Science.gov

Sample records for sequence backbone composition

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

    SciTech Connect

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

    2015-10-15

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

  2. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.

    PubMed

    Lapidoth, Gideon D; Baran, Dror; Pszolla, Gabriele M; Norn, Christoffer; Alon, Assaf; Tyka, Michael D; Fleishman, Sarel J

    2015-08-01

    Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exert control over all polypeptide degrees of freedom--remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity. PMID:25670500

  3. ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

    PubMed Central

    2011-01-01

    Background The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection) sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP) calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs) were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf.comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin. PMID:21635747

  4. Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies.

    PubMed

    Gardner, Andrew G; Sessa, Emily B; Michener, Pryce; Johnson, Eden; Shepherd, Kelly A; Howarth, Dianella G; Jabaily, Rachel S

    2016-01-01

    Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia+Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A+Goodenia B) (Velleia+Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera. PMID:26463342

  5. Composition for nucleic acid sequencing

    DOEpatents

    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

    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.

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

    NASA Astrophysics Data System (ADS)

    Harper, Brett; Miladi, Mahsan; Solouki, Touradj

    2014-10-01

    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.

  7. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus sidechain groups to chain expansion via chemical denaturation

    PubMed Central

    Holehouse, Alex S.; Garai, Kanchan; Lyle, Nicholas; Vitalis, Andreas; Pappu, Rohit V.

    2015-01-01

    In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones and therefore backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of sidechains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that sidechains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of sidechain-mediated interactions as determinants of the conformational properties of unfolded states in water and in influencing chain expansion upon denaturation. PMID:25664638

  8. 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 motion with a near critical drift towards an absorbing barrier at the origin. #12;3/ 17 Spines, backbones

  9. Methods and compositions for efficient nucleic acid sequencing

    DOEpatents

    Drmanac, Radoje

    2006-07-04

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

  10. Methods and compositions for efficient nucleic acid sequencing

    DOEpatents

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

    2002-01-01

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

  11. Sequence-specific 1HN, 13C and 15N backbone resonance assignments of the 34 kDa Paramecium bursaria Chlorella virus 1 (PBCV1) DNA ligase

    PubMed Central

    Piserchio, Andrea; Nair, Pravin A.; Shuman, Stewart; Ghose, Ranajeet

    2009-01-01

    Chlorella virus DNA ligase (ChVLig) is a minimal (298-amino acid) pluripotent ATP-dependent ligase composed of three structural modules – a nucleotidyltransferase domain, an OB domain, and a ?-hairpin latch – that forms a circumferential clamp around nicked DNA. ChVLig provides an instructive model to understand the chemical and conformational steps of nick repair. Here we report the assignment of backbone 13C, 15N, 1HN resonances of this 34.2 kDa protein, the first for a DNA ligase in full-length form. PMID:19636951

  12. Predicting bacterial essential genes using only sequence composition information.

    PubMed

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

    2014-01-01

    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

  13. Identification of base and backbone contacts used for DNA sequence recognition and high-affinity binding by LAC9, a transcription activator containing a C6 zinc finger

    SciTech Connect

    Halvorsen, Yuan-Di C.; Nandabalan, K.; Dickson, R.C. )

    1991-04-01

    The LAC9 protein of Kluyveromyces lactis is a transcriptional regulator of genes in the lactose-galactose regulon. To regulate transcription, LAC9 must bind to 17-bp upstream activator sequences (UASs) located in front of each target gene. LAC9 is homologous to the GAL4 protein of Saccharomyces cerevisiae, and the two proteins must bind DNA in a very similar manner. In this paper the authors show that high-affinity, sequence-specific binding by LAC9 dimers is mediated primarily by 3 bp at each end of the UAS. In addition, at least one half of the UAS must have a GC or CG base pair at position 1 for high-affinity binding; LAC9k binds preferentially to the half containing the GC base pair. Hydroxyl radical footprinting shows that a LAC9 dimer binds an unusually broad region on one face of the DNA helix. Because of the data, they suggest that LAC9 contacts positions 6, 7, and 8, both plus and minus, of the UAS, which are separated by more than one turn of the DNA helix, and twists part way around the DNA, thus protecting the broad region of the minor groove between the major-groove contacts.

  14. Plausible classification codes and local compositional complexity of nucleotide sequences

    SciTech Connect

    Konopka, A.K.

    1993-12-31

    Genomic DNA fragments are initially represented by sequences of symbols from an elementary alphabet (such as the one that contains A, C, G, T, and N symbols for nucleotides). Although in theory scientists could consider alphabets of symbols that represent secondary and tertiary structures of biopolymers, the sequences of monomers are the only solid data they have thus far. Even in the presence of sequencing errors the reliability of sequence representation is far greater than higher-order structure representations available thus far. For this reason the author will focus on sequence representations only. Sequences can be classified according to a description of their biological function (``extrasequencial`` factual data). The result of such classification are collections of Functionally Equivalent Sequences (abbreviated as FESs in plural and as FES in singular). In order for FESs to be suitable for statistical analyses they should not contain sequences that are identical or almost identical to each other. As far as computational biology is concerned functions are represented by FESS. The challenge is to find patterns that could serve as indicators of a given sequence belonging to a given FES and not to other FESS. Before the search for function-associated patterns can be performed, patterns have to be defined and their (not necessarily statistical) significance has to be evaluated.

  15. Characterization of microbiome composition and function through shotgun sequencing has provided many insights

    E-print Network

    Reports Characterization of microbiome composition and function through shotgun sequencing has provided many insights into its roles in health and disease. Gene calling (1, 2), func- tional single nucleotide polymorphism (SNP) detec- tion (11) have all shown associations between microbiome

  16. Diverse nucleotide compositions and sequence fluctuation in Rubisco protein genes

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

    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.

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

    PubMed

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

    2015-06-01

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

  18. Automated protein backbone assignment using the projection-decomposition approach.

    PubMed

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

    2012-09-01

    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

  19. Backbone upgrades and DEC equipment replacement

    NASA Technical Reports Server (NTRS)

    Vancamp, Warren

    1991-01-01

    The NASA Science Internet (NSI) dual protocol backbone is outlined. It includes DECnet link upgrades to match TCP/IP link performance. It also includes the integration of backbone resources and central management. The phase 1 transition process is outlined.

  20. Nucleic acid compositions with scissile linkage useful for detecting nucleic acid sequences

    SciTech Connect

    Duck, P.; Bender, R.; Crosby, W.; Robertson, J.G.

    1989-10-24

    This patent describes a composition. It comprises the structure: S-L(NA{sub 1}-S-NA{sub 2}){sub n}M. NA{sub 1} and NA{sub 2} are nucleic acid sequences; -S- is a scissile linkage which is capable of being cleaved or disrupted without cleaving or disrupting the nuclei acid sequences of NA{sub 1} or NA{sub 2} or of a target nuclei acid sequence capable of hybridizing to the NA{sub 1} and NA{sub 2} sequences, or to the NA{sub 1} and NA{sub 2} sequences and the scissile linkage of the composition, wherein if the scissile linkage is a nuclei acid sequence it is RNA when both NA{sub 1} and NA{sub 2} are DNA sequences, or the scissile linkage is DNA when both NA{sub 1} and NA{sub 2} are RNA sequences; and n is an integer from 1 to 4. The solid lines represent chemical bonds; X is a solid support; L is a chemical entity which links NA{sub 1} to the solid support; and M is a marker.

  1. Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

    PubMed Central

    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

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

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

    PubMed

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

    2008-09-21

    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

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

    SciTech Connect

    Cherian, Betsy Sheena; Nair, Achuthsankar S.

    2010-01-22

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

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

    PubMed Central

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

    2015-01-01

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

  5. Composite Sequences for Triple-dot Qubits that Compensate for Miscalibration and Hyperfine Gradients

    NASA Astrophysics Data System (ADS)

    Ladd, Thaddeus

    2014-03-01

    Exchange-only qubits defined in triple quantum dots form a promising means for all-electrical semiconductor quantum control, but they suffer from both charge noise and random magnetic field gradients. Low-frequency noise sources can be compensated using composite sequences, but the development of such sequences is constrained by the fact that exchange energies are always positive and the control axes are non-orthogonal. Here, we present the results of both analytical approaches and computational searches for composite pulse sequences, which compensate for simultaneous low-frequency miscalibration (due to fixed random electric fields) and hyperfine effects (due to nuclear magnetic fields) in a single triple-dot qubit. We also present compensation sequences for multi-qubit gates. These results can substantially improve the working fidelity of quantum operations in semiconductor quantum dot devices. Sponsored by United States Department of Defense. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressly or implied, of the United States Department of Defense or the U.S. Government.

  6. Flexible backbone aromatic polyimide adhesives

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

    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.

  7. Flexible backbone aromatic polyimide adhesives

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

    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.

  8. Continuous Backbone "Continuum" Robot Manipulators: A Review

    E-print Network

    gripper. However, the continuum robot was able to use its compliant, actively controlled continuous1 Continuous Backbone "Continuum" Robot Manipulators: A Review Ian D. Walker Department of Electrical and Computer Engineering Clemson University Clemson, South Carolina, 29634 USA iwalker

  9. Simple Sequence Repeats in Escherichia coli: Abundance, Distribution, Composition, and Polymorphism

    PubMed Central

    Gur-Arie, Riva; Cohen, Cyril J.; Eitan, Yuval; Shelef, Leora; Hallerman, Eric M.; Kashi, Yechezkel

    2000-01-01

    Computer-based genome-wide screening of the DNA sequence of Escherichia coli strain K12 revealed tens of thousands of tandem simple sequence repeat (SSR) tracts, with motifs ranging from 1 to 6 nucleotides. SSRs were well distributed throughout the genome. Mononucleotide SSRs were over-represented in noncoding regions and under-represented in open reading frames (ORFs). Nucleotide composition of mono- and dinucleotide SSRs, both in ORFs and in noncoding regions, differed from that of the genomic region in which they occurred, with 93% of all mononucleotide SSRs proving to be of A or T. Computer-based analysis of the fine position of every SSR locus in the noncoding portion of the genome relative to downstream ORFs showed SSRs located in areas that could affect gene regulation. DNA sequences at 14 arbitrarily chosen SSR tracts were compared among E. coli strains. Polymorphisms of SSR copy number were observed at four of seven mononucleotide SSR tracts screened, with all polymorphisms occurring in noncoding regions. SSR polymorphism could prove important as a genome-wide source of variation, both for practical applications (including rapid detection, strain identification, and detection of loci affecting key phenotypes) and for evolutionary adaptation of microbes.[The sequence data described in this paper have been submitted to the GenBank data library under accession numbers AF209020–209030 and AF209508–209518.] PMID:10645951

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

    PubMed

    Fuglsang, Anders

    2004-11-01

    A Windows application for compositional analysis of sequenced genomes (EMBL or GenBank flat files) is available as freeware. The application allows the user to quantify word bias using Markov chain analysis and it allows the user to generate sliding window data for GC-skew, AT-skew, purine excess, keto excess and discrete word counts. The mathematical routines reside in a dynamic link library (DLL), which can be used independently by other applications. The software is available for download at http://www.dfuni.dk/~anfu/Bioinformatics/Main.htm. PMID:15702383

  11. Analytical Singular Value Decomposition of infrared image sequences: microcrack detection on ceramic composites under mechanical stresses

    NASA Astrophysics Data System (ADS)

    Bamford, Matthieu; Batsale, Jean Christophe

    2008-05-01

    In this Note, infrared image sequences of a SiC f/SiC composite excited with a uniform heat pulse are processed using a modal approach. A new analytical integral transform (called analytical SVD or ASVD) inspired by the classical Singular Value Decomposition is developed and implemented on the raw experimental data. The second resulting spatial mode (out of a thousand) yielded by the ASVD provides, without further processing, a 2D mapping of the normalized local transverse diffusivity variations around a nominal value. Such mapping yields information on the inner structure of the material, and can be used to reveal the presence of voids inside the medium. This method is thus implemented on a tensile testing machine, to detect microcracks in a SiC f/SiC composite sample under mechanical stress in almost real time. To cite this article: M. Bamford, J.C. Batsale, C. R. Mecanique 336 (2008).

  12. External Tank - The Structure Backbone

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  13. Unimolecular antiparallel G-quadruplex folding topology of 2'-5'-isoTBA sequences remains unaltered by loop composition.

    PubMed

    Aher, Manisha N; Erande, Namrata D; Fernandes, Moneesha; Kumar, Vaijayanti A

    2015-12-28

    A 2'-5'-linked isoTBA 15 mer sequence with (232) loop composition formed stable antiparallel quadruplex structures similar to the SELEX derived 15 mer TBA sequence with (232) loop composition. A parallel versus antiparallel topology of 3'-5'-G-quadruplexes is largely dictated by the loop length, and it is known that the truncated loops favour parallel quadruplexes. In contrast to TBA, systematic reduction of the loop length in isoTBA from (232) to (222), (131) or even (111) did not alter the antiparallel topology of the resulting 14 mer, 13 mer and 11 mer G-rich modified isoTBA-like sequences. PMID:26478215

  14. Sequence composition and environment effects on residue fluctuations in protein structures

    NASA Astrophysics Data System (ADS)

    Ruvinsky, Anatoly M.; Vakser, Ilya A.

    2010-10-01

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

  15. Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition

    PubMed Central

    Ulpinnis, Chris; Scholz, Uwe; Altmann, Thomas

    2015-01-01

    A major goal of maize genomic research is to identify sequence polymorphisms responsible for phenotypic variation in traits of economic importance. Large-scale detection of sequence variation is critical for linking genes, or genomic regions, to phenotypes. However, due to its size and complexity, it remains expensive to generate whole genome sequences of sufficient coverage for divergent maize lines, even with access to next generation sequencing (NGS) technology. Because methods involving reduction of genome complexity, such as genotyping-by-sequencing (GBS), assess only a limited fraction of sequence variation, targeted sequencing of selected genomic loci offers an attractive alternative. We therefore designed a sequence capture assay to target 29 Mb genomic regions and surveyed a total of 4,648 genes possibly affecting biomass production in 21 diverse inbred maize lines (7 flints, 14 dents). Captured and enriched genomic DNA was sequenced using the 454 NGS platform to 19.6-fold average depth coverage, and a broad evaluation of read alignment and variant calling methods was performed to select optimal procedures for variant discovery. Sequence alignment with the B73 reference and de novo assembly identified 383,145 putative single nucleotide polymorphisms (SNPs), of which 42,685 were non-synonymous alterations and 7,139 caused frameshifts. Presence/absence variation (PAV) of genes was also detected. We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions. This diversification has the potential to broaden functional diversity and generate phenotypic variation that may lead to new adaptations and the modification of important agronomic traits. Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation. In summary, we demonstrated that sequencing of captured DNA is a powerful approach for variant discovery in maize genes. PMID:26151830

  16. Hidden Markov Models That Use Predicted Local Structure for Fold Recognition: Alphabets of Backbone Geometry

    E-print Network

    Mandel-Gutfreund, Yael

    Hidden Markov Models That Use Predicted Local Structure for Fold Recognition: Alphabets of Backbone, California 2 Affymetrix, Inc., Emeryville, California 3 Department of Chemistry and Biochemistry, University the structure of the large number of putative proteins discovered by genome sequencing projects. Fold

  17. Exploring the Gastrointestinal "Nemabiome": Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities.

    PubMed

    Avramenko, Russell W; Redman, Elizabeth M; Lewis, Roy; Yazwinski, Thomas A; Wasmuth, James D; Gilleard, John S

    2015-01-01

    Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. We describe the first application of deep amplicon sequencing to study parasitic nematode communities as well as introduce the concept of the gastro-intestinal "nemabiome". The approach is analogous to 16S rDNA deep sequencing used to explore microbial communities, but utilizes the nematode ITS-2 rDNA locus instead. Gastro-intestinal parasites of cattle were used to develop the concept, as this host has many well-defined gastro-intestinal nematode species that commonly occur as complex co-infections. Further, the availability of pure mono-parasite populations from experimentally infected cattle allowed us to prepare mock parasite communities to determine, and correct for, species representation biases in the sequence data. We demonstrate that, once these biases have been corrected, accurate relative quantitation of gastro-intestinal parasitic nematode communities in cattle fecal samples can be achieved. We have validated the accuracy of the method applied to field-samples by comparing the results of detailed morphological examination of L3 larvae populations with those of the sequencing assay. The results illustrate the insights that can be gained into the species composition of parasite communities, using grazing cattle in the mid-west USA as an example. However, both the technical approach and the concept of the 'nemabiome' have a wide range of potential applications in human and veterinary medicine. These include investigations of host-parasite and parasite-parasite interactions during co-infection, parasite epidemiology, parasite ecology and the response of parasite populations to both drug treatments and control programs. PMID:26630572

  18. Exploring the Gastrointestinal “Nemabiome”: Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities

    PubMed Central

    Avramenko, Russell W.; Redman, Elizabeth M.; Lewis, Roy; Yazwinski, Thomas A.; Wasmuth, James D.; Gilleard, John S.

    2015-01-01

    Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. We describe the first application of deep amplicon sequencing to study parasitic nematode communities as well as introduce the concept of the gastro-intestinal “nemabiome”. The approach is analogous to 16S rDNA deep sequencing used to explore microbial communities, but utilizes the nematode ITS-2 rDNA locus instead. Gastro-intestinal parasites of cattle were used to develop the concept, as this host has many well-defined gastro-intestinal nematode species that commonly occur as complex co-infections. Further, the availability of pure mono-parasite populations from experimentally infected cattle allowed us to prepare mock parasite communities to determine, and correct for, species representation biases in the sequence data. We demonstrate that, once these biases have been corrected, accurate relative quantitation of gastro-intestinal parasitic nematode communities in cattle fecal samples can be achieved. We have validated the accuracy of the method applied to field-samples by comparing the results of detailed morphological examination of L3 larvae populations with those of the sequencing assay. The results illustrate the insights that can be gained into the species composition of parasite communities, using grazing cattle in the mid-west USA as an example. However, both the technical approach and the concept of the ‘nemabiome’ have a wide range of potential applications in human and veterinary medicine. These include investigations of host-parasite and parasite-parasite interactions during co-infection, parasite epidemiology, parasite ecology and the response of parasite populations to both drug treatments and control programs. PMID:26630572

  19. Backbone Motions in a Crystalline Protein from

    E-print Network

    Griffin, Robert G.

    the role of fluctuations in facilitating enzyme­substrate engagement,1­3 enzy- matic activity,4 indicating that backbone motions are fast compared to the nmr frequencies. However, as the temperature slightly in amplitude as the temperature rises toward 290 K, but the correlation time, as is also observed

  20. Proc. AAAI-02, to appear. Searching for Backbones and Fat

    E-print Network

    Zhang, Weixiong

    Proc. AAAI-02, to appear. Searching for Backbones and Fat: A Limit-Crossing Approach solution fat variables. Identification of backbone and fat variables is a valuable as- set when attempting to solve complex problems. In this pa- per, we demonstrate a method for identifying backbones and fat. Our

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

    PubMed Central

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

    2012-01-01

    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

  2. The nucleotide composition of the spacer sequence influences the expression yield of heterologously expressed genes in Bacillus subtilis.

    PubMed

    Liebeton, Klaus; Lengefeld, Jette; Eck, Jürgen

    2014-12-10

    Bacillus subtilis is a commonly used host for the heterologous expression of genes in academia and industry. Many factors are known to influence the expression yield in this organism e.g. the complementarity between the Shine-Dalgarno sequence (SD) and the 16S-rRNA or secondary structures in the translation initiation region of the transcript. In this study, we analysed the impact of the nucleotide composition between the SD sequence and the start codon (the spacer sequence) on the expression yield. We demonstrated that a polyadenylate-moiety spacer sequence moderately increases the expression level of laccase CotA from B. subtilis. By screening a library of artificially generated spacer variants, we identified clones with greatly increased expression levels of two model enzymes, the laccase CotA from B. subtilis (11 fold) and the metagenome derived protease H149 (30 fold). Furthermore, we demonstrated that the effect of the spacer sequence is specific to the gene of interest. These results prove the high impact of the spacer sequence on the expression yield in B. subtilis. PMID:24997355

  3. Telephone wire is backbone of security system

    SciTech Connect

    Brede, K.; Rackson, L.T.

    1995-09-01

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

  4. Resonant magnetoelectric response of composite cantilevers: Theory of short vs. open circuit operation and layer sequence effects

    NASA Astrophysics Data System (ADS)

    Krantz, Matthias C.; Gugat, Jascha L.; Gerken, Martina

    2015-11-01

    The magnetoelectric effect in layered composite cantilevers consisting of strain coupled layers of magnetostrictive (MS), piezoelectric (PE), and substrate materials is investigated for magnetic field excitation at bending resonance. Analytic theories are derived for the transverse magnetoelectric (ME) response in short and open circuit operation for three different layer sequences and results presented and discussed for the FeCoBSi-AlN-Si and the FeCoBSi-PZT-Si composite systems. Response optimized PE-MS layer thickness ratios are found to greatly change with operation mode shifting from near equal MS and PE layer thicknesses in the open circuit mode to near vanishing PE layer thicknesses in short circuit operation for all layer sequences. In addition the substrate layer thickness is found to differently affect the open and short circuit ME response producing shifts and reversal between ME response maxima depending on layer sequence. The observed rich ME response behavior for different layer thicknesses, sequences, operating modes, and PE materials can be explained by common neutral plane effects and different elastic compliance effects in short and open circuit operation.

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

    PubMed

    Aita, Takuyo; Nishigaki, Koichi

    2012-11-01

    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

  6. RNA-Redesign: a web server for fixed-backbone 3D design of RNA

    PubMed Central

    Yesselman, Joseph D.; Das, Rhiju

    2015-01-01

    RNA is rising in importance as a design medium for interrogating fundamental biology and for developing therapeutic and bioengineering applications. While there are several online servers for design of RNA secondary structure, there are no tools available for the rational design of 3D RNA structure. Here we present RNA-Redesign (http://rnaredesign.stanford.edu), an online 3D design tool for RNA. This resource utilizes fixed-backbone design to optimize the sequence identity and nucleobase conformations of an RNA to match a desired backbone, analogous to fundamental tools that underlie rational protein engineering. The resulting sequences suggest thermostabilizing mutations that can be experimentally verified. Further, sequence preferences that differ between natural and computationally designed sequences can suggest whether natural sequences possess functional constraints besides folding stability, such as cofactor binding or conformational switching. Finally, for biochemical studies, the designed sequences can suggest experimental tests of 3D models, including concomitant mutation of base triples. In addition to the designs generated, detailed graphical analysis is presented through an integrated and user-friendly environment. PMID:25964298

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

    E-print Network

    Bystroff, Chris

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

  8. HASH: a program to accurately predict protein H? shifts from neighboring backbone shifts.

    PubMed

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    2013-01-01

    Chemical shifts provide not only peak identities for analyzing nuclear magnetic resonance (NMR) data, but also an important source of conformational information for studying protein structures. Current structural studies requiring H(?) chemical shifts suffer from the following limitations. (1) For large proteins, the H(?) chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of C(?) that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict H(?) chemical shifts. Predicting accurate H(?) chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called HASH, to predict H(?) chemical shifts. HASH combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate H(?) chemical shifts. Our testing results on different possible combinations of input data indicate that HASH has a wide rage of potential NMR applications in structural and biological studies of proteins. PMID:23242797

  9. Static magnetoelectric and magnetoelastic response of composite cantilevers: Theory of short vs. open circuit operation and layer sequence effects

    NASA Astrophysics Data System (ADS)

    Krantz, Matthias C.; Gugat, Jascha L.; Gerken, Martina

    2015-11-01

    The static bending-mode transverse magnetoelectric effect and the magnetic field-induced bending response of composite cantilevers with thin magnetostrictive (MS), piezoelectric (PE), and substrate (Sub) layers is investigated for the PE layer subjected to open and short circuit conditions. Analytic theories are presented for strain-coupled three layer composites of PE, MS, and Sub layers in all layer sequences. We use constitutive equations with linear coupling of stress, strain, H, E, and D fields and present results for the open and short circuit magnetoelectric and bending responses for arbitrary layer thickness ratios for the FeCoBSi-AlN-Si materials system. Besides a rich sequence dependent behavior the theory predicts great and systematic differences between the open and short circuit magnetoelectric response yielding maxima at similar MS and PE layer thicknesses in the open circuit and near vanishing PE layer thicknesses in the short circuit cases. In contrast, the open vs. short circuit bending response differences are pronounced but much smaller. Layer sequence systematics and implications for static H-field sensors will be discussed.

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

    PubMed

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

    2009-01-01

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

  11. Polyarylether composition and membrane

    DOEpatents

    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

    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.

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

    USGS Publications Warehouse

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

    2012-01-01

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

  13. Using DGGE and 16S rRNA Gene Sequence Analysis to Evaluate Changes in Oral Bacterial Composition

    PubMed Central

    CHEN, Zhou; TRIVEDI, Harsh M.; CHHUN, Nok; BARNES, Virginia M.; SAXENA, Deepak; XU, Tao; LI, Yihong

    2015-01-01

    Objective To investigate whether a standard dental prophylaxis followed by tooth brushing with an antibacterial dentifrice will affect the oral bacterial community, as determined by denaturing gradient gel electrophoresis (DGGE) combined with 16S rRNA gene sequence analysis. Methods Twenty-four healthy adults were instructed to brush their teeth using commercial dentifrice for 1 week during a washout period. An initial set of pooled supragingival plaque samples was collected from each participant at baseline (0 h) before prophylaxis treatment. The subjects were given a clinical examination and dental prophylaxis and asked to brush for 1 min with a dentifrice containing 0.3% triclosan/2.0% PVM/MA copolymer/0.243% sodium fluoride (Colgate Total). On the following day, a second set of pooled supragingival plaque samples (24 h) was collected. Total bacterial genomic DNA was isolated from the samples. Differences in the microbial composition before and after the prophylactic procedure and tooth brushing were assessed by comparing the DGGE profiles of PCR-amplified and 16S rRNA gene segments sequence analysis. Results Two distinct clusters of DGGE profiles were found, suggesting that a shift in the microbial composition had occurred 24 h after the prophylaxis and brushing. A detailed sequencing analysis of 16S rRNA gene segments further identified six phyla and 29 genera, including known and unknown bacterial species. Importantly, an increase in bacterial diversity was observed after 24 h, including members of the Streptococcaceae family, Prevotella, Corynebacterium, TM7 and other commensal bacteria. Conclusion The results suggest that the use of a standard prophylaxis followed by the use of the dentifrice containing 0.3% triclosan/2.0% PVM/MA copolymer/0.243% sodium fluoride may promote a healthier composition within the oral bacterial community. PMID:22319750

  14. Algorithm for Rapid Reconstruction of Protein Backbone from Alpha

    E-print Network

    Skolnick, Jeff

    of Molecular Biology, 10666 North Torrey Pines Road, La Jolla, California 92037; and 2 Department of Chemistry folding algorithms to rapidly generate approximate coordinates of backbone atoms. 1997 by John Wiley 1997 by John Wiley & Sons CCC 0192-8651 / 97 / 010080-06 #12;RECONSTRUCTION OF A PROTEIN BACKBONE

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

    NASA Technical Reports Server (NTRS)

    Hodges, F. N.; Kushiro, I.

    1974-01-01

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

  16. Sequence stratigraphy and composition of late quaternary shelf-margin deltas, Northern Gulf of Mexico

    SciTech Connect

    Morton, R.A.; Suter, J.R.

    1996-04-01

    High-resolution seismic profiles and foundation borings from the northwestern Gulf of Mexico record the physical attributes and depositional histories of several late Quaternary sequences that were deposited by wave-modified, river-dominated shelf-margin deltas during successive periods of lowered sea level. Each progressively younger deltaic sequence is thinner and exhibits a systematic decrease in the abundance and concentration of sand, which is attributed to a shift in the axes of trunk streams and greater structural influence through time. Our study shows that (1) contemporaneous structural deformation controlled the thickness of each sequence, the oblique directions of delta progradation, the axes of major fluvial channels, and the geometries of delta lobes at the shelf margin; (2) sedimentation was rapid in response to rapid eustatic fluctuations and structural influence; (3) boundaries of these high-frequency sequences are the correlative conformities of updip fluvial incision and coincide with downlap surfaces at the shelf margin; (4) the downlap surfaces are not true surfaces, but zones of parallel reflections that become progressively higher and younger in the direction of progradation; (5) the downlap zones are composed of marine muds that do not contain the high concentrations of shell debris expected in condensed sections; (6) possible paleosols capping the two oldest sequences are regressive surfaces of subaerial exposure that were preserved during transgressions; and (7) no incised valleys or submarine canyons breach the paleoshelf margin, even though incised drainages were present updip and sea level curves indicate several periods of rapid fall.

  17. Backbone of credit relationships in the Japanese credit market

    E-print Network

    Marotta, Luca; Fujiwara, Yoshi; Iyetomi, Hiroshi; Aoyama, Hideaki; Gallegati, Mauro; Mantegna, Rosario N

    2015-01-01

    We detect the backbone of the weighted bipartite network of the Japanese credit market relationships. The backbone is detected by adapting a general method used in the investigation of weighted networks. With this approach we detect a backbone that is statistically validated against a null hypothesis of uniform diversification of loans for banks and firms. Our investigation is done year by year and it covers more than thirty years during the period from 1980 to 2011. We relate some of our findings with economic events that have characterized the Japanese credit market during the last years. The study of the time evolution of the backbone allows us to detect changes occurred in network size, fraction of credit explained, and attributes characterizing the banks and the firms present in the backbone.

  18. A fractographic investigation of the influence of stacking sequence on the strength of notched laminated composites

    NASA Technical Reports Server (NTRS)

    Harris, Charles E.; Morris, Don H.

    1987-01-01

    The fracture behavior of T300/5208 CFRP laminate panels with 12 different combinations of ply orientation and stacking sequence is investigated experimentally, using optical microscopy, SEM, and X-ray radiography to characterize the notch-tip damage zones and fracture surfaces of center-cracked tension specimens subjected to tensile loading at constant crosshead displacement rate 20 micron/s. The results are presented graphically and analyzed in detail. Significant differences in notched strength are found for different ply fiber orientations and stacking sequences; the laminates with few major delaminations had a greater percentage of fracture due to broken fibers and also higher notched strength.

  19. Backbones of evolutionary history test biodiversity theory for microbes

    PubMed Central

    O’Dwyer, James P.; Kembel, Steven W.; Sharpton, Thomas J.

    2015-01-01

    Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities. PMID:26106159

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

    SciTech Connect

    Fidanza, J.A.

    1992-01-01

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

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

    PubMed Central

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

    2010-01-01

    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

  2. High Speed Fibre Optic Backbone LAN

    NASA Astrophysics Data System (ADS)

    Tanimoto, Masaaki; Hara, Shingo; Kajita, Yuji; Kashu, Fumitoshi; Ikeuchi, Masaru; Hagihara, Satoshi; Tsuzuki, Shinji

    1987-09-01

    Our firm has developed the SUMINET-4100 series, a fibre optic local area network (LAN), to serve the communications system trunk line needs for facilities, such as steel refineries, automobile plants and university campuses, that require large transmission capacity, and for the backbone networks used in intelligent building systems. The SUMINET-4100 series is already in service in various fields of application. Of the networks available in this series, the SUMINET-4150 has a trunk line speed of 128 Mbps and the multiplexer used for time division multiplexing (TDM) was enabled by designing an ECL-TTL gate array (3000 gates) based custom LSI. The synchronous, full-duplex V.24 and V.3.5 interfaces (SUMINET-2100) are provided for use with general purpose lines. And the IBM token ring network, the SUMINET-3200, designed for heterogeneous PCs and the Ethernet can all be connected to sub loops. Further, the IBM 3270 TCA and 5080 CADAM can be connected in the local mode. Interfaces are also provided for the NTT high-speed digital service, the digital PBX systems, and the Video CODEC system. The built-in loop monitor (LM) and network supervisory processor (NSP) provide management of loop utilization and send loop status signals to the host CPU's network configuration and control facility (NCCF). These built-in functions allow both the computer system and LAN to be managed from a single source at the host. This paper outlines features of the SUMINET-4150 and provides an example of its installation.

  3. Manipulating the backbone structure of semiconducting polymers

    NASA Astrophysics Data System (ADS)

    Luscombe, Christine

    2015-03-01

    Pi-Conjugated polymers are being used in the fabrication of a wide variety of organic electronic devices such as organic field-effect transistors (OFETs), organic photovoltaic (OPV) devices, and organic light-emitting diodes (OLEDs). The advances made in organic electronics have been driven by the syntheses of pi-conjugated polymers with increasingly complex structures but have heavily relied on an Edisonian approach. Despite these advances, there are many contradictory reports in the literature about our understanding of the performance of ?-conjugated polymers in many applications. Our group has been studying and developing techniques to grow semiconducting polymers using a living polymerization method. This has allowed us to synthesize polymer architectures that we haven't been able to access till now including polythiophene brushes, star-shaped P3HT, as well as hyperbranched P3HT. It also allows us to accurately control the molecular weights of P3HT and produce materials with a narrow molecular weight distribution. In this presentation, our work towards creating brush polymers will be presented where a series of fully conjugated graft copolymers containing poly(3-hexylthiophene) (P3HT) side chains and a p-type carbazole-diketopyrrolopyrrole donor-acceptor backbone were synthesized via a graft through Suzuki polymerization.

  4. Extracting the Information Backbone in Online System

    PubMed Central

    Zhang, Qian-Ming; Zeng, An; Shang, Ming-Sheng

    2013-01-01

    Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity) of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such “less can be more” feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency. PMID:23690946

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

    NASA Astrophysics Data System (ADS)

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

    1998-12-01

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

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

    SciTech Connect

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

    1998-12-01

    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.

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

    SciTech Connect

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

    1998-12-10

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

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

    SciTech Connect

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

    1998-12-01

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

  9. Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins

    PubMed Central

    2015-01-01

    We present a generic solvated coarse-grained protein model that can be used to characterize the driving forces behind protein folding. Each amino acid is coarse-grained with two beads, a backbone, and a side chain. Although the backbone beads are modeled as polar entities, side chains are hydrophobic, polar, or charged, thus allowing the exploration of how sequence patterning determines a protein fold. The change in orientation of the atoms of the coarse-grained unit is captured by the addition of two oppositely charged dummy particles inside the backbone coarse-grained bead. These two dummy charges represent a dipole that can fluctuate, thus introducing structural polarization into the coarse-grained model. Realistic ?/? content is achieved de novo without any biases in the force field toward a particular secondary structure. The dipoles created by the dummy particles interact with each other and drive the protein models to fold into unique structures depending on the amino acid patterning and presence of capping residues. We have also characterized the role of dipole–dipole and dipole–charge interactions in shaping the secondary and supersecondary structure of proteins. Formation of helix bundles and ?-strands are also discussed. PMID:24932137

  10. Resilience Characteristics of the Internet Backbone Routing Infrastructure

    E-print Network

    Resilience Characteristics of the Internet Backbone Routing Infrastructure Craig Labovitz, Roger inter- domain routing infrastructure. Further, we explore large-scale vulnerabilities in Inter- net infrastructure in the presence of failure or malicious attacks. The Internet's sustained exponential growth

  11. A backbone lever-arm effect enhances polymer mechanochemistry.

    PubMed

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

    2013-02-01

    Mechanical forces along a polymer backbone can be used to bring about remarkable reactivity in embedded mechanically active functional groups, but little attention has been paid to how a given polymer backbone delivers that force to the reactant. Here, single-molecule force spectroscopy was used to directly quantify and compare the forces associated with the ring opening of gem-dibromo and gem-dichlorocyclopropanes affixed along the backbone of cis-polynorbornene and cis-polybutadiene. The critical force for isomerization drops by about one-third in the polynorbornene scaffold relative to polybutadiene. The root of the effect lies in more efficient chemomechanical coupling through the polynorbornene backbone, which acts as a phenomenological lever with greater mechanical advantage than polybutadiene. The experimental results are supported computationally and provide the foundation for a new strategy by which to engineer mechanochemical reactivity. PMID:23344431

  12. A backbone lever-arm effect enhances polymer mechanochemistry

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

  13. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data

    PubMed Central

    El-Kebir, Mohammed; Oesper, Layla; Acheson-Field, Hannah; Raphael, Benjamin J.

    2015-01-01

    Motivation: DNA sequencing of multiple samples from the same tumor provides data to analyze the process of clonal evolution in the population of cells that give rise to a tumor. Results: We formalize the problem of reconstructing the clonal evolution of a tumor using single-nucleotide mutations as the variant allele frequency (VAF) factorization problem. We derive a combinatorial characterization of the solutions to this problem and show that the problem is NP-complete. We derive an integer linear programming solution to the VAF factorization problem in the case of error-free data and extend this solution to real data with a probabilistic model for errors. The resulting AncesTree algorithm is better able to identify ancestral relationships between individual mutations than existing approaches, particularly in ultra-deep sequencing data when high read counts for mutations yield high confidence VAFs. Availability and implementation: An implementation of AncesTree is available at: http://compbio.cs.brown.edu/software. Contact: braphael@brown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26072510

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

    PubMed

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

    2013-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

    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.

  16. Bioinformatical parsing of folding-on-binding proteins reveals their compositional and evolutionary sequence design

    PubMed Central

    Narasumani, Mohanalakshmi; Harrison, Paul M

    2015-01-01

    Intrinsic disorder occurs when (part of) a protein remains unfolded during normal functioning. Intrinsically-disordered regions can contain segments that ‘fold on binding’ to another molecule. Here, we perform bioinformatical parsing of human ‘folding-on-binding’ (FB) proteins, into four subsets: Ordered regions, FB regions, Disordered regions that surround FB regions (‘Disordered-around-FB’), and Other-Disordered regions. We examined the composition and evolutionary behaviour (across vertebrate orthologs) of these subsets. From a convergence of three separate analyses, we find that for hydrophobicity, Ordered regions segregate from the other subsets, but the Ordered and FB regions group together as highly conserved, and the Disordered-around-FB and Other-Disordered regions as less conserved (with a lesser significant difference between Ordered and FB regions). FB regions are highly-conserved with net positive charge, whereas Disordered-around-FB have net negative charge and are relatively less hydrophobic than FB regions. Indeed, these Disordered-around-FB regions are excessively hydrophilic compared to other disordered regions generally. We describe how our results point towards a possible compositionally-based steering mechanism of folding-on-binding. PMID:26678310

  17. Radical-driven peptide backbone dissociation tandem mass spectrometry.

    PubMed

    Oh, Han Bin; Moon, Bongjin

    2015-01-01

    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. PMID:24863492

  18. Identification of protein N-termini in Cyanophora paradoxa cyanelles: transit peptide composition and sequence determinants for precursor maturation

    PubMed Central

    Köhler, Daniel; Dobritzsch, Dirk; Hoehenwarter, Wolfgang; Helm, Stefan; Steiner, Jürgen M.; Baginsky, Sacha

    2015-01-01

    Glaucophyta, rhodophyta, and chloroplastida represent the three main evolutionary lineages that diverged from a common ancestor after primary endosymbiosis. Comparative analyses between members of these three lineages are a rich source of information on ancestral plastid features. We analyzed the composition and the cleavage site of cyanelle transit peptides from the glaucophyte Cyanophora paradoxa by terminal amine labeling of substrates (TAILS), and compared their characteristics to those of representatives of the chloroplastida. Our data show that transit peptide architecture is similar between members of these two lineages. This entails a comparable modular structure, an overrepresentation of serine or alanine and similarities in the amino acid composition around the processing peptidase cleavage site. The most distinctive difference is the overrepresentation of phenylalanine in the N-terminal 1–10 amino acids of cyanelle transit peptides. A quantitative proteome analysis with periplasm-free cyanelles identified 42 out of 262 proteins without the N-terminal phenylalanine, suggesting that the requirement for phenylalanine in the N-terminal region is not absolute. Proteins in this set are on average of low abundance, suggesting that either alternative import pathways are operating specifically for low abundance proteins or that the gene model annotation is incorrect for proteins with fewer EST sequences. We discuss these two possibilities and provide examples for both interpretations. PMID:26257763

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

    PubMed

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

    2015-03-01

    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

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

    PubMed

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

    2014-04-01

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

  1. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

    PubMed Central

    Ollikainen, Noah; de Jong, René M.; Kortemme, Tanja

    2015-01-01

    Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein–ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art “fixed backbone” design methods perform poorly on these tests, we develop a new “coupled moves” design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein – ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution. PMID:26397464

  2. A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences

    PubMed Central

    Tsay, Jyh-Jong; Su, Shih-Chieh; Yu, Chin-Sheng

    2015-01-01

    Protein structure prediction (PSP) is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD) of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP. PMID:26151847

  3. A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences.

    PubMed

    Tsay, Jyh-Jong; Su, Shih-Chieh; Yu, Chin-Sheng

    2015-01-01

    Protein structure prediction (PSP) is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD) of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP. PMID:26151847

  4. PS1-10jh: The disruption of a main-sequence star of near-solar composition

    SciTech Connect

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

    2014-03-01

    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.

  5. Contribution of Peptide Backbone to Anti-Citrullinated Peptide Antibody Reactivity

    PubMed Central

    Trier, Nicole Hartwig; Dam, Catharina Essendrup; Olsen, Dorthe Tange; Hansen, Paul Robert; Houen, Gunnar

    2015-01-01

    Rheumatoid arthritis (RA) is one of the most common autoimmune diseases, affecting approximately 1–2% of the world population. One of the characteristic features of RA is the presence of autoantibodies. Especially the highly specific anti-citrullinated peptide antibodies (ACPAs), which have been found in up to 70% of RA patients’ sera, have received much attention. Several citrullinated proteins are associated with RA, suggesting that ACPAs may react with different sequence patterns, separating them from traditional antibodies, whose reactivity usually is specific towards a single target. As ACPAs have been suggested to be involved in the development of RA, knowledge about these antibodies may be crucial. In this study, we examined the influence of peptide backbone for ACPA reactivity in immunoassays. The antibodies were found to be reactive with a central Cit-Gly motif being essential for ACPA reactivity and to be cross-reactive between the selected citrullinated peptides. The remaining amino acids within the citrullinated peptides were found to be of less importance for antibody reactivity. Moreover, these findings indicated that the Cit-Gly motif in combination with peptide backbone is essential for antibody reactivity. Based on these findings it was speculated that any amino acid sequence, which brings the peptide into a properly folded structure for antibody recognition is sufficient for antibody reactivity. These findings are in accordance with the current hypothesis that structural homology rather than sequence homology are favored between citrullinated epitopes. These findings are important in relation to clarifying the etiology of RA and to determine the nature of ACPAs, e.g. why some Cit-Gly-containing sequences are not targeted by ACPAs. PMID:26657009

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

    NASA Astrophysics Data System (ADS)

    Paredes, Eduardo

    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.

