associated protein 1B (MAP1B) is a classical high molecular mass microtubule-associated protein expressed at high levels in the brain. It confers specific properties to neuronal microtubules and is essential for neuronal differentiation, brain development and synapse maturation. Misexpression of the protein contributes to the development of brain disorders in humans. However, despite numerous reports demonstrating the importance of MAP1B in regulation of the neuronal cytoskeleton during neurite extension and axon guidance, its mechanism of action is still elusive. Here we focus on the intrinsically disordered microtubule binding domain of the light chain of MAP1B. In order to obtain more detailed structural information about this domain we assigned NMR chemical shifts of backbone and aliphatic side chain atoms. PMID:23339032

Orbán-Németh, Zsuzsanna; Henen, Morkos A; Geist, Leonhard; ?erko, Szymon; Saxena, Saurabh; Stanek, Jan; Ko?mi?ski, Wiktor; Propst, Friedrich; Konrat, Robert

2014-04-01

425

(1)H, (13)C and (15)N backbone assignment of the EC-1 domain of human E-cadherin.  

PubMed

The Extracellular 1 (EC1) domain of E-cadherin has been shown to be important for cadherin-cadherin homophilic interactions. Cadherins are responsible for calcium-mediated cell-cell adhesion located at the adherens junction of the biological barriers (i.e., intestinal mucosa and the blood-brain barrier (BBB)). Cadherin peptides can modulate cadherin interactions to improve drug delivery through the BBB. However, the mechanism of modulating the E-cadherin interactions by cadherin peptides has not been fully elucidated. To provide a basis for subsequent examination of the structure and peptide-binding properties of the EC1 domain of human E-cadherin using solution NMR spectroscopy, the (1)H, (13)C and (15)N backbone resonance of the uniformly labeled-EC1 were assigned and the secondary structure was determined based on the chemical shift values. These resonance assignments are essential for assessing protein-ligand interactions and are reported here. PMID:24510398

Prasasty, Vivitri D; Krause, Mary E; Tambunan, Usman S F; Anbanandam, Asokan; Laurence, Jennifer S; Siahaan, Teruna J

2015-04-01

426

Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins  

NASA Astrophysics Data System (ADS)

Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing 13C detection only a single set of resonances was observed.

Chevelkov, Veniamin; Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam

2014-05-01

427

Backbone and stereospecific (13)C methyl Ile (?1), Leu and Val side-chain chemical shift assignments of Crc.  

PubMed

Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (?1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W. PMID:24496608

Sharma, Rakhi; Sahu, Bhubanananda; Ray, Malay K; Deshmukh, Mandar V

2015-04-01

428

ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization  

NASA Astrophysics Data System (ADS)

Non-adiabatic on-the-fly molecular dynamics (NA-O-MD) simulations require the electronic wavefunction, energy gradients, and derivative coupling vectors in every timestep. Thus, they are commonly restricted to the excited state dynamics of molecules with up to ?20 atoms. We discuss an approximation that combines the ONIOM(QM:QM) method with NA-O-MD simulations to allow calculations for larger molecules. As a proof of principle we present the excited state dynamics of a (6-4)-lesion containing dinucleotide (63 atoms), and especially the importance to include the confinement effects of the DNA backbone. The method is able to include electron correlation on a high level of theory and offers an attractive alternative to QM:MM approaches for moderate sized systems with unknown force fields.

Fingerhut, Benjamin P.; Oesterling, Sven; Haiser, Karin; Heil, Korbinian; Glas, Andreas; Schreier, Wolfgang J.; Zinth, Wolfgang; Carell, Thomas; de Vivie-Riedle, Regina

2012-05-01

429

Preparation and structures of 1,2-dihydro-1,2-diphosphaacenaphthylenes and rigid backbone stabilized triphosphenium cation.  

PubMed

The effect of the special peri-geometry of rigid naphthalene-1,8-diyl backbone in phosphenium formation reaction was investigated. 1,8-Bis(diphenylphosphino) naphthalene and P2I4 afforded triphosphenium iodide in a clean reaction. The reaction of 1,8-bis(dimethylaminophosphino) naphthalene with P2I4 is complex, it afforded four products, all containing the 1,2-dihydro-1,2-diphosphaacenaphthylene motif and heterophosphonium functionalities. Two examples of the rare structural motif of two acenaphthylene units connected head to head and thus a contiguous chain of four phosphorus atoms were also isolated, one compound showing diastereomerization in the solution. All new compounds were fully characterised including single crystal X-ray diffraction. PMID:16673031

Kilian, Petr; Slawin, Alexandra M Z; Woollins, J Derek

2006-05-14

430

The C-terminal domain of Nup93 is essential for assembly of the structural backbone of nuclear pore complexes  

PubMed Central

Nuclear pore complexes (NPCs) are large macromolecular assemblies that control all transport across the nuclear envelope. They are formed by about 30 nucleoporins (Nups), which can be roughly categorized into those forming the structural skeleton of the pore and those creating the central channel and thus providing the transport and gating properties of the NPC. Here we show that the conserved nucleoporin Nup93 is essential for NPC assembly and connects both portions of the NPC. Although the C-terminal domain of the protein is necessary and sufficient for the assembly of a minimal structural backbone, full-length Nup93 is required for the additional recruitment of the Nup62 complex and the establishment of transport-competent NPCs. PMID:22171326

Sachdev, Ruchika; Sieverding, Cornelia; Flötenmeyer, Matthias; Antonin, Wolfram

2012-01-01

431

Biosynthesis of 4D-hydroxysphinganine by the rat. En bloc incorporation of the sphinganine carbon backbone.  

PubMed

Rats were injected intravenously with erythro-DL-[1-3H]sphinganine. Radiolabeled 4D-hydroxysphinganine (phytosphingosine) was detected (in addition to sphinganine and 4-sphingenine) in glycolipid- and sphingomyelin-rich fractions from intestine and kidney. Identification of these bases was achieved following hydrolysis of the these fractions and conversion of the long chain bases to their N-dinitrophenyl (Dnp) derivatives. Dnp-4D-hydroxy[3H]sphinganine was characterized by: comigration on thin-layer chromatography with authentic standard and detection of pentadecanol and Dnp-[3H]serinol. These results strongly suggest that in mammalian tissues the C18 carbon backbone of 4D-hydroxysphinganine can be derived (en bloc) from sphinganine. PMID:6477953

Crossman, M W; Hirschberg, C B

1984-09-12