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1

TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences  

Microsoft Academic Search

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

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

2012-01-01

2

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

E-print Network

Solution rheology of hydrophobically modified associative polymers: Effects of backbone composition of polymer molecular structure on the solution rheology of a hydrophobically modified associative polymer ethoxylate urethane polymers, forming transient networks through mo- lecular associations. Due

Khan, Saad A.

3

Protein backbone angle restraints from searching a database for chemical shift and sequence homology  

Microsoft Academic Search

Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database

Gabriel Cornilescu; Frank Delaglio; Ad Bax

1999-01-01

4

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

5

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

6

Backbone dynamics of sequence specific recognition and binding by the yeast Pho4 bHLH domain probed by NMR.  

PubMed Central

Backbone dynamics of the basic/helix-loop-helix domain of Pho4 from Saccharomyces cerevisae have been probed by NMR techniques, in the absence of DNA, nonspecifically bound to DNA and bound to cognate DNA. Alpha proton chemical shift indices and nuclear Overhauser effect patterns were used to elucidate the secondary structure in these states. These secondary structures are compared to the co-crystal complex of Pho4 bound to a cognate DNA sequence (Shimizu T. Toumoto A, Ihara K, Shimizu M, Kyogou Y, Ogawa N, Oshima Y, Hakoshima T, 1997, EMBO J 15: 4689-4697). The dynamic information provides insight into the nature of this DNA binding domain as it progresses from free in solution to a specifically bound DNA complex. Relative to the unbound form, we show that formation of either the nonspecific and cognate DNA bound complexes involves a large change in conformation and backbone dynamics of the basic region. The nonspecific and cognate complexes, however, have nearly identical secondary structure and backbone dynamics. We also present evidence for conformational flexibility at a highly conserved glutamate basic region residue. These results are discussed in relation to the mechanism of sequence specific recognition and binding. PMID:11206057

Cave, J. W.; Kremer, W.; Wemmer, D. E.

2000-01-01

7

Thiophene-thiazolothiazole copolymers: significant impact of side chain composition on backbone orientation and solar cell performances.  

PubMed

The backbone orientation in the thiophene-thiazolothiazole (TzTz) copolymer system can be altered by tuning of the alky side chain composition. We highlight that the orientation significantly impact their solar cell efficiency in particular when using thicker active layers. PMID:24403117

Osaka, Itaru; Saito, Masahiko; Koganezawa, Tomoyuki; Takimiya, Kazuo

2014-01-15

8

Pulse Sequences for Measurement of One-Bond 15N- 1H Coupling Constants in the Protein Backbone  

NASA Astrophysics Data System (ADS)

A set of three improved two-dimensional (2D) NMR methods for measuring one-bond 15N- 1H coupling constants in the protein backbone is presented. They are tailored to suit the size of the TROSY effect, i.e., the degree of interference between dipolar and chemical shift anisotropy relaxation mechanisms. The methods edit 2D spectra into two separate subspectra corresponding to the two possible spin states of the coupling partner. Cross talk between the two subspectra is a second order effect in the difference between the actual coupling constants and the one used in setting the pertinent delays of the pulse sequences. This relatively high degree of editing accuracy makes the methods useful for applications to molecules subjected to weak alignment where the one-bond coupling constants are linear combinations of a scalar J and a residual dipolar contribution containing important structural information. A demonstration of the new methods is shown for the 15N-labeled protein chymotrypsin inhibitor 2 in a lipid bicelle mixture.

Lerche, Mathilde H.; Meissner, Axel; Poulsen, Flemming M.; Sørensen, Ole Winneche

1999-09-01

9

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

10

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

11

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

12

Foldamers with Heterogeneous Backbones  

PubMed Central

Conspectus The functions carried out by proteins and nucleic acids provide the foundation for life, and chemists have begun to ask whether it is possible to design synthetic oligomers that approach the structural and functional complexity of these biopolymers. The study of foldamers, non-natural oligomers with discrete folding propensities, has demonstrated that a variety of synthetic backbones can show biopolymer-like conformational behavior. Early work in this area focused on oligomers comprised of a single type of monomer subunit, but recent efforts have highlighted the potential of mixed or “heterogeneous” backbones to expand the structural and functional repertoire of foldamers. In this Account, we illustrate the promise of heterogeneous backbone foldamers by focusing on examples containing both ?- and ?-amino acid residues. The use of heterogeneous backbone foldamers offers advantages over homogeneous backbone counterparts, including access to many new molecular shapes, based on variations in the stoichiometries and patterns of subunit combination, and improved prospects for side chain diversification. Recent efforts to develop ?/?-peptide foldamers can be divided into two conceptually distinct classes. The first includes entities prepared by a “block” strategy, in which ?-peptide segments and ?-peptide segments are combined to form a hybrid oligomer. The second class encompasses designs in which ?- and ?-amino acid monomers are interspersed in a regular pattern throughout an oligomer sequence. A variety of secondary structures has been generated from ?/?-peptides via these approaches. Helical secondary structures available to ?/?-peptides have recently been parlayed into higher order structure, specifically, helix bundle quaternary structure. Desirable biological functions have been elicited from ?/?-peptide foldamers. Efforts to mimic naturally occurring host-defense ?-peptides have yielded new antimicrobial agents and led to a re-examination of the long-held views regarding structure-activity relationships among ?-peptides and other amphiphilic oligomers. Foldamers offer new platforms for mimicry of molecular surfaces involved in specific protein-protein recognition events; recent achievements with ?/?-peptide inhibitors of protein-protein interactions involved in apoptotic signaling have revealed benefits of heterogeneous backbones relative to homogeneous backbones for foldamer-based designs. These initial successes in the development of ?/?-peptides with specific biological activities highlight the potential of heterogeneous backbone foldamers for biomedical applications and provide guidelines for the future work on new target functions. PMID:18590282

Horne, W. Seth; Gellman, Samuel H.

2008-01-01

13

Sequence Analysis and Anomaly Detection of Web Service Composition  

Microsoft Academic Search

Traditional security solutions for web services or service composition are access control based models. In this paper, a new approach, sequence analysis based anomaly detection (SABAD) model for service composition is proposed to deal with the insecurity factors. SABAD model includes two parts, one is to mine abnormal service sequence patterns by extracting and analyzing service sequences, the other is

Cairong Yan; Zhidong Qin; Youqun Shi

2008-01-01

14

Inferring phylogenies from DNA sequences of unequal base compositions.  

PubMed Central

A new method for computing evolutionary distances between DNA sequences is proposed. Contrasting with classical methods, the underlying model does not assume that sequence base compositions (A, C, G, and T contents) are at equilibrium, thus allowing unequal base compositions among compared sequences. This makes the method more efficient than the usual ones in recovering phylogenetic trees from sequence data when base composition is heterogeneous within the data set, as we show by using both simulated and empirical data. When applied to small-subunit ribosomal RNA sequences from several prokaryotic or eukaryotic organisms, this method provides evidence for an early divergence of the microsporidian Vairimorpha necatrix in the eukaryotic lineage. PMID:7479987

Galtier, N; Gouy, M

1995-01-01

15

The Completely Sequenced Plasmid pEST4011 Contains a Novel IncP1 Backbone and a Catabolic Transposon Harboring tfd Genes for 2,4-Dichlorophenoxyacetic Acid Degradation  

PubMed Central

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Achromobacter xylosoxidans subsp. denitrificans strain EST4002 contains plasmid pEST4011. This plasmid ensures its host a stable 2,4-D+ phenotype. We determined the complete 76,958-bp nucleotide sequence of pEST4011. This plasmid is a deletion and duplication derivative of pD2M4, the 95-kb highly unstable laboratory ancestor of pEST4011, and was self-generated during different laboratory manipulations performed to increase the stability of the 2,4-D+ phenotype of the original strain, strain D2M4(pD2M4). The 47,935-bp catabolic region of pEST4011 forms a transposon-like structure with identical copies of the hybrid insertion element IS1071::IS1471 at the two ends. The catabolic regions of pEST4011 and pJP4, the best-studied 2,4-D-degradative plasmid, both contain homologous, tfd-like genes for complete 2,4-D degradation, but they have little sequence similarity other than that. The backbone genes of pEST4011 are most similar to the corresponding genes of broad-host-range self-transmissible IncP1 plasmids. The backbones of the other three IncP1 catabolic plasmids that have been sequenced (the 2,4-D-degradative plasmid pJP4, the haloacetate-catabolic plasmid pUO1, and the atrazine-catabolic plasmid pADP-1) are nearly identical to the backbone of R751, the archetype plasmid of the IncP1 ? subgroup. We show that despite the overall similarity in plasmid organization, the pEST4011 backbone is sufficiently different (51 to 86% amino acid sequence identity between individual backbone genes) from the backbones of members of the three IncP1 subgroups (the ?, ?, and ? subgroups) that it belongs to a new IncP1subgroup, the ? subgroup. This conclusion was also supported by a phylogenetic analysis of the trfA2, korA, and traG gene products of different IncP1 plasmids. PMID:15489427

Vedler, Eve; Vahter, Merle; Heinaru, Ain

2004-01-01

16

Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein  

E-print Network

to the under- lying theory, e.g. classification based on N-terminal targeting sequences, overall amino acidUsing N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting. A key step in this annotation process is the definition of a protein's subcellular lo- calization

Shatkay, Hagit

17

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.

18

Conserved sequences of prokaryotic proteomes and their compositional age.  

PubMed

A full repertoire of octapeptides which are present in at least 30 bacterial proteomes of total 131 currently available is computationally derived and filtered. An original search technique is used that, in terms of computational time and memory, is similar to the Suffix tree method. The presence of a given sequence in a large number of proteomes qualifies it as a conserved sequence. The larger the number of proteomes where it is found, the higher is the conservation. The concept of compositional age of the amino acid sequences ("compositional clock") is introduced for the first time. The compositional age is calculated on the basis of the consensus temporal order of appearance of amino acids in early evolution. The correlation between the compositional age and the sequence conservation is established. PMID:16205982

Sobolevsky, Yehoshua; Trifonov, Edward N

2005-11-01

19

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

20

Problems with Parsimony in Sequences of Biased Base Composition  

Microsoft Academic Search

.   Parsimony is commonly used to infer the direction of substitution and mutation. However, it is known that parsimony is biased\\u000a when the base composition of the DNA sequence is skewed. Here I quantify this effect for several simple cases. The analysis\\u000a demonstrates that parsimony can be misleading even when levels of sequence divergence are as low as 10%; parsimony

Adam Eyre-Walker

1998-01-01

21

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

22

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

23

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

24

Monolithic Backbone Railgun  

Microsoft Academic Search

The vast majority of all operational railguns in the world employ a metallic containment housing. Often composed of thousands of precision sheet metal laminates to prevent induced eddy currents, the launchers are labor intensive to build. The backbone railgun provides a monolithic metallic containment structure. Induced eddy currents are inhibited by the introduction of a large number of slits along

Eric L. Kathe; John A. Mallick

2007-01-01

25

Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks  

PubMed Central

The ability of DNA to adopt non-canonical structures can affect transcription and has broad implications for genome functioning. We have recently reported that guanine-rich (G-rich) homopurine-homopyrimidine sequences cause significant blockage of transcription in vitro in a strictly orientation-dependent manner: when the G-rich strand serves as the non-template strand [Belotserkovskii et al. (2010) Mechanisms and implications of transcription blockage by guanine-rich DNA sequences., Proc. Natl Acad. Sci. USA, 107, 12816–12821]. We have now systematically studied the effect of the sequence composition and single-stranded breaks on this blockage. Although substitution of guanine by any other base reduced the blockage, cytosine and thymine reduced the blockage more significantly than adenine substitutions, affirming the importance of both G-richness and the homopurine-homopyrimidine character of the sequence for this effect. A single-strand break in the non-template strand adjacent to the G-rich stretch dramatically increased the blockage. Breaks in the non-template strand result in much weaker blockage signals extending downstream from the break even in the absence of the G-rich stretch. Our combined data support the notion that transcription blockage at homopurine-homopyrimidine sequences is caused by R-loop formation. PMID:23275544

Belotserkovskii, Boris P.; Neil, Alexander J.; Saleh, Syed Shayon; Shin, Jane Hae Soo; Mirkin, Sergei M.; Hanawalt, Philip C.

2013-01-01

26

Predicting bacterial essential genes using only sequence composition information.  

PubMed

Essential genes are those genes that are needed by organisms at any time and under any conditions. It is very important for us to identify essential genes from bacterial genomes because of their vital role in synthetic biology and biomedical practices. In this paper, we developed a support vector machine (SVM)-based method to predict essential genes of bacterial genomes using only compositional features. These features are all derived from the primary sequences, i.e., nucleotide sequences and protein sequences. After training on the multiple samplings of the labeled (essential or not essential) features using a library for SVM, we obtained an average area under the ROC curve (AUC) of about 0.82 in a 5-fold cross-validation for Escherichia coli and about 0.74 for Mycoplasma pulmonis. We further evaluated the performance of the method proposed using the dataset consisting of 16 bacterial genomes, and an average AUC of 0.76 was achieved. Based on this training dataset, a model for essential gene prediction was established. Another two independent genomes, Shewanella oneidensis RW1 and Salmonella enterica serovar Typhimurium SL1344 were used to evalutate the model. Results showed that the AUC sores were 0.77 and 0.81, respectively. For the convenience of the vast majority of experimental scientists, a web server has been constructed, which is freely available at http://cefg.uestc.edu.cn:9999/egp. PMID:25036505

Ning, L W; Lin, H; Ding, H; Huang, J; Rao, N; Guo, F B

2014-01-01

27

Backbone cyclic insulin.  

PubMed

Backbone cyclic insulin was designed and prepared by reverse proteolysis in partial organic solvent of a single-chain precursor expressed in yeast. The precursor contains two loops to bridge the two chains of native insulin. The cyclisation method uses Achromobacter lyticus protease and should be generally applicable to proteins with C-terminal lysine and proximal N-terminal. The presence of the ring-closing bond and the native insulin disulfide patterns were documented by LC-MS peptide maps. The cyclic insulin was shown to be inert towards degradation by CPY, but was somewhat labile towards chymotrypsin. Intravenous administration of the cyclic insulin to Wistar rats showed the compounds to be equipotent to HI despite much lower insulin receptor affinity. PMID:20641002

Andersen, Asser S; Palmqvist, Eva; Bang, Susanne; Shaw, Allan C; Hubalek, Frantisek; Ribel, Ulla; Hoeg-Jensen, Thomas

2010-09-01

28

Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition.  

PubMed

Membrane proteins are vital type of proteins that serve as channels, receptors, and energy transducers in a cell. Prediction of membrane protein types is an important research area in bioinformatics. Knowledge of membrane protein types provides some valuable information for predicting novel example of the membrane protein types. However, classification of membrane protein types can be both time consuming and susceptible to errors due to the inherent similarity of membrane protein types. In this paper, neural networks based membrane protein type prediction system is proposed. Composite protein sequence representation (CPSR) is used to extract the features of a protein sequence, which includes seven feature sets; amino acid composition, sequence length, 2 gram exchange group frequency, hydrophobic group, electronic group, sum of hydrophobicity, and R-group. Principal component analysis is then employed to reduce the dimensionality of the feature vector. The probabilistic neural network (PNN), generalized regression neural network, and support vector machine (SVM) are used as classifiers. A high success rate of 86.01% is obtained using SVM for the jackknife test. In case of independent dataset test, PNN yields the highest accuracy of 95.73%. These classifiers exhibit improved performance using other performance measures such as sensitivity, specificity, Mathew's correlation coefficient, and F-measure. The experimental results show that the prediction performance of the proposed scheme for classifying membrane protein types is the best reported, so far. This performance improvement may largely be credited to the learning capabilities of neural networks and the composite feature extraction strategy, which exploits seven different properties of protein sequences. The proposed Mem-Predictor can be accessed at http://111.68.99.218/Mem-Predictor. PMID:21110985

Hayat, Maqsood; Khan, Asifullah

2011-02-21

29

Recombinant Expression of Backbone-Cyclized Polypeptides  

PubMed Central

Here we review the different biochemical approaches available for the expression of backbone-cyclized polypeptides, including peptides and proteins. These methods allow for the production of circular polypeptides either in vitro or in vivo using standard recombinant DNA expression techniques. Polypeptide circularization provides a valuable tool to study the effects of topology on protein stability and folding kinetics. Furthermore, having biosynthetic access to backbone-cyclized polypeptides makes the production of genetically-encoded libraries of cyclic polypeptides possible. The production of such libraries, which was previously restricted to the domain of synthetic chemistry, now offers biologists access to highly diverse and stable molecular libraries that can be screened using high-throughput methods for the rapid selection of novel cyclic polypeptide sequences with new biological activities. PMID:23893781

Borra, Radhika; Camarero, Julio A.

2013-01-01

30

Analytical expressions and lineshape simulations for Levitt-Suter-Ernst composite-pulse quadrupolar echo sequences  

NASA Astrophysics Data System (ADS)

Analytical expressions are derived for the Levitt-Suter-Emst composite quadrupolar echo sequences, allowing facile lineshape calculations for comparison with experiment. Large phase distortions in the lineshape obtained with the first-order sequence are significantly reduced with the second-order sequence. For 90° pulse lengths greater than ˜5?s, both sequences produce large phase errors for typical 2H quadrupolar coupling strengths in solids.

Barbara, Thomas M.

31

Amino acid sequence determination of protein biomarkers of Campylobacter upsaliensis and C. helveticus by "composite" sequence proteomic analysis.  

PubMed

We have identified the protein biomarkers observed in the matrix-assisted laser desorption/ionization time-of-flight mass spectra (MALDI-TOF-MS) of cell lysates of five strains of Campylobacter upsaliensis and one strain of C. helveticus by "bottom-up" proteomic techniques. Only one C. upsaliensis strain had previously been genomically sequenced. The significant findings are as follows: (1) The protein biomarkers identified were: 10 kD chaperonin, protein of unknown function (DUF465), phnA protein, probable periplasmic protein, D-methionine-binding lipoprotein MetQ, cytochrome c family protein, DNA-binding protein HU, thioredoxin, asparigenase family protein, helix-turn-helix domain protein, as well as several ribosomal and conserved hypothetical proteins. (2) Amino acid substitutions in protein biomarkers across species and strains account for variations in biomarker ion mass-to-charge (m/z). (3) The most common post-translational modifications (PTMs) identified were cleavage of N-terminal methionine and N-terminal signal peptides. The rule that predicts N-terminal methionine cleavage, based on the penultimate residue, does not appear to apply to C. upsaliensis proteins when the penultimate residue is threonine. (4) It was discovered that some protein biomarker genes of the genomically sequenced C. upsaliensis strain were found to have nucleotide sequences with GTG or TTG "start" codons that were not the actual start codon (ATG) of the protein based on proteomic analysis. (5) Proteomic identification of the protein biomarkers of the non-genomically sequenced C. upsaliensis and C. helveticus strains involved identification of homologous protein amino acid sequences to that of the sequenced strain. Interestingly, some protein sequence regions that were not completely homologous to the sequenced strain, due to amino acid substitutions, were found to have homologous sequence regions from more phyogenetically distant species/strains, e.g., C. jejuni. Exploiting this partial homology of more distant species/strains, it was possible to construct a "composite" amino acid sequence using multiple non-overlapping sequence regions from both phylogenetically proximate and distant strains. The new composite sequence was confirmed by both MS and MS/MS data. Thus, it was possible in some cases to determine the amino acid sequence of an unknown protein biomarker from a genomically non-sequenced bacterial strain without the necessity of either genetically sequencing the biomarker gene or resorting to de novo MS/MS analysis of the full protein sequence. PMID:17508732

Fagerquist, Clifton K

2007-07-01

32

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

33

Effects of laminate sequencing on thermoforming of thermoplastic matrix composites  

Microsoft Academic Search

Continuous fiber-reinforced thermoplastic composites are promising materials for light-weight structural components. Their medium to high processing and temperature-dependent properties, and the complex deformation mechanisms that occur within the composite sheet during the forming, are main problems in the practical production of parts. Thermoforming is an effective fabrication method due to the reversible solid–liquid phase transformation of thermoplastic materials. Deep drawing

M. Sadighi; E. Rabizadeh; F. Kermansaravi

2008-01-01

34

Conserved Sequences of Prokaryotic Proteomes and Their Compositional Age  

Microsoft Academic Search

A full repertoire of octapeptides which are present in at least 30 bacterial proteomes of total 131 currently available is computationally derived and filtered. An original search technique is used that, in terms of computational time and memory, is similar to the Suffix tree method. The presence of a given sequence in a large number of proteomes qualifies it as

Yehoshua Sobolevsky; Edward N. Trifonov

2005-01-01

35

A base composition analysis of natural patterns for the preprocessing of metagenome sequences  

PubMed Central

Background On the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. Our tool uses these natural patterns to determine relatedness across sequence data. We introduce spectrum sets (sets of motifs) which are permutations of bacterial restriction sites and the base composition analysis framework to measure their proportional content in sequence data. We suggest that this framework will increase the efficiency during the pre-processing stages of metagenome sequencing and assembly projects. Results Our method is able to differentiate organisms and their reads or contigs. The framework shows how to successfully determine the relatedness between these reads or contigs by comparison of base composition. In particular, we show that two types of organismal-sequence data are fundamentally different by analyzing their spectrum set motif proportions (coverage). By the application of one of the four possible spectrum sets, encompassing all known restriction sites, we provide the evidence to claim that each set has a different ability to differentiate sequence data. Furthermore, we show that the spectrum set selection having relevance to one organism, but not to the others of the data set, will greatly improve performance of sequence differentiation even if the fragment size of the read, contig or sequence is not lengthy. Conclusions We show the proof of concept of our method by its application to ten trials of two or three freshly selected sequence fragments (reads and contigs) for each experiment across the six organisms of our set. Here we describe a novel and computationally effective pre-processing step for metagenome sequencing and assembly tasks. Furthermore, our base composition method has applications in phylogeny where it can be used to infer evolutionary distances between organisms based on the notion that related organisms often have much conserved code. PMID:24564274

2013-01-01

36

Automated protein backbone assignment using the projection-decomposition approach.  

PubMed

Spectral projection experiments by NMR in conjunction with decomposition analysis have been previously introduced for the backbone assignment of proteins; various pulse sequences as well as the behaviour with low signal-to-noise or chemical shift degeneracy have been illustrated. As a guide for routine applications of this combined tool, we provide here a systematic analysis on different types of proteins using welldefined run-time parameters. As a second result of this study, the backbone assignment module SHABBA was extensively rewritten and improved. Calculations on ubiquitin yielded again fully correct and nearly complete backbone and CH? assignments. For the 128 residue long azurin, missing assignments mostly affect H? and H?. Among the remaining backbone (plus C?) nuclei 97.5 % could be assigned with 1.0 % differences to a reference. Finally, the new SHABBA algorithm was applied to projections recorded for a yeast histone protein domain at room temperature, where the protein is subject to partial unfolding: this leads to unobservable resonances (about a dozen missing signals in a normal 15N-HSQC) and extensive degeneracy among the resonances. From the clearly observable residues, 97.5 % of the backbone and CH?resonances could be assigned, of which only 0.8 % showed differences to published shifts. An additional study on the protein MMP20, which exhibits spectral difficulties to an even larger extent, explores the limitations of the approach. PMID:22806129

Fredriksson, Jonas; Bermel, Wolfgang; Staykova, Doroteya K; Billeter, Martin

2012-09-01

37

Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.  

PubMed

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, [Formula: see text]-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

Drew, Kevin; Renfrew, P Douglas; 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

38

SARP: A Novel Algorithm to Assess Compositional Biases in Protein Sequences  

PubMed Central

The composition of a defined set of subunits (nucleotides, amino acids) is one of the key features of biological sequences. Compositional biases are local shifts in amino acid or nucleotide frequencies that can occur as an adaptation of an organism to an extreme ecological niche, or as the signature of a specific function or localization of the corresponding protein. The calculation of probability is a method for annotating compositional bias and providing accurate detection of biased subsequences. Here, we present a Sequence Analysis based on the Ranking of Probabilities (SARP), a novel algorithm for the annotation of compositional biases based on ranking subsequences by their probabilities. SARP provides the same accuracy as the previously published Lower Probability Subsequences (LPS) algorithm but performs at an approximately 230-fold faster rate. It can be recommended for use when working with large datasets to reduce the time and resources required. PMID:23919085

Antonets, Kirill S.; Nizhnikov, Anton A.

2013-01-01

39

Enzymes/non-enzymes classification model complexity based on composition, sequence, 3D and topological indices.  

PubMed

The huge amount of new proteins that need a fast enzymatic activity characterization creates demands of protein QSAR theoretical models. The protein parameters that can be used for an enzyme/non-enzyme classification includes the simpler indices such as composition, sequence and connectivity, also called topological indices (TIs) and the computationally expensive 3D descriptors. A comparison of the 3D versus lower dimension indices has not been reported with respect to the power of discrimination of proteins according to enzyme action. A set of 966 proteins (enzymes and non-enzymes) whose structural characteristics are provided by PDB/DSSP files was analyzed with Python/Biopython scripts, STATISTICA and Weka. The list of indices includes, but it is not restricted to pure composition indices (residue fractions), DSSP secondary structure protein composition and 3D indices (surface and access). We also used mixed indices such as composition-sequence indices (Chou's pseudo-amino acid compositions or coupling numbers), 3D-composition (surface fractions) and DSSP secondary structure amino acid composition/propensities (obtained with our Prot-2S Web tool). In addition, we extend and test for the first time several classic TIs for the Randic's protein sequence Star graphs using our Sequence to Star Graph (S2SG) Python application. All the indices were processed with general discriminant analysis models (GDA), neural networks (NN) and machine learning (ML) methods and the results are presented versus complexity, average of Shannon's information entropy (Sh) and data/method type. This study compares for the first time all these classes of indices to assess the ratios between model accuracy and indices/model complexity in enzyme/non-enzyme discrimination. The use of different methods and complexity of data shows that one cannot establish a direct relation between the complexity and the accuracy of the model. PMID:18606172

Munteanu, Cristian Robert; González-Díaz, Humberto; Magalhães, Alexandre L

2008-09-21

40

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

41

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

42

The "universal polymer backbone" concept  

NASA Astrophysics Data System (ADS)

This thesis begins with a brief analysis of the synthetic methodologies utilized in polymer science. A conclusion is drawn inferring that upper limits in molecular design are inevitable, arising as a direct consequence of the predominance of covalent strategies in the field. To address these concerns, the 'universal polymer backbone' (UPB) concept has been hypothesized. A UPB has been defined as any copolymer, side-chain functionalized with multiple recognition elements that are individually capable of forming strong, directional, and reversible non-covalent bonds. Non-covalent functionalization of these scaffolds can lead to the formation of a multitude of new polymer structures, each stemming from a single parent or 'universal polymer backbone'. To prepare such a UPB, isomerically pure exo-norbornene esters containing either a PdII SCS pincer complex or a diaminopyridine residue were synthesized, polymerized, and copolymerized via ROMP. All polymerizations were living under mild reaction conditions. Kinetic studies showed that the kp values are highly dependent upon the isomeric purity but completely independent of the terminal recognition units. Non-covalent functionalization of these copolymers was accomplished via (1) directed self-assembly, (2) multi-step self-assembly , and (3) one-step orthogonal self-assembly. This system shows complete specificity of each recognition motif for its complementary unit with no observable changes in the association constant upon functionalization. To explore potential applications of this UPB concept, random terpolymers possessing high concentrations of pendant alkyl chains and small amounts of recognition units were synthesized. Non-covalent crosslinking using a directed functionalization strategy resulted in dramatic increases in solution viscosities for metal crosslinked polymers with only minor changes in viscosity for hydrogen bonding motifs. The crosslinked materials were further functionalized via self-assembly by employing the second recognition motif, which gave rise to functionalized materials with tailored crosslinks. This non-covalent crosslinking/functionalization strategy could allow for rapid and tunable materials synthesis by overcoming many difficulties inherent to the preparation of covalently crosslinked polymers. Finally, the current status of the UPB concept is reviewed and methodological extensions of the concept are suggested. Evaluation of how UPBs may be used to optimize materials and their potential use in fabricating unique electro-optical materials, sensors, and drug delivery vesicles are explored.

Pollino, Joel Matthew

43

Composite sequence proteomic analysis of protein biomarkers of Campylobacter coli, C. lari and C. concisus for bacterial identification.  

PubMed

Protein biomarkers observed in the matrix-assisted laser desorption/ionization time-of-flight mass spectra (MALDI-TOF-MS) of cell lysates of three strains of Campylobacter coli, two strains of C. lari and one strain of C. concisus have been identified by 'bottom-up' proteomic techniques. The significant findings are as follows. First, the protein biomarkers identified were: PhnA-related protein, 4-oxalocrotonate tautomerase (DmpI)-related protein, NifU-like protein, cytochrome c, DNA-binding protein HU, 10 kDa chaperonin, thioredoxin, as well as several conserved hypothetical and ribosomal proteins. Second, variations in the biomarker ion m/z in MALDI-TOF-MS spectra across species and strains are the result of variations in the amino acid sequence of the protein due to non-synonymous mutations of the biomarker gene. Third, the most common post-translational modifications (PTMs) were the removal of the N-terminal methionine and N-terminal signal peptides. However, in the case of the NifU protein (an iron-sulfur cluster transport protein), post-translational cleavage occurred from the C-terminus. Fourth, only the genomes of the C. coli strain RM2228 and C. lari strain RM2100 have been sequenced; thus, proteomic identification of the proteins of the other strains in this study relied upon sequence homology to the genomic sequence of these strains as well as the genomes of sequences of other Campylobacter strains. In some cases, the determination of the full amino acid sequence of a protein biomarker from a genomically non-sequenced strain was accomplished by combining non-overlapping partial sequences from proteomic identifications of genomically-sequenced strains that were of the same species (or of a different species) to that of the non-sequenced strain. The accuracy of this composite sequence was confirmed by both MS and MS/MS. It was necessary, in some cases, to perform de novo sequencing on 'gaps' in the composite sequence that were not homologous to any genomically-sequenced strain. In order to validate the composite sequence approach, composite sequences were further confirmed by subsequent DNA sequencing of the biomarker gene. Thus, using the composite sequence approach, it was possible to determine the full amino acid sequence of an unknown protein from a genomically non-sequenced bacterial strain without the necessity of either sequencing the biomarker gene or performing full de novo MS/MS sequencing. The sequence obtained could then be used as a strain-specific biomarker for analysis by 'top-down' proteomics techniques. PMID:17893805

Fagerquist, Clifton K; Yee, Emma; Miller, William G

2007-10-01

44

Flexible backbone aromatic polyimide adhesives  

NASA Technical Reports Server (NTRS)

Continuing research at Langley Research Center on the synthesis and development of new inexpensive flexible aromatic polyimides as adhesives has resulted in a material identified as LARC-F-SO2 with similarities to polyimidesulfone, PISO2, and other flexible backbone polyimides recently reported by Progar and St. Clair. Also prepared and evaluated was an endcapped version of PISO2. These two polymers were compared with LARC-TPI and LARC-STPI, polyimides research in our laboratory and reported in the literature. The adhesive evaluation, primarily based on lap shear strength (LSS) tests at RT, 177 C and 204 C, involved preparing adhesive tapes, conducting bonding studies and exposing lap shear specimens to 204 C air for up to 1000 hrs and to a 72-hour water boil. The type of adhesive failure as well as the Tg was determined for the fractured specimens. The results indicate that LARC-TPI provides the highest LSSs. LARC-F-SO2, LARC-TPI and LARC-STPI all retain their strengths after thermal exposure for 1000 hrs and PISO2 retains greater than 80 percent of its control strengths. After a 72-hr water boil exposure, most of the four adhesive systems showed reduced strengths for all test temperatures although still retaining a high percentage of their original strength (greater than 60 percent) except for one case. The predominant failure type was cohesive with no significant change in the Tgs.

Progar, Donald J.; St.clair, Terry L.

1988-01-01

45

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

46

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 done? Important: If you have had an accident that started your neck pain or if ...

47

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

48

Evidence of evolutionary constraints that influences the sequence composition and diversity of mitochondrial matrix targeting signals.  

PubMed

Mitochondrial targeting signals (MTSs) are responsible for trafficking nuclear encoded proteins to their final destination within mitochondria. These sequences are diverse, sharing little amino acid homology and vary significantly in length, and although the formation of a positively-charged amphiphilic alpha helix within the MTS is considered to be necessary and sufficient to mediate import, such a feature does not explain their diversity, nor how such diversity influences target sequence function, nor how such dissimilar signals interact with a single, evolutionarily conserved import mechanism. An in silico analysis of 296 N-terminal, matrix destined MTSs from Homo sapiens, Mus musculus, Saccharomyces cerevisiae, Arabidopsis thaliana, and Oryza sativa was undertaken to investigate relationships between MTSs, and/or, relationships between an individual targeting signal sequence and the protein that it imports. We present evidence that suggests MTS diversity is influenced in part by physiochemical and N-terminal characteristics of their mature sequences, and that some of these correlated characteristics are evolutionarily maintained across a number of taxa. Importantly, some of these associations begin to explain the variation in MTS length and composition. PMID:23825690

Doyle, Stephen R; Kasinadhuni, Naga R P; Chan, Chee Kai; Grant, Warwick N

2013-01-01

49

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

Microsoft Academic Search

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

Bruno Vincent; Martha Kaeslin; Thomas Roth; Manfred Heller; Julie Poulain; François Cousserans; Johann Schaller; Marylène Poirié; Beatrice Lanzrein; Jean-Michel Drezen; Sébastien JM Moreau

2010-01-01

50

31P NMR investigation of backbone dynamics in DNA binding sites.  

PubMed

The backbone conformation of DNA plays an important role in the indirect readout mechanisms for protein--DNA recognition events. Thus, investigating the backbone dynamics of each step in DNA binding sequences provides useful information necessary for the characterization of these interactions. Here, we use 31P dynamic NMR to characterize the backbone conformation and dynamics in the Dickerson dodecamer, a sequence containing the EcoRI binding site, and confirm solid-state 2H NMR results showing that the C3pG4 and C9pG10 steps experience unique dynamics and that these dynamics are quenched upon cytosine methylation. In addition, we show that cytosine methylation affects the conformation and dynamics of neighboring nucleotide steps, but this effect is localized to only near neighbors and base-pairing partners. Last, we have been able to characterize the percent BII in each backbone step and illustrate that the C3pG4 and C9pG10 favor the noncanonical BII conformation, even at low temperatures. Our results demonstrate that 31P dynamic NMR provides a robust and efficient method for characterizing the backbone dynamics in DNA. This allows simple, rapid determination of sequence-dependent dynamical information, providing a useful method for studying trends in protein-DNA recognition events. PMID:18717548

Tian, Ye; Kayatta, Michael; Shultis, Katharine; Gonzalez, Alejandro; Mueller, Leonard J; Hatcher, Mary E

2009-03-01

51

Efficient Distributed Low-Cost Backbone Formation for Wireless Networks  

E-print Network

1 Efficient Distributed Low-Cost Backbone Formation for Wireless Networks Yu Wang Weizhao Wang with low cost is proposed. We prove that the total cost of the constructed backbone is within a small backbone is needed. Therefore, by defining different costs, our proposed low-cost backbone formation

Li, Xiang-Yang

52

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

53

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

54

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

55

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

56

Effect of annealing on phase sequence and their composition in the Pt-coated Mo system  

NASA Astrophysics Data System (ADS)

The phase formation sequence and the composition of phases induced by thermal annealing in a platinum (Pt) coated molybdenum (Mo) system were investigated by X-ray diffraction (XRD), Rutherford backscattering spectrometry (RBS) and transmission electron microscopy (TEM). The X-ray diffraction study of a 0.2 ?m thick platinum layer deposited on a Mo substrate and annealed at temperatures between 800 °C and 900 °C for different periods of time shows the formation of MoPt2 and MoPt phases. It was also found that these phases nucleate sequentially and the MoPt2 phase becomes unstable at 900 °C after a longer annealing time of 8 h. Rutherford backscattering spectroscopy and transmission electron microscopy showed that the coating thickness approximately doubled after thermal annealing, from 0.22 ?m to 0.46 ?m, due to the formation of the Pt-Mo phases.