  7. A Consistent Phylogenetic Backbone for the Fungi

    PubMed Central

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

    2012-01-01

    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

  8. Ultradeep 16S rRNA Sequencing Analysis of Geographically Similar but Diverse Unexplored Marine Samples Reveal Varied Bacterial Community Composition

    PubMed Central

    Karutha Pandian, Shunmugiah

    2013-01-01

    Background Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. Methods and Principal Findings In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62–71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples. Conclusion This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater) and the host associated marine samples (Seaweed and Seagrass) at higher depths from uncharacterised coastal region of Palk Bay, India using next generation sequencing technology. PMID:24167548

  9. LARC-IA: A flexible backbone polyimide

    NASA Technical Reports Server (NTRS)

    Progar, Donald J.; Stclair, Terry L.

    1990-01-01

    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.

  10. Transforming Plastic Surfaces with Electrophilic Backbones from Hydrophobic to Hydrophilic

    E-print Network

    Zare, Richard N.

    Transforming Plastic Surfaces with Electrophilic Backbones from Hydrophobic to Hydrophilic Samuel demonstrate a simple nonaqueous reaction scheme for transforming the surface of plastics from hydrophobic. It is permanent, does not release contaminants, and causes no optical or mechanical distortion of the plastic. We

  11. Cooperative UAV-Based Communications Backbone for Sensor Networks

    SciTech Connect

    Roberts, R S

    2001-10-07

    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.

  12. Provisioning IP Backbone Networks to Support Latency Sensitive Traffic

    E-print Network

    Tobagi, Fouad

    collected from the Sprint IP network. We then develop a procedure which uses this model to find the amountProvisioning IP Backbone Networks to Support Latency Sensitive Traffic Chuck Fraleigh and Fouad this procedure to the Sprint network, we find that satisfying end-to-end delay requirements as low as 3 ms

  13. The Graphical Representation of the Digital Astronaut Physiology Backbone

    NASA Technical Reports Server (NTRS)

    Briers, Demarcus

    2010-01-01

    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.

  14. A six-dimensional alpha proton detection-based APSY experiment for backbone assignment of intrinsically disordered proteins.

    PubMed

    Yao, Xuejun; Becker, Stefan; Zweckstetter, Markus

    2014-12-01

    Sequence specific resonance assignment is the prerequisite for the NMR-based analysis of the conformational ensembles and their underlying dynamics of intrinsically disordered proteins. However, rapid solvent exchange in intrinsically disordered proteins often complicates assignment strategies based on HN-detection. Here we present a six-dimensional alpha proton detection-based automated projection spectroscopy (APSY) experiment for backbone assignment of intrinsically disordered proteins. The 6D HCACONCAH APSY correlates the six different chemical shifts, H(?)(i - 1), C(?)(i - 1), C'(i - 1), N(i), C?(i) and H?(i). Application to two intrinsically disordered proteins, 140-residue ?-synuclein and a 352-residue isoform of Tau, demonstrates that the chemical shift information provided by the 6D HCACONCAH APSY allows efficient backbone resonance assignment of intrinsically disordered proteins. PMID:25367087

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

    PubMed Central

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

    2013-01-01

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

  16. Tackling speciose genera: species composition and phylogenetic position of Senecio sect. Jacobaea (Asteraceae) based onplastid and nrDNA sequences.

    PubMed

    Pelser, Pieter B; Gravendeel, Barbara; van der Meijden, Ruud

    2002-06-01

    The molecular phylogeny of Senecio sect. Jacobaea (Asteraceae; Senecioneae) was studied to clarify species composition and interspecific relationships of Senecio sect. Jacobaea. This information is necessary for studies seeking explanations of the evolutionary success of Senecio, in terms of high species numbers and the evolution of chemical defense mechanisms. Parsimony analyses with 60 species of the tribe Senecioneae, representing 23 genera and 11 sections of Senecio, based on DNA sequence data of the plastid genome (the trnT-L intergenic spacer, the trnL intron, and two parts of the trnK intron, flanking both sides of the matK gene) and nuclear genome (ITS1, 5.8S, and ITS2 gene and spacers) show that sect. Jacobaea is a strongly supported monophyletic group. Fifteen species have been identified as members of section Jacobaea, including three species that have been consistently ascribed to this section in taxonomic literature and 12 species that were either placed in other sections of Senecio or not exclusively ascribed to sect. Jacobaea. This section was traditionally circumscribed as a group of European, biennial, or perennial herbs with pinnately incised leaves, but the results of this study show that one annual species, a species from northeastern Asia, and a species growing in the Himalayas are members of sect. Jacobaea as well. Furthermore, not all species in the section have pinnately incised leaves. The genera Emilia, Packera, and Pseudogynoxys form the sister clade of sect. Jacobaea, but this relationship lacks strong bootstrap support and thus remains provisional. PMID:21665692

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

    PubMed Central

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

    2013-01-01

    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

  18. 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)

    Terentiev, R. A.

    2014-03-01

    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.

  19. Active and Passive Measurements on Campus, Regional and National Network Backbone Paths

    E-print Network

    Calyam, Prasad

    1 Active and Passive Measurements on Campus, Regional and National Network Backbone Paths 1 Prasad of the active and passive measurement data collected along network backbone paths within typical campus traffic dynamics in the different academic network backbones and can be used for better design and control

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

    E-print Network

    Simaan, Nabil

    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

  1. Efficient and Resilient Backbones for Multihop Wireless Networks Seungjoon Lee Bobby Bhattacharjee Aravind Srinivasan Samir Khuller

    E-print Network

    Srinivasan, Aravind

    failures or high mobility. We present a parameterized backbone construction algorithm that permits explicit tradeoffs between backbone size, resilience to node movement and failure, energy consumption, and path dominating set is NP-hard. battery-powered, the use of low-battery nodes in the backbone can shorten

  2. Strong liquid-crystalline polymeric compositions

    DOEpatents

    Dowell, Flonnie (Los Alamos, NM)

    1993-01-01

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

  3. Strong liquid-crystalline polymeric compositions

    DOEpatents

    Dowell, F.

    1993-12-07

    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.

  4. Extracting the Globally and Locally Adaptive Backbone of Complex Networks

    PubMed Central

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

    2014-01-01

    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

  5. Backbone decomposition for continuous-state branching processes with immigration

    E-print Network

    Ren, A E Kyprianou Y-X

    2011-01-01

    In the spirit of Duqesne and Winkel (2007) and Berestycki et al. (2011) we show that supercritical continuous-state branching process with a general branching mechanism and general immigration mechanism is equal in law to a continuous-time Galton Watson process with immigration with Poissonian dressing. The result also characterises the limiting backbone decomposition which is predictable from the work on consistent growth of Galton-Watson trees with immigration in Cao and Winkel (2010).

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

    PubMed Central

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

    2008-01-01

    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

  7. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning

    PubMed Central

    Heffernan, Rhys; Paliwal, Kuldip; Lyons, James; Dehzangi, Abdollah; Sharma, Alok; Wang, Jihua; Sattar, Abdul; Yang, Yuedong; Zhou, Yaoqi

    2015-01-01

    Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary structure and torsion angle prediction. In this study, we expand the iterative features to include solvent accessible surface area and backbone angles and dihedrals based on C? atoms. By using a deep learning neural network in three iterations, we achieved 82% accuracy for secondary structure prediction, 0.76 for the correlation coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute errors of backbone ? and ? angles, respectively, and 8° and 32° for mean absolute errors of C?-based ? and ? angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking. PMID:26098304

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

    PubMed

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

    2013-02-26

    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

  9. Origin of the Temporal-compositional Variations in Monogenetic Vent Eruptions: Insights from the Crystal Cargo in the Papoose Canyon Sequence, Big Pine Volcanic Field, CA

    NASA Astrophysics Data System (ADS)

    Gao, R.; Ramirez, G.; Lassiter, J. C.

    2014-12-01

    Systematic temporal-compositional variations observed in many monogenetic vent eruption sequences (e.g. decreasing incompatible element concentrations, variation in major element and isotopic compositions) may reflect varying extents of crustal contamination (c.f., [1]), or melting and mixing of small-scale mantle heterogeneities (c.f., [2]). During eruption of the Papoose Canyon (PC) monogenetic vent incompatible trace element concentrations decreased a factor of 2, 87Sr/86Sr decreased (from ~0.7063 to 0.7055), and 143Nd/144Nd increased (from ~0.51246 to 0.51258) (c.f., [2]). Blondes et al. (2008) argued that the relatively primitive melt MgO content and apparent presence of mantle xenoliths in the sequence indicate limited melt storage and crustal contamination prior to eruption, and proposed melting and mixing of two distinct mantle components to explain the variations. However, PC olivine phenocryst compositions (Fo# ~76-89) span a wide range, extending to evolved (low-Fo) compositions, and the vast majority of phenocrysts are more evolved than olivines in equilibrium with the host scoria (Mg# ~87-89). In addition, olivine and clinopyroxene from xenoliths within the early sequence have Mg# (73-87) similar to the phenocrysts, and lower than typical mantle peridotites. Sr-Nd isotopic compositions of the xenoliths are similar to the early PC lavas, but less enriched than the host melts. Therefore, the xenoliths are most likely cognate xenoliths derived from fractionated PC magmas. Finally, both phenocryst and xenolith olivines have ?18O (~5.5 to 5.7 ‰) higher than most mantle peridotites (~5.2 ±0.2 ‰), and clinopyroxene trace element abundances indicate derivation from melts with trace element abundances higher than the most enriched PC lavas. In conjunction, these features suggest that the phenocrysts and xenoliths derive from early PC melts that ponded and fractionated and assimilated continental crust, possibly in crustal sills. These melts were drained and mixed with more primitive melts as the eruption began, and the temporal-compositional trends in part reflect decreasing contaminated sill component over time. These results indicate that even "primitive" melts may contain a significant signature of crustal contamination. [1] Erlund et al., 2010. [2] Blondes et al., 2008.

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

    SciTech Connect

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

    2008-09-23

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

  11. 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)

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

    2015-01-01

    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.

  12. Composite-180° Pulse-Based Symmetry Sequences to Recouple Proton Chemical Shift Anisotropy Tensors under Ultrafast MAS Solid-State NMR Spectroscopy

    PubMed Central

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

    2015-01-01

    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. PMID:25497846

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

    PubMed Central

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

    2014-01-01

    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

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

    DOE PAGESBeta

    None

    2014-12-01

    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 Illuminamore »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.« less

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

    SciTech Connect

    2014-12-01

    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.

  16. High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis

    PubMed Central

    Liu, Aicui; Wang, Chao; Liang, Zhijuan; Zhou, Zhi-Wei; Wang, Lin; Ma, Qiaoli; Wang, Guowei; Zhou, Shu-Feng; Wang, Zhenhai

    2015-01-01

    Purulent meningitis (PM) is a severe infectious disease that is associated with high rates of morbidity and mortality. It has been recognized that bacterial infection is a major contributing factor to the pathogenesis of PM. However, there is a lack of information on the bacterial composition in PM, due to the low positive rate of cerebrospinal fluid bacterial culture. Herein, we aimed to discriminate and identify the main pathogens and bacterial composition in cerebrospinal fluid sample from PM patients using high-throughput sequencing approach. The cerebrospinal fluid samples were collected from 26 PM patients, and were determined as culture-negative samples. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 26 samples of PM were sequenced using the 454 GS FLX system. The results showed that there were 71,440 pyrosequencing reads, of which, the predominant phyla were Proteobacteria and Firmicutes; and the predominant genera were Streptococcus, Acinetobacter, Pseudomonas, and Neisseria. The bacterial species in the cerebrospinal fluid were complex, with 61.5% of the samples presenting with mixed pathogens. A significant number of bacteria belonging to a known pathogenic potential was observed. The number of operational taxonomic units for individual samples ranged from six to 75 and there was a comparable difference in the species diversity that was calculated through alpha and beta diversity analysis. Collectively, the data show that high-throughput sequencing approach facilitates the characterization of the pathogens in cerebrospinal fluid and determine the abundance and the composition of bacteria in the cerebrospinal fluid samples of the PM patients, which may provide a better understanding of pathogens in PM and assist clinicians to make rational and effective therapeutic decisions. PMID:26300628

  17. Composite

    NASA Astrophysics Data System (ADS)

    Kim, Su-Hyeon; Cho, Young-Hee; Lee, Jung-Moo

    2014-06-01

    Particle distribution and hot workability of an in situ Al-TiCp composite were investigated. The composite was fabricated by an in situ casting method using the self-propagating high-temperature synthesis of an Al-Ti-C system. Hot-compression tests were carried out, and power dissipation maps were constructed using a dynamic material model. Small globular TiC particles were not themselves fractured, but the clustering and grain boundary segregation of the particles contributed to the cracking of the matrix by causing the debonding of matrix/particle interfaces and providing a crack propagation path. The efficiency of power dissipation increased with increasing temperature and strain rate, and the maximum efficiency was obtained at a temperature of 723 K (450 °C) and a strain rate of 1/s. The microstructural mechanism occurring in the maximum efficiency domain was dynamic recrystallization. The role of particles in the plastic flow and the microstructure evolution were discussed.

  18. Composite Sequence–Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development

    PubMed Central

    Manocheewa, Siriphan; Mittler, John E; Samudrala, Ram; Mullins, James I

    2015-01-01

    Rapid evolution and high sequence diversity enable Human Immunodeficiency Virus (HIV) populations to acquire mutations to escape antiretroviral drugs and host immune responses, and thus are major obstacles for the control of the pandemic. One strategy to overcome this problem is to focus drugs and vaccines on regions of the viral genome in which mutations are likely to cripple function through destabilization of viral proteins. Studies relying on sequence conservation alone have had only limited success in determining critically important regions. We tested the ability of two structure-based computational models to assign sites in the HIV-1 capsid protein (CA) that would be refractory to mutational change. The destabilizing mutations predicted by these models were rarely found in a database of 5811 HIV-1 CA coding sequences, with none being present at a frequency greater than 2%. Furthermore, 90% of variants with the low predicted stability (from a set of 184 CA variants whose replication fitness or infectivity has been studied in vitro) had aberrant capsid structures and reduced viral infectivity. Based on the predicted stability, we identified 45 CA sites prone to destabilizing mutations. More than half of these sites are targets of one or more known CA inhibitors. The CA regions enriched with these sites also overlap with peptides shown to induce cellular immune responses associated with lower viral loads in infected individuals. Lastly, a joint scoring metric that takes into account both sequence conservation and protein structure stability performed better at identifying deleterious mutations than sequence conservation or structure stability information alone. The computational sequence–structure stability approach proposed here might therefore be useful for identifying immutable sites in a protein for experimental validation as potential targets for drug and vaccine development. PMID:26556362

  19. Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development.

    PubMed

    Manocheewa, Siriphan; Mittler, John E; Samudrala, Ram; Mullins, James I

    2015-01-01

    Rapid evolution and high sequence diversity enable Human Immunodeficiency Virus (HIV) populations to acquire mutations to escape antiretroviral drugs and host immune responses, and thus are major obstacles for the control of the pandemic. One strategy to overcome this problem is to focus drugs and vaccines on regions of the viral genome in which mutations are likely to cripple function through destabilization of viral proteins. Studies relying on sequence conservation alone have had only limited success in determining critically important regions. We tested the ability of two structure-based computational models to assign sites in the HIV-1 capsid protein (CA) that would be refractory to mutational change. The destabilizing mutations predicted by these models were rarely found in a database of 5811 HIV-1 CA coding sequences, with none being present at a frequency greater than 2%. Furthermore, 90% of variants with the low predicted stability (from a set of 184 CA variants whose replication fitness or infectivity has been studied in vitro) had aberrant capsid structures and reduced viral infectivity. Based on the predicted stability, we identified 45 CA sites prone to destabilizing mutations. More than half of these sites are targets of one or more known CA inhibitors. The CA regions enriched with these sites also overlap with peptides shown to induce cellular immune responses associated with lower viral loads in infected individuals. Lastly, a joint scoring metric that takes into account both sequence conservation and protein structure stability performed better at identifying deleterious mutations than sequence conservation or structure stability information alone. The computational sequence-structure stability approach proposed here might therefore be useful for identifying immutable sites in a protein for experimental validation as potential targets for drug and vaccine development. PMID:26556362

  20. Tuning the guest-binding ability of a helically folded capsule by in situ modification of the aromatic oligoamide backbone.

    PubMed

    Lautrette, Guillaume; Aube, Christophe; Ferrand, Yann; Pipelier, Muriel; Blot, Virginie; Thobie, Christine; Kauffmann, Brice; Dubreuil, Didier; Huc, Ivan

    2014-02-01

    Starting from a previously described aromatic oligoamide helically folded capsule that binds tartaric acid with high affinity and diastereoselectivity, we demonstrate the feasibility of the direct in situ modification of the helix backbone, which results in a conformational change that reduces its affinity for guests by two orders of magnitude. Specifically, ring contraction of the central pyridazine unit into a pyrrole in the full helical sequence was investigated by using electrochemical and chemical processes. The sequence containing the pyrrole was synthesized independently in a convergent manner to ascertain its structure. The conformation of the pyrrolic folded capsule was elucidated in the solid state by X-ray crystallography and in solution by using (1)H and (13)C?NMR spectroscopy. Solution studies revealed an unanticipated solvent-dependent equilibrium between the anti-anti and syn-syn conformations of the pyrrole ring with respect to its two adjacent pyridine units. Titrations of the pyrrole-containing sequence monitored by (1)H?NMR spectroscopy confirmed the expected drop in affinity for tartaric acid and malic acid that arises from the conformation change in the backbone that follows the replacement of the pyridazine by a pyrrole. The reduction of the pyridazine to a pyrrole was characterized by cyclic voltammetry both on the entire sequence and on a shorter precursor. The lower cathodic potential of the precursor made its preparative-scale electroreduction possible. Direct in situ modification of the pyridazine within the entire capsule sequence was achieved chemically by using zinc in acetic acid. PMID:24402735

  1. Composition and variation analysis of the TCR ?-chain CDR3 repertoire in systemic lupus erythematosus using high-throughput sequencing.

    PubMed

    Sui, Weiguo; Hou, Xianliang; Zou, Guimian; Che, Wenti; Yang, Ming; Zheng, Can; Liu, Fuhua; Chen, Peng; Wei, Xiaolian; Lai, Liusheng; Dai, Yong

    2015-10-01

    The ability of T lymphocytes to mount an immune response against a diverse array of pathogens is primarily conveyed by the amino acid (aa) sequence of the hypervariable complementarity-determining region 3 (CDR3) segments of the T cell receptor (TCR). In this study, we used a combination of multiplex-PCR, Illumina sequencing and IMGT/HighV-QUEST for a standardized analysis of the characteristics and polymorphisms of the T-cell receptor BV complementarity-determining region 3 (TCR BV CDR3) gene in peripheral blood mononuclear cells (PBMCs) from SLE patients and healthy donors (NC). We found the distributions of CDR3, VD indel, and DJ indel lengths to be comparable between the SLE and NC groups. The degree of clonal expansion in the SLE group was significantly greater than in the NC group, and the expression levels of 10 TR?V segments and 6 TR?J segments were also significantly different in the SLE group. Regarding public T cell responses, 3CDR3 DNA sequences and 4 aa sequences were shared by all SLE patients and may serve as biomarkers for SLE disease risk, diagnosis and/or prognosis. PMID:26227771

  2. Bacterial Pathogens and Community Composition in Advanced Sewage Treatment Systems Revealed by Metagenomics Analysis Based on High-Throughput Sequencing

    PubMed Central

    Lu, Xin; Zhang, Xu-Xiang; Wang, Zhu; Huang, Kailong; Wang, Yuan; Liang, Weigang; Tan, Yunfei; Liu, Bo; Tang, Junying

    2015-01-01

    This study used 454 pyrosequencing, Illumina high-throughput sequencing and metagenomic analysis to investigate bacterial pathogens and their potential virulence in a sewage treatment plant (STP) applying both conventional and advanced treatment processes. Pyrosequencing and Illumina sequencing consistently demonstrated that Arcobacter genus occupied over 43.42% of total abundance of potential pathogens in the STP. At species level, potential pathogens Arcobacter butzleri, Aeromonas hydrophila and Klebsiella pneumonia dominated in raw sewage, which was also confirmed by quantitative real time PCR. Illumina sequencing also revealed prevalence of various types of pathogenicity islands and virulence proteins in the STP. Most of the potential pathogens and virulence factors were eliminated in the STP, and the removal efficiency mainly depended on oxidation ditch. Compared with sand filtration, magnetic resin seemed to have higher removals in most of the potential pathogens and virulence factors. However, presence of the residual A. butzleri in the final effluent still deserves more concerns. The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment. Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence. PMID:25938416

  3. A highly selective and sensitive electrochemical CS-MWCNTs/Au-NPs composite DNA biosensor for Staphylococcus aureus gene sequence detection.

    PubMed

    Sun, Yange; He, Xingxing; Ji, Jian; Jia, Min; Wang, Zhouping; Sun, Xiulan

    2015-08-15

    This paper presents a new electrochemical DNA biosensor constructed using a substrate electrode composed of a novel nanocomposite material prepared using gold nanoparticles (Au-NPs) and multiwalled carbon nanotubes (MWCNTs) and further modified with an Au electrode (AuE), which was used as the substrate electrode. A single-stranded DNA (ssDNA) probe was immobilized on the Au-NPs/CS-MWCNTs/AuE electrode by means of facile gold-thiol affinity, which resulted in hybridization with the target ssDNA sequence. Hybridization reactions were assessed by using the reduction peak current of methylene blue (MB) as an electrochemical indicator. The advantages of the nanomaterials were found to include high surface area, favorable electronic properties, and strong electrocatalytic activity. The amount of ssDNA adsorbed on the electrode surface was increased and the electrochemical response of MB accelerated. The differential pulse voltammetric responses of MB were in line with the specific target ssDNA sequence within the concentration range 1.0×10(-15)-1.0×10(-8)M with the detection limit 3.3×10(-16)M (3?). In the colony forming unit (CFU) we were able to detect 10CFU mL(-1)of Staphylococcus aureus in the tap water, achieving good discrimination ability between one- and three-base mismatched ssDNA sequences. The polymerase chain reaction (PCR) amplification products of S. aureus nuc gene sequence were also detected with satisfactory results. PMID:25966418

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

    PubMed Central

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

    2015-01-01

    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

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

    PubMed

    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

    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

  6. Composites

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

    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.

  7. Deep sequencing reveals different compositions of mRNA transcribed from the F8 gene in a panel of FVIII-producing CHO cell lines.

    PubMed

    Kaas, Christian S; Bolt, Gert; Hansen, Jens J; Andersen, Mikael R; Kristensen, Claus

    2015-07-01

    Coagulation factor VIII (FVIII) is one of the most complex biopharmaceuticals due to the large size, poor protein stability and extensive post-translational modifications. As a consequence, efficient production of FVIII in mammalian cells poses a major challenge, with typical yields two to three orders of magnitude lower than for antibodies. In the present study we investigated CHO DXB11 cells transfected with a plasmid encoding human coagulation factor VIII. Single cell clones were isolated from the pool of transfectants and a panel of 14 clones representing a dynamic range of FVIII productivities was selected for RNA sequencing analysis. The analysis showed distinct differences in F8 RNA composition between the clones. The exogenous F8-dhfr transcript was found to make up the most abundant transcript in the present clones. No correlation was seen between F8 mRNA levels and the measured FVIII productivity. It was found that three MTX resistant, nonproducing clones had different truncations of the F8 transcripts. We find that by using deep sequencing, in contrast to microarray technology, for determining the transcriptome from CHO transfectants, we are able to accurately deduce the mature mRNA composition of the transgene and identify significant truncations that would probably otherwise have remained undetected. PMID:25963793

  8. Complex of B-DNA with polyamides freezes DNA backbone flexibility.

    PubMed

    Wellenzohn, B; Flader, W; Winger, R H; Hallbrucker, A; Mayer, E; Liedl, K R

    2001-05-30

    The development of sequence-specific minor groove binding ligands is a modern and rapidly growing field of research because of their extraordinary importance as transcription-controlling drugs. We performed three molecular dynamics simulations in order to clarify the influence of minor groove binding of two ImHpPyPy-beta-Dp polyamides to the d(CCAGTACTGG)(2) decamer in the B-form. This decamer contains the recognition sequence for the trp repressor (5'-GTACT-3'), and it was investigated recently by X-ray crystallography. On one hand we are able to reproduce X-ray-determined DNA--drug contacts, and on the other hand we provide new contact information which is important for the development of potential ligands. The new insights show how the beta-tail of the polyamide ligands contributes to binding. Our simulations also indicate that complexation freezes the DNA backbone in a specific B(I) or B(II) substate conformation and thus optimizes nonbonded contacts. The existence of this distinct B(I)/B(II) substate pattern also allows the formation of water-mediated contacts. Thus, we suggest the B(I) <==> B(II) substate behavior to be an important part of the indirect readout of DNA. PMID:11457333

  9. Backbone and side-chain dynamics of residues in a partially folded beta-sheet peptide from platelet factor-4.

    PubMed Central

    Daragan, V. A.; Ilyina, E. E.; Fields, C. G.; Fields, G. B.; Mayo, K. H.

    1997-01-01

    Structurally characterizing partially folded states is problematic given the nature of these transient species. A peptide 20mer, T38AQLIATLKNGRKISLDLQA57 (P20), which has been shown to partially fold in a relatively stable turn/loop conformation (LKNGR) and transient beta-sheet structure, is a good model for studying backbone and side-chain mobilities in a transiently folded peptide by using 13C-NMR relaxation. Here, four residues in P20, A43, T44, G48, and 151, chosen for their positions in or near the loop conformation and for compositional variety, have been selectively 13C-enriched. Proton-coupled and decoupled 13C-NMR relaxation experiments have been performed to obtain the temperature dependencies (278 K to 343 K) of auto- and cross-correlation motional order parameters and correlation times. In order to differentiate sequence-neighbor effects from folding effects, two shorter peptides derived from P20, IATLK (P5) and NGRKIS (P6), were similarly 13C-enriched and investigated. For A43, T44, G48, and 151 residues in P20 relative to those in P5/P6, several observations are consistent with partial folding in P20: (1) C alpha H motional tendencies are all about the same, vary less with temperature, and are relatively more restricted, (2) G48 C alpha H2 phi (t) psi (t) rotations are more correlated, and (3) methyl group rotations are slower and yield lower activation energies consistent with formation of hydrophobic "pockets." In addition, T44 and 151 C beta H mobilities in P20 are more restricted at lower temperature than those of their C alpha H and display significantly greater sensitivity to temperature suggesting a larger enthalpic contribution to side-chain mobility. Moreover, at higher temperatures, side-chain methyls and methylenes in P20 are more motionally restricted than those in P5/P6, suggesting that some type of "folded" or "collapsed" structure remains in P20 for what normally would be considered an "unfolded" state. PMID:9041637

  10. Abundances of Triacylglycerol Positional Isomers and Enantiomers Comprised of a Dipalmitoylglycerol Backbone and Short- or Medium-chain Fatty Acids in Bovine Milk Fat.

    PubMed

    Nagai, Toshiharu; Watanabe, Natsuko; Yoshinaga, Kazuaki; Mizobe, Hoyo; Kojima, Koichi; Kuroda, Ikuma; Odanaka, Yuki; Saito, Tadao; Beppu, Fumiaki; Gotoh, Naohiro

    2015-01-01

    Bovine milk fat (BMF) is composed of triacylglycerols (TAG) rich in palmitic acid (P), oleic acid (O), and short-chain or medium-chain fatty acids (SCFAs or MCFAs). The composition and binding positions of the fatty acids on the glycerol backbone determine their physical and nutritional properties. SCFAs and MCFAs are known to characteristically bind to the sn-3 position of the TAGs in BMF; however, there are very few non-destructive analyses of TAG enantiomers binding the fatty acids at this position. We previously reported a method to resolve the enantiomers of TAGs, binding both long-chain saturated fatty acid and unsaturated fatty acid at the sn-1 and 3 positions, in palm oil, fish oil, and marine mammal oil using chiral HPLC. Here, we further developed a method to resolve several TAG enantiomers containing a dipalmitoyl (PP) glycerol backbone and one SCFA (or MCFA) in BMF. We revealed that the predominant TAG structure in BMF was homochiral, such as 1,2-dipalmitoyl-3-butyroyl-sn-glycerol. This is the first quantitative determination of many TAG enantiomers, which bind to a SCFA or MCFA, in BMF was evaluated simultaneously. Furthermore, the results indicated that the amount ratios of the positional isomers and enantiomers of TAGs consisting of a dipalmitoyl (PP) glycerol backbone and SCFA (or MCFA), resembled the whole TAG structures containing the other diacylglycerol backbones consisting of P, O, myristic acid, and/or stearic acid in BMF. PMID:26329769

  11. Thin Films Formed from Conjugated Polymers with Ionic, Water-Soluble Backbones.

    PubMed

    Voortman, Thomas P; Chiechi, Ryan C

    2015-12-30

    This paper compares the morphologies of films of conjugated polymers in which the backbone (main chain) and pendant groups are varied between ionic/hydrophilic and aliphatic/hydrophobic. We observe that conjugated polymers in which the pendant groups and backbone are matched, either ionic-ionic or hydrophobic-hydrophobic, form smooth, structured, homogeneous films from water (ionic) or tetrahydrofuran (hydrophobic). Mismatched conjugated polymers, by contrast, form inhomogeneous films with rough topologies. The polymers with ionic backbone chains are conjugated polyions (conjugated polymers with closed-shell charges in the backbone), which are semiconducting materials with tunable bad-gaps, not unlike uncharged conjugated polymers. PMID:25723354

  12. Refined solution structure and backbone dynamics of HIV-1 Nef.

    PubMed Central

    Grzesiek, S.; Bax, A.; Hu, J. S.; Kaufman, J.; Palmer, I.; Stahl, S. J.; Tjandra, N.; Wingfield, P. T.

    1997-01-01

    The tendency of HIV-1 Nef to form aggregates in solution, particularly at pH values below 8, together with its large fraction of highly mobile residues seriously complicated determination of its three-dimensional structure, both for heteronuclear solution NMR (Grzesiek et al., 1996a, Nat Struct Biol 3:340-345) and for X-ray crystallography (Lee et al., 1996, Cell 85:931-942). Methods used to determine the Nef structure by NMR at pH 8 and 0.6 mM concentration are presented, together with a detailed description of Nef's secondary and tertiary structure. The described techniques have general applicability for the NMR structure determination of proteins that are aggregating and/or have limited stability at low pH values. Extensive chemical shift assignments are reported for backbone and side chain 1H, 13C, and 15N resonances of the HIV-1 Nef deletion mutants NEF delta 2-39, NEF delta 2-39, delta 159-173, and of NEF delta 2-39, delta 159-173 in complex with the SH3 domain of the Hck tyrosine protein kinase. Besides a type II polyproline helix, Nef's structure consists of three alpha-helices, a 3(10) helix, and a five-stranded anti-parallel beta-sheet. The analysis of 15N relaxation parameters of the backbone amide sites reveals that all the secondary structure elements are non-mobile on the picosecond to nanosecond and on the millisecond time scale. A large number of slowly exchanging amide protons provides evidence for the stability of the Nef core even on the time scale of hours. Significant internal motions on the ps to ns time scale are detected for residues 60 to 71 and for residues 149 to 180, which form solvent-exposed loops. The residues of the HIV-1 protease cleavage site (W57/L58) do not exhibit large amplitude motions on the sub-nanosecond time scale, and their side chains insert themselves into a hydrophobic crevice formed between the C-terminus of helix 1 and the N-terminus of helix 2. A refined structure has been determined based on additional constraints for side-chain and backbone dihedral angles derived from a large number of three-bond J-coupling and ROE data. PMID:9194185

  13. Backbone dynamics of barstar: a (15)N NMR relaxation study.

    PubMed

    Sahu, S C; Bhuyan, A K; Majumdar, A; Udgaonkar, J B

    2000-12-01

    Backbone dynamics of uniformly (15)N-labeled barstar have been studied at 32 degrees C, pH 6.7, by using (15)N relaxation data obtained from proton-detected 2D (1)H-(15)N NMR spectroscopy. (15)N spin-lattice relaxation rate constants (R(1)), spin-spin relaxation rate constants (R(2)), and steady-state heteronuclear (1)H-(15)N NOEs have been determined for 69 of the 86 (excluding two prolines and the N-terminal residue) backbone amide (15)N at a magnetic field strength of 14.1 Tesla. The primary relaxation data have been analyzed by using the model-free formalism of molecular dynamics, using both isotropic and axially symmetric diffusion of the molecule, to determine the overall rotational correlation time (tau(m)), the generalized order parameter (S(2)), the effective correlation time for internal motions (tau(e)), and NH exchange broadening contributions (R(ex)) for each residue. As per the axially symmetric diffusion, the ratio of diffusion rates about the unique and perpendicular axes (D( parallel)/D( perpendicular)) is 0.82 +/- 0.03. The two results have only marginal differences. The relaxation data have also been used to map reduced spectral densities for the NH vectors of these residues at three frequencies: 0, omega(H), and omega(N), where omega(H),(N) are proton and nitrogen Larmor frequencies. The value of tau(m) obtained from model-free analysis of the relaxation data is 5.2 ns. The reduced spectral density analysis, however, yields a value of 5.7 ns. The tau(m) determined here is different from that calculated previously from time-resolved fluorescence data (4.1 ns). The order parameter ranges from 0.68 to 0.98, with an average value of 0.85 +/- 0.02. A comparison of the order parameters with the X-ray B-factors for the backbone nitrogens of wild-type barstar does not show any considerable correlation. Model-free analysis of the relaxation data for seven residues required the inclusion of an exchange broadening term, the magnitude of which ranges from 2 to 9.1 s(-1), indicating the presence of conformational averaging motions only for a small subset of residues. PMID:11056034

  14. A Native to Amyloidogenic Transition Regulated by a Backbone Trigger

    SciTech Connect

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

    2006-01-01

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

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

    E-print Network

    Gunner, Marilyn

    Department, City College of New York, New York 10031 ABSTRACT Asymmetry in packing the peptide amide dipole 40% bases. The positive backbone potential stabilizes ionization of 20% of the acids by 3 pH units of the protein backbone is the most prev- alent polar group in any protein, and it plays several well established

  16. Solution Structure and Backbone Dynamics of the Holo Form of the Frenolicin Acyl Carrier Protein,)

    E-print Network

    Puglisi, Joseph

    Solution Structure and Backbone Dynamics of the Holo Form of the Frenolicin Acyl Carrier Protein-phosphopantetheine prosthetic group of a holo-ACP is a long and flexible arm that can reach into different active linkage. We have determined the solution structure and characterized backbone dynamics of the holo form

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

    E-print Network

    Baker, David

    Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope Campbell Family Cancer Research Institute, Ontario Cancer Institute/Princess Margaret Hospital, Toronto, ON Edited by I. Wilson Keywords: protein grafting; flexible backbone design; epitope scaffold; immunogen

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

    E-print Network

    Williams, Loren

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

  19. Evaluation of A Wireless Enterprise Backbone Network Architecture Ashish Raniwala Tzi-cker Chiueh

    E-print Network

    Chiueh, Tzi-cker

    Evaluation of A Wireless Enterprise Backbone Network Architecture Ashish Raniwala Tzi-cker Chiueh enterprises. All the WLAN access points are eventually connected to a wired back- bone to reach the Internet or enterprise computing resources. In this project, we aim to expand WLAN into an enterprise- scale backbone

  20. Distributed Mobile Disk Cover A Building Block for Mobile Backbone Networks

    E-print Network

    Zussman, Gil

    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 related to the design and operation of such networks is the problem of constructing and maintaining

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. The sequence of intermetallic formation and solidification pathway of an Al–13Mg–7Si–2Cu in-situ composite

    SciTech Connect

    Farahany, Saeed; Nordin, Nur Azmah; Ourdjini, Ali; Abu Bakar, TutyAsma; Hamzah, Esah; Idris, Mohd Hasbullah; Hekmat-Ardakan, Alireza

    2014-12-15

    The phase transformation sequence and solidification behaviour of an Al–13Mg–7Si–2Cu in-situ composite was examined using a combination of computer-aided cooling curve thermal analysis and interrupted quenching techniques. Five different phases were identified by analysing the derivative cooling curves, the X-ray diffraction profile, optical and scanning electron microscopy images and the corresponding energy dispersive spectroscopy. It has been found that the solidification of this alloy begins with primary Mg{sub 2}Si precipitation and continues with the formation of eutectic Al–Mg{sub 2}Si, followed by Al{sub 5}FeSi and simultaneous precipitation of Al{sub 5}Cu{sub 2}Mg{sub 8}Si{sub 6} and Al{sub 2}Cu complex intermetallic phases. The formation of the last three intermetallic compounds changes the solidification behaviour of these composites remarkably due to their complex eutectic formation reactions. The solidification of the alloy, calculated using the Factsage thermochemical analysis software, has demonstrated a good agreement with the experiments in terms of compound prediction, their weight fractions and reaction temperatures. - Highlights: • Solidification path of a commercial Al-13Mg-7Si-2Cu composite was characterized. • Five different phases were identified and then confirmed with EDS and XRD results. • Mg{sub 2}Si, Al-Mg{sub 2}Si,Al{sub 5}FeSi (?),Al{sub 5}Cu{sub 2}Mg{sub 8}Si{sub 6} (Q) and Al{sub 2}Cu(?) precipitated respectively. • Solidification was predicted using the Factsage thermochemical analysis software.

  3. Effects of the alternating backbone configuration on the secondary structure and self-assembly of beta-peptides.

    PubMed

    Martinek, Tamás A; Mándity, István M; Fülöp, Lívia; Tóth, Gábor K; Vass, Elemér; Hollósi, Miklós; Forró, Eniko; Fülöp, Ferenc

    2006-10-18

    Heterochiral homo-oligomers with alternating backbone configurations were constructed by using the different enantiomers of the cis- and trans-2-aminocyclopentanecarboxylic acid (ACPC) monomers. Molecular modeling and the spectroscopic techniques (NMR, ECD, and VCD) unequivocally proved that the alternating heterochiral cis-ACPC sequences form an H10/12 helix, where extra stabilization can be achieved via the cyclic side chains. The ECD and TEM measurements, together with molecular modeling, revealed that the alternating heterochiral trans-ACPC oligomers tend to attain a polar-strand secondary structure in solution, which can self-assemble into nanostructured fibrils. The observations indicate that coverage of all the possible secondary structures (various helix types and strand-mimicking conformations) can be attained with the help of cyclic beta-amino acid diastereomers. A relationship has been established between the backbone chirality pattern and the prevailing secondary structure, which underlines the role of stereochemical control in the beta-peptide secondary structure design and may contribute to future biological applications. PMID:17031967

  4. TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition.

    PubMed

    He, Xue; Han, Ke; Hu, Jun; Yan, Hui; Yang, Jing-Yu; Shen, Hong-Bin; Yu, Dong-Jun

    2015-12-01

    Antifreeze proteins (AFPs) are indispensable for living organisms to survive in an extremely cold environment and have a variety of potential biotechnological applications. The accurate prediction of antifreeze proteins has become an important issue and is urgently needed. Although considerable progress has been made, AFP prediction is still a challenging problem due to the diversity of species. In this study, we proposed a new sequence-based AFP predictor, called TargetFreeze. TargetFreeze utilizes an enhanced feature representation method that weightedly combines multiple protein features and takes the powerful support vector machine as the prediction engine. Computer experiments on benchmark datasets demonstrate the superiority of the proposed TargetFreeze over most recently released AFP predictors. We also implemented a user-friendly web server, which is openly accessible for academic use and is available at http://csbio.njust.edu.cn/bioinf/TargetFreeze . TargetFreeze supplements existing AFP predictors and will have potential applications in AFP-related biotechnology fields. PMID:26058944

  5. Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin.

    PubMed

    Denesvre, Caroline; Dumarest, Marine; Rémy, Sylvie; Gourichon, David; Eloit, Marc

    2015-10-01

    Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics. PMID:26223320

  6. Ruthenium-catalyzed olefin metathesis accelerated by the steric effect of the backbone substituent in cyclic (alkyl)(amino) carbenes.

    PubMed

    Zhang, Jun; Song, Shangfei; Wang, Xiao; Jiao, Jiajun; Shi, Min

    2013-10-21

    Three ruthenium complexes bearing backbone-monosubstituted CAACs were prepared and displayed dramatic improvement in catalytic efficiency not only in RCM reaction but also in the ethenolysis of methyl oleate, compared to those bearing backbone-disubstituted CAACs. PMID:24013192

  7. Analysis of Polygala tenuifolia Transcriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing.

    PubMed

    Tian, Hongling; Xu, Xiaoshuang; Zhang, Fusheng; Wang, Yaoqin; Guo, Shuhong; Qin, Xuemei; Du, Guanhua

    2015-01-01

    Radix polygalae, the dried roots of Polygala tenuifolia and P. sibirica, is one of the most well-known traditional Chinese medicinal plants. Radix polygalae contains various saponins, xanthones, and oligosaccharide esters and these compounds are responsible for several pharmacological properties. To provide basic breeding information, enhance molecular biological analysis, and determine secondary metabolite biosynthetic pathways of P. tenuifolia, we applied Illumina sequencing technology and de novo assembly. We also applied this technique to gain an overview of P. tenuifolia transcriptome from samples with different years. Using Illumina sequencing, approximately 67.2% of unique sequences were annotated by basic local alignment search tool similarity searches against public sequence databases. We classified the annotated unigenes by using Nr, Nt, GO, COG, and KEGG databases compared with NCBI. We also obtained many candidates CYP450s and UGTs by the analysis of genes in the secondary metabolite biosynthetic pathways, including putative terpenoid backbone and phenylpropanoid biosynthesis pathway. With this transcriptome sequencing, future genetic and genomics studies related to the molecular mechanisms associated with the chemical composition of P. tenuifolia may be improved. Genes involved in the enrichment of secondary metabolite biosynthesis-related pathways could enhance the potential applications of P. tenuifolia in pharmaceutical industries. PMID:26543847

  8. Analysis of Polygala tenuifolia Transcriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing

    PubMed Central

    Tian, Hongling; Xu, Xiaoshuang; Zhang, Fusheng; Wang, Yaoqin; Guo, Shuhong; Qin, Xuemei; Du, Guanhua

    2015-01-01

    Radix polygalae, the dried roots of Polygala tenuifolia and P. sibirica, is one of the most well-known traditional Chinese medicinal plants. Radix polygalae contains various saponins, xanthones, and oligosaccharide esters and these compounds are responsible for several pharmacological properties. To provide basic breeding information, enhance molecular biological analysis, and determine secondary metabolite biosynthetic pathways of P. tenuifolia, we applied Illumina sequencing technology and de novo assembly. We also applied this technique to gain an overview of P. tenuifolia transcriptome from samples with different years. Using Illumina sequencing, approximately 67.2% of unique sequences were annotated by basic local alignment search tool similarity searches against public sequence databases. We classified the annotated unigenes by using Nr, Nt, GO, COG, and KEGG databases compared with NCBI. We also obtained many candidates CYP450s and UGTs by the analysis of genes in the secondary metabolite biosynthetic pathways, including putative terpenoid backbone and phenylpropanoid biosynthesis pathway. With this transcriptome sequencing, future genetic and genomics studies related to the molecular mechanisms associated with the chemical composition of P. tenuifolia may be improved. Genes involved in the enrichment of secondary metabolite biosynthesis-related pathways could enhance the potential applications of P. tenuifolia in pharmaceutical industries. PMID:26543847

  9. Quantitative Analysis of PMLA Nanoconjugate Components after Backbone Cleavage

    PubMed Central

    Ding, Hui; Patil, Rameshwar; Portilla-Arias, Jose; Black, Keith L.; Ljubimova, Julia Y.; Holler, Eggehard

    2015-01-01

    Multifunctional polymer nanoconjugates containing multiple components show great promise in cancer therapy, but in most cases complete analysis of each component is difficult. Polymalic acid (PMLA) based nanoconjugates have demonstrated successful brain and breast cancer treatment. They consist of multiple components including targeting antibodies, Morpholino antisense oligonucleotides (AONs), and endosome escape moieties. The component analysis of PMLA nanoconjugates is extremely difficult using conventional spectrometry and HPLC method. Taking advantage of the nature of polyester of PMLA, which can be cleaved by ammonium hydroxide, we describe a method to analyze the content of antibody and AON within nanoconjugates simultaneously using SEC-HPLC by selectively cleaving the PMLA backbone. The selected cleavage conditions only degrade PMLA without affecting the integrity and biological activity of the antibody. Although the amount of antibody could also be determined using the bicinchoninic acid (BCA) method, our selective cleavage method gives more reliable results and is more powerful. Our approach provides a new direction for the component analysis of polymer nanoconjugates and nanoparticles. PMID:25894227

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

    SciTech Connect

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

    2000-10-31

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

  11. The Dominant Folding Route Minimizes Backbone Distortion in SH3

    PubMed Central

    Lammert, Heiko; Noel, Jeffrey K.; Onuchic, José N.

    2012-01-01

    Energetic frustration in protein folding is minimized by evolution to create a smooth and robust energy landscape. As a result the geometry of the native structure provides key constraints that shape protein folding mechanisms. Chain connectivity in particular has been identified as an essential component for realistic behavior of protein folding models. We study the quantitative balance of energetic and geometrical influences on the folding of SH3 in a structure-based model with minimal energetic frustration. A decomposition of the two-dimensional free energy landscape for the folding reaction into relevant energy and entropy contributions reveals that the entropy of the chain is not responsible for the folding mechanism. Instead the preferred folding route through the transition state arises from a cooperative energetic effect. Off-pathway structures are penalized by excess distortion in local backbone configurations and contact pair distances. This energy cost is a new ingredient in the malleable balance of interactions that controls the choice of routes during protein folding. PMID:23166485

  12. MCBT: Multi-Hop Cluster Based Stable Backbone Trees for Data Collection and Dissemination in WSNs

    PubMed Central

    Shin, Inyoung; Kim, Moonseong; Mutka, Matt W.; Choo, Hyunseung; Lee, Tae-Jin

    2009-01-01

    We propose a stable backbone tree construction algorithm using multi-hop clusters for wireless sensor networks (WSNs). The hierarchical cluster structure has advantages in data fusion and aggregation. Energy consumption can be decreased by managing nodes with cluster heads. Backbone nodes, which are responsible for performing and managing multi-hop communication, can reduce the communication overhead such as control traffic and minimize the number of active nodes. Previous backbone construction algorithms, such as Hierarchical Cluster-based Data Dissemination (HCDD) and Multicluster, Mobile, Multimedia radio network (MMM), consume energy quickly. They are designed without regard to appropriate factors such as residual energy and degree (the number of connections or edges to other nodes) of a node for WSNs. Thus, the network is quickly disconnected or has to reconstruct a backbone. We propose a distributed algorithm to create a stable backbone by selecting the nodes with higher energy or degree as the cluster heads. This increases the overall network lifetime. Moreover, the proposed method balances energy consumption by distributing the traffic load among nodes around the cluster head. In the simulation, the proposed scheme outperforms previous clustering schemes in terms of the average and the standard deviation of residual energy or degree of backbone nodes, the average residual energy of backbone nodes after disseminating the sensed data, and the network lifetime. PMID:22454570

  13. 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 and creative expression rather than professional skill. General Psychology: A study of the basic topics in psychology that lay the foundation for courses leading to a major in psychology and are relevant to assisting

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

    SciTech Connect

    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.

    2012-02-07

    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.

  15. 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

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

    2014-01-01

    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

  16. 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

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

    2014-01-01

    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

  17. Composition and interrelationships of a large Neotropical freshwater fish group, the subfamily Cheirodontinae (Characiformes: Characidae): a case study based on mitochondrial and nuclear DNA sequences.

    PubMed

    Mariguela, T C; Ortí, G; Avelino, G S; Abe, K T; Oliveira, C

    2013-07-01

    Characidae is the most species-rich family of freshwater fishes in the order Characiformes, with more than 1000 valid species that correspond to approximately 55% of the order. Few hypotheses about the composition and internal relationships within this family are available and most fail to reach an agreement. Among Characidae, Cheirodontinae is an emblematic group that includes 18 genera (1 fossil) and approximately 60 described species distributed throughout the Neotropical region. The taxonomic and systematic history of Cheirodontinae is complex, and only two hypotheses about the internal relationships in this subfamily have been reported to date. In the present study, we test the composition and relationships of fishes assigned to Cheirodontinae based on a broad taxonomic sample that also includes some characid incertae sedis taxa that were previously considered to be part of Cheirodontinae. We present phylogenetic analyses of a large molecular dataset of mitochondrial and nuclear DNA sequences. Our results reject the monophyly of Cheirodontinae as previously conceived, as well as the tribes Cheirodontini and Compsurini, and the genera Cheirodon, Compsura, Leptagoniates, Macropsobrycon, Odontostilbe, and Serrapinnus. On the basis of these results we propose: (1) the exclusion of Amazonspinther and Spintherobolus from the subfamily Cheirodontinae since they are the sister-group of all remaining Characidae; (2) the removal of Macropsobrycon xinguensis of the genus Macropsobrycon; (3) the removal of Leptagoniates pi of the genus Leptagoniates; (4) the inclusion of Leptagoniates pi in the subfamily Cheirodontinae; (5) the removal of Cheirodon stenodon of the genus Cheirodon and its inclusion in the subfamily Cheirodontinae under a new genus name; (6) the need to revise the polyphyletic genera Compsura, Odontostilbe, and Serrapinnus; and (7) the division of Cheirodontinae in three newly defined monophyletic tribes: Cheirodontini, Compsurini, and Pseudocheirodontini. Our results suggest that our knowledge about the largest Neotropical fish family, Characidae, still is incipient. PMID:23541838

  18. The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

    PubMed Central

    Kennedy, Nicholas A.; Walker, Alan W.; Berry, Susan H.; Duncan, Sylvia H.; Farquarson, Freda M.; Louis, Petra; Thomson, John M.; Ahmad, T; Anderson, CA; Barrett, JC; Drummond, H; Edwards, C; Hart, A; Hawkey, C; Henderson, P; Khan, M; Lamb, CA; Lee, JC; Mansfield, JC; Mathew, CG; Mowat, C; Newman, WG; Prescott, NJ; Simmons, A; Simpson, P; Taylor, K; Taylor, K; Wilson, DC; Satsangi, Jack; Flint, Harry J.; Parkhill, Julian

    2014-01-01

    Introduction Determining bacterial community structure in fecal samples through DNA sequencing is an important facet of intestinal health research. The impact of different commercially available DNA extraction kits upon bacterial community structures has received relatively little attention. The aim of this study was to analyze bacterial communities in volunteer and inflammatory bowel disease (IBD) patient fecal samples extracted using widely used DNA extraction kits in established gastrointestinal research laboratories. Methods Fecal samples from two healthy volunteers (H3 and H4) and two relapsing IBD patients (I1 and I2) were investigated. DNA extraction was undertaken using MoBio Powersoil and MP Biomedicals FastDNA SPIN Kit for Soil DNA extraction kits. PCR amplification for pyrosequencing of bacterial 16S rRNA genes was performed in both laboratories on all samples. Hierarchical clustering of sequencing data was done using the Yue and Clayton similarity coefficient. Results DNA extracted using the FastDNA kit and the MoBio kit gave median DNA concentrations of 475 (interquartile range 228-561) and 22 (IQR 9-36) ng/µL respectively (p<0.0001). Hierarchical clustering of sequence data by Yue and Clayton coefficient revealed four clusters. Samples from individuals H3 and I2 clustered by patient; however, samples from patient I1 extracted with the MoBio kit clustered with samples from patient H4 rather than the other I1 samples. Linear modelling on relative abundance of common bacterial families revealed significant differences between kits; samples extracted with MoBio Powersoil showed significantly increased Bacteroidaceae, Ruminococcaceae and Porphyromonadaceae, and lower Enterobacteriaceae, Lachnospiraceae, Clostridiaceae, and Erysipelotrichaceae (p<0.05). Conclusion This study demonstrates significant differences in DNA yield and bacterial DNA composition when comparing DNA extracted from the same fecal sample with different extraction kits. This highlights the importance of ensuring that samples in a study are prepared with the same method, and the need for caution when cross-comparing studies that use different methods. PMID:24586470

  19. RNA Backbone: Consensus All-angle Conformers and Modular String Nomenclature

    E-print Network

    Richardson, David

    found favorable for the sugar-to-sugar "suite" unit within which the angle correlations are strongest (e with the backbone, however (except for very high resolution crystal structures, seldom attainable for RNA molecules

  20. NMR determination of the secondary structure and the three-dimensional polypeptide backbone fold of the human sterol carrier protein 2.

    PubMed

    Szyperski, T; Scheek, S; Johansson, J; Assmann, G; Seedorf, U; Wüthrich, K

    1993-11-29

    Nuclear magnetic resonance (NMR) spectroscopy was used to determine the secondary structure and the three-dimensional polypeptide backbone fold of the human sterol carrier protein 2 (hSCP2), which is a basic protein with 123 residues believed to participate in the intracellular transport of cholesterol and various other lipids. Sequence-specific assignments were obtained for nearly all backbone 1H and 15N resonances, as well as for about two-thirds of the side-chain 1H resonances, using uniform 15N-labeling of the protein combined with homonuclear two-dimensional 1H NMR and three-dimensional 15N-correlated 1H NMR. Three alpha-helices comprising the polypeptide segments of residues 9-22, 25-30 and 78-84 were identified by sequential and medium-range nuclear Overhauser effects (NOE). The analysis of long-range backbone-backbone NOEs showed that hSCP2 further contains a five-stranded beta-sheet including the residues 33-41, 47-54, 60-62, 71-76 and 100-102, which is a central feature of the molecular architecture. The first three strands are arranged in an antiparallel fashion, the polypeptide chain then crosses over this three-stranded sheet in a right-handed sense so that the fourth strand is added parallel to the first one. The fifth strand runs antiparallel to the fourth one, so that the overall topology is +1, +1, -3x, -1. The three-dimensional arrangement of the beta-sheet and the first two helices was determined using an input of 625 NOE upper distance constraints and 95 scalar coupling constants for a preliminary structure calculation with the distance geometry program DIANA. PMID:8243660

  1. Displacements of backbone vibrational modes of A-DNA and B-DNA.

    PubMed Central

    Lu, K C; Van Zandt, L L; Prohofsky, E W

    1979-01-01

    We display the displacement vectors or eigenvectors of calculations of the A- and B-DNA backbones. These calculations are based on a refinement scheme that simultaneously fit several backbone modes of A-DNA, B-DNA, and A-RNA. We discuss the role of symmetry operations in mode calculations and the relevance of these displacement vectors to the interpretation of linear dichroism measurements performed on the A- and B-DNA helix. PMID:262445

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

    PubMed Central

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

    2015-01-01

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

  3. Persistence and epidemic propagation of a Pseudomonas aeruginosa sequence type 235 clone harboring an IS26 composite transposon carrying the blaIMP-1 integron in Hiroshima, Japan, 2005 to 2012.

    PubMed

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

    2015-05-01

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

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

    PubMed Central

    Ginsberg, Stephen D.; Che, Shaoli

    2015-01-01

    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

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

    E-print Network

    Wu, Sitao; Zhang, Yang

    2008-10-15

    as training (validation/testing) data. The total residues in the 500 (460/1,029) proteins are 72,918 (89,653/146,517). We use DSSP program [27] to extract the experimental values of the phi and psi angles. The phi/psi angles of the N- and C-terminal residues... predictor based only on secondary structure predictions. For this purpose, we first calculate the average torsion angles in three secondary structures (a helices, b strands and coils) by DSSP program [27] on the 500 training proteins with solved 3D...

  6. Complete backbone and DENQ side chain NMR assignments in proteins from a single experiment: implications to structure-function studies.

    PubMed

    Reddy, Jithender G; Hosur, Ramakrishna V

    2014-03-01

    Resonance assignment is the first and the most crucial step in all nuclear magnetic resonance (NMR) investigations on structure-function relationships in biological macromolecules. Often, the assignment exercise has to be repeated several times when specific interactions with ligands, substrates etc., have to be elucidated for understanding the functional mechanisms. While the protein backbone serves to provide a scaffold, the side chains interact directly with the ligands. Such investigations will be greatly facilitated, if there are rapid methods for obtaining exhaustive information with minimum of NMR experimentation. In this context, we present here a pulse sequence which exploits the recently introduced technique of parallel detection of multiple nuclei, e.g. (1)H and (13)C, and results in two 3D-data sets simultaneously. These yield complete backbone resonance assignment ((1)H(N), (15)N, (13)CO, (1)H?/(13)C?, and (1)H?/(13)C? chemical shifts) and side chain assignment of D, E, N and Q residues. Such an exhaustive assignment has the potential of yielding accurate 3D structures using one or more of several algorithms which calculate structures of the molecules very reliably on the basis of NMR chemical shifts alone. The side chain assignments of D, E, N, and Q will be extremely valuable for interaction studies with different ligands; D and E side chains are known to be involved in majority of catalytic activities. Utility of this experiment has been demonstrated with Ca(2+) bound M-crystallin, which contains largely D, E, N and Q residues at the metal binding sites. PMID:24535112

  7. Sequence Preference for BI/BII Conformations in DNA: MD and Crystal Structure Data Analysis

    E-print Network

    Bansal, Manju

    Sequence Preference for BI/BII Conformations in DNA: MD and Crystal Structure Data Analysis http://www.jbsdonline.com Abstract Deciphering sequence information from sugar-phosphate backbone is finely tuned through is negative in BI and positive in BII. Our analysis of MD and crystal structures shows that BII conformation

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  10. Fast Bayesian identification of a class of elastic weakly nonlinear systems using backbone curves

    NASA Astrophysics Data System (ADS)

    Hill, T. L.; Green, P. L.; Cammarano, A.; Neild, S. A.

    2016-01-01

    This paper introduces a method for the identification of the parameters of nonlinear structures using a probabilistic Bayesian framework, employing a Markov chain Monte Carlo algorithm. This approach uses analytical models to describe the unforced, undamped dynamic responses of structures in the frequency-amplitude domain, known as the backbone curves. The analytical models describing these backbone curves are then fitted to measured responses, found using the resonant-decay method. To investigate the proposed identification method, a nonlinear two-degree-of-freedom example structure is simulated numerically and analytical expressions describing the backbone curves are found. These expressions are then used, in conjunction with the backbone curve data found through simulated experiment, to estimate the system parameters. It is shown that the use of these computationally-cheap analytical expressions allows for an extremely efficient method for modelling the dynamic behaviour, providing an identification procedure that is both fast and accurate. Furthermore, for the example structure, it is shown that the estimated parameters may be used to accurately predict the existence of dynamic behaviours that are well-away from the backbone curve data provided; specifically the existence of an isola is predicted.

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

    PubMed Central

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

    2012-01-01

    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

  12. Anion-Conducting Polymer, Composition, and Membrane

    DOEpatents

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

    2008-10-21

    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.

  13. Anion-conducting polymer, composition, and membrane

    DOEpatents

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

    2010-12-07

    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.

  14. Anion-conducting polymer, composition, and membrane

    DOEpatents

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

    2009-09-01

    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.

  15. Anion-conducting polymer, composition, and membrane

    DOEpatents

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

    2011-11-22

    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.

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

    SciTech Connect

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

    2014-09-15

    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.

  17. Solvation thermodynamics of amino acid side chains on a short peptide backbone

    NASA Astrophysics Data System (ADS)

    Hajari, Timir; van der Vegt, Nico F. A.

    2015-04-01

    The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.

  18. Solvation thermodynamics of amino acid side chains on a short peptide backbone

    SciTech Connect

    Hajari, Timir; Vegt, Nico F. A. van der

    2015-04-14

    The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.

  19. Influence of backbone conformational rigidity in temperature-sensitive amphiphilic supramolecular assemblies.

    PubMed

    Raghupathi, Krishna R; Sridhar, Uma; Byrne, Kevin; Raghupathi, Kishore; Thayumanavan, S

    2015-04-29

    Molecular design features that endow amphiphilic supramolecular assemblies with a unique temperature-sensitive transition have been investigated. We find that conformational rigidity in the backbone is an important feature for eliciting this feature. We also find that intramolecular hydrogen-bonding can induce such rigidity in amphiphile backbone. Guest encapsulation stability of these assemblies was found to be significantly altered within a narrow temperature window, which correlates with the temperature-sensitive size transition of the molecular assembly. Molecular design principles demonstrated here could have broad implications in developing future temperature-responsive systems. PMID:25893806

  20. Convenient and Scalable Synthesis of Fmoc-Protected Peptide Nucleic Acid Backbone

    PubMed Central

    Feagin, Trevor A.; Shah, Nirmal I.; Heemstra, Jennifer M.

    2012-01-01

    The peptide nucleic acid backbone Fmoc-AEG-OBn has been synthesized via a scalable and cost-effective route. Ethylenediamine is mono-Boc protected, then alkylated with benzyl bromoacetate. The Boc group is removed and replaced with an Fmoc group. The synthesis was performed starting with 50?g of Boc anhydride to give 31?g of product in 32% overall yield. The Fmoc-protected PNA backbone is a key intermediate in the synthesis of nucleobase-modified PNA monomers. Thus, improved access to this molecule is anticipated to facilitate future investigations into the chemical properties and applications of nucleobase-modified PNA. PMID:22848796

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

    PubMed Central

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

    2013-01-01

    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

  2. Comparison of sequence masking algorithms and the detection of biased protein sequence

    E-print Network

    Kreil, David

    Comparison of sequence masking algorithms and the detection of biased protein sequence regions;Abstract Motivation Separation of protein sequence regions according to their local information complexity by sequence similarity. Comparison with alternative methods that focus on compositional sequence bias rather

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

    NASA Astrophysics Data System (ADS)

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

    2004-12-01

    In the preceding report we showed experimentally that the dunite-harzburgite-lherzolite (DHL) sequence found in the mantle sections of ophiolite could be formed by reactive dissolution of lherzolite in a basaltic liquid. The most striking results of our lherzolite dissolution experiments are the sharp mineralogical boundaries between adjacent lithologies and simple monotonic composition variations in minerals across the DHL sequence. Here we present a detailed compositional traverse across a dunite (3.64 m wide) - harzburgite-lherzolite (5.64 m) - plagioclase lherzolite (> 10 m) sequence (referred to as DHL-PL) at the Trinity ophiolite that shows complicated composition trends and melt flow history. With the exception of a small (1 m wide) anomalous region within the dunite, less than 1 m away from the dunite-harzburgite contact, the Mg#s of olivine (90), cpx (92.8), opx (90.4 in harzburgite) and spinel (40), as well as Al2O3 and TiO2 abundance in cpx, opx and spinel are essentially constant from dunite to lherzolite. The CaO content in olivine (0.02%), opx (1%) and cpx (23.5%) are also uniform throughout the harzburgite-plagioclase lherzolite sequence. However, the Mg# of olivine and opx, Al2O3, TiO2 and Cr2O3 in cpx and opx, as well as Na2O in cpx increase 2 meters into the plagioclase lherzolite. In addition, asymmetric concentration gradients are observed for CaO in olivine and Cr2O3, Al2O3, MgO, and FeO in spinel. These asymmetric concentration gradients are mostly in the dunite-side of the dunite-harzburgite contact. And finally, the 1 m wide anomalous region within the dunite is characterized by elevated Mg# and NiO in olivine, Al2O3, TiO2, Cr2O3, and REE in cpx, and very distinct elemental abundance in spinel. The composition variations reported here are substantially different from those of Quick (1981) who measured a smaller (1 m) DHL-PL sequence at the Trinity ophiolite. Together these two Trinity data sets show a large variation in DHL-PL chemistry within the same ophiolite. Concentration gradients across DHL-PL sequences have been observed in the mantle sections of ophiolites around the world. Based on our lherzolite dissolution experiments, preliminary numerical calculations, and previous studies we suggest that the DHL-PL sequence at Trinity was formed by pervasive melt flow and reactive dissolution of a plagioclase lherzolite in basaltic liquids. Although the details are still unknown, the complicated concentration profiles reported in this study can be explained by a model that involves multiple episodes of melt flow and melt-rock reaction in an evolving dunite channel system. Multiple episodes of melt flow in the mantle, each with distinct elemental and isotopic characteristics, have already been documented in olivine-hosted melt inclusions. The spatial distributions of the compositional variations reported here can be used to further constrain the time interval between different episodes of melt flow in the dunite channel. For example, the two (or more) episodes of melt flow that created the anomalous region in the dunite and the DHL-PL sequence could at most be separated by less than a few hundred years.

  4. Molecular phylogenetics before sequences

    PubMed Central

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

    2014-01-01

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

  5. Remote Enantioselection Transmitted by an Achiral Peptide Nucleic Acid Backbone

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

    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.

  6. NMR Structure Determination for Larger Proteins Using Backbone-Only Data

    E-print Network

    Baker, David

    NMR Structure Determination for Larger Proteins Using Backbone-Only Data Srivatsan Raman1 intensive and prone to error. Here we show that structures can be accurately determined without NMR enable routine NMR structure determination for larger proteins. The first step in protein structure

  7. Interpreting the forced responses of a two-degree-of-freedom nonlinear oscillator using backbone curves

    NASA Astrophysics Data System (ADS)

    Hill, T. L.; Cammarano, A.; Neild, S. A.; Wagg, D. J.

    2015-08-01

    In this paper the backbone curves of a two-degree-of-freedom nonlinear oscillator are used to interpret its behaviour when subjected to external forcing. The backbone curves describe the loci of dynamic responses of a system when unforced and undamped, and are represented in the frequency-amplitude projection. In this study we provide an analytical method for relating the backbone curves, found using the second-order normal form technique, to the forced responses. This is achieved using an energy-based analysis to predict the resonant crossing points between the forced responses and the backbone curves. This approach is applied to an example system subjected to two different forcing cases: one in which the forcing is applied directly to an underlying linear mode and the other subjected to forcing in both linear modes. Additionally, a method for assessing the accuracy of the prediction of the resonant crossing points is then introduced, and these predictions are then compared to responses found using numerical continuation.

  8. RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

    E-print Network

    Baker, David

    RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design Po-Ssu Huang1 , Yih of America, 2 Interdisciplinary Program in Biomolecular Structure and Design, University of Washington University, Lund, Sweden, 4 Program in Molecular Structure and Function, Hospital for Sick Children, Toronto

  9. Link Estimation and Routing in Sensor Network Backbones: Beacon-based or Data-driven?

    E-print Network

    Zhang, Hongwei

    1 Link Estimation and Routing in Sensor Network Backbones: Beacon-based or Data-driven? Hongwei of broadcast beacons even if we make the length and transmission rate of beacons be the same as those of data directly via data traffic itself without using periodic beacons. To this end, we design a data

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

    ERIC Educational Resources Information Center

    Jerome, Brian; Fuqua, Paul

    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…

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

    E-print Network

    Kelly, Maggi

    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

  12. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

    E-print Network

    Bax, Ad

    determination process has been well recognized (Billeter et al. 2008), and it is clear that recent chemical of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National InstitutesARTICLE TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical

  13. Searching for Backbones An Efficient Parallel Algorithm for Finding Groundstates in Spin Glass Models

    E-print Network

    Schneider, Johannes Josef

    , one usually finds structures which are common to all solutions. Thus, one can assume is iterated until all optimization runs end at the same solution. INTRODUCTION Spin glasses are unorderedSearching for Backbones ­ An Efficient Parallel Algorithm for Finding Groundstates in Spin Glass

  14. Anharmonic Backbone Vibrations in Ultrafast Processes at the DNA-Water Interface.

    PubMed

    Siebert, Torsten; Guchhait, Biswajit; Liu, Yingliang; Costard, Rene; Elsaesser, Thomas

    2015-07-30

    The vibrational modes of the deoxyribose-phosphodiester backbone moiety of DNA and their interactions with the interfacial aqueous environment are addressed with two-dimensional (2D) infrared spectroscopy on a femto- to picosecond time scale. Beyond the current understanding in the harmonic approximation, the anharmonic character and delocalization of the backbone modes in the frequency range from 900 to 1300 cm(-1) are determined with both diagonal anharmonicities and intermode couplings on the order of 10 cm(-1). Mediated by the intermode couplings, energy transfer between the backbone modes takes place on a picosecond time scale, parallel to vibrational relaxation and energy dissipation into the environment. Probing structural dynamics noninvasively via the time evolution of the 2D lineshapes, limited structural fluctuations are observed on a 300 fs time scale of low-frequency motions of the helix, counterions, and water shell. Structural disorder of the DNA-water interface and DNA-water hydrogen bonds are, however, preserved for times beyond 10 ps. The different interactions of limited strength ensure ultrafast vibrational relaxation and dissipation of excess energy in the backbone structure, processes that are important for the structural integrity of hydrated DNA. PMID:26125542

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

    E-print Network

    Sullivan, Jack

    Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene *Corresponding author: E-mail: jacks@uidaho.edu. Associate editor: Andrew Roger Abstract Plasmids are transferred horizontally between plasmids, recent studies have also provided examples of recombination

  16. RNA Tetraloop Folding Reveals Tension between Backbone Restraints and Molecular Interactions

    E-print Network

    Williams, Loren

    RNA Tetraloop Folding Reveals Tension between Backbone Restraints and Molecular Interactions observation that release of torsional restraints upon conversion of one or more loop riboses to more flexible improved stacking and hydrogen-bonding interactions upon release of torsional restraints. The most obvious

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

    E-print Network

    Schofield, Jeremy

    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

  18. Supporting Internet Protocol TV (IPTV) in Backbone Networks: Design of Robust Routing Strategies

    E-print Network

    Greenberg, Albert

    Backbone Distribution Network Super Head-End (SHE) SHE VHO Video Hub Office (VHO) VHO Broadcast TV Figure 1 commercial-grade live broadcast Television ser- vice over IP ­ known as the Internet Protocol TV (IPTV) [10 reliable and cost effective network infrastructure ­ all the way from the central head ends where the video

  19. Synthesis and properties of DNA oligonucleotides with a zwitterionic backbone structure.

    PubMed

    Schmidtgall, Boris; Spork, Anatol P; Wachowius, Falk; Höbartner, Claudia; Ducho, Christian

    2014-11-18

    The nucleosyl amino acid (NAA)-modification of oligonucleotides is introduced, which enables the preparation of oligonucleotides with zwitterionic backbone structures. It is demonstrated that partially zwitterionic NAA-modified DNA oligonucleotides are capable of duplex formation with native polyanionic counterstrands and show retained sensitivity towards base-pairing mismatches. PMID:25251903

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

    E-print Network

    Richardson, David

    . (c) Proposed correction with good van der Waals contacts. (d) Original and altered conformation.W. Murray, J.S. Richardson1 , W.B. Arendall III and D.C. Richardson Department of Biochemistry, DukeRNA Structure and Function 485 RNA backbone rotamers ­ finding your way in seven dimensions L.J

  1. On the consequences of side chain flexibility and backbone conformation on hydration and proton dissociation in perfluorosulfonic acid membranes

    E-print Network

    Elliott, James

    On the consequences of side chain flexibility and backbone conformation on hydration and proton in the backbone on hydration and proton transfer in the short-side-chain (SSC) perfluorosulfonic acid fuel cell proteins16­18 (e.g. proton channels19 and pumps20 ), carbon nanotubes,21 and polymer electrolyte membranes

  2. Folding a protein by discretizing its backbone torsional dynamics

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel

    1999-05-01

    The aim of this work is to provide a coarse codification of local conformational constraints associated with each folding motif of a peptide chain in order to obtain a rough solution to the protein folding problem. This is accomplished by implementing a discretized version of the soft-mode dynamics on a personal computer (PC). Our algorithm mimics a parallel process as it evaluates concurrent folding possibilities by pattern recognition. It may be implemented in a PC as a sequence of perturbation-translation-renormalization (p-t-r) cycles performed on a matrix of local topological constraints (LTM). This requires suitable representational tools and a periodic quenching of the dynamics required for renormalization. We introduce a description of the peptide chain based on a local discrete variable the values of which label the basins of attraction of the Ramachandran map for each residue. Thus, the local variable indicates the basin in which the torsional coordinates of each residue lie at a given time. In addition, a coding of local topological constraints associated with each secondary and tertiary structural motif is introduced. Our treatment enables us to adopt a computation time step of 81 ps, a value far larger than hydrodynamic drag time scales. Folding pathways are resolved as transitions between patterns of locally encoded structural signals that change within the 10 ?s-100 ms time scale range. These coarse folding pathways are generated by the periodic search for structural patterns in the time-evolving LTM. Each pattern is recorded as a contact matrix, an operation subject to a renormalization feedback loop. The validity of our approach is tested vis-a-vis experimentally-probed folding pathways eventually generating tertiary interactions in proteins which recover their active structure under in vitro renaturation conditions. As an illustration, we focus on determining significant folding intermediates and late kinetic bottlenecks that occur within the first 10 ms of the bovine pancreatic trypsin inhibitor renaturation process. The probed cooperativity and nucleation effects, as well as diffusion-collision stabilization of secondary structure are shown to result from the persistence of relatively stable patterns through successive (p-t-r) cycles, thus acting as seeding patterns for further growth or hierarchical development.

  3. 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.

    PubMed

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

    2012-07-01

    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 a B-DNA biomolecule are then studied as examples, where the model systems have been constructed by extracting from the perfect or an 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, or di-Thy) and a surrounding physical/chemical environment of interest (e.g. backbone, adjacent stacking nucleobases) in gas phase and examine how the excitation properties of the core vary in response to the environment. We find that the orbitals contributed by the DNA backbone and surrounding nucleobases often participate in a transition of Thy-related excitations affecting their composition, absorption energy, and oscillator strength. A vast number of strongly backbone-orbital involved excitations are also found at an absorption wavelength below ?180 nm predicted by TD-?B97X. 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 may from time to time exhibit very different photo-induced physical and/or chemical processes. PMID:22641198

  4. Peptide backbone fragmentation initiated by side-chain loss at cysteine residue in matrix-assisted laser desorption/ionization in-source decay mass spectrometry.

    PubMed

    Asakawa, Daiki; Smargiasso, Nicolas; Quinton, Loïc; De Pauw, Edwin

    2013-03-01

    Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) is initiated by hydrogen transfer from matrix molecules to the carbonyl oxygen of peptide backbone with subsequent radical-induced cleavage leading to c'/z• fragments pair. MALDI-ISD is a very powerful method to obtain long sequence tags from proteins or to do de novo sequencing of peptides. Besides classical fragmentation, MALDI-ISD also shows specific fragments for which the mechanism of formation enlightened the MALDI-ISD process. In this study, the MALDI-ISD mechanism is reviewed, and a specific mechanism is studied in details: the N-terminal side of Cys residue (Xxx-Cys) is described to promote the generation of c' and w fragments in MALDI-ISD. Our data suggest that for sequences containing Xxx-Cys motifs, the N-C? bond cleavage occurs following the hydrogen attachment to the thiol group of Cys side-chain. The c•/w fragments pair is formed by side-chain loss of the Cys residue with subsequent radical-induced cleavage at the N-C? bond located at the left side (N-terminal direction) of the Cys residue. This fragmentation pathway preferentially occurs at free Cys residue and is suppressed when the cysteines are involved in disulfide bonds. Hydrogen attachment to alkylated Cys residues using iodoacetamide gives free Cys residue by the loss of •CH2CONH2 radical. The presence of alkylated Cys residue also suppress the formation of c•/w fragments pair via the (C?)-centered radical, whereas w fragment is still observed as intense signal. In this case, the z• fragment formed by hydrogen attachment of carbonyl oxygen followed side-chain loss at alkylated Cys leads to a w fragment. Hydrogen attachment on peptide backbone and side-chain of Cys residue occurs therefore competitively during MALDI-ISD process. PMID:23494792

  5. Sequence composition of BAC clones and SSR markers mapped to Upland cotton chromosomes 11 and 21 targeting resistance to soil-borne pathogens

    PubMed Central

    Wang, Congli; Ulloa, Mauricio; Shi, Xinyi; Yuan, Xiaohui; Saski, Christopher; Yu, John Z.; Roberts, Philip A.

    2015-01-01

    Genetic and physical framework mapping in cotton (Gossypium spp.) were used to discover putative gene sequences involved in resistance to common soil-borne pathogens. Chromosome (Chr) 11 and its homoeologous Chr 21 of Upland cotton (G. hirsutum) are foci for discovery of resistance (R) or pathogen-induced R (PR) genes underlying QTLs involved in response to root-knot nematode (Meloidogyne incognita), reniform nematode (Rotylenchulus reniformis), Fusarium wilt (Fusarium oxysporum f.sp. vasinfectum), Verticillium wilt (Verticillium dahliae), and black root rot (Thielaviopsis basicola). Simple sequence repeat (SSR) markers and bacterial artificial chromosome (BAC) clones from a BAC library developed from the Upland cotton Acala Maxxa were mapped on Chr 11 and Chr 21. DNA sequence through Gene Ontology (GO) of 99 of 256 Chr 11 and 109 of 239 Chr 21 previously mapped SSRs revealed response elements to internal and external stimulus, stress, signaling process, and cell death. The reconciliation between genetic and physical mapping of gene annotations from new DNA sequences of 20 BAC clones revealed 467 (Chr 11) and 285 (Chr 21) G. hirsutum putative coding sequences, plus 146 (Chr 11) and 98 (Chr 21) predicted genes. GO functional profiling of Unigenes uncovered genes involved in different metabolic functions and stress response elements (SRE). Our results revealed that Chrs 11 and 21 harbor resistance gene rich genomic regions. Sequence comparisons with the ancestral diploid D5 (G. raimondii), A2 (G. arboreum) and domesticated tetraploid TM-1 AD1 (G. hirsutum) genomes revealed abundance of transposable elements and confirmed the richness of resistance gene motifs in these chromosomes. The sequence information of SSR markers and BAC clones and the genetic mapping of BAC clones provide enhanced genetic and physical frameworks of resistance gene-rich regions of the cotton genome, thereby aiding discovery of R and PR genes and breeding for resistance to cotton diseases. PMID:26483808

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

    SciTech Connect

    Radhakrishnan, R.; Bhaduri, S.B.; Henager, C.H. Jr.

    1995-05-01

    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.

  7. 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)

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

    2014-12-01

    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.

  8. Sequence of phase transitions induced by chemical composition and high temperature in [Ba2CaWO6](1-x)[Sr2CaWO6]x double perovskite tungsten oxides

    NASA Astrophysics Data System (ADS)

    Mirinioui, F.; Manoun, Bouchaib; Tamraoui, Y.; Lazor, P.

    2015-12-01

    [Ba2CaWO6]1-x[Sr2CaWO6]x (0?x?1) materials were synthesized by the high temperature solid state reaction and firing methods, and characterized using techniques of X-ray diffraction and Raman spectroscopy. The crystal structures were determined by Rietveld refinements on the laboratory X-ray powder diffraction data. As a function of composition, upon increasing the strontium content, the samples exhibit a sequence of three phase transitions: from cubic (Fm 3 ?m) to tetragonal (I4/m) to monoclinic structural phases (I2/m, P21/n). These transitions have been confirmed by Raman studies Fm 3 bar m x = 0 ? I 4 / m 0.1 ? x ? 0.2 ? I 2 / m 0.3 ? x ? 0.5 ? P21 / n 0.6 ? x ? 1 Furthermore, increasing the temperature for the compositions [Ba2CaWO6]1-x[Sr2CaWO6]x (0.1?x<1), manifests the P21/n to I2/m, the I2/m to I4/m and the I4/m to Fm 3 ?m phase transitions. For the compositions (0.1?x?0.2) the tetragonal to cubic phase transition is well illustrated. For the room temperature I2/m monoclinic compositions, two phase transitions were observed for all the compositions with x ranging from 0.3 to 0.5: from the monoclinic (I2/m) to tetragonal (I4/m), and from I4/m to Fm 3 ?m structures. Finally, for the room temperature P21/n monoclinic compositions, only two phase transitions are observed in the temperature range probed by Raman spectroscopy, the temperature was not high enough to reach the tetragonal-to-cubic phase transition.

  9. Self-assembly of diphenylalanine backbone homologues and their combination with functionalized carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Dinesh, Bhimareddy; Squillaci, Marco A.; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto

    2015-09-01

    The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of ? and ? homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, ? and ? peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of ? and ? peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of ? and ? peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing.The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of ? and ? homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, ? and ? peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of ? and ? peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of ? and ? peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04665c

  10. Electrochemical DNA biosensor with chitosan-Co(3)O(4) nanorod-graphene composite for the sensitive detection of Staphylococcus aureus nuc gene sequence.

    PubMed

    Qi, Xiaowei; Gao, Hongwei; Zhang, Yuanyuan; Wang, Xiuzhen; Chen, Ying; Sun, Wei

    2012-12-01

    In this paper a novel nanocomposite material prepared by Co(3)O(4) nanorods (nano-Co(3)O(4)), graphene (GR) and chitosan (CTS) was fabricated and further modified on carbon ionic liquid electrode (CILE), which was used as the substrate electrode to construct a new electrochemical DNA biosensor. The single-stranded DNA (ssDNA) probe was immobilized on the CTS-Co(3)O(4)-GR/CILE surface by electrostatic attraction, which could hybridize with the target ssDNA sequence under the selected conditions. By using methylene blue (MB) as the electrochemical indicator, the hybridization reactions were monitored with the reduction peak current. By combining the biocompatibility of Co(3)O(4) nanorods, excellent electron transfer ability and big surface of GR, good film-forming ability of CTS and the high conductivity of CILE, the amount of ssDNA adsorbed on the electrode surface was increased and the electrochemical response of MB was accelerated. Under the optimal conditions differential pulse voltammetric responses of MB were in linear with the specific target ssDNA sequence in the concentration range from 1.0×10(-12) to 1.0×10(-6)M with the detection limit as 4.3×10(-13)M (3?). Good discrimination ability to the one-base and three-base mismatched ssDNA sequences could be achieved and the polymerase chain reaction (PCR) amplification products of Staphylococcus aureus nuc gene sequence were detected with satisfactory results. PMID:22765971

  11. The Manufacturing Process for the NASA Composite Crew Module Demonstration Structure

    NASA Technical Reports Server (NTRS)

    Pelham, Larry; Higgins, John E.

    2008-01-01

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

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

    PubMed Central

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

    2010-01-01

    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

  13. Influence of Backbone Fluorination in Regioregular Poly(3-alkyl-4-fluoro)thiophenes.

    PubMed

    Fei, Zhuping; Boufflet, Pierre; Wood, Sebastian; Wade, Jessica; Moriarty, John; Gann, Eliot; Ratcliff, Erin L; McNeill, Christopher R; Sirringhaus, Henning; Kim, Ji-Seon; Heeney, Martin

    2015-06-01

    We report two strategies toward the synthesis of 3-alkyl-4-fluorothiophenes containing straight (hexyl and octyl) and branched (2-ethylhexyl) alkyl groups. We demonstrate that treatment of the dibrominated monomer with 1 equiv of alkyl Grignard reagent leads to the formation of a single regioisomer as a result of the pronounced directing effect of the fluorine group. Polymerization of the resulting species affords highly regioregular poly(3-alkyl-4-fluoro)thiophenes. Comparison of their properties to those of the analogous non-fluorinated polymers shows that backbone fluorination leads to an increase in the polymer ionization potential without a significant change in optical band gap. Fluorination also results in an enhanced tendency to aggregate in solution, which is ascribed to a more co-planar backbone on the basis of Raman and DFT calculations. Average charge carrier mobilities in field-effect transistors are found to increase by up to a factor of 5 for the fluorinated polymers. PMID:25994804

  14. Tension trapping of carbonyl ylides facilitated by a change in polymer backbone.

    PubMed

    Klukovich, Hope M; Kean, Zachary S; Black Ramirez, Ashley L; Lenhardt, Jeremy M; Lin, Jiaxing; Hu, Xiangqian; Craig, Stephen L

    2012-06-13

    Epoxidized polybutadiene and epoxidized polynorbornene were subjected to pulsed ultrasound in the presence of small molecules capable of being trapped by carbonyl ylides. When epoxidized polybutadiene was sonicated, there was no observable small molecule addition to the polymer. Concurrently, no appreciable isomerization (cis to trans epoxide) was observed, indicating that the epoxide rings along the backbone are not mechanically active under the experimental conditions employed. In contrast, when epoxidized polynorbornene was subjected to the same conditions, both addition of ylide trapping reagents and net isomerization of cis to trans epoxide were observed. The results demonstrate the mechanical activity of epoxides, show that mechanophore activity is determined not only by the functional group but also the polymer backbone in which it is embedded, and facilitate a characterization of the reactivity of the ring-opened dialkyl epoxide. PMID:22650366

  15. Sequence Recombination Improves Target Specificity in a Redesigned Collagen Peptide abc-type Heterotrimer

    PubMed Central

    Giddu, Sumana; Xu, Fei; Nanda, Vikas

    2012-01-01

    Stability of the collagen triple helix is largely governed by its imino acid content, namely the occurrence of proline and 4R-hydroxyproline at the X and Y positions respectively of the periodic (Gly-X-Y)n sequence. Although other amino acids at these positions reduce stability of the triple helix, this can be partially compensated by introducing intermolecular side chain salt bridges. This approach was previously used to design an abc-type heterotrimer composed of one basic, one acidic and one neutral imino acid rich chain (Gauba & Hartgerink, 2007). In this study, an abc-type heterotrimer was designed to be the most stable species using a sequence recombination strategy that preserved both the amino acid composition and the network of interchain salt-bridges of the original design. The target heterotrimer had the highest Tm of 50°C, 7°C greater than the next most stable species. Stability of the heterotrimer decreased with increasing ionic strength, consistent with the role of intermolecular salt bridges in promoting stability. Quantitative meta-analysis of these results and published stability measurements on closely related peptides was used to discriminate the contributions of backbone propensity and side chain electrostatics to collagen stability. PMID:23042255

  16. Biosensors for DNA sequence detection

    NASA Technical Reports Server (NTRS)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    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.