Khumalo, Z. M.; Topi?, M.; Comrie, C. M.; Blumenthal, M.; Pineda-Vargas, C. A.; Bucher, R.; Kisslinger, K.

2014-11-01

57

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

58

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

PubMed

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 approximately 0.3, high sulfate content: 1.75 g/l) in aerobic metabolic function. Reactor was operated under anoxic-aerobic-anoxic microenvironment conditions with a total cycle period of 24 h [fill: 15 min; reaction: 23 h (aeration along with recirculation); settle: 30 min; decant: 15 min] and the performance of the system was studied at organic loading rates (OLR) of 0.92, 1.50, 3.07 and 4.76 kg COD/cum-day. Substrate utilization showed a steady increase with increase in OLR and system performance sustained at higher loading rates. Maximum non-cumulative substrate utilization was observed after 4h of the cycle operation. Sulfate removal efficiency of 20% was observed due to the induced anoxic conditions prevailing during the sequence phase operation of the reactor and the existing internal anoxic zones in the biofilm matrix. Biofilm configured sequencing batch reactor (SBR) showed comparatively higher efficiency to the corresponding suspended growth and granular activated carbon (GAC) configured systems studied with same wastewater. Periodic discontinuous batch mode operation of the biofilm reactors results in a more even distribution of the biomass throughout the reactor and was able to treat large shock loads than the continuous flow process. Biofilm configured system coupled with periodic discontinuous batch mode operation imposes regular variations in the substrate concentration on biofilm organisms. As a result, organisms throughout the film achieve maximum growth rates resulting in improved reaction potential leading to stable and robust system which is well suited for treating highly variable wastes. PMID:17097228

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

2007-06-01

59

Treatment of composite chemical wastewater by aerobic GAC-biofilm sequencing batch reactor (SBGR).  

PubMed

The performance of granular activated carbon (GAC)-biofilm configured sequencing batch reactor (SBGR) in aerobic environment was investigated for the treatment of composite chemical wastewater [low BOD/COD ratio ( approximately 0.3), high sulfate content (1.75 g/l) and high TDS concentration (11 g/l)]. Composite wastewater was a combined mixture of effluents from about 100 chemical based industries. Reactor was operated under anoxic-aerobic-anoxic microenvironment conditions with a total cycle period of 24 h (fill: 15 min; reaction (aeration with recirculation): 23 h; settle: 30 min; decant: 15 min) and the performance of the system was studied at organic loading rates (OLR) of 1.7 kg COD/cum-day, 3.5 kg COD/cum-day and 5.5 kg COD/cum-day. The reactor showed efficient performance with respect to substrate degradation rate and sustained its performance at higher operating OLR (5.5 kg COD/cum-day) and at low BOD/COD ratio. Substrate utilization was found to increase with increase in the operating OLR. Maximum non-cumulative substrate utilization of 1.837 kg COD/cum-h, 2.99 kg COD/cum-h and 3.821 kg COD/cum-h was observed after 15 h of the cycle operation for operating OLRs of 1.7 kg COD/cum-day, 3.5 kg COD/cum-day and 5.5 kg COD/cum-day, respectively. Sulfate removal efficiency of 11+/-2% was recorded in the SBGR due to the induced anoxic conditions prevailing during the sequence phase operation of the reactor and the existing internal anoxic zones in the biofilm. Effective performance of the reactor may be attributed to sorption capacity of GAC as carrier material facilitating low toxicant concentration in the mixed liquor. The existing high flow rates around the GAC particle results in good mass transfer of the substrate from the bulk liquid. The long retention of biofilm on GAC increases the potential for the treatment of recalcitrant industrial wastewater. GAC configured biofilm configuration coupled with sequencing batch mode operation appears to be promising for the effective treatment of complex industrial wastewater containing poorly degradable compounds. PMID:16019144

Rao, N Chandrasekhara; Mohan, S Venkata; Muralikrishna, P; Sarma, P N

2005-09-30

60

Efficient Distributed Low-Cost Backbone Formation for Wireless Networks  

E-print Network

Efficient Distributed Low-Cost Backbone Formation for Wireless Networks Yu Wang, Member, IEEE distributed method to construct a weighted backbone with low cost is proposed. We prove that the total cost proposed low-cost backbone formation algorithms can be used in various practical applications. Recently

Wang, Yu

61

Seafloor spreading and the ophiolitic sequences of the Troodos complex - A principal component analysis of lava and dike compositions  

Microsoft Academic Search

The Troodos complex of Cyprus has been interpreted as a slice of oceanic crest formed from ultramafic magma in a back-arc basin. Recent investigations, however, have suggested that only the upper gabbros, the sheeted dike complex, and the lower lava sequence formed as a direct consequence of seafloor spreading and that the primary magma was of basaltic composition. According to

P. Thy; K. H. Esbensen

1993-01-01

62

Gallium: the backbone of the electronics industry  

Microsoft Academic Search

Gallium is a silvery blue and soft metallic element that enjoys vast application in optoelectronics (e.g., LED’s), telecommunication, aerospace, and many commercial and household items such as alloys, computers and DVD’s. Albeit that gallium represents a small annual tonnage of material, its important impact as the backbone of the worldwide electronics sector goes unnoticed by the popularity of key base

R. R. Moskalyk

2003-01-01

63

Disorder Predictors Also Predict Backbone Dynamics for a Family of Disordered Proteins  

PubMed Central

Several algorithms have been developed that use amino acid sequences to predict whether or not a protein or a region of a protein is disordered. These algorithms make accurate predictions for disordered regions that are 30 amino acids or longer, but it is unclear whether the predictions can be directly related to the backbone dynamics of individual amino acid residues. The nuclear Overhauser effect between the amide nitrogen and hydrogen (NHNOE) provides an unambiguous measure of backbone dynamics at single residue resolution and is an excellent tool for characterizing the dynamic behavior of disordered proteins. In this report, we show that the NHNOE values for several members of a family of disordered proteins are highly correlated with the output from three popular algorithms used to predict disordered regions from amino acid sequence. This is the first test between an experimental measure of residue specific backbone dynamics and disorder predictions. The results suggest that some disorder predictors can accurately estimate the backbone dynamics of individual amino acids in a long disordered region. PMID:22195023

Daughdrill, Gary W.; Borcherds, Wade M.; Wu, Hongwei

2011-01-01

64

Dead-End Elimination with Perturbations (“DEEPer”): A provable protein design algorithm with continuous sidechain and backbone flexibility  

PubMed Central

Computational protein and drug design generally require accurate modeling of protein conformations. This modeling typically starts with an experimentally-determined protein structure and considers possible conformational changes due to mutations or new ligands. The DEE/A* algorithm provably finds the GMEC (global minimum-energy conformation) of a protein assuming the backbone does not move and the sidechains take on conformations from a set of discrete, experimentally-observed conformations called rotamers. DEE/A* can efficiently find the overall GMEC for exponentially many mutant sequences. Previous improvements to DEE/A* include modeling ensembles of sidechain conformations and either continuous sidechain or backbone flexibility. We present a new algorithm, DEEPer (Dead-End Elimination with Perturbations), that combines these advantages and can also handle much more extensive backbone flexibility and backbone ensembles. DEEPer provably finds the GMEC or, if desired by the user, all conformations and sequences within a specified energy window of the GMEC. It includes the new abilities to handle arbitrarily large backbone perturbations and to generate ensembles of backbone conformations. It also incorporates the shear, an experimentally-observed local backbone motion never before used in design. Additionally, we derive a new method to accelerate DEE/A*-based calculations, indirect pruning, that is particularly useful for DEEPer. In 67 benchmark tests on 64 proteins, DEEPer consistently identified lower-energy conformations than previous methods did, indicating more accurate modeling. Additional tests demonstrated its ability to incorporate larger, experimentally-observed backbone conformational changes and to model realistic conformational ensembles. These capabilities provide significant advantages for modeling protein mutations and protein-ligand interactions. PMID:22821798

Hallen, Mark A.; Keedy, Daniel A.; Donald, Bruce R.

2012-01-01

65

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

66

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

67

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

68

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

69

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

70

BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution.  

PubMed

Coffee is one of the world's most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome. PMID:23708951

Dereeper, Alexis; Guyot, Romain; Tranchant-Dubreuil, Christine; Anthony, François; Argout, Xavier; de Bellis, Fabien; Combes, Marie-Christine; Gavory, Frederick; de Kochko, Alexandre; Kudrna, Dave; Leroy, Thierry; Poulain, Julie; Rondeau, Myriam; Song, Xiang; Wing, Rod; Lashermes, Philippe

2013-10-01

71

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

72

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks  

PubMed Central

A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ? 90% fraction of the residues, with an error rate smaller than ca 3.5%, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (?,?) torsion angles of ca 12°. TALOS-N also reports sidechain ?1 rotameric states for about 50% of the residues, and a consistency with reference structures of 89%. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts. PMID:23728592

Shen, Yang; Bax, Ad

2013-01-01

73

An Selenide-Based Approach to Photochemical Cleavage of Peptide and Protein Backbones at Engineered Backbone Esters  

PubMed Central

A strategy for photochemical cleavage of peptide and protein backbones is described, which is based on a selenide-mediated cleavage of a backbone ester moiety. Studies in model systems establish the viability of the chemistry and suggest the method could be a valuable tool for chemical biology studies of proteins. PMID:19902952

Eastwood, Amy L.; Blum, Angela P.; Zacharias, Niki M.; Dougherty, Dennis A.

2010-01-01

74

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

75

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

76

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

77

A composite map of expressed sequences and phenotypic traits of the sunflower (Helianthus annuus L.) genome  

Microsoft Academic Search

A map of the sunflower genome, based on expressed sequences and consisting of 273 loci, was constructed. The map incorporates\\u000a data from seven F2 populations, for a total of 1115 individuals. Two hundred and fourty five loci corresponding to 170 anonymous cDNA markers\\u000a and four loci for morphological markers were mapped. We also mapped 18 loci corresponding to previously described

L. Gentzbittel; E. Mestries; S. Mouzeyar; F. Mazeyrat; S. Badaoui; F. Vear; D. Tourvieille de Labrouhe; P. Nicolas

1999-01-01

78

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

79

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

80

A renormalization approach to describe charge transport in quasiperiodic dangling backbone ladder (DBL)-DNA molecules  

NASA Astrophysics Data System (ADS)

We study the charge transport properties of a dangling backbone ladder (DBL)-DNA molecule focusing on a quasiperiodic arrangement of its constituent nucleotides forming a Rudin-Shapiro (RS) and Fibonacci (FB) Poly (CG) sequences, as well as a natural DNA sequence (Ch22) for the sake of comparison. Making use of a one-step renormalization process, the DBL-DNA molecule is modeled in terms of a one-dimensional tight-binding Hamiltonian to investigate its transmissivity and current-voltage (I-V) profiles. Beyond the semiconductor I-V characteristics, a striking similarity between the electronic transport properties of the RS quasiperiodic structure and the natural DNA sequence was found.

Sarmento, R. G.; Fulco, U. L.; Albuquerque, E. L.; Caetano, E. W. S.; Freire, V. N.

2011-10-01

81

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

82

First survey of the wheat chromosome 5A composition through a next generation sequencing approach.  

PubMed

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

83

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

84

Basic Design I: A foundation studio course exploring two-dimensional design problems through a controlled sequence of exercises in drawing, abstract black and white composition, and basic color  

E-print Network

a controlled sequence of exercises in drawing, abstract black and white composition, and basic color theory equations and inequalities, rational and radical functions, logarithmic and exponential functions

85

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

86

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.

Research, Cornell C.

2003-01-01

87

Purification, identification, and in vivo activity of angiotensin I-converting enzyme inhibitory peptide, from ribbonfish (Trichiurus haumela) backbone.  

PubMed

Ribbonfish (Trichiurus haumela) backbone is normally discarded as an industrial waste from fish processing. A method of developing angiotensin I-converting enzyme inhibitory (ACEI) peptides from ribbonfish backbone was previously optimized. The purposes of the study were to characterize the active peptides in the hydrolysate and to evaluate its in vivo activity. Ribbonfish backbone protein hydrolysate prepared by acid protease was fractionated into 4 fractions (I, MW < 1 kDa; II, MW = 1 to 5 kDa; III, MW = 5 to 10 kDa; and IV, MW > 10 kDa) through ultrafiltration membranes. Fraction I, showing the highest ACEI activity, was further purified using consecutive chromatographic techniques including gel filtration and reversed phase high-performance liquid chromatography. The purified ACE inhibitory peptide was determined to have a molecular weight of 317.25 Da, with a sequence of Leu-Trp and an IC?? value of 5.6 ?M. Systolic blood pressure of spontaneously hypertensive rats was significantly decreased from 181 ± 2.0 to 161.3 ± 2.3 mm Hg after 4 h of oral administration of Leu-Trp at a dose of 10 mg/kg of body weight. These results indicated that ribbonfish backbone protein could be used for development of antihypertensive agent. PMID:24344998

Zou, Ping; Wang, Jin-Ling; He, Guo-Qing; Wu, Jianping

2014-01-01

88

PS1-10jh: The Disruption of a Main-sequence Star of Near-solar Composition  

NASA Astrophysics Data System (ADS)

When a star comes within a critical distance to a supermassive black hole (SMBH), immense tidal forces disrupt the star, resulting in a stream of debris that falls back onto the SMBH and powers a luminous flare. In this paper, we perform hydrodynamical simulations of the disruption of a main-sequence star by an SMBH to characterize the evolution of the debris stream after a tidal disruption. We demonstrate that this debris stream is confined by self-gravity in the two directions perpendicular to the original direction of the star's travel and as a consequence has a negligible surface area and makes almost no contribution to either the continuum or line emission. We therefore propose that any observed emission lines are not the result of photoionization in this unbound debris, but are produced in the region above and below the forming elliptical accretion disk, analogous to the broad-line region (BLR) in steadily accreting active galactic nuclei. As each line within a BLR is observationally linked to a particular location in the accretion disk, we suggest that the absence of a line indicates that the accretion disk does not yet extend to the distance required to produce that line. This model can be used to understand the spectral properties of the tidal disruption event PS1-10jh, for which He II lines are observed, but the Balmer series and He I are not. Using a maximum likelihood analysis, we show that the disruption of a main-sequence star of near-solar composition can reproduce this event.

Guillochon, James; Manukian, Haik; Ramirez-Ruiz, Enrico

2014-03-01

89

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

90

Native protein sequences are close to optimal for their structures  

Microsoft Academic Search

How large is the volume of sequence space that is compatible with a given protein structure? Starting from random sequences, low free energy sequences were generated for 108 protein backbone structures by using a Monte Carlo optimization procedure and a free energy function based primarily on Lennard-Jones packing interactions and the Lazaridis-Karplus implicit solvation model. Remarkably, in the designed sequences

Brian Kuhlman; David Baker

2000-01-01

91

A Consistent Phylogenetic Backbone for the Fungi  

PubMed Central

The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

2012-01-01

92

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

93

A distributed scheduler for airborne backbone networks with directional antennas  

Microsoft Academic Search

Airborne backbone networks are useful in tactical applications to interconnect sub-networks. A major challenge in such networks, normally comprising large numbers of highly mobile nodes, is the design of the medium access control (MAC) and routing protocols. We propose integration of MAC and routing functions, which use the attributes of a clustering scheme that addresses scalability. The reactive routing protocol

William Huba; Nicholas Martin; Yamin Al-Mousa; Chukwuchebem Orakwue; Nirmala Shenoy

2011-01-01

94

A Circle Limit III Backbone Arc Formula Douglas Dunham1  

E-print Network

A Circle Limit III Backbone Arc Formula Douglas Dunham1 1 Department of Computer Science University tessellation. · Later in 1958: Inspired by that tessellation, Escher cre- ates Circle Limit I. · Late 1959: Solving the "problems" of Circle Limit I, Escher creates Circle Limit III. · 1979: In a Leonardo article

Dunham, Doug

95

A "Circle Limit III" Backbone Arc Formula Douglas Dunham1  

E-print Network

A "Circle Limit III" Backbone Arc Formula Douglas Dunham1 1 Department of Computer Science@luns.org Abstract M.C. Escher considered Circle Limit III to be the most successful of his four "Circle Limit lines make with the bounding circle, and (2) are other such patterns of fish possible? H.S.M. Coxeter

Dunham, Doug

96

Backbone additivity in the transfer model of protein solvation  

PubMed Central

The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (?Gtr) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and ?Gtr values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of ?54 cal/mol/M compares quite favorably with ?43 cal/mol/M determined experimentally. PMID:20306490

Hu, Char Y; Kokubo, Hironori; Lynch, Gillian C; Bolen, D Wayne; Pettitt, B Montgomery

2010-01-01

97

Cooperative UAV-Based Communications Backbone for Sensor Networks  

SciTech Connect

The objective of this project is to investigate the use of unmanned air vehicles (UAVs) as mobile, adaptive communications backbones for ground-based sensor networks. In this type of network, the UAVs provide communication connectivity to sensors that cannot communicate with each other because of terrain, distance, or other geographical constraints. In these situations, UAVs provide a vertical communication path for the sensors, thereby mitigating geographic obstacles often imposed on networks. With the proper use of UAVs, connectivity to a widely disbursed sensor network in rugged terrain is readily achieved. Our investigation has focused on networks where multiple cooperating UAVs are used to form a network backbone. The advantage of using multiple UAVs to form the network backbone is parallelization of sensor connectivity. Many widely spaced or isolated sensors can be connected to the network at once using this approach. In these networks, the UAVs logically partition the sensor network into sub-networks (subnets), with one UAV assigned per subnet. Partitioning the network into subnets allows the UAVs to service sensors in parallel thereby decreasing the sensor-to-network connectivity. A UAV services sensors in its subnet by flying a route (path) through the subnet, uplinking data collected by the sensors, and forwarding the data to a ground station. An additional advantage of using multiple UAVs in the network is that they provide redundancy in the communications backbone, so that the failure of a single UAV does not necessarily imply the loss of the network.

Roberts, R S

2001-10-07

98

Scalable Cycle-Breaking Algorithms for Gigabit Ethernet Backbones  

E-print Network

-and-play functionalities as its Ethernet (10 Mb/s) and Fast Ethernet (100 Mb/s) pre- cursors, requiring minimal manual1 Scalable Cycle-Breaking Algorithms for Gigabit Ethernet Backbones Francesco De Pellegrini, David Starobinski, Mark G. Karpovsky, and Lev B. Levitin Abstract-- Ethernet networks rely on the so-called spanning

Karpovsky, Mark

99

Ethernet VPN (EVPN) & Provider Backbone Bridging Ethernet VPN  

E-print Network

Ethernet VPN (EVPN) & Provider Backbone Bridging Ethernet VPN (PBBEVPN) MS Scholarly Paper and a set of new requirements for Ethernet multipoint VPN service. Virtual Private LAN Services (VPLS. However, there exist a number of limitations. Ethernet Virtual Private Network (EVPN) and Provider

100

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

101

Traffic Characteristics of the T1 NSFNET Backbone  

Microsoft Academic Search

This paper presents the results of a measurementstudy of the T1 NSFNET backbone. We first discussthe measurement environment and approach to datacollection. We then present measurements results for:long-term growth in traffic volume, including attributionto domains and protocols; trend in average packetsize on the network, both over long and medium termintervals; most popular sources, destinations, and sitepairs; traffic locality; international distribution

Kimberly C. Claffy; George C. Polyzos; Hans-werner Braun

1993-01-01

102

UV resonance Raman monitors polyglutamine backbone and side chain hydrogen bonding and fibrillization1  

PubMed Central

We utilize 198 and 204 nm excited UV resonance Raman spectroscopy (UVRR) and circular dichroism spectroscopy (CD) to monitor the backbone conformation and the GLN side chain hydrogen bonding (HB) of a short, mainly polyGLN peptide of sequence D2Q10K2 (Q10). We measured the UVRR spectra of valeramide to determine the dependence of the primary amide vibrations on amide HB. We observe that non-disaggregated Q10 (NDQ10) solution (prepared by directly dissolving the original synthesized peptide in pure water) occurs in a ?-sheet conformation, where the GLN side chains form HB to either the backbone or other GLN side chains. At 60 °C, these solutions readily form amyloid fibrils. We used the polyGLN disaggregation protocol of Wetzel et al (Methods Enzymol, 2006, 413, 34–74) to dissolve the Q10 ?-sheet aggregates. We observe that the disaggregated Q10 (DQ10) solutions adopt PPII-like and 2.51-helix conformations where the GLN side chains form HB to water. In contrast, these samples do not form fibrils. The NDQ10 ?-sheet solution structure is essentially identical to that found in the NDQ10 solid formed upon solution evaporation. The DQ10 PPII and 2.51-helix solution structure is essentially identical to that in the DQ10 solid. Although the NDQ10 solution readily forms fibrils when heated, the DQ10 solution does not form fibrils unless seeded by NDQ10 solution. This result demonstrates very high activation barriers between these solution conformations. The NDQ10 fibril secondary structure is essentially identical to that of the NDQ10 solution, except that the NDQ10 fibril backbone conformational distribution is narrower than in the dissolved species. The NDQ10 fibril GLN side chain geometry is more constrained than when NDQ10 is in solution. The NDQ10 fibril structure is identical to that of the DQ10 fibril seeded by the NDQ10 solution. PMID:22746095

Xiong, Kan; Punihaole, David

2012-01-01

103

Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition  

PubMed Central

Background The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum) which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses. Results In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC) clone library (87 Mb) and sequencing of 22 potato BAC clones (2.9 Mb). The GC content of potato is very similar to Solanum lycopersicon (tomato) and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed. Conclusion Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that this conservation can be leveraged in genomic applications including cross-species annotation and genome sequencing initiatives. While tomato and potato share genic features, they differ in their repetitive sequence content and composition suggesting that repetitive sequences may have a more significant role in shaping speciation than previously reported. PMID:18554403

Zhu, Wei; Ouyang, Shu; Iovene, Marina; O'Brien, Kimberly; Vuong, Hue; Jiang, Jiming; Buell, C Robin

2008-01-01

104

Photodegradation of human growth hormone: a novel backbone cleavage between Glu-88 and Pro-89.  

PubMed

The exposure of protein pharmaceuticals to light can cause loss of potency, oxidation, structural changes and aggregation. To elucidate the chemical pathways of photodegradation, we irradiated human growth hormone (hGH) at ? = 254 nm, ? ? 265-340 nm, and ? ? 295-340 nm (using the spectral cutoff of borosilicate glass) and analyzed the products by mass spectrometry. By means of LC-MS/MS analysis, we observed an unusual peptide backbone cleavage between Glu-88 and Pro-89. The crystal structure of hGH indicates that these residues are in proximity to Trp-86, which likely mediates this backbone cleavage. The two cleavage fragments observed by MS/MS analysis indicate the loss of CO from the amide bond and replacement of the Glu-C(? O)Pro bond with a Glu-H bond, accompanied by double bond formation on proline. The reaction is oxygen-independent and likely involves hydrogen transfer to the C? of Glu-88. To probe the influence of the protein fold, we irradiated hGH in its unfolded state, in 1:1 (v/v) acetonitrile/water, and also the isolated tryptic peptide Ile-78-Arg-90, which contains the Glu-88-Pro-89 sequence. In both cases, the cleavage between Glu-88 and Pro-89 was largely suppressed, while other cleavage pathways became dominant, notably between Gln-84 and Ser-85, as well as Ser-85 and Trp-86. PMID:23721578

Steinmann, Daniel; Ji, J Andrea; Wang, Y John; Schöneich, Christian

2013-07-01

105

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

106

A method to assess compositional bias in biological sequences and its application to prion-like glutamine\\/asparagine-rich domains in eukaryotic proteomes  

Microsoft Academic Search

We have derived a novel method to assess compositional biases in biological sequences, which is based on finding the lowest-probability subsequences for a given residue-type set. As a case study, the distribution of prion-like glutamine\\/asparagine-rich ((Q+N)-rich) domains (which are linked to amyloidogenesis) was assessed for budding and fission yeasts and four other eukaryotes. We find more than 170 prion-like (Q+N)-rich

Paul M Harrison; Mark Gerstein

2003-01-01

107

Mobility Control for Joint Coverage-Connectivity Optimization in Directional Wireless Backbone Networks  

Microsoft Academic Search

The use of directional wireless communications to form flexible mesh backbone networks, which provide broadband connectivity to capacity-limited wireless networks or hosts, promises to circumvent the scalability limitations of traditional wireless networks. The main challenge in the design of directional wireless backbone (DWB) networks is to assure backbone network requirements such as coverage and connectivity in a dynamic wireless environment.

Jaime Llorca; Stuart D. Milner; Christopher C. Davis

2007-01-01

108

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

109

Damage of DNA backbone by nanoscale shock waves  

NASA Astrophysics Data System (ADS)

By means of full-atom molecular dynamics simulations we investigate the process of DNA backbone damage by nanoscale shock waves in a water environment. These shock waves are created by ions penetrating the medium with high linear energy transfer. The high rate of the ions' energy transfer to the surrounding molecules leads to the rapid increase of the temperature in the vicinity of the ion trajectory, which causes the formation of shock waves propagating through the medium. We have investigated the ions' linear energy transfer of 900, 2000 and 5000 eV/nm. In the case of a linear energy transfer of 5000 eV/nm the deposition exerts unsustainable stress onthe DNA molecule, which leads to the breakage of DNA backbone covalent bonds by thermomechanical effects.

Yakubovich, Alexander V.; Surdutovich, Eugene; Solov'yov, Andrey V.

2012-07-01

110

Extracting the globally and locally adaptive backbone of complex networks.  

PubMed

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

111

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

112

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

113

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

114

Induced helical backbone conformations of self-organizable dendronized polymers.  

PubMed

Control of function through the primary structure of a molecule presents a significant challenge with valuable rewards for nanoscience. Dendritic building blocks encoded with information that defines their three-dimensional shape (e.g., flat-tapered or conical) and how they associate with each other are referred to as self-assembling dendrons. Self-organizable dendronized polymers possess a flat-tapered or conical self-assembling dendritic side chain on each repeat unit of a linear polymer backbone. When appended to a covalent polymer, the self-assembling dendrons direct a folding process (i.e., intramolecular self-assembly). Alternatively, intermolecular self-assembly of dendrons mediated by noncovalent interactions between apex groups can generate a supramolecular polymer backbone. Self-organization, as we refer to it, is the spontaneous formation of periodic and quasiperiodic arrays from supramolecular elements. Covalent and supramolecular polymers jacketed with self-assembling dendrons self-organize. The arrays are most often comprised of cylindrical or spherical objects. The shape of the object is determined by the primary structure of the dendronized polymer: the structure of the self-assembling dendron and the length of the polymer backbone. It is therefore possible to predictably generate building blocks for single-molecule nanotechnologies or arrays of supramolecules for bottom-up self-assembly. We exploit the self-organization of polymers jacketed with self-assembling dendrons to elucidate how primary structure determines the adopted conformation and fold (i.e., secondary and tertiary structure), how the supramolecules associate (i.e., quaternary structure), and their resulting functions. A combination of experimental techniques is employed to interrogate the primary, secondary, tertiary, and quaternary structure of the self-organizable dendronized polymers. We refer to the process by which we interpolate between the various levels of structural information to rationalize function as retrostructural analysis. Retrostructural analysis validates our hypothesis that the self-assembling dendrons induce a helical backbone conformation in cylindrical self-organizable dendronized polymers. This helical conformation mediates unprecedented functions. Self-organizable dendronized polymers have emerged as powerful building blocks for nanoscience by virtue of their dimensions and ability to self-organize. Discrete cylindrical and spherical structures with well-defined dimensions can be visualized and manipulated individually. More importantly, they provide a robust framework for elucidating functions available only at the nanoscale. This Account will highlight structures and functions generated from self-organizable dendronized polymers that enable integration of the nanoworld with its macroscopic universe. Emphasis is placed on those structures and functions derived from the induced helical backbone conformation of cylindrical self-organizable dendronized polymers. PMID:18605742

Rudick, Jonathan G; Percec, Virgil

2008-12-01

115

Backbone (1)H, (15)N, and (13)C resonance assignments and secondary structure of the Tollip CUE domain.  

PubMed

The Toll-interacting protein (Tollip) is a negative regulator of the Toll-like receptor (TLR)-mediated inflammation response. Tollip is a modular protein that contains an Nterminal Tom1-binding domain (TBD), a central conserved domain 2 (C2), and a C-terminal coupling of ubiquitin to endoplasmic reticulum degradation (CUE) domain. Here, we report the sequence-specific backbone (1)H, (15)N, and (13)C assignments of the human Tollip CUE domain. The CUE domain was found to be a stable dimer as determined by size-exclusion chromatography and molecular crosslinking studies. Analysis of the backbone chemical shift data indicated that the CUE domain exhibits three helical elements corresponding to 52% of the protein backbone. Circular dichroism spectrum analysis confirmed the helical nature of this domain. Comparison of the location of these helical regions with those reported for yeast CUE domains suggest differences in length for all helical elements. We expect the structural analysis presented here will be the foundation for future studies on the biological significance of the Tollip CUE domain, its molecular interactions, and the mechanisms that modulate its function during the inflammatory response. PMID:20957454

Azurmendi, Hugo F; Mitra, Sharmistha; Ayala, Iriscilla; Li, Liwu; Finkielstein, Carla V; Capelluto, Daniel G S

2010-12-01

116

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

117

Animal protection and structural studies of a consensus sequence vaccine targeting the receptor binding domain of the type IV pilus of Pseudomonas aeruginosa.  

PubMed

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 A 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. PMID:17936788

Kao, Daniel J; Churchill, Mair E A; Irvin, Randall T; Hodges, Robert S

2007-11-23

118

Novel electrochemical biosensor based on functional composite nanofibers for sensitive detection of p53 tumor suppressor gene.  

PubMed

A novel electrochemical biosensor based on functional composite nanofibers for sensitive hybridization detection of p53 tumor suppressor using methylene blue (MB) as an electrochemical indicator is developed. The carboxylated multi-walled carbon nanotubes (MWNTs) doped nylon 6 (PA6) composite nanofibers (MWNTs-PA6) was prepared using electrospinning, which served as the nanosized backbone for pyrrole (Py) electropolymerization. The functional composite nanofibers (MWNTs-PA6-PPy) used as supporting scaffolds for ssDNA immobilization can dramatically increase the amount of DNA attachment and the hybridization sensitivity. The biosensor displayed good sensitivity and specificity. The target wild type p53 sequence (wtp53) can be detected as low as 50 fM and the discrimination is up to 57.5% between the wtp53 and the mutant type p53 sequence (mtp53). It holds promise for the early diagnosis of cancer development and monitoring of patient therapy. PMID:23410627

Wang, Xiaoying; Wang, Xiaobing; Wang, Xiaoning; Chen, Fentian; Zhu, Kehui; Xu, Qian; Tang, Meng

2013-02-26

119

Scientific Laser Market Still The Backbone Of The Industry  

NASA Astrophysics Data System (ADS)

Good morning. I would like to thank Gary Forrest and Laser Focus for giving me the opportunity to participate in this seminar. After listening to Moe Levitt's overview of the industry outlook for 1988, it is a pleasure for me to represent one of the 'hot' sectors in the market - the old research market. My mission today is to provide a perspective of this market to you as one of the healthier parts of the industry, as one of the backbones of our industry.

Tomkins, Jon

1988-06-01

120

Composite-180° pulse-based symmetry sequences to recouple proton chemical shift anisotropy tensors under ultrafast MAS solid-state NMR spectroscopy  

NASA Astrophysics Data System (ADS)

There is considerable interest in the measurement of proton (1H) chemical shift anisotropy (CSA) tensors to obtain deeper insights into H-bonding interactions which find numerous applications in chemical and biological systems. However, the presence of strong 1H/1H dipolar interaction makes it difficult to determine small size 1H CSAs from the homogeneously broadened NMR spectra. Previously reported pulse sequences for 1H CSA recoupling are prone to the effects of radio frequency field (B1) inhomogeneity. In the present work we have carried out a systematic study using both numerical and experimental approaches to evaluate ?-encoded radio frequency (RF) pulse sequences based on R-symmetries that recouple 1H CSA in the indirect dimension of a 2D 1H/1H anisotropic/isotropic chemical shift correlation experiment under ultrafast magic angle spinning (MAS) frequencies. The spectral resolution and sensitivity can be significantly improved in both frequency dimensions of the 2D 1H/1H correlation spectrum without decoupling 1H/1H dipolar couplings but by using ultrafast MAS rates up to 70 kHz. We successfully demonstrate that with a reasonable RF field requirement (<200 kHz) a set of symmetry-based recoupling sequences, with a series of phase-alternating 270°0-90°180 composite-180° pulses, are more robust in combating B1 inhomogeneity effects. In addition, our results show that the new pulse sequences render remarkable 1H CSA recoupling efficiency and undistorted CSA lineshapes. Experimental results on citric acid and malonic acid comparing the efficiencies of these newly developed pulse sequences with that of previously reported CSA recoupling pulse sequences are also reported under ultrafast MAS conditions.

Pandey, Manoj Kumar; Malon, Michal; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

2015-01-01

121

Composite-180° pulse-based symmetry sequences to recouple proton chemical shift anisotropy tensors under ultrafast MAS solid-state NMR spectroscopy.  

PubMed

There is considerable interest in the measurement of proton ((1)H) chemical shift anisotropy (CSA) tensors to obtain deeper insights into H-bonding interactions which find numerous applications in chemical and biological systems. However, the presence of strong (1)H/(1)H dipolar interaction makes it difficult to determine small size (1)H CSAs from the homogeneously broadened NMR spectra. Previously reported pulse sequences for (1)H CSA recoupling are prone to the effects of radio frequency field (B1) inhomogeneity. In the present work we have carried out a systematic study using both numerical and experimental approaches to evaluate ?-encoded radio frequency (RF) pulse sequences based on R-symmetries that recouple (1)H CSA in the indirect dimension of a 2D (1)H/(1)H anisotropic/isotropic chemical shift correlation experiment under ultrafast magic angle spinning (MAS) frequencies. The spectral resolution and sensitivity can be significantly improved in both frequency dimensions of the 2D (1)H/(1)H correlation spectrum without decoupling (1)H/(1)H dipolar couplings but by using ultrafast MAS rates up to 70kHz. We successfully demonstrate that with a reasonable RF field requirement (<200kHz) a set of symmetry-based recoupling sequences, with a series of phase-alternating 270°0-90°180 composite-180° pulses, are more robust in combating B1 inhomogeneity effects. In addition, our results show that the new pulse sequences render remarkable (1)H CSA recoupling efficiency and undistorted CSA lineshapes. Experimental results on citric acid and malonic acid comparing the efficiencies of these newly developed pulse sequences with that of previously reported CSA recoupling pulse sequences are also reported under ultrafast MAS conditions. PMID:25497846

Pandey, Manoj Kumar; Malon, Michal; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

2015-01-01

122

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

123

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

124

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

125

Error tolerant NMR backbone resonance assignment and automated structure generation.  