  17. 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

  18. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    E-print Network

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  19. Tritium containing polymers having a polymer backbone substantially void of tritium

    DOEpatents

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

    1992-03-31

    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.

  20. Tritium containing polymers having a polymer backbone substantially void of tritium

    DOEpatents

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

    1992-01-01

    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.

  1. Conjugated backbone orientation variation in high mobility regioregular PT based copolymers

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    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 cm2 V-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.

  2. On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent

    PubMed Central

    Riml, Christian; Glasner, Heidelinde; Rodgers, M. T.; Micura, Ronald; Breuker, Kathrin

    2015-01-01

    Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in ‘top-down’ strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively charged RNA. We found that CAD of RNA is a stepwise reaction that is facilitated by, but does not require, the presence of positive charge. Preferred backbone cleavage next to adenosine and guanosine in CAD of (M+nH)n+ and (M?nH)n? ions, respectively, is based on hydrogen bonding between nucleobase and phosphodiester moieties. Moreover, CAD of RNA involves an intermediate that is sufficiently stable to survive extension of the RNA structure and intramolecular proton redistribution according to simple Coulombic repulsion prior to backbone cleavage into c and y ions from phosphodiester bond cleavage. PMID:25904631

  3. Efficient backbone cyclization of linear peptides by a recombinant asparaginyl endopeptidase.

    PubMed

    Harris, Karen S; Durek, Thomas; Kaas, Quentin; Poth, Aaron G; Gilding, Edward K; Conlan, Brendon F; Saska, Ivana; Daly, Norelle L; van der Weerden, Nicole L; Craik, David J; Anderson, Marilyn A

    2015-01-01

    Cyclotides are diverse plant backbone cyclized peptides that have attracted interest as pharmaceutical scaffolds, but fundamentals of their biosynthetic origin remain elusive. Backbone cyclization is a key enzyme-mediated step of cyclotide biosynthesis and confers a measure of stability on the resultant cyclotide. Furthermore, cyclization would be desirable for engineered peptides. Here we report the identification of four asparaginyl endopeptidases (AEPs), proteases implicated in cyclization, from the cyclotide-producing plant Oldenlandia affinis. We recombinantly express OaAEP1b and find it functions preferably as a cyclase by coupling C-terminal cleavage of propeptide substrates with backbone cyclization. Interestingly, OaAEP1b cannot cleave at the N-terminal site of O. affinis cyclotide precursors, implicating additional proteases in cyclotide biosynthesis. Finally, we demonstrate the broad utility of this enzyme by cyclization of peptides unrelated to cyclotides. We propose that recombinant OaAEP1b is a powerful tool for use in peptide engineering applications where increased stability of peptide products is desired. PMID:26680698

  4. Multiplex sequencing

    SciTech Connect

    Church, G.M.; Kieffer-Higgins, S.

    1990-07-17

    This patent describes a method for sequencing a DNA specimen. It comprises: providing a set of at least two vectors, each vector of the set comprising a cloning site and including at least one tag sequence at a position within 50 bases of the cloning site, each tag sequence in each vector differing from each tag sequence of every other vector of the set, and each being incapable of hybridizing to the DNA specimen under stringent conditions, providing a first and a second DNA sequence from the DNA specimen. The first DNA sequence being different from the second DNA sequence, ligating the first DNA sequence into the cloning site of one of the vectors, and the second DNA sequence into the cloning side of the second of the vectors, thereby producing a plurality of hybrid vectors, providing a pool of the hybrid vectors, treating separate aliquots of the pool in a plurality of vessels to produce fragments, separating the fragments comprising tag sequences from each the vessel according to their size, hybridizing the separated fragments under stringent conditions with a first oligonucleotide probe able to hybridize specifically with one of the tag sequences, and detecting the pattern of hybridization wherein the pattern reflects the nucleotide sequence of the DNA specimen.

  5. Methylene Blue Binding to DNA with Alternating GC Base Sequence: A Modeling Study

    E-print Network

    Rohs, Remo

    Methylene Blue Binding to DNA with Alternating GC Base Sequence: A Modeling Study Remo Rohs, HeinzVed January 18, 2000 Abstract: Photoactive methylene blue is one of the most efficient singlet oxygen-specific cleavage of the DNA backbone. Photophysical data obtained for methylene blue in complexes with DNA indicate

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

    PubMed

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

    2013-07-01

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

  7. High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in bronchoalveolar lavage fluid in patients with ventilator-associated pneumonia.

    PubMed

    Yang, Xiao-Jun; Wang, Yan-Bo; Zhou, Zhi-Wei; Wang, Guo-Wei; Wang, Xiao-Hong; Liu, Qing-Fu; Zhou, Shu-Feng; Wang, Zhen-Hai

    2015-01-01

    Ventilator-associated pneumonia (VAP) is a life-threatening disease that is associated with high rates of morbidity and likely mortality, placing a heavy burden on an individual and society. Currently available diagnostic and therapeutic approaches for VAP treatment are limited, and the prognosis of VAP is poor. The present study aimed to reveal and discriminate the identification of the full spectrum of the pathogens in patients with VAP using high-throughput sequencing approach and analyze the species richness and complexity via alpha and beta diversity analysis. The bronchoalveolar lavage fluid samples were collected from 27 patients with VAP in intensive care unit. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 27 samples of VAP were sequenced using the 454 GS FLX system. A total of 103,856 pyrosequencing reads and 638 operational taxonomic units were obtained from these 27 samples. There were four dominant phyla, including Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. There were 90 different genera, of which 12 genera occurred in over ten different samples. The top five dominant genera were Streptococcus, Acinetobacter, Limnohabitans, Neisseria, and Corynebacterium, and the most widely distributed genera were Streptococcus, Limnohabitans, and Acinetobacter in these 27 samples. Of note, the mixed profile of causative pathogens was observed. Taken together, the results show that the high-throughput sequencing approach facilitates the characterization of the pathogens in bronchoalveolar lavage fluid samples and the determination of the profile for bacteria in the bronchoalveolar lavage fluid samples of the patients with VAP. This study can provide useful information of pathogens in VAP and assist clinicians to make rational and effective therapeutic decisions. PMID:26345636

  8. High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in bronchoalveolar lavage fluid in patients with ventilator-associated pneumonia

    PubMed Central

    Yang, Xiao-Jun; Wang, Yan-Bo; Zhou, Zhi-Wei; Wang, Guo-Wei; Wang, Xiao-Hong; Liu, Qing-Fu; Zhou, Shu-Feng; Wang, Zhen-Hai

    2015-01-01

    Ventilator-associated pneumonia (VAP) is a life-threatening disease that is associated with high rates of morbidity and likely mortality, placing a heavy burden on an individual and society. Currently available diagnostic and therapeutic approaches for VAP treatment are limited, and the prognosis of VAP is poor. The present study aimed to reveal and discriminate the identification of the full spectrum of the pathogens in patients with VAP using high-throughput sequencing approach and analyze the species richness and complexity via alpha and beta diversity analysis. The bronchoalveolar lavage fluid samples were collected from 27 patients with VAP in intensive care unit. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 27 samples of VAP were sequenced using the 454 GS FLX system. A total of 103,856 pyrosequencing reads and 638 operational taxonomic units were obtained from these 27 samples. There were four dominant phyla, including Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. There were 90 different genera, of which 12 genera occurred in over ten different samples. The top five dominant genera were Streptococcus, Acinetobacter, Limnohabitans, Neisseria, and Corynebacterium, and the most widely distributed genera were Streptococcus, Limnohabitans, and Acinetobacter in these 27 samples. Of note, the mixed profile of causative pathogens was observed. Taken together, the results show that the high-throughput sequencing approach facilitates the characterization of the pathogens in bronchoalveolar lavage fluid samples and the determination of the profile for bacteria in the bronchoalveolar lavage fluid samples of the patients with VAP. This study can provide useful information of pathogens in VAP and assist clinicians to make rational and effective therapeutic decisions. PMID:26345636

  9. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    SciTech Connect

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

    2007-02-21

    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.

  10. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

    PubMed Central

    Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry

    2015-01-01

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Overall, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems. PMID:26506617

  11. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions†

    PubMed Central

    2015-01-01

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C–H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P–N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https://zenodo.org/collection/user-nmrlipids) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers. PMID:26509669

  12. Membrane Curvature Sensing by Amphipathic Helices Is Modulated by the Surrounding Protein Backbone

    PubMed Central

    Doucet, Christine M.; Esmery, Nina; de Saint-Jean, Maud; Antonny, Bruno

    2015-01-01

    Membrane curvature is involved in numerous biological pathways like vesicle trafficking, endocytosis or nuclear pore complex assembly. In addition to its topological role, membrane curvature is sensed by specific proteins, enabling the coordination of biological processes in space and time. Amongst membrane curvature sensors are the ALPS (Amphipathic Lipid Packing Sensors). ALPS motifs are short peptides with peculiar amphipathic properties. They are found in proteins targeted to distinct curved membranes, mostly in the early secretory pathway. For instance, the ALPS motif of the golgin GMAP210 binds trafficking vesicles, while the ALPS motif of Nup133 targets nuclear pores. It is not clear if, besides curvature sensitivity, ALPS motifs also provide target specificity, or if other domains in the surrounding protein backbone are involved. To elucidate this aspect, we studied the subcellular localization of ALPS motifs outside their natural protein context. The ALPS motifs of GMAP210 or Nup133 were grafted on artificial fluorescent probes. Importantly, ALPS motifs are held in different positions and these contrasting architectures were mimicked by the fluorescent probes. The resulting chimeras recapitulated the original proteins localization, indicating that ALPS motifs are sufficient to specifically localize proteins. Modulating the electrostatic or hydrophobic content of Nup133 ALPS motif modified its avidity for cellular membranes but did not change its organelle targeting properties. In contrast, the structure of the backbone surrounding the helix strongly influenced targeting. In particular, introducing an artificial coiled-coil between ALPS and the fluorescent protein increased membrane curvature sensitivity. This coiled-coil domain also provided membrane curvature sensitivity to the amphipathic helix of Sar1. The degree of curvature sensitivity within the coiled-coil context remains correlated to the natural curvature sensitivity of the helices. This suggests that the chemistry of ALPS motifs is a key parameter for membrane curvature sensitivity, which can be further modulated by the surrounding protein backbone. PMID:26366573

  13. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions.

    PubMed

    Botan, Alexandru; Favela-Rosales, Fernando; Fuchs, Patrick F J; Javanainen, Matti; Kandu?, Matej; Kulig, Waldemar; Lamberg, Antti; Loison, Claire; Lyubartsev, Alexander; Miettinen, Markus S; Monticelli, Luca; Määttä, Jukka; Ollila, O H Samuli; Retegan, Marius; Róg, Tomasz; Santuz, Hubert; Tynkkynen, Joona

    2015-12-10

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files ( https://zenodo.org/collection/user-nmrlipids ) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers. PMID:26509669

  14. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.

    PubMed

    Keedy, Daniel A; Fraser, James S; van den Bedem, Henry

    2015-10-01

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the "flap" regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Overall, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems. PMID:26506617

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

    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.

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

    PubMed

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

    2013-05-01

    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

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

    PubMed

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

    2014-06-01

    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

  18. Molecular mechanical studies of DNA flexibility: coupled backbone torsion angles and base-pair openings.

    PubMed

    Keepers, J W; Kollman, P A; Weiner, P K; James, T L

    1982-09-01

    Molecular mechanics studies have been carried out on "B-DNA-like" structures of [d(C-G-C-G-A-A-T-T-C-G-C-G)](2) and [d(A)](12).[d(T)](12). Each of the backbone torsion angles (psi, phi, omega, omega', phi') has been "forced" to alternative values from the normal B-DNA values (g(+), t, g(-), g(-), t conformations). Compensating torsion angle changes preserve most of the base stacking energy in the double helix. In a second part of the study, one purine N3-pyrimidine N1 distance at a time has been forced to a value of 6 A in an attempt to simulate the base opening motions required to rationalize proton exchange data for DNA. When the 6-A constraint is removed, many of the structures revert to the normal Watson-Crick hydrogen-bonded structure, but a number are trapped in structures approximately 5 kcal/mol higher in energy than the starting B-DNA structure. The relative energy of these structures, some of which involve a non-Watson-Crick thymine C2(carbonyl)[unk]adenine 6NH(2) hydrogen bond, are qualitatively consistent with the DeltaH for a "base pair-open state" suggested by Mandal et al. of 4-6 kcal/mol [Mandal, C., Kallenbach, N. R. & Englander, S. W. (1979) J. Mol. Biol. 135, 391-411]. The picture of DNA flexibility emerging from this study depicts the backbone as undergoing rapid motion between local torsional minima on a nanosecond time scale. Backbone motion is mainly localized within a dinucleoside segment and generally not conformationally coupled along the chain or across the base pairs. Base motions are much smaller in magnitude than backbone motions. Base sliding allows imino N-H exchange, but it is localized, and only a small fraction of the N-H groups is exposed at any one time. Stacking and hydrogen bonding cause a rigid core of bases in the center of the molecule accounting for the hydrodynamic properties of DNA. PMID:6957879

  19. Localization of strain in the RNA backbone and its functional implication

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel; Rabitz, Herschel

    1992-07-01

    It is known that an RNA molecule capable of self-splicing shares a common pattern of Watson-Crick base paris with other RNA species endowed with the same capability. The aim of this work is to introduce a minimal model Hamiltonian which determines a localized strain in the RNA backbone as the search for the molecular conformation is subject to the constraint imposed by the concensus secondary structure. The site where the strain is localized is shown to coincide with the splicing site of the molecule. As justified posteriori, the level of structural complexity of the model is sufficient to account for energy localization in a nontrivial fashion.

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

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    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.

  1. The assignment of the resonances of the backbone amide protons of arginine vasopressin and gramicidin S in D 2O by decoupling during exchange

    NASA Astrophysics Data System (ADS)

    Fischman, Alan J.; Live, David H.; Wittbold, William M.; Wyssbrod, Herman R.

    The resonances of six of the seven backbone amide protons of [8-arginine]vasopressin (AVP) and of all four nonequivalent backbone amide protons of gramicidin S (GS) in D 2O were assigned by decoupling of the amide protons from their respective vicinal C ? protons while exchange of the amide protons for deuterons was occurring. The simple pulsed Fourier transform method involving only a (?/2-FID) sequence of pulses was used. This method of assigning resonances of exchangeable protons is termed on-the-fly decoupling. Values for the chemical shifts of the amide protons ( ?N H) and for the coupling constants between vicinal amide and C ? protons of AVP in D 2O are shown to be quite similar to the corresponding ones previously published for [8-lysine]vasopressin in H 2O at a slightly different acidity and temperature [ J. D. Glickson, D. W. Urry, and R. Walter, Proc. Nat. Acad. Sci. USA69, 2566 (1972) ]. Values for the ?N HS of GS in D 2O are shown to be quite similar to the corresponding ones previously published for this peptide in CH 3OH at the same temperature [ D. W. Urry, in "The Enzymes of Biological Membranes" (A. Martonosi, Ed.), Vol. 1, pp. 31-69, Plenum, New York, 1976 ]. It is concluded that on-the-fly decoupling can be used to assign resonances of exchangeable protons in compounds dissolved at millimolar concentrations in solvents with exchangeable deuterons and that the spectral simplification that results when signals from rapidly exchanging protons are not observed may be advantageous.

  2. Helium-abundance and other composition effects on the properties of stellar surface convection in solar-like main-sequence stars

    SciTech Connect

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

    2013-12-01

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

  3. Towards atomistic resolution structure of phosphatidylcholine glycerol backbone and choline headgroup at different ambient conditions

    E-print Network

    Alexandru Botan; Andrea Catte; Fernando Favela; Patrick Fuchs; Matti Javanainen; Waldemar Kulig; Antti Lamberg; Markus S. Miettinen; Luca Monticelli; Jukka Määttä; Vasily S. Oganesyan; O. H. Samuli Ollila; Marius Retegan; Hubert Santuz; Joona Tynkkynen

    2015-01-14

    Phospholipids are essential building blocks of biological membranes. Despite of vast amount of accurate experimental data the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulation model would automatically resolve the structures giving an interpretation of experimental results, if the model would reproduce the experimental data. In this work we compare the C-H bond vector order parameters for glycerol backbone and choline headgroup between 14 different atomistic resolution models and experiments in fully hydrated lipid bilayer. The current models are not accurately enough to resolve the structure. However, closer inspection of three best performing models (CHARMM36, GAFFlipid and MacRog) suggest that improvements in the sampled dihedral angle distributions would potentilly lead to the model which would resolve the structure. Despite of the inaccuracy in the fully hydrated structures, the response to the dehydration, i.e. P-N vector tilting more parallel to membrane normal, is qualitatively correct in all models. The CHARMM36 and MacRog models describe the interactions between lipids and cholesterol better than Berger/H\\"oltje model. This work has been, and continues to be, progressed and discussed through the blog: nmrlipids.blogspot.fi. Everyone is invited to join the discussion and make contributions through the blog. The manuscript will be eventually submitted to an appropriate scientific journal. Everyone who has contributed to the work through the blog will be offered coauthorship. For more details see: nmrlipids.blogspot.fi.

  4. Fragmentation-Rearrangement of Peptide Backbones Mediated by the Air Pollutant NO2 (.).

    PubMed

    Gamon, Luke F; Nathanael, Joses G; Taggert, Bethany I; Henry, Fraser A; Bogena, Jana; Wille, Uta

    2015-10-12

    The fragmentation-rearrangement of peptide backbones mediated by nitrogen dioxide, NO2 (.) , was explored using di-, tri-, and tetrapeptides 8-18 as model systems. The reaction, which is initiated through nonradical N-nitrosation of the peptide bond, shortens the peptide chain by the expulsion of one amino acid moiety with simultaneous fusion of the remaining molecular termini through formation of a new peptide bond. The relative rate of the fragmentation-rearrangement depends on the nature of the amino acids and decreases with increasing steric bulk at the ? carbon in the order Gly>Ala>Val. Peptides that possessed consecutive aromatic side chains only gave products that resulted from nitrosation of the sterically less congested N-terminal amide. Such backbone fragmentation-rearrangement occurs under physiologically relevant conditions and could be an important reaction pathway for peptides, in which sections without readily oxidizable side chains are exposed to the air pollutant NO2 (.) . In addition to NO2 (.) -induced radical oxidation processes, this outcome shows that ionic reaction pathways, in particular nitrosation, should be factored in when assessing NO2 (.) reactivity in biological systems. PMID:26333002

  5. First-principles study of the effect of functional groups on polyaniline backbone.

    PubMed

    Chen, X P; Jiang, J K; Liang, Q H; Yang, N; Ye, H Y; Cai, M; Shen, L; Yang, D G; Ren, T L

    2015-01-01

    We present a first-principles density functional theory study focused on how the chemical and electronic properties of polyaniline are adjusted by introducing suitable substituents on a polymer backbone. Analyses of the obtained energy barriers, reaction energies and minimum energy paths indicate that the chemical reactivity of the polyaniline derivatives is significantly enhanced by protonic acid doping of the substituted materials. Further study of the density of states at the Fermi level, band gap, HOMO and LUMO shows that both the unprotonated and protonated states of these polyanilines are altered to different degrees depending on the functional group. We also note that changes in both the chemical and electronic properties are very sensitive to the polarity and size of the functional group. It is worth noting that these changes do not substantially alter the inherent chemical and electronic properties of polyaniline. Our results demonstrate that introducing different functional groups on a polymer backbone is an effective approach to obtain tailored conductive polymers with desirable properties while retaining their intrinsic properties, such as conductivity. PMID:26584671

  6. Ultraviolet Spectroscopy of Protein Backbone Transitions in Aqueous Solution: combined QM and MM Simulations

    PubMed Central

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

    2010-01-01

    A generalized approach combining Quantum Mechanics (QM) and Molecular Mechanics (MM) calculations is developed to simulate the n ? ?* and ? ? ?* backbone transitions of proteins in aqueous solution. These transitions, which occur in the ultraviolet (UV) at 180–220 nm, provide a sensitive probe for secondary structures. The excitation Hamiltonian is constructed using high level electronic structure calculations of N-methylacetamide (NMA). Its electrostatic fluctuations are modeled using a new algorithm, EHEF, which combines a molecular dynamics (MD) trajectory obtained with a molecular mechanics forcefield, and electronic structures of sampled MD snapshots calculated by QM. The lineshapes and excitation split-tings induced by the electrostatic environment in the experimental UV linear absorption (LA) and circular dichroism (CD) spectra of several proteins in aqueous solution are reproduced by our calculations. The distinct CD features of ?-helix and ?-sheet protein structures are observed in the simulations and can be assigned to different backbone geometries. The fine structure of the UV spectra is accurately characterized and enables us to identify signatures of secondary structures. PMID:20503991

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-02-01

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

  9. Structure and Assembly of Group B Streptococcus Pilus 2b Backbone Protein

    PubMed Central

    Cozzi, Roberta; Malito, Enrico; Lazzarin, Maddalena; Nuccitelli, Annalisa; Castagnetti, Andrea; Bottomley, Matthew J.; Margarit, Immaculada; Maione, Domenico; Rinaudo, C. Daniela

    2015-01-01

    Group B Streptococcus (GBS) is a major cause of invasive disease in infants. Like other Gram-positive bacteria, GBS uses a sortase C-catalyzed transpeptidation mechanism to generate cell surface pili from backbone and ancillary pilin precursor substrates. The three pilus types identified in GBS contain structural subunits that are highly immunogenic and are promising candidates for the development of a broadly-protective vaccine. Here we report the X-ray crystal structure of the backbone protein of pilus 2b (BP-2b) at 1.06Å resolution. The structure reveals a classical IgG-like fold typical of the pilin subunits of other Gram-positive bacteria. The crystallized portion of the protein (residues 185-468) encompasses domains D2 and D3 that together confer high stability to the protein due to the presence of an internal isopeptide bond within each domain. The D2+D3 region, lacking the N-terminal D1 domain, was as potent as the entire protein in conferring protection against GBS challenge in a well-established mouse model. By site-directed mutagenesis and complementation studies in GBS knock-out strains we identified the residues and motives essential for assembly of the BP-2b monomers into high-molecular weight complexes, thus providing new insights into pilus 2b polymerization. PMID:25942637

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

    PubMed Central

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

    2015-01-01

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

  11. NMR Polypeptide Backbone Conformation of the E. coli Outer Membrane Protein W

    PubMed Central

    Horst, Reto; Stanczak, Pawel; Wüthrich, Kurt

    2014-01-01

    SUMMARY The outer membrane proteins (Omp) are key factors for bacterial survival and virulence. Among the Omps which have been structurally characterized either by X-ray crystallography or by NMR in solution, the crystal structure of OmpW stands out because three of its four extracellular loops are well defined, whereas long extracellular loops in other E. coli Omps are disordered in the crystals as well as in NMR structures. OmpW thus presented an opportunity for detailed comparison of the extracellular loops in a ?-barrel membrane protein structure in crystals and in non-crystalline milieus. Here the polypeptide backbone conformation of OmpW in 30-Fos micelles was determined. Complete backbone NMR assignments were obtained and the loops were structurally characterized. In combination with the OmpW crystal structure, NMR line shape analyses and 15N{1H}-NOE data, these results showed that intact regular secondary structures in the loops undergo slow hinge motions at the detergent–solvent interface. PMID:25017731

  12. Solution Structure and Backbone Dynamics of Human Liver Fatty Acid Binding Protein: Fatty Acid Binding Revisited

    PubMed Central

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

    2012-01-01

    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

  13. Ultraviolet spectroscopy of protein backbone transitions in aqueous solution: combined QM and MM simulations.

    PubMed

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

    2010-06-24

    A generalized approach combining quantum mechanics (QM) and molecular mechanics (MM) calculations is developed to simulate the n --> pi* and pi --> pi* backbone transitions of proteins in aqueous solution. These transitions, which occur in the ultraviolet (UV) at 180-220 nm, provide a sensitive probe for secondary structures. The excitation Hamiltonian is constructed using high-level electronic structure calculations of N-methylacetamide (NMA). Its electrostatic fluctuations are modeled using a new algorithm, EHEF, which combines a molecular dynamics (MD) trajectory obtained with a MM forcefield and electronic structures of sampled MD snapshots calculated by QM. The lineshapes and excitation splittings induced by the electrostatic environment in the experimental UV linear absorption (LA) and circular dichroism (CD) spectra of several proteins in aqueous solution are reproduced by our calculations. The distinct CD features of alpha-helix and beta-sheet protein structures are observed in the simulations and can be assigned to different backbone geometries. The fine structure of the UV spectra is accurately characterized and enables us to identify signatures of secondary structures. PMID:20503991

  14. First-principles study of the effect of functional groups on polyaniline backbone

    PubMed Central

    Chen, X. P.; Jiang, J. K.; Liang, Q. H.; Yang, N.; Ye, H. Y.; Cai, M.; Shen, L.; Yang, D. G.; Ren, T. L.

    2015-01-01

    We present a first-principles density functional theory study focused on how the chemical and electronic properties of polyaniline are adjusted by introducing suitable substituents on a polymer backbone. Analyses of the obtained energy barriers, reaction energies and minimum energy paths indicate that the chemical reactivity of the polyaniline derivatives is significantly enhanced by protonic acid doping of the substituted materials. Further study of the density of states at the Fermi level, band gap, HOMO and LUMO shows that both the unprotonated and protonated states of these polyanilines are altered to different degrees depending on the functional group. We also note that changes in both the chemical and electronic properties are very sensitive to the polarity and size of the functional group. It is worth noting that these changes do not substantially alter the inherent chemical and electronic properties of polyaniline. Our results demonstrate that introducing different functional groups on a polymer backbone is an effective approach to obtain tailored conductive polymers with desirable properties while retaining their intrinsic properties, such as conductivity. PMID:26584671

  15. Combination cytotoxicity of backbone degradable HPMA copolymer gemcitabine and platinum conjugates toward human ovarian carcinoma cells

    PubMed Central

    Duangjai, Acharaporn; Luo, Kui; Zhou, Yan; Yang, Jiyuan; Kope?ek, Jind?ich

    2014-01-01

    Multiblock, backbone degradable HPMA copolymer-drug conjugates containing gemcitabine and DACH platinum (mP-GEM and mP-DACH Pt), respectively were synthesized by reversible addition fragmentation (RAFT) polymerization and subsequent chain extension by click chemistry. Using combination index analysis, the cytotoxicities of the two multiblock conjugates, as single agents and in combination, were evaluated in vitro in A2780 human ovarian cancer cells, with free drugs as controls. The greatest synergistic cytotoxic effect was observed when A2780 cells were sequentially exposed to mP-GEM for 24 h and mP-DACH Pt for 48 h. In addition, mechanistic studies support the rationale of the synergy between mP-GEM and mP-DACH Pt: mP-GEM pretreatment was able to enhance the platinum-DNA adduct accumulation and inhibit cell proliferation to a higher extent than single mPDACH Pt treatment. These observations are useful for the development of combination macromolecular therapeutics for ovarian cancer based on the second-generation backbone degradable HPMA copolymers. PMID:24316339

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

    SciTech Connect

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

    2014-06-17

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

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

    DOE PAGESBeta

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

    2014-06-17

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

  18. Differential ordering of the protein backbone and side chains during protein folding revealed by site-specific recombinant infrared probes

    PubMed Central

    Nagarajan, Sureshbabu; Taskent-Sezgin, Humeyra; Parul, Dzmitry; Carrico, Isaac; Raleigh, Daniel P.; Dyer, R. Brian

    2011-01-01

    The timescale for ordering of the polypeptide backbone relative to the side chains is a critical issue in protein folding. The interplay between ordering of the backbone and side chains is particularly important for the formation of ?-sheet structures, as the polypeptide chain searches for the native stabilizing cross-strand interactions. We have studied these issues in the N-terminal domain of protein L9 (NTL9), a model protein with mixed ?/? structure. We have developed a general approach for introducing site-specific IR probes for the side chains (azide) and backbone (13C=18O) using recombinant protein expression. T-jump, time-resolved IR spectroscopy combined with site-specific labeling enables independent measurement of the respective backbone and side chain dynamics with single residue resolution. We find that side chain ordering in a key region of the ?-sheet structure occurs on a slower time scale than ordering of the backbone during the folding of NTL9, likely due to the transient formation of nonnative side chain interactions. PMID:22039909

  19. The Inherent Conformational Preferences of Glutamine-Containing Peptides: the Role for Side-Chain Backbone Hydrogen Bonds

    NASA Astrophysics Data System (ADS)

    Walsh, Patrick S.; McBurney, Carl; Gellman, Samuel H.; Zwier, Timothy S.

    2015-06-01

    Glutamine is widely known to be found in critical regions of peptides which readily fold into amyloid fibrils, the structures commonly associated with Alzheimer's disease and glutamine repeat diseases such as Huntington's disease. Building on previous single-conformation data on Gln-containing peptides containing an aromatic cap on the N-terminus (Z-Gln-OH and Z-Gln-NHMe), we present here single-conformation UV and IR spectra of Ac-Gln-NHBn and Ac-Ala-Gln-NHBn, with its C-terminal benzyl cap. These results point towards side-chain to backbone hydrogen bonds dominating the structures observed in the cold, isolated environment of a molecular beam. We have identified and assigned three main conformers for Ac-Gln-NHBn all involving primary side-chain to backbone interactions. Ac-Ala-Gln-NHBn extends the peptide chain by one amino acid, but affords an improvement in the conformational flexibility. Despite this increase in the flexibility, only a single conformation is observed in the gas-phase: a structure which makes use of both side-chain-to-backbone and backbone-to-backbone hydrogen bonds.

  20. 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

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

    2014-01-01

    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

  1. 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

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

    2014-01-01

    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

  2. Dna Sequencing

    DOEpatents

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

    1995-04-25

    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.

  3. Thermoplastic copolyimides and composites therefrom

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

    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.

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

    PubMed

    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

    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

  5. Backbone and side chain dynamics of uncomplexed human adipocyte and muscle fatty acid-binding proteins.

    PubMed

    Constantine, K L; Friedrichs, M S; Wittekind, M; Jamil, H; Chu, C H; Parker, R A; Goldfarb, V; Mueller, L; Farmer, B T

    1998-06-01

    Adipocyte lipid-binding protein (A-LBP) and muscle fatty acid-binding protein (M-FABP) are members of a family of small ( approximately 15 kDa) cytosolic proteins that are involved in the metabolism of fatty acids and other lipid-soluble molecules. Although highly homologous (65%) and structurally very similar, A-LBP and M-FABP display distinct ligand binding characteristics. Since ligand binding may be influenced by intrinsic protein dynamical properties, we have characterized the backbone and side chain dynamics of uncomplexed (apo) human A-LBP and M-FABP. Backbone dynamics were characterized by measurements of 15N T1 and T2 values and ¿1H¿-15N NOEs. These data were analyzed using model-free spectral density functions and reduced spectral density mapping. The dynamics of methyl-containing side chains were charaterized by measurements of 2H T1 and T1rho relaxation times of 13C1H22H groups. The 2H relaxation data were analyzed using the model-free approach. For A-LBP, 15N relaxation data were obtained for 111 residues and 2H relaxation data were obtained for 42 methyl groups. For M-FABP, 15N relaxation data were obtained for 111 residues and 2H relaxation data were obtained for 53 methyl groups. The intrinsic flexibilities of these two proteins are compared, with particular emphasis placed on binding pocket residues. There are a number of distinct dynamical differences among corresponding residues between the two proteins. In particular, many residues display greater backbone picosecond to nanosecond and/or microsecond to millisecond time scale mobility in A-LBP relative to M-FABP, including F57, K58, and most residues in alpha-helix 2 (residues 28-35). Variations in the dynamics of this region may play a role in ligand selectivity. The side chains lining the fatty acid binding pocket display a wide range of motional restriction in both proteins. Side chains showing distinct dynamical differences between the two proteins include those of residues 20, 29, and 51. This information provides a necessary benchmark for determining dynamical changes induced by ligand binding and may ultimately lead to an enhanced understanding of ligand affinity and selectivity among fatty acid-binding proteins. PMID:9609689

  6. Exact solution for a diffusive process on a backbone structure: Green function approach and external force

    NASA Astrophysics Data System (ADS)

    Lenzi, E. K.; da Silva, L. R.; Tateishi, A. A.; Lenzi, M. K.; Ribeiro, H. V.

    2014-03-01

    The effects of an external force on a diffusive process subjected to a backbone structure are investigated. This analysis is performed by considering the system governed by the Fokker-Planck equation {?ial _t}? = {D_y}?ial _y^2? + {D_x}? (y)?ial _x^2? - nabla \\cdot ({?c F_? }) with ?c F = v_x + ? (y)v^prime_x,v_y. The equation is subjected to the boundary conditions ?(±?, y; t) = 0 and ?(x, ±? t) = 0 with ? (x,y;0) = hat ? (x,y), where hat ? (x,y) is normalized. Applying the Green function approach, we obtain exact solutions and analyze the relaxation process through the mean square displacement evaluated for the x and y directions. Our results show an anomalous spreading of the system characterized by one or several diffusive regimes connected to anomalous diffusion and stationary states.

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

    NASA Astrophysics Data System (ADS)

    Cazon, L.

    2013-06-01

    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.

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

    E-print Network

    Cazon, L

    2013-01-01

    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.

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

    PubMed

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

    2014-08-14

    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

  10. The Effects of NHC-Backbone Substitution on Efficiency in Ruthenium-based Olefin Metathesis

    PubMed Central

    Kuhn, Kevin M.; Bourg, Jean-Baptiste; Chung, Cheol K.; Virgil, Scott C.; Grubbs, Robert H.

    2009-01-01

    A series of ruthenium olefin metathesis catalysts bearing N-heterocyclic carbene (NHC) ligands with varying degrees of backbone and N-aryl substitution have been prepared. These complexes show greater resistance to decomposition through C–H activation of the N-aryl group, resulting in increased catalyst lifetimes. This work has utilized robotic technology to examine the activity and stability of each catalyst in metathesis, providing insights into the relationship between ligand architecture and enhanced efficiency. The development of this robotic methodology has also shown that, under optimized conditions, catalyst loadings as low as 25 ppm can lead to 100% conversion in the ring-closing metathesis of diethyl diallylmalonate. PMID:19351207

  11. Modeling the Backbone Dynamics of Reduced and Oxidized Solvated Rat Microsomal Cytochrome b5

    PubMed Central

    Giachetti, Andrea; Penna, Giovanni La; Perico, Angelo; Banci, Lucia

    2004-01-01

    In this article, a description of the statistics and dynamics of cytochrome b5 in both reduced and oxidized forms is given. Results of molecular dynamics computer simulations in the explicit solvent have been combined with mode-coupling diffusion models including and neglecting the molecule-solvent correlations. R1 and R1? nuclear magnetic relaxation parameters of 15N in the protein backbone have been calculated and compared with experiments. Slight changes in charge density in the heme upon oxidation produces a cascade of changes in charge distributions from heme propionates up to charged residues ?1.5 nm from Fe. These changes in charge distributions modify the molecular surface and the water shell surrounding the protein. The statistical changes upon oxidation can be included in diffusive models that physically explain the upper and lower limits of R1? relaxation parameters at high off-resonance fields. PMID:15240483

  12. Modification of Rifamycin Polyketide Backbone Leads to Improved Drug Activity against Rifampicin-resistant Mycobacterium tuberculosis*

    PubMed Central

    Nigam, Aeshna; Almabruk, Khaled H.; Saxena, Anjali; Yang, Jongtae; Mukherjee, Udita; Kaur, Hardeep; Kohli, Puneet; Kumari, Rashmi; Singh, Priya; Zakharov, Lev N.; Singh, Yogendra; Mahmud, Taifo; Lal, Rup

    2014-01-01

    Rifamycin B, a product of Amycolatopsis mediterranei S699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and AIDS-related mycobacterial infections. However, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of Mycobacterium tuberculosis. As part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of module 2 of rapamycin polyketide synthase. The resulting mutants (rifAT6::rapAT2) of A. mediterranei S699 produced new rifamycin analogs, 24-desmethylrifamycin B and 24-desmethylrifamycin SV, which contained modification in the polyketide backbone. 24-Desmethylrifamycin B was then converted to 24-desmethylrifamycin S, whose structure was confirmed by MS, NMR, and X-ray crystallography. Subsequently, 24-desmethylrifamycin S was converted to 24-desmethylrifampicin, which showed excellent antibacterial activity against several rifampicin-resistant M. tuberculosis strains. PMID:24923585

  13. Modification of rifamycin polyketide backbone leads to improved drug activity against rifampicin-resistant Mycobacterium tuberculosis.

    PubMed

    Nigam, Aeshna; Almabruk, Khaled H; Saxena, Anjali; Yang, Jongtae; Mukherjee, Udita; Kaur, Hardeep; Kohli, Puneet; Kumari, Rashmi; Singh, Priya; Zakharov, Lev N; Singh, Yogendra; Mahmud, Taifo; Lal, Rup

    2014-07-25

    Rifamycin B, a product of Amycolatopsis mediterranei S699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and AIDS-related mycobacterial infections. However, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of Mycobacterium tuberculosis. As part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of module 2 of rapamycin polyketide synthase. The resulting mutants (rifAT6::rapAT2) of A. mediterranei S699 produced new rifamycin analogs, 24-desmethylrifamycin B and 24-desmethylrifamycin SV, which contained modification in the polyketide backbone. 24-Desmethylrifamycin B was then converted to 24-desmethylrifamycin S, whose structure was confirmed by MS, NMR, and X-ray crystallography. Subsequently, 24-desmethylrifamycin S was converted to 24-desmethylrifampicin, which showed excellent antibacterial activity against several rifampicin-resistant M. tuberculosis strains. PMID:24923585

  14. Essential roles of four-carbon backbone chemicals in the control of metabolism

    PubMed Central

    Chriett, Sabrina; Pirola, Luciano

    2015-01-01

    The increasing incidence of obesity worldwide and its related cardiometabolic complications is an urgent public health problem. While weight gain results from a negative balance between the energy expenditure and calorie intake, recent research has demonstrated that several small organic molecules containing a four-carbon backbone can modulate this balance by favoring energy expenditure, and alleviating endoplasmic reticulum stress and oxidative stress. Such small molecules include the bacterially produced short chain fatty acid butyric acid, its chemically produced derivative 4-phenylbutyric acid, the main ketone body D-?-hydroxybutyrate - synthesized by the liver - and the recently discovered myokine ?-aminoisobutyric acid. Conversely, another butyrate-related molecule, ?-hydroxybutyrate, has been found to be an early predictor of insulin resistance and glucose intolerance. In this minireview, we summarize recent advances in the understanding of the mechanism of action of these molecules, and discuss their use as therapeutics to improve metabolic homeostasis or their detection as early biomarkers of incipient insulin resistance. PMID:26322177

  15. Essential roles of four-carbon backbone chemicals in the control of metabolism.

    PubMed

    Chriett, Sabrina; Pirola, Luciano

    2015-08-26

    The increasing incidence of obesity worldwide and its related cardiometabolic complications is an urgent public health problem. While weight gain results from a negative balance between the energy expenditure and calorie intake, recent research has demonstrated that several small organic molecules containing a four-carbon backbone can modulate this balance by favoring energy expenditure, and alleviating endoplasmic reticulum stress and oxidative stress. Such small molecules include the bacterially produced short chain fatty acid butyric acid, its chemically produced derivative 4-phenylbutyric acid, the main ketone body D-?-hydroxybutyrate - synthesized by the liver - and the recently discovered myokine ?-aminoisobutyric acid. Conversely, another butyrate-related molecule, ?-hydroxybutyrate, has been found to be an early predictor of insulin resistance and glucose intolerance. In this minireview, we summarize recent advances in the understanding of the mechanism of action of these molecules, and discuss their use as therapeutics to improve metabolic homeostasis or their detection as early biomarkers of incipient insulin resistance. PMID:26322177

  16. "Chameleonic" backbone hydrogen bonds in protein binding and as drug targets.

    PubMed

    Menéndez, C A; Accordino, S R; Gerbino, D C; Appignanesi, G A

    2015-10-01

    We carry out a time-averaged contact matrix study to reveal the existence of protein backbone hydrogen bonds (BHBs) whose net persistence in time differs markedly form their corresponding PDB-reported state. We term such interactions as "chameleonic" BHBs, CBHBs, precisely to account for their tendency to change the structural prescription of the PDB for the opposite bonding propensity in solution. We also find a significant enrichment of protein binding sites in CBHBs, relate them to local water exposure and analyze their behavior as ligand/drug targets. Thus, the dynamic analysis of hydrogen bond propensity might lay the foundations for new tools of interest in protein binding-site prediction and in lead optimization for drug design. PMID:26486885

  17. Side chain and backbone contributions of Phe508 to CFTR folding

    SciTech Connect

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J.

    2010-12-07

    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.

  18. Analysis of Polypeptide Backbone T1 Relaxation Data Using an Experimentally Derived Model

    NASA Astrophysics Data System (ADS)

    North, C. L.; Cross, T. A.

    The time scale of internal motion of the Ala 3-Leu 4 peptide linkage plane of gramicidin A in its channel conformation is analyzed by interpreting solid-state 15N T1 measurements taken at 4.7 and 9.4 T. The T1 relaxation measurements have been interpreted using a structural model of local motion which has previously been experimentally determined. According to this model, the individual peptide plane motion is a rotational diffusion subject to a harmonic restoring potential about an axis through successive ? carbons. The results which best fit the model to the data reported here and to previously determined information about the motions of the gramicidin channel suggest that the correlation time for librations of the Ala 3-Leu 4 peptide linkage is 36 ns. This suggests that the peptide backbone motions of the gramicidin channel may be on the same time scale as the translational motion of a cation in the channel.

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

    E-print Network

    L. Cazon

    2013-01-15

    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.

  20. Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics.

    PubMed

    Cheng, Lingpeng; Zhu, Jiang; Hui, Wong Hoi; Zhang, Xiaokang; Honig, Barry; Fang, Qin; Zhou, Z Hong

    2010-04-01

    Grass carp reovirus (GCRV) is a member of the aquareovirus genus in the Reoviridae family and has a capsid with two shells-a transcription-competent core surrounded by a coat. We report a near-atomic-resolution reconstruction of the GCRV virion by cryo-electron microscopy and single-particle reconstruction. A backbone model of the GCRV virion, including seven conformers of the five capsid proteins making up the 1500 molecules in both the core and the coat, was derived using cryo-electron microscopy density-map-constrained homology modeling and refinement. Our structure clearly showed that the amino-terminal segment of core protein VP3B forms an approximately 120-A-long alpha-helix-rich extension bridging across the icosahedral 2-fold-symmetry-related molecular interface. The presence of this unique structure across this interface and the lack of an external cementing molecule at this location in GCRV suggest a stabilizing role of this extended amino-terminal density. Moreover, part of this amino-terminal extension becomes invisible in the reconstruction of transcription-competent core particles, suggesting its involvement in endogenous viral RNA transcription. Our structure of the VP1 turret represents its open state, and comparison with its related structures at the closed state suggests hinge-like domain movements associated with the mRNA-capping machinery. Overall, this first backbone model of an aquareovirus virion provides a wealth of structural information for understanding the structural basis of GCRV assembly and transcription. PMID:20036256

  1. Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation.