PubMed

Error tolerant backbone resonance assignment is the cornerstone of the NMR structure determination process. Although a variety of assignment approaches have been developed, none works sufficiently well on noisy fully automatically picked peaks to enable the subsequent automatic structure determination steps. We have designed an integer linear programming (ILP) based assignment system (IPASS) that has enabled fully automatic protein structure determination for four test proteins. IPASS employs probabilistic spin system typing based on chemical shifts and secondary structure predictions. Furthermore, IPASS extracts connectivity information from the inter-residue information and the (automatically picked) (15)N-edited NOESY peaks which are then used to fix reliable fragments. When applied to automatically picked peaks for real proteins, IPASS achieves an average precision and recall of 82% and 63%, respectively. In contrast, the next best method, MARS, achieves an average precision and recall of 77% and 36%, respectively. The assignments generated by IPASS are then fed into our protein structure calculation system, FALCON-NMR, to determine the 3D structures without human intervention. The final models have backbone RMSDs of 1.25Å, 0.88Å, 1.49Å, and 0.67Å to the reference native structures for proteins TM1112, CASKIN, VRAR, and HACS1, respectively. The web server is publicly available at http://monod.uwaterloo.ca/nmr/ipass. PMID:21328705

Alipanahi, Babak; Gao, Xin; Karakoc, Emre; Li, Shuai Cheng; Balbach, Frank; Feng, Guangyu; Donaldson, Logan; Li, Ming

2011-02-01

126

Long-term forecasting of internet backbone traffic.  

PubMed

We introduce a methodology to predict when and where link additions/upgrades have to take place in an Internet protocol (IP) backbone network. Using simple network management protocol (SNMP) statistics, collected continuously since 1999, we compute aggregate demand between any two adjacent points of presence (PoPs) and look at its evolution at time scales larger than 1 h. We show that IP backbone traffic exhibits visible long term trends, strong periodicities, and variability at multiple time scales. Our methodology relies on the wavelet multiresolution analysis (MRA) and linear time series models. Using wavelet MRA, we smooth the collected measurements until we identify the overall long-term trend. The fluctuations around the obtained trend are further analyzed at multiple time scales. We show that the largest amount of variability in the original signal is due to its fluctuations at the 12-h time scale. We model inter-PoP aggregate demand as a multiple linear regression model, consisting of the two identified components. We show that this model accounts for 98% of the total energy in the original signal, while explaining 90% of its variance. Weekly approximations of those components can be accurately modeled with low-order autoregressive integrated moving average (ARIMA) models. We show that forecasting the long term trend and the fluctuations of the traffic at the 12-h time scale yields accurate estimates for at least 6 months in the future. PMID:16252820

Papagiannaki, Konstantina; Taft, Nina; Zhang, Zhi-Li; Diot, Christophe

2005-09-01

127

Anatomy of high-sediment supply, transgressive tracts in the Vilomara composite sequence, Sant Llorenç del Munt, Ebro Basin, NE Spain  

NASA Astrophysics Data System (ADS)

The Sant Llorenç del Munt fan-delta succession forms a clastic wedge (ca. 3 m.y. duration) that built out into the NE Ebro Basin in response to transpression and uplift along the Catalan Coastal Range. The wedge contains a series of composite transgressive-regressive sequences. The transgressive part of one of these sequences, the Vilomara composite sequence, has been examined to highlight the character of 'transgressive' successions in a highly aggradational setting. The analysis focuses on the nature of the component high-frequency (fundamental) sequences. There is a marked difference in how alluvial and marine sediment volumes are partitioned within the transgressive and regressive tracts of the three fundamental sequences within this overall landward-stepping succession. In transgressive tracts, the marine shoreline clastics are well developed, but only in narrow (250 m wide) strike-parallel zones, which are closely associated with ravinement clusters. The time-equivalent alluvial strata are thick and extensive. In regressive tracts, the marine clastics are extensively developed along both dip and strike as prograding shoreline sheets, whereas the interfingering alluvial deposits are only thinly developed or eroded out completely by their overlying sequence boundary. In regressive intervals, there was significant sediment bypass in the alluvial reaches, with feeding to the shorezone and shelf; in transgressive intervals, in contrast, great volumes of sediment were stored in the coastal plains. This partitioning of sediment volumes commonly led to wedge-shaped, seaward-thickening regressive geometries, and wedge-shaped, landward-thickening transgressive geometries. The unusual thickness of transgressive strata, the aggradationally-stacked nature of successive ravinement surfaces, and the thick development of nonmarine strata during times of transgression are symptomatic of an unusually high supply of sediment to the system during high rates of accommodation creation and a near-continuous rise of relative sea level. An unusual type of parasequence in the transgressive tracts, showing well-developed transgressive and regressive components, is probably also symptomatic of the high sediment supply setting.

Steel, R.; Rasmussen, H.; Eide, S.; Neuman, B.; Siggerud, E.

2000-12-01

128

Composites  

NASA Astrophysics Data System (ADS)

It is commonly known that the properties of sintered materials are strongly related to technological conditions of the densification process. This paper shows the sintering behavior of a NiAl-Al2O3 composite, and its individual components sintered separately. Each kind of material was processed via the powder metallurgy route (hot pressing). The progress of sintering at different stages of the process was tested. Changes in the microstructure were examined using scanning and transmission electron microscopy. Metal-ceramics interface was clean and no additional phases were detected. Correlation between the microstructure, density, and mechanical properties of the sintered materials was analyzed. The values of elastic constants of NiAl/Al2O3 were close to intermetallic ones due to the volume content of the NiAl phase particularly at low densities, where small alumina particles had no impact on the composite's stiffness. The influence of the external pressure of 30 MPa seemed crucial for obtaining satisfactory stiffness for three kinds of the studied materials which were characterized by a high dense microstructure with a low number of isolated spherical pores.

Chmielewski, M.; Nosewicz, S.; Pietrzak, K.; Rojek, J.; Strojny-N?dza, A.; Mackiewicz, S.; Dutkiewicz, J.

2014-11-01

129

Indirect readout of the trp-repressor-operator complex by B-DNA's backbone conformation transitions.  

PubMed

Although the trp-repressor-operator complex is one of the best studied transcriptional controlling systems, some questions regarding the specific recognition of the operator by the repressor remain. We performed a 2.35 ns long molecular dynamics simulation to clarify the influence of the two B-DNA backbone conformational substates B(I) and B(II) on complexation. The trp-repressor-operator is an ideal biological system for this study because experimental results have already figured out that the interaction between the internucleotide phosphates and the protein is essential for the formation of the high affinity complex. Our simulation supports these results, but more important it shows a strong correlation between the B(I)/B(II) phosphate substate and the number of interactions with this phosphate. In particular the B(I) <==> B(II) transitions occur synchronous to hydrogen bond breaking or formation. To the best of our knowledge, this was observed for the first time. Thus, we conclude that the sequence specific B(I)/B(II) behavior contributes via indirect readout to sequence specific recognition. These results have implication for the design of transcription-controlling drugs in view of the recently published influence of minor groove binders on the B(I)/B(II) pattern. The simulation also agrees with crystallographically observed hydration sites. This is consistent with experimental results and indicates the correctness of the model used. PMID:11900552

Wellenzohn, Bernd; Flader, Wolfgang; Winger, Rudolf H; Hallbrucker, Andreas; Mayer, Erwin; Liedl, Klaus R

2002-03-26

130

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome.  

PubMed

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are "novel" to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence. PMID:24833511

Gill, Navdeep; Buti, Matteo; Kane, Nolan; Bellec, Arnaud; Helmstetter, Nicolas; Berges, Hélène; Rieseberg, Loren H

2014-01-01

131

Trimethylamine ?-oxide Influence on the Backbone of Proteins: An Oligoglycine Model  

SciTech Connect

The study of organic osmolytes has been pivotal in demonstrating the role of solvent effects on the protein backbone in the folding process. Although a thermodynamic description of the interactions between the protein backbone and osmolyte has been well defined, the structural analysis of the effect of osmolyte on the protein backbone has been incomplete. Therefore, we have performed simulations of a peptide backbone model, glycine??, in protecting osmolyte trimethylamine ?-oxide (TMAO) solution, in order to determine the effect of the solution structure on the conformation of the peptide backbone. We show that the models chosen show that the ensemble of backbone structures shifts toward a more collapsed state in TMAO solution as compared with pure water solution. The collapse is consistent with preferential exclusion of the osmolyte caused by unfavorable interactions between osmolyte and peptide backbone. The exclusion is caused by strong triplet correlations of osmolyte, water, and peptide backbone. This provides a clear mechanism showing that even a modest concentration of TMAO forces the protein backbone to adopt a more collapsed structure in the absence of side chain effects.

Hu, Char Y.; Lynch, Gillian C.; Kokubo, Hironori; Pettitt, Bernard M.

2010-02-15

132

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

NASA Astrophysics Data System (ADS)

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). Holographic recording was attempted by photopolymerization of the monomers in the photopolymer film using a 532 nm laser. Holographic gratings were written into the photopolymer samples by interfering two collimated plane wave beams. The temporal growth of the diffracted power was monitored in real-time at 785 nm laser. Contents of monomer and TESPEG were changed in the range of 0-60 wt% and the composition were optimized in terms of diffraction efficiency. Photopolymer film exhibited very high diffraction efficiency of 93.5% and low shrinkage (<0.5%) after the contents of monomer, binder, and TSPEG were optimized.

Chang, Yu Mi; Yoon, Sung Cheol; Han, Mijeong

2007-12-01

133

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

134

Emergence of sequence type 779 methicillin-resistant Staphylococcus aureus harboring a novel pseudo staphylococcal cassette chromosome mec (SCCmec)-SCC-SCCCRISPR composite element in Irish hospitals.  

PubMed

Methicillin-resistant Staphylococcus aureus (MRSA) has been a major cause of nosocomial infection in Irish hospitals for 4 decades, and replacement of predominant MRSA clones has occurred several times. An MRSA isolate recovered in 2006 as part of a larger study of sporadic MRSA exhibited a rare spa (t878) and multilocus sequence (ST779) type and was nontypeable by PCR- and DNA microarray-based staphylococcal cassette chromosome mec (SCCmec) element typing. Whole-genome sequencing revealed the presence of a novel 51-kb composite island (CI) element with three distinct domains, each flanked by direct repeat and inverted repeat sequences, including (i) a pseudo SCCmec element (16.3 kb) carrying mecA with a novel mec class region, a fusidic acid resistance gene (fusC), and two copper resistance genes (copB and copC) but lacking ccr genes; (ii) an SCC element (17.5 kb) carrying a novel ccrAB4 allele; and (iii) an SCC element (17.4 kb) carrying a novel ccrC allele and a clustered regularly interspaced short palindromic repeat (CRISPR) region. The novel CI was subsequently identified by PCR in an additional 13 t878/ST779 MRSA isolates, six from bloodstream infections, recovered between 2006 and 2011 in 11 hospitals. Analysis of open reading frames (ORFs) carried by the CI showed amino acid sequence similarity of 44 to 100% to ORFs from S. aureus and coagulase-negative staphylococci (CoNS). These findings provide further evidence of genetic transfer between S. aureus and CoNS and show how this contributes to the emergence of novel SCCmec elements and MRSA strains. Ongoing surveillance of this MRSA strain is warranted and will require updating of currently used SCCmec typing methods. PMID:23147725

Kinnevey, Peter M; Shore, Anna C; Brennan, Grainne I; Sullivan, Derek J; Ehricht, Ralf; Monecke, Stefan; Slickers, Peter; Coleman, David C

2013-01-01

135

Emergence of Sequence Type 779 Methicillin-Resistant Staphylococcus aureus Harboring a Novel Pseudo Staphylococcal Cassette Chromosome mec (SCCmec)-SCC-SCCCRISPR Composite Element in Irish Hospitals  

PubMed Central

Methicillin-resistant Staphylococcus aureus (MRSA) has been a major cause of nosocomial infection in Irish hospitals for 4 decades, and replacement of predominant MRSA clones has occurred several times. An MRSA isolate recovered in 2006 as part of a larger study of sporadic MRSA exhibited a rare spa (t878) and multilocus sequence (ST779) type and was nontypeable by PCR- and DNA microarray-based staphylococcal cassette chromosome mec (SCCmec) element typing. Whole-genome sequencing revealed the presence of a novel 51-kb composite island (CI) element with three distinct domains, each flanked by direct repeat and inverted repeat sequences, including (i) a pseudo SCCmec element (16.3 kb) carrying mecA with a novel mec class region, a fusidic acid resistance gene (fusC), and two copper resistance genes (copB and copC) but lacking ccr genes; (ii) an SCC element (17.5 kb) carrying a novel ccrAB4 allele; and (iii) an SCC element (17.4 kb) carrying a novel ccrC allele and a clustered regularly interspaced short palindromic repeat (CRISPR) region. The novel CI was subsequently identified by PCR in an additional 13 t878/ST779 MRSA isolates, six from bloodstream infections, recovered between 2006 and 2011 in 11 hospitals. Analysis of open reading frames (ORFs) carried by the CI showed amino acid sequence similarity of 44 to 100% to ORFs from S. aureus and coagulase-negative staphylococci (CoNS). These findings provide further evidence of genetic transfer between S. aureus and CoNS and show how this contributes to the emergence of novel SCCmec elements and MRSA strains. Ongoing surveillance of this MRSA strain is warranted and will require updating of currently used SCCmec typing methods. PMID:23147725

Kinnevey, Peter M.; Shore, Anna C.; Brennan, Grainne I.; Sullivan, Derek J.; Ehricht, Ralf; Monecke, Stefan; Slickers, Peter

2013-01-01

136

Laccase-assisted grafting of poly(3-hydroxybutyrate) onto the bacterial cellulose as backbone polymer: development and characterisation.  

PubMed

Bacterial cellulose (BC) exhibits high purity, mechanical strength and an ultra-fine fibrous 3-D network structure with bio-compatible and bio-degradable characteristics, while P(3 HB) are a bio-degradable matrix material derived from natural resources. Herein, we report a mild and eco-friendly fabrication of indigenously isolated P(3 HB) based novel composites consisting of BC (a straight-chain polysaccharide) as a backbone polymer and laccase was used as a grafting tool. The resulting composites were characterised by Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), X-ray diffraction (XRD), differential scanning calorimetry (DSC), dynamic mechanical analyser (DMA) and water contact angle analyser (WCA). The FTIR spectra of the pure P(3 HB) and P(3 HB) containing graft composites [P(3 HB)-g-BC] showed their strong characteristic bands at 3358 cm(-1), 1721 cm(-1) and 1651 cm(-1), respectively. A homogenous dispersion of P(3 HB) in the backbone polymer of BC was achieved as evident by the SEM micrographs. XRD pattern for P(3 HB) showed distinct peaks at 2? values that represent the crystalline nature of P(3 HB). While, in comparison with those of neat P(3 HB), the degree of crystallinity for P(3 HB)-g-BC decreased and this reduction is mainly because of the new cross-linking of P(3 HB) within the backbone polymer that changes the morphology and destroys the crystallites. Laccase-assisted graft composite prepared from P(3 HB) and BC was fairly flexible and strong, judged by the tensile strength (64.5 MPa), elongations at break (15.7%), and Young's modulus (0.98 GPa) because inherently high strength of BC allowed the mechanical properties of P(3 HB) to improve in the P(3 HB)-g-BC composite. The hydrophilic property of the P(3 HB)-g-BC was much better than that of the individual counterparts which is also a desired characteristic to enhance the biocompatibility of the materials for proper cell adhesion and proliferation. PMID:25256467

Iqbal, Hafiz M N; Kyazze, Godfrey; Tron, Thierry; Keshavarz, Tajalli

2014-11-26

137

Backbone cleavages of [M - H](-) anions of peptides. Cyclisation of citropin 1 peptides involving reactions between the C-terminal [CONH](-) residue and backbone amide carbonyl groups. A new type of beta cleavage: a joint experimental and theoretical study.  

PubMed

This paper reports the study of backbone cleavages in the collision-induced negative-ion mass spectra of the [M - H](-) anions of some synthetic modifications of the bioactive amphibian peptide citropin 1 (GLFDVIKKVASVIGGL-NH(2)). The peptides chosen for study contain no amino acid residues which could effect facile side-chain cleavage, i.e. Ser (-CH(2)O, side-chain cleavage) and Asp (-H(2)O) are replaced by Ala or Lys. We expected that such peptides should exhibit standard and pronounced peaks due to alpha cleavage ions (and to a lesser extent beta cleavage ions) in their collision-induced negative-ion spectra. This expectation was realised, but the spectra also contained peaks formed by a new series of cleavage anions. These are produced following cyclisation of the C-terminal CONH(-) moiety at carbonyl functions of amide groups along the peptide backbone; effectively transferring the NH of the C-terminal CONH(-) group to other amino acid residues. We have called the product anions of these processes beta' ions, in order to distinguish them from standard beta ions. Some beta' ions also fragment directly to some other beta' ions of smaller mass. The reaction coordinates of alpha,beta and beta' backbone processes have been calculated at the HF/6-31G*//AM1 level theory for simple model systems. The initial cyclisation step of the beta' sequence is barrierless and exothermic. Subsequent steps have a maximum barrier of +40 kcal mol(-1), with the overall reaction being endothermic by some 30 kcal mol(-1) at the level of theory used. These calculations take no account of the complexity of the conformationally flexible peptide system, and it is surprising that each of the two reacting centres can 'find' each other in such a large system. PMID:11921251

Brinkworth, Craig S; Dua, Suresh; Bowie, John H

2002-01-01

138

Tactical network design and simulator with Wireless Mesh Network-based Backbone architecture  

Microsoft Academic Search

For tactical networks, rapid reconfiguration and recovery of network topology is highly required. In this paper, we propose an effective tactical network architecture with WMN(Wireless Mesh Network)-based backbone. To reduce the computational and maintenance complexities of tactical networks, a hierarchical architecture is considered in the proposed architecture. The proposed architecture is called called TMB (Tactical Mesh Backbone). In addition, we

Bosung Kim; Kwangsoo Kim; Hye-lim Koo; Byeong-hee Roh; Yu-Seon Kim; Jong-Sam Jin

2010-01-01

139

Novel photochromic compounds based on the 1-thienyl-2-vinylcyclopentene backbone.  

PubMed

[reaction: see text] A new class of photochromic compounds based on the hexatriene backbone has been developed. The backbone, composed of a thiophene ring, a perfluorocyclopentene ring, and a trisubstituted olefin, undergoes reversible ring-opening and ring-closing photoisomerization reactions when irradiated with ultraviolet and visible light, respectively. PMID:12688714

Peters, Andrea; Vitols, Colin; McDonald, Robert; Branda, Neil R

2003-04-17

140

Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope  

E-print Network

Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope Edited by I. Wilson Keywords: protein grafting; flexible backbone design; epitope scaffold; immunogen epitopes onto heterologous proteins to design novel "epitope-scaffold" antigens. However, side

Baker, David

141

Distributed Mobile Disk Cover A Building Block for Mobile Backbone Networks  

E-print Network

1 Distributed Mobile Disk Cover ­ A Building Block for Mobile Backbone Networks Anand Srinivas, Gil of Mobile Backbone Networks has been recently studied by a few different approaches. An important subproblem a Geometric Disk Cover (GDC) under mobility. While from the context of static nodes and centralized solutions

Zussman, Gil

142

Supplemental Material of "Efficient Virtual Backbone Construction without a Common Control  

E-print Network

1 Supplemental Material of "Efficient Virtual Backbone Construction without a Common Control. The existing approaches of building virtual backbones rely on a common channel to exchange control messages, no matter if it is exchanging information among 1- hop or 2-hop neighbors, or neighbors with even further

Wu, Jie

143

Short communication Backbone conformation study of a side chain polyacrylate through  

E-print Network

polar low molecular weight liquid crystals present strange polymorphisms [1-3] such as, for instance [1.41 Introduction. Our aim is to compare the conformations of the backbone of a liquid crystal polymer in the usual). Abstract.2014 The backbone conformation of a liquid crystalline side-chain polyacrylate was studied

Boyer, Edmond

144

TACN-based oligomers with aromatic backbones for efficient nucleic acid delivery.  

PubMed

Cationic oligomers with a rigid aromatic backbone were first applied as non-viral gene delivery vectors. These materials showed better DNA condensation ability than their flexible analogues. In vitro transfection experiments revealed that the materials with more rigid backbone exhibited considerably higher TE and lower cytotoxicity than 25 kDa PEI. PMID:24811979

Yi, Wen-Jing; Yu, Xing-Chi; Wang, Bing; Zhang, Ji; Yu, Qing-Ying; Zhou, Xue-Dong; Yu, Xiao-Qi

2014-06-21

145

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

146

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

147

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

148

Data Acquisition Backbone Core DABC release v1.0  

NASA Astrophysics Data System (ADS)

The Data Acquisition Backbone Core (DABC) is a general purpose software framework designed for the implementation of a wide-range of data acquisition systems - from various small detector test beds to high performance systems. DABC consists of a compact data-flow kernel and a number of plug-ins for various functional components like data inputs, device drivers, user functional modules and applications. DABC provides configurable components for implementing event building over fast networks like InfiniBand or Gigabit Ethernet. A generic Java GUI provides the dynamic control and visualization of control parameters and commands, provided by DIM servers. A first set of application plug-ins has been implemented to use DABC as event builder for the front-end components of the GSI standard DAQ system MBS (Multi Branch System). Another application covers the connection to DAQ readout chains from detector front-end boards (N-XYTER) linked to read-out controller boards (ROC) over UDP into DABC for event building, archiving and data serving. This was applied for data taking in the September 2008 test beamtime for the CBM experiment at GSI. DABC version 1.0 is released and available from the website.

Adamczewski-Musch, J.; Essel, H. G.; Kurz, N.; Linev, S.

2010-04-01

149

Solution structure and backbone dynamics of Mason-Pfizer monkey virus (MPMV) nucleocapsid protein.  

PubMed

Retroviral nucleocapsid proteins (NCPs) are CCHC-type zinc finger proteins that mediate virion RNA binding activities associated with retrovirus assembly and genomic RNA encapsidation. Mason-Pfizer monkey virus (MPMV), a type D retrovirus, encodes a 96-amino acid nucleocapsid protein, which contains two Cys-X2-Cys-X4-His-X4-Cys (CCHC) zinc fingers connected by an unusually long 15-amino acid linker. Homonuclear, two-dimensional sensitivity-enhanced 15N-1H, three-dimensional 15N-1H, and triple resonance NMR spectroscopy have been used to determine the solution structure and residue-specific backbone dynamics of the structured core domain of MPMV NCP containing residues 21-80. Structure calculations and spectral density mapping of N-H bond vector mobility reveal that MPMV NCP 21-80 is best described as two independently folded, rotationally uncorrelated globular domains connected by a seven-residue flexible linker consisting of residues 42-48. The N-terminal CCHC zinc finger domain (residues 24-37) appears to adopt a fold like that described previously for HIV-1 NCP; however, residues within this domain and the immediately adjacent linker region (residues 38-41) are characterized by extensive conformational averaging on the micros-ms time scale at 25 degrees C. In contrast to other NCPs, residues 49-77, which includes the C-terminal CCHC zinc-finger (residues 53-66), comprise a well-folded globular domain with the Val49-Pro-Gly-Leu52 sequence and C-terminal tail residues 67-77 characterized by amide proton exchange properties and 15N R1, R2, and (1H-15N) NOE values indistinguishable to residues in the core C-terminal finger. Twelve refined structural models of MPMV NCP residues 49-80 (pairwise backbone RMSD of 0.77 A) reveal that the side chains of the conserved Pro50 and Trp62 are in van der Waals contact with one another. Residues 70-73 in the C-terminal tail adopt a reverse turn-like structure. Ile77 is involved in extensive van der Waals contact with the core finger domain, while the side chains of Ser68 and Asn75 appear to form hydrogen bonds that stabilize the overall fold of this domain. These residues outside of the core finger structure are conserved in D-type and related retroviral NCPs, e.g., MMTV NCP, suggesting that the structure of MPMV NCP may be representative of this subclass of retroviral NCPs. PMID:9827993

Gao, Y; Kaluarachchi, K; Giedroc, D P

1998-11-01

150

dndDB: A Database Focused on Phosphorothioation of the DNA Backbone  

PubMed Central

Background The Dnd DNA degradation phenotype was first observed during electrophoresis of genomic DNA from Streptomyces lividans more than 20 years ago. It was subsequently shown to be governed by the five-gene dnd cluster. Similar gene clusters have now been found to be widespread among many other distantly related bacteria. Recently the dnd cluster was shown to mediate the incorporation of sulphur into the DNA backbone via a sequence-selective, stereo-specific phosphorothioate modification in Escherichia coli B7A. Intriguingly, to date all identified dnd clusters lie within mobile genetic elements, the vast majority in laterally transferred genomic islands. Methodology We organized available data from experimental and bioinformatics analyses about the DNA phosphorothioation phenomenon and associated documentation as a dndDB database. It contains the following detailed information: (i) Dnd phenotype; (ii) dnd gene clusters; (iii) genomic islands harbouring dnd genes; (iv) Dnd proteins and conserved domains. As of 25 December 2008, dndDB contained data corresponding to 24 bacterial species exhibiting the Dnd phenotype reported in the scientific literature. In addition, via in silico analysis, dndDB identified 26 syntenic dnd clusters from 25 species of Eubacteria and Archaea, 25 dnd-bearing genomic islands and one dnd plasmid containing 114 dnd genes. A further 397 other genes coding for proteins with varying levels of similarity to Dnd proteins were also included in dndDB. A broad range of similarity search, sequence alignment and phylogenetic tools are readily accessible to allow for to individualized directions of research focused on dnd genes. Conclusion dndDB can facilitate efficient investigation of a wide range of aspects relating to dnd DNA modification and other island-encoded functions in host organisms. dndDB version 1.0 is freely available at http://mml.sjtu.edu.cn/dndDB/. PMID:19357771

Ou, Hong-Yu; He, Xinyi; Shao, Yucheng; Tai, Cui; Rajakumar, Kumar; Deng, Zixin

2009-01-01

151

FDDI (Fiber Distributed Data Interface) as a backbone for large campus Ethernet networks  

SciTech Connect

Many large campus environments rely heavily on multiple Ethernet Local Area Networks, LANs, interconnected with bridges and/or routers, operating over Backbone LANs also based on Ethernet. Although the use of Ethernets for direct user attachments will be viable for quite some time to come, the use of Ethernets in the Backbone is more limited. A Fiber Distributed Data Interface (FDDI) Backbone, interconnected to existing Ethernets with FDDI to Ethernet MAC level bridges, will provide the principal evolutionary path for these large campus networks due to its combination of high speed, low delay time and reliability. 7 refs.

Fink, R.L.

1987-08-01

152

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

153

Peptide Backbone Sampling Convergence with the Adaptive Biasing Force Algorithm  

PubMed Central

Complete Boltzmann sampling of reaction coordinates in biomolecular systems continues to be a challenge for unbiased molecular dynamics simulations. A growing number of methods have been developed for applying biases to biomolecular systems to enhance sampling while enabling recovery of the unbiased (Boltzmann) distribution of states. The Adaptive Biasing Force (ABF) algorithm is one such method, and works by canceling out the average force along the desired reaction coordinate(s) using an estimate of this force progressively accumulated during the simulation. Upon completion of the simulation, the potential of mean force, and therefore Boltzmann distribution of states, is obtained by integrating this average force. In an effort to characterize the expected performance in applications such as protein loop sampling, ABF was applied to the full ranges of the Ramachandran ?/? backbone dihedral reaction coordinates for dipeptides of the 20 amino acids using all-atom explicit-water molecular dynamics simulations. Approximately half of the dipeptides exhibited robust and rapid convergence of the potential of mean force as a function of ?/? in triplicate 50-ns simulations, while the remainder exhibited varying degrees of less complete convergence. The greatest difficulties in achieving converged ABF sampling were seen in the branched-sidechain amino acids threonine and valine, as well as the special case of proline. Proline dipeptide sampling was further complicated by trans-to-cis peptide bond isomerization not observed in unbiased control molecular dynamics simulations. Overall, the ABF method was found to be a robust means of sampling the entire ?/? reaction coordinate for the 20 amino acids, including high free-energy regions typically inaccessible in standard molecular dynamics simulations. PMID:23215032

Faller, Christina E.; Reilly, Kyle A.; Hills, Ronald D.; Guvench, Olgun

2013-01-01

154

Peptide backbone sampling convergence with the adaptive biasing force algorithm.  

PubMed

Complete Boltzmann sampling of reaction coordinates in biomolecular systems continues to be a challenge for unbiased molecular dynamics simulations. A growing number of methods have been developed for applying biases to biomolecular systems to enhance sampling while enabling recovery of the unbiased (Boltzmann) distribution of states. The adaptive biasing force (ABF) algorithm is one such method and works by canceling out the average force along the desired reaction coordinate(s) using an estimate of this force progressively accumulated during the simulation. Upon completion of the simulation, the potential of mean force, and therefore Boltzmann distribution of states, is obtained by integrating this average force. In an effort to characterize the expected performance in applications such as protein loop sampling, ABF was applied to the full ranges of the Ramachandran ?/? backbone dihedral reaction coordinates for dipeptides of the 20 amino acids using all-atom explicit-water molecular dynamics simulations. Approximately half of the dipeptides exhibited robust and rapid convergence of the potential of mean force as a function of ?/? in triplicate 50 ns simulations, while the remainder exhibited varying degrees of less complete convergence. The greatest difficulties in achieving converged ABF sampling were seen in the branched-side chain amino acids threonine and valine, as well as the special case of proline. Proline dipeptide sampling was further complicated by trans-to-cis peptide bond isomerization not observed in unbiased control molecular dynamics simulations. Overall, the ABF method was found to be a robust means of sampling the entire ?/? reaction coordinate for the 20 amino acids, including high free-energy regions typically inaccessible in standard molecular dynamics simulations. PMID:23215032

Faller, Christina E; Reilly, Kyle A; Hills, Ronald D; Guvench, Olgun

2013-01-17

155

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

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

156

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

157

Mobile backbone architecture for wireless ad-hoc networks : algorithms and performance analysis  

E-print Network

In this thesis, 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 ...

Srinivas, Anand, 1979-

2007-01-01

158

Chemorheology of phenylboronate-salicylhydroxamate crosslinked hydrogel networks with a sulfonated polymer backbone  

PubMed Central

Hydrogel networks crosslinked with polymer-bound phenylboronic acid (PBA) and salicylhydroxamic acid (SHA) demonstrate pH-reversible gel behavior due to the pH-dependent equilibrium of the crosslinking moieties that form the gel network. Furthermore, the pH at which gels behave dynamically can be controlled by use of a polyelectrolyte backbone. Here we report on the frequency-dependent chemorheological characterization of PBA-SHA crosslinked hydrogel networks with a sulfonated polymer backbone. Our results suggest that the anionic nature of the polymers allows reversible crosslinking at neutral pH that an otherwise neutral-backboned PBA-SHA crosslinked network cannot, and that these charge-induced dynamics can be effectively screened by ions in solution. Moreover, moduli-frequency data can effectively be reduced into a single master curve with a neutral-backboned PBA-SHA gel data set as the reference condition. PMID:23132956

Roberts, Meredith C.; Mahalingam, Alamelu; Hanson, Melissa C.; Kiser, Patrick F.

2012-01-01

159

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

Microsoft Academic Search

Galacturonan, the main constituent of the backbone (core) of the comaruman macromolecule, a pectin from the marsh cinquefoil\\u000a Comarum palustre L., was obtained on partial acid hydrolysis of the pectin. Using atomic force microscopy and methylation analysis of the\\u000a galacturonan, the backbone of the comaruman macromolecule was shown to contain branches as side chains consisting of ?-1,4-linked\\u000a residues of D-galactopyranosyl

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

2006-01-01

160

On the Geometry and Electronic Structure of the As-DNA Backbone  

SciTech Connect

High-level quantum chemical calculations have been applied to investigate the geometry and electronic properties of the arsenate analogue of the DNA backbone. The optimized geometries as well as hyperconjugation effects along the C30 O30 X O50 C50 linkage (X = P,As) exhibit a remarkable similarity for both arsenates and phosphates. This suggests that arsenates, if present, might serve as a potential substitute for phosphates in the DNA backbone.

Fuentes-Cabrera, Miguel A [ORNL; Sponer, Jiri [Academy of Sciences of the Czech Republic; Sponer, Judit [Academy of Sciences of the Czech Republic; Sumpter, Bobby G [ORNL; Mladek, Arnost [Academy of Sciences of the Czech Republic

2011-01-01

161

Effects of solvents on the intrinsic propensity of peptide backbone conformations  

NASA Astrophysics Data System (ADS)

We investigated the effects of solvents on the intrinsic propensity of peptide backbone conformations based on molecular dynamics simulations. The results show that compared with pure water, aqueous urea decreases the helix propensity. In comparison, methanol decreases the polyproline II (PPII) propensity. Such a solvent dependence of the intrinsic propensity of the backbone conformation is correlated with the solvent dependence of the hydration of the backbone groups and the formation probability of the local intrapeptide hydrogen bonds. Aqueous urea which has low ability to stabilize the local intrapeptide hydrogen bonds disfavors the helical conformation. Whereas, methanol which has low ability to hydrate the backbone groups disfavors the polyproline II conformation. In addition, the solvent effects can be further modulated by the side chains of the peptides. The solvent effects of the intrinsic propensity of peptide backbone conformations observed in this work suggest that changing the intrinsic propensity of the protein backbone conformations can partly contribute to the solvent-induced protein structure and dynamics variations. These results will be useful in understanding the solvent dependence of the conformational distributions of the unfolded proteins or peptides (or intrinsically disordered proteins) in which the global tertiary interactions are less important than that in the well-folded proteins.

Li, Wenfei; Qin, Meng; Tie, Zuoxiu; Wang, Wei

2011-10-01

162

Investigation into the structural composition of hydroalcoholic solutions as basis for the development of multiple suppression pulse sequences for NMR measurement of alcoholic beverages.  

PubMed

An eight-fold suppression pulse sequence was recently developed to improve sensitivity in (1) H NMR measurements of alcoholic beverages [Magn. Res. Chem. 2011 (49): 734-739]. To ensure that only one combined hydroxyl peak from water and ethanol appears in the spectrum, adjustment to a certain range of ethanol concentrations was required. To explain this observation, the structure of water-ethanol solutions was studied. Hydroalcoholic solutions showed extreme behavior at 25% vol, 46% vol, and 83% vol ethanol according to (1) H NMR experiments. Near-infrared spectroscopy confirmed the occurrence of four significant compounds ('individual' ethanol and water structures as well as two water-ethanol complexes of defined composition - 1?:?1 and 1?:?3). The successful multiple suppression can be achieved for every kind of alcoholic beverage with different alcoholic strengths, when the final ethanol concentration is adjusted to a range between 25% vol and 46% vol (e.g. using dilution or pure ethanol addition). In this optimum region, an individual ethanol peak was not detected, because the 'individual' water structure and the 1?:?1 ethanol-water complex predominate. The nature of molecular association in ethanol-water solutions is essential to elucidate NMR method development for measurement of alcoholic beverages. The presented approach can be used to optimize other NMR suppression protocols for binary water-organic solvent mixtures, where hydrogen bonding plays a dominant role. Copyright © 2014 John Wiley & Sons, Ltd. PMID:25139252

Monakhova, Yulia B; Mushtakova, Svetlana P; Kuballa, Thomas; Lachenmeier, Dirk W

2014-12-01

163

Deriving High-Resolution Protein Backbone Structure Propensities from All Crystal Data Using the Information Maximization Device  

PubMed Central

The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), totaling more than 77,000 chains, permits the derivation of a large number of optimized sequence-dependent PDFs. This work demonstrates the effectiveness of the IMD and the superiority of the resulting PDFs by extensive fold recognition experiments and rigorous comparisons with previously published triplet PDFs. Because it automatically optimizes PDFs, IMD results in improved performance of knowledge-based potentials, which rely on such PDFs. Furthermore, it provides an easy computational recipe for empirically deriving other kinds of sequence-dependent structural PDFs with greater detail and precision. The high-resolution phi-psi maps derived in this work are available for download. PMID:24896099

Solis, Armando D.

2014-01-01

164

Backbone Degradable Multiblock N-(2-Hydroxypropyl)methacrylamide Copolymer Conjugates via Reversible Addition Fragmentation Chain Transfer Polymerization and Thiol-ene Coupling Reaction  

PubMed Central

Telechelic water-soluble HPMA copolymers and HPMA copolymer-doxorubicin (DOX) conjugates have been synthesized by RAFT polymerization mediated by a new bifunctional chain transfer agent (CTA) that contains an enzymatically degradable oligopeptide sequence. Post-polymerization aminolysis followed by chain extension with a bis-maleimide resulted in linear high molecular weight multiblock HPMA copolymer conjugates. These polymers are enzymatically degradable; in addition to releasing the drug (DOX), the degradation of the polymer backbone resulted in products with molecular weights similar to the starting material and below the renal threshold. The new multiblock HPMA copolymers hold potential as new carriers of anticancer drugs. PMID:21158387

Pan, Huaizhong; Yang, Jiyuan; Kope?ková, Pavla

2011-01-01

165

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

E-print Network

predictor (or a purely secondary-structure-based predictor) with p-value <1.0×10?300 (or <1.0×10?148) by Wilcoxon signed rank test. For some residues (ILE, LEU, PRO and VAL) and especially the residues in helix and buried regions, the MAE of phi angles...

Wu, Sitao; Zhang, Yang

2008-10-15

166

Methods and Compositions for Amplification and Detection of microRNAs (miRNAs) and Noncoding RNAs (ncRNAs) Using the Signature Sequence Amplification Method (SSAM)  

PubMed Central

The signature sequence amplification method (SSAM) described herein is an approach for amplifying noncoding RNA (ncRNA), microRNA (miRNA), and small polynucleotide sequences. A key point of the SSAM technology is the generation of signature sequences. The signature sequences include target sequences (miRNA, ncRNA, and/or any small polynucleotide sequence) flanked by two DNA fragments. Target sequences can be amplified through DNA synthesis, RNA synthesis, or the combination of DNA and RNA synthesis. The amplification of signature sequences provides an efficient and reproducible mechanism to determine the presence or absence of the target miRNAs/ncRNAs, to analyze the quantities of the miRNAs in biological samples, and for miRNA/ncRNA profiling. PMID:25564022

Ginsberg, Stephen D.; Che, Shaoli

2015-01-01

167

Journal of Artificial Intelligence Research 12 (2000) 235270 Submitted 12/99; published 5/00 Backbone Fragility and the Local Search Cost Peak  

E-print Network

/00 Backbone Fragility and the Local Search Cost Peak Josh Singer joshuas@dai.ed.ac.uk Division of Informatics early in WSat's search. This pattern leads us to introduce a measure of the backbone fragility­cost random instances for local search are those with very large backbones which are also backbone­fragile. We

Gent, Ian

168

Design of peptide standards with the same composition and minimal sequence variation to monitor performance/selectivity of reversed-phase matrices.  

PubMed

The present manuscript extends our de novo peptide design approach to the synthesis and evaluation of a new generation of reversed-phase HPLC peptide standards with the same composition and minimal sequence variation (SCMSV). Thus, we have designed and synthesized four series of peptide standards with the sequences Gly-X-Leu-Gly-Leu-Ala-Leu-Gly-Gly-Leu-Lys-Lys-amide, where the N-terminal is either N(?)-acetylated (Series 1) or contains a free ?-amino group (Series 3); and Gly-Gly-Leu-Gly-Gly-Ala-Leu-Gly-X-Leu-Lys-Lys-amide, where the N-terminal is either N(?)-acetylated (Series 2) or contains a free ?-amino group (Series 4). In this initial study, the single substitution position, X, was substituted with alkyl side-chains (Ala

Mant, Colin T; Hodges, Robert S

2012-03-23

169

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

170

Catalytic mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: a quantum mechanical/molecular mechanical analysis.  

PubMed

Endonucleases, such as the restriction enzyme EcoRV, cleave the DNA backbone at a specific recognition sequence. We have investigated the catalytic mechanism of backbone phosphodiester hydrolysis by the restriction enzyme EcoRV by means of hybrid quantum mechanical/molecular mechanical calculations. An exhaustive computation of different reaction pathways is performed, thus generating a network of pathways. Comparison of the computed (AM1d/MM) enzymatic reaction pathways with an analogous mechanism for small-molecule model systems [AM1/d and B3LYP/6-31++G(d,p)] reveals that the transition barriers for associative hydrolysis, which is more probable in the model systems, are not lowered by the enzyme. Instead, a reaction mechanism which has mostly dissociative character is more likely. The protein environment is tuned to significantly electrostatically stabilize the transition state structures. The direct catalytic impact of essential residues is determined: The magnesium metal ion activates a water molecule, thus facilitating protonation of the leaving group. A reduction of the coordination number of the magnesium metal ion from six to four upon the positioning of the attacking water molecule explains why larger metal ions, such as calcium, are not catalytically active. The nucleophile is generated by the transfer of a proton from the attacking water molecule to a carboxylic oxygen atom of aspartate 90. The catalytic effect of lysine 92 involves proper positioning of the scissile phosphate group and, more importantly, stabilization of the metaphosphate intermediate in an orientation optimal for attack of the nucleophile. PMID:19678693

Imhof, Petra; Fischer, Stefan; Smith, Jeremy C

2009-09-29

171

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

172

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

173

Synthesis and utilization of 13C and 15N backbone-labeled proline: NMR study of synthesized oxytocin with backbone-labeled C-terminal tripeptide amide.  

PubMed

The 13C and 15N backbone-labeled proline was prepared using Oppolzer's method based on application of a sultam as chiral auxiliary. This isotopomer was used in the synthesis of the 13C, 15N backbone-labeled C-terminal tripeptide amide fragment of neurohypophyseal hormone oxytocin. Finally, this tripeptide amide was coupled by segment condensation with N-Boc- or N-Fmoc-tocinoic acid, followed by N-deprotection with TFA or piperidine. The labeled oxytocin exhibited biological activity identical with that of natural oxytocin. A detailed 1H, 13C and 15N NMR study confirmed the assigned oxytocin conformation containing a beta-turn in the cyclic part of the molecule, stabilized by H-bond(s) that can be perturbed by the C-terminal tripeptide amide moiety as indicated by comparison of NMR data for both the tocine ring in oxytocin and tocinoic acid. PMID:15791394

Budesínský, M; Ragnarsson, U; Lankiewicz, L; Grehn, L; Slaninová, J; Hlavácek, J

2005-08-01

174

Electric field induced localization phenomena in a ladder network with superlattice configuration: Effect of backbone environment  

NASA Astrophysics Data System (ADS)

Electric field induced localization properties of a tight-binding ladder network in presence of backbone sites are investigated. Based on Green's function formalism we numerically calculate two-terminal transport together with density of states for different arrangements of atomic sites in the ladder and its backbone. Our results lead to a possibility of getting multiple mobility edges which essentially plays a switching action between a completely opaque to fully or partly conducting region upon the variation of system Fermi energy, and thus, support in fabricating mesoscopic or DNA-based switching devices.

Dutta, Paramita; Maiti, Santanu K.; Karmakar, S. N.

2014-09-01

175

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

176

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

177

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

178

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

179

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 that the early evolution of life was dominated by RNA, which can both transfer information from generation of heterogeneous nucleic acid molecules could evolve reproducible function. For such evolution to be possible

Heller, Eric

180

Backbone Dynamics of Detergent-Solubilized Alamethicin from Amide Hydrogen Exchange Measurements  

E-print Network

synthesized N-acetyl-R-aminoisobutyric acid-N-methyl and N-acetyl-alanine- N-methyl and measured the p is significantly more stable than the backbones of alanine-based helical peptides. Rapid exchange at Gly-11 insoluble in water, they do not crystallize easily, and they are difficult to obtain in large quantities

O'Neil, Joe

181

Recognition of tRNA backbone for aminoacylation with cysteine: evolution from Escherichia coli to human.  

PubMed

The underlying basis of the genetic code is specific aminoacylation of tRNAs by aminoacyl-tRNA synthetases. Although the code is conserved, bases in tRNA that establish aminoacylation are not necessarily conserved. Even when the bases are conserved, positions of backbone groups that contribute to aminoacylation may vary. We show here that, although the Escherichia coli and human cysteinyl-tRNA synthetases both recognize the same bases (U73 and the GCA anticodon) of tRNA for aminoacylation, they have different emphasis on the tRNA backbone. The E. coli enzyme recognizes two clusters of phosphate groups. One is at A36 in the anticodon and the other is in the core of the tRNA structure and includes phosphate groups at positions 9, 12, 14, and 60. Metal-ion rescue experiments show that those at positions 9, 12, and 60 are involved with binding divalent metal ions that are important for aminoacylation. The E. coli enzyme also recognizes 2'-hydroxyl groups within the same two clusters: at positions 33, 35, and 36 in the anticodon loop, and at positions 49, 55, and 61 in the core. The human enzyme, by contrast, recognizes few phosphate or 2'-hydroxy groups for aminoacylation. The evolution from the backbone-dependent recognition by the E. coli enzyme to the backbone-independent recognition by the human enzyme demonstrates a previously unrecognized shift that nonetheless has preserved the specificity for aminoacylation with cysteine. PMID:12083512

Ming, Xiaotian; Smith, Kristina; Suga, Hiroaki; Hou, Ya-Ming

2002-05-17

182

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

183

Animals without Backbones: The Invertebrate Story. Grade Level 5-9.  

ERIC Educational Resources Information Center

This guide, when used in tandem with the videotape "Animals Without Backbones," helps students learn about invertebrates. These materials promote hands-on discovery and learning. The guide is composed of six curriculum-based teaching units: (1) "Getting Started"; (2) "Porifera"; (3) "Cnidarians"; (4) "Worms"; (5) "Mollusks"; (6) "Arthropods"; and…

Jerome, Brian; Fuqua, Paul

184

Interconnection of FDDI-II Networks Through an ATM Backbone -An Analysis  

E-print Network

address space, i.e. global addressing. Remote address is determined either through learning or explicit that the gateway is part of) and remote stations. 0 Virtual Paths through ATM backbone are pre- established network. It implements all the modules of a non-monitor station of FDDI-11. Some of the assumptions

Jayasumana, Anura P.

185

Photophysics of Backbone Fluorescent DNA Modifications: Reducing Uncertainties in FRET Suman Ranjit,,  

E-print Network

Photophysics of Backbone Fluorescent DNA Modifications: Reducing Uncertainties in FRET Suman Ranjit of uncertainty commonly encountered in Fo¨rster resonance energy transfer (FRET) measurements. We show. Unusually large FRET efficiencies for donor-acceptor pairs separated by 102 � (three helical turns) were

Thorpe, Michael

186

Cost and Reliability Considerations in Designing the Next-Generation IP over WDM Backbone Networks  

E-print Network

Cost and Reliability Considerations in Designing the Next-Generation IP over WDM Backbone Networks@cse.unl.edu,{kkrama,sinha}@research.att.com Abstract--To accommodate the increasing demands for band- width, Internet Service Providers (ISPs) have networks. To address the reliability challenges due to failures and planned outages, ISPs typically use two

Fisher, Kathleen

187

A Practical Solution for Aligning and Simplifying Pairs of Protein Backbones Under the Discrete Frechet  

E-print Network

A Practical Solution for Aligning and Simplifying Pairs of Protein Backbones Under the Discrete Fr´echet as the dis- tance measure. Recently, the discrete Fr´echet distance has been applied to align and simplify simultaneously under the discrete Fr´echet distance. However, it is still open whether CPS-3F is NP

Zhu, Binhai

188

alifornia's oak savannas and woodlands have been the backbone of the state's rangeland  

E-print Network

C alifornia's oak savannas and woodlands have been the backbone of the state's rangeland livestock privately owned, with domestic livestock grazing about 80% of all oak rangelands. Aside from their importance to the state's live- stock industry, oak rangelands are one of the most biologically diverse

Kelly, Maggi

189

Carboxamide versus sulfonamide in peptide backbone folding: a case study with a hetero foldamer.  

PubMed

Strikingly dissimilar hydrogen-bonding patterns have been observed for two sets of closely similar hetero foldamers containing carboxamide and sulfonamides at regular intervals. Although both foldamers maintain conformational ordering, the hydrogen-bonding pattern and backbone helical handedness differ diametrically. PMID:23473041

Ramesh, Veera V E; Kale, Sangram S; Kotmale, Amol S; Gawade, Rupesh L; Puranik, Vedavati G; Rajamohanan, P R; Sanjayan, Gangadhar J

2013-04-01

190

Helical folding in heterogeneous foldamers without inter-residual backbone hydrogen-bonding.  

PubMed

This communication describes a set of hybrid foldamers that do not feature inter-residual, but intra-residual backbone hydrogen-bonding, yet adopt a preferentially folded conformation displaying right-handed helical architecture. Conformational ordering is apparently due to the combined conformational restrictions imposed by the conformationally restricted individual amino acid residues with which the oligomers are made of. PMID:22850490

Priya, Gowri; Kotmale, Amol S; Gawade, Rupesh L; Mishra, Deepti; Pal, Sourav; Puranik, Vedavadi G; Rajamohanan, Pattuparambil R; Sanjayan, Gangadhar J

2012-09-14

191

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

192

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

193

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

194

Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing  

PubMed Central

The crystal structure of the duplex formed by oligo(2?,3?-dideoxy-?-d-glucopyranosyl)nucleotides (homo-DNA) revealed strongly inclined backbone and base-pair axes [Egli,M., Pallan,P.S., Pattanayek,R., Wilds,C.J., Lubini,P., Minasov,G., Dobler,M., Leumann,C.J. and Eschenmoser,A. (2006) Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J. Am. Chem. Soc., 128, 10847–10856]. This inclination is easily perceived because homo-DNA exhibits only a modest helical twist. Conversely, the tight coiling of strands conceals that the backbone-base inclinations for A- (DNA and RNA) and B-form (DNA) duplexes differ considerably. We have defined a parameter ?B that corresponds to the local inclination between sugar-phosphate backbone and base plane in nucleic acid strands. Here, we show its biological significance as a predictive measure for the relative strand polarities (antiparallel, aps, or parallel, ps) in duplexes of DNA, RNA and artificial nucleic acid pairing systems. The potential of formation of ps duplexes between complementary 16-mers with eight A and U(T) residues each was investigated with DNA, RNA, 2?-O-methylated RNA, homo-DNA and p-RNA, the ribopyranosyl isomer of RNA. The thermodynamic stabilities of the corresponding aps duplexes were also measured. As shown previously, DNA is capable of forming both ps and aps duplexes. However, all other tested systems are unable to form stable ps duplexes with reverse Watson–Crick (rWC) base pairs. This observation illustrates the handicap encountered by nucleic acid systems with inclinations ?B that differ significantly from 0° to form a ps rWC paired duplex. Accordingly, RNA with a backbone-base inclination of ?30°, pairs strictly in an aps fashion. On the other hand, the more or less perpendicular orientation of backbone and bases in DNA allows it to adopt a ps rWC paired duplex. In addition to providing a rationalization of relative strand polarity with nucleic acids, the backbone-base inclination parameter is also a determinant of cross-pairing. Thus, systems with strongly deviating ?B angles will not pair with each other. Nucleic acid pairing systems with significant backbone-base inclinations can also be expected to display different stabilities depending on which terminus carries unpaired nucleotides. The negative inclination of RNA is consistent with the higher stability of duplexes with 3?- compared to those with 5?-dangling ends. PMID:17905816

Pallan, Pradeep S.; Lubini, Paolo; Bolli, Martin; Egli, Martin

2007-01-01

195

Lactobacillus plantarum possesses the capability for wall teichoic acid backbone alditol switching  

PubMed Central

Background Specific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA) in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background. Results Through genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-?B reporter cells expressing Toll like receptor (TLR)-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-? after stimulation with the WTA mutants as compared to the wild-type. Conclusions The study presented here correlates structural differences in WTA to their functional characteristics, thereby providing important information aiding to improve our understanding of molecular host-microbe interactions and probiotic functionality. PMID:22967304

2012-01-01

196

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

197

FiberDock: Flexible induced-fit backbone refinement in molecular docking  

PubMed Central

Upon binding, proteins undergo conformational changes. These changes often prevent rigid-body docking methods from predicting the 3D structure of a complex from the unbound conformations of its proteins. Handling protein backbone flexibility is a major challenge for docking methodologies, as backbone flexibility adds a huge number of degrees of freedom to the search space, and therefore considerably increases the running time of docking algorithms. Normal mode analysis permits description of protein flexibility as a linear combination of discrete movements (modes). Low-frequency modes usually describe the large-scale conformational changes of the protein. Therefore, many docking methods model backbone flexibility by using only few modes, which have the lowest frequencies. However, studies show that due to molecular interactions, many proteins also undergo local and small-scale conformational changes, which are described by high-frequency normal modes. Here we present a new method, FiberDock, for docking refinement which models backbone flexibility by an unlimited number of normal modes. The method iteratively minimizes the structure of the flexible protein along the most relevant modes. The relevance of a mode is calculated according to the correlation between the chemical forces, applied on each atom, and the translation vector of each atom, according to the normal mode. The results show that the method successfully models backbone movements that occur during molecular interactions and considerably improves the accuracy and the ranking of rigid-docking models of protein–protein complexes. A web server for the FiberDock method is available at: http://bioinfo3d.cs.tau.ac.il/FiberDock. PMID:20077569

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

2015-01-01

198

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

199

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

200

Structural conservation, variability, and immunogenicity of the T6 backbone pilin of serotype M6 Streptococcus pyogenes.  

PubMed

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

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

2014-07-01

201

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

202

Analysis on the sequence of formation of Ti{sub 3}SiC{sub 2} and Ti{sub 3}SiC{sub 2}/SiC composites  

SciTech Connect

Ti{sub 3}SiC{sub 2}, a compound in the ternary Ti-Si-C system, is reported to be ductile. This paper reports the sequence of formation of Ti{sub 3}SiC{sub 2} and Ti{sub 3}SiC{sub 2}/SiC composites involving either combustion synthesis or by displacement reaction, respectively. Onset of exothermic reaction temperatures were determined using Differential Thermal Analysis (DTA). Phases present after the exothermic temperatures were analyzed by X-Ray diffraction. Based on these observations, a route to formation of Ti{sub 3}SiC{sub 2} and Ti{sub 3}SiC{sub 2}/SiC composites is proposed for the two`s thesis methods.

Radhakrishnan, R.; Bhaduri, S.B. [Idaho Univ., Moscow, ID (United States). Dept. of Mining and Metallurgy; Henager, C.H. Jr. [Pacific Northwest Lab., Richland, WA (United States)

1995-05-01

203

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

204

Genetic characterization by composite sequence analysis of a new pathogenic field strain of equine infectious anemia virus from the 2006 outbreak in Ireland.  

PubMed

Equine infectious anemia virus (EIAV), the causative agent of equine infectious anaemia (EIA), possesses the least-complex genomic organization of any known extant lentivirus. Despite this relative genetic simplicity, all of the complete genomic sequences published to date are derived from just two viruses, namely the North American EIAV(WYOMING) (EIAV(WY)) and Chinese EIAV(LIAONING) (EIAV(LIA)) strains. In 2006, an outbreak of EIA occurred in Ireland, apparently as a result of the importation of contaminated horse plasma from Italy and subsequent iatrogenic transmission to foals. This EIA outbreak was characterized by cases of severe, sometimes fatal, disease. To begin to understand the molecular mechanisms underlying this pathogenic phenotype, complete proviral genomic sequences in the form of 12 overlapping PCR-generated fragments were obtained from four of the EIAV-infected animals, including two of the index cases. Sequence analysis of multiple molecular clones produced from each fragment demonstrated the extent of diversity within individual viral genes and permitted construction of consensus whole-genome sequences for each of the four viral isolates. In addition, complete env gene sequences were obtained from 11 animals with differing clinical profiles, despite exposure to a common EIAV source. Although the overall genomic organization of the Irish EIAV isolates was typical of that seen in all other strains, the European viruses possessed ?80?% nucleotide sequence identity with either EIAV(WY) or EIAV(LIA). Furthermore, phylogenetic analysis suggested that the Irish EIAV isolates developed independently of the North American and Chinese viruses and that they constitute a separate monophyletic group. PMID:23175240

Quinlivan, Michelle; Cook, Frank; Kenna, Rachel; Callinan, John J; Cullinane, Ann

2013-03-01

205

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

206

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

207

Simulation study of chiral two dimensional ultraviolet (2DUV) spectroscopy of the protein backbone  

PubMed Central

Amide n –?* and ?-?* excitations around 200 nm are prominent spectroscopic signatures of the protein backbone, which are routinely used in ultraviolet (UV) circular dichroism for structure characterization. Recently developed ultrafast laser sources may be used to extend these studies to two dimensions (2D). We apply a new algorithm for modelling protein electronic transitions to simulate two-dimensional ultraviolet (2DUV) photon echo signals in this regime and to identify signatures of protein backbone secondary (and tertiary) structure. Simulated signals for a set of globular and fibrillar proteins and their specific regions reveal characteristic patterns of helical and sheet secondary structures. We investigate how these patterns vary and converge with the size of the structural motif. Specific chiral polarization configurations of the UV pulses are found to be sensitive to aspects of the protein structure. This information significantly augments that available from linear circular dichroism. PMID:20481498

Abramavicius, Darius; Jiang, Jun; Bulheller, Benjamin M.; Hirst, Jonathan D.; Mukamel, Shaul

2010-01-01

208

SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace  

PubMed Central

SABBAC is an on-line service devoted to protein backbone reconstruction from alpha-carbon trace. It is based on the assembly of fragments taken from a library of reduced size, selected from the encoding of the protein trace in a hidden Markov model-derived structural alphabet. The assembly of the fragments is achieved by a greedy algorithm, using an energy-based scoring. Alpha-carbon coordinates remain unaffected. SABBAC simply positions the missing backbone atoms, no further refinement is performed. From our tests, SABBAC performs equal or better than other similar on-line approach and is robust to deviations on the alpha-carbon coordinates. It can be accessed at . PMID:16844979

Maupetit, Julien; Gautier, R.; Tufféry, Pierre

2006-01-01

209

Hybrid molecular brushes with chitosan backbone: facile synthesis and surface grafting.  

PubMed

We developed a facile route toward amphiphilic hybrid molecular brushes (HMB) with chitosan backbone and concurrently grafted chains of poly(acrylamide) and polystyrene. The grafting occurs through amino groups of chitosan; no extra modification of chitosan is required. The kinetic and molecular weight characteristics of the primary molecular brush CHI-graft-PAAm are studied. The second step is grafting of PS by emulsion polymerization. The resulting HMB CHI-graft-PAAm-graft-PS form very stable emulsions. We attached the HMB on solid substrates using chitosan backbone by the "grafting to" approach. Thin films of the immobilized HMB of 3-11 nm thickness completely cover the surface. Being amphiphilic by nature, the immobilized HMB reveal the ability to adapt to the medium, which results in shifting of the hydrophobic/hydrophilic balance over a wide range. PMID:25438297

Hall-Edgefield, Desirae L; Shi, Tony; Nguyen, Kimmy; Sidorenko, Alexander

2014-12-24

210

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

211

Phosphate backbone neutralization increases duplex DNA flexibility: A model for protein binding  

PubMed Central

An important component of protein–DNA recognition is the charge neutralization of DNA backbone phosphates and subsequent protein-induced DNA bending. Replacement of phosphates by neutral methylphosphonates has previously been shown to be a model for protein-induced bending. In addition to bending, the neutralization process may change the inherent flexibility of the DNA—a feature never before tested. We have developed a method to measure the differential flexibility of duplex DNA when methylphosphonate substitutions are made and find that the local flexibility is increased up to 40%. These results imply that backbone-neutralization-dependent DNA flexibility augments DNA-binding motifs in protein–DNA recognition processes. PMID:11929991

Okonogi, Tamara M.; Alley, Stephen C.; Harwood, Eric A.; Hopkins, Paul B.; Robinson, Bruce H.

2002-01-01

212

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

Microsoft Academic Search

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

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

1994-01-01

213

Approach to detection of protein structural motifs using an encoding scheme of backbone conformations  

SciTech Connect

This paper presents an approach to detection of protein structural motifs. In our approach, first all protein backbone conformations are converted into character strings using an encoding scheme. Then we use the Smith-Waterman local alignment algorithm to detect common structural motifs. By comparing results with the PROSITE regular expression patterns, our method can detect several motifs which the PROSITE patterns fail to detect. 18 refs., 9 figs.

Matsuda, H.; Taniguchi, F.; Hashimoto, A. [Osaka Univ. (Japan)

1996-12-31

214

Cytokinin vectors mediate marker-free and backbone-free plant transformation  

Microsoft Academic Search

Conventional Agrobacterium-mediated transformation methods rely on complex and genotype-specific tissue culture media for\\u000a selection, proliferation, and regeneration of genetically modified cells. Resulting transgenic plants may not only contain\\u000a selectable marker genes but also carry fragments of the vector backbone. Here, we describe a new method for the production\\u000a of transgenic plants that lack such foreign DNA. This method employs vectors

Craig M. Richael; Marina Kalyaeva; Robert C. Chretien; Hua Yan; Sathya Adimulam; Artesia Stivison; Caius M. Rommens

2008-01-01

215

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

216

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.

Jensen, George A. (Richland, WA); Nelson, David A. (Richland, WA); Molton, Peter M. (Richland, WA)

1992-01-01

217

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

218

Proposed BackBone API Preliminary Draft v1.0  

E-print Network

Smart Trek Proposed BackBone API Preliminary Draft v1.0 Table of Contents 1.0) API diagram / Introduction 2.0) Requirements 3.0) Class skeletons 4.0) Isp Examples 4.1) Domain Inbound API example 4.2) SDD Inbound API example 4.3) SDD Outbound API example 4.4) ItsFrame Inbound API example 4.5) ItsFrame Outbound

219

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

220

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

221

Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain  

PubMed Central

Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: 13C? longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, 13C?/13C??13C? CSA/dipolar and 13C?/13C??15N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular motions in the 2–16°C temperature range. There is a gradual deviation from this assumption from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization of the potential and other thermodynamics characteristics of protein backbone. PMID:21416162

Vugmeyster, Liliya; Ostrovsky, Dmitry

2012-01-01

222

Sequence Recognition in the Pairing of DNA Duplexes  

NASA Astrophysics Data System (ADS)

Pairing of DNA fragments with homologous sequences occurs in gene shuffling, DNA repair, and other vital processes. While chemical individuality of base pairs is hidden inside the double helix, x ray and NMR revealed sequence-dependent modulation of the structure of DNA backbone. Here we show that the resulting modulation of the DNA surface charge pattern enables duplexes longer than ~50 base pairs to recognize sequence homology electrostatically at a distance of up to several water layers. This may explain the local recognition observed in pairing of homologous chromosomes and the observed length dependence of homologous recombination.

Kornyshev, A. A.; Leikin, S.

2001-04-01

223

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions.  

PubMed

High-throughput molecular technologies can profile microbial communities at high resolution even in complex environments like the intestinal microbiota. Recent improvements in next-generation sequencing technologies allow for even finer resolution. We compared phylogenetic profiling of both longer (454 Titanium) sequence reads with shorter, but more numerous, paired-end reads (Illumina). For both approaches, we targeted six tandem combinations of 16S rRNA gene variable regions, in microbial DNA extracted from a human faecal sample, in order to investigate their limitations and potentials. In silico evaluations predicted that the V3/V4 and V4/V5 regions would provide the highest classification accuracies for both technologies. However, experimental sequencing of the V3/V4 region revealed significant amplification bias compared to the other regions, emphasising the necessity for experimental validation of primer pairs. The latest developments of 454 and Illumina technologies offered higher resolution compared to their previous versions, and showed relative consistency with each other. However, the majority of the Illumina reads could not be classified down to genus level due to their shorter length and higher error rates beyond 60 nt. Nonetheless, with improved quality and longer reads, the far greater coverage of Illumina promises unparalleled insights into highly diverse and complex environments such as the human gut. PMID:20880993

Claesson, Marcus J; Wang, Qiong; O'Sullivan, Orla; Greene-Diniz, Rachel; Cole, James R; Ross, R Paul; O'Toole, Paul W

2010-12-01

224

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

225

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."

2011-11-23

226

Sequencing Puzzle  

NSDL National Science Digital Library

The sequencing puzzle is designed to teach high school students, and perhaps even middle school, and the general public about the basics of genome sequencing. The sequencing of the tomato genome is used as the basis for this activity. It is an interactive puzzle. In addition to the puzzle, the site also contains background information on tomatoes, DNA, and various molecular terms.

227

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

228

“Splicing up” drug discovery. Cell-Based Expression and Screening of Genetically-Encoded Libraries of Backbone Cyclized Polypeptides  

PubMed Central

The present paper reviews the use of protein splicing for the biosynthesis of backbone cyclic polypeptides. This general method allows the in vivo and in vitro biosynthesis of cyclic polypeptides using recombinant DNA expression techniques. Biosynthetic access to backbone cyclic peptides opens the possibility to generate cell-based combinatorial libraries that can be screened inside living cells for their ability to attenuate or inhibit cellular processes thus providing a new way for finding therapeutic agents. PMID:19628015

Sancheti, Harshkumar; Camarero, Julio A.

2012-01-01

229

Low-Dielectric-Constant Polyimide/Glass Composites  

NASA Technical Reports Server (NTRS)

Advance in polymer technology yields composites having relatively low dielectric constants. Reduction achieved by reducing interactions between linear polyimide chains and by incorporation of fluorine into polymer backbones. Further reductions obtained by physically incorporating selected diamic acid additives into polyimides. Strong potential for use in microelectronics industry for fabrication of printed-circuit boards and fabrication of components for military aircraft.

Stoakley, Diane M.; St. Clair, Anne K.; Baucom, Robert M.; Proctor, K. Mason; Smith, Ricky E.; Smith, Janice Y.

1994-01-01

230

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics.  

PubMed

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the ?-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit. PMID:23656161

Krokhotin, Andrey; Niemi, Antti J; Peng, Xubiao

2013-05-01

231

Solution NMR analysis of the interaction between the actinoporin sticholysin I and DHPC micelles--correlation with backbone dynamics.  

PubMed

Sticholysin I (StI), an actinoporin expressed as a water-soluble protein by the sea anemone Stichodactyla helianthus, binds to natural and model membranes, forming oligomeric pores. It is proposed that the first event of a multistep pore formation mechanism consists of the monomeric protein attachment to the lipid bilayer. To date there is no high-resolution structure of the actinoporin pore or other membrane-bound form available. Here we evaluated StI:micelle complexes of variable lipid composition to look for a suitable model for NMR studies. Micelles of pure or mixed lysophospholipids and of dihexanoyl phosphatidylcholine (DHPC) were examined. The StI:DHPC micelle was found to be the best system, yielding a stable sample and good quality spectra. A comprehensive chemical shift perturbation analysis was performed to map the StI membrane recognition site in the presence of DHPC micelles. The region mapped (residues F(51), R(52), S(53) in loop 3; F(107), D(108), Y(109), W(111), Y(112), W(115) in loop 7; Q(129), Y(132), D(134), M(135), Y(136), Y(137), G(138) in helix-?2) is in agreement with previously reported data, but additional residues were found to interact, especially residues V(81), A(82), T(83), G(84) in loop 5, and A(85), A(87) in strand-?5. Backbone dynamics measurements of StI free in solution and bound to micelles highlighted the relevance of protein flexibility for membrane binding and suggested that a conformer selection process may take place during protein-membrane interaction. We conclude that the StI:DHPC micelles system is a suitable model for further characterization of an actinoporin membrane-bound form by solution NMR. PMID:24218049

López-Castilla, Aracelys; Pazos, Fabiola; Schreier, Shirley; Pires, José Ricardo

2014-06-01

232

NMR backbone assignments of the tyrosine kinase domain of human fibroblast growth factor receptor 1.  

PubMed

Members of the fibroblast growth factor receptor tyrosine kinase family (FGFR1-4) play an important role in many signalling cascades. Although tightly regulated, aberrant activity of these enzymes may lead to, or become features of, disease pathologies including cancer. FGFR isoforms have been the subject of drug discovery programmes, with a number of kinase-domain inhibitors in pre-clinical and clinical development. Here, we present the first (83% complete) backbone resonance assignments of apo-FGFR1 kinase. PMID:23325512

Vajpai, Navratna; Schott, Anne-Kathrin; Vogtherr, Martin; Breeze, Alexander L

2014-04-01

233

TOAC Spin Labels in the Backbone of Alamethicin: EPR Studies in Lipid Membranes  

Microsoft Academic Search

Alamethicin is a 19-amino-acid residue hydrophobic peptide that produces voltage-dependent ion channels in membranes. Analogues of the Glu(OMe)7,18,19 variant of alamethicin F50\\/5 that are rigidly spin-labeled in the peptide backbone have been synthesized by replacing residue 1, 8, or 16 with 2,2,6,6-tetramethyl-piperidine-1-oxyl-4-amino-4-carboxyl (TOAC), a helicogenic nitroxyl amino acid. Conventional electron paramagnetic resonance spectra are used to determine the insertion and

Derek Marsh; Micha Jost; Cristina Peggion; Claudio Tonioloy

2007-01-01

234

An algorithm for converting a virtual-bond chain into a complete polypeptide backbone chain  

NASA Technical Reports Server (NTRS)

A systematic analysis is presented of the algorithm for converting a virtual-bond chain, defined by the coordinates of the alpha-carbons of a given protein, into a complete polypeptide backbone. An alternative algorithm, based upon the same set of geometric parameters used in the Purisima-Scheraga algorithm but with a different "linkage map" of the algorithmic procedures, is proposed. The global virtual-bond chain geometric constraints are more easily separable from the loal peptide geometric and energetic constraints derived from, for example, the Ramachandran criterion, within the framework of this approach.

Luo, N.; Shibata, M.; Rein, R.

1991-01-01

235

Aftershock Sequences  

NSDL National Science Digital Library

In this activity, learners will look at some of the characteristic properties of aftershock sequences, and relate them to variables in two equations: the modified version of Omori's Law, and the Gutenberg-Richter relation for aftershock sequences. The database provided in this link can be searched to extract the magnitude and time-after-mainshock for selected earthquakes. From this information, users can discover the real-world meanings of various properties of aftershock sequences.