    PubMed

    Waldhauer, Max C; Schmitz, Silvan N; Ahlmann-Eltze, Constantin; Gleixner, Jan G; Schmelas, Carolin C; Huhn, Anna G; Bunne, Charlotte; Büscher, Magdalena; Horn, Max; Klughammer, Nils; Kreft, Jakob; Schäfer, Elisabeth; Bayer, Philipp A; Krämer, Stephen G; Neugebauer, Julia; Wehler, Pierre; Mayer, Matthias P; Eils, Roland; Di Ventura, Barbara

    2015-11-10

    The activity of proteins is dictated by their three-dimensional structure, the native state, and is influenced by their ability to remain in or return to the folded native state under physiological conditions. Backbone circularization is thought to increase protein stability by decreasing the conformational entropy in the unfolded state. A positive effect of circularization on stability has been shown for several proteins. Here, we report the development of a cloning standard that facilitates implementing the SICLOPPS technology to circularize proteins of interest using split inteins. To exemplify the usage of the cloning standard we constructed two circularization vectors based on the Npu DnaE and gp41-1 split inteins, respectively. We use these vectors to overexpress in Escherichia coli circular forms of the Bacillus subtilis enzyme family 11 xylanase that differ in the identity and number of additional amino acids used for circularization (exteins). We found that the variant circularized with only one additional serine has increased thermostability of 7 °C compared to native xylanase. The variant circularized with six additional amino acids has only a mild increase in thermostability compared to the corresponding exteins-bearing linear xylanase, but is less stable than native xylanase. However, this circular xylanase retains more than 50% of its activity after heat shock at elevated temperatures, while native xylanase and the corresponding exteins-bearing linear xylanase are largely inactivated. We correlate this residual activity to the fewer protein aggregates found in the test tubes of circular xylanase after heat shock, suggesting that circularization protects the protein from aggregation under these conditions. Taken together, these data indicate that backbone circularization has a positive effect on xylanase and can lead to increased thermostability, provided the appropriate exteins are selected. We believe that our cloning standard and circularization vectors will facilitate testing the effects of circularization on other proteins. PMID:26434634

  2. An avian live attenuated master backbone for potential use in epidemic and pandemic influenza vaccines.

    PubMed

    Hickman, Danielle; Hossain, Md Jaber; Song, Haichen; Araya, Yonas; Solórzano, Alicia; Perez, Daniel R

    2008-11-01

    The unprecedented emergence in Asia of multiple avian influenza virus (AIV) subtypes with a broad host range poses a major challenge in the design of vaccination strategies that are both effective and available in a timely manner. The present study focused on the protective effects of a genetically modified AIV as a source for the preparation of vaccines for epidemic and pandemic influenza. It has previously been demonstrated that a live attenuated AIV based on the internal backbone of influenza A/Guinea fowl/Hong Kong/WF10/99 (H9N2), called WF10att, is effective at protecting poultry species against low- and high-pathogenicity influenza strains. More importantly, this live attenuated virus provided effective protection when administered in ovo. In order to characterize the WF10att backbone further for use in epidemic and pandemic influenza vaccines, this study evaluated its protective effects in mice. Intranasal inoculation of modified attenuated viruses in mice provided adequate protective immunity against homologous lethal challenges with both the wild-type influenza A/WSN/33 (H1N1) and A/Vietnam/1203/04 (H5N1) viruses. Adequate heterotypic immunity was also observed in mice vaccinated with modified attenuated viruses carrying H7N2 surface proteins. The results presented in this report suggest that the internal genes of a genetically modified AIV confer similar protection in a mouse model and thus could be used as a master donor strain for the generation of live attenuated vaccines for epidemic and pandemic influenza. PMID:18931063

  3. Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit.

    PubMed

    Kruse, Holger; Mladek, Arnost; Gkionis, Konstantinos; Hansen, Andreas; Grimme, Stefan; Sponer, Jiri

    2015-10-13

    We have created a benchmark set of quantum chemical structure-energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO-CCSD(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0?OL3 force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of ?0.4-0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields. PMID:26574283

  4. 40-Gbps optical backbone network deep packet inspection based on FPGA

    NASA Astrophysics Data System (ADS)

    Zuo, Yuan; Huang, Zhiping; Su, Shaojing

    2014-11-01

    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.

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

    NASA Astrophysics Data System (ADS)

    Itoh, Kazuhito; Sasai, Masaki

    2011-03-01

    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.

  6. DNA sequencing

    SciTech Connect

    Tabor, S.; Richardson, C.C.

    1991-02-19

    This patent describes a method for determining the nucleotide base sequence of a DNA molecule. It comprises: providing the DNA molecule annealed with a primer molecule able to hybridize to the DNA molecule; incubating the annealed molecules in a vessel containing four different deoxynucleoside triphosphates, a processive DNA polymerase, wherein the polymerase is able to remain bound for at least 500 bases to the DNA molecule in an environmental condition used in the extension reaction of a DNA sequencing reaction, the polymerase having less than 500 units of exonuclease activity per mg of the polymerase, and one of four DNA synthesis terminating agents which terminate DNA synthesis at a specific nucleotide base, wherein each the agent terminates DNA synthesis at a different nucleotide base, and separating the DNA products of the incubating reaction according to their size, whereby at least a part of the nucleotide base sequence of the DNA molecule can be determined.

  7. SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles.

    PubMed

    Faraggi, Eshel; Zhang, Tuo; Yang, Yuedong; Kurgan, Lukasz; Zhou, Yaoqi

    2012-01-30

    Accurate prediction of protein secondary structure is essential for accurate sequence alignment, three-dimensional structure modeling, and function prediction. The accuracy of ab initio secondary structure prediction from sequence, however, has only increased from around 77 to 80% over the past decade. Here, we developed a multistep neural-network algorithm by coupling secondary structure prediction with prediction of solvent accessibility and backbone torsion angles in an iterative manner. Our method called SPINE X was applied to a dataset of 2640 proteins (25% sequence identity cutoff) previously built for the first version of SPINE and achieved a 82.0% accuracy based on 10-fold cross validation (Q(3)). Surpassing 81% accuracy by SPINE X is further confirmed by employing an independently built test dataset of 1833 protein chains, a recently built dataset of 1975 proteins and 117 CASP 9 targets (critical assessment of structure prediction techniques) with an accuracy of 81.3%, 82.3% and 81.8%, respectively. The prediction accuracy is further improved to 83.8% for the dataset of 2640 proteins if the DSSP assignment used above is replaced by a more consistent consensus secondary structure assignment method. Comparison to the popular PSIPRED and CASP-winning structure-prediction techniques is made. SPINE X predicts number of helices and sheets correctly for 21.0% of 1833 proteins, compared to 17.6% by PSIPRED. It further shows that SPINE X consistently makes more accurate prediction in helical residues (6%) without over prediction while PSIPRED makes more accurate prediction in coil residues (3-5%) and over predicts them by 7%. SPINE X Server and its training/test datasets are available at http://sparks.informatics.iupui.edu/ PMID:22045506

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

    NASA Astrophysics Data System (ADS)

    Naritomi, Yusuke; Fuchigami, Sotaro

    2013-12-01

    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.

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

    SciTech Connect

    Naritomi, Yusuke; Fuchigami, Sotaro

    2013-12-07

    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.

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

    E-print Network

    Theodorakis, Panagiotis E.

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

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

    PubMed

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

    2010-11-17

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

  12. Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities

    E-print Network

    Bing-Sui Lu; Ali Naji; Rudolf Podgornik

    2015-03-18

    We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van der Waals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel $r^{-5}$ scaling behavior of the van der Waals interaction energy for small inter-polymer separation $r$, in contradistinction to the $r^{-4}$ scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently aligned identical polymers. Such behavior can assist the molecular recognition between polymers.

  13. Methods and compositions for chromosome-specific staining

    DOEpatents

    Gray, Joe W.; Pinkel, Daniel

    2003-07-22

    Methods and compositions for chromosome-specific staining are provided. Compositions comprise heterogenous mixtures of labeled nucleic acid fragments having substantially complementary base sequences to unique sequence regions of the chromosomal DNA for which their associated staining reagent is specific. Methods include methods for making the chromosome-specific staining compositions of the invention, and methods for applying the staining compositions to chromosomes.

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

    SciTech Connect

    Wang, Jinfeng; Mooberry, E.S.; Walkenhorst, W.F.; Markley, J.L. )

    1992-01-28

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

  15. Molecular basis for nanoscopic membrane curvature generation from quantum mechanical models and synthetic transporter sequences

    PubMed Central

    Schmidt, Nathan W.; Lis, Michael; Zhao, Kun; Lai, Ghee Hwee; Alexandrova, Anastassia; Tew, Gregory N.; Wong, Gerard C. L.

    2013-01-01

    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

  16. Backbone, side chain and heme resonance assignments of cytochrome OmcF from Geobacter sulfurreducens.

    PubMed

    Dantas, Joana M; Silva E Sousa, Marta; Salgueiro, Carlos A; Bruix, Marta

    2015-10-01

    Gene knockout studies on Geobacter sulfurreducens (Gs) cells showed that the outer membrane cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) citrate and U(VI) oxide. In addition, microarray analysis of OmcF-deficient mutant versus the wild-type strain revealed that many of the genes with decreased transcript level were those whose expression is upregulated in cells grown with a graphite electrode as electron acceptor. This suggests that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electrical current production by Gs in microbial fuel cells. Extracellular electron transfer processes (EET) constitute nowadays the foundations to develop biotechnological applications in biofuel production, bioremediation and bioenergy. Therefore, the structural characterization of OmcF is a fundamental step to understand the mechanisms underlying EET. Here, we report the complete assignment of the heme proton signals together with (1)H, (13)C and (15)N backbone and side chain assignments of the OmcF, excluding the hydrophobic residues of the N-terminal predicted lipid anchor. PMID:25939275

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

    PubMed Central

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

    2014-01-01

    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

  18. Backbone switch to abacavir/lamivudine fixed-dose combination: implications for antiretroviral therapy optimization.

    PubMed

    Fantauzzi, Alessandra; Floridia, Marco; Falasca, Francesca; Spanedda, Pierpaolo; Turriziani, Ombretta; Vullo, Vincenzo; Mezzaroma, Ivano

    2015-11-01

    Current guidelines recommend treatment optimization in virologically suppressed patients through switching/ simplification strategies to minimize long-term toxicities and improve adherence. The assessment of inflammation/ coagulation profiles may support therapeutic decisions. We undertook a prospective, non-randomized study to evaluate the efficacy and safety of switching to ABC/3TC from ZDV/3TC or TDF/FTC backbones, in 40 HIV-1 infected patients with HIV-RNA levels <37 copies/mL (>24 months). Main endpoints were viral load levels, CD4+ T cells and toxicities after 48 weeks. Serum inflammation/coagulation markers (ESR, CRP, D-dimer and fibrinogen) and pro-inflammatory cytokines (IL-6, TNF-?, adiponectin, resistin) were evaluated. Baseline characteristics were similar in the two arms, with significantly lower values of e-GFR in patients on TDF/FTC. Markers of inflammation/ coagulation and cytokine profile were also similar, except for higher values of resistin in patients on TDF/ FTC. During follow up, CD4+ T cells increased and viral load remained undetectable in both groups. Patient from ZDV/3TC had significantly greater changes in total cholesterol and serum creatinine. Markers of inflammation/ coagulation remained unchanged. Adiponectin significantly increased in patients from ZDV/3TC. Switching to ABC/3TC was effective and safe. Inflammatory markers remained low in both groups. Some changes in metabolic, kidney and cytokine profiles were apparently specific for baseline cART treatment. PMID:26485011

  19. Purification, crystallization and halide phasing of a Streptococcus agalactiae backbone pilin GBS80 fragment

    PubMed Central

    Vengadesan, Krishnan; Ma, Xin; Dwivedi, Prabhat; Ton-That, Hung; Narayana, Sthanam V. L.

    2010-01-01

    The Gram-positive pathogen Streptococcus agalactiae or group B streptococcus (GBS) is the leading cause of bacterial septicemia, pneumonia and meningitis among neonates around the world. The pathogen assembles two types of pili on its surface, named PI-1 and PI-2, that mediate bacterial adherence to host cells. The GBS PI-1 pilus is formed by the major pilin GBS80, which forms the pilus shaft, and two minor pilins GBS104 and GBS52, which are incorporated into the pilus structure. While considerable structural information exists on Gram-negative pili, the structural study of Gram-positive pili is an emerging area of research. Here, the purification, crystallization and initial phasing of the 35?kDa major fragment of the backbone pilin GBS80 are reported. Crystals were obtained in two different space groups: P21 and C2. SAD data collected from an iodide-derivative crystal at the home source were used to obtain initial phases and interpretable electron-density maps. PMID:21139220

  20. Toward High Performance n-Type Thermoelectric Materials by Rational Modification of BDPPV Backbones.

    PubMed

    Shi, Ke; Zhang, Fengjiao; Di, Chong-An; Yan, Tian-Wei; Zou, Ye; Zhou, Xu; Zhu, Daoben; Wang, Jie-Yu; Pei, Jian

    2015-06-10

    Three n-type polymers BDPPV, ClBDPPV, and FBDPPV which exhibit outstanding electrical conductivities when mixed with an n-type dopant, N-DMBI ((4-(1,3-dimethyl-2,3-dihydro-1H-benzoimidazol-2-yl)phenyl)dimethylamine), in solution. High electron mobility and an efficient doping process endow FBDPPV with the highest electrical conductivities of 14 S cm(-1) and power factors up to 28 ?W m(-1) K(-2), which is the highest thermoelectric (TE) power factor that has been reported for solution processable n-type conjugated polymers. Our investigations reveal that introduction of halogen atoms to the polymer backbones has a dramatic influence on not only the electron mobilities but also the doping levels, both of which are critical to the electrical conductivities. This work suggests the significance of rational modification of polymer structures and opens the gate for applying the rapidly developed organic semiconductors with high carrier mobilities to thermoelectric field. PMID:25997085

  1. An Enhanced Backbone-Assisted Reliable Framework for Wireless Sensor Networks

    PubMed Central

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

    2010-01-01

    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

  2. Navigating the massive world of reddit: Using backbone networks to map user interests in social media

    E-print Network

    Olson, Randal S

    2013-01-01

    In the massive online worlds of social media, users frequently rely on organizing themselves around specific topics of interest to find and engage with like-minded people. However, navigating these massive worlds and finding topics of specific interest often proves difficult because the worlds are mostly organized haphazardly, leaving users to find relevant interests by word of mouth or using a basic search feature. Here, we report on a method using the backbone of a network to create a map of the primary topics of interest in any social network. To demonstrate the method, we build an interest map for the social news web site reddit and show how such a map could be used to navigate a social media world. Moreover, we analyze the network properties of the reddit social network and find that it has a scale-free, small-world, and modular community structure, much like other online social networks such as Facebook and Twitter. We suggest that the integration of interest maps into popular social media platforms wil...

  3. Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential.

    PubMed

    Mukherjee, Sudipto; Zhou, Guangfeng; Michel, Chris; Voelz, Vincent A

    2015-12-17

    Peptoids (N-substituted oligoglycines) are biomimetic polymers that can fold into a variety of unique structural scaffolds. Peptoid helices, which result from the incorporation of bulky chiral side chains, are a key peptoid structural motif whose formation has not yet been accurately modeled in molecular simulations. Here, we report that a simple modification of the backbone ?-angle potential in GAFF is able to produce well-folded cis-amide helices of (S)-N-(1-phenylethyl)glycine (Nspe), consistent with experiment. We validate our results against both QM calculations and NMR experiments. For this latter task, we make quantitative comparisons to sparse NOE data using the Bayesian Inference of Conformational Populations (BICePs) algorithm, a method we have recently developed for this purpose. We then performed extensive REMD simulations of Nspe oligomers as a function of chain length and temperature to probe the molecular forces driving cooperative helix formation. Analysis of simulation data by Lifson-Roig helix-coil theory show that the modified potential predicts much more cooperative folding for Nspe helices. Unlike peptides, per-residue entropy changes for helix nucleation and extension are mostly positive, suggesting that steric bulk provides the main driving force for folding. We expect these results to inform future work aimed at predicting and designing peptoid peptidomimetics and tertiary assemblies of peptoid helices. PMID:26584227

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

    NASA Technical Reports Server (NTRS)

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

    2004-01-01

    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.

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

    PubMed Central

    2010-01-01

    Background Hypnales comprise over 50% of all pleurocarpous mosses. They provide a young radiation complicating phylogenetic analyses. To resolve the hypnalean phylogeny, it is necessary to use a phylogenetic marker providing highly variable features to resolve species on the one hand and conserved features enabling a backbone analysis on the other. Therefore we used highly variable internal transcribed spacer 2 (ITS2) sequences and conserved secondary structures, as deposited with the ITS2 Database, simultaneously. Findings We built an accurate and in parts robustly resolved large scale phylogeny for 1,634 currently available hypnalean ITS2 sequence-structure pairs. Conclusions Profile Neighbor-Joining revealed a possible hypnalean backbone, indicating that most of the hypnalean taxa classified as different moss families are polyphyletic assemblages awaiting taxonomic changes. PMID:21108782

  6. Small-Time Scaling Behaviors of Internet Backbone Traffic: An Empirical Study

    E-print Network

    Moon, Sue B.

    Moon, and Christophe Diot Sprint ATL Email: {sbmoon,cdiot}@sprintlabs.com Abstract-- We study the small the traffic composition of the traces along two dimensions ­ flow size and flow density. Our study uncovers in small time scales, and reveals that the traffic composition in terms of proportions of dense vs. sparse

  7. Preform fiber architecture for ceramic-matrix composites

    SciTech Connect

    Ko, F.K. )

    1989-02-01

    Similar to the steel frames in a skyscraper, fiber architectures are the structural backbone of a composite. Starting with linear assemblies of fibers in continuous and/or discrete form, these microfiber beams can be organized into two-and three-dimensional structures by means of interlacing, intertwining, or interlooping. This article discusses fiber architecture. The role of fiber architecture in designing composites are illustrated through an examination of the structural features and the properties of ceramic-matrix composites (CMC) reinforced by textile structures.

  8. Are Proteins Just Coiled Cords? Local and Global Analysis of Contact Maps Reveals the Backbone-Dependent Nature of Proteins.

    PubMed

    Santoni, Daniele; Paci, Paola; Di Paola, Luisa; Giuliani, Alessandro

    2016-01-01

    In this work, we present an extensive analysis of protein contact network topology applied to a wide data set. We extended the concept of degree distribution to graphlets, describing local connectivity patterns. We compared results to those derived from artificial networks of the same size (number of nodes), reproducing the average degree of each protein network. The artificial networks resemble the coiling of immaterial cords and we tried to understand if they could catch the protein structure topology upon the sole constraint of backbone (cord). We found a surprisingly similar pattern for local topological descriptors (graphlets distribution) while real proteins and cords differ at large extent in the global topological invariant average shortest path that presumably catches the systemic nature of protein and the non negligible encumbrance of backbone (residues steric hindrance). We demonstrated average shortest path to link polymer length and physical size of the molecule, and its minimization plays the role of `target function` of folding process. PMID:26412790

  9. Direct measurement of the correlated dynamics of the protein-backbone and proximal waters of hydration in mechanically strained elastin

    E-print Network

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

    2011-04-05

    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.

  10. The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

    PubMed

    Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

    2015-11-01

    The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ? and/or ?. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(?) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. Proteins 2015; 83:1973-1986. © 2015 Wiley Periodicals, Inc. PMID:26264789

  11. Electron-impact total ionization cross sections of DNA sugar-phosphate backbone and an additivity principle

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.; Dateo, Christopher E.

    2005-01-01

    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.

  12. Altered Backbone and Side-Chain Interactions Result in Route Heterogeneity during the Folding of Interleukin-1? (IL-1?)

    PubMed Central

    Capraro, Dominique T.; Lammert, Heiko; Heidary, David K.; Roy, Melinda; Gross, Larry A.; Onuchic, José N.; Jennings, Patricia A.

    2013-01-01

    Deletion of the ?-bulge trigger-loop results in both a switch in the preferred folding route, from the functional loop packing folding route to barrel closure, as well as conversion of the agonist activity of IL-1? into antagonist activity. Conversely, circular permutations of IL-1? conserve the functional folding route as well as the agonist activity. These two extremes in the folding-functional interplay beg the question of whether mutations in IL-1? would result in changes in the populations of heterogeneous folding routes and the signaling activity. A series of topologically equivalent water-mediated ?-strand bridging interactions within the pseudosymmetric ?-trefoil fold of IL-1? highlight the backbone water interactions that stabilize the secondary and tertiary structure of the protein. Additionally, conserved aromatic residues lining the central cavity appear to be essential for both stability and folding. Here, we probe these protein backbone-water molecule and side chain-side chain interactions and the role they play in the folding mechanism of this geometrically stressed molecule. We used folding simulations with structure-based models, as well as a series of folding kinetic experiments to examine the effects of the F42W core mutation on the folding landscape of IL-1?. This mutation alters water-mediated backbone interactions essential for maintaining the trefoil fold. Our results clearly indicate that this perturbation in the primary structure alters a structural water interaction and consequently modulates the population of folding routes accessed during folding and signaling activity. PMID:23972849

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

    NASA Astrophysics Data System (ADS)

    Choi, Eunwoo

    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.

  14. DNA sequencing

    SciTech Connect

    Tabor, S.; Richardson, C.C.

    1990-10-09

    A method for sequencing a strand of DNA. It comprises providing the strand hybridized with a primer able to hybridize to the strand, to give an hybridized mixture, incubating the hybridized mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and a first chain terminating agent, wherein the DNA polymerase causes the primer to be elongated to form a first series of first DNA products differing in the length of the elongated primer, each the first DNA product having a the chain terminating agent at its elongated end. The number of molecules of each the first DNA products is approximately the same for substantially all DNA products differing in length by no more than 20 bases, and providing a second chain terminating agent in the hybridized mixture at a concentration different from the first chain terminating agent.

  15. AdorAdorni ni AguaAgua Tibia Tibia AmerAmerican Canican Canyyon on Antelope Creek LakAntelope Creek Lakes Babes Babbitt Pbitt Peakeak Backbone Creek Bald Mountain Bell MeadoBackbone Creek Bald Mountain Bell Meadow Big Grw Big Grizzlizzly Mount

    E-print Network

    Antelope Creek Lakes · Babes · Babbitt Pbitt Peakeak Backbone Creek · Bald Mountain · Bell MeadoBackbone Creek · Bald Mountain · Bell Meadow · Big Grw · Big Grizzlizzly Mountain · Big Piney Mountain · Big Pine Mountain · Bishop Creek PMountain · Bishop Creek Ponderosa Pine · Black Butte · BlacksMountain

  16. Biases in Illumina transcriptome sequencing caused by random hexamer priming

    E-print Network

    Biases in Illumina transcriptome sequencing caused by random hexamer priming Kasper D. Hansen1 composition at the beginning of transcriptome sequencing reads from the Illumina Genome Analyzer. The bias structure. General biases in DNA sequencing using the Illumina platform have been studied in (2). Dohm et al

  17. Molecular Characterization of Transgene Integration by Next-Generation Sequencing in Transgenic Cattle

    PubMed Central

    Zhang, Ran; Yin, Yinliang; Zhang, Yujun; Li, Kexin; Zhu, Hongxia; Gong, Qin; Wang, Jianwu; Hu, Xiaoxiang; Li, Ning

    2012-01-01

    As the number of transgenic livestock increases, reliable detection and molecular characterization of transgene integration sites and copy number are crucial not only for interpreting the relationship between the integration site and the specific phenotype but also for commercial and economic demands. However, the ability of conventional PCR techniques to detect incomplete and multiple integration events is limited, making it technically challenging to characterize transgenes. Next-generation sequencing has enabled cost-effective, routine and widespread high-throughput genomic analysis. Here, we demonstrate the use of next-generation sequencing to extensively characterize cattle harboring a 150-kb human lactoferrin transgene that was initially analyzed by chromosome walking without success. Using this approach, the sites upstream and downstream of the target gene integration site in the host genome were identified at the single nucleotide level. The sequencing result was verified by event-specific PCR for the integration sites and FISH for the chromosomal location. Sequencing depth analysis revealed that multiple copies of the incomplete target gene and the vector backbone were present in the host genome. Upon integration, complex recombination was also observed between the target gene and the vector backbone. These findings indicate that next-generation sequencing is a reliable and accurate approach for the molecular characterization of the transgene sequence, integration sites and copy number in transgenic species. PMID:23185606

  18. Using SEQUEST with Theoretically Complete Sequence Databases

    NASA Astrophysics Data System (ADS)

    Sadygov, Rovshan G.

    2015-08-01

    SEQUEST has long been used to identify peptides/proteins from their tandem mass spectra and protein sequence databases. The algorithm has proven to be hugely successful for its sensitivity and specificity in identifying peptides/proteins, the sequences of which are present in the protein sequence databases. In this work, we report on work that attempts a new use for the algorithm by applying it to search a complete list of theoretically possible peptides, a de novo-like sequencing. We used freely available mass spectral data and determined a number of unique peptides as identified by SEQUEST. Using masses of these peptides and the mass accuracy of 0.001 Da, we have created a database of all theoretically possible peptide sequences corresponding to the precursor masses. We used our recently developed algorithm for determining all amino acid compositions corresponding to a mass interval, and used a lexicographic ordering to generate theoretical sequences from the compositions. The newly generated theoretical database was many-fold more complex than the original protein sequence database. We used SEQUEST to search and identify the best matches to the spectra from all theoretically possible peptide sequences. We found that SEQUEST cross-correlation score ranked the correct peptide match among the top sequence matches. The results testify to the high specificity of SEQUEST when combined with the high mass accuracy for intact peptides.

  19. Using SEQUEST with Theoretically Complete Sequence Databases

    NASA Astrophysics Data System (ADS)

    Sadygov, Rovshan G.

    2015-11-01

    SEQUEST has long been used to identify peptides/proteins from their tandem mass spectra and protein sequence databases. The algorithm has proven to be hugely successful for its sensitivity and specificity in identifying peptides/proteins, the sequences of which are present in the protein sequence databases. In this work, we report on work that attempts a new use for the algorithm by applying it to search a complete list of theoretically possible peptides, a de novo-like sequencing. We used freely available mass spectral data and determined a number of unique peptides as identified by SEQUEST. Using masses of these peptides and the mass accuracy of 0.001 Da, we have created a database of all theoretically possible peptide sequences corresponding to the precursor masses. We used our recently developed algorithm for determining all amino acid compositions corresponding to a mass interval, and used a lexicographic ordering to generate theoretical sequences from the compositions. The newly generated theoretical database was many-fold more complex than the original protein sequence database. We used SEQUEST to search and identify the best matches to the spectra from all theoretically possible peptide sequences. We found that SEQUEST cross-correlation score ranked the correct peptide match among the top sequence matches. The results testify to the high specificity of SEQUEST when combined with the high mass accuracy for intact peptides.

  20. Self-assembled peptide amphiphile nanofibers and peg composite hydrogels as tunable ECM mimetic microenvironment.

    PubMed

    Goktas, Melis; Cinar, Goksu; Orujalipoor, Ilghar; Ide, Semra; Tekinay, Ayse B; Guler, Mustafa O

    2015-04-13

    Natural extracellular matrix (ECM) consists of complex signals interacting with each other to organize cellular behavior and responses. This sophisticated microenvironment can be mimicked by advanced materials presenting essential biochemical and physical properties in a synergistic manner. In this work, we developed a facile fabrication method for a novel nanofibrous self-assembled peptide amphiphile (PA) and poly(ethylene glycol) (PEG) composite hydrogel system with independently tunable biochemical, mechanical, and physical cues without any chemical modification of polymer backbone or additional polymer processing techniques to create synthetic ECM analogues. This approach allows noninteracting modification of multiple niche properties (e.g., bioactive ligands, stiffness, porosity), since no covalent conjugation method was used to modify PEG monomers for incorporation of bioactivity and porosity. Combining the self-assembled PA nanofibers with a chemically cross-linked polymer network simply by facile mixing followed by photopolymerization resulted in the formation of porous bioactive hydrogel systems. The resulting porous network can be functionalized with desired bioactive signaling epitopes by simply altering the amino acid sequence of the self-assembling PA molecule. In addition, the mechanical properties of the composite system can be precisely controlled by changing the PEG concentration. Therefore, nanofibrous self-assembled PA/PEG composite hydrogels reported in this work can provide new opportunities as versatile synthetic mimics of ECM with independently tunable biological and mechanical properties for tissue engineering and regenerative medicine applications. In addition, such systems could provide useful tools for investigation of how complex niche cues influence cellular behavior and tissue formation both in two-dimensional and three-dimensional platforms. PMID:25751623

  1. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.

    PubMed

    Zgarbová, Marie; Šponer, Ji?í; Otyepka, Michal; Cheatham, Thomas E; Galindo-Murillo, Rodrigo; Jure?ka, Petr

    2015-12-01

    Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ?/? and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar-phosphate backbone torsion angle ?. We suggest a refinement of this potential, ?OL1, which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. We recommend using ?OL1 in combination with our previously introduced corrections, ??OL1 and ?OL4, (the combination being named OL15) as a possible alternative to the current ? torsion potential for more accurate modeling of nucleic acids. PMID:26588601

  2. Development of novel bifunctional chelating agents containing rigid cyclic hydrocarbon backbones

    SciTech Connect

    Sweet, M.P.; Joshi, V.; Mease, R.C.

    1995-05-01

    We are developing a new class of ligands in which the metal-binding polyaminocarboxylate groups are incorporated onto rigid cyclic hydrocarbon backbones. These ligands, with increased preorganization, should produce radiometal-bioconjugates with higher in-vivo stability. The synthesis of the first in this series of ligands (2,3-diaminobicyclo[2.2.2] octanetetraacetic acid, BODTA) began with a Diels-Alder reaction of 1,3-diacetylimidazolin-2-one and 1,3-cyclohexadiene. Base hydrolysis, alkylation with ethyl iodoacetate, hydrolysis of the esters, and catalytic hydrogenation gave BODTA. For conjugation to MAbs, an average of one COOH group of unsaturated BODTA was converted into an NHS ester using 0.8 equivalent of DCC. The second ligand under development is the decadentate tethered bis-cyclohexyl-EDTA (bis-CDTA) in which 2 cyclohexyl rings are tied together with an ethylene tether. Acylation of monotrityl-1,2-diaminocyclohexane with the di-NHS ester of oxalic acid, reduction of the amide moieties, and removal of the trityl groups followed by cyanomethylation has afforded a hexanitrile whose hydrolysis will produce tethered bis-CDTA. An anti-CEA F(ab{prime}){sub 2} MAb was conjugated with an average of 0.6 BODTA per MAb molecule, labeled with Co-57, and purified by size-exclusion HPLC. Stability of this radioconjugate in mouse serum at 48 h was somewhat better (2% loss) than that of the conventional DTPA-dianhydride (DTPA-DA) conjugate (8% loss). In human tumor-xenografted nude mice (LS-174T cells), tumor (T), blood (B), liver (L), and kidney (K) uptakes (% ID/g) at 24h were: TODTA, 21.6, 4.4, 4.8, 6.0; DTPA-DA, 13.6, 2.5, 5.0, 2.9. The tumor to normal tissue ratios at 48 h for BODTA and DTPA-DA respectively were: T/B, 18.0, 13.9; T/L 4.9, 2.3; T/K, 5.4, 3.9. These preliminary results show promise for using the basic BODTA structure to produce improved bioconjugates with small radiometal ions.

  3. Protein inhibitors of serine proteinases: role of backbone structure and dynamics in controlling the hydrolysis constant.

    PubMed

    Song, Jikui; Markley, John L

    2003-05-13

    Standard mechanism protein inhibitors of serine proteinases bind as substrates and are cleaved by cognate proteinases at their reactive sites. The hydrolysis constant for this cleavage reaction at the P(1)-P(1)' peptide bond (K(hyd)) is determined by the relative concentrations at equilibrium of the "intact" (uncleaved, I) and "modified" (reactive site cleaved, I*) forms of the inhibitor. The pH dependence of K(hyd) can be explained in terms of a pH-independent term, K(hyd) degrees, plus the proton dissociation constants of the newly formed amino and carboxylate groups at the cleavage site. Two protein inhibitors that differ from one another by a single residue substitution have been found to have K(hyd) degrees values that differ by a factor of 5 [Ardelt, W., and Laskowski, M., Jr. (1991) J. Mol. Biol. 220, 1041-1052]: turkey ovomucoid third domain (OMTKY3) has K(hyd) degrees = 1.0, and Indian peafowl ovomucoid third domain (OMIPF3), which differs from OMTKY3 by the substitution P(2)'-Tyr(20)His, has K(hyd) degrees = 5.15. What mechanism is responsible for this small difference? Is it structural (enthalpic) or dynamic (entropic)? Does the mutation affect the free energy of the I state, the I* state, or both? We have addressed these questions through NMR investigations of the I and I forms of OMTKY3 and OMIPF3. Information about structure was derived from measurements of NMR chemical shift changes and trans-hydrogen-bond J-couplings; information about dynamics was obtained through measurements of (15)N relaxation rates and (1)H-(15)N heteronuclear NOEs with model-free analysis of the results. Although the I forms of each variant are more dynamic than the corresponding I forms, the study revealed no appreciable difference in the backbone dynamics of either intact inhibitor (OMIPF3 vs OMTKY3) or modified inhibitor (OMIPF3* vs OMTKY3*). Instead, changes in chemical shifts and trans-hydrogen-bond J-couplings suggested that the K(hyd) degrees difference arises from differential intramolecular interactions within the intact inhibitors (OMIPF3 vs OMTKY3) in a region of each protein that becomes disordered upon reactive site cleavage (to OMIPF3* and OMTKY3*). PMID:12731859

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

    PubMed Central

    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

    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

  5. {{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)

    Asakawa, Daiki; Takayama, Mitsuo

    2011-07-01

    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.

  6. Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea.

    PubMed

    Goldsmith, Dawn B; Parsons, Rachel J; Beyene, Damitu; Salamon, Peter; Breitbart, Mya

    2015-01-01

    Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS) site in the summer (September) and winter (March) of three years. Viral phoH sequences reveal differences in the viral communities throughout a depth profile and between seasons in the same year. Variation was also detected between the same seasons in subsequent years, though these differences were not as great as the summer/winter distinctions. Over 3,600 phoH operational taxonomic units (OTUs; 97% sequence identity) were identified. Despite high richness, most phoH sequences belong to a few large, common OTUs whereas the majority of the OTUs are small and rare. While many OTUs make sporadic appearances at just a few times or depths, a small number of OTUs dominate the community throughout the seasons, depths, and years. PMID:26157645

  7. Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea

    PubMed Central

    Goldsmith, Dawn B.; Parsons, Rachel J.; Beyene, Damitu; Salamon, Peter

    2015-01-01

    Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS) site in the summer (September) and winter (March) of three years. Viral phoH sequences reveal differences in the viral communities throughout a depth profile and between seasons in the same year. Variation was also detected between the same seasons in subsequent years, though these differences were not as great as the summer/winter distinctions. Over 3,600 phoH operational taxonomic units (OTUs; 97% sequence identity) were identified. Despite high richness, most phoH sequences belong to a few large, common OTUs whereas the majority of the OTUs are small and rare. While many OTUs make sporadic appearances at just a few times or depths, a small number of OTUs dominate the community throughout the seasons, depths, and years. PMID:26157645

  8. Dissecting the relationship between protein structure and sequence variation

    NASA Astrophysics Data System (ADS)

    Shahmoradi, Amir; Wilke, Claus; Wilke Lab Team

    2015-03-01

    Over the past decade several independent works have shown that some structural properties of proteins are capable of predicting protein evolution. The strength and significance of these structure-sequence relations, however, appear to vary widely among different proteins, with absolute correlation strengths ranging from 0 . 1 to 0 . 8 . Here we present the results from a comprehensive search for the potential biophysical and structural determinants of protein evolution by studying more than 200 structural and evolutionary properties in a dataset of 209 monomeric enzymes. We discuss the main protein characteristics responsible for the general patterns of protein evolution, and identify sequence divergence as the main determinant of the strengths of virtually all structure-evolution relationships, explaining ~ 10 - 30 % of observed variation in sequence-structure relations. In addition to sequence divergence, we identify several protein structural properties that are moderately but significantly coupled with the strength of sequence-structure relations. In particular, proteins with more homogeneous back-bone hydrogen bond energies, large fractions of helical secondary structures and low fraction of beta sheets tend to have the strongest sequence-structure relation. BEACON-NSF center for the study of evolution in action.

  9. Novel animal papillomavirus sequences and accurate phylogenetic placement.

    PubMed

    Mengual-Chuliá, Beatriz; García-Pérez, Raquel; Gottschling, Marc; Nindl, Ingo; Bravo, Ignacio G

    2012-12-01

    All amniotes are probably infected by specific papillomaviruses (PVs), but knowledge about PV diversity remains sparse. An insufficient taxon sampling, and a focus on humans as hosts, may perturb phylogenetic analyses leading to wrong conclusions about PV evolution. We performed a systematic approach to explore the diversity of PVs combining rolling circle amplification with the use of "universal" primers to search for the presence of novel PV sequences in animal samples. We communicate 12 sequences putatively corresponding to novel PVs gained from 10 host species in eight mammal families: Bovidae, Canidae, Cervidae, Equidae, Hominidae, Phocoenidae, Procyonidae and Pteropodidae. The phylogenetic position of the new sequences was inferred with an evolutionary placement algorithm under a Maximum Likelihood framework using a pre-computed, well-resolved tree constructed with the E1-E2-L1 gene sequences as a backbone. The new sequences were phylogenetically diverse and could be respectively placed with confidence within all four PV crown groups. The prevailing presence of sequences from the crown groups Alpha+Omikron-PVs and Beta+Xi-PVs may correspond to an increased viral diversity in these taxa, or rather reflect a combination of anthropocentric bias and preferential amplification from commonly used "universal" primers. Our results combined with literature data support the view that the number and diversity of animal PVs is overwhelmingly large. PMID:22960206

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

    E-print Network

    Nemat-Nasser, Sia

    of counterions that balance the electrical charge of anions covalently fixed to the backbone membrane. IPMCs electric potential waveforms. 1. Introduction Ionic polymer-metal composites (IPMCs) are electroactive conducted so far. Electrical-chemical-mechanical actuation of Nafion-based IPMCs upon application of applied

  11. Differential backbone dynamics of companion helices in the extended helical coiled-coil domain of a bacterial chemoreceptor.

    PubMed

    Bartelli, Nicholas L; Hazelbauer, Gerald L

    2015-11-01

    Cytoplasmic domains of transmembrane bacterial chemoreceptors are largely extended four-helix coiled coils. Previous observations suggested the domain was structurally dynamic. We probed directly backbone dynamics of this domain of the transmembrane chemoreceptor Tar from Escherichia coli using site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy. Spin labels were positioned on solvent-exposed helical faces because EPR spectra for such positions reflect primarily polypeptide backbone movements. We acquired spectra for spin-labeled, intact receptor homodimers solubilized in detergent or inserted into native E. coli lipid bilayers in Nanodiscs, characterizing 16 positions distributed throughout the cytoplasmic domain and on both helices of its helical hairpins, one amino terminal to the membrane-distal tight turn (N-helix), and the other carboxyl terminal (C-helix). Detergent solubilization increased backbone dynamics for much of the domain, suggesting that loss of receptor activities upon solubilization reflects wide-spread destabilization. For receptors in either condition, we observed an unanticipated difference between the N- and C-helices. For bilayer-inserted receptors, EPR spectra from sites in the membrane-distal protein-interaction region and throughout the C-helix were typical of well-structured helices. In contrast, for approximately two-thirds of the N-helix, from its origin as the AS-2 helix of the membrane-proximal HAMP domain to the beginning of the membrane-distal protein-interaction region, spectra had a significantly mobile component, estimated by spectral deconvolution to average approximately 15%. Differential helical dynamics suggests a four-helix bundle organization with a pair of core scaffold helices and two more dynamic partner helices. This newly observed feature of chemoreceptor structure could be involved in receptor function. PMID:26257396

  12. Lens Sequences Jerzy Kocik

    E-print Network

    Kocik, Jerzy

    Carbondale, IL 62901, USA jkocik@math.siu.edu Abstract A family of sequences produced by a non it a seed of the sequence. Notice that any three consecutive terms of a lens sequence may form a seed. Two that a triplet of circles (a, b, c) generates the lens sequence, and we will call it a seed of the sequence

  13. Shotgun protein sequencing.

    SciTech Connect

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  14. Hybrid character of a large neurofilament protein (NF-M): intermediate filament type sequence followed by a long and acidic carboxy-terminal extension.

    PubMed Central

    Geisler, N; Fischer, S; Vandekerckhove, J; Plessmann, U; Weber, K

    1984-01-01

    The sequence of the amino-terminal 436 residues of porcine neurofilament component NF-M (apparent mol. wt. in gel electrophoresis 160 kd), one of the two high mol. wt. components of mammalian neurofilaments, reveals the typical structural organization of an intermediate filament (IF) protein of the non-epithelial type. A non-alpha-helical arginine-rich headpiece with multiple beta-turns (residues 1-98) precedes a highly alpha-helical rod domain able to form double-stranded coiled-coils (residues 99-412) and a non-alpha-helical tailpiece array starting at residue 413. All extra mass of NF-M forms, as a carboxy-terminal tailpiece extension of approximately 500 residues, an autonomous domain of unique composition. Limited sequence data in the amino-terminal region of this domain document a lysine- and particularly glutamic acid-rich array somewhat reminiscent of the much shorter tailpiece extension of NF-L (apparent mol. wt. 68 kd), the major neurofilament protein. NF-M is therefore a true intermediate filament protein co-polymerized with NF-L via presumptive coiled-coil type interactions and not a peripherally bound associated protein of a filament backbone built exclusively from NF-L. Along the structurally conserved coiled-coil domains the two neurofilament proteins show only approximately 65% sequence identity, a value similar to that seen when NF-L and NF-M are compared with mesenchymal vimentin. The highly charged and acidic tailpiece extensions of all triplet proteins particularly rich in glutamic acid seem unique to the neurofilament type of IFs. They could form extra-filamentous scaffolds suitable for interactions with other neuronal components.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:6439558

  15. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.