236

Hydrogels Containing Peptide or Aminosugar Sequences Implanted into the Rat Brain: Influence on Cellular Migration and Axonal Growth  

Microsoft Academic Search

Biocompatible polymer matrices for implantation into lesion sites in the brain were synthesized by incorporating peptide or aminosugar sequences intoN-(2-hydroxypropyl)methacrylamide (HPMA) hydrogels. RGD peptide sequences were chemically linked to the hydrogel backbone via a glycylglycine spacer; aminosugars were glucosamine (NHGlc) orN-acetylglucosamine residues. Unmodified or sequence containing HPMA hydrogels were implanted into the lesioned optic tract or cerebral cortex of juvenile

Giles W. Plant; Stèphane Woerly; Alan R. Harvey

1997-01-01

237

Applications of Recursive Segmentation to the Analysis of DNA Sequences  

Microsoft Academic Search

Recursive segmentation is a procedure that partitions a DNA sequence into domains with a homogeneous composition of the four nucleotides A, C, G and T. This procedure can also be applied to any sequence converted from a DNA sequence, such as to a binary strong(G + C)\\/weak(A+ T) sequence, to a binary sequence indicating the presence or absence of the

Wentian Li; Pedro Bernaola-galván; Fatameh Haghighi; Ivo Grosse

2002-01-01

238

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

239

Original article The effect of feeding sequence  

E-print Network

under the CH treatment. dairy cow / feeding sequence / milk composition Résumé — Effet de lOriginal article The effect of feeding sequence on fat concentration in milk* C Chassaing JB Coulon% of the total dry matter in the diet. The feeding sequence had no effect on the resultant milk yield (20

Paris-Sud XI, Université de

240

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

241

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.

Institute, Wellcome T.

2012-06-26

242

Potter's Sequence  

PubMed Central

Potter's sequence is a rare fatal disorder that occurs in sporadic and autosomal recessive forms with an incidence of 1 in 4000 births. Babies born with this condition are either still born or die very early within the neonatal period. We report a case of Potter's sequence with the typical physical findings and histological findings. PMID:24027716

Shastry, Srikanth M.; Kolte, Sachin S.; Sanagapati, Panduranga R.

2012-01-01

243

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

PubMed

RNA interference (RNAi) has great potential to treat human disease. However, in vivo delivery of short interfering RNAs (siRNAs), which are negatively charged double-stranded RNA macromolecules, remains a major hurdle. Current siRNA delivery has begun to move away from large lipid and synthetic nanoparticles to more defined molecular conjugates. 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; Berg, Arjen van den; 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

2014-12-01

244

Chemical structure of the carbohydrate backbone of the lipopolysaccharide from Piscirickettsia salmonis.  

PubMed

Elucidation of the carbohydrate backbone structure of the lipopolysaccharide (LPS) from Piscirickettsia salmonis, the etiological agent of the salmonid rickettsial septicemia, is described. Structural information was established by a combination of monosaccharide and methylation analyses of LPS, and by NMR and mass spectrometries of oligosaccharides obtained through the use of various chemical degradations of the native polymer. The following structure of the backbone sugars was determined on the basis of the combined data from these experiments: [formula see text] The presence of two consecutive residues of diacetylated pseudaminic acid (Pse5,7Ac, 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid) in the LPS appears to be unique among polysaccharides containing this acidic sugar. Similarly, the presence of 4-aminoarabinose (Ara4N, 4-amino-4-deoxy-l-arabinopyranose) on O-4 of the ?-GlcN1P of the lipid A moiety is a unique feature of this LPS. PMID:23673236

Vinogradov, Evgeny; Frimmelova, Martina; Toman, Rudolf

2013-08-30

245

Solution structure and backbone dynamics of human liver fatty acid binding protein: fatty acid binding revisited.  

PubMed

Liver fatty acid binding protein (L-FABP), a cytosolic protein most abundant in liver, is associated with intracellular transport of fatty acids, nuclear signaling, and regulation of intracellular lipolysis. Among the members of the intracellular lipid binding protein family, L-FABP is of particular interest as it can i), bind two fatty acid molecules simultaneously and ii), accommodate a variety of bulkier physiological ligands such as bilirubin and fatty acyl CoA. To better understand the promiscuous binding and transport properties of L-FABP, we investigated structure and dynamics of human L-FABP with and without bound ligands by means of heteronuclear NMR. The overall conformation of human L-FABP shows the typical ?-clam motif. Binding of two oleic acid (OA) molecules does not alter the protein conformation substantially, but perturbs the chemical shift of certain backbone and side-chain protons that are involved in OA binding according to the structure of the human L-FABP/OA complex. Comparison of the human apo and holo L-FABP structures revealed no evidence for an "open-cap" conformation or a "swivel-back" mechanism of the K90 side chain upon ligand binding, as proposed for rat L-FABP. Instead, we postulate that the lipid binding process in L-FABP is associated with backbone dynamics. PMID:22713574

Cai, Jun; Lücke, Christian; Chen, Zhongjing; Qiao, Ye; Klimtchuk, Elena; Hamilton, James A

2012-06-01

246

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

247

BEST-HNN and 2D-(HN) NH experiments for rapid backbone assignment in proteins  

NASA Astrophysics Data System (ADS)

HNN has proven to be an extremely valuable experiment for rapid and unambiguous backbone (H N, 15N) assignment in ( 13C, 15N) labeled proteins. However, low sensitivity of the experiment is often a limiting factor, especially when the transverse relaxation times ( T2) are short. We show here that BEST modification Schanda et al. (2006) [2] increases the sensitivity per unit time by more than a factor of 2.0 and thus substantially increases the speed of data collection; good 3D data can be collected in 8-10 h. Next, we present a simple method for amino-acid type identification based on simple 2D versions of the HNN experiment, labeled here as 2D-(HN) NH. Each of these experiments which produce anchor points for Gly, Ala, Ser/Thr residues, can be recorded in less than an hour. These enable rapid data acquisition, rapid analysis, and consequently rapid assignment of backbone (H N, 15N) resonances. The 2D-(HN) NH experiment does not involve aliphatic/aromatic protons and hence can be applied to deuterated protein samples as well, which is an additional advantage. The experiments have been demonstrated with human ubiquitin (76 aa) and acetic-acid denatured HIV-1 protease (99 aa), as representatives of folded and unfolded protein systems, respectively.

Kumar, Dinesh; Paul, Subhradip; Hosur, Ramakrishna V.

2010-05-01

248

The influence of helix morphology on co-operative polyamide backbone conformational flexibility in peptide nucleic acid complexes.  

PubMed

A systematic analysis of peptide nucleic acid (PNA) complexes deposited in the Protein Data Bank has been carried out using a set of contiguous atom torsion angle definitions. The analysis is complemented by molecular mechanics adiabatic potential energy calculations on hybrid PNA-nucleic acid model systems. Hitherto unobserved correlations in the values of the (alpha and epsilon) dihedral angles flanking the backbone secondary amide bond are found. This dihedral coupling forms the basis of a PNA backbone conformation classification scheme. Six conformations are thus characterised in experimental structures. Helix morphology is found to exert a significant influence on backbone conformation and flexibility: Watson-Crick PNA strands in complexes with DNA and RNA, that possess A-like base-pair stacking, adopt backbone conformations distinct from those in PNA.DNA-PNA triplex and PNA-PNA duplex P-helix forms. Solvation effects on Watson-Crick PNA backbone conformation in heterotriplexes are discussed and the possible involvement of inter-conformational transitions and dihedral angle uncoupling in asymmetric heteroduplex base-pair breathing is suggested. PMID:10512700

Topham, C M; Smith, J C

1999-10-01

249

Performance and microbial community composition dynamics of aerobic granular sludge from sequencing batch bubble column reactors operated at 20 degrees C, 30 degrees C, and 35 degrees C.  

PubMed

Two bubble column sequencing batch reactors fed with an artificial wastewater were operated at 20 degrees C, 30 degrees C, and 35 degrees C. In a first stage, stable granules were obtained at 20 degrees C, whereas fluffy structures were observed at 30 degrees C. Molecular analysis revealed high abundance of the operational taxonomic unit 208 (OTU 208) affiliating with filamentous bacteria Leptothrix spp. at 30 degrees C, an OTU much less abundant at 20 degrees C. The granular sludge obtained at 20 degrees C was used for the second stage during which one reactor was maintained at 20 degrees C and the second operated at 30 degrees C and 35 degrees C after prior gradual increase of temperature. Aerobic granular sludge with similar physical properties developed in both reactors but it had different nutrient elimination performances and microbial communities. At 20 degrees C, acetate was consumed during anaerobic feeding, and biological phosphorous removal was observed when Rhodocyclaceae-affiliating OTU 214 was present. At 30 degrees C and 35 degrees C, acetate was mainly consumed during aeration and phosphorous removal was insignificant. OTU 214 was almost absent but the Gammaproteobacteria-affiliating OTU 239 was more abundant than at 20 degrees C. Aerobic granular sludge at all temperatures contained abundantly the OTUs 224 and 289 affiliating with Sphingomonadaceae indicating that this bacterial family played an important role in maintaining stable granular structures. PMID:20461512

Ebrahimi, Sirous; Gabus, Sébastien; Rohrbach-Brandt, Emmanuelle; Hosseini, Maryam; Rossi, Pierre; Maillard, Julien; Holliger, Christof

2010-07-01

250

Significant role of the DNA backbone in mediating the transition origin of electronic excitations of B-DNA - implication from long range corrected TDDFT and quantified NTO analysis  

NASA Astrophysics Data System (ADS)

We systematically investigate the possible complex transition origin of electronic excitations of giant molecular systems by using the recently proposed QNTO analysis [J.-H. Li, J.-D. Chai, G. Y. Guo and M. Hayashi, Chem. Phys. Lett., 2011, 514, 362.] combined with long-range corrected TDDFT calculations. Thymine (Thy) related excitations of biomolecule B-DNA are then studied as examples, where the model systems have been constructed extracting from the perfect or a X-ray crystal (PDB code 3BSE) B-DNA structure with at least one Thy included. In the first part, we consider the systems composed of a core molecular segment (e.g. Thy, di-Thy) and a surrounding physical/chemical environment of interest (e.g. backbone, adjacent stacking nucleobases) and examine how the excitation properties of the core vary in response to the environment. We find that the orbitals contributed from DNA backbone and surrounding nucleobases often participate in a transition of Thy-related excitations affecting their composition, absorption energy, and oscillator strength. In the second part, we take into account geometrically induced variation of the excitation properties of various B-DNA segments, e.g. di-Thy, dTpdT etc., obtained from different sources (ideal and 3BSE). It is found that the transition origin of several Thy-related excitations of these segments is sensitive to slight conformational variations, suggesting that DNA with thermal motions in cells may from time to time exhibit very different photo-induced physical and/or chemical processes.

Li, Jian-Hao; Chai, Jeng-Da; Guo, Guang-Yu; Hayashi, Michitoshi

251

Biocatalytic fabrication of fast-degradable, water-soluble polycarbonate functionalized with tertiary amine groups in backbone.  

PubMed

Degradable polymers with specifically designed functionality have wide applications in biomedical fields. We reported herein the synthesis and characterization of a water-soluble and fast-degradable polycarbonate, functionalized with tertiary amine groups in the backbone. A novel cyclic carbonate monomer, namely, 6,14-dimethyl-1,3,9,11-tetraoxa-6,14-diaza-cyclohexadecane-2,10-dione (ADMC)(2), was synthesized and polymerized to provide the title polycarbonate [poly(ADMC)] via Novozym-435 lipase or tin(II) 2-ethylheaxanoate [Sn(Oct)(2)] catalyzed ring-opening polymerization (ROP). Novozym-435 lipase exhibited high activity toward the ROP in terms of molecular weight (M(n)) and monomer conversion, whereas the attempt with Sn(Oct)(2) failed. In the presence of molecular sieves-4 Å, the highest M(n) value of 1.2 × 10(4) g/mol was obtained in toluene with an initial monomer concentration of 0.58 M at 75 °C in the presence of 10 wt % of Novozym-435 to the monomer. Parameters that influence the polymerization, including reaction temperature, enzyme concentration, monomer concentration, and solvent composition, were investigated systematically. The resultant data suggested "living" characteristics for this enzyme-catalyzed polymerization, and the "living" feature seemed independent of the lipase concentration. The polymerization conducted in mixed solvents (toluene/isooctane) showed that product M(n)s were heavily dependent on the solvent composition. Poly(ADMC) was demonstrated to be amorphous by DSC technique. The obtained poly(ADMC) was found to be soluble in most of the organic solvents and interestingly in H(2)O as well. In vitro hydrolytic degradation of poly(ADMC) as monitored by GPC indicated the degradation was a relatively fast process. HPLC-ESI/MS and (1)H NMR analyses demonstrated that N-methyl diethanolamine was the main product after degradation. Poly(ADMC) presented low cytotoxicity toward human cervix carcinoma (HeLa) cells and hepatoblastoma cells (Hep G2), as demonstrated by MTT assay. PMID:20836520

Wang, Hua-Fen; Su, Wei; Zhang, Chao; Luo, Xiao-hua; Feng, Jun

2010-10-11

252

Sequential HNCACB and CBCANH Protein NMR Pulse Sequences  

NASA Astrophysics Data System (ADS)

The pulse sequences HNCACB and CBCANH correlating side chain C ? resonances with amide resonances in the protein backbone do not distinguish between inter- and intraresidue correlations. The new pulse sequences sequential HNCACB and sequential CBCANH make this distinction by suppressing coherence transfer between 13C ? and 15N via the one-bond J(NC ?) coupling so that only the sequential correlations are observed in the spectrum. The experimental results of applying sequential HNCACB in a clean-TROSY-adapted implementation to the protein Chymotrypsin Inhibitor 2 at 800 MHz are presented.

Meissner, Axel; Sørensen, Ole Winneche

2001-08-01

253

Backbone 1H, 13C, and 15N NMR assignments for the Cyanothece 51142 protein cce_0567: a protein associated with nitrogen fixation in the DUF683 family  

SciTech Connect

The recently sequenced genome of the diurnal cyanobacterium Cyanothece sp. PCC 51142 (contig 83.1_1_243_746) contains the sequence for an hypothetical protein that falls into the DUF683 family. As observed for the other 54 DUF683 proteins currently listed in the GenBank database, this 78-residue (9.0 kDa) protein in Cyanothece is also found in a nitrogen fixation gene cluster suggesting that it is involved in the process. To date no structural information exists for any of the proteins in the DUF683 family. In an effort to elucidate the biochemical role DUF683 may play in nitrogen fixation and to obtain structural information for a member of the DUF683 protein family, a construct containing DUF683 from Cyanothece 51142 was generated, expressed, purified, and the solution properties characterized. A total rotational correlation time (tc) of 17.1 ns was estimated by nuclear magnetic resonance (NMR) spectroscopy suggesting a molecular weight of ~ 40 kDa, an observation dictating that DUF683 is a tetramer in solution. Using triple-labeled (2H, 13C, 15N) and residue-specific 15N-labeled amino acids (L, K, V, and E/Q) samples, most of the backbone and side chain resonances for DUF683 were assigned. The 13C alpha chemical shifts and NOESY NMR data indicate that the protein is helical from K18-E75.

Buchko, Garry W.; Sofia, Heidi J.

2008-06-01

254

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 Central

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

255

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

256

Solution structure and backbone dynamics of human epidermal-type fatty acid-binding protein (E-FABP).  

PubMed Central

Human epidermal-type fatty acid-binding protein (E-FABP) belongs to a family of intracellular 14-15 kDa lipid-binding proteins, whose functions have been associated with fatty acid signalling, cell growth, regulation and differentiation. As a contribution to understanding the structure-function relationship, we report in the present study features of its solution structure and backbone dynamics determined by NMR spectroscopy. Applying multi-dimensional high-resolution NMR techniques on unlabelled and 15N-enriched recombinant human E-FABP, the 1H and 15N resonance assignments were completed. On the basis of 2008 distance restraints, the three-dimensional solution structure of human E-FABP was subsequently obtained (backbone atom root-mean-square deviation of 0.92+/-0.11 A; where 1 A=0.1 nm), consisting mainly of 10 anti-parallel beta-strands that form a beta-barrel structure. 15N relaxation experiments (T1, T2 and heteronuclear nuclear Overhauser effects) at 500, 600 and 800 MHz provided information on the internal dynamics of the protein backbone. Nearly all non-terminal backbone amide groups showed order parameters S(2)>0.8, with an average value of 0.88+/-0.04, suggesting a uniformly low backbone mobility in the nanosecond-to-picosecond time range. Moreover, hydrogen/deuterium exchange experiments indicated a direct correlation between the stability of the hydrogen-bonding network in the beta-sheet structure and the conformational exchange in the millisecond-to-microsecond time range. The features of E-FABP backbone dynamics elaborated in the present study differ markedly from those of the phylogenetically closely related heart-type FABP and the more distantly related ileal lipid-binding protein, implying a strong interdependence with the overall protein stability and possibly also with the ligand-binding affinity for members of the lipid-binding protein family. PMID:12049637

Gutiérrez-González, Luis H; Ludwig, Christian; Hohoff, Carsten; Rademacher, Martin; Hanhoff, Thorsten; Rüterjans, Heinz; Spener, Friedrich; Lücke, Christian

2002-01-01

257

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

258

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

259

Chemical and isotopic composition of modern water bodies in the Lake Kopais Basin, central Greece: analogues for the interpretation of the lacustrine sedimentary sequence  

NASA Astrophysics Data System (ADS)

Stable-isotope measurements and modern aquatic chemistry are used to aid the reconstruction of past hydrological changes recorded in a 126 ka-long sediment core from Lake Kopais, Greece. This is the most southeasterly European site with a long Late Quaternary sequence. Although the lake has been artificially drained, calcareous sediments from the centre of the basin, 38°26'16?N, 23°03'01?E, provide a continuous record from the early part of the last interglacial to the Early Holocene. Because the physiography and hydrology are complex, modern analogues for past environmental conditions are essential. The modern waters are of Ca-Mg-HCO 3 or Mg-Ca-HCO 3 type, reflecting the prevalence of limestones and metamorphic rocks in the catchment. They show a clear evolutionary trend in ? 18O and ?D values from the source areas to the modern lakes. However, the modern water bodies are less evolved than the palaeolake. A larger evaporating surface, higher values of ? 18O in precipitation, decreased precipitation/evaporation ratios and hydrological closure increased the ? 18O values of endogenic carbonates at different times in the past. However, Palaeolake Kopais never desiccated completely or became saline. Analyses of the organic fraction from the core show that: (i) it is mainly of algal origin; (ii) productivity and carbon cycling in the lake waters were relatively stable through time; and (iii) the bulk ? 13C values vary between -29‰ and -25‰, indicating that the lake waters were never appreciably carbon-limited and that C 4 plants did not invade the catchment. Although significant shifts in the ? 18O and ? 13C values of endogenic low-Mg calcite are attributable mainly to past variations in water balance, weak ? 18O-? 13C covariance during marine isotope stages (MIS) 5e-5c suggests that the palaeolake leaked significantly through karstic sinkholes. Since it was effectively operating as an open system, ? 18O may have retained the isotopic imprint of increased summer precipitation. Between MIS 5a and MIS 4, strong isotopic covariance suggests minimal outflow and drier conditions than today. After an increase in winter snowmelt during MIS 3, the climate again became cold and dry in the full-glacial (MIS 2). A fluctuating increase in moisture occurred during the late-glacial to early Holocene transition (MIS 2-1).

Griffiths, Susan J.; Street-Perrott, F. Alayne; Holmes, Jonathan A.; Leng, Melanie J.; Tzedakis, Chronis

2002-04-01

260

Proteoglycan sequence  

PubMed Central

Proteoglycans (PGs) are among the most structurally complex biomacromolecules in nature. They are present in all animal cells and frequently exert their critical biological functions through interactions with protein ligands and receptors. PGs are comprised of a core protein to which one or multiple, heterogeneous, and polydisperse glycosaminoglycan (GAG) chains are attached. Proteins, including the protein core of PGs, are now routinely sequenced either directly using proteomics or indirectly using molecular biology through their encoding DNA. The sequencing of the GAG component of PGs poses a considerably more difficult challenge because of the relatively underdeveloped state of glycomics and because the control of their biosynthesis in the endoplasmic reticulum and the Golgi is poorly understood and not believed to be template driven. Recently, the GAG chain of the simplest PG has been suggested to have a defined sequence based on its top-down Fourier transform mass spectral sequencing. This review examines the advances made over the past decade in the sequencing of GAG chains and the challenges the field face in sequencing complex PGs having critical biological functions in developmental biology and pathogenesis. PMID:22513887

Li, Lingyun; Ly, Mellisa

2012-01-01

261

Extensive Air Showers: from the muonic smoking guns to the hadronic backbone  

E-print Network

Extensive Air Showers are complex macroscopic objects initiated by single ultra-high energy particles. They are the result of millions of high energy reactions in the atmosphere and can be described as the superposition of hadronic and electromagnetic cascades. The hadronic cascade is the air shower backbone, and it is mainly made of pions. Decays of neutral pions initiate electromagnetic cascades, while the decays of charged pions produce muons which leave the hadronic core and travel many kilometers almost unaffected. Muons are smoking guns of the hadronic cascade: the energy, transverse momentum, spatial distribution and depth of production are key to reconstruct the history of the air shower. In this work, we overview the phenomenology of muons on the air shower and its relation to the hadronic cascade. We briefly review the experimental efforts to analyze muons within air showers and discuss possible paths to use this information.

L. Cazon

2013-01-15

262

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

263

On the photostability of peptides after selective photoexcitation of the backbone: prompt versus slow dissociation.  

PubMed

Vulnerability of biomolecules to ultraviolet radiation is intimately linked to deexcitation pathways: photostability requires fast internal conversion to the electronic ground state, but also intramolecular vibrational redistribution and cooling on a time scale faster than dissociation. Here we present a protocol to disentangle slow and non-hazardous statistical dissociation from prompt cleavage of peptide bonds by 210 nm light based on experiments on protonated peptides isolated in vacuo and tagged by 18-crown-6 ether (CE). The weakest link in the system is between the charged site and CE, which is remote from the initial site of excitation. Hence loss of CE serves as direct proof that energy has reached the charge-site end, leaving the backbone intact. Our work demonstrates that excitation of tertiary amide moieties (proline linkages) results in both prompt dissociation and statistical dissociation after energy randomisation over all vibrational degrees of freedom. PMID:24945849

Byskov, Camilla Skinnerup; Jensen, Frank; Jørgensen, Thomas J D; Nielsen, Steen Brøndsted

2014-08-14

264

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

2014-12-10

265

Extensive Air Showers: from the muonic smoking guns to the hadronic backbone  

NASA Astrophysics Data System (ADS)

Extensive Air Showers are complex macroscopic objects initiated by single ultra-high energy particles. They are the result of millions of high energy reactions in the atmosphere and can be described as the superposition of hadronic and electromagnetic cascades. The hadronic cascade is the air shower backbone, and it is mainly made of pions. Decays of neutral pions initiate electromagnetic cascades, while the decays of charged pions produce muons which leave the hadronic core and travel many kilometers almost unaffected. Muons are smoking guns of the hadronic cascade: the energy, transverse momentum, spatial distribution and depth of production are key to reconstruct the history of the air shower. In this work, we overview the phenomenology of muons on the air shower and its relation to the hadronic cascade. We briefly review the experimental efforts to analyze muons within air showers and discuss possible paths to use this information.

Cazon, L.

2013-06-01

266

Correlation between protein secondary structure, backbone bond angles, and side-chain orientations  

NASA Astrophysics Data System (ADS)

We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C? carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the C? carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the C?-C? structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

Lundgren, Martin; Niemi, Antti J.

2012-08-01

267

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

268

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

269

Experimental Study of Nafion-and Flemion-based Ionic Polymer-metal Composites (IPMCs) with Ethylene Glycol as Solvent  

E-print Network

Experimental Study of Nafion- and Flemion-based Ionic Polymer- metal Composites (IPMCs-metal composites (IPMCs) consist of a perfluorinated ionomer membrane (usually Nafion® or Flemion® ) plated on both that balance the electrical charge of anions covalently fixed to the membrane backbone. IPMCs are electroactive

Nemat-Nasser, Sia

270

Controlled actuation of Nafion-based Ionic Polymer-metal Composites (IPMCs) with Ethylene Glycol as Solvent  

E-print Network

Controlled actuation of Nafion-based Ionic Polymer-metal Composites (IPMCs) with Ethylene Glycol for Advanced Materials 9500 Gilman Drive La Jolla, CA 92093-0416 Abstract Ionic polymer-metal composites (IPMCs of counterions that balance the electrical charge of anions covalently fixed to the backbone membrane. IPMCs

Nemat-Nasser, Sia

271

Alternative off-lattice model with continuous backbone mass for polymers Gunther Schoppe and Dieter W. Heermann*  

E-print Network

. Promi- nent examples for this are plastic bags made out of polyeth- ylene or compact discs which mainlyAlternative off-lattice model with continuous backbone mass for polymers Gunther Scho¨t Heidelberg, Heidelberg, Germany Received 29 May 1998 We present an alternative model for polymers

Heermann, Dieter W.

272

Numerical modeling and Hardware-in-the-Loop simulation of undersea networks, ocean observatories and offshore communications backbones  

Microsoft Academic Search

This paper discusses the importance of taking a systems engineering approach when designing undersea networks, ocean observatories and offshore communications backbones. A design that utilizes modular components and systems, and places diligence in modeling and testing communications, power and data bandwidth requirements is essential for sustained operation and economic feasibility. An example is the modular seafloor communications network described -

Andrew M. Clark; Donna M. Kocak; Ken Martindale; Adrian Woodroffe

2009-01-01

273

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

NASA Astrophysics Data System (ADS)

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? 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; Fuchigami, Sotaro

2013-12-01

274

Peptide backbone orientation and dynamics in spider dragline silk and two-photon excitation in nuclear magnetic and quadrupole resonance  

Microsoft Academic Search

In the first part of the dissertation, spider dragline silk is studied by solid state NMR techniques. The dependence of NMR frequency on molecular orientation is exploited using the DECODER experiment to determine the orientation of the protein backbone within the silk fibre. Practical experimental considerations require that the silk fibres be wound about a cylindrical axis perpendicular to the

Philip Thomas Eles

2005-01-01

275

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

276

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

277

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

278

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins  

E-print Network

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales

Shaw, David E.

279

Two-dimensional NMR spectroscopy reveals cation-triggered backbone degradation in polysulfone-based anion exchange membranes  

PubMed Central

Anion exchange membranes (AEMs) find widespread applications as an electrolyte and/or electrode binder in fuel cells, electrodialysis stacks, flow and metal-air batteries, and electrolyzers. AEMs exhibit poor stability in alkaline media; their degradation is induced by the hydroxide ion, a potent nucleophile. We have used 2D NMR techniques to investigate polymer backbone stability (as opposed to cation stability) of the AEM in alkaline media. We report the mechanism behind a peculiar, often-observed phenomenon, wherein a demonstrably stable polysulfone backbone degrades rapidly in alkaline solutions upon derivatization with alkaline stable fixed cation groups. Using COSY and heteronuclear multiple quantum correlation spectroscopy (2D NMR), we unequivocally demonstrate that the added cation group triggers degradation of the polymer backbone in alkaline via quaternary carbon hydrolysis and ether hydrolysis, leading to rapid failure. This finding challenges the existing perception that having a stable cation moiety is sufficient to yield a stable AEM and emphasizes the importance of the often ignored issue of backbone stability. PMID:23335629

Arges, Christopher G.; Ramani, Vijay

2013-01-01

280

Switching the H-bonding network of a foldamer by modulating the backbone chirality and constitutional ratio of amino acids.  

PubMed

This communication describes the folding propensity of a heterofoldamer motif featuring proline (Pro) and anthranilic acid (Ant) residues in a 1:2:1 (?:?:?) constitutional ratio. Structural investigations unequivocally suggest that the hydrogen-bonding network of this foldamer motif can be switched between 9-membered and 6-membered by modulating the backbone chirality and constitutional ratio of the amino acid residues. PMID:24057152

Ramesh, Veera V E; Vijayadas, Kuruppanthara N; Dhokale, Snehal; Gonnade, Rajesh G; Rajamohanan, Pattuparambil R; Sanjayan, Gangadhar J

2013-11-01

281

Exploring the correlation between the sequence composition of the nucleotide binding G5 loop of the FeoB GTPase domain (NFeoB) and intrinsic rate of GDP release  

PubMed Central

GDP release from GTPases is usually extremely slow and is in general assisted by external factors, such as association with guanine exchange factors or membrane-embedded GPCRs (G protein-coupled receptors), which accelerate the release of GDP by several orders of magnitude. Intrinsic factors can also play a significant role; a single amino acid substitution in one of the guanine nucleotide recognition motifs, G5, results in a drastically altered GDP release rate, indicating that the sequence composition of this motif plays an important role in spontaneous GDP release. In the present study, we used the GTPase domain from EcNFeoB (Escherichia coli FeoB) as a model and applied biochemical and structural approaches to evaluate the role of all the individual residues in the G5 loop. Our study confirms that several of the residues in the G5 motif have an important role in the intrinsic affinity and release of GDP. In particular, a T151A mutant (third residue of the G5 loop) leads to a reduced nucleotide affinity and provokes a drastically accelerated dissociation of GDP. PMID:25374115

Guilfoyle, Amy P.; Deshpande, Chandrika N.; Schenk, Gerhard; Maher, Megan J.; Jormakka, Mika

2014-01-01

282

Backbone cleavages of [M - H](-) anions derived from caerin 1 peptides and some synthetic modifications. Molecular recognition initiating internal cyclisation of Glu23.  

PubMed

The collision induced spectra of [M - H](-) anions from of caerin 1 peptides and some synthetic modifications show the usual alpha, beta and beta' backbone cleavages together with Ser (epsilon,gamma) and Glu (gamma) cleavages which break the peptide backbone in the vicinity of those residues. All of these cleavages require the peptide backbone to be flexible. There is also a backbone cleavage of a type not observed before. This cleavage involves nucleophilic attack of the carboxylate anion of the Glu23 side chain at the backbone CH of Ile 21. We propose that this cleavage requires the caerin peptide to be in an alpha helical conformation (the 3D structure that this peptide adopts in solution) in order that the interacting groups are held in close proximity. PMID:12112614

Brinkworth, Craig S; Bowie, John H

2002-01-01

283

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

284

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

285

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

286

The carbohydrate–polypeptide linkages, the amino acid sequences of the peptides adjacent to some of these bonds, and the composition and size of the carbohydrate units of ?1-acid glycoprotein  

PubMed Central

1. The glycopeptides derived from a proteolytic digest of sialic acid-free ?1-acid glycoprotein were separated on a DEAE-cellulose column into five main fractions. 2. The average molecular weight of these glycopeptides was 2400, except for one fraction whose molecular weight was 3100. The average molecular weight of the sialic acid-free carbohydrate units was found to be 2200. From these data and the carbohydrate content of the native protein and the assumed molecular weight of 44000, it was concluded that ?1-acid glycoprotein probably possesses five carbohydrate units. The sialic acid-containing carbohydrate units of this glycoprotein have an average molecular weight of 3000, except for one unit the molecular weight of which is significantly higher. 3. The N-, non-N- and C-terminal amino acids of the main glycopeptides were determined. Aspartic acid and threonine occur in most peptides. Alanine, glycine, proline, serine and lysine were present in varying amounts. Traces of other amino acids were also found. 4. The amino acid sequence of three main glycopeptides was established and indicated that these glycopeptides are located at different positions of the polypeptide chain of the glycoprotein. These sequences are: Asp(NH2)-Pro-Lys; Thr-Asp(NH2)-Ala; Asp(NH2)-Gly-Thr. 5. From the results of a series of chemical reactions (periodate oxidation, hydrazinolysis, dinitrophenylation, mild acid hydrolysis) it was shown that the hydroxyl group of the N-terminal threonine and the ?-amino group of lysine are free and that the ?-carboxyl group of aspartic acid is present as amide. It was concluded that this amide group is involved in the carbohydrate–polypeptide linkages of at least four carbohydrate units of ?1-acid glycoprotein. 6. The carbohydrate composition of the sialic acid-free glycopeptides was determined in terms of moles of neutral hexoses, glucosamine and fucose/mole. 7. Fucose, at least to the larger part, is not linked to sialic acid, and its (glycosidic) linkage is significantly more stable toward acid hydrolysis than the bond of the sialyl residues. 8. Heterogeneity of the carbohydrate units of ?1-acid glycoprotein was found with regard to size and to content of fucose and sialic acid. PMID:14342511

Satake, M.; Okuyama, T.; Ishihara, K.; Schmid, K.

1965-01-01

287

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

288

Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution.  

PubMed

Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported. Current working hypotheses for a spider "backbone" phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis of spiders including taxa representing all major spider lineages. Our robust phylogenetic hypothesis recovers some fundamental and uncontroversial spider clades, but rejects the prevailing paradigm of a monophyletic Orbiculariae, the most diverse lineage, containing orb-weaving spiders. Based on our results, the orb web either evolved much earlier than previously hypothesized and is ancestral for a majority of spiders or else it has multiple independent origins, as hypothesized by precladistic authors. Cribellate deinopoid orb weavers that use mechanically adhesive silk are more closely related to a diverse clade of mostly webless spiders than to the araneoid orb-weaving spiders that use adhesive droplet silks. The fundamental shift in our understanding of spider phylogeny proposed here has broad implications for interpreting the evolution of spiders, their remarkable biomaterials, and a key extended phenotype--the spider web. PMID:25042592

Bond, Jason E; Garrison, Nicole L; Hamilton, Chris A; Godwin, Rebecca L; Hedin, Marshal; Agnarsson, Ingi

2014-08-01

289

Degenerate primer MOB typing of multiresistant clinical isolates of E. coli uncovers new plasmid backbones.  

PubMed

Degenerate Primer MOB Typing is a PCR-based protocol for the classification of ?-proteobacterial transmissible plasmids in five phylogenetic relaxase MOB families. It was applied to a multiresistant E. coli collection, previously characterized by PCR-based replicon-typing, in order to compare both methods. Plasmids from 32 clinical isolates of multiresistant E. coli (19 extended spectrum beta-lactamase producers and 13 non producers) and their transconjugants were analyzed. A total of 95 relaxases were detected, at least one per isolate, underscoring the high potential of these strains for antibiotic-resistance transmission. MOBP12 and MOBF12 plasmids were the most abundant. Most MOB subfamilies detected were present in both subsets of the collection, indicating a shared mobilome among multiresistant E. coli. The plasmid profile obtained by both methods was compared, which provided useful data upon which decisions related to the implementation of detection methods in the clinic could be based. The phylogenetic depth at which replicon and MOB-typing classify plasmids is different. While replicon-typing aims at plasmid replication regions with non-degenerate primers, MOB-typing classifies plasmids into relaxase subfamilies using degenerate primers. As a result, MOB-typing provides a deeper phylogenetic depth than replicon-typing and new plasmid groups are uncovered. Significantly, MOB typing identified 17 plasmids and an integrative and conjugative element, which were not detected by replicon-typing. Four of these backbones were different from previously reported elements. PMID:25463772

Garcillán-Barcia, M Pilar; Ruiz Del Castillo, Belén; Alvarado, Andrés; de la Cruz, Fernando; Martínez-Martínez, Luis

2015-01-01

290

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

291

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

292

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

293

Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling.  