    PubMed

    Karchin, Rachel; Cline, Melissa; Mandel-Gutfreund, Yael; Karplus, Kevin

    2003-06-01

    An important problem in computational biology is predicting the structure of the large number of putative proteins discovered by genome sequencing projects. Fold-recognition methods attempt to solve the problem by relating the target proteins to known structures, searching for template proteins homologous to the target. Remote homologs that may have significant structural similarity are often not detectable by sequence similarities alone. To address this, we incorporated predicted local structure, a generalization of secondary structure, into two-track profile hidden Markov models (HMMs). We did not rely on a simple helix-strand-coil definition of secondary structure, but experimented with a variety of local structure descriptions, following a principled protocol to establish which descriptions are most useful for improving fold recognition and alignment quality. On a test set of 1298 nonhomologous proteins, HMMs incorporating a 3-letter STRIDE alphabet improved fold recognition accuracy by 15% over amino-acid-only HMMs and 23% over PSI-BLAST, measured by ROC-65 numbers. We compared two-track HMMs to amino-acid-only HMMs on a difficult alignment test set of 200 protein pairs (structurally similar with 3-24% sequence identity). HMMs with a 6-letter STRIDE secondary track improved alignment quality by 62%, relative to DALI structural alignments, while HMMs with an STR track (an expanded DSSP alphabet that subdivides strands into six states) improved by 40% relative to CE. PMID:12784210

  16. Adaptive seeds tame genomic sequence comparison.

    PubMed

    Kie?basa, Szymon M; Wan, Raymond; Sato, Kengo; Horton, Paul; Frith, Martin C

    2011-03-01

    The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use adaptive seeds. Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches. This method guarantees that the number of matches, and thus the running time, increases linearly, instead of quadratically, with sequence length. LAST, our open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition. PMID:21209072

  17. Whole Genome Sequencing

    MedlinePLUS

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  18. From protein sequence to dynamics and disorder with DynaMine

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    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.

  19. Coordinate cytokine regulatory sequences

    DOEpatents

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  20. Color Tuning of Core-Shell Fluorescent Microspheres by Controlling the Conjugation of Poly(p-phenylenevinylene) Backbone.

    PubMed

    Chen, Yun; Chen, Hong; Zhang, Heng; Fan, Li-Juan

    2015-12-01

    A series of poly(p-phenylenevinylene) (PPV)-coated microspheres with varied fluorescent emission colors have been prepared by controlling the average length of the conjugated segments on the polymer backbone. A modified Wessling method was used for preparing PPV with different conjugation segments. The labile sulfonium groups of the initial polymer precursor of PPV (pre-PPV) were partly substituted by relatively stable methoxyl groups. A series of precursors with different degrees of substitution were prepared by controlling the time of reaction; these precursors were adsorbed onto the negatively charged substrate spheres. Subsequently, heterogeneous thermal treatment eliminated the sulfonium groups selectively to form the conjugated segments on the PPV backbone with varied average conjugation lengths. Under UV exposure, the as-prepared PPV-coated microspheres displayed emission colors ranging from blue to green; a 65 nm shift in the emission maximum was observed in the fluorescence spectra. The gradual color change in emission of spheres was also confirmed in a confocal microscopy study. Further characterizations indicated that these microspheres possessed clear core-shell structure, good monodispersity in size, smooth surfaces, uniform emission, and superior thermal and photo stability. Flow cytometry measurements indicated that these spheres have very different patterns of intensity combination from four-signal receiving channels. The simple method reported herein, which can effectively and efficiently tune the emission color of the fluorescent microspheres, is a promising approach for preparation of microspheres used as encoded signal carrier in flow cytometry and other high-throughput techniques. PMID:26553581

  1. Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid

    PubMed Central

    Babbitt, Gregory A.; Alawad, Mohammed A.; Schulze, Katharina V.; Hudson, André O.

    2014-01-01

    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

  2. DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations.

    PubMed

    Robertson, James C; Cheatham, Thomas E

    2015-11-01

    BI and BII conformational substates in the DNA backbone typify canonical B-form DNA. The BI and BII substates are important for structural variation of DNA and have been implicated in protein-nucleic acid recognition mechanisms. Recent refinements have been made to nucleic acid force fields employed in molecular dynamics simulations that demonstrate a better ability to model the BI and BII states, leading to overall improved modeling of DNA structure and dynamics. These force field improvements have yet to be significantly demonstrated in the context of a protein-DNA system extended to long time scales. Our plan was to run molecular dynamics simulations of a well-studied protein-DNA system (E2-DNA) into the microsecond time scale and determine the ability of the force field to populate BII states in the DNA backbone consistent with dinucleotide steps crystallized in the BII conformation. The results showed that the dinucleotide steps in the E2-DNA complex with the highest BII populations from simulation trajectories corresponded to the dinucleotide steps crystallized in the BII state and that decoy BI and BII states converge to the same results within approximately one microsecond. PMID:26482568

  3. Synthesis and structure-activity relationship studies of peptidomimetic PKB/Akt inhibitors: the significance of backbone interactions.

    PubMed

    Tal-Gan, Yftah; Freeman, Noam S; Klein, Shoshana; Levitzki, Alexander; Gilon, Chaim

    2010-04-15

    Elevated levels of activated Protein Kinase B (PKB/Akt) have been detected in many types of human cancer. In contrast to ATP site inhibitors, substrate-based inhibitors are more likely to be selective because of extensive interactions with the specific substrate binding site. Unfortunately, peptide-based inhibitors lack important pharmacological properties that are required of drug candidates. Chemical modifications of potent peptide inhibitors, such as peptoids and N(alpha)-methylated amino acids, may overcome these drawbacks, while maintaining potency. We present a structure-activity relationship study of a potent, peptide-based PKB/Akt inhibitor, PTR6154. The study was designed to evaluate backbone modifications on the inhibitory activity of PTR6154. Two peptidomimetic libraries, peptoid and N(alpha)-methylation, based on PTR6154, were synthesized and evaluated for in vitro PKB/Akt inhibition efficiency. All the peptoid analogs reduced potency significantly, as well as most of the members of the N-methyl library, suggesting that the backbone conformation and/or hydrogen bond interactions of PTR6154 derivatives are essential for inhibition activity. Two N-terminal members of the N-methyl library did not decrease potency and can be used as future drug leads. PMID:20347317

  4. Solubility of polyethers in hydrocarbons at low temperatures. A model for potential genetic backbones on warm titans.

    PubMed

    McLendon, Christopher; Opalko, F Jeffrey; Illangkoon, Heshan I; Benner, Steven A

    2015-03-01

    Ethers are proposed here as the repeating backbone linking units in linear genetic biopolymers that might support Darwinian evolution in hydrocarbon oceans. Hydrocarbon oceans are found in our own solar system as methane mixtures on Titan. They may be found as mixtures of higher alkanes (propane, for example) on warmer hydrocarbon-rich planets in exosolar systems ("warm Titans"). We report studies on the solubility of several short polyethers in propane over its liquid range (from 85 to 231 K, or -188 °C to -42 °C). These show that polyethers are reasonably soluble in propane at temperatures down to ca. 200 K. However, their solubilities drop dramatically at still lower temperatures and become immeasurably low below 170 K, still well above the ? 95 K in Titan's oceans. Assuming that a liquid phase is essential for any living system, and genetic biopolymers must dissolve in that biosolvent to support Darwinism, these data suggest that we must look elsewhere to identify linear biopolymers that might support genetics in Titan's surface oceans. However, genetic molecules with polyether backbones may be suitable to support life in hydrocarbon oceans on warm Titans, where abundant organics and environments lacking corrosive water might make it easier for life to originate. PMID:25761113

  5. Improved site-specific recombinase-based method to produce selectable marker- and vector-backbone-free transgenic cells

    NASA Astrophysics Data System (ADS)

    Yu, Yuan; Tong, Qi; Li, Zhongxia; Tian, Jinhai; Wang, Yizhi; Su, Feng; Wang, Yongsheng; Liu, Jun; Zhang, Yong

    2014-02-01

    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.

  6. Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: 2H NMR studies on perdeuterated C-phycocyanin.

    PubMed

    Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

    2014-03-01

    Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high. PMID:24730877

  7. Solid State Nuclear Magnetic Resonance Investigation of Polymer Backbone Dynamics in Poly(Ethylene Oxide) Based Lithium and Sodium Polyether-ester-sulfonate Ionomers

    SciTech Connect

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

    2013-01-01

    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.

  8. Nearest-neighbor effects on backbone alpha and beta carbon chemical shifts in proteins.

    PubMed

    Wang, Liya; Eghbalnia, Hamid R; Markley, John L

    2007-11-01

    We present a method for analyzing the chemical shift database to yield information on nearest-neighbor effects on carbon-13 chemical shift values for alpha and beta carbons of amino acids in proteins. For each amino acid sequence XYZ, we define two correction factors, Delta(XY) s and Delta(YZ) s , representing the effects on (delta13 Calpha-delta13 Cbeta) for residue Y from the preceding residue (X) and the following residue (Z), where X, Y, and Z represent one of the 20 naturally occurring amino acids, Delta designates the change in value or the correction factor (in ppm), and s is an index standing for one of three "pseudo secondary structure states" derived from chemical shift dispersions, which we show represent residues in primarily alpha-helix, beta-strand, and non-alphabeta(coil). The correction factors were obtained from maximum likelihood fitting of (delta13 Calpha-delta13 Cbeta) values from the chemical shifts of 651 proteins to a mixture of three Gaussians. These correction factors were derived strictly from the analysis of assigned chemical shifts, without regard to the three-dimensional structures of these proteins. The corrections factors were found to differ according to the secondary structural environment of the central residue (deduced from the chemical shift distribution) as well as by different identities of the nearest neighboring residues in the sequence. The areas subsumed by the sequence-dependent chemical shift distributions report on the relative energies of the sequences in different pseudo secondary structural environments, and the positions of the peaks indicate the chemical shifts of lowest energy conformations. As such, these results have potential applications to the determination of dihedral angle restraints from chemical shifts for structure determination and to more accurate predictions of chemical shifts in proteins of known structure. From a database of chemical shifts associated well-defined three-dimensional structures, comparisons were made between DSSP designations derived from three-dimensional structure and pseudo secondary structure designations derived from nearest-neighbor corrected chemical shift analysis. The high level of agreement between the two approaches to classifying secondary structure provides a measure of confidence in this chemical shift-based approach to the analysis of protein structure. PMID:17899393

  9. Accurate measurements of the effects of deuteration at backbone amide positions on the chemical shifts of ¹?N, ¹³C?, ¹³C?, ¹³CO and ¹H? nuclei in proteins.

    PubMed

    Zhang, Daoning; Tugarinov, Vitali

    2013-06-01

    An approach towards accurate NMR measurements of deuterium isotope effects on the chemical shifts of all backbone nuclei in proteins ((15)N, (13)C?, (13)CO, (1)H?) and (13)C? nuclei arising from (1)H-to-D substitutions at amide nitrogen positions is described. Isolation of molecular species with a defined protonation/deuteration pattern at successive backbone nitrogen positions in the polypeptide chain allows quantifying all deuterium isotope shifts of these nuclei from the first to the fourth order. Some of the deuterium isotope shifts measured in the proteins ubiquitin and GB1 can be interpreted in terms of backbone geometry via empirical relationships describing their dependence on (?; ?) backbone dihedral angles. Because of their relatively large variability and notable dependence on the protein secondary structure, the two- and three-bond (13)C? isotope shifts, (2)?C?(NiD) and (3)?C?(Ni+1D), and three-bond (13)C? isotope shifts, (3)?C?(NiD), are useful reporters of the local geometry of the protein backbone. PMID:23612994

  10. Enzyme IIBcellobiose of the phosphoenol-pyruvate-dependent phosphotransferase system of Escherichia coli: backbone assignment and secondary structure determined by three-dimensional NMR spectroscopy.

    PubMed Central

    Ab, E.; Schuurman-Wolters, G. K.; Saier, M. H.; Reizer, J.; Jacuinod, M.; Roepstorff, P.; Dijkstra, K.; Scheek, R. M.; Robillard, G. T.

    1994-01-01

    The assignment of backbone resonances and the secondary structure determination of the Cys 10 Ser mutant of enzyme IIBcellobiose of the Escherichia coli cellobiose-specific phosphoenol-pyruvate-dependent phosphotransferase system are presented. The backbone resonances were assigned using 4 triple resonance experiments, the HNCA and HN(CO)CA experiments, correlating backbone 1H, 15N, and 13C alpha resonances, and the HN(CA)CO and HNCO experiments, correlating backbone 1H,15N and 13CO resonances. Heteronuclear 1H-NOE 1H-15N single quantum coherence (15N-NOESY-HSQC) spectroscopy and heteronuclear 1H total correlation 1H-15N single quantum coherence (15N-TOCSY-HSQC) spectroscopy were used to resolve ambiguities arising from overlapping 13C alpha and 13CO frequencies and to check the assignments from the triple resonance experiments. This procedure, together with a 3-dimensional 1H alpha-13C alpha-13CO experiment (COCAH), yielded the assignment for all observed backbone resonances. The secondary structure was determined using information both from the deviation of observed 1H alpha and 13C alpha chemical shifts from their random coil values and 1H-NOE information from the 15N-NOESY-HSQC. These data show that enzyme IIBcellobiose consists of a 4-stranded parallel beta-sheet and 5 alpha-helices. In the wild-type enzyme IIBcellobiose, the catalytic residue appears to be located at the end of a beta-strand. PMID:8003964

  11. Enzyme IIBcellobiose of the phosphoenol-pyruvate-dependent phosphotransferase system of Escherichia coli: backbone assignment and secondary structure determined by three-dimensional NMR spectroscopy.

    PubMed

    Ab, E; Schuurman-Wolters, G K; Saier, M H; Reizer, J; Jacuinod, M; Roepstorff, P; Dijkstra, K; Scheek, R M; Robillard, G T

    1994-02-01

    The assignment of backbone resonances and the secondary structure determination of the Cys 10 Ser mutant of enzyme IIBcellobiose of the Escherichia coli cellobiose-specific phosphoenol-pyruvate-dependent phosphotransferase system are presented. The backbone resonances were assigned using 4 triple resonance experiments, the HNCA and HN(CO)CA experiments, correlating backbone 1H, 15N, and 13C alpha resonances, and the HN(CA)CO and HNCO experiments, correlating backbone 1H,15N and 13CO resonances. Heteronuclear 1H-NOE 1H-15N single quantum coherence (15N-NOESY-HSQC) spectroscopy and heteronuclear 1H total correlation 1H-15N single quantum coherence (15N-TOCSY-HSQC) spectroscopy were used to resolve ambiguities arising from overlapping 13C alpha and 13CO frequencies and to check the assignments from the triple resonance experiments. This procedure, together with a 3-dimensional 1H alpha-13C alpha-13CO experiment (COCAH), yielded the assignment for all observed backbone resonances. The secondary structure was determined using information both from the deviation of observed 1H alpha and 13C alpha chemical shifts from their random coil values and 1H-NOE information from the 15N-NOESY-HSQC. These data show that enzyme IIBcellobiose consists of a 4-stranded parallel beta-sheet and 5 alpha-helices. In the wild-type enzyme IIBcellobiose, the catalytic residue appears to be located at the end of a beta-strand. PMID:8003964

  12. Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

    PubMed Central

    Mládek, Arnošt; Šponer, Judit E.; Kulhánek, Petr; Lu, Xiang-Jun; Olson, Wilma K.; Šponer, Ji??

    2012-01-01

    Folded RNA molecules are shaped by an astonishing variety of highly conserved noncanonical molecular interactions and backbone topologies. The dinucleotide platform is a widespread recurrent RNA modular building submotif formed by the side-by-side pairing of bases from two consecutive nucleotides within a single strand, with highly specific sequence preferences. This unique arrangement of bases is cemented by an intricate network of noncanonical hydrogen bonds and facilitated by a distinctive backbone topology. The present study investigates the gas-phase intrinsic stabilities of the three most common RNA dinucleotide platforms — 5?-GpU-3?, ApA, and UpC — via state-of-the-art quantum-chemical (QM) techniques. The mean stability of base-base interactions decreases with sequence in the order GpU > ApA > UpC. Bader’s atoms-in-molecules analysis reveals that the N2(G)…O4(U) hydrogen bond of the GpU platform is stronger than the corresponding hydrogen bonds in the other two platforms. The mixed-pucker sugar-phosphate backbone conformation found in most GpU platforms, in which the 5?-ribose sugar (G) is in the C2?-endo form and the 3?-sugar (U) in the C3?-endo form, is intrinsically more stable than the standard A-RNA backbone arrangement, partially as a result of a favorable O2?…O2P intra-platform interaction. Our results thus validate the hypothesis of Lu et al. (Lu Xiang-Jun, et al. Nucleic Acids Res. 2010, 38, 4868-4876), that the superior stability of GpU platforms is partially mediated by the strong O2?…O2P hydrogen bond. In contrast, ApA and especially UpC platform-compatible backbone conformations are rather diverse and do not display any characteristic structural features. The average stabilities of ApA and UpC derived backbone conformers are also lower than those of GpU platforms. Thus, the observed structural and evolutionary patterns of the dinucleotide platforms can be accounted for, to a large extent, by their intrinsic properties as described by modern QM calculations. In contrast, we show that the dinucleotide platform is not properly described in the course of atomistic explicit-solvent simulations. Our work also gives methodological insights into QM calculations of experimental RNA backbone geometries. Such calculations are inherently complicated by rather large data and refinement uncertainties in the available RNA experimental structures, which often preclude reliable energy computations. PMID:22712001

  13. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

    PubMed

    Delaneau, Olivier; Marchini, Jonathan

    2014-01-01

    A major use of the 1000 Genomes Project (1000 GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000 GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. PMID:25653097

  14. The Shannon information entropy of protein sequences.

    PubMed Central

    Strait, B J; Dewey, T G

    1996-01-01

    A comprehensive data base is analyzed to determine the Shannon information content of a protein sequence. This information entropy is estimated by three methods: a k-tuplet analysis, a generalized Zipf analysis, and a "Chou-Fasman gambler." The k-tuplet analysis is a "letter" analysis, based on conditional sequence probabilities. The generalized Zipf analysis demonstrates the statistical linguistic qualities of protein sequences and uses the "word" frequency to determine the Shannon entropy. The Zipf analysis and k-tuplet analysis give Shannon entropies of approximately 2.5 bits/amino acid. This entropy is much smaller than the value of 4.18 bits/amino acid obtained from the nonuniform composition of amino acids in proteins. The "Chou-Fasman" gambler is an algorithm based on the Chou-Fasman rules for protein structure. It uses both sequence and secondary structure information to guess at the number of possible amino acids that could appropriately substitute into a sequence. As in the case for the English language, the gambler algorithm gives significantly lower entropies than the k-tuplet analysis. Using these entropies, the number of most probable protein sequences can be calculated. The number of most probable protein sequences is much less than the number of possible sequences but is still much larger than the number of sequences thought to have existed throughout evolution. Implications of these results for mutagenesis experiments are discussed. PMID:8804598

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

    PubMed

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

    2014-12-01

    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

  16. Sequencing Analysis Technical Guide

    E-print Network

    Xie, Xiaoliang Sunney

    the sequencing reaction. To test the methodology, the team designed three random DNA templates. In the first Turnaround, Low DNA Input, High Accuracy Will Enable Clinical Apps Harvard Team Says Fluorogenic SequencingSequencing Analysis Technical Guide Home » News » In Sequence Harvard Team Says Fluorogenic

  17. 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)

    Wippo, Harald; Reck, Folkert; Kudick, Rene; Ramaseshan, Mahesh; Ceulemans, Griet; Bolli, Martin; Krishnamurthy, Ramanarayanan; Eschenmoser, Albert

    2001-01-01

    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.

  18. Gramicidin A Backbone and Side Chain Dynamics Evaluated by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Experiments. II: Nuclear Magnetic Resonance Experiments

    PubMed Central

    Vostrikov, Vitaly V.; Gu, Hong; Ingólfsson, Helgi I.; Hinton, James F.; Andersen, Olaf S.; Roux, Benoît; Koeppe, Roger E.

    2011-01-01

    Motional properties are important for understanding protein function and are accessible to NMR relaxation measurements. The goal of this study is to investigate the internal dynamics occurring in gramicidin A (gA) channels, in order to provide benchmark experimental data for comparison with the results of molecular dynamics simulations. We therefore synthesized several 15N isotope-enriched gA samples, covering all backbone residues as well as the Trp indole side chains for NMR relaxation experiments. Based on the 15N-NMR spectra for labeled gA samples incorporated in sodium dodecylsulfate (SDS) micelles, we have determined T1, T2, and heteronuclear NOE values for backbone and indole 15NH groups. The results indicate that the SDS-incorporated gA channel is a constrained structure, without an especially “floppy” region. The NMR observables, particularly those for backbone groups, are predicted well by the molecular dynamics simulations in the accompanying article. PMID:21574558

  19. Radical Additions to Aromatic Residues in Peptides Facilitate Unexpected Side Chain and Backbone Losses

    NASA Astrophysics Data System (ADS)

    Zhang, Xing; Julian, Ryan R.

    2014-04-01

    Accurate identification of fragments in tandem mass spectrometry experiments is aided by knowledge of relevant fragmentation mechanisms. Herein, novel radical addition reactions that direct unexpected side-chain dissociations at tryptophan and tyrosine residues are reported. Various mechanisms that can account for the observed dissociation channels are investigated by experiment and theory. The propensity for radical addition at a particular site is found to be primarily under kinetic control, which is largely dictated by molecular structure. In certain peptides, intramolecular radical addition reactions are favored, which leads to the observation of numerous unexpected fragments. In one pathway, radical addition leads to migration of an aromatic side chain to another residue. Alternatively, radical addition followed by hydrogen atom loss leads to cyclization of the peptide and increased observation of internal sequence fragments. Radical addition reactions should be considered when assigning fragmentation spectra obtained from activation of hydrogen deficient peptides.

  20. RNA global alignment in the joint sequence–structure space using elastic shape analysis

    PubMed Central

    Laborde, Jose; Robinson, Daniel; Klassen, Eric; Zhang, Jinfeng

    2013-01-01

    The functions of RNAs, like proteins, are determined by their structures, which, in turn, are determined by their sequences. Comparison/alignment of RNA molecules provides an effective means to predict their functions and understand their evolutionary relationships. For RNA sequence alignment, most methods developed for protein and DNA sequence alignment can be directly applied. RNA 3-dimensional structure alignment, on the other hand, tends to be more difficult than protein structure alignment due to the lack of regular secondary structures as observed in proteins. Most of the existing RNA 3D structure alignment methods use only the backbone geometry and ignore the sequence information. Using both the sequence and backbone geometry information in RNA alignment may not only produce more accurate classification, but also deepen our understanding of the sequence–structure–function relationship of RNA molecules. In this study, we developed a new RNA alignment method based on elastic shape analysis (ESA). ESA treats RNA structures as three dimensional curves with sequence information encoded on additional dimensions so that the alignment can be performed in the joint sequence–structure space. The similarity between two RNA molecules is quantified by a formal distance, geodesic distance. Based on ESA, a rigorous mathematical framework can be built for RNA structure comparison. Means and covariances of full structures can be defined and computed, and probability distributions on spaces of such structures can be constructed for a group of RNAs. Our method was further applied to predict functions of RNA molecules and showed superior performance compared with previous methods when tested on benchmark datasets. The programs are available at http://stat.fsu.edu/ ?jinfeng/ESA.html. PMID:23585278

  1. MRO Sequence Checking Tool

    NASA Technical Reports Server (NTRS)

    Fisher, Forest; Gladden, Roy; Khanampornpan, Teerapat

    2008-01-01

    The MRO Sequence Checking Tool program, mro_check, automates significant portions of the MRO (Mars Reconnaissance Orbiter) sequence checking procedure. Though MRO has similar checks to the ODY s (Mars Odyssey) Mega Check tool, the checks needed for MRO are unique to the MRO spacecraft. The MRO sequence checking tool automates the majority of the sequence validation procedure and check lists that are used to validate the sequences generated by MRO MPST (mission planning and sequencing team). The tool performs more than 50 different checks on the sequence. The automation varies from summarizing data about the sequence needed for visual verification of the sequence, to performing automated checks on the sequence and providing a report for each step. To allow for the addition of new checks as needed, this tool is built in a modular fashion.

  2. Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution

    PubMed Central

    Desai, Bijoy J.; Goto, Yuki; Cembran, Alessandro; Fedorov, Alexander A.; Almo, Steven C.; Gao, Jiali; Suga, Hiroaki; Gerlt, John A.

    2014-01-01

    Hydrogen bonds between backbone amide groups of enzymes and their substrates are often observed, but their importance in substrate binding and/or catalysis is not easy to investigate experimentally. We describe the generation and kinetic characterization of a backbone amide to ester substitution in the orotidine 5?-monophosphate (OMP) decarboxylase from Methanobacter thermoautotrophicum (MtOMPDC) to determine the importance of a backbone amide–substrate hydrogen bond. The MtOMPDC-catalyzed reaction is characterized by a rate enhancement (?1017) that is among the largest for enzyme-catalyzed reactions. The reaction proceeds through a vinyl anion intermediate that may be stabilized by hydrogen bonding interaction between the backbone amide of a conserved active site serine residue (Ser-127) and oxygen (O4) of the pyrimidine moiety and/or electrostatic interactions with the conserved general acidic lysine (Lys-72). In vitro translation in conjunction with amber suppression using an orthogonal amber tRNA charged with l-glycerate (HOS) was used to generate the ester backbone substitution (S127HOS). With 5-fluoro OMP (FOMP) as substrate, the amide to ester substitution increased the value of Km by ?1.5-fold and decreased the value of kcat by ?50-fold. We conclude that (i) the hydrogen bond between the backbone amide of Ser-127 and O4 of the pyrimidine moiety contributes a modest factor (?102) to the 1017 rate enhancement and (ii) the stabilization of the anionic intermediate is accomplished by electrostatic interactions, including its proximity of Lys-72. These conclusions are in good agreement with predictions obtained from hybrid quantum mechanical/molecular mechanical calculations. PMID:25275007

  3. Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study.

    PubMed

    Sahu, S C; Bhuyan, A K; Udgaonkar, J B; Hosur, R V

    2000-10-01

    Backbone dynamics of uniformly 15N-labeled free barnase and its complex with unlabelled barstar have been studied at 40 degrees C, pH 6.6, using 15N relaxation data obtained from proton-detected 2D [1H]-15N NMR spectroscopy. 15N spin-lattice relaxation rate constants (R1), spin-spin relaxation rate constants (R2), and steady-state heteronuclear [1H]-15N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues of free barnase and for 90 residues out of a total of 106 in the complex (excluding three prolines and the N-terminal residue) backbone amide 15N sites of barnase. The primary relaxation data for both the cases have been analyzed in the framework of the model-free formalism using both isotropic and axially symmetric models of the rotational diffusion tensor. As per the latter, the overall rotational correlation times (tau(m)) are 5.0 and 9.5 ns for the free and complexed barnase, respectively. The average order parameter is found to be 0.80 for free barnase and 0.86 for the complex. However, the changes are not uniform along the backbone and for about 5 residues near the binding interface there is actually a significant decrease in the order parameters on complex formation. These residues are not involved in the actual binding. For the residues where the order parameter increases, the magnitudes vary significantly. It is observed that the complex has much less internal mobility, compared to free barnase. From the changes in the order parameters, the entropic contribution of NH bond vector motion to the free energy of complex formation has been calculated. It is apparent that these motion's cause significant unfavorable contributions and therefore must be compensated by many other favorable contributions to effect tight complex formation. The observed variations in the motion and their different locations with regard to the binding interface may have important implications for remote effects and regulation of the enzyme action. PMID:11101215

  4. Genome Sequencing Centers

    Cancer.gov

    The Cancer Genome Atlas (TCGA) Genome Sequencing Centers (GSCs) perform large-scale DNA sequencing using the latest sequencing technologies. Supported by the National Human Genome Research Institute (NHGRI) large-scale sequencing program, the GSCs generate the enormous volume of data required by TCGA, while continually improving existing technologies and methods to expand the frontier of what can be achieved in cancer genome sequencing.

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

    SciTech Connect

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

    2008-10-27

    We report the X-ray crystal structure of a Thermoanaerobacter tengcongensis ribose binding protein (tteRBP) determined to 1.9 {angstrom} resolution. We find that tteRBP is significantly more stable ({sup app}T{sub m} value {approx} 102 C) than the mesophilic Escherichia coli ribose binding protein (ecRBP) ({sup app}T{sub m} value {approx} 56 C). The tteRBP has essentially the identical backbone conformation (0.41 {angstrom} RMSD of 235/271 C{sub {alpha}} positions and 0.65 {angstrom} RMSD of 270/271 C{sub {alpha}} 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.

  6. Design and Synthesis of Peptide YY Analogues with C-terminal Backbone Amide-to-Ester Modifications

    PubMed Central

    2013-01-01

    Peptide YY (PYY) is a gut hormone that activates the G protein-coupled neuropeptide Y (NPY) receptors, and because of its appetite reducing actions, it is evaluated as an antiobesity drug candidate. The C-terminal tail of PYY is crucial for activation of the NPY receptors. Here, we describe the design and preparation of a series of PYY(3–36) depsipeptide analogues, in which backbone amide-to-ester modifications were systematically introduced in the C-terminal. Functional NPY receptor assays and circular dichroism revealed that the ?(CONH) bonds at positions 30–31 and 33–34 are particularly important for receptor interaction and that the latter is implicated in Y2 receptor selectivity. PMID:24900634

  7. Prenylation and Backbone Structure of Flavonoids and Isoflavonoids from Licorice and Hop Influence Their Phase I and II Metabolism.

    PubMed

    van de Schans, Milou G M; Bovee, Toine F H; Stoopen, Geert M; Lorist, Marlies; Gruppen, Harry; Vincken, Jean-Paul

    2015-12-16

    In vitro liver metabolism of 11 prenylated flavonoids and isoflavonoids was investigated by determining their phase I glucuronyl and sulfate metabolites using pork liver preparations. One hundred metabolites were annotated using RP-UHPLC-ESI-MS(n). A mass spectrometry-based data interpretation guideline was proposed for the tentative annotation of the position of hydroxyl groups, considering its relevance for estrogenic activity. To relate structure to metabolism, compounds were classified on the basis of three criteria: backbone structure (isoflavene, isoflavan, or flavanone), number of prenyl groups (0, 1, or 2), and prenyl configuration (chain or pyran). Glucuronidation was most extensive for isoflavenes and for unprenylated compounds (yield of 90-100%). Pyran and chain prenylation gave more complex hydroxylation patterns with 4 or more than 6 hydroxyl isomers, respectively, as compared to unprenylated compounds (only 1 hydroxyl isomer). Moreover, the number of hydroxyl isomers also increased with the number of prenyl groups. PMID:26567868

  8. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation.

    PubMed

    Marassi, Francesca M; Ding, Yi; Schwieters, Charles D; Tian, Ye; Yao, Yong

    2015-09-01

    The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential. PMID:26143069

  9. The polypeptide backbone of recombinant human zona pellucida glycoprotein-3 initiates acrosomal exocytosis in human spermatozoa in vitro.

    PubMed Central

    Chapman, N; Kessopoulou, E; Andrews, P; Hornby, D; Barratt, C R

    1998-01-01

    Human gamete interaction is of fundamental biological importance, yet the molecular interactions between spermatozoa and the zona pellucida are poorly understood. Surprisingly, the role of the polypeptide backbone of zona pellucida glycoprotein 3 (ZP3), the putative ligand for spermatozoa activation, has been largely overlooked. Purified recombinant human ZP3 was expressed in Escherichia coli as a C-terminal fusion to the dimeric glutathione S-transferase (GST) from Schistosoma japonicum and was shown to induce acrosomal exocytosis in live, capacitated human spermatozoa. The level of exocytosis is comparable with that obtained using purified, glycosylated, recombinant human ZP3 [van Duin, M., Polman, J.E.M., DeBreet, I.T.M., Van Ginneken, K., Bunschoten, H., Grootenhuis, A., Brindle, J. and Aitken, R.J. (1994). Biol Reprod. 51, 607-617]. These data imply that the polypeptide chain of human ZP3 contributes to recognition of spermatozoa during acrosomal exocytosis in vitro. PMID:9480899

  10. Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

    NASA Astrophysics Data System (ADS)

    Chevelkov, Veniamin; Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam

    2014-05-01

    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.

  11. Backbone cyclised peptides from plants show molluscicidal activity against the rice pest Pomacea canaliculata (golden apple snail).

    PubMed

    Plan, Manuel Rey R; Saska, Ivana; Cagauan, Arsenia G; Craik, David J

    2008-07-01

    Golden apple snails ( Pomacea canaliculata) are serious pests of rice in South East Asia. Cyclotides are backbone cyclized peptides produced by plants from Rubiaceae and Violaceae. In this study, we investigated the molluscicidal activity of cyclotides against golden apple snails. Crude cyclotide extracts from both Oldenlandia affinis and Viola odorata plants showed molluscicidal activity comparable to the synthetic molluscicide metaldehyde. Individual cyclotides from each extract demonstrated a range of molluscicidal activities. The cyclotides cycloviolacin O1, kalata B1, and kalata B2 were more toxic to golden apple snails than metaldehyde, while kalata B7 and kalata B8 did not cause significant mortality. The toxicity of the cyclotide kalata B2 on a nontarget species, the Nile tilapia ( Oreochromis niloticus), was three times lower than the common piscicide rotenone. Our findings suggest that the existing diversity of cyclotides in plants could be used to develop natural molluscicides. PMID:18557620

  12. Naphthodithiophene-Based Conjugated Polymer with Linear, Planar Backbone Conformation and Strong Intermolecular Packing for Efficient Organic Solar Cells.

    PubMed

    Lee, Jaewon; Ko, Hyomin; Song, Eunjoo; Kim, Heung Gyu; Cho, Kilwon

    2015-09-30

    Two donor-acceptor copolymers, PBDT and PNDT, containing 4,8-bis(2-ethylhexyloxy)benzo[1,2-b:3,4-b']dithiophene (BDT) and 4,9-bis(2-ethylhexyloxy)naphtho[1,2-b:5,6-b']dithiophene (NDT), respectively, as an electron-rich unit and 5,6-difluoro-2,1,3-benzothiadiazole (2FBT) as an electron-deficient unit, were synthesized and compared. The introduction of the NDT core into the conjugated backbone was found to effectively improve both light harvesting and the charge carrier mobility by enhancing chain planarity and backbone linearity; the NDT copolymer has stronger noncovalent interactions and smaller bond angles than those of the BDT-based polymer. Moreover, the introduction of the NDT core brings about a drastic change in the molecular orientation into the face-on motif and results in polymer:PCBM blend films with well-mixed interpenetrating nanofibrillar bulk-heterojunction networks with small-scale phase separation, which produce solar cells with higher short-circuit current density and fill factor values. A conventional optimized device structure containing PNDT:PC71BM was found to exhibit a maximum solar efficiency of 6.35%, an open-circuit voltage of 0.84 V, a short-circuit current density of 11.92 mA cm(-2), and a fill factor of 63.5% with thermal annealing, which demonstrates that the NDT and DT2FBT moieties are a promising electron-donor/acceptor combination for high-performance photovoltaics. PMID:26360662

  13. Isolation of Pristine Electronics Grade Semiconducting Carbon Nanotubes by Switching the Rigidity of the Wrapping Polymer Backbone on Demand.

    PubMed

    Joo, Yongho; Brady, Gerald J; Shea, Matthew J; Oviedo, M Belén; Kanimozhi, Catherine; Schmitt, Samantha K; Wong, Bryan M; Arnold, Michael S; Gopalan, Padma

    2015-10-27

    Conjugated polymers are among the most selective carbon nanotube sorting agents discovered and enable the isolation of ultrahigh purity semiconducting singled-walled carbon nanotubes (s-SWCNTs) from heterogeneous mixtures that contain problematic metallic nanotubes. The strong selectivity though highly desirable for sorting, also leads to irreversible adsorption of the polymer on the s-SWCNTs, limiting their electronic and optoelectronic properties. We demonstrate how changes in polymer backbone rigidity can trigger its release from the nanotube surface. To do so, we choose a model polymer, namely poly[(9,9-dioctylfluorenyl-2,7-diyl)-alt-co-(6,60-(2,20-bipyridine))] (PFO-BPy), which provides ultrahigh selectivity for s-SWCNTs, which are useful specifically for FETs, and has the chemical functionality (BPy) to alter the rigidity using mild chemistry. Upon addition of Re(CO)5Cl to the solution of PFO-BPy wrapped s-SWCNTs, selective chelation with the BPy unit in the copolymer leads to the unwrapping of PFO-BPy. UV-vis, XPS, and Raman spectroscopy studies show that binding of the metal ligand complex to BPy triggers up to 85% removal of the PFO-BPy from arc-discharge s-SWCNTs (diameter = 1.3-1.7 nm) and up to 72% from CoMoCAT s-SWCNTs (diameter = 0.7-0.8 nm). Importantly, Raman studies show that the electronic structure of the s-SWCNTs is preserved through this process. The generalizability of this method is demonstrated with two other transition metal salts. Molecular dynamics simulations support our experimental findings that the complexation of BPy with Re(CO)5Cl in the PFO-BPy backbone induces a dramatic conformational change that leads to a dynamic unwrapping of the polymer off the nanotube yielding pristine s-SWCNTs. PMID:26348205

  14. Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting.

    PubMed

    Vlijm, Rifka; V D Torre, Jaco; Dekker, Cees

    2015-01-01

    The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a lower binding energy than GC-rich sequences. In cells, however, the double-stranded backbone of DNA is destabilized by negative supercoiling, and not by temperature. To investigate what the effect of GC content is on DNA melting induced by negative supercoiling, we studied DNA molecules with a GC content ranging from 38% to 77%, using single-molecule magnetic tweezer measurements in which the length of a single DNA molecule is measured as a function of applied stretching force and supercoiling density. At low force (<0.5pN), supercoiling results into twisting of the dsDNA backbone and loop formation (plectonemes), without inducing any DNA melting. This process was not influenced by the DNA sequence. When negative supercoiling is introduced at increasing force, local melting of DNA is introduced. We measured for the different DNA molecules a characteristic force Fchar, at which negative supercoiling induces local melting of the dsDNA. Surprisingly, GC-rich sequences melt at lower forces than AT-rich sequences: Fchar = 0.56pN for 77% GC but 0.73pN for 38% GC. An explanation for this counterintuitive effect is provided by the realization that supercoiling densities of a few percent only induce melting of a few percent of the base pairs. As a consequence, denaturation bubbles occur in local AT-rich regions and the sequence-dependent effect arises from an increased DNA bending/torsional energy associated with the plectonemes. This new insight indicates that an increased GC-content adjacent to AT-rich DNA regions will enhance local opening of the double-stranded DNA helix. PMID:26513573

  15. Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting

    PubMed Central

    Vlijm, Rifka; v.d. Torre, Jaco; Dekker, Cees

    2015-01-01

    The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a lower binding energy than GC-rich sequences. In cells, however, the double-stranded backbone of DNA is destabilized by negative supercoiling, and not by temperature. To investigate what the effect of GC content is on DNA melting induced by negative supercoiling, we studied DNA molecules with a GC content ranging from 38% to 77%, using single-molecule magnetic tweezer measurements in which the length of a single DNA molecule is measured as a function of applied stretching force and supercoiling density. At low force (<0.5pN), supercoiling results into twisting of the dsDNA backbone and loop formation (plectonemes), without inducing any DNA melting. This process was not influenced by the DNA sequence. When negative supercoiling is introduced at increasing force, local melting of DNA is introduced. We measured for the different DNA molecules a characteristic force Fchar, at which negative supercoiling induces local melting of the dsDNA. Surprisingly, GC-rich sequences melt at lower forces than AT-rich sequences: Fchar = 0.56pN for 77% GC but 0.73pN for 38% GC. An explanation for this counterintuitive effect is provided by the realization that supercoiling densities of a few percent only induce melting of a few percent of the base pairs. As a consequence, denaturation bubbles occur in local AT-rich regions and the sequence-dependent effect arises from an increased DNA bending/torsional energy associated with the plectonemes. This new insight indicates that an increased GC-content adjacent to AT-rich DNA regions will enhance local opening of the double-stranded DNA helix. PMID:26513573

  16. Automated DNA Sequencing System

    SciTech Connect

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  17. Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

    PubMed Central

    Maadooliat, Mehdi; Huang, Jianhua Z.

    2013-01-01

    Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence–structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu.edu/?madoliat/LagSVD) that can be used to produce informative animations. PMID:22926831

  18. Molecular contacts of ribose-phosphate backbone of mRNA with human ribosome.

    PubMed

    Sharifulin, Dmitri E; Grosheva, Anastasia S; Bartuli, Yulia S; Malygin, Alexey A; Meschaninova, Maria I; Ven'yaminova, Aliya G; Stahl, Joachim; Graifer, Dmitri M; Karpova, Galina G

    2015-08-01

    In this work, intimate contacts of riboses of mRNA stretch from nucleotides in positions +3 to +12 with respect to the first nucleotide of the P site codon were studied using cross-linking of short mRNA analogs with oxidized 3'-terminal riboses bound to human ribosomes in the complexes stabilized by codon-anticodon interactions and in the binary complexes. It was shown that in all types of complexes cross-links of the mRNA analogs to ribosomal protein (rp) uS3 occur and the yield of these cross-links does not depend on the presence of tRNA and on sequences of the mRNA analogs. Site of the mRNA analogs cross-linking in rp uS3 was mapped to the peptide in positions 55-64 that is located away from the mRNA binding site. Additionally, in complexes with P site-bound tRNA, riboses of mRNA nucleotides in positions +4 to +7 cross-linked to the C-terminal tail of rp uS19 displaying a contact specific to the decoding site of the mammalian ribosome, and tRNA bound at the A site completely blocked this cross-linking. Remarkably, rps uS3 and uS19 were also able to cross-link to the fragment of HCV IRES containing unstructured 3'-terminal part restricted by the AUGC tetraplet with oxidized 3'-terminal ribose. However, no cross-linking to rp uS3 was observed in the 48S preinitiation complex assembled in reticulocyte lysate with this HCV IRES derivative. The results obtained show an ability of rp uS3 to interact with single-stranded RNAs. Possible roles of rp uS3 region 55-64 in the functioning of ribosomes are discussed. PMID:26066980

  19. Genome Sequence Databases (Overview): Sequencing and Assembly

    SciTech Connect

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  20. Biochemistry 1990, 29, 7387-7401 7387 Analysis of the Backbone Dynamics of Interleukin-1,6 Using Two-Dimensional

    E-print Network

    Clore, G. Marius

    -order parameter with an average value of 0.82 f 0.05. For a model comprising free diffusion within a cone symmetric diffusion within a cone, while the slower motion comprisesjumps between two different orientations are exchange broadened are directly involved in backbone hydrogen bonding with bound internal water molecules

  1. High-Resolution NMR Structure and Backbone Dynamics of the Bacillus subtilis Response Regulator, Spo0F: Implications for Phosphorylation and Molecular

    E-print Network

    McIntosh, Lawrence P.

    High-Resolution NMR Structure and Backbone Dynamics of the Bacillus subtilis Response Regulator in Bacillus subtilis. Three-dimensional 1H, 15N, and 13C experiments have been used to obtain full side chain-protein interactions and for determining the lifetimes of the phosphorylated state. Bacillus subtilis responds

  2. Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences

    E-print Network

    Stadler, Peter F.

    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

  3. Contamination of sequence databases with adaptor sequences

    SciTech Connect

    Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D.

    1997-02-01

    Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

  4. DNA sequencing conference, 2

    SciTech Connect

    Cook-Deegan, R.M.; Venter, J.C.; Gilbert, W.; Mulligan, J.; Mansfield, B.K.

    1991-06-19

    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.

  5. Roles of repetitive sequences

    SciTech Connect

    Bell, G.I.

    1991-12-31

    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.

  6. Cellulases and coding sequences

    DOEpatents

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

    2001-02-20

    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.

  7. Cellulases and coding sequences

    DOEpatents

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

    2001-01-01

    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.

  8. Sequence information signal processor

    DOEpatents

    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

    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.

  9. Roles of repetitive sequences

    SciTech Connect

    Bell, G.I.

    1991-01-01

    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.

  10. Single-molecule sequence detection via microfluidic planar extensional flow at a stagnation point

    PubMed Central

    Dylla-Spears, Rebecca; Townsend, Jacqueline E.; Jen-Jacobson, Linda; Sohn, Lydia L.; Muller, Susan J.

    2012-01-01

    We demonstrate the use of a microfluidic stagnation point flow to trap and extend single molecules of double-stranded (ds) genomic DNA for detection of target sequences along the DNA backbone. Mutant EcoRI-based fluorescent markers are bound sequence-specifically to fluorescently labeled ds ?-DNA. The marker-DNA complexes are introduced into a microfluidic cross slot consisting of flow channels that intersect at ninety degrees. Buffered solution containing the marker-DNA complexes flows in one channel of the cross slot, pure buffer flows in the opposing channel at the same flow rate, and fluid exits the two channels at ninety degrees from the inlet channels. This creates a stagnation point at the center of a planar extensional flow, where marker-DNA complexes may be trapped and elongated along the outflow axis. The degree of elongation can be controlled using the flow strength (i.e., a non-dimensional flow rate) in the device. Both the DNA backbone and the markers bound along the stretched DNA are observed directly using fluorescence microscopy and the location of the markers along the DNA backbone is measured. We find that our method permits detection of each of the five expected target site positions to within 1.5 kb with standard deviations of <1.5 kb. We compare the method’s precision and accuracy at molecular extensions of 68% and 88% of the contour length to binding distributions from similar data obtained via molecular combing. We also provide evidence that increased mixing of the sample during binding of the marker to the DNA improves binding to internal target sequences of dsDNA, presumably by extending the DNA and making the internal binding sites more accessible. PMID:20358051

  11. Assignment of congested NMR spectra: Carbonyl backbone enrichment via the Entner Doudoroff pathway

    NASA Astrophysics Data System (ADS)

    Goldbourt, Amir; Day, Loren A.; McDermott, Ann E.

    2007-12-01

    In NMR spectra of complex proteins, sparse isotope enrichment can be important, in that the removal of many 13C- 13C homonuclear J-couplings can narrow the lines and thereby facilitate the process of spectral assignment and structure elucidation. We present a simple scheme for selective yet extensive isotopic enrichment applicable for production of proteins in organisms utilizing the Entner-Doudoroff (ED) metabolic pathway. An enrichment scheme so derived is demonstrated in the context of a magic-angle spinning solid-state NMR (MAS SSNMR) study of Pf1 bacteriophage, the host of which is Pseudomonas aeruginosa, strain K (PAK), an organism that uses the ED pathway for glucose catabolism. The intact and infectious Pf1 phage in this study was produced by infected PAK cells grown on a minimal medium containing 1- 13C D-glucose ( 13C in position 1) as the sole carbon source, as well as 15NH 4Cl as the only nitrogen source. The 37 MDa Pf1 phage consists of about 93% major coat protein, 1% minor coat proteins, and 6% single-stranded, circular DNA. As a consequence of this composition and the enrichment scheme, the resonances in the MAS SSNMR spectra of the Pf1 sample were almost exclusively due to carbonyl carbons in the major coat protein. Moreover, 3D heteronuclear NCOCX correlation experiments also show that the amino acids leucine, serine, glycine, and tyrosine were not isotopically enriched in their carbonyl positions (although most other amino acids were), which is as expected based upon considerations of the ED metabolic pathway. 3D NCOCX NMR data and 2D 15N- 15N data provided strong verification of many previous assignments of 15N amide and 13C carbonyl shifts in this highly congested spectrum; both the semi-selective enrichment patterns and the narrowed linewidths allowed for greater certainty in the assignments as compared with use of uniformly enriched samples alone.

  12. Sequence finishing and mapping of Drosophila melanogasterheterochromatin

    SciTech Connect

    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

    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.

  13. Asphaltic compositions

    SciTech Connect

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

    1987-02-24

    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.

  14. Electrocatalyst compositions

    DOEpatents

    Mallouk, Thomas E.; Chan, Benny C.; Reddington, Erik; Sapienza, Anthony; Chen, Guoying; Smotkin, Eugene; Gurau, Bogdan; Viswanathan, Rameshkrishnan; Liu, Renxuan

    2001-09-04

    Compositions for use as catalysts in electrochemical reactions are described. The compositions are alloys prepared from two or more elemental metals selected from platinum, molybdenum, osmium, ruthenium, rhodium, and iridium. Also described are electrode compositions including such alloys and electrochemical reaction devices including such catalysts.

  15. Methods for making nucleotide probes for sequencing and synthesis

    DOEpatents

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

    2014-07-08

    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.

  16. Career Academy Course Sequences.

    ERIC Educational Resources Information Center

    Markham, Thom; Lenz, Robert

    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)…

  17. Amino acid sequence and posttranslational modifications of human factor VII sub a from plasma and transfected baby hamster kidney cells

    SciTech Connect

    Thim, L.; Bjoern, S.; Christensen, M.; Nicolaisen, E.M.; Lund-Hansen, T.; Pedersen, A.H.; Hedner, U. )

    1988-10-04

    Blood coagulation factor VII is a vitamin K dependent glycoprotein which in its activated form, factor VII{sub a}, participates in the coagulation process by activating factor X and/or factor IX in the presence of Ca{sup 2+} and tissue factor. Three types of potential posttranslational modifications exist in the human factor VII{sub a} molecule, namely, 10 {gamma}-carboxylated, N-terminally located glutamic acid residues, 1 {beta}-hydroxylated aspartic acid residue, and 2 N-glycosylated asparagine residues. In the present study, the amino acid sequence and posttranslational modifications of recombinant factor VII{sub a} as purified from the culture medium of a transfected baby hamster kidney cell line have been compared to human plasma factor VII{sub a}. By use of HPLC, amino acid analysis, peptide mapping, and automated Edman degradation, the protein backbone of recombinant factor VII{sub a} was found to be identical with human factor VII{sub a}. Asparagine residues 145 and 322 were found to be fully N-glycosylated in human plasma factor VII{sub a}. In the recombinant factor VII{sub a}, asparagine residue 322 was fully glycosylated whereas asparagine residue 145 was only partially (approximately 66%) glycosylated. Besides minor differences in the sialic acid and fucose contents, the overall carbohydrate compositions were nearly identical in recombinant factor VII{sub a} and human plasma factor VII{sub a}. These results show that factor VII{sub a} as produced in the transfected baby hamster kidney cells is very similar to human plasma factor VII{sub a} and that this cell line thus might represent an alternative source for human factor VII{sub a}.

  18. Complete Nucleotide Sequence of a Conjugative Plasmid Carrying blaPER-1

    PubMed Central

    Li, Ruichao; Zhou, Yuanjie; Chan, Edward Wai-chi

    2015-01-01

    The nucleotide sequence of a self-transmissible plasmid pVPH1 harboring blaPER-1 from Vibrio parahaemolyticus was determined. pVPH1 was 183,730 bp in size and shared a backbone similar to pAQU1 and pAQU2, differing mainly in an ?40-kb multidrug resistance (MDR) region. A complex class 1 integron was identified together with ISCR1 and blaPER-1 (ISCR1-blaPER-1-gst-abct-qacE?1-sul1), which was shown to form a circular intermediate playing an important role in the dissemination of blaPER-1. PMID:25779581

  19. Enhanced virome sequencing using targeted sequence capture

    PubMed Central

    Wylie, Todd N.; Wylie, Kristine M.; Herter, Brandi N.; Storch, Gregory A.

    2015-01-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ?1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications. PMID:26395152

  20. Enhanced virome sequencing using targeted sequence capture.

    PubMed

    Wylie, Todd N; Wylie, Kristine M; Herter, Brandi N; Storch, Gregory A

    2015-12-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ?1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications. PMID:26395152

  1. Computational methods in sequence and structure prediction

    NASA Astrophysics Data System (ADS)

    Lang, Caiyi

    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.)

  2. Broadly Neutralizing Anti-Influenza Virus Antibodies: Enhancement of Neutralizing Potency in Polyclonal Mixtures and IgA Backbones

    PubMed Central

    He, Wenqian; Mullarkey, Caitlin E.; Duty, J. Andrew; Moran, Thomas M.; Palese, Peter

    2015-01-01

    ABSTRACT Current influenza virus vaccines rely upon the accurate prediction of circulating virus strains months in advance of the actual influenza season in order to allow time for vaccine manufacture. Unfortunately, mismatches occur frequently, and even when perfect matches are achieved, suboptimal vaccine efficacy leaves several high-risk populations vulnerable to infection. However, the recent discovery of broadly neutralizing antibodies that target the hemagglutinin (HA) stalk domain has renewed hope that the development of “universal” influenza virus vaccines may be within reach. Here, we examine the functions of influenza A virus hemagglutinin stalk-binding antibodies in an endogenous setting, i.e., as polyclonal preparations isolated from human sera. Relative to monoclonal antibodies that bind to the HA head domain, the neutralization potency of monoclonal stalk-binding antibodies was vastly inferior in vitro but was enhanced by several orders of magnitude in the polyclonal context. Furthermore, we demonstrated a surprising enhancement in IgA-mediated HA stalk neutralization relative to that achieved by antibodies of IgG isotypes. Mechanistically, this could be explained in two ways. Identical variable regions consistently neutralized virus more potently when in an IgA backbone compared to an IgG backbone. In addition, HA-specific memory B cells isolated from human peripheral blood were more likely to be stalk specific when secreting antibodies of IgA isotypes compared to those secreting IgG. Taken together, our data provide strong evidence that HA stalk-binding antibodies perform optimally when in a polyclonal context and that the targeted elicitation of HA stalk-specific IgA should be an important consideration during “universal” influenza virus vaccine design. IMPORTANCE Influenza viruses remain one of the most worrisome global public health threats due to their capacity to cause pandemics. While seasonal vaccines fail to protect against the emergence of pandemic strains, a new class of broadly neutralizing antibodies has been recently discovered and may be the key to developing a “universal” influenza virus vaccine. While much has been learned about the biology of these antibodies, most studies have focused only on monoclonal antibodies of IgG subtypes. However, the study of monoclonal antibodies often fails to capture the complexity of antibody functions that occur during natural polyclonal responses. Here, we provide the first detailed analyses of the biological activity of these antibodies in polyclonal contexts, comparing both IgG and IgA isotypes isolated from human donors. The striking differences observed in the functional properties of broadly neutralizing antibodies in polyclonal contexts will be essential for guiding design of “universal” influenza virus vaccines and therapeutics. PMID:25589655

  3. RNA-Binding Affinities and Crystal Structure of Oligonucleotides Containing Five-Atom Amide-Based Backbone Structures

    SciTech Connect

    Pallan, Pradeep S.; von Matt, Peter; Wilds, Christopher J.; Altmann, Karl-Heinz; Egli, Martin

    2010-03-08

    Among the hundreds of nucleic acid analogues that have been studied over the last two decades only very few exhibit backbones with linkers between residues that are either shorter or longer than the four-atom linker O3{prime}-P-O5{prime}-C5{prime} connecting sugar ring moieties in DNA and RNA. 2{prime}-Deoxyribonucleoside dimers connected by a five-atom linker O3{prime}-CH*(CH{sub 3})-CO-NH-CH{sub 2} (* designates a chiral center) were reported to lead to only a slight destabilization of RNA-DNA hybrids in which the DNA strand contained one or several of these amide-linked dimers (De Napoli, L., Iadonisi, A., Montesarchio, D., Varra, M., and Piccialli, G. (1995) Synthesis of thymidine dimers containing a new internucleosidic amide linkage and their incorporation into oligodeoxyribonucleotides, Bioorg. Med. Chem. Lett. 5, 1647-1652). To analyze the influence of various chemistries of such five-atom amide linkers on the RNA-binding affinity of modified DNA strands, we have synthesized five different amide-linked dimers, including structures with homochiral linkers of the type X3{prime}-C*H(CH{sub 3})-CO-NH-CH{sub 2} (X = O, CH{sub 2}) as well as the corresponding analogues carrying methoxy groups at the 2{prime}-position of the 3{prime}-nucleosides. We have conducted a detailed thermodynamic analysis of duplex formation between the modified DNA and RNA, with the DNA strands containing between one and seven consecutive modified dimers. Some of the five-atom-linked dimers lead to significantly higher RNA-binding affinities compared with that of native DNA. Interestingly, the linkers with opposite stereochemistry at the chiral center stabilize duplexes between the modified DNA and RNA to different degrees. CD spectroscopy in solution and a crystal structure of an RNA-DNA duplex with a single amide-linked dimer demonstrate that the longer amide backbones do not disrupt the duplex geometry. These observations provide further evidence that stable cross-pairing between two different types of nucleic acids does not require the numbers of atoms linking their individual residues to match.

  4. Identifying features in biological sequences: Sixth workshop report

    SciTech Connect

    Burks, C.; Myers, E.; Pearson, W.R.

    1995-12-31

    This report covers the sixth of an annual series of workshops held at the Aspen Center for Physics concentrating particularly on the identification of features in DNA sequence, and more broadly on related topics in computational molecular biology. The workshop series originally focused primarily on discussion of current needs and future strategies for identifying and predicting the presence of complex functional units on sequenced, but otherwise uncharacterized, genomic DNA. We addressed the need for computationally-based, automatic tools for synthesizing available data about individual consensus sequences and local compositional patterns into the composite objects (e.g., genes) that are -- as composite entities -- the true object of interest when scanning DNA sequences. The workshop was structured to promote sustained informal contact and exchange of expertise between molecular biologists, computer scientists, and mathematicians.

  5. Polymer support for exonucleolytic sequencing.

    PubMed

    Hinz, M; Gura, S; Nitzan, B; Margel, S; Seliger, H

    2001-04-13

    Different kinds of particles were investigated for their potential use as supports for exonucleolytic sequence analysis. Composite beads composed of an unreactive polystyrene "core" and a "shell" of functionalized silica nanoparticles were found to best fulfill the various prerequisites. The biotin/streptavidin system was used for attachment of DNA to composite beads of 6 microm diameter. Applying M13 ssDNA in extremely high dilution (approximately 1 molecule versus 100 beads) with internal fluorescent labels, only a small fraction of beads was found to be associated with fluorescent entities, which likely correspond to a very small number of bound DNA molecules per particle. For better selection and transfer of DNA-containing beads into microstructures for exonuclease degradation the loading experiments were repeated with composite beads of 2.3 microm diameter. In this case a covalent bond was formed between carboxylate-functionalized beads and amino-terminated oligonucleotides, which were detected through external labelling with fluorescent nanoparticles interacting with biotinylated segments of the complementary strand. PMID:11257537

  6. Natural melanin composites by layer-by-layer assembly

    NASA Astrophysics Data System (ADS)

    Eom, Taesik; Shim, Bong Sub

    2015-04-01

    Melanin is an electrically conductive and biocompatible material, because their conjugated backbone structures provide conducting pathways from human skin, eyes, brain, and beyond. So there is a potential of using as materials for the neural interfaces and the implantable devices. Extracted from Sepia officinalis ink, our natural melanin was uniformly dispersed in mostly polar solvents such as water and alcohols. Then, the dispersed melanin was further fabricated to nano-thin layered composites by the layer-by-layer (LBL) assembly technique. Combined with polyvinyl alcohol (PVA), the melanin nanoparticles behave as an LBL counterpart to from finely tuned nanostructured films. The LBL process can adjust the smart performances of the composites by varying the layering conditions and sandwich thickness. We further demonstrated the melanin loading degree of stacked layers, combination nanostructures, electrical properties, and biocompatibility of the resulting composites by UV-vis spectrophotometer, scanning electron microscope (SEM), multimeter, and in-vitro cell test of PC12, respectively.

  7. Improving computational protein design by using structure-derived sequence profile

    PubMed Central

    Dai, Liang; Yang, Yuedong; Kim, Hyung Rae; Zhou, Yaoqi

    2011-01-01

    Designing a protein sequence that will fold into a predefined structure is of both practical and fundamental interest. Many successful, computational designs in the last decade resulted from improved understanding of hydrophobic and polar interactions between side chains of amino acid residues in stabilizing protein tertiary structures. However, the coupling between main-chain backbone structure and local sequence has yet to be fully addressed. Here, we attempt to account for such coupling by using a sequence profile derived from the sequences of five residue fragments in a fragment library that are structurally matched to the five-residue segments contained in a target structure. We further introduced a term to reduce low complexity regions of designed sequences. These two terms together with optimized reference states for amino-acid residues were implemented in the RosettaDesign program. The new method, called RosettaDesign-SR, makes a 12% increase (from 34 to 46%) in fraction of proteins whose designed sequences are more than 35% identical to wild-type sequences. Meanwhile, it reduces 8% (from 22% to 14%) to the number of designed sequences that are not homologous to any known protein sequences according to psi-blast. More importantly, the sequences designed by RosettaDesign-SR have 2–3% more polar residues at the surface and core regions of proteins and these surface and core polar residues have about 4% higher sequence identity to wild-type sequences than by RosettaDesign. Thus, the proteins designed by RosettaDesign-SR should be less likely to aggregate and more likely to have unique structures due to more specific polar interactions. PMID:20544969

  8. Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences

    E-print Network

    Stadler, Peter F.

    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

  9. A Network Flow Approach to Predict Protein Targets and Flavonoid Backbones to Treat Respiratory Syncytial Virus Infection

    PubMed Central

    Poloni, Joice de Faria; Saraiva Macedo Timmers, Luis Fernando; Bonatto, Diego; Condessa Pitrez, Paulo Márcio; Tetelbom Stein, Renato

    2015-01-01

    Background. Respiratory syncytial virus (RSV) infection is the major cause of respiratory disease in lower respiratory tract in infants and young children. Attempts to develop effective vaccines or pharmacological treatments to inhibit RSV infection without undesired effects on human health have been unsuccessful. However, RSV infection has been reported to be affected by flavonoids. The mechanisms underlying viral inhibition induced by these compounds are largely unknown, making the development of new drugs difficult. Methods. To understand the mechanisms induced by flavonoids to inhibit RSV infection, a systems pharmacology-based study was performed using microarray data from primary culture of human bronchial cells infected by RSV, together with compound-proteomic interaction data available for Homo sapiens. Results. After an initial evaluation of 26 flavonoids, 5 compounds (resveratrol, quercetin, myricetin, apigenin, and tricetin) were identified through topological analysis of a major chemical-protein (CP) and protein-protein interacting (PPI) network. In a nonclustered form, these flavonoids regulate directly the activity of two protein bottlenecks involved in inflammation and apoptosis. Conclusions. Our findings may potentially help uncovering mechanisms of action of early RSV infection and provide chemical backbones and their protein targets in the difficult quest to develop new effective drugs. PMID:25879022

  10. ProCS15: a DFT-based chemical shift predictor for backbone and C? atoms in proteins

    PubMed Central

    Larsen, Anders S.; Bratholm, Lars A.; Christensen, Anders S.; Channir, Maher

    2015-01-01

    We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and C? atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively. PMID:26623185

  11. Scaffolding of peptides using a coarse-grained representation of residues with side chain and backbone nodes

    NASA Astrophysics Data System (ADS)

    Pandey, Ras; Farmer, Barry

    2011-03-01

    Monte Carlo simulations are performed to study scaffolding of peptides (KSL) on a cubic lattice. A residue is represented by three backbone nodes (C-terminal, C-alpha, N-terminal) and a side node connected to the central C-alpha node each connected by fluctuating bond. A peptide is a chain of residues. A solvent constituent is represented by a particle of the same size as that of a node. Peptides and solvent are distributed randomly in the cubic box with concentration Cp and Cw respectively. Each residue interacts with other residues and solvent particles via its side chain with the Lennard-Jones (LJ) potential where a knowledge-based interaction matrix is used for the residue-residue interaction. We examine local and global physical quantities such as mobility and energy of each residue, radial distribution function, and structure factor. We find that the scaffolding of peptides depends on the interaction strength and concentration of the solvent. The structure factor shows multi-scale structure of the aggregates. This work is supported by the Air Force Research Laboratory.

  12. Isoindigo-Containing Molecular Semiconductors: Effect of Backbone Extension on Molecular Organization and Organic Solar Cell Performance

    PubMed Central

    2015-01-01

    We have synthesized three new isoindigo-based small molecules by extending the conjugated length through the incorporation of octyl-thiophene units between the isoindigo core and benzothiophene terminal units. Both UV–vis and Grazing incidence X-ray diffraction experiments show that such extension of the ?-conjugated backbone can induce H-aggregation, and enhance crystallinity and molecular ordering of these isoindigo-based small molecules in the solid state. Compared to two other isoindigo-based derivatives in the series, the derivative with two octyl-thiophene units, BT-T2-ID, is the most crystalline and ordered, and its molecular packing motif appears to be substantially different. Devices utilizing these new extended isoindigo-based small molecules as the electron donor exhibit higher performance than those utilizing nonextended BT-ID as the electron donor. Particularly, devices containing BT-T2-ID in an as-cast blend with PC61BM show power conversion efficiencies up to 3.4%, which is comparable to the best devices containing isoindigo-based molecular semiconductors and is a record among devices containing isoindigo-based small molecules that were processed in the absence of any additives. PMID:25678745

  13. MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data.

    PubMed

    Mantsyzov, Alexey B; Shen, Yang; Lee, Jung Ho; Hummer, Gerhard; Bax, Ad

    2015-09-01

    MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts ((15)N, (13)C(?), and (13)C'), six types of J couplings ((3)JHNH?, (3)JC'C', (3)JC'H?, (1)JH?C?, (2)JC?N and (1)JC?N), as well as the (15)N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein ?-synuclein, as well as for several static and dynamic residues in the folded protein GB3. PMID:26219516

  14. Information Measures for Long-Range Correlated Sequences: the Case of the 24 Human Chromosome Sequences

    E-print Network

    Carbone, A

    2013-01-01

    The Shannon (block) entropy of the clusters generated by intersecting a long-range correlated sequence with its moving average is studied. The entropy is given by two terms, respectively increasing logarithmically and linearly (besides a constant term), corresponding to clusters with power-law or exponentially distributed lengths. Then, the entropy measure is implemented on the 24 human chromosome sequences. Interestingly, it is found that, for the power-law correlated clusters, the nucleotide composition is, on the average, equal to the nucleotide composition of the whole sequence, while, for the exponentially correlated clusters, it fluctuates around the average value. Even more interestingly, it is found that the variance of the fluctuations is a characteristic property of each chromosome. How these fluctuations correlate to biological properties such as segmental duplications, gene density of each chromosome is finally discussed.

  15. Composites review

    NASA Technical Reports Server (NTRS)

    Hordonneau, A.

    1987-01-01

    The properties and applications of composite materials are reviewed. Glass, carbon, Kevlar, ceramic, whisker, and metal fibers are discussed along with polyester, epoxy, polyimide, Peek, carbon, ceramic, and metal matrices. The quantitative distribution of high technology fiber in various applications is given. The role of aerospace industry in the development and promotion of composite utilization is discussed. Consumption trends indicate a rapid development of the composite market.

  16. Unlocking hidden genomic sequence

    PubMed Central

    Keith, Jonathan M.; Cochran, Duncan A. E.; Lala, Gita H.; Adams, Peter; Bryant, Darryn; Mitchelson, Keith R.

    2004-01-01

    Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs. PMID:14973330

  17. Energetic composites

    DOEpatents

    Danen, Wayne C. (Los Alamos, NM); Martin, Joe A. (Espanola, NM)

    1993-01-01

    A method for providing chemical energy and energetic compositions of matter consisting of thin layers of substances which will exothermically react with one another. The layers of reactive substances are separated by thin layers of a buffer material which prevents the reactions from taking place until the desired time. The reactions are triggered by an external agent, such as mechanical stress or an electric spark. The compositions are known as metastable interstitial composites (MICs). This class of compositions includes materials which have not previously been capable of use as energetic materials. The speed and products of the reactions can be varied to suit the application.

  18. Energetic composites

    DOEpatents

    Danen, W.C.; Martin, J.A.

    1993-11-30

    A method for providing chemical energy and energetic compositions of matter consisting of thin layers of substances which will exothermically react with one another. The layers of reactive substances are separated by thin layers of a buffer material which prevents the reactions from taking place until the desired time. The reactions are triggered by an external agent, such as mechanical stress or an electric spark. The compositions are known as metastable interstitial composites (MICs). This class of compositions includes materials which have not previously been capable of use as energetic materials. The speed and products of the reactions can be varied to suit the application. 3 figures.

  19. Small-time scaling behavior of Internet backbone traffic q Vinay J. Ribeiro a,*, Zhi-Li Zhang b

    E-print Network

    Moon, Sue B.

    , Sue Moon c , Christophe Diot d a Department of Electrical and Computer Engineering, Rice University causes of the observed scaling behavior, we analyze the flow composition of the traffic along two that the traffic composition in terms of proportions of dense vs. sparse flows plays a major role in influencing

  20. Cryogenic Spectroscopy and Quantum Molecular Dynamics Determine the Structure of Cyclic Intermediates Involved in Peptide Sequence Scrambling.

    PubMed

    Aseev, Oleg; Perez, Marta A S; Rothlisberger, Ursula; Rizzo, Thomas R

    2015-07-01

    Collision-induced dissociation (CID) is a key technique used in mass spectrometry-based peptide sequencing. Collisionally activated peptides undergo statistical dissociation, forming a series of backbone fragment ions that reflect their amino acid (AA) sequence. Some of these fragments may experience a "head-to-tail" cyclization, which after proton migration, can lead to the cyclic structure opening in a different place than the initially formed bond. This process leads to AA sequence scrambling that may hinder sequencing of the initial peptide. Here we combine cryogenic ion spectroscopy and ab initio molecular dynamics simulations to isolate and characterize the precise structures of key intermediates in the scrambling process. The most stable peptide fragments show intriguing symmetric cyclic structures in which the proton is situated on a C2 symmetry axis and forms exceptionally short H-bonds (1.20 Å) with two backbone oxygens. Other nonsymmetric cyclic structures also exist, one of which is protonated on the amide nitrogen, where ring opening is likely to occur. PMID:26266729

  1. Interpretation of DNA vibration modes: IV--A single-helical approach to assign the phosphate-backbone contribution to the vibrational spectra in A and B conformations.

    PubMed

    Letellier, R; Ghomi, M; Taillandier, E

    1989-02-01

    A calculated approach based on the Higgs method for assigning the vibration modes of an infinite helicoidal polymeric chain has been performed on the basis of a reliable valence force field. The calculated results allowed the phosphate-backbone marker modes of the A and B forms, to be interpreted. In the dynamic models used, the bases have been omitted and no interchain interaction was considered. The calculation can also interprete quite satisfactorily the characteristic Raman peaks and infrared bands in the 1250-700 cm-1 spectral region arising from the sugar or sugar-phosphate association and reproduce their evolution upon the B----A DNA conformational transition. They clearly show that the phosphate-backbone modes in the above mentioned spectral region constitute the optical branches of the phonon dispersion curves with no detectable variation in the first Brillouin-zone. PMID:2619939

  2. New theories for smectic and nematic liquid-crystal polymers: Backbone LCPs (liquid crystalline polymers) and their mixtures and side-chain LCPs

    SciTech Connect

    Dowell, F.

    1987-01-01

    A summary of predictions and explanations from statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with backbone LCPs are presented. Trends in the thermodynamic and molecular ordering properties have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. The theoretical results are found to be in good agreement with existing experimental data. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories can be used to design new LCPs and new solvents as well as to predict and explain properties. 27 refs., 4 tabs.

  3. Electrode compositions

    DOEpatents

    Block, J.; Fan, X.

    1998-10-27

    An electrode composition is described for use as an electrode in a non-aqueous battery system. The electrode composition contains an electrically active powder in a solid polymer and, as a dispersant, a C{sub 8}-C{sub 15} alkyl capped oligomer of a hexanoic acid that is electrochemically inert at 2.5--4.5 volts.

  4. Electrode compositions

    DOEpatents

    Block, Jacob (Rockville, MD); Fan, Xiyun (Orange, TX)

    1998-01-01

    An electrode composition for use as an electrode in a non-aqueous battery system. The electrode composition contains an electrically active powder in a solid polymer and, as a dispersant, a C.sub.8 -C.sub.15 alkyl capped oligomer of a hexanoic acid that is electrochemically inert at 2.5-4.5 volts.

  5. Sulfur-infiltrated graphene-backboned mesoporous carbon nanosheets with a conductive polymer coating for long-life lithium-sulfur batteries.

    PubMed

    Dong, Yanfeng; Liu, Shaohong; Wang, Zhiyu; Liu, Yang; Zhao, Zongbin; Qiu, Jieshan

    2015-05-01

    Sandwich-type, two-dimensional hybrid nanosheets were fabricated by the infiltration of nanosized sulfur into graphene-backboned mesoporous carbon with a PPy nanocoating. They exhibit a high reversible capacity for as long as 400 cycles with an ultra slow decay rate of 0.05% per cycle at the high rate of 1-3 C due to the efficient immobilization of polysulfides. PMID:25832361

  6. Small Angle Neutron Scattering Study of Conformation of Oligo(ethylene glycol) Grafted Polystyrene in Dilute Solutions: Effect of the Backbone Length

    SciTech Connect

    Cheng, Gang; Hong, Kunlun; Hua, Fengjun; Melnichenko, Yuri B; Wignall, George D; Mays, Jimmy

    2008-01-01

    The conformation and clusterization of comb like polymers of polystyrene densely grafted with oligo(ethylene glycol) (OEG) side chains in 1.0 wt% solutions of D2O, toluene-d8 and methanol-d4 was investigated as a function of the degree of polymerization (DP) of the backbone by small angle neutron scattering (SANS). Each side chain had four EG repeat units and the DP of the polystyrene backbone was varied from 8 to 85. The global conformation of the polymers in toluene and methanol was shown to assume ellipsoidal, cylindrical or worm-like chain morphologies with increasing DP of the polystyrene backbone. At the same time, in D2O, the polymer conformation was described by the form factor of rigid cylinders. The second viral coefficient was measured for the polymer with a DP of 85 in all three solvents and the solvent quality of toluene, methanol and D2O was identified as good, marginal and poor for this polymer. Due to a poor solvent quality, the PS backbone (DP = 85) is partially collapsed in D2O whereas it is moderately expanded in toluene and methanol. Polymers with the DP of 8 were found to aggregate into clusters in all three solvents, with the characteristic size between 100 and 200 ?and a fractal dimension of 2. With increase of the DP, the clusters diminished in D2O and completely disappeared in toluene and methanol. This observation suggests that the clusterization of these short side-chain polymers is caused by end group and hydrogen bonding interactions between different chains.

  7. Improving sequencing by tunneling with multiplexing and cross-correlations

    E-print Network

    P. Boynton; A. V. Balatsky; I. K. Schuller; M. Di Ventra

    2015-09-22

    Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original idea considered a single pair of electrodes to read out the current and distinguish the bases [1, 2]. Here, we propose an improvement to the original sequencing by tunneling method, in which $N$ pairs of electrodes are built in series along a synthetic nanochannel. While the ssDNA is forced through the channel using a longitudinal field it passes by each pair of electrodes for long enough time to gather a minimum of $m$ tunneling current measurements, where $m$ is determined by the level of sequencing error desired. Each current time series for each nucleobase is then cross-correlated together, from which the DNA bases can be distinguished. We show using random sampling of data from classical molecular dynamics, that indeed the sequencing error is significantly reduced as the number of pairs of electrodes, $N$, increases. Compared to the sequencing ability of a single pair of electrodes, cross-correlating $N$ pairs of electrodes is exponentially better due to the approximate log-normal nature of the tunneling current probability distributions. We have also used the Fenton-Wilkinson approximation to analytically describe the mean and variance of the cross-correlations that are used to distinguish the DNA bases. The method we suggest is particularly useful when the measurement bandwidth is limited, allowing a smaller electrode gap residence time while still promising to consistently identify the DNA bases correctly.

  8. Layered metal matrix composites

    SciTech Connect

    Lu, L.; Li, G.; Lai, M.O.

    1996-10-01

    Metal matrix composite (MMC) with composition of Al-4.5 wt.%Cu reinforced by 10wt.%TiB{sub 2} or 15wt.%SiC particulate has been successfully fabricated using powder metallurgy technique. Disk, compression and beam specimens were prepared with (a) layered structure containing ductile Al-4.5wt.%Cu with brittle Al-4.5wt.%Cu/TiB{sub 2} or Al-4.5wt.%Cu/SiC layers, and (b) homogeneous constituent with composition of Al-4.5wt.%Cu/10wt.%TiB{sub 2}. The specimens for the fracture toughness measurement were built through three ductile-brittle-ductile alternating layers. For the beam specimens, the layers were built through brittle-ductile-brittle sequence. The brittle layer consisted of Al-4.5%Cu with fixed amount of reinforcement. Fracture toughness testing revealed an increase for layered composites although the total amount of the reinforcement was the same for all disk specimens. The increase in fracture toughness is due to the existence of ductile layers which manifests a strong influence on delaying the occurrence of fracture. It acts as a barrier to resist the propagation of crack and hence increases the fracture toughness of the layered MMC specimens. Delamination in the beam specimens was observed to be due to shear stresses. Fracture surfaces of both disk, compress and beam specimens were characterized using the SEM.

  9. Effect of Hydroxyl Concentration on Chemical Sensitivity of Polyvinyl Alcohol/Carbon-Black Composite Chemiresistors

    SciTech Connect

    Hughes, Robert C.; Patel, Sanjay V.; Yelton, W. Graham

    1999-05-19

    The sensitivity and selectivity of polyvinyl alcohol (PVA) / carbon black composite films have been found to vary depending upon the hydroxylation percentage ("-OH") of the polymer. These chemiresistors made from PVA films whose polymer backbone is 88% hydroxylated (PVA88) have a high sensitivity to water, while chemiresistors made from PVA75 have a higher sensitivity to methanol. The minor differences in polymer composition result in films with different Hildebrand volubility parameters. The relative responses of several different PVA-based chemiresistors to solvents with different volubility parameters are presented. In addition, polyvinyl acetate (PVAC) films with PVA88 are used in an array to distinguish the responses to methanol-water mixtures.

  10. In Sup35p filaments (the [PSI+] prion), the globular C-terminal domains are widely offset from the amyloid fibril backbone

    SciTech Connect

    Baxa, U.; Wall, J.; Keller, P. W.; Cheng, N.; Steven, A. C.

    2011-01-01

    In yeast cells infected with the [PSI+] prion, Sup35p forms aggregates and its activity in translation termination is downregulated. Transfection experiments have shown that Sup35p filaments assembled in vitro are infectious, suggesting that they reproduce or closely resemble the prion. We have used several EM techniques to study the molecular architecture of filaments, seeking clues as to the mechanism of downregulation. Sup35p has an N-terminal 'prion' domain; a highly charged middle (M-)domain; and a C-terminal domain with the translation termination activity. By negative staining, cryo-EM and scanning transmission EM (STEM), filaments of full-length Sup35p show a thin backbone fibril surrounded by a diffuse 65-nm-wide cloud of globular C-domains. In diameter ({approx}8 nm) and appearance, the backbones resemble amyloid fibrils of N-domains alone. STEM mass-per-unit-length data yield -1 subunit per 0.47 nm for N-fibrils, NM-filaments and Sup35p filaments, further supporting the fibril backbone model. The 30 nm radial span of decorating C-domains indicates that the M-domains assume highly extended conformations, offering an explanation for the residual Sup35p activity in infected cells, whereby the C-domains remain free enough to interact with ribosomes.

  11. Agriculture: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This guide, which was written as an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and sequence of a 3-year program in agriculture. The guide consists of a course description; general course objectives;…

  12. Cosmetology: Scope and Sequence.

    ERIC Educational Resources Information Center

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  13. Sequences for Student Investigation

    ERIC Educational Resources Information Center

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  14. M&m Sequences

    ERIC Educational Resources Information Center

    Schultz, Harris S.; Shiflett, Ray C.

    2005-01-01

    Consider a sequence recursively formed as follows: Start with three real numbers, and then when k are known, let the (k +1)st be such that the mean of all k +1 equals the median of the first k. The authors conjecture that every such sequence eventually becomes stable. This article presents results related to their conjecture.

  15. Lichenase and coding sequences

    DOEpatents

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

    2000-08-15

    The present invention provides a fungal lichenase, i.e., an endo-1,3-1,4-.beta.-D-glucanohydrolase, its coding sequence, recombinant DNA molecules comprising the lichenase coding sequences, recombinant host cells and methods for producing same. The present lichenase is from Orpinomyces PC-2.

  16. Sequence harmony: detecting functional specificity from alignments

    PubMed Central

    Feenstra, K. Anton; Pirovano, Walter; Krab, Klaas; Heringa, Jaap

    2007-01-01

    Multiple sequence alignments are often used for the identification of key specificity-determining residues within protein families. We present a web server implementation of the Sequence Harmony (SH) method previously introduced. SH accurately detects subfamily specific positions from a multiple alignment by scoring compositional differences between subfamilies, without imposing conservation. The SH web server allows a quick selection of subtype specific sites from a multiple alignment given a subfamily grouping. In addition, it allows the predicted sites to be directly mapped onto a protein structure and displayed. We demonstrate the use of the SH server using the family of plant mitochondrial alternative oxidases (AOX). In addition, we illustrate the usefulness of combining sequence and structural information by showing that the predicted sites are clustered into a few distinct regions in an AOX homology model. The SH web server can be accessed at www.ibi.vu.nl/programs/seqharmwww. PMID:17584793

  17. The 3'-untranslated region of p21WAF1 mRNA is a composite cis-acting sequence bound by RNA-binding proteins from breast cancer cells, including HuR and poly(C)-binding protein.

    PubMed

    Giles, Keith M; Daly, John M; Beveridge, Dianne J; Thomson, Andrew M; Voon, Dominic C; Furneaux, Henry M; Jazayeri, Jalal A; Leedman, Peter J

    2003-01-31

    Despite promoting growth in many cell types, epidermal growth factor (EGF) induces growth inhibition in a variety of cancer cells that overexpress its receptor. The cyclin-dependent kinase inhibitor p21(WAF1) is a central component of this pathway. We found in human MDA-468 breast cancer cells that EGF up-regulates p21(WAF1) mRNA and protein, through a combination of increased mRNA stability and transcription. The decay rate of a hybrid luciferase reporter full-length p21(WAF1) 3'-untranslated region (UTR) mRNA was significantly faster than that of a control mRNA. Transfections with a variety of p21(WAF1) 3'-UTR constructs identified multiple cis-acting elements capable of reducing basal reporter activity. Short wavelength ultraviolet light induced reporter activity in constructs containing the 5' region of the p21(WAF1) 3'-UTR, whereas EGF induced reporter activity in constructs containing sequences 3' of the UVC-responsive region. These cis-elements bound multiple proteins from MDA-468 cells, including HuR and poly(C)-binding protein 1 (CP1). Immunoprecipitation studies confirmed that HuR and CP1 associate with p21(WAF1) mRNA in MDA-468 cells. Over- and underexpression of HuR in MDA-468 cells did not affect EGF-induced p21(WAF1) protein expression or growth inhibition. However, binding of HuR to its target 3'-UTR cis-element was regulated by UVC but not by EGF, suggesting that these stimuli modulate the stability of p21(WAF1) mRNA via different mechanisms. We conclude that EGF-induced p21(WAF1) protein expression is mediated largely by stabilization of p21(WAF1) mRNA elicited via multiple 3'-UTR cis-elements. Although HuR binds at least one of these elements, it does not appear to be a major modulator of p21(WAF1) expression or growth inhibition in this system. CP1 is a novel p21(WAF1) mRNA-binding protein that may function cooperatively with other mRNA-binding proteins to regulate p21(WAF1) mRNA stability. PMID:12431987

  18. A semisynthetic strategy leads to alteration of the backbone amidate ligand in the NiSOD active site

    SciTech Connect

    Campeciño, Julius O.; Dudycz, Lech W.; Tumelty, David; Berg, Volker; Cabelli, Diane E.; Maroney, Michael J.

    2015-07-01

    Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, N?5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategy that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ~1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N2S2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ~11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with gz < gx,y. 14N-hyperfine is observed on gz

  19. Characterization of the Burkholderia mallei tonB Mutant and Its Potential as a Backbone Strain for Vaccine Development

    PubMed Central

    Mott, Tiffany M.; Vijayakumar, Sudhamathi; Sbrana, Elena; Endsley, Janice J.; Torres, Alfredo G.

    2015-01-01

    Background In this study, a Burkholderia mallei tonB mutant (TMM001) deficient in iron acquisition was constructed, characterized, and evaluated for its protective properties in acute inhalational infection models of murine glanders and melioidosis. Methodology/Principal Findings Compared to the wild-type, TMM001 exhibits slower growth kinetics, siderophore hyper-secretion and the inability to utilize heme-containing proteins as iron sources. A series of animal challenge studies showed an inverse correlation between the percentage of survival in BALB/c mice and iron-dependent TMM001 growth. Upon evaluation of TMM001 as a potential protective strain against infection, we found 100% survival following B. mallei CSM001 challenge of mice previously receiving 1.5 x 104 CFU of TMM001. At 21 days post-immunization, TMM001-treated animals showed significantly higher levels of B. mallei-specific IgG1, IgG2a and IgM when compared to PBS-treated controls. At 48 h post-challenge, PBS-treated controls exhibited higher levels of serum inflammatory cytokines and more severe pathological damage to target organs compared to animals receiving TMM001. In a cross-protection study of acute inhalational melioidosis with B. pseudomallei, TMM001-treated mice were significantly protected. While wild type was cleared in all B. mallei challenge studies, mice failed to clear TMM001. Conclusions/Significance Although further work is needed to prevent chronic infection by TMM001 while maintaining immunogenicity, our attenuated strain demonstrates great potential as a backbone strain for future vaccine development against both glanders and melioidosis. PMID:26114445

  20. A semisynthetic strategy leads to alteration of the backbone amidate ligand in the NiSOD active site

    DOE PAGESBeta

    Campeciño, Julius O.; Dudycz, Lech W.; Tumelty, David; Berg, Volker; Cabelli, Diane E.; Maroney, Michael J.