PubMed

Most dsRNA viruses have a genome-enclosing capsid that comprises 120 copies of a single coat protein (CP). These 120 CP subunits are arranged as asymmetrical dimers that surround the icosahedral fivefold axes, forming pentamers of dimers that are thought to be assembly intermediates. This scheme is violated, however, in recent structures of two dsRNA viruses, a fungal virus from family Partitiviridae and a rabbit virus from family Picobirnaviridae, both of which have 120 CP subunits organized as dimers of quasisymmetrical dimers. In this study, we report the CP backbone trace of a second fungal partitivirus, determined in this case by electron cryomicroscopy and homology modeling. This virus also exhibits quasisymmetrical CP dimers that are connected by prominent surface arches and stabilized by domain swapping between the two CP subunits. The CP fold is dominated by alpha-helices, although beta-strands mediate several important contacts. A dimer-of-dimers assembly intermediate is again implicated. The disordered N-terminal tail of each CP subunit protrudes into the particle interior and likely interacts with the genome during packaging and/or transcription. These results broaden our understanding of conserved and variable aspects of partitivirus structure and reflect the growing use of electron cryomicroscopy for atomic modeling of protein folds. PMID:20643089

Tang, Jinghua; Pan, Junhua; Havens, Wendy M; Ochoa, Wendy F; Guu, Tom S Y; Ghabrial, Said A; Nibert, Max L; Tao, Yizhi Jane; Baker, Timothy S

2010-07-21

294

Backbone Trace of Partitivirus Capsid Protein from Electron Cryomicroscopy and Homology Modeling  

PubMed Central

Abstract Most dsRNA viruses have a genome-enclosing capsid that comprises 120 copies of a single coat protein (CP). These 120 CP subunits are arranged as asymmetrical dimers that surround the icosahedral fivefold axes, forming pentamers of dimers that are thought to be assembly intermediates. This scheme is violated, however, in recent structures of two dsRNA viruses, a fungal virus from family Partitiviridae and a rabbit virus from family Picobirnaviridae, both of which have 120 CP subunits organized as dimers of quasisymmetrical dimers. In this study, we report the CP backbone trace of a second fungal partitivirus, determined in this case by electron cryomicroscopy and homology modeling. This virus also exhibits quasisymmetrical CP dimers that are connected by prominent surface arches and stabilized by domain swapping between the two CP subunits. The CP fold is dominated by ?-helices, although ?-strands mediate several important contacts. A dimer-of-dimers assembly intermediate is again implicated. The disordered N-terminal tail of each CP subunit protrudes into the particle interior and likely interacts with the genome during packaging and/or transcription. These results broaden our understanding of conserved and variable aspects of partitivirus structure and reflect the growing use of electron cryomicroscopy for atomic modeling of protein folds. PMID:20643089

Tang, Jinghua; Pan, Junhua; Havens, Wendy M.; Ochoa, Wendy F.; Guu, Tom S.Y.; Ghabrial, Said A.; Nibert, Max L.; Tao, Yizhi Jane; Baker, Timothy S.

2010-01-01

295

Structurally diverse cyclisation linkers impose different backbone conformations in bicyclic peptides.  

PubMed

Combinatorial libraries of structurally diverse peptide macrocycles offer a rich source for the development of high-affinity ligands to targets of interest. In this work we have developed linkers for the generation of genetically encoded bicyclic peptides and tested whether the peptides cyclised by them have significant variations in their backbone conformations. Two new cyclisation reagents, each containing three thiol-reactive groups, efficiently and selectively cyclised linear peptides containing three cysteine moieties. When the mesitylene linker of the bicyclic peptide PK15, a potent inhibitor of plasma kallikrein (K(i)=2 nM), was replaced by the new linkers, its inhibitory activity dropped by a factor of more than 1000, suggesting that the linkers impose different conformations on the peptide. Indeed, structural analysis by solution-state NMR revealed different NOE constraints in the three bicyclic peptides, indicating that these relatively small linkers at the centres of bicyclic peptide structures significantly influence the conformations of the peptides. These results demonstrate the prominent structural role of linkers in peptide macrocycles and suggest that application of different cyclisation linkers in a combinatorial fashion could be an attractive means to generate topologically diverse macrocycle libraries. PMID:22492661

Chen, Shiyu; Morales-Sanfrutos, Julia; Angelini, Alessandro; Cutting, Brian; Heinis, Christian

2012-05-01

296

An enhanced backbone-assisted reliable framework for wireless sensor networks.  

PubMed

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

297

Fragment orbital based description of charge transfer in peptides including backbone orbitals.  

PubMed

Charge transfer in peptides and proteins can occur on different pathways, depending on the energetic landscape as well as the coupling between the involved orbitals. Since details of the mechanism and pathways are difficult to access experimentally, different modeling strategies have been successfully applied to study these processes in the past. These can be based on a simple empirical pathway model, efficient tight binding type atomic orbital Hamiltonians or ab initio and density functional calculations. An interesting strategy, which allows an efficient calculations of charge transfer parameters, is based on a fragmentation of the system into functional units. While this works well for systems like DNA, where the charge transfer pathway is naturally divided into distinct molecular fragments, this is less obvious for charge transfer along peptide and protein backbones. In this work, we develop and access a strategy for an effective fragmentation approach, which allows one to compute electronic couplings for large systems along nanosecond time scale molecular dynamics trajectories. The new methodology is applied to a solvated peptide, for which charge transfer properties have been studied recently using an empirical pathway model. As could be expected, dynamical effects turn out to be important, which emphasizes the importance of using effective quantum approaches which allow for sufficient sampling. However, the computed rates are orders of magnitude smaller than experimentally determined, which indicates the shortcomings of present modeling approaches. PMID:24655342

Heck, Alexander; Woiczikowski, P Benjamin; Kuba?, Tomáš; Welke, Kai; Niehaus, Thomas; Giese, Bernd; Skourtis, Spiros; Elstner, Marcus; Steinbrecher, Thomas B

2014-04-24

298

A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella  

PubMed Central

A novel, site-specific, DNA backbone S-modification (phosphorothioation) has been discovered, but its in vivo function(s) have remained obscure. Here, we report that the enteropathogenic Salmonella enterica serovar Cerro 87, which possesses S-modified DNA, restricts DNA isolated from Escherichia coli, while protecting its own DNA by site-specific phosphorothioation. A cloned 15-kb gene cluster from S. enterica conferred both host-specific restriction and DNA S-modification on E. coli. Mutational analysis of the gene cluster proved unambiguously that the S-modification prevented host-specific restriction specified by the same gene cluster. Restriction activity required three genes in addition to at least four contiguous genes necessary for DNA S-modification. This functional overlap ensures that restriction of heterologous DNA occurs only when the host DNA is protected by phosphorothioation. Meanwhile, this novel type of host-specific restriction and modification system was identified in many diverse bacteria. As in the case of methylation-specific restriction systems, targeted inactivation of this gene cluster should facilitate genetic manipulation of these bacteria, as we demonstrate in Salmonella. PMID:20627870

Xu, Tiegang; Yao, Fen; Zhou, Xiufen; Deng, Zixin; You, Delin

2010-01-01

299

Elastic a-silicon nanoparticle backboned graphene hybrid as a self-compacting anode for high-rate lithium ion batteries.  

PubMed

Although various Si-based graphene nanocomposites provide enhanced electrochemical performance, these candidates still yield low initial coloumbic efficiency, electrical disconnection, and fracture due to huge volume changes after extended cycles lead to severe capacity fading and increase in internal impedance. Therefore, an innovative structure to solve these problems is needed. In this study, an amorphous (a) silicon nanoparticle backboned graphene nanocomposite (a-SBG) for high-power lithium ion battery anodes was prepared. The a-SBG provides ideal electrode structures-a uniform distribution of amorphous silicon nanoparticle islands (particle size <10 nm) on both sides of graphene sheets-which address the improved kinetics and cycling stability issues of the silicon anodes. a-Si in the composite shows elastic behavior during lithium alloying and dealloying: the pristine particle size is restored after cycling, and the electrode thickness decreases during the cycles as a result of self-compacting. This noble architecture facilitates superior electrochemical performance in Li ion cells, with a specific energy of 468 W h kg(-1) and 288 W h kg(-1) under a specific power of 7 kW kg(-1) and 11 kW kg(-1), respectively. PMID:25078072

Ko, Minseong; Chae, Sujong; Jeong, Sookyung; Oh, Pilgun; Cho, Jaephil

2014-08-26

300

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

301

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

302

Effect of solvents on the chemical and physical properties of ionic polymer-metal composites  

E-print Network

online 25 May 2006 Ionic polymer-metal composites IPMCs consist of a perfluorinated ionomer membrane of a perfluorinated backbone ionomer usually Nafion® or Flemion®; CF2CF m CF2CF2 n; see Fig. 1 plated on both faces

Nemat-Nasser, Sia

303

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

304

Paucity of moderately repetitive sequences  

SciTech Connect

We examined clones of renatured repetitive human DNA to find novel repetitive DNAs. After eliminating known repeats, the remaining clones were subjected to sequence analysis. These clones also corresponded to known repeats, but with greater sequence diversity. This indicates that either these libraries were depleted of short interspersed repeats in construction, or these repeats are much less prevalent in the human genome than is indicated by data from {und Xenopus} or sea urchin studies. We directly investigated the sequence composition of human DNA through traditional renaturation techniques with the goal of estimating the limits of abundance of repetitive sequence classes in human DNA. Our results sharply limit the maximum possible abundance to 1--2% of the human genome. Our estimate, minus the known repeats in this fraction, leaves about 1% (3 {times} 10{sup 7} nucleotides) of the human genome for novel repetitive elements. 2 refs. (MHB)

Schmid, C.W.

1991-01-01

305

Functional RNAs exhibit tolerance for non-heritable 2?–5? vs. 3?–5? backbone heterogeneity  

PubMed Central

A plausible process for non-enzymatic RNA replication would greatly simplify models of the transition from prebiotic chemistry to simple biology. However, all known conditions for the chemical copying of an RNA template result in the synthesis of a complementary strand containing a mixture of 2?–5? and 3?–5? linkages, rather than the selective synthesis of only 3?–5? linkages as found in contemporary RNA. Here we show that such backbone heterogeneity is compatible with RNA folding into defined three-dimensional structures that retain molecular recognition and catalytic properties and, therefore, would not prevent the evolution of functional RNAs such as ribozymes. Moreover, the same backbone heterogeneity lowers the melting temperature of RNA duplexes that would otherwise be too stable for thermal strand separation. By allowing copied strands to dissociate, this heterogeneity may have been one of the essential features that allowed RNA to emerge as the first biopolymer. PMID:23609089

Engelhart, Aaron E.; Powner, Matthew W.; Szostak, Jack W.

2014-01-01

306

Structural Basis for Intumescence – Part III – Thermal Degradation Study of Intumescent Polymers Containing Spirophosphorus Moiety in the Backbone  

Microsoft Academic Search

3,9-Dichloro-2,4,8,10-tetraoxo-3,9-disphosphaspiro-[5.5]-undecane-3,9-dioxide (spiro) was melt condensed with structurally different dihydric phenols to form poly aromatic spirophosphates. The thermal volatilization analysis showed eruptive release of gases above 300°C and the temperature region of release depends on the nature of the aromatic units incorporated in the polymer backbone. The thermal degradation in nitrogen atmosphere indicated the formation of phenol, substituted phenols, aromatics, alkyl

Palanichamy Sivasamy; Bashyam Geetha; Chinnaswamy Thangavel Vijayakumar; Johannes Karl Fink

2010-01-01

307

On the merging of millimeter-wave fiber-radio backbone with 25GHz WDM ring networks  

Microsoft Academic Search

We present an optical modulation and distribution scheme that incorporates subcarrier-multiplexed (SCM) transport with remote local oscillator (LO) delivery for a millimeter-wave (mm-wave) fiber-radio backbone driving a sectorized antenna interface. The proposed method is compatible with a standard wavelength-division multiplexing infrastructure with a 25-GHz channel spacing. We also characterize the profiles and bandwidths of the optical filters, which are essential

Christina Lim; Ampalavanapillai Nirmalathas; Manik Attygalle; Dalma Novak; Rod Waterhouse

2003-01-01

308

Localization of electrons in the sugar\\/phosphate backbone in DNA investigated via resonant Auger decay spectra  

Microsoft Academic Search

In order to elucidate the localized nature of electrons in sugar\\/phosphate backbone in DNA molecules, resonant Auger decay spectra excited by soft x-rays around the inner-shell ionization thresholds have been measured for single-strand DNA. The systems investigated are thin films of DNA as well as related phosphorus compounds such as nucleotide (adenosine triphosphate, ATP), sodium phosphate, and indium phosphide. For

Yuji Baba; Tetsuhiro Sekiguchi; Iwao Shimoyama; Norie Hirao; Krishna G. Nath

2006-01-01

309

One-pot total syntheses of natural products containing a THP-ring backbone: (±)-centrolobine and (±)-civet cat secretion  

Microsoft Academic Search

A one-pot strategy is devised and applied to the total syntheses of natural products with a THP-ring backbone. A special feature of this one-pot synthesis is the recyclability of the indium complex byproduct generated from the indium-mediated allylation reaction for concurrent catalysis in subsequent steps. Centrolobine and civet cat secretion are synthesized via this new method in overall yields of

Hai Zhou; Teck-Peng Loh

2009-01-01

310

Direct Formation of the C5?-Radical in the Sugar-Phosphate Backbone of DNA by High Energy Radiation  

PubMed Central

Neutral sugar radicals formed in DNA sugar-phosphate backbone are well-established as precursors of biologically important damage such as DNA-strand scission and crosslinking. In this work, we present electron spin resonance (ESR) evidence showing that the sugar radical at C5? (C5?•) is one of the most abundant (ca. 30%) sugar radicals formed by ?- and Ar ion-beam irradiated hydrated DNA samples. Taking dimethyl phosphate as a model of sugar-phosphate backbone, ESR and theoretical (DFT) studies of ?-irradiated dimethyl phosphate were carried out. CH3OP(O2?)OCH2• is formed via deprotonation from the methyl group of directly ionized dimethyl phosphate at 77 K. Formation of CH3OP(O2?)OCH2• is independent of dimethyl phosphate concentration (neat or in aqueous solution) or pH. ESR spectra of C5?• found in DNA and of CH3OP(O2?)OCH2• do not show an observable ?-phosphorous hyperfine coupling (HFC). Further, C5?• found in DNA does not show a significant C4?-H ?–proton HFC. Applying the DFT/B3LYP/6-31G(d) method, a study of conformational dependence of the phosphorous HFC in CH3OP(O2?)OCH2• shows that in its minimum energy conformation, CH3OP(O2?)OCH2• has a negligible ?-phosphorous HFC. Based on these results, formation of radiation-induced C5?• is proposed to occur via a very rapid deprotonation from the directly ionized sugar-phosphate backbone and rate of this deprotonation must be faster than that of energetically downhill transfer of the unpaired spin (hole) from ionized sugar-phosphate backbone to the DNA bases. Moreover, C5?• in irradiated DNA is found to be in a conformation that does not exhibit ? proton or ? phosphorous HFCs. PMID:22553971

Adhikary, Amitava; Becker, David; Palmer, Brian J.; Heizer, Alicia N.; Sevilla, Michael D.

2012-01-01

311

Complete Genome Sequence and Comparative Genomics of Shigella flexneri Serotype 2a Strain 2457T  

Microsoft Academic Search

We determined the complete genome sequence of Shigella flexneri serotype 2a strain 2457T (4,599,354 bp). Shigella species cause >1 million deaths per year from dysentery and diarrhea and have a lifestyle that is markedly different from those of closely related bacteria, including Escherichia coli. The genome exhibits the backbone and island mosaic structure of E. coli pathogens, albeit with much

J. Wei; M. B. Goldberg; V. Burland; M. M. Venkatesan; W. Deng; G. Fournier; G. F. Mayhew; G. Plunkett; D. J. Rose; A. Darling; B. Mau; N. T. Perna; S. M. Payne; L. J. Runyen-Janecky; S. Zhou; D. C. Schwartz; F. R. Blattner

2003-01-01

312

A maximum entropy approach to the study of residue-specific backbone angle distributions in ?-synuclein, an intrinsically disordered protein.  

PubMed

?-Synuclein is an intrinsically disordered protein of 140 residues that switches to an ?-helical conformation upon binding phospholipid membranes. We characterize its residue-specific backbone structure in free solution with a novel maximum entropy procedure that integrates an extensive set of NMR data. These data include intraresidue and sequential H(N) ? H(?) and H(N) ? H(N) NOEs, values for (3) JHNH?, (1) JH?C?, (2) JC?N, and (1) JC?N, as well as chemical shifts of (15)N, (13)C(?), and (13)C' nuclei, which are sensitive to backbone torsion angles. Distributions of these torsion angles were identified that yield best agreement to the experimental data, while using an entropy term to minimize the deviation from statistical distributions seen in a large protein coil library. Results indicate that although at the individual residue level considerable deviations from the coil library distribution are seen, on average the fitted distributions agree fairly well with this library, yielding a moderate population (20-30%) of the PPII region and a somewhat higher population of the potentially aggregation-prone ? region (20-40%) than seen in the database. A generally lower population of the ?R region (10-20%) is found. Analysis of (1)H ? (1)H NOE data required consideration of the considerable backbone diffusion anisotropy of a disordered protein. PMID:24976112

Mantsyzov, Alexey B; Maltsev, Alexander S; Ying, Jinfa; Shen, Yang; Hummer, Gerhard; Bax, Ad

2014-09-01

313

Deformation of redox-active polymer gel based on polysiloxane backbone and bis(benzodithiolyl)bithienyl scaffold.  

PubMed

Redox-active polymer gels consisting of polysiloxane backbone and bis(benzodithiolyl)bithienyl units have been designed and synthesized. The bis(benzodithiolyl)bithienyl units, which undergo interconversion between cyclic form and opened dicationic form, have been incorporated into polysiloxane backbone via hydrosilylation of vinyl-terminated bis(benzodithiolyl)bithienyl derivative and poly(methylhydrosiloxane) (PMHS) or poly(dimethylsiloxane-co-hydrogenmethylsiloxane) (PDMS-co-PMHS), resulting in polymer gels cross-linked with bis(benzodithiolyl)bithienyl units. After the incorporation of M1 into polysiloxane backbone, these polymer gels (P1 and P2) also exhibit redox responses associated with the electrochemical interconversion of the bis(benzodithiolyl)bithienyl moieties. The polymer gels show swelling behavior upon chemical oxidization, and bending behavior has been observed for the polymer gel immobilized poly(vinylidene difluoride) (PVdF) film. These results provide a useful perspective for fabricating redox-triggered polymer gel actuators based on the conformational change of the functional molecular unit. PMID:25400032

Ohtake, Toshihiro; Tanaka, Hideki; Matsumoto, Tetsuro; Ohta, Akira; Kimura, Mutsumi

2014-12-01

314

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

315

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

316

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.

Schmidtgall, Boris; Höbartner, Claudia

2015-01-01

317

Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling  

PubMed Central

Conformational dynamics play a key role in the properties and functions of proteins and nucleic acids. Heteronuclear NMR spin relaxation is a uniquely powerful site-specific probe of dynamics in proteins and has found increasing applications to nucleotide base side chains and anomeric sites in RNA. Applications to the nucleic acid ribose backbone, however, have been hampered by strong magnetic coupling among ring carbons in uniformly 13C-labeled samples. In this work, we apply a recently-developed, metabolically-directed isotope labeling scheme that places 13C with high efficiency and specificity at the nucleotide ribose C2’ and C4’ sites. We take advantage of this scheme to explore backbone dynamics in the well-studied GCAA RNA tetraloop. Using a combination of CPMG (Carr-Purcell-Meiboom-Gill) and R1? relaxation dispersion spectroscopy to explore exchange processes on the microsecond to millisecond timescale, we find an extensive pattern of dynamic transitions connecting a set of relatively well-defined conformations. In many cases, the observed transitions appear to be linked to C3’-endo/C2’-endo sugar pucker transitions of the corresponding nucleotides, and may also be correlated across multiple nucleotides within the tetraloop. These results demonstrate the power of NMR spin relaxation based on alternate-site isotope labeling to open a new window into the dynamic properties of ribose backbone groups in RNA. PMID:19049467

Johnson, James E.; Hoogstraten, Charles G.

2009-01-01

318

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A-T phosphoramidite building blocks.  

PubMed

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; Ducho, Christian

2015-01-01

319

The Construction of Metal-Organic Framework with Active Backbones by the Utilization of Reticular Chemistry  

NASA Astrophysics Data System (ADS)

With the principles of reticular chemistry, metal-organic frameworks with ultra-high porosity, chiral-recognition unit as a chiral stationary phase, metalloporhyrins for enhanced hydrogen adsorption and an intrinsic conductivity to form porous conductors, have been prepared. This dissertation presents how the principles of reticular chemistry were utilized to achieve in the preparations of metal-organic frameworks with a large surface area and active backbones. Through the simple isoreticular (having the same framework topology) expansion from MOF-177 composed with 1,3,5-tris(4'-carboxyphenyl-)benzene (BTB3-) as the strut; MOF-200 was prepared with 4,4',4"-(benzene-1,3,5-triyl-tris(benzene-4,1-diy1))tribenzoic acid an extension from BTB3- by a phenylene unit to yield one of the most porous MOFs with a Langmuir surface area of 10,400 m2. and the lowest density of 0.22 cm3.g-1. A successful thermal polymerization reaction at 325 °C inside of the pores of highly porous MOF, MOF-177, was performed and verified the integrity of the MOF structure even after the thermal reaction. 1,4-Diphenylbutadiyne that is known to polymerize upon heating to form a conjugated backbone was impregnated via solution-diffusion into MOF-177 and then subsequently polymerized by heat to form polymer impregnated MOF-177. Characterization was carried out using powder X-ray diffraction and volumetric sorption analyzer. MOF-1020 with a linear quaterphenyl dicarboxylate-based strut was designed to contain a chiral bisbinaphthyl crown-ether moiety for alkyl ammonium resolution was precisely placed into a Zn4O(CO2)6-based cubic MOF structure. Unfortunately, the chiral resolution was not achieved due to the sensitivity and the pore environment of MOF-1020. However, an interesting phenomenon was observed, where the loss of crystallinity occurs upon solvent removal while the crystallites remain shiny and crystalline, but it readily is restored upon re-solvation of the crystallites. This rare phenomenon was studied by powder X-ray diffraction and supported by gas adsorption and thermogravimetric analysis. Layered MOFs with metalloporphyrins with Zn, Cu, Co and Fe at their +2 oxidation states as struts were prepared to facilitate non-structural metal sites and tested for hydrogen adsorption and the binding enthalpies. Steep uptakes are indeed observed, but rather due to the optimal interlayer distance of 9 A for dihydrogen, and the binding enthalpies are 6.7 -- 7.6 kJ . mo1-1 which are not ·extraordinary. Although the metals did not seem to play a large role, a trend was observed where the binding enthalpies increase as the metals in the metalloporphyrins go from late to early transition metals. With the concept of conductive metal oxides, a journey of constructing conductive MOFs was taken by attempting the formation of metal-carbon bonds by linking transition metal ions with conjugated organic struts which are 1,4-benzenediisonitrile, 1,4-benzenediethynylide and p-cyanophenylethynylide. Among the attempted systems, a reaction of Cr(III) and 1,4-benzenediethynylide yielded an amorphous material with a BET (Brunauer-Emmett-Teller) surface area of 80 m2.g-1, hydrogen uptake of 47 cm 3. g-1 and a resistance of 20 MO. Also a crystalline compound was prepared by mimicking Prussian blue by using p-cyanophenylethynylide where one end can bind metal with ethynylic carbon and the other end with the cyano nitrogen by following the similar synthesis of Prussian blue analogues. The principles of reticular chemistry are demonstrated through each chapter and show how powerful and beneficial reticular chemistry is by allowing the predetermination of the structure and function. The details of the ways to approach an ideal compound and the synthetic aspects are also described in this dissertation.

Choi, Eunwoo

320

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

321

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

322

Functional implications of large backbone amplitude motions of the glycoprotein 130-binding epitope of interleukin-6.  

PubMed

Human interleukin (IL)-6 plays a pivotal role in the immune response, hematopoiesis, the acute-phase response, and inflammation. IL-6 has three distinct receptor epitopes, termed sites I, II, and III, that facilitate the formation of a signaling complex. IL-6 signals via a homodimer of glycoprotein 130 (gp130) after initially forming a heterodimer with the nonsignaling ?-receptor [IL-6 ?-receptor (IL-6R)] via site I. Here, we present the backbone dynamics of apo-IL-6 as determined by analysis of NMR relaxation data with the extended model-free formalism of Lipari and Szabo. To alleviate significant resonance overlap in the HSQC-type spectra, cell-free protein synthesis was used to selectively (15) N-label residues, thereby ensuring a complete set of residue-specific dynamics. The calculated order parameters [square of the generalized model-free order parameter (S(2))] showed significant conformational heterogeneity among clusters of residues in IL-6. In particular, the N-terminal region of the long AB-loop, which corresponds spatially to one of the gp130 receptor binding epitopes (i.e. site III), experiences substantial fluctuations along the conformation of the main chain (S(2) = 0.3-0.8) that are not observed at the other two epitopes or in other cytokines. Thus, we postulate that dynamic properties of the AB-loop are responsible for inhibiting the interaction of IL-6 with gp130 in the absence of the IL-6R, and that binding of IL-6R at site I shifts the dynamic equilibrium to favor interaction with gp130 at site III. In addition, molecular dynamics simulations corroborated the NMR-derived dynamics, and showed that the BC-loop adopts different substates that possibly play a role in facilitating receptor assembly. PMID:24712547

Bobby, Romel; Robustelli, Paul; Kralicek, Andrew V; Mobli, Mehdi; King, Glenn F; Grötzinger, Joachim; Dingley, Andrew J

2014-05-01

323

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

324

Backbone dynamics of (1-71)bacterioopsin studied by two-dimensional 1H-15N NMR spectroscopy.  

PubMed

The backbone dynamics of a uniformly 15N-labelled proteolytic fragment (residues 1-71) of bacteriorhodopsin, solubilized in two media [methanol/chloroform (1:1), 0.1 M 2HCO2NH4 and SDS micelles] have been investigated using two-dimensional proton-detected heteronuclear 1H-15N NMR spectroscopy. A set of longitudinal and transverse relaxation rates of 15N nuclei and 1H-15N NOE were obtained for 61 backbone amide groups. The contribution of the conformational exchange to transverse relaxation rates of individual nitrogens was elucidated using a set of different rates of the Carr-Purcell-Meiboom-Gill (CPMG) spin-lock pulse train. We found that most of the backbone amide groups are involved in the co-operative exchange process over the rate range 10(3)-10(4) s-1, with the chemical-shift dispersion near 1 ppm. Contributions of conformational exchange to the measured transverse relaxation were essentially suppressed by the 3-kHz (spin-echo period tau = 0.083 ms) CPMG spin-lock. Under these conditions, the measured longitudinal, transverse relaxation rates and NOE values were interpreted using the model-free approach of Lipari and Szabo [Lipari, G. & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559]. In both media used, the protein exhibits very similar dynamic properties, and has overall rotational correlation times of 7.0 ns and 6.6 ns in organic mixture and in SDS micelles, respectively. In addition to overall rotation of the molecule, the backbone N-H vectors are involved in two types of internal motions; fast, on a time scale of < 20 ps, and intermediate, close to 1 ns. Distinctly mobile regions are identified by a large decrease in the overall order parameter and correspond to N-terminal residues (residues 1-7 both for organic solvent and micelles), C-terminal residues (residues 65-71 and 69-71 for organic solvent and micelles, respectively) and residues connecting alpha helices (residues 33-41 and 33-38, for organic solvent and micelles, respectively). A decrease in the order parameter was also observed for residues next to Pro50, indicating a higher flexibility in this region. Thus, backbone dynamic parameters of (1-71)bacterioopsin are in good correspondence with its spatial structure [Pervushin, K. V., Orekhov, V. Yu., Popov, A., Musina, L. Yu., Arseniev, A. S., (1994) Eur. J. Biochem., in the press]. The observed conformational exchange behavior of alpha helices seems to be induced by the flickering helix-helix interaction and could be important for the functioning of bacteriorhodopsin. PMID:8112340

Orekhov VYu; Pervushin, K V; Arseniev, A S

1994-02-01

325

Backbone and side chain 1H, 13C, and 15N NMR assignments for the organic hydroperoxide resistance protein (Ohr) from Burkholderia pseudomallei  

PubMed Central

Burkholderia pseudomallei is a NIAID Category B microorganism responsible for melioidosis. Here we report backbone and side chain NMR assignments for the 139-residue, homodimeric, organic hydroperoxide resistance protein (Ohr) from this organism. PMID:19888681

Buchko, Garry W.; Hewitt, Stephen N.; Napuli, Alberto J.; van Voorhis, Wesley C.; Myler, Peter J.

2009-01-01

326

Multi-objective optimization of fiber reinforced composite laminates for strength, stiffness and minimal mass  

E-print Network

Multi-objective optimization of fiber reinforced composite laminates for strength, stiffness and material properties of the matrix and fibers. The lamina stresses for thin composite coupons subjected composite materials; Stacking sequence; Composite pressure vessel 1. Introduction Fiber reinforced

Vel, Senthil

327

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

328

Preserving sequence annotations across reference sequences  

PubMed Central

Background Matching and comparing sequence annotations of different reference sequences is vital to genomics research, yet many annotation formats do not specify the reference sequence types or versions used. This makes the integration of annotations from different sources difficult and error prone. Results As part of our effort to create linked data for interoperable sequence annotations, we present an RDF data model for sequence annotation using the ontological framework established by the OBO Foundry ontologies and the Basic Formal Ontology (BFO). We defined reference sequences as the common domain of integration for sequence annotations, and identified three semantic relationships between sequence annotations. In doing so, we created the Reference Sequence Annotation to compensate for gaps in the SO and in its mapping to BFO, particularly for annotations that refer to versions of consensus reference sequences. Moreover, we present three integration models for sequence annotations using different reference assemblies. Conclusions We demonstrated a working example of a sequence annotation instance, and how this instance can be linked to other annotations on different reference sequences. Sequence annotations in this format are semantically rich and can be integrated easily with different assemblies. We also identify other challenges of modeling reference sequences with the BFO. PMID:25093075

2014-01-01

329

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

330

A chimera carrying the functional domain of the orphan protein SLC7A14 in the backbone of SLC7A2 mediates trans-stimulated arginine transport.  

PubMed

In human skin fibroblasts, a lysosomal transport system specific for cationic amino acids has been described and named system c. We asked if SLC7A14 (solute carrier family 7 member A14), an orphan protein assigned to the SLC7 subfamily of cationic amino acid transporters (CATs) due to sequence homology, may represent system c. Fusion proteins between SLC7A14 and enhanced GFP localized to intracellular vesicles, co-staining with the lysosomal marker LysoTracker(®). To perform transport studies, we first tried to redirect SLC7A14 to the plasma membrane (by mutating putative lysosomal targeting motifs) but without success. We then created a chimera carrying the backbone of human (h) CAT-2 and the protein domain of SLC7A14 corresponding to the so-called "functional domain" of the hCAT proteins, a protein stretch of 81 amino acids that determines the apparent substrate affinity, sensitivity to trans-stimulation, and (as revealed in this study) pH dependence. The chimera mediated arginine transport and exhibited characteristics similar but not identical to hCAT-2A (the low affinity hCAT-2 isoform). Western blot and microscopic analyses confirmed localization of the chimera in the plasma membrane of Xenopus laevis oocytes. Noticeably, arginine transport by the hCAT-2/SLC7A14 chimera was pH-dependent, trans-stimulated, and inhibited by ?-trimethyl-L-lysine, properties assigned to lysosomal transport system c in human skin fibroblasts. Expression analysis showed strong expression of SLC7A14 mRNA in these cells. Taken together, these data strongly suggest that SLC7A14 is a lysosomal transporter for cationic amino acids. PMID:22787143

Jaenecke, Isabel; Boissel, Jean-Paul; Lemke, Matthias; Rupp, Johanna; Gasnier, Bruno; Closs, Ellen I

2012-08-31

331

UV-driven switching of chain orientation and liquid crystal alignment in nanoscale thin films of a novel polyimide bearing stilbene moieties in the backbone.  

PubMed

A novel photosensitive polyimide, poly(4,4'-stilbenylene 4,4'-oxidiphthalimide) (ODPA-Stilbene PSPI) was newly synthesized. The most surprising feature of this PSPI is that the PSPI films irradiated with linear polarized ultraviolet light (LPUVL) can favorably induce a unidirectional alignment of liquid crystals (LCs) in contact with the film surface and further switch the director of the unidirectionally aligned LCs from a perpendicular direction to a parallel direction with respect to the polarization direction of LPUVL by simply controlling the exposure dose in the irradiation process. These LPUVL-irradiated films were found to provide high anchoring energy to LCs, always giving very stable, homogeneous cells with unidirectionally aligned LCs regardless of the LC alignment directions. In the films, the PSPI polymer chains were found to undergo favorably unidirectional orientation via a specific orientation sequence of the polymer chain segments led by the directionally selective trans-cis photoisomerization of the stilbene chromophore units in the backbone induced by LPUVL exposure. Such unidirectionally oriented polymer chains of the films induce alignment of the LCs along the orientation direction of the polymer chains via favorable anisotropic molecular interactions between the oriented polymer chain segments and the LC molecules. In addition, the PSPI has an excellent film formation processibility; good quality PSPI thin films with a smooth surface are easily produced by simple spin-coating of the soluble poly(amic acid) precursor and subsequent thermal imidization process. In summary, this new PSPI is the promising LC alignment layer candidate with rubbing-free processing for the production of advanced LC display devices, including LC display televisions with large display areas. PMID:18386867

Hahm, Suk Gyu; Lee, Seung Woo; Lee, Taek Joon; Cho, Seon Ah; Chae, Boknam; Jung, Young Mee; Kim, Seung Bin; Ree, Moonhor

2008-04-24

332

{{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

333

Phase behaviors, molecular and supramolecular structures in polymers containing rigid-rod backbones with cyanobiphenyl side chains  

NASA Astrophysics Data System (ADS)

One of the most important and challenging topics in materials chemistry involves designing nano-structures in synthetic materials via self-assembly for various highly technical applications. A specially designed combined liquid crystalline polymer containing a polyester backbone with cyanobiphenyl side chains has been studied in aspects of phase behaviors and crystal structures. The triclinic crystal phases identified in this series of polymer are all found to be constricted by 4-monomer unit cells. This discovery of 4-monomer triclinic unit cells motivates a search for the existence of supramolecular phases and understanding the possible molecular packing. A series of newly designed polyimides, which are composed of aromatic polyimide backbones with 4-cyanobiphenyl mesogens on the side chains has been synthesized. This series of polymers possesses a lesser degree of coupling between the backbones and side chains, which indicates the possibility of microphase separation between them. The representative polyimides of BPDA-7CBBP and BPDA-11CBBP in this series, in which 4-cyanobiphenyl side chains are connected onto the backbones through seven and eleven methylene units respectively have systematically studied in this research. Two crystal forms were recognized in BPDA-11CBBA, and one of them possesses six repeating units in one monoclinic unit cell. Moreover, the existence of a supramolecular phase has been proposed based on 2D WAXD fiber patterns. In the case of BPDA-7CBBP, three crystal forms were identified: two of them are constructed by triclinic lattices with large unit cells. The numbers of repeating units in those unit cells are seven and eight, respectively. Complicated phase behaviors including a second-order transition between the supramolecular phase and a high-order liquid crystal phase have been explored. The fact that large unit cells in both polymers with the numbers of repeating units in unit cells being 6, 7, and 8 leads to an important issue for our study: how are these molecules packed into these large unit cells? For understanding the various numbers of repeating units found in those low-symmetry unit cells, a waved-layer type of motif has been considered responsible for constructing the crystal phases with big unit cells. The distributions of order domains in the supramolecular phase are found less likely to possess cylindrical symmetry. Furthermore, the waviness of the layer-type motif has been realized to be a necessary element as long as the layer-type motif is the packing unit in crystal phases with large unit cell. (Abstract shortened by UMI.)

Ruan, Jrjeng

334

Depurination of N7-methylguanine by DNA glycosylase AlkD is dependent on the DNA backbone  

PubMed Central

DNA glycosylase AlkD excises N7-methylguanine (7mG) by a unique but unknown mechanism, in which the damaged nucleotide is positioned away from the protein and the phosphate backbone distorted. Here, we show by methylphosphonate substitution that a phosphate proximal to the lesion has a significant effect on the rate enhancement of 7mG depurination by the enzyme. Thus, instead of a conventional mechanism whereby protein side chains participate in N-glycosidic bond cleavage, AlkD remodels the DNA into an active site composed exclusively of DNA functional groups that provide the necessary chemistry to catalyze depurination. PMID:24090276

Rubinson, Emily H.; Christov, Plamen P.; Eichman, Brandt F.

2013-01-01

335

Depurination of N7-methylguanine by DNA glycosylase AlkD is dependent on the DNA backbone.  

PubMed

DNA glycosylase AlkD excises N7-methylguanine (7mG) by a unique but unknown mechanism, in which the damaged nucleotide is positioned away from the protein and the phosphate backbone is distorted. Here, we show by methylphosphonate substitution that a phosphate proximal to the lesion has a significant effect on the rate enhancement of 7mG depurination by the enzyme. Thus, instead of a conventional mechanism whereby protein side chains participate in N-glycosidic bond cleavage, AlkD remodels the DNA into an active site composed exclusively of DNA functional groups that provide the necessary chemistry to catalyze depurination. PMID:24090276

Rubinson, Emily H; Christov, Plamen P; Eichman, Brandt F

2013-10-22

336

Incorporation of Heterocycles into the Backbone of Peptoids to Generate Diverse Peptoid-Inspired One Bead One Compound Libraries  

PubMed Central

Combinatorial libraries of peptoids (oligo-N-substituted glycines) have proven to be useful sources of protein ligands. Each unit of the peptoid oligomer is derived from 2-haloacetic acid and a primary amine. In order to increase the chemical diversity available in peptoid libraries, we demonstrate here that heterocyclic halomethyl carboxylic acids can be employed as backbone building blocks in the synthesis of peptoid-based oligomers. Optimized conditions are reported that allow the creation of large, high quality combinatorial libraries containing these units. PMID:22320121

Aditya, Animesh; Kodadek, Thomas

2012-01-01

337

?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

338

?ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.  

PubMed

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

2014-10-29

339

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

340

De Novo Backbone Trace of GroEL from Single Particle Electron Cryomicroscopy  

Microsoft Academic Search

SUMMARY In this work, we employ single-particle electron cryo- microscopy (cryo-EM) to reconstruct GroEL to 4A ? resolution with both D7 and C7 symmetry. Using a newly developed skeletonization algorithm and secondary structure element identification in combi- nation with sequence-based secondary structure prediction, we demonstrate that it is possible to achieve a de novo Ca trace directly from a cryo-EM

Steven J. Ludtke; Matthew L. Baker; Dong-Hua Chen; Jiu-Li Song; David T. Chuang; Wah Chiu

2008-01-01

341

alpha Helical stabilization by side chain shielding of backbone hydrogen bonds  

Microsoft Academic Search

We study atomic models of the thermodynamics of the structural transition of peptides that form -helices. The effect of sequence variation on -helix formation for alanine-rich peptides, Ac-Ala21- methyl amide (A21) and Ac-A5 (AAARA)3A-methyl amide (Fs peptide), is investigated by atomic simulation studies of the ther- modynamics of the helix-coil transition in explicit water. The simulations show that the guanidinium

Angel E. Garcia; Kevin Y. Sanbonmatsu

2002-01-01

342

Transcription and reverse transcription of artificial nucleic acids involving backbone modification by template-directed DNA polymerase reactions.  

PubMed

Oligodeoxyribonucleotides (ODN) where the phosphodiester linkage had been replaced with an amide-type linker [-CH(2)C=ONH-] or an amine-type linker [-CH(2)CH(2)NH-] were synthesized to investigate the effect of these backbone modifications on polymerase reactions. In addition, a triphosphate analogue of thymidine dinucleotide with the amide-type linker was synthesized and enzymatic insertion of the amide linkage into ODN was attempted using this analogue for the polymerase reaction. Primer extension reactions using three types of thermostable DNA polymerases, KOD(exo-), Vent(exo-) and Taq were performed for the assays. Analysis of these data indicate that (i) the polymerase reaction tends to be affected much more by insertion of the cationic flexible amine-type linker than by insertion of the neutral rigid amide-type linker; (ii) the backbone modification has a greater effect on the polymerase reaction when it is adjacent to the 3'-end of a primer as the elongation terminus than when it is on the template, as well as in base or sugar modification; (iii) although the modified linker in the modified DNA template is passed beyond by the polymerase, it still affects the extension reaction several bases downstream from its location; (iv) the modified linker in the template, in some cases, also affects the extension reaction upstream from its location; (v) further improvement of the chemical structure is required for dinucleotide-mimic incorporation. PMID:19427792

Kuwahara, Masayasu; Takeshima, Hidetoshi; Nagashima, Jun-ichi; Minezaki, Satoshi; Ozaki, Hiroaki; Sawai, Hiroaki

2009-06-01

343

Localization of electrons in the sugar/phosphate backbone in DNA investigated via resonant Auger decay spectra  

SciTech Connect

In order to elucidate the localized nature of electrons in sugar/phosphate backbone in DNA molecules, resonant Auger decay spectra excited by soft x-rays around the inner-shell ionization thresholds have been measured for single-strand DNA. The systems investigated are thin films of DNA as well as related phosphorus compounds such as nucleotide (adenosine triphosphate, ATP), sodium phosphate, and indium phosphide. For ATP and DNA, it was observed that the resonant excitations from P 1s to valence unoccupied {pi}* orbitals are followed by spectator-type Auger decays where the excited electrons remain in valence orbitals during the core-hole decays. It was also found that the energy of the P KL{sub 2,3}L{sub 2,3} (2p{sup -1}{center_dot}{pi}*) spectator Auger peak shifts linearly with the photon energy due to the resonant Auger Raman scattering. Most of the decay channel at the core-to-valence resonant excitation is spectator-type Auger decay in DNA, which is quite different from the Auger decay processes in metallic and semiconducting materials. We conclude that the excited electrons in valence unoccupied states around the phosphates in DNA molecules are strongly localized, resulting in the insulating properties in a one-dimensional direction along sugar/phosphate backbone.

Baba, Yuji; Sekiguchi, Tetsuhiro; Shimoyama, Iwao; Hirao, Norie [Japan Atomic Energy Agency, Tokai-mura, Naka-gun, Ibaraki-ken, 319-1195 (Japan); Nath, Krishna G. [INRS-EMT, University of Quebec, 1650 Boul. Lionel Boulet, Varennes, QC, J3X 1S2 (Canada)

2006-11-15

344

Localization of electrons in the sugar/phosphate backbone in DNA investigated via resonant Auger decay spectra  

NASA Astrophysics Data System (ADS)

In order to elucidate the localized nature of electrons in sugar/phosphate backbone in DNA molecules, resonant Auger decay spectra excited by soft x-rays around the inner-shell ionization thresholds have been measured for single-strand DNA. The systems investigated are thin films of DNA as well as related phosphorus compounds such as nucleotide (adenosine triphosphate, ATP), sodium phosphate, and indium phosphide. For ATP and DNA, it was observed that the resonant excitations from P 1s to valence unoccupied ?* orbitals are followed by spectator-type Auger decays where the excited electrons remain in valence orbitals during the core-hole decays. It was also found that the energy of the P KL2,3L2,3 (2p-1•?*) spectator Auger peak shifts linearly with the photon energy due to the resonant Auger Raman scattering. Most of the decay channel at the core-to-valence resonant excitation is spectator-type Auger decay in DNA, which is quite different from the Auger decay processes in metallic and semiconducting materials. We conclude that the excited electrons in valence unoccupied states around the phosphates in DNA molecules are strongly localized, resulting in the insulating properties in a one-dimensional direction along sugar/phosphate backbone.

Baba, Yuji; Sekiguchi, Tetsuhiro; Shimoyama, Iwao; Hirao, Norie; Nath, Krishna G.

2006-11-01

345

Effect of distribution of stickers along backbone on temperature-dependent structural properties in associative polymer solutions  

E-print Network

Effect of distribution of stickers along the backbone on structural properties in associating polymer solutions is studied using self-consistent field lattice model. Only two inhomogeneous morphologies, i.e., microfluctuation homogenous (MFH) and micelle morphologies, are observed. If the system is cooled, the solvent content within the aggregates decreases. When the spacing of stickers along the backbone is increased the temperature-dependent range of aggregation in MFH morphology and half-width of specific heat peak for homogenous solutions-MFH transition increase, and the symmetry of the peak decreases. However, with increasing spacing of stickers, the above three corresponding quantities related to micelles behave differently. It is demonstrated that the broad nature of the observed transitions can be ascribed to the structural changes which accompany the replacement of solvents in aggregates by polymer, which is consistent with the experimental conclusion. It is found that different effect of spacing of stickers on the two transitions can be interpreted in terms of intrachain and interchain associations.

X. -G. Han; X. -F. Zhang; Y. -H. Ma

2012-10-05

346

Metal coordination architectures of triazole-based ligands: Effect of the backbone of bridging ligands on the construction of polymers  

NASA Astrophysics Data System (ADS)

In our efforts to investigate the influence of the backbone of different triazole-based bridging ligands on the structure of their metal complexes, four new coordination polymers, {[Cu(L1)2(H2O)2]Cl2}n (1), [Cu(L2)2Cl2]n (2), [Co(L2)2(SCN)2]n (3), and [Cu(L3)2(NO3)2]n (4), (L1 = 1,2-bis(triazol-1-ylmethyl)benzene, L2 = 1,3-bis(triazol-1-ylmethyl)benzene, L3 = 1,4-bis(triazol-1-ylmethyl)benzene), have been synthesized. All the complexes have been structurally characterized by IR, elemental analysis and single-crystal X-ray diffraction. Structural analyses show that 1 and 4 possess 2D coordination networks with (4,4) topology, and 1 shows a diagonal-diagonal inclined interpenetration. 2 and 3 are isostructural and feature 1D double chain, which further connected by C-H···Cl or ?···? weak interactions to form 2D supramolecular frameworks. The results show that the structures of ligands (with different non-coordination backbone spacers) play important roles in the formation of such coordination architectures. Furthermore, EPR (Electron Paramagnetic Resonance) spectra of CuII complexes (1, 2, and 4) have been investigated in the solid state at room temperature.

Du, Jian-Long; Hu, Tong-Liang; Bu, Xian-He

2012-04-01

347

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

348

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

349

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

350

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

351

Solid state nuclear magnetic resonance investigation of polymer backbone dynamics in poly(ethylene oxide) based lithium and sodium polyether-ester-sulfonate ionomers.  

PubMed

Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (T(g)) have been investigated using solid-state nuclear magnetic resonance. Experiments detecting (13)C with (1)H 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) (1)H-(13)C 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 (1)H spin-lattice relaxation rate measurements. Previous (1)H and (7)Li 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 (13)C linewidths were used to both qualitatively and quantitatively examine the effects of cation content and identity on PEO spacer mobility. Variable contact time (1)H-(13)C 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 (1)H to (13)C nuclei, becomes similar for T?1.1 T(g) 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. PMID:23697441

Roach, David J; Dou, Shichen; Colby, Ralph H; Mueller, Karl T

2013-05-21

352

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

353

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

354

Simulating Microfracture In Metal-Matrix Composites  

NASA Technical Reports Server (NTRS)

Computational procedures developed for simulating microfracture in metal-matrix/fiber composite materials under mechanical and/or thermal loads at ambient and high temperatures. Procedures evaluate microfracture behavior of composites, establish hierarchies and sequences of fracture modes, and examine influences of compliant layers and partial debonding on properties of composites and on initiation of microfractures in them.

Mital, Subodh K.; Chamis, Christos C.; Gotsis, Pascal K.

1994-01-01

355

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

356

Full genome characterization of human Rotavirus A strains isolated in Cameroon, 2010-2011: diverse combinations of the G and P genes and lack of reassortment of the backbone genes.  

PubMed

Over the past few years whole genome sequencing of rotaviruses has become a routine laboratory method in many strain surveillance studies. To study the molecular evolutionary pattern of representative Cameroonian Rotavirus A (RVA) strains, the semiconductor sequencing approach was used following random amplification of genomic RNA. In total, 31 RVA strains collected during 2010-2011 in three Cameroonian study sites located 120 to 1240 km from each other were sequenced and analyzed. Sequence analysis of the randomly selected representative strains showed that 18 RVAs were Wa-like, expressing G1P[6], G12P[6], or G12P[8] neutralization antigens on the genotype 1 genomic constellation (I1-R1-C1-M1-A1-N1-T1-E1-H1), whereas 13 other strains were DS-1-like, expressing G2P[4], G2P[6], G3P[6], and G6P[6] on the genotype 2 genomic constellation (I2-R2-C2-M2-A2-N2-T2-E2-H2). No inter-genogroup reassortment in the backbone genes was observed. Phylogenetic analysis of the Cameroonian G6P[6] strains indicated the separation of the strains identified in the Far North region (Maroua) and the Northwest region (Bamenda and Esu) into two branches that is consistent with multiple introductions of G6P[6] strains into this country. The present whole genome based molecular characterization study indicates that the emerging G6P[6] strain is fully heterotypic to Rotarix, the vaccine introduced during 2014 in childhood immunization program in Cameroon. Continuous strain monitoring is therefore needed in this area and elsewhere to see if G6s, besides genotype G1 to G4, G8, G9 and G12, may become a new, regionally important genotype in the post vaccine licensure era in Africa. PMID:25460824

Ndze, Valentine Ngum; Esona, Mathew Dioh; Achidi, Eric Akum; Gonsu, Kamga Hortense; Dóró, Renáta; Marton, Szilvia; Farkas, Szilvia; Ngeng, Marxcel Bong; Ngu, Akum Felix; Obama-Abena, Marie Therese; Bányai, Krisztián

2014-12-01

357

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

358

Backbone and side-chain ¹H, ¹?N and ¹³C assignments of mouse peptide ESP4.  

PubMed

A peptide or a small protein released from an exocrine gland or in urine is utilized as a chemosignal that elicits social or reproductive behavior in mice. Recently, we identified the male-specific peptide, exocrine gland-secreting peptide 1 (ESP1), in mouse tear fluids that enhanced female sexual receptive behavior, and determined the three dimensional structure. ESP1 appears to be a member of multigene family that consists of 38 genes in mice, which we call the ESP family. ESP4, a member of the ESP family, is expressed in various exocrine glands, and shows the highest sequence similarity with ESP1. Here, we report the NMR assignments of ESP4 which provides a basis for NMR analyses of this protein. Our results will give insight into structural relationships within the ESP family. PMID:23179060

Taniguchi, Masahiro; Yoshinaga, Sosuke; Haga-Yamanaka, Sachiko; Touhara, Kazushige; Terasawa, Hiroaki

2014-04-01

359

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

360

Qualifying high-throughput immune repertoire sequencing.  

PubMed

Diversity of B and T cell receptors, achieved by gene recombination and somatic hypermutation, allows the immune system for recognition and targeted reaction against various threats. Next-generation sequencing for assessment of a cell's gene composition and variation makes deep analysis of one individual's immune spectrum feasible. An easy to apply but detailed analysis and visualization strategy is necessary to process all sequences generated. We performed sequencing utilizing the 454 system for CLL and control samples, utilized the IMGT database and applied the presented analysis tools. With the applied protocol, malignant clones are found and characterized, mutational status compared to germline identity is elaborated in detail showing that the CLL mutation status is not as monoclonal as generally thought. On the other hand, this strategy is not solely applicable to the 454 sequencing system but can easily be transferred to any other next-generation sequencing platform. PMID:24607567

Niklas, Norbert; Pröll, Johannes; Weinberger, Johannes; Zopf, Agnes; Wiesinger, Karin; Krismer, Konstantin; Bettelheim, Peter; Gabriel, Christian

2014-01-01

361

Electrochemical biosensor based on functional composite nanofibers for detection of K-ras gene via multiple signal amplification strategy.  

PubMed

An electrochemical biosensor based on functional composite nanofibers for hybridization detection of specific K-ras gene that is highly associated with colorectal cancer via multiple signal amplification strategy has been developed. The carboxylated multiwalled carbon nanotubes (MWCNTs) doped nylon 6 (PA6) composite nanofibers (MWCNTs-PA6) was prepared using electrospinning, which served as the nanosized backbone for thionine (TH) electropolymerization. The functional composite nanofibers [MWCNTs-PA6-PTH, where PTH is poly(thionine)] used as supporting scaffolds for single-stranded DNA1 (ssDNA1) immobilization can dramatically increase the amount of DNA attachment and the hybridization sensitivity. Through the hybridization reaction, a sandwich format of ssDNA1/K-ras gene/gold nanoparticle-labeled ssDNA2 (AuNPs-ssDNA2) was fabricated, and the AuNPs offered excellent electrochemical signal transduction. The signal amplification was further implemented by forming network-like thiocyanuric acid/gold nanoparticles (TA/AuNPs). A significant sensitivity enhancement was obtained; the detection limit was down to 30fM, and the discriminations were up to 54.3 and 51.9% between the K-ras gene and the one-base mismatched sequences including G/C and A/T mismatched bases, respectively. The amenability of this method to the analyses of K-ras gene from the SW480 colorectal cancer cell lysates was demonstrated. The results are basically consistent with those of the K-ras Kit (HRM: high-resolution melt). The method holds promise for the diagnosis and management of cancer. PMID:25173509

Wang, Xiaoying; Shu, Guofang; Gao, Chanchan; Yang, Yu; Xu, Qian; Tang, Meng

2014-12-01

362

Picoeukaryotic sequences in the Sargasso Sea metagenome  

PubMed Central

Background With genome sequencing becoming more and more affordable, environmental shotgun sequencing of the microorganisms present in an environment generates a challenging amount of sequence data for the scientific community. These sequence data enable the diversity of the microbial world and the metabolic pathways within an environment to be investigated, a previously unthinkable achievement when using traditional approaches. DNA sequence data assembled from extracts of 0.8 ?m filtered Sargasso seawater unveiled an unprecedented glimpse of marine prokaryotic diversity and gene content. Serendipitously, many sequences representing picoeukaryotes (cell size <2 ?m) were also present within this dataset. We investigated the picoeukaryotic diversity of this database by searching sequences containing homologs of eight nuclear anchor genes that are well conserved throughout the eukaryotic lineage, as well as one chloroplastic and one mitochondrial gene. Results We found up to 41 distinct eukaryotic scaffolds, with a broad phylogenetic spread on the eukaryotic tree of life. The average eukaryotic scaffold size is 2,909 bp, with one gap every 1,253 bp. Strikingly, the AT frequency of the eukaryotic sequences (51.4%) is significantly lower than the average AT frequency of the metagenome (61.4%). This represents 4% to 18% of the estimated prokaryotic diversity, depending on the average prokaryotic versus eukaryotic genome size ratio. Conclusion Despite similar cell size, eukaryotic sequences of the Sargasso Sea metagenome have higher GC content, suggesting that different environmental pressures affect the evolution of their base composition. PMID:18179699

Piganeau, Gwenael; Desdevises, Yves; Derelle, Evelyne; Moreau, Herve

2008-01-01

363

Backbone and side chain 1H, 13C and 15N resonance assignments of the catalytic domain of diphtheria toxin.  

PubMed

Diphtheria is a serious upper respiratory tract disease caused by the diphtheria toxin (DT) secreted from the bacteria Corynebacterium diphtheriae. Vaccination is the best way to protect against this infectious disease. Diphtheria vaccines are prepared by isolating, purifying and chemically deactivating DT. Although toxoids have been used for decades in immunization, there is still little understanding at the molecular level of the process of toxoid preparation, and how chemical treatment enhances their immunogenicity. We have undertaken an NMR study of the catalytic domain as a first step in understanding the molecular details involved in vaccine antigen preparation. Here we report a near complete assignment for the backbone and side chain resonances of the diphtheria toxin catalytic domain. PMID:22205447

Sauvé, Simon; Gingras, Geneviève; Aubin, Yves

2012-10-01

364

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

365

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

366

Access to c? backbone dynamics of biological solids by (13)c t1 relaxation and molecular dynamics simulation.  

PubMed

We introduce a labeling scheme for magic angle spinning (MAS) solid-state NMR that is based on deuteration in combination with dilution of the carbon spin system. The labeling strategy achieves spectral editing by simplification of the H?C? and aliphatic side chain spectral region. A reduction in both proton and carbon spin density in combination with fast spinning (?50 kHz) is essential to retrieve artifact-free (13)C-R1 relaxation data for aliphatic carbons. We obtain good agreement between the NMR experimental data and order parameters extracted from a molecular dynamics (MD) trajectory, which indicates that carbon based relaxation parameters can yield complementary information on protein backbone as well as side chain dynamics. PMID:25564702

Asami, Sam; Porter, Justin R; Lange, Oliver F; Reif, Bernd

2015-01-28

367

A synthetic zipper peptide motif orchestrated via co-operative interplay of hydrogen bonding, aromatic stacking, and backbone chirality.  

PubMed

Here, we report on a new class of synthetic zipper peptide which assumes its three-dimensional zipper-like structure via a co-operative interplay of hydrogen bonding, aromatic stacking, and backbone chirality. Structural studies carried out in both solid- and solution-state confirmed the zipper-like structural architecture assumed by the synthetic peptide which makes use of unusually remote inter-residual hydrogen-bonding and aromatic stacking interactions to attain its shape. The effect of chirality modulation and the extent of noncovalent forces in the structure stabilization have also been comprehensively explored via single-crystal X-ray diffraction and solution-state NMR studies. The results highlight the utility of noncovalent forces in engineering complex synthetic molecules with intriguing structural architectures. PMID:23865816

Nair, Roshna V; Kheria, Sanjeev; Rayavarapu, Suresh; Kotmale, Amol S; Jagadeesh, Bharatam; Gonnade, Rajesh G; Puranik, Vedavati G; Rajamohanan, Pattuparambil R; Sanjayan, Gangadhar J

2013-08-01

368

The role of proline and glycine in determining the backbone flexibility of a channel-forming peptide.  

PubMed

Alamethicin is a helical 20-amino acid voltage-gated channel-forming peptide, which is known to exhibit segmental flexibility in solution along its backbone near alpha-methylalanine (MeA)-10 and Gly-11. In an alpha-helical configuration, MeA at position 10 would normally hydrogen-bond with position 14, but the presence of proline at this position prevents the formation of this interhelical hydrogen bond. To determine whether the presence of proline at position 14 contributes to the flexibility of this helix, two analogs of alamethicin were synthesized, one with proline 14 replaced by alanine and another with both proline 14 and glycine 11 replaced by alanine. The C-termini of these peptides were derivatized with a proxyl nitroxide, and paramagnetic enhancements produced by the nitroxide on the Calpha protons were used to estimate r-6 weighted distances between the nitroxide and the backbone protons. When compared to native alamethicin, the analog lacking proline 14 exhibited similar C-terminal to Calpha proton distances, indicating that substitution of proline alone does not alter the flexibility of this helix; however, the subsequent removal of glycine 11 resulted in a significant increase in the averaged distances between the C- and N-termini. Thus, the G-X-X-P motif found in alamethicin appears to be largely responsible for mediating high-amplitude bending motions that have been observed in the central helical domain of alamethicin in methanol. To determine whether these substitutions alter the channel behavior of alamethicin, the macroscopic and single-channel currents produced by these analogs were compared. Although the substitution of the G-X-X-P motif produces channels with altered characteristics, this motif is not essential to achieve voltage-dependent gating or alamethicin-like behavior. PMID:10049319

Jacob, J; Duclohier, H; Cafiso, D S

1999-03-01

369

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs  

PubMed Central

Background We introduce Sequence Bundles--a novel data visualisation method for representing multiple sequence alignments (MSAs). We identify and address key limitations of the existing bioinformatics data visualisation methods (i.e. the Sequence Logo) by enabling Sequence Bundles to give salient visual expression to sequence motifs and other data features, which would otherwise remain hidden. Methods For the development of Sequence Bundles we employed research-led information design methodologies. Sequences are encoded as uninterrupted, semi-opaque lines plotted on a 2-dimensional reconfigurable grid. Each line represents a single sequence. The thickness and opacity of the stack at each residue in each position indicates the level of conservation and the lines' curved paths expose patterns in correlation and functionality. Several MSAs can be visualised in a composite image. The Sequence Bundles method is designed to favour a tangible, continuous and intuitive display of information. Results We have developed a software demonstration application for generating a Sequence Bundles visualisation of MSAs provided for the BioVis 2013 redesign contest. A subsequent exploration of the visualised line patterns allowed for the discovery of a number of interesting features in the dataset. Reported features include the extreme conservation of sequences displaying a specific residue and bifurcations of the consensus sequence. Conclusions Sequence Bundles is a novel method for visualisation of MSAs and the discovery of sequence motifs. It can aid in generating new insight and hypothesis making. Sequence Bundles is well disposed for future implementation as an interactive visual analytics software, which can complement existing visualisation tools. PMID:25237395

2014-01-01

370

Ignimbrite sequence on Gran Canaria  

Microsoft Academic Search

The Miocene sequence of felsic extrusive rocks of about 1000 m total thickness on Gran Canaria is divided into three units:\\u000a \\u000a \\u000a a) \\u000a \\u000a A lower unit of trachytic rhyolites (lavas, composite flows, ignimbrites) characterized by a phenocryst assemblage of anorthoclase\\u000a (Or15–20, wt%), clinopyroxene, hypersthene (amphibole substituted for both in ignimbrites), and Fe\\/Ti-oxides. The commonest groundmass\\u000a minerals are anorthoclase and alkali-amphibole, with

H. U. Schmincke

1969-01-01

371

The structure of a novel neutral lipid A from the lipopolysaccharide of Bradyrhizobium elkanii containing three mannose units in the backbone.  

PubMed

The chemical structure of the lipid A of the lipopolysaccharide (LPS) from Bradyrhizobium elkanii USDA 76 (a member of the group of slow-growing rhizobia) has been established. It differed considerably from lipids A of other Gram-negative bacteria, in that it completely lacks negatively charged groups (phosphate or uronic acid residues); the glucosamine (GlcpN) disaccharide backbone is replaced by one consisting of 2,3-dideoxy-2,3-diamino-D-glucopyranose (GlcpN3N) and it contains two long-chain fatty acids, which is unusual among rhizobia. The GlcpN3N disaccharide was further substituted by three D-mannopyranose (D-Manp) residues, together forming a pentasaccharide. To establish the structural details of this molecule, 1D and 2D NMR spectroscopy, chemical composition analyses and high-resolution mass spectrometry methods (electrospray ionisation Fourier-transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) and tandem mass spectrometry (MS/MS)) were applied. By using 1D and 2D NMR spectroscopy experiments, it was confirmed that one D-Manp was linked to C-1 of the reducing GlcpN3N and an alpha-(1-->6)-linked D-Manp disaccharide was located at C-4' of the non-reducing GlcpN3N (alpha-linkage). Fatty acid analysis identified 12:0(3-OH) and 14:0(3-OH), which were amide-linked to GlcpN3N. Other lipid A constituents were long (omega-1)-hydroxylated fatty acids with 26-33 carbon atoms, as well as their oxo forms (28:0(27-oxo) and 30:0(29-oxo)). The 28:0(27-OH) was the most abundant acyl residue. As confirmed by high-resolution mass spectrometry techniques, these long-chain fatty acids created two acyloxyacyl residues with the 3-hydroxy fatty acids. Thus, lipid A from B. elkanii comprised six acyl residues. It was also shown that one of the acyloxyacyl residues could be further acylated by 3-hydroxybutyric acid (linked to the (omega-1)-hydroxy group). PMID:20087912

Komaniecka, Iwona; Choma, Adam; Lindner, Buko; Holst, Otto

2010-03-01

372

1 H, 13 C and 15 N backbone assignments for the ligand binding domain of the Pseudomonas aeruginosa virulence regulator LasR  

Microsoft Academic Search

LasR regulates toxin production in Pseudomonas aeruginosa and its inhibition can attenuate the virulence of this opportunistic human pathogen. To aid studies of interactions with\\u000a inhibitors, we report the NMR backbone assignments for the dimeric LasR ligand-binding domain.

Matthew James Bottomley; Ester Muraglia; Renzo Bazzo

2007-01-01

373

Backbone and side-chain assignment of the lipidated and non-lipidated forms of the meningococcal outer membrane protein LP2086.  

PubMed

LP2086 is a lipidated outer membrane protein from Neisseria meningitidis that elicits bactericidal antibodies and represents a promising vaccine candidate against meningococcal infections. Here we report the backbone and side-chain assignment for two forms of LP2086: non-lipidated in aqueous buffer and the lipidated protein in micellar solution. PMID:19636959

Mascioni, A; Jacob, J; Moy, F; Dilts, D; Fink, P; Malakian, K; Sigethy, S; Wen, Y; Novikova, E; Zlotnick, G W; Tsao, D H H

2009-06-01

374

1 H, 13 C, 15 N backbone and side-chain resonance assignments of the Bright\\/ARID domain from the human histone demethylase JARID1B  

Microsoft Academic Search

We report backbone and side-chain resonance assignments of the Bright\\/ARID domain from the human JARID1B protein. These assignments\\u000a provide a basis for the detailed structural investigation of the interaction between DNA and ARID domains.

Wenming Yao; Yu Peng; Qun Chen; Donghai Lin

2009-01-01

375

Backbone assignments of the 26 kDa neuron-specific ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1)  

E-print Network

of Parkinson's disease. Herein, we present the NMR backbone assignments of human UCH-L1, thus enabling future De-ubiquitination Á Ubiquitin C-terminal hydrolase Á Knotted proteins Á Parkinson's disease with Parkinson's disease (PD) (the UCH-L1 gene is also referred to as PARK5). The I93 M mutation has been

Jackson, Sophie

376

DNA Microarray Profiling of a Diverse Collection of Nosocomial Methicillin-Resistant Staphylococcus aureus Isolates Assigns the Majority to the Correct Sequence Type and Staphylococcal Cassette Chromosome mec (SCCmec) Type and Results in the Subsequent Identification and Characterization of Novel SCCmec-SCCM1 Composite Islands  

PubMed Central

One hundred seventy-five isolates representative of methicillin-resistant Staphylococcus aureus (MRSA) clones that predominated in Irish hospitals between 1971 and 2004 and that previously underwent multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) typing were characterized by spa typing (175 isolates) and DNA microarray profiling (107 isolates). The isolates belonged to 26 sequence type (ST)-SCCmec types and subtypes and 35 spa types. The array assigned all isolates to the correct MLST clonal complex (CC), and 94% (100/107) were assigned an ST, with 98% (98/100) correlating with MLST. The array assigned all isolates to the correct SCCmec type, but subtyping of only some SCCmec elements was possible. Additional SCCmec/SCC genes or DNA sequence variation not detected by SCCmec typing was detected by array profiling, including the SCC-fusidic acid resistance determinant Q6GD50/fusC. Novel SCCmec/SCC composite islands (CIs) were detected among CC8 isolates and comprised SCCmec IIA-IIE, IVE, IVF, or IVg and a ccrAB4-SCC element with 99% DNA sequence identity to SCCM1 from ST8/t024-MRSA, SCCmec VIII, and SCC-CI in Staphylococcus epidermidis. The array showed that the majority of isolates harbored one or more superantigen (94%; 100/107) and immune evasion cluster (91%; 97/107) genes. Apart from fusidic acid and trimethoprim resistance, the correlation between isolate antimicrobial resistance phenotype and the presence of specific resistance genes was ?97%. Array profiling allowed high-throughput, accurate assignment of MRSA to CCs/STs and SCCmec types and provided further evidence of the diversity of SCCmec/SCC. In most cases, array profiling can accurately predict the resistance phenotype of an isolate. PMID:22869569

Brennan, Orla M.; Deasy, Emily C.; Rossney, Angela S.; Kinnevey, Peter M.; Ehricht, Ralf; Monecke, Stefan; Coleman, David C.

2012-01-01

377

The Connell Sum Sequence  

NASA Astrophysics Data System (ADS)

The Connell sum sequence refers to the partial sums of the Connell sequence. In this paper, the Connell sequence, Connell sum sequence and generalizations from Iannucci and Mills-Taylor are interpreted as sums of elements of triangles, relating them to polygonal number-stuttered arithmetic progressions. The n-th element of the Connell sum sequence is established as a sharp upper bound for the value of a gamma-labeling of a graph of size n. The limiting behavior and a explicit formula for the Connell (m,r)-sum sequence are also given.

Bullington, Grady D.

2007-01-01

378

Bonobos extract meaning from call sequences.  

PubMed

Studies on language-trained bonobos have revealed their remarkable abilities in representational and communication tasks. Surprisingly, however, corresponding research into their natural communication has largely been neglected. We address this issue with a first playback study on the natural vocal behaviour of bonobos. Bonobos produce five acoustically distinct call types when finding food, which they regularly mix together into longer call sequences. We found that individual call types were relatively poor indicators of food quality, while context specificity was much greater at the call sequence level. We therefore investigated whether receivers could extract meaning about the quality of food encountered by the caller by integrating across different call sequences. We first trained four captive individuals to find two types of foods, kiwi (preferred) and apples (less preferred) at two different locations. We then conducted naturalistic playback experiments during which we broadcasted sequences of four calls, originally produced by a familiar individual responding to either kiwi or apples. All sequences contained the same number of calls but varied in the composition of call types. Following playbacks, we found that subjects devoted significantly more search effort to the field indicated by the call sequence. Rather than attending to individual calls, bonobos attended to the entire sequences to make inferences about the food encountered by a caller. These results provide the first empirical evidence that bonobos are able to extract information about external events by attending to vocal sequences of other individuals and highlight the importance of call combinations in their natural communication system. PMID:21556149

Clay, Zanna; Zuberbühler, Klaus

2011-01-01

379

Bonobos Extract Meaning from Call Sequences  

PubMed Central

Studies on language-trained bonobos have revealed their remarkable abilities in representational and communication tasks. Surprisingly, however, corresponding research into their natural communication has largely been neglected. We address this issue with a first playback study on the natural vocal behaviour of bonobos. Bonobos produce five acoustically distinct call types when finding food, which they regularly mix together into longer call sequences. We found that individual call types were relatively poor indicators of food quality, while context specificity was much greater at the call sequence level. We therefore investigated whether receivers could extract meaning about the quality of food encountered by the caller by integrating across different call sequences. We first trained four captive individuals to find two types of foods, kiwi (preferred) and apples (less preferred) at two different locations. We then conducted naturalistic playback experiments during which we broadcasted sequences of four calls, originally produced by a familiar individual responding to either kiwi or apples. All sequences contained the same number of calls but varied in the composition of call types. Following playbacks, we found that subjects devoted significantly more search effort to the field indicated by the call sequence. Rather than attending to individual calls, bonobos attended to the entire sequences to make inferences about the food encountered by a caller. These results provide the first empirical evidence that bonobos are able to extract information about external events by attending to vocal sequences of other individuals and highlight the importance of call combinations in their natural communication system. PMID:21556149

Clay, Zanna; Zuberbühler, Klaus

2011-01-01

380

Composite solders  

Microsoft Academic Search

The characterization of composite solders has been performed, specifically on tin\\/lead\\/Cu6Sn5 composition. This characterization includes both microstructural and mechanical analysis. Scanning electron microscope (SEM) characterization of cross sections of the composite solder was preferred over optical inspection, owing to the similar appearance of the Sn and Cu6Sn5 phases by the latter method. The mechanical properties of composites were examined and

James L. Marshall; Jose Calderon; Jennifer Sees; George Lucey; Jennie S. Hwang

1991-01-01

381

DNA sequencing conference, 2  

SciTech Connect

This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

1991-06-19

382

Cellulases and coding sequences  

DOEpatents

The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

Li, Xin-Liang (Athens, GA); Ljungdahl, Lars G. (Athens, GA); Chen, Huizhong (Lawrenceville, GA)

2001-02-20

383

Cellulases and coding sequences  

DOEpatents

The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

Li, Xin-Liang (Athens, GA); Ljungdahl, Lars G. (Athens, GA); Chen, Huizhong (Lawrenceville, GA)

2001-01-01

384

Sequence information signal processor  

DOEpatents

An electronic circuit is used to compare two sequences, such as genetic sequences, to determine which alignment of the sequences produces the greatest similarity. The circuit includes a linear array of series-connected processors, each of which stores a single element from one of the sequences and compares that element with each successive element in the other sequence. For each comparison, the processor generates a scoring parameter that indicates which segment ending at those two elements produces the greatest degree of similarity between the sequences. The processor uses the scoring parameter to generate a similar scoring parameter for a comparison between the stored element and the next successive element from the other sequence. The processor also delivers the scoring parameter to the next processor in the array for use in generating a similar scoring parameter for another pair of elements. The electronic circuit determines which processor and alignment of the sequences produce the scoring parameter with the highest value.