    2015-07-01

    Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, N?5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategymore »that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ~1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N2S2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ~11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with gz x,y. 14N-hyperfine is observed on gz« less

  1. High-Efficiency Polymer LEDs with Fast Response Times Fabricated via Selection of Electron-Injecting Conjugated Polyelectrolyte Backbone Structure.

    PubMed

    Suh, Minwon; Bailey, Jim; Kim, Sung Wook; Kim, Kyungmok; Yun, Dong-Jin; Jung, Youngsuk; Hamilton, Iain; Chander, Nathan; Wang, Xuhua; Bradley, Donal D C; Jeon, Duk Young; Kim, Ji-Seon

    2015-12-01

    Imidazolium ionic side-group-containing fluorene-based conjugated polyelectrolytes (CPEs) with different ?-conjugated structures, poly[(9,9-bis(8'-(3?-methyl-1?-imidazolium)octyl)-2,7-fluorene)-alt-2,7-(9,9-dioctylfluorene)] dibromide (F8im-Br) and poly[(9,9-bis(8'-(3?-methyl-1?-imidazolium)octyl)-2,7-fluorene)-alt-(benzo(2,1,3)thiadiazol-4,8-diyl) dibromide (F8imBT-Br), are synthesized and utilized as an electron injection layer (EIL) in green-emitting F8BT polymer light-emitting diodes (PLEDs). Both CPE EIL devices significantly outperform Ca cathode devices; 17.9 cd A(-1) (at 3.8 V) and 16.6 lm W(-1) (at 3.0 V) for F8imBT-Br devices, 11.1 cd A(-1) (at 4.2 V) and 9.1 lm W(-1) (at 3.4 V) for F8im-Br devices, and 7.2 cd A(-1) (at 3.6 V) and 7.0 lm W(-1) (at 3.0 V) for Ca devices. Importantly, unlike the F8im-Br EIL devices, F8imBT-Br PLEDs exhibit much faster electroluminescence turn-on times (<10 ?s) despite both EILs possessing the same tethered imidazolium and mobile bromide ions. The F8imBT-Br devices represent, to the best of our knowledge, the highest efficiency in thin (70 nm) single-layer F8BT PLEDs in conventional device architecture with the fastest EL response time using CPE EIL with mobile ions. Our results clearly indicate the importance of an additional factor of EIL materials, specifically the conjugated backbone structure, to determine the device efficiency and response times. PMID:26562214

  2. Sequence History Update Tool

    NASA Technical Reports Server (NTRS)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  3. Structural gene and complete amino acid sequence of Vibrio alginolyticus collagenase.

    PubMed Central

    Takeuchi, H; Shibano, Y; Morihara, K; Fukushima, J; Inami, S; Keil, B; Gilles, A M; Kawamoto, S; Okuda, K

    1992-01-01

    The DNA encoding the collagenase of Vibrio alginolyticus was cloned, and its complete nucleotide sequence was determined. When the cloned gene was ligated to pUC18, the Escherichia coli expression vector, bacteria carrying the gene exhibited both collagenase antigen and collagenase activity. The open reading frame from the ATG initiation codon was 2442 bp in length for the collagenase structural gene. The amino acid sequence, deduced from the nucleotide sequence, revealed that the mature collagenase consists of 739 amino acids with an Mr of 81875. The amino acid sequences of 20 polypeptide fragments were completely identical with the deduced amino acid sequences of the collagenase gene. The amino acid composition predicted from the DNA sequence was similar to the chemically determined composition of purified collagenase reported previously. The analyses of both the DNA and amino acid sequences of the collagenase gene were rigorously performed, but we could not detect any significant sequence similarity to other collagenases. Images Fig. 2. PMID:1311172

  4. Nitrogen Backbone Oligomers

    NASA Astrophysics Data System (ADS)

    Wang, Hongbo; Eremets, Mikhail I.; Troyan, Ivan; Liu, Hanyu; Ma, Yanming; Vereecken, Luc

    2015-08-01

    We found that nitrogen and hydrogen directly react at room temperature and pressures of ~35?GPa forming chains of single-bonded nitrogen atom with the rest of the bonds terminated with hydrogen atoms - as identified by IR absorption, Raman, X-ray diffraction experiments and theoretical calculations. At releasing pressures below ~10?GPa, the product transforms into hydrazine. Our findings might open a way for the practical synthesis of these extremely high energetic materials as the formation of nitrogen-hydrogen compounds is favorable already at pressures above 2?GPa according to the calculations.

  5. Nitrogen Backbone Oligomers

    PubMed Central

    Wang, Hongbo; Eremets, Mikhail I.; Troyan, Ivan; Liu, Hanyu; Ma, Yanming; Vereecken, Luc

    2015-01-01

    We found that nitrogen and hydrogen directly react at room temperature and pressures of ~35?GPa forming chains of single-bonded nitrogen atom with the rest of the bonds terminated with hydrogen atoms - as identified by IR absorption, Raman, X-ray diffraction experiments and theoretical calculations. At releasing pressures below ~10?GPa, the product transforms into hydrazine. Our findings might open a way for the practical synthesis of these extremely high energetic materials as the formation of nitrogen-hydrogen compounds is favorable already at pressures above 2?GPa according to the calculations. PMID:26286836

  6. Generalized Euler Sequences Revisited

    NASA Astrophysics Data System (ADS)

    de Ruiter, Anton H. J.; Forbes, James Richard

    2015-03-01

    It has previously been shown in the literature that the generalized Euler sequences (also known as Davenport sequences) provide a universal set of attitude representations. However, while these works assert the existence of generalized Euler angles for a given attitude, they do not provide explicit ranges that those angles must lie within. In addition, they do not generally provide physical insight into what a generalized Euler sequence is. This paper addresses these two points. As such, this paper contains a comprehensive self-contained treatment of generalized Euler sequences. In particular, a constructive approach is taken to proving that the generalized Euler sequences provide a universal set of attitude representations. In doing so, specific ranges that contain the generalized Euler angles are obtained, and physical insight is provided into the generalized Euler sequences. The singularity of the generalized Euler sequences is characterized, and it is shown that the generalized Euler angles are uniquely specified within their restricted ranges when away from the singularity condition.

  7. HIV Sequence Compendium 2015

    SciTech Connect

    Foley, Brian Thomas; Leitner, Thomas Kenneth; Apetrei, Cristian; Hahn, Beatrice; Mizrachi, Ilene; Mullins, James; Rambaut, Andrew; Wolinsky, Steven; Korber, Bette Tina Marie

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  8. A Nucleolar PUF RNA-binding Protein with Specificity for a Unique RNA Sequence.

    PubMed

    Zhang, Chi; Muench, Douglas G

    2015-12-11

    PUF proteins are a conserved group of sequence specific RNA-binding proteins that bind to RNA in a modular fashion. The RNA-binding domain of PUF proteins typically consists of eight clustered Puf repeats. Plant genomes code for large families of PUF proteins that show significant variability in their predicted Puf repeat number, organization, and amino acid sequence. Here we sought to determine whether the observed variability in the RNA-binding domains of four plant PUFs results in a preference for nonclassical PUF RNA target sequences. We report the identification of a novel RNA binding sequence for a nucleolar Arabidopsis PUF protein that contains an atypical RNA-binding domain. The Arabidopsis PUM23 (APUM23) binding sequence was 10 nucleotides in length, contained a centrally located UUGA core element, and had a preferred cytosine at nucleotide position 8. These RNA sequence characteristics differ from those of other PUF proteins, because all natural PUFs studied to date bind to RNAs that contain a conserved UGU sequence at their 5' end and lack specificity for cytosine. Gel mobility shift assays validated the identity of the APUM23 binding sequence and supported the location of 3 of the 10 predicted Puf repeats in APUM23, including the cytosine-binding repeat. The preferred 10-nucleotide sequence bound by APUM23 is present within the 18S rRNA sequence, supporting the known role of APUM23 in 18S rRNA maturation. This work also reveals that APUM23, an ortholog of yeast Nop9, could provide an advanced structural backbone for Puf repeat engineering and target-specific regulation of cellular RNAs. PMID:26487722

  9. Fuel composition

    SciTech Connect

    Johnson, T.H.

    1990-06-26

    This patent describes a motor fuel composition. It comprises: a mixture of hydrocarbons in the gasoline boiling range containing a deposit preventing or reducing effective amount of poly(olefin)-N-substituted- carbamate.

  10. Phylogenetic Trees From Sequences

    NASA Astrophysics Data System (ADS)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  11. Automatic Command Sequence Generation

    NASA Technical Reports Server (NTRS)

    Fisher, Forest; Gladded, Roy; Khanampompan, Teerapat

    2007-01-01

    Automatic Sequence Generator (Autogen) Version 3.0 software automatically generates command sequences for the Mars Reconnaissance Orbiter (MRO) and several other JPL spacecraft operated by the multi-mission support team. Autogen uses standard JPL sequencing tools like APGEN, ASP, SEQGEN, and the DOM database to automate the generation of uplink command products, Spacecraft Command Message Format (SCMF) files, and the corresponding ground command products, DSN Keywords Files (DKF). Autogen supports all the major multi-mission mission phases including the cruise, aerobraking, mapping/science, and relay mission phases. Autogen is a Perl script, which functions within the mission operations UNIX environment. It consists of two parts: a set of model files and the autogen Perl script. Autogen encodes the behaviors of the system into a model and encodes algorithms for context sensitive customizations of the modeled behaviors. The model includes knowledge of different mission phases and how the resultant command products must differ for these phases. The executable software portion of Autogen, automates the setup and use of APGEN for constructing a spacecraft activity sequence file (SASF). The setup includes file retrieval through the DOM (Distributed Object Manager), an object database used to store project files. This step retrieves all the needed input files for generating the command products. Depending on the mission phase, Autogen also uses the ASP (Automated Sequence Processor) and SEQGEN to generate the command product sent to the spacecraft. Autogen also provides the means for customizing sequences through the use of configuration files. By automating the majority of the sequencing generation process, Autogen eliminates many sequence generation errors commonly introduced by manually constructing spacecraft command sequences. Through the layering of commands into the sequence by a series of scheduling algorithms, users are able to rapidly and reliably construct the desired uplink command products. With the aid of Autogen, sequences may be produced in a matter of hours instead of weeks, with a significant reduction in the number of people on the sequence team. As a result, the uplink product generation process is significantly streamlined and mission risk is significantly reduced. Autogen is used for operations of MRO, Mars Global Surveyor (MGS), Mars Exploration Rover (MER), Mars Odyssey, and will be used for operations of Phoenix. Autogen Version 3.0 is the operational version of Autogen including the MRO adaptation for the cruise mission phase, and was also used for development of the aerobraking and mapping mission phases for MRO.

  12. Sequence-specific mapping of the interaction between urea and unfolded ubiquitin from ensemble analysis of NMR and small angle scattering data.

    PubMed

    Huang, Jie-rong; Gabel, Frank; Jensen, Malene Ringkjøbing; Grzesiek, Stephan; Blackledge, Martin

    2012-03-01

    The molecular details of how urea interacts with, and eventually denatures proteins, remain largely unknown. In this study we have used extensive experimental NMR data, in combination with statistical coil ensemble modeling and small-angle scattering, to analyze the conformational behavior of the protein ubiquitin in the presence of urea. In order to develop an atomic resolution understanding of the denatured state, conformational ensembles of full-atom descriptions of unfolded proteins, including side chain conformations derived from rotamer libraries, are combined with random sampling of explicit urea molecules in interaction with the protein. Using this description of the conformational equilibrium, we demonstrate that the direct-binding model of urea to the protein backbone is compatible with available experimental data. We find that, in the presence of 8 M urea, between 30 and 40% of the backbone peptide groups bind a urea molecule, independently reproducing results from a model-free analysis of small-angle neutron and X-ray scattering data. Crucially, this analysis also provides sequence specific details of the interaction between urea and the protein backbone. The pattern of urea-binding along the amino-acid sequence reveals a higher level of binding in the central part of the protein, a trend which resembles independent results derived from chemical shift mapping of the urea-protein interaction. Together these results substantiate the direct-binding model and provide a framework for studying the physical basis of interactions between proteins and solvent molecules. PMID:22309138

  13. Computer Music Synthesis and Composition

    NASA Astrophysics Data System (ADS)

    Ayers, Lydia

    What is computer music composition? Composers are using the computer for everything from MIDI instruments communicating with computer sequencers, pitch trackers analyzing the sounds of acoustic instruments and converting them to pitch information, live performers with recorded music, performers with interactive computer programs, computer music produced by dancers using sensors, automatic music composition with the computer programs composing the music, composing with sounds or parts of sounds rather than notes, how to structure the use of time, composing with timbres, or the colors of sounds, and timbre morphing, such as a gong morphing to a voice, composing with textures and texture morphing, such as fluttertonguing morphing to pitch, granular synthesis, trills and convolution.

  14. Symmetries in laminated composite plates

    NASA Technical Reports Server (NTRS)

    Noor, A. K.

    1976-01-01

    The different types of symmetry exhibited by laminated anisotropic fibrous composite plates are identified and contrasted with the symmetries of isotropic and homogeneous orthotropic plates. The effects of variations in the fiber orientation and the stacking sequence of the layers on the symmetries exhibited by composite plates are discussed. Both the linear and geometrically nonlinear responses of the plates are considered. A simple procedure is presented for exploiting the symmetries in the finite element analysis. Examples are given of square, skew and polygonal plates where use of symmetry concepts can significantly reduce the scope and cost of analysis.

  15. Hydride compositions

    DOEpatents

    Lee, Myung W. (North Augusta, SC)

    1995-01-01

    A composition for use in storing hydrogen, and a method for making the composition. The composition comprises a mixture of two or more hydrides, each hydride having a different series of hydrogen sorption isotherms that contribute to the overall isotherms of the mixture. The hydrides are chosen so that the isotherms of the mixture have regions wherein the hydrogen equilibrium pressure increases with increasing hydrogen, preferably linearly. The isotherms of the mixture can be adjusted by selecting hydrides with different isotherms and by varying the amounts of the individual hydrides, or both. Preferably, the mixture is made up of hydrides that have isotherms with substantially flat plateaus and in nearly equimolar amounts. The composition is activated by degassing, exposing to hydrogen and then heating at a temperature below the softening temperature of any of the. constituents so that their chemical and structural integrity is preserved. When the composition is used to store hydrogen, its hydrogen content can be found simply by measuring P.sub.H.sbsb.2 and determining H/M from the isothermic function of the composition.

  16. Hydride compositions

    DOEpatents

    Lee, Myung, W.

    1994-01-01

    Disclosed are a composition for use in storing hydrogen and a method for making the composition. The composition comprises a mixture of two or more hydrides, each hydride having a different series of hydrogen sorption isotherms that contribute to the overall isotherms of the mixture. The hydrides are chosen so that the isotherms of the mixture have regions wherein the H equilibrium pressure increases with increasing hydrogen, preferably linearly. The isotherms of the mixture can be adjusted by selecting hydrides with different isotherms and by varying the amounts of the individual hydrides, or both. Preferably, the mixture is made up of hydrides that have isotherms with substantially flat plateaus and in nearly equimolar amounts. The composition is activated by degassing, exposing to H, and then heating below the softening temperature of any of the constituents. When the composition is used to store hydrogen, its hydrogen content can be found simply by measuring P{sub H}{sub 2} and determining H/M from the isothermic function of the composition.

  17. Sequence Learning & Speech Recognition

    E-print Network

    Keysers, Daniel

    Jelinek: Statistical Methods for Speech Recognition, MIT Press, 1998 Lawrence R. Rabiner: A Tutorial (i.e. visual surveillance) bioinformatics: sequence alignment, gene finding, protein with Bioinformatics Applications #12;Hidden Markov Models Three Basic Problems Evaluation Problem: given observation

  18. Authentication of byte sequences

    SciTech Connect

    Stearns, S.D.

    1991-06-01

    Algorithms for the authentication of byte sequences are described. The algorithms are designed to authenticate data in the Storage, Retrieval, Analysis, and Display (SRAD) Test Data Archive of the Radiation Effects and Testing Directorate (9100) at Sandia National Laboratories, and may be used in similar situations where authentication of stored data is required. The algorithms use a well-known error detection method called the Cyclic Redundancy Check (CRC). When a byte sequence is authenticated and stored, CRC bytes are generated and attached to the end of the sequence. When the authenticated data is retrieved, the authentication check consists of processing the entire sequence, including the CRC bytes, and checking for a remainder of zero. The error detection properties of the CRC are extensive and result in a reliable authentication of SRAD data.

  19. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 2 of 2

  20. Sequencing Complex Genomic Regions

    SciTech Connect

    Eichler, Evan

    2009-05-28

    Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 1 of 2

  1. Genome sequencing conference II

    SciTech Connect

    Not Available

    1990-01-01

    Genome Sequencing Conference 2 was held September 30 to October 30, 1990. 26 speaker abstracts and 33 poster presentations were included in the program report. New and improved methods for DNA sequencing and genetic mapping were presented. Many of the papers were concerned with accuracy and speed of acquisition of data with computers and automation playing an increasing role. Individual papers have been processed separately for inclusion on the database.

  2. HIV Sequence Compendium 2010

    SciTech Connect

    Kuiken, Carla; Foley, Brian; Leitner, Thomas; Apetrei, Christian; Hahn, Beatrice; Mizrachi, Ilene; Mullins, James; Rambaut, Andrew; Wolinsky, Steven; Korber, Bette

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  3. Donor Properties of a New Class of Guanidinate Ligands Possessing Ketimine Backbones: A Comparative Study Using Iron.

    PubMed

    Maity, Arnab K; Metta-Magaña, Alejandro J; Fortier, Skye

    2015-10-19

    Addition of 1 equiv of LiN?C(t)Bu2 or LiN?Ad (Ad = 2-adamantyl) to the aryl carbodiimide C(NDipp)2 (Dipp = 2,6-diisopropylphenyl) readily generates the lithium ketimine-guanidinates Li(THF)2[(X)C(NDipp)2] (X = N?C(t)Bu2 (1-(t)Bu), N?Ad (1-Ad)) in excellent yields. These new ligands can be readily metalated with iron to give the N,N'-bidentate chelates [{(X)C(NDipp)2}FeBr]2 (X = N?C(t)Bu2 (5-(t)Bu), N?Ad (5-Ad)), in which the ketimines behave as noncoordinating backbone substituents. In an effort to understand the potential electronic contributions of the ketimine group to the ligand architecture, a thorough structural and electronic study was conducted comparing the features and properties of 5-(t)Bu and 5-Ad to their guanidinate and amidinate analogues [{(X)C(NDipp)2}FeBr]2 (X = (i)Pr2N (6), (t)Bu (7)). Solid-state structural analyses indicate little electronic contribution from the N-ketimine nitrogen atom, while solution-phase electronic absorption spectra of 5-(t)Bu and 5-Ad are qualitatively similar to the amidinate complex 7. Yet, electrochemical measurements do show the donor properties of the ketimine-guanidinate in 5-(t)Bu to be intermediate between its guanidinate and amidinate counterparts in 6 and 7. Preliminary reactivity studies also show that the reduction chemistry of 5-(t)Bu diverges significantly from that of 6 and 7. Treatment of 5-(t)Bu with excess magnesium or 1 equiv of KC8 leads to the formation of the Fe(I)-Fe(I) complex [{?-((t)Bu2C?N)C(NDipp)2}2Fe2] (11), which possesses an exceedingly short Fe?Fe bond (2.1516(5) Å), while neither 6 nor 7 forms dinuclear complexes upon reduction. This result demonstrates that ketimine-guanidinates do not simply behave as amidinate variants but can contribute to distinctive metal chemistry of their own. PMID:26419613

  4. Tridentate Lewis Acids Based on 1,3,5-Trisilacyclohexane Backbones and an Example of Their Host-Guest Chemistry.

    PubMed

    Weisheim, Eugen; Reuter, Christian G; Heinrichs, Peter; Vishnevskiy, Yury V; Mix, Andreas; Neumann, Beate; Stammler, Hans-Georg; Mitzel, Norbert W

    2015-08-24

    Directed tridentate Lewis acids based on the 1,3,5-trisilacyclohexane skeleton with three ethynyl groups [CH2Si(Me)(C2H)]3 were synthesised and functionalised by hydroboration with HB(C6F5)2, yielding the ethenylborane {CH2Si(Me)[C2H2B(C6F5)2]}3, and by metalation with gallium and indium organyls affording {CH2Si(Me)[C2M(R)2]}3 (M = Ga, In, R = Me, Et). In the synthesis of the backbone the influence of substituents (MeO, EtO and iPrO groups at Si) on the orientation of the methyl group was studied with the aim to increase the abundance of the all-cis isomer. New compounds were identified by elemental analyses, multi-nuclear NMR spectroscopy and in some cases by IR spectroscopy. Crystal structures were obtained for cis-trans-[CH2Si(Me)(Cl)]3, all-cis-[CH2Si(Me)(H)]3, all-cis-[CH2Si(Me)(C2H)]3, cis-trans-[CH2Si(Me)(C2H)]3 and all-cis-[CH2Si(Me)(C2SiMe3)]3. A gas-phase electron diffraction experiment for all-cis-[CH2Si(Me)(C2H)]3 provides information on the relative stabilities of the all-equatorial and all-axial form; the first is preferred in both solid and gas phase. The gallium-based Lewis acid {CH2Si(Me)[C2Ga(Et)2]}3 was reacted with a tridentate Lewis base (1,3,5-trimethyl-1,3,5-triazacyclohexane) in an NMR titration experiment. The generated host-guest complexes involved in the equilibria during this reaction were identified by DOSY NMR spectroscopy by comparing measured diffusion coefficients with those of the suitable reference compounds of same size and shape. PMID:26213228

  5. Synthesis and evaluation of a backbone biodegradable multiblock HPMA copolymer nanocarrier for the systemic delivery of paclitaxel.

    PubMed

    Zhang, Rui; Luo, Kui; Yang, Jiyuan; Sima, Monika; Sun, Yongen; Janát-Amsbury, Margit M; Kope?ek, Jind?ich

    2013-02-28

    The performance and safety of current antineoplastic agents, particularly water-insoluble drugs, are still far from satisfactory. For example, the currently widely used Cremophor EL®-based paclitaxel (PTX) formulation exhibits pharmacokinetic concerns and severe side effects. Thus, the concept of a biodegradable polymeric drug-delivery system, which can significantly improve therapeutic efficacy and reduce side effects is advocated. The present work aims to develop a new-generation of long-circulating, biodegradable carriers for effective delivery of PTX. First, a multiblock backbone biodegradable N-(2-hydroxypropyl)methacrylamide(HPMA) copolymer-PTX conjugate (mP-PTX) with molecular weight (Mw) of 335 kDa was synthesized by RAFT (reversible addition-fragmentation chain transfer) copolymerization, followed by chain extension. In vitro studies on human ovarian carcinoma A2780 cells were carried out to investigate the cytotoxicity of free PTX, HPMA copolymer-PTX conjugate with Mw of 48 kDa (P-PTX), and mP-PTX. The experiments demonstrated that mP-PTX has a similar cytotoxic effect against A2780 cells as free PTX and P-PTX. To further compare the behavior of this new biodegradable conjugate (mP-PTX) with free PTX and P-PTX in vivo evaluation was performed using female nu/nu mice bearing orthotopic A2780 ovarian tumors. Pharmacokinetics study showed that high Mw mP-PTX was cleared more slowly from the blood than commercial PTX formulation and low Mw P-PTX. SPECT/CT imaging and biodistribution studies demonstrated biodegradability as well as elimination of mP-PTX from the body. The tumors in the mP-PTX treated group grew more slowly than those treated with saline, free PTX, and P-PTX (single dose at 20 mg PTX/kg equivalent). Moreover, mice treated with mP-PTX had no obvious ascites and body-weight loss. Histological analysis indicated that mP-PTX had no toxicity in liver and spleen, but induced massive cell death in the tumor. In summary, this biodegradable drug delivery system has a great potential to improve performance and safety of current antineoplastic agents. PMID:23262201

  6. Pairwise Sequence Alignment Library

    SciTech Connect

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  7. Pairwise Sequence Alignment Library

    Energy Science and Technology Software Center (ESTSC)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprintmore »that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

  8. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

    PubMed Central

    2011-01-01

    Despite the ever-increasing output of Illumina sequencing data, loci with extreme base compositions are often under-represented or absent. To evaluate sources of base-composition bias, we traced genomic sequences ranging from 6% to 90% GC through the process by quantitative PCR. We identified PCR during library preparation as a principal source of bias and optimized the conditions. Our improved protocol significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate. PMID:21338519

  9. Program Synthesizes UML Sequence Diagrams

    NASA Technical Reports Server (NTRS)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  10. Phosphorescent compositions, methods of making the compositions, and methods of using the compositions

    DOEpatents

    Jia, Weiyi; Wang, Xiaojun; Yen, William; Yen, Laurel C.; Jia, George D.

    2012-12-04

    Compositions, methods of making compositions, materials including compositions, crayons including compositions, paint including compositions, ink including compositions, waxes including compositions, polymers including compositions, vesicles including the compositions, methods of making each, and the like are disclosed.

  11. Phosphorescent compositions, methods of making the compositions, and methods of using the compositions

    DOEpatents

    Jia, Weiyi; Wang, Xiaojun; Jia, George D.; Lewis, Linda; Yen, Laurel C.

    2014-06-24

    Compositions, methods of making compositions, materials including compositions, crayons including compositions, paint including compositions, ink including compositions, waxes including compositions, polymers including compositions, vesicles including the compositions, methods of making each, and the like are disclosed.

  12. Photoimageable composition

    SciTech Connect

    Dentinger, Paul; Krafick, Karen L.; Simison, Kelby Liv

    2005-02-22

    The use of photoacid generators including an alkoxyphenylphenyliodonium salt and/or bis(t-butylphenyl)iodonium salt in a photoimageable composition helps improve resolution. Suitable photoimageable compositions includes: (a) a multifuctional polymeric epoxy resin that is dissolved in an organic solvent wherein the epoxy resin comprises oligomers of bisphenol A that is quantitatively protected by glycidyl ether and wherein the oligomers have an average functionality that ranges from about 3 to 12; and a photoacid generator comprising an alkoxyphenylphenyliodonium salt and/or bis(t-butylphenyl)iodonium salt. Preferred alkoxyphenylphenyliodonium salts include 4-octyloxyphenyl phenyliodonium hexafluoroantimonate and 4-methoxyphenyl phenyliodonium hexafluoroantimonate. The photoimageable composition is particularly suited for producing high aspect ratio microstructures.

  13. Photoimageable composition

    DOEpatents

    Simison, Kelby Liv; Dentinger, Paul

    2003-11-11

    The use of selected buffering amines in a photoimageable composition prevents process bias which with conventional photoresists causes designed features to be distorted, especially in corners and high resolution features. It is believed that the amines react with the catalysts, e.g., photoacids, generated to create an inert salt. The presence of the amines also increases resolution. Suitable photoimageable compositions includes: (a) a multifunctional polymeric epoxy resin that is dissolved in an organic solvent wherein the epoxy resin comprises oligomers of bisphenol A that is quantitatively protected by glycidyl ether and wherein the oligomers have an average functionality that ranges from about 3 to 12; (b) a photoactive compound; and (c) an amine that is selected from the group consisting of triisobutylamine, 1,8-bis(dimethylamino)naphthalene (also known as PROTON SPONGET.TM.), 2,2'-diazabicyclo[2.2.2] octane and mixtures thereof. The photoimageable composition is particularly suited for producing high aspect ratio metal microstructures.

  14. Composite material

    DOEpatents

    Hutchens, Stacy A. (Knoxville, TN); Woodward, Jonathan (Solihull, GB); Evans, Barbara R. (Oak Ridge, TN); O'Neill, Hugh M. (Knoxville, TN)

    2012-02-07

    A composite biocompatible hydrogel material includes a porous polymer matrix, the polymer matrix including a plurality of pores and providing a Young's modulus of at least 10 GPa. A calcium comprising salt is disposed in at least some of the pores. The porous polymer matrix can comprise cellulose, including bacterial cellulose. The composite can be used as a bone graft material. A method of tissue repair within the body of animals includes the steps of providing a composite biocompatible hydrogel material including a porous polymer matrix, the polymer matrix including a plurality of pores and providing a Young's modulus of at least 10 GPa, and inserting the hydrogel material into cartilage or bone tissue of an animal, wherein the hydrogel material supports cell colonization in vitro for autologous cell seeding.

  15. Binning metagenomic contigs by coverage and composition.

    PubMed

    Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino; Schirmer, Melanie; Quick, Joshua; Ijaz, Umer Z; Lahti, Leo; Loman, Nicholas J; Andersson, Anders F; Quince, Christopher

    2014-11-01

    Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets. PMID:25218180

  16. Pressure Modulation of Backbone Conformation and Intermolecular Distance of Conjugated Polymers Toward Understanding the Dynamism of ?-Figuration of their Conjugated System.

    PubMed

    Noguchi, Yuki; Saeki, Akinori; Fujiwara, Takenori; Yamanaka, Sho; Kumano, Masataka; Sakurai, Tsuneaki; Matsuyama, Naoto; Nakano, Motohiro; Hirao, Naohisa; Ohishi, Yasuo; Seki, Shu

    2015-06-18

    Continuous tuning of the backbone conformation and interchain distance of a ?-conjugated polymer is an essential prerequisite to unveil the inherent electrical and optical features of organic electronics. To this end, applying pressure in a hydrostatic medium or diamond anvil cell is a facile approach without the need for side-chain synthetic engineering. We report the development of high-pressure, time-resolved microwave conductivity (HP-TRMC) and evaluation of transient photoconductivity in the regioregular poly(3-hexylthiophene) (P3HT) film and its bulk heterojunction blend with methanofullerene (PCBM). X-ray diffraction experiments under high pressure were performed to detail the pressure dependence of ?-stacking and interlamellar distances in P3HT crystallites and PCBM aggregates. The HP-TRMC results were further correlated with high-pressure Raman spectroscopy and density functional theory calculation. The increased HP-TRMC conductivity of P3HT under pressure was found to be relevant to the planarity of the backbone conformation and intramolecular hole mobility. The effects of pressure on the backbone planarity are estimated to be ?0.3 kJ mol(-1) based on the compressibility derived from the X-ray diffraction under high pressure, suggesting the high enough energy to cause modulation of the planarity in terms of the Landau-de Gennes free energy of isolated P3HT chains as 0.23 kJ mol(-1). In contrast, the P3HT:PCBM blend showed a simple decrease in photoconductivity irrespective of the identical compressive behavior of P3HT. A mechanistic insight into the interplay of intra- and intermolecular mobilities is a key to tailoring the dynamic ?-figuration associated with electrical properties, which may lead to the use of HP-TRMC for exploring divergent ?-conjugated materials at the desired molecular arrangement and conformation. PMID:25563063

  17. The role of backbone conformational heat capacity in protein stability: temperature dependent dynamics of the B1 domain of Streptococcal protein G.

    PubMed Central

    Seewald, M. J.; Pichumani, K.; Stowell, C.; Tibbals, B. V.; Regan, L.; Stone, M. J.

    2000-01-01

    The contributions of backbone NH group dynamics to the conformational heat capacity of the B1 domain of Streptococcal protein G have been estimated from the temperature dependence of 15N NMR-derived order parameters. Longitudinal (R1) and transverse (R2) relaxation rates, transverse cross-relaxation rates (eta(xy)), and steady state [1H]-15N nuclear Overhauser effects were measured at temperatures of 0, 10, 20, 30, 40, and 50 degrees C for 89-100% of the backbone secondary amide nitrogen nuclei in the B1 domain. The ratio R2/eta(xy) was used to identify nuclei for which conformational exchange makes a significant contribution to R2. Relaxation data were fit to the extended model-free dynamics formalism, incorporating an axially symmetric molecular rotational diffusion tensor. The temperature dependence of the order parameter (S2) was used to calculate the contribution of each NH group to conformational heat capacity (Cp) and a characteristic temperature (T*), representing the density of conformational energy states accessible to each NH group. The heat capacities of the secondary structure regions of the B1 domain are significantly higher than those of comparable regions of other proteins, whereas the heat capacities of less structured regions are similar to those in other proteins. The higher local heat capacities are estimated to contribute up to approximately 0.8 kJ/mol K to the total heat capacity of the B1 domain, without which the denaturation temperature would be approximately 9 degrees C lower (78 degrees C rather than 87 degrees C). Thus, variation of backbone conformational heat capacity of native proteins may be a novel mechanism that contributes to high temperature stabilization of proteins. PMID:10892810

  18. The complete mitochondrial genome sequence of Schizothorax dolichonema (Cypriniformes: Cyprinidae).

    PubMed

    Yue, Xingjian; Zhou, Chuanjiang; Shi, Jinrong; Zou, Yuanchao

    2016-01-01

    The complete mitochondrial genome sequence of Schizothorax dolichonema has been sequenced, which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and 2 non-coding regions: origin of light-strand replication and control region, with the total length of 16,583?bp. The gene order and composition are similar to most of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The mitogenome sequence of S. dolichonema would contribute for better understanding of biogeography and evolution of Schizothoracine fishes. PMID:24617487

  19. Method to amplify variable sequences without imposing primer sequences

    DOEpatents

    Bradbury, Andrew M.; Zeytun, Ahmet

    2006-11-14

    The present invention provides methods of amplifying target sequences without including regions flanking the target sequence in the amplified product or imposing amplification primer sequences on the amplified product. Also provided are methods of preparing a library from such amplified target sequences.

  20. Sequencing a Genome by Walking With Clone-end Sequences

    E-print Network

    Sequencing a Genome by Walking With Clone-end Sequences: A Mathematical Analysis Serafim Batzoglou-insert clones (such as bacterial artificial chromosomes (BACs)) and then (ii) to take successive 'walking' steps by selecting and sequencing minimally overlapping clones, using information such as clone-end sequences

  1. DNA sequencing: Clinical applications of new DNA sequencing technologies

    E-print Network

    Quake, Stephen R.

    DNA sequencing: Clinical applications of new DNA sequencing technologies Frederick E. Dewey, MD1-PAAuthorManuscriptNIH-PAAuthorManuscriptNIH-PAAuthorManuscript #12;Gilbert and Sanger sequencing,5,6 that DNA sequencing became widely available to the research community. The Sanger method, which is based on DNA chain termination with a small concentration of radio

  2. Controlled processing during sequencing

    PubMed Central

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region’s activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations. PMID:26578941

  3. Backbone chemical shift assignments for the sensor domain of the Burkholderia pseudomallei histidine kinase RisS: "missing" resonances at the dimer interface.

    PubMed

    Buchko, Garry W; Edwards, Thomas E; Hewitt, Stephen N; Phan, Isabelle Q H; Van Voorhis, Wesley C; Miller, Samuel I; Myler, Peter J

    2015-10-01

    Using a deuterated sample, all the observable backbone (1)H(N), (15)N, (13)C(a), and (13)C' chemical shifts for the dimeric, periplasmic sensor domain of the Burkholderia pseudomallei histidine kinase RisS were assigned. Approximately one-fifth of the amide resonances are "missing" in the (1)H-(15)N HSQC spectrum and map primarily onto ?-helices at the dimer interface observed in a crystal structure suggesting this region either undergoes intermediate timescale motion (?s-ms) and/or is heterogeneous. PMID:25957069

  4. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

    PubMed Central

    2014-01-01

    Background The recent introduction of the Pacific Biosciences RS single molecule sequencing technology has opened new doors to scaffolding genome assemblies in a cost-effective manner. The long read sequence information is promised to enhance the quality of incomplete and inaccurate draft assemblies constructed from Next Generation Sequencing (NGS) data. Results Here we propose a novel hybrid assembly methodology that aims to scaffold pre-assembled contigs in an iterative manner using PacBio RS long read information as a backbone. On a test set comprising six bacterial draft genomes, assembled using either a single Illumina MiSeq or Roche 454 library, we show that even a 50× coverage of uncorrected PacBio RS long reads is sufficient to drastically reduce the number of contigs. Comparisons to the AHA scaffolder indicate our strategy is better capable of producing (nearly) complete bacterial genomes. Conclusions The current work describes our SSPACE-LongRead software which is designed to upgrade incomplete draft genomes using single molecule sequences. We conclude that the recent advances of the PacBio sequencing technology and chemistry, in combination with the limited computational resources required to run our program, allow to scaffold genomes in a fast and reliable manner. PMID:24950923

  5. Magnetic and mechanical properties of Ni-Mn-Ga/Fe-Ga ferromagnetic shape memory composite

    NASA Astrophysics Data System (ADS)

    Tan, Chang-Long; Zhang, Kun; Tian, Xiao-Hua; Cai, Wei

    2015-05-01

    A ferromagnetic shape memory composite of Ni-Mn-Ga and Fe-Ga was fabricated by using spark plasma sintering method. The magnetic and mechanical properties of the composite were investigated. Compared to the Ni-Mn-Ga alloy, the threshold field for magnetic-field-induced strain in the composite is clearly reduced owing to the assistance of internal stress generated from Fe-Ga. Meanwhile, the ductility has been significantly improved in the composite. A fracture strain of 26% and a compressive strength of 1600 MPa were achieved. Projects supported by the National Natural Science Foundation of China (Grant Nos. 51271065 and 51301054), the Program for New Century Excellent Talents in Heilongjiang Provincial Education Department, China (Grant No. 1253-NCET-009), the Youth Academic Backbone in Heilongjiang Provincial Education Department, China (Grant No. 1251G022), the Projects of Heilongjiang, China, and China Postdoctoral Science Foundation.

  6. Processing and Characterization of Basalt Fiber Reinforced Ceramic Composites for High Temperature Applications Using Polymer Precursors

    NASA Technical Reports Server (NTRS)

    Cox, Sarah B.; Lui, Donovan; Gou, Jihua

    2014-01-01

    The development of high temperature structural composite materials has been very limited due to the high cost of the materials and the processing needed. Ceramics can take much higher temperatures, but they are difficult to produce and form in bulk volumes. Polymer Derived Ceramics (PDCs) begin as a polymer matrix, allowing a shape to be formed and cured and then to be pyrolized in order to obtain a ceramic with the associated thermal and mechanical properties. The two PDCs used in this development are polysiloxane and polycarbosilane. Polysiloxanes contain a silicon oxycarbide backbone when pyrolized up to 1000C. Polycarbosilane, an organosilicon polymer, contain a silicon-carbon backbone; around 1200C, beta-SiC begins to crystallize. The use of basalt in structural and high temperature applications has been under development for over 50 years, yet there has been little published research on the incorporation of basalt fibers as a reinforcement in composites. Basalt is a naturally occurring material found in volcanic rock. Continuous basalt fiber reinforced PDCs have been fabricated and tested for the applicability of this composite system as a high temperature structural composite material. Thermal and mechanical testing includes oxyacetylene torch testing and three point bend testing.

  7. Processing and Characterization of Basalt Fiber Reinforced Ceramic Composites for High Temperature Applications Using Polymer Precursors

    NASA Technical Reports Server (NTRS)

    Cox, Sarah; Lui, Donovan; Gou, Jihua

    2014-01-01

    The development of high temperature structural composite materials has been very limited due to the high cost of the materials and the processing needed. Ceramics can take much higher temperatures, but they are difficult to produce and form in bulk volumes. Polymer Derived Ceramics (PDCs) begin as a polymer matrix, allowing a shape to be formed, to be cured, and be pyrolized in order to obtain a ceramic with the associated thermal and mechanical properties. The two PDCs used in this development are polysiloxane and polycarbosilane. Polysiloxanes contain a silicon oxycarbide backbone when pyrolized up to 1000degC. Polycarbosilane, an organosilicon polymer, contain a silicon-carbon backbone; around 1200degC, -SiC begins to crystallize. The use of basalt in structural and high temperature applications has been under development for over 50 years, yet there has been little published research on the incorporation of basalt fibers as a reinforcement in composites. Basalt is a naturally occurring material found in volcanic rock. Continuous basalt fiber reinforced PDCs have been fabricated and tested for the applicability of this composite system as a high temperature structural composite material. Testing for this included thermal and mechanical testing per ASTM standard tests.

  8. Processing and Characterization of Basalt Fiber Reinforced Ceramic Composites for High Temperature Applications Using Polymer Precursors

    NASA Technical Reports Server (NTRS)

    Cox, Sarah B.; Lui, Donovan; Wang, Xin; Gou, Jihua

    2014-01-01

    The development of high temperature structural composite materials has been very limited due to the high cost of the materials and the processing needed. Ceramics can take much higher temperatures, but they are difficult to produce and form in bulk volumes. Polymer Derived Ceramics (PDCs) begin as a polymer matrix, allowing a shape to be formed and cured and then to be pyrolized in order to obtain a ceramic with the associated thermal and mechanical properties. The two PDCs used in this development are polysiloxane and polycarbosilane. Polysiloxanes contain a silicon oxycarbide backbone when pyrolized up to 1000 deg C. Polycarbosilane, an organosilicon polymer, contain a silicon-carbon backbone; around 1200 deg C, Beta-SiC begins to crystallize. The use of basalt in structural and high temperature applications has been under development for over 50 years, yet there has been little published research on the incorporation of basalt fibers as a reinforcement in composites. Basalt is a naturally occurring material found in volcanic rock. Continuous basalt fiber reinforced PDCs have been fabricated and tested for the applicability of this composite system as a high temperature structural composite material. Thermal and mechanical testing includes oxyacetylene torch testing and three point bend testing.

  9. Highly efficient broadband conversion of light polarization by composite retarders

    E-print Network

    S. S. Ivanov; A. A. Rangelov; N. V. Vitanov; T. Peters; T. Halfmann

    2011-10-06

    Driving on an analogy with the technique of composite pulses in quantum physics, we propose highly efficient broadband polarization converters composed of sequences of ordinary retarders rotated at specific angles with respect to their fast-polarization axes.

  10. Generations of sequencing technologies.

    PubMed

    Pettersson, Erik; Lundeberg, Joakim; Ahmadian, Afshin

    2009-02-01

    Advancements in the field of DNA sequencing are changing the scientific horizon and promising an era of personalized medicine for elevated human health. Although platforms are improving at the rate of Moore's Law, thereby reducing the sequencing costs by a factor of two or three each year, we find ourselves at a point in history where individual genomes are starting to appear but where the cost is still too high for routine sequencing of whole genomes. These needs will be met by miniaturized and parallelized platforms that allow a lower sample and template consumption thereby increasing speed and reducing costs. Current massively parallel, state-of-the-art systems are providing significantly improved throughput over Sanger systems and future single-molecule approaches will continue the exponential improvements in the field. PMID:18992322

  11. Polyolefin composition

    SciTech Connect

    Takagi, K.; Kawai, Y.; Kamiya, Y.

    1986-07-15

    A polyolefin composition is described comprising: 100 parts by weight of polyolefin, not less than 0.5 part by weight of a polyamide selected from the group consisting of nylon 6 and nylon 66, and from 3 to 30 percent by weight of a novolak based on the weight of the polyamide.

  12. Exchange biasing