Peterson, John C. (Alta Loma, CA); Chow, Edward T. (San Dimas, CA); Waterman, Michael S. (Culver City, CA); Hunkapillar, Timothy J. (Pasadena, CA)

1999-01-01

385

Roles of repetitive sequences  

SciTech Connect

The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

Bell, G.I.

1991-12-31

386

Roles of repetitive sequences  

SciTech Connect

The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

Bell, G.I.

1991-01-01

387

Sequencing with graphene pores  

NASA Astrophysics Data System (ADS)

Solid-state nanopores are often used for biomolecular analysis, but have so far been unable to sequence DNA. Marija Drndi? asks whether nanopores made in graphene could fulfil all of the requirements needed for sequencing.

Drndi?, Marija

2014-10-01

388

Asphaltic compositions  

SciTech Connect

This patent describes an asphaltic composition of enhanced utility for vehicular pavement which composition comprises a road paving grade of asphalt in admixture with at least one alkylene dithiocarbamate. The composition is characterized by having a reduced increase in absolute viscosity to original absolute viscosity after thin film aging as measured by ASTM Test D 1754 at 140/sup 0/F.

Wright, W.E.; Zaweski, E.F.

1987-02-24

389

Schur monotone decreasing sequences  

NASA Astrophysics Data System (ADS)

In this paper, we introduce Schur monotone decreasing sequences in an n-dimensional space by considering a majorization pre-order. By means of down arrow mappings, we study omega limiting points of bounded Schur monotone decreasing sequences. We provide convergence criteria for such kinds of sequences. We prove that a Cesaro mean (or an arithmetic mean) of any bounded Schur monotone decreasing sequences converges to a unique limiting point.

Ganikhodjaev, Rasul; Saburov, Mansoor; Saburov, Khikmat

2013-09-01

390

The DynaMine webserver: predicting protein dynamics from sequence  

PubMed Central

Protein dynamics are important for understanding protein function. Unfortunately, accurate protein dynamics information is difficult to obtain: here we present the DynaMine webserver, which provides predictions for the fast backbone movements of proteins directly from their amino-acid sequence. DynaMine rapidly produces a profile describing the statistical potential for such movements at residue-level resolution. The predicted values have meaning on an absolute scale and go beyond the traditional binary classification of residues as ordered or disordered, thus allowing for direct dynamics comparisons between protein regions. Through this webserver, we provide molecular biologists with an efficient and easy to use tool for predicting the dynamical characteristics of any protein of interest, even in the absence of experimental observations. The prediction results are visualized and can be directly downloaded. The DynaMine webserver, including instructive examples describing the meaning of the profiles, is available at http://dynamine.ibsquare.be. PMID:24728994

Cilia, Elisa; Pancsa, Rita; Tompa, Peter; Lenaerts, Tom; Vranken, Wim F.

2014-01-01

391

Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences  

E-print Network

Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences Roman R. Stocsits 1 , Ivo L sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however

Stadler, Peter F.

392

Career Academy Course Sequences.  

ERIC Educational Resources Information Center

This career academy course sequence guide is designed to give teachers a quick overview of the course sequences of well-known career academy and career pathway programs from across the country. The guide presents a variety of sample course sequences for the following academy themes: (1) arts and communication; (2) business and finance; (3)…

Markham, Thom; Lenz, Robert

393

Effects of intermolecular forces and backbone architecture on the phase behavior of fluorocopolymer-supercritical fluid mixtures  

NASA Astrophysics Data System (ADS)

The impact of polymer backbone architecture on fluorocopolymer solubility in supercritical fluid (SCF) solvents is studied by systematically varying the chemical type of the repeat units in the main chain. The fluorocopolymers investigated include nonpolar copolymers of tetrafluoroethylene with 19 mol% hexafluoropropylene (FEPsb{19}) and 48 mol% hexafluoropropylene (FEPsb{48}) and a polar copolymer of vinylidene fluoride with 22 mol% hexafluoropropylene (Fluorelsp°ler ). The solvents are methodically varied from nonpolar perfluoroalkanes and SFsb6 to polar fluorocarbons and COsb2. Low molecular weight solvents are used to facilitate in interpreting the intermolecular forces that control fluorocopolymer solubility, although pressures in excess of 2,500 bar are sometimes needed to dissolve the fluorocopolymers in these simple solvents. Polarity effects, which vary inversely with temperature, are moderated by operating over a large temperature range from 0 to 300sp° C. A variable-volume view cell, capable of operating to high temperatures and high pressures, was designed and implemented to meet these extreme operating conditions. Increasing the polarizability of nonpolar solvents reduces the pressures required to dissolve FEPsb{19} by as much as 1,500 bar going from perfluoromethane to perfluoropropane. However, in polar solvents, the pressures required for FEPsb{19} solubility rise dramatically as the temperature is decreased due to the increase in polar, solvent-solvent interactions that do not favor the solubility of a nonpolar copolymer. Replacing semi-crystalline FEPsb{19} with amorphous FEPsb{48} yields the same trends in phase behavior. Therefore, crystallinity does not control the shape of these fluorocopolymer-SCF cloud-point curves. Adding a cosolvent to the solution can dramatically lower the pressures needed to dissolve the copolymer. Introducing the "cosolvent" directly into the polymer backbone by changing copolymer architecture is another method of modifying fluorocopolymer solubility as seen with the results for Fluorel-SCF mixtures compared to those for FEPsb{19}-SCF mixtures. A supercritical fractionation of FEPsb{19} provides information on the impact of molecular weight and end-group content on fluorocopolymer solubility. Challenges remain for modeling fluorocopolymer-solvent mixtures. The Sanchez-Lacombe equation cannot capture the characteristics of FEPsb{19}-SCF solvent phase behavior unless two empirical mixture parameters, one of which varies with temperature, are used.

Mertdogan, Cynthia Asli

394

Peptide backbone orientation and dynamics in spider dragline silk and two-photon excitation in nuclear magnetic and quadrupole resonance  

NASA Astrophysics Data System (ADS)

In the first part of the dissertation, spider dragline silk is studied by solid state NMR techniques. The dependence of NMR frequency on molecular orientation is exploited using the DECODER experiment to determine the orientation of the protein backbone within the silk fibre. Practical experimental considerations require that the silk fibres be wound about a cylindrical axis perpendicular to the external magnetic field, complicating the reconstruction of the underlying orientation distribution and necess-itating the development of numerical techniques for this purpose. A two-component model of silk incorporating static b-sheets and polyglycine II helices adequately fits the NMR data and suggests that the b-sheets are well aligned along the silk axis (20 FWHM) while the helices are poorly aligned (68 FWHM). The effects of fibre strain, draw rate and hydration on orientation are measured. Measurements of the time-scale for peptide backbone motion indicate that when wet, a strain-dependent frac-tion of the poorly aligned component becomes mobile. This suggests a mechanism for the supercontraction of silk involving latent entropic springs that undergo a local strain-dependent phase transition, driving supercontraction. In the second part of this dissertation a novel method is developed for exciting NMR and nuclear quadrupole resonance (NQR) by rf irradiation at multiple frequencies that sum to (or differ by) the resonance frequency. This is fundamentally different than traditional NMR experiments where irradiation is applied on-resonance. With excitation outside the detection bandwidth, two-photon excitation allows for detection of free induction signals during excitation, completely eliminating receiver dead-time. A theoretical approach to describing two-photon excitation is developed based on average Hamiltonian theory. An intuition for two-photon excitation is gained by analogy to the coherent absorption of multiple photons requiring conservation of total energy and momentum. It is shown that two-photon excitation efficiency impro-ves when the two applied rf frequencies deviate from half-resonance. For two-photon NQR, it is shown that observable magnetization appears perpendicular to the excita-tion coil, requiring a second coil for detection, and that double quantum coherences are also generated. Several model systems and experimental geometries are used to demonstrate the peculiarities of two-photon excitation in NMR and NQR.

Eles, Philip Thomas

2005-07-01

395

Sequence finishing and mapping of Drosophila melanogasterheterochromatin  

SciTech Connect

Genome sequences for most metazoans are incomplete due tothe presence of repeated DNA in the pericentromeric heterochromatin. Theheterochromatic regions of D. melanogaster contain 20 Mb of sequenceamenable to mapping, sequence assembly and finishing. Here we describethe generation of 15 Mb of finished or improved heterochromatic sequenceusing available clone resources and assembly and mapping methods. We alsoconstructed a BAC-based physical map that spans approximately 13 Mb ofthe pericentromeric heterochromatin, and a cytogenetic map that positionsapproximately 11 Mb of BAC contigs and sequence scaffolds in specificchromosomal locations. The integrated sequence assembly and maps greatlyimprove our understanding of the structure and composition of this poorlyunderstood fraction of a metazoan genome and provide a framework forfunctional analyses.

Hoskins, Roger A.; Carlson, Joseph W.; Kennedy, Cameron; Acevedo,David; Evans-Holm, Martha; Frise, Erwin; Wan, Kenneth H.; Park, Soo; Mendez-Lago, Maria; Rossi, Fabrizio; Villasante, Alfredo; Dimitri,Patrizio; Karpen, Gary H.; Celniker, Susan E.

2007-06-15

396

Complete Nucleotide Sequence of Two Multidrug-Resistant IncR Plasmids from Klebsiella pneumoniae  

PubMed Central

We report here the complete nucleotide sequence of two IncR replicons encoding multidrug resistance determinants, including ?-lactam (blaDHA-1, blaSHV-12), aminoglycoside (aphA1, strA, strB), and fluoroquinolone (qnrB4, aac6?-1b-cr) resistance genes. The plasmids have backbones that are similar to each other, including the replication and stability systems, and contain a wide variety of transposable elements carrying known antibiotic resistance genes. This study confirms the increasing clinical importance of IncR replicons as resistance gene carriers. PMID:24752259

Compain, Fabrice; Frangeul, Lionel; Drieux, Laurence; Verdet, Charlotte; Brisse, Sylvain; Arlet, Guillaume

2014-01-01

397

Complete nucleotide sequence of two multidrug-resistant IncR plasmids from Klebsiella pneumoniae.  

PubMed

We report here the complete nucleotide sequence of two IncR replicons encoding multidrug resistance determinants, including ?-lactam (blaDHA-1, blaSHV-12), aminoglycoside (aphA1, strA, strB), and fluoroquinolone (qnrB4, aac6'-1b-cr) resistance genes. The plasmids have backbones that are similar to each other, including the replication and stability systems, and contain a wide variety of transposable elements carrying known antibiotic resistance genes. This study confirms the increasing clinical importance of IncR replicons as resistance gene carriers. PMID:24752259

Compain, Fabrice; Frangeul, Lionel; Drieux, Laurence; Verdet, Charlotte; Brisse, Sylvain; Arlet, Guillaume; Decré, Dominique

2014-07-01

398

Methods for making nucleotide probes for sequencing and synthesis  

DOEpatents

Compositions and methods for making a plurality of probes for analyzing a plurality of nucleic acid samples are provided. Compositions and methods for analyzing a plurality of nucleic acid samples to obtain sequence information in each nucleic acid sample are also provided.

Church, George M; Zhang, Kun; Chou, Joseph

2014-07-08

399

DIMACS Technical Report 956 Relation between Protein Structure, Sequence  

E-print Network

. Classification of proteins based on sequence homology and based on amino acid composition were compared and Composition of Amino Acids by Eddy N. Mayoraz 1 RUTCOR--Rutgers University's Center for Operations Research, P residue identity they have a similar fold. This threshold of 50% is usually used as a ``safe definition

400

Computational methods in sequence and structure prediction  

NASA Astrophysics Data System (ADS)

This dissertation is organized into two parts. In the first part, we will discuss three computational methods for cis-regulatory element recognition in three different gene regulatory networks as the following: (a) Using a comprehensive "Phylogenetic Footprinting Comparison" method, we will investigate the promoter sequence structures of three enzymes (PAL, CHS and DFR) that catalyze sequential steps in the pathway from phenylalanine to anthocyanins in plants. Our result shows there exists a putative cis-regulatory element "AC(C/G)TAC(C)" in the upstream of these enzyme genes. We propose this cis-regulatory element to be responsible for the genetic regulation of these three enzymes and this element, might also be the binding site for MYB class transcription factor PAP1. (b) We will investigate the role of the Arabidopsis gene glutamate receptor 1.1 (AtGLR1.1) in C and N metabolism by utilizing the microarray data we obtained from AtGLR1.1 deficient lines (antiAtGLR1.1). We focus our investigation on the putatively co-regulated transcript profile of 876 genes we have collected in antiAtGLR1.1 lines. By (a) scanning the occurrence of several groups of known abscisic acid (ABA) related cisregulatory elements in the upstream regions of 876 Arabidopsis genes; and (b) exhaustive scanning of all possible 6-10 bps motif occurrence in the upstream regions of the same set of genes, we are able to make a quantative estimation on the enrichment level of each of the cis-regulatory element candidates. We finally conclude that one specific cis-regulatory element group, called "ABRE" elements, are statistically highly enriched within the 876-gene group as compared to their occurrence within the genome. (c) We will introduce a new general purpose algorithm, called "fuzzy REDUCE1", which we have developed recently for automated cis-regulatory element identification. In the second part, we will discuss our newly devised protein design framework. With this framework we have developed a software package which is capable of designing novel protein structures at the atomic resolution. This software package allows us to perform protein structure design with a flexible backbone. The backbone flexibility includes loop region relaxation as well as a secondary structure collective mode relaxation scheme. (Abstract shortened by UMI.)

Lang, Caiyi

401

Conformational Analysis of Peptides and Glycopeptides Derived from the Consensus Sequence for ?-O-Glucosylation.  

PubMed

Cys-Xxx-Ser-Xxx-Pro-Cys (Xxx= any amino acid but Pro) is the most common sequence present in naturally occurring peptides and proteins glycosylated with ?-O-glucose (?-O-Glc). Taking into account the lack of studies concerning the spatial disposition of this sequence, we have synthesized and analyzed, in aqueous solution, the conformational behavior of peptides and a glycopeptide derived from the particular fragment Cys-Ala-Ser-Ser-Pro-Cys. This sequence is found in the crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Our studies, based on the use of NOESY experiments in combination with molecular dynamics (MD) simulations, indicate that for this particular fragment, initially characterized by a type I ?-turn motif, the glycosylation with ?-O-Glc forces the peptide backbone into an extended conformation. This conformation is stabilized by the presence of both hydrogen bonds and water pockets between the peptide and the sugar moieties. PMID:25515748

Somovilla, Victor J; Martinez-Saez, Nuria; Fernandez-Tejada, Alberto; de la Torre, Beatriz G; Andreu, David; Jimenez-Barbero, Jesus; L Asensio, Juan; Avenoza, Alberto; Busto, Jesus H; Corzana, Francisco; Peregrina, Jesus M

2015-01-01

402

The Fibonacci Sequence & Robots  

NSDL National Science Digital Library

Using the LEGO® NXT robotics kit, students construct and program robots to illustrate and explore the Fibonacci sequence. Within teams, students are assigned roles: group leader, chassis builder, arm builder, chief programmer, and Fibonacci verifier. By designing a robot that moves based on the Fibonacci sequence of numbers, they can better visualize how quickly the numbers in the sequence grow. To program the robot to move according to these numbers, students break down the sequence into simple algebraic equations so that the computer can understand the Fibonacci sequence.

AMPS GK-12 Program,

403

Simultaneously high stiffness and damping in nanoengineered microtruss composites.  

PubMed

Materials combining high stiffness and mechanical energy dissipation are needed in automotive, aviation, construction, and other technologies where structural elements are exposed to dynamic loads. In this paper we demonstrate that a judicious combination of carbon nanotube engineered trusses held in a dissipative polymer can lead to a composite material that simultaneously exhibits both high stiffness and damping. Indeed, the combination of stiffness and damping that is reported is quite high in any single monolithic material. Carbon nanotube (CNT) microstructures grown in a novel 3D truss topology form the backbone of these nanocomposites. The CNT trusses are coated by ceramics and by a nanostructured polymer film assembled using the layer-by-layer technique. The crevices of the trusses are then filled with soft polyurethane. Each constituent of the composite is accurately modeled, and these models are used to guide the manufacturing process, in particular the choice of the backbone topology and the optimization of the mechanical properties of the constituent materials. The resulting composite exhibits much higher stiffness (80 times) and similar damping (specific damping capacity of 0.8) compared to the polymer. Our work is a step forward in implementing the concept of materials by design across multiple length scales. PMID:24620996

Meaud, Julien; Sain, Trisha; Yeom, Bongjun; Park, Sei Jin; Shoultz, Anna Brieland; Hulbert, Gregory; Ma, Zheng-Dong; Kotov, Nicholas A; Hart, A John; Arruda, Ellen M; Waas, Anthony M

2014-04-22

404

Nucleotide Sequence of HS-beta Satellite DNA from Kangaroo Rat Dipodomys ordii  

Microsoft Academic Search

The sequence of the highly repetitive satellite HS-beta DNA fraction from kangaroo rat Dipodomys ordii was determined independently by RNA and DNA sequencing techniques. A basic iterated sequence of 10 nucleotides with several mutational variations was found. Base-composition data are consistent with the proposed sequence and revealed a high content of 5-methylcytosine. DNA and RNA sequencing techniques used gave identical

K. Fry; R. Poon; P. Whitcome; J. Idriss; W. Salser; J. Mazrimas; F. Hatch

1973-01-01

405

Alkali metal salts of formazanate ligands: diverse coordination modes as a result of the nitrogen-rich [NNCNN] ligand backbone.  

PubMed

Alkali metal salts of redox-active formazanate ligands were prepared, and their structures in the solid-state and in solution are determined. The nitrogen-rich [NNCNN] backbone of formazanates results in a varied coordination chemistry, with both the internal and terminal nitrogen atoms available for bonding with the alkali metal. The potassium salt K[PhNNC(p-tol)NNPh]·2THF (1-K) is dimeric in the solid state and even in THF solution, as a result of the K atom bridging via interaction with a terminal N atom and the aromatic ring of a second unit. Conversely, for the compounds Na[MesNNC(CN)NNMes]·2THF (2-Na) and Na[PhNNC((t)Bu)NNPh] (3-Na) polymeric and hexameric structures are found in the solid state respectively. The preference for binding the alkali metal through internal N atoms (1-K and 2-Na) to give a 4-membered chelate, or via internal/external N atoms (5-membered chelate in 3-Na), contrasts with the 6-membered chelate mode observed in our recently reported formazanate zinc complexes. PMID:25351633

Travieso-Puente, Raquel; Chang, Mu-Chieh; Otten, Edwin

2014-12-28

406

Backbone nuclear relaxation characteristics and calorimetric investigation of the human Grb7-SH2/erbB2 peptide complex  

PubMed Central

Grb7 is a member of the Grb7 family of proteins, which also includes Grb10 and Grb14. All three proteins have been found to be overexpressed in certain cancers and cancer cell lines. In particular, Grb7 (along with the receptor tyrosine kinase erbB2) is overexpressed in 20%–30% of breast cancers. Grb7 binds to erbB2 and may be involved in cell signaling pathways that promote the formation of metastases and inflammatory responses. In a prior study, we reported the solution structure of the Grb7-SH2/erbB2 peptide complex. In this study, T1, T2, and steady-state NOE measurements were performed on the Grb7-SH2 domain, and the backbone relaxation behavior of the domain is discussed with respect to the potential function of an insert region present in all three members of this protein family. Isothermal titration calorimetry (ITC) studies were completed measuring the thermodynamic parameters of the binding of a 10-residue phosphorylated peptide representative of erbB2 to the SH2 domain. These measurements are compared to calorimetric studies performed on other SH2 domain/phosphorylated peptide complexes available in the literature. PMID:15930003

Ivancic, Monika; Spuches, Anne M.; Guth, Ethan C.; Daugherty, Margaret A.; Wilcox, Dean E.; Lyons, Barbara A.

2005-01-01

407

High accuracy of karplus equations for relating three-bond j couplings to protein backbone torsion angles.  

PubMed

(3) JC'C' and (3) JHNH? couplings are related to the intervening backbone torsion angle ${\\varphi }$ by standard Karplus equations. Although these couplings are known to be affected by parameters other than ${\\varphi }$, including H-bonding, valence angles and residue type, experimental results and quantum calculations indicate that the impact of these latter parameters is typically very small. The solution NMR structure of protein GB3, newly refined by using extensive sets of residual dipolar couplings, yields 50-60?% better Karplus equation agreement between ${\\varphi }$ angles and experimental (3) JC'C' and (3) JHNH? values than does the high-resolution X-ray structure. In intrinsically disordered proteins, (3) JC'C' and (3) JHNH? couplings can be measured at even higher accuracy, and the impact of factors other than the intervening torsion angle on (3) J will be smaller than in folded proteins, making these couplings exceptionally valuable reporters on the ensemble of ${\\varphi }$ angles sampled by each residue. PMID:25511552

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

2015-02-23

408

Synthesis and in vitro antioxidant functions of protein hydrolysate from backbones of Rastrelliger kanagurta by proteolytic enzymes  

PubMed Central

Every year, a huge quantity of fishery wastes and by-products are generated by fish processing industries. These wastes are either underutilized to produce low market value products or dumped leading to environmental issues. Complete utilization of fishery wastes for recovering value added products would be beneficial to the society and individual. The fish protein hydrolysates and derived peptides of fishery resources are widely used as nutritional supplements, functional ingredients, and flavor enhancers in food, beverage and pharmaceutical industries. Antioxidants from fishery resources have attracted the attention of researchers as they are cheaper in cost, easy to derive, and do not have side effects. Thus the present investigation was designed to produce protein hydrolysate by pepsin and papain digestion from the backbones of Rastrelliger kanagurta (Indian mackerel) and evaluate its antioxidant properties through various in vitro assays. The results reveal that both hydrolysates are potent antioxidants, capable of scavenging 46% and 36% of DPPH (1,1-diphenyl-2 picrylhydrazyl) and 58.5% and 37.54% of superoxide radicals respectively. The hydrolysates exhibit significant (p < 0.05) reducing power and lipid peroxidation inhibition. Among the two hydrolysates produced, pepsin derived fraction is superior than papain derived fraction in terms of yield, DH (Degree of hydrolysis), and antioxidant activity. PMID:24596496

Sheriff, Sheik Abdulazeez; Sundaram, Balasubramanian; Ramamoorthy, Baranitharan; Ponnusamy, Ponmurugan

2013-01-01

409

Synthetic and structural study of the coordination chemistry of a peri-backbone-supported phosphino-phosphonium salt.  

PubMed

Coordination chemistry of an acenaphthene peri-backbone-supported phosphino-phosphonium chloride (1) was investigated, revealing three distinct modes of reactivity. The reaction of 1 with Mo(CO)4(nor) gives the Mo(0) complex [(1)Mo(CO)4Cl] (2), in which the ligand 1 exhibits monodentate coordination through the phosphine donor and the P-P bond is retained. PtCl2(cod) reacts with the chloride and triflate salts of 1 to form a mononuclear complex [(1Cl)PtCl2] (3) and a binuclear complex [((1Cl)PtCl)2][2TfO] (4), respectively. In both of these complexes, the platinum center adds across the P-P bond, and subsequent chloride transfer to the phosphenium center results in phosphine-chlorophosphine bidentate coordination. [((1)PdCl)2] (5) was isolated from the reaction of 1 and Pd2(dba)3 (dba = dibenzylideneacetone). Oxidative addition to palladium(0) results in a heteroleptic phosphine bridging phosphide coordination to the Pd(II) center. In addition, reaction of 1 with BH3·SMe2 leads to the bis(borane) adduct of the corresponding mixed tertiary/secondary phosphine (6), with BH3 acting as both a reducing agent and a Lewis acid. The new compounds were fully characterized, including X-ray diffraction. The ligand properties of 1 and related bonding issues are discussed with help of DFT computations. PMID:25073081

Ray, Matthew J; Bühl, Michael; Taylor, Laurence J; Athukorala Arachchige, Kasun S; Slawin, Alexandra M Z; Kilian, Petr

2014-08-18

410

Polymeric micelles with citraconic amide as pH-sensitive bond in backbone for anticancer drug delivery.  

PubMed

A novel pH-sensitive polymeric micelle was reported. Methoxy poly(ethylene glycol)-b-poly(?-caprolactone) copolymer with citraconic amide as pH-sensitive bond was synthesized (mPEG-pH-PCL). The copolymers self-assembled into micelles to encapsulate anticancer drug doxorubicin (DOX). The morphology, size and size distribution, drug release profile and in vitro anticancer activity of the DOX loaded mPEG-pH-PCL micelles were studied. The results showed that the mean size of the micelles was around 120 nm, the drug loading content and encapsulation efficiency of the mPEG-pH-PCL micelles were 6.8% and 54.3%, respectively. The mean diameter and size distribution of the mPEG-pH-PCL micelles increased significantly when soaking in medium with pH 5.5. The drug release of micelles in pH 5.5 was much faster than that in pH 7.4. The confocal laser microscopy and flow cytometry measurements indicated that the weak acidity of endosomes broke the citraconic amide bonds in the copolymer backbones and triggered the fast release of DOX. The in vitro IC50 of the drug loaded mPEG-pH-PCL micelles was lower than that of drug loaded polymeric micelles without pH-sensitivity to both HepG2 and 4T1 cancer cells. PMID:24836667

Cao, Jun; Su, Ting; Zhang, Longgui; Liu, Rong; Wang, Gang; He, Bin; Gu, Zhongwei

2014-08-25

411

Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory.  

PubMed

The DNA sugar-phosphate backbone has a substantial influence on the DNA structural dynamics. Structural biology and bioinformatics studies revealed that the DNA backbone in experimental structures samples a wide range of distinct conformational substates, known as rotameric DNA backbone conformational families. Their correct description is essential for methods used to model nucleic acids and is known to be the Achilles heel of force field computations. In this study we report the benchmark database of MP2 calculations extrapolated to the complete basis set of atomic orbitals with aug-cc-pVTZ and aug-cc-pVQZ basis sets, MP2(T,Q), augmented by ?CCSD(T)/aug-cc-pVDZ corrections. The calculations are performed in the gas phase as well as using a COSMO solvent model. This study includes a complete set of 18 established and biochemically most important families of DNA backbone conformations and several other salient conformations that we identified in experimental structures. We utilize an electronically sufficiently complete DNA sugar-phosphate-sugar (SPS) backbone model system truncated to prevent undesired intramolecular interactions. The calculations are then compared with other QM methods. The BLYP and TPSS functionals supplemented with Grimme's D3(BJ) dispersion term provide the best tradeoff between computational demands and accuracy and can be recommended for preliminary conformational searches as well as calculations on large model systems. Among the tested methods, the best agreement with the benchmark database has been obtained for the double-hybrid DSD-BLYP functional in combination with a quadruple-? basis set, which is, however, computationally very demanding. The new hybrid density functionals PW6B95-D3 and MPW1B95-D3 yield outstanding results and even slightly outperform the computationally more demanding PWPB95 double-hybrid functional. B3LYP-D3 is somewhat less accurate compared to the other hybrids. Extrapolated MP2(D,T) calculations are not as accurate as the less demanding DFT-D3 methods. Preliminary force field tests using several charge sets reveal an almost order of magnitude larger deviations from the reference QM data compared to modern DFT-D3, underlining the challenges facing force field simulations of nucleic acids. As expected, inclusion of the solvent environment approximated by a continuum approach has a large impact on the relative stabilities of different backbone substates and is important when comparing the QM data with structural bioinformatics and other experimental data. PMID:23575975

Mládek, Arnošt; Krepl, Miroslav; Svozil, Daniel; Cech, Petr; Otyepka, Michal; Banáš, Pavel; Zgarbová, Marie; Jure?ka, Petr; Sponer, Ji?í

2013-05-21

412

Substitution of Wild-Type Yellow Fever Asibi Sequences for 17D Vaccine Sequences in ChimeriVax–Dengue 4 Does Not Enhance Infection of Aedes aegypti Mosquitoes  

PubMed Central

To address concerns that a flavivirus vaccine/wild-type recombinant virus might have a high mosquito infectivity phenotype, the yellow fever virus (YFV) 17D backbone of the ChimeriVax– dengue 4 virus was replaced with the corresponding gene sequences of the virulent YFV Asibi strain. Field-collected and laboratory-colonized Aedes aegypti mosquitoes were fed on blood containing each of the viruses under investigation and held for 14 days after infection. Infection and dissemination rates were based on antigen detection in titrated body or head triturates. Our data indicate that, even in the highly unlikely event of recombination or substantial backbone reversion, virulent sequences do not enhance the transmissibility of ChimeriVax viruses. In light of the low-level viremias that have been observed after vaccination in human volunteers coupled with low mosquito infectivity, it is predicted that the risk of mosquito infection and transmission of ChimeriVax vaccine recombinant/revertant viruses in nature is minimal. PMID:18266608

McGee, Charles E.; Tsetsarkin, Konstantin; Vanlandingham, Dana L.; McElroy, Kate L.; Lang, Jean; Guy, Bruno; Decelle, Thierry; Higgs, Stephen

2008-01-01

413

Substitution of wild-type yellow fever Asibi sequences for 17D vaccine sequences in ChimeriVax-dengue 4 does not enhance infection of Aedes aegypti mosquitoes.  

PubMed

To address concerns that a flavivirus vaccine/wild-type recombinant virus might have a high mosquito infectivity phenotype, the yellow fever virus (YFV) 17D backbone of the ChimeriVax-dengue 4 virus was replaced with the corresponding gene sequences of the virulent YFV Asibi strain. Field-collected and laboratory-colonized Aedes aegypti mosquitoes were fed on blood containing each of the viruses under investigation and held for 14 days after infection. Infection and dissemination rates were based on antigen detection in titrated body or head triturates. Our data indicate that, even in the highly unlikely event of recombination or substantial backbone reversion, virulent sequences do not enhance the transmissibility of ChimeriVax viruses. In light of the low-level viremias that have been observed after vaccination in human volunteers coupled with low mosquito infectivity, it is predicted that the risk of mosquito infection and transmission of ChimeriVax vaccine recombinant/revertant viruses in nature is minimal. PMID:18266608

McGee, Charles E; Tsetsarkin, Konstantin; Vanlandingham, Dana L; McElroy, Kate L; Lang, Jean; Guy, Bruno; Decelle, Thierry; Higgs, Stephen

2008-03-01

414

Estimating Linear Models for Compositional Distributional Semantics  

Microsoft Academic Search

In distributional semantics studies, there is a growing attention in compositionally determining the distributional meaning of word sequences. Yet, compositional dis- tributional models depend on a large set of parameters that have not been explored. In this paper we propose a novel approach to estimate parameters for a class of com- positional distributional models: the addi- tive models. Our approach

Fabio Massimo Zanzotto; Ioannis Korkontzelos; Francesca Fallucchi; Suresh Manandhar

2010-01-01

415

sup 1 H NMR studies of plastocyanin from Scenedesmus obliquus: Complete sequence-specific assignment, secondary structure analysis, and global fold  

SciTech Connect

Two-dimensional {sup 1}H NMR methods have been used to make sequence-specific resonance assignments for the 97 amino acid residues of the plastocyanin from the green alga Scenedesmus obliquus. Assignments were obtained for all backbone protons and the majority of the side-chain protons. Spin system identification relied heavily on the observation of relayed connectivities to the backbone amide proton. Sequence-specific assignments were made by using the sequential assignment procedure. During this process, an extra valine residue was identified that had not been detected in the original amino acid sequence. Elements of regular secondary structure were identified from characteristic NOE connectivities between backbone protons, coupling constant values, and the observation of slowly exchanging amide protons. The protein in solution contains eight {beta}-strands, one short segment of helix, five reverse turns, and five loops. The {beta}-strands may be arranged into two {beta}sheets on the basis of extensive cross-strand NOE connectivities. The chain-folding topology determined from the NMR experiments is that of a Greek key {beta}-barrel and is similar to that observed for French bean plastocyanin in solution and poplar plastocyanin in the crystalline state. While the overall structures are similar, several differences in local structure between the S. obliquus and higher plant plastocyanins have been identified.

Moore, J.M.; Chazin, W.J.; Wright, P.E. (Research Institute of Scripps Clinic, La Jolla, CA (USA)); Powls, R. (The University, Liverpool (England))

1988-10-04

416

Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences  

E-print Network

Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences Roman R. Stocsits1 , Ivo L data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however

Stadler, Peter F.

417

Sequence-structure relationships in DNA oligomers: a computational approach.  

PubMed

A collective-variable model for DNA structure is used to predict the conformation of a set of 30 octamer, decamer, and dodecamer oligomers for which high-resolution crystal structures are available. The model combines an all-atom base pair representation with an empirical backbone, emphasizing the role of base stacking in fixing sequence-dependent structure. We are able to reproduce trends in roll and twist to within 5 degrees across a large database of both A- and B-DNA oligomers. A genetic algorithm approach is used to search for global minimum structures and this is augmented by a grid search to identify local minimums. We find that the number of local minimums is highly sequence dependent, with certain sequences having a set of minimums that span the entire range between canonical A- and B-DNA conformations. Although the global minimum does not always agree with the crystal structure, for 24 of the 30 oligomers, we find low-energy local minimums that match the experimental step parameters. Discrepancies throw some light on the role of crystal packing in determining the solid-state conformation of double-helical DNA. PMID:11472171

Packer, M J; Hunter, C A

2001-08-01

418

Quantifying sequence and structural features of protein-RNA interactions.  

PubMed

Increasing awareness of the importance of protein-RNA interactions has motivated many approaches to predict residue-level RNA binding sites in proteins based on sequence or structural characteristics. Sequence-based predictors are usually high in sensitivity but low in specificity; conversely structure-based predictors tend to have high specificity, but lower sensitivity. Here we quantified the contribution of both sequence- and structure-based features as indicators of RNA-binding propensity using a machine-learning approach. In order to capture structural information for proteins without a known structure, we used homology modeling to extract the relevant structural features. Several novel and modified features enhanced the accuracy of residue-level RNA-binding propensity beyond what has been reported previously, including by meta-prediction servers. These features include: hidden Markov model-based evolutionary conservation, surface deformations based on the Laplacian norm formalism, and relative solvent accessibility partitioned into backbone and side chain contributions. We constructed a web server called aaRNA that implements the proposed method and demonstrate its use in identifying putative RNA binding sites. PMID:25063293

Li, Songling; Yamashita, Kazuo; Amada, Karlou Mar; Standley, Daron M

2014-09-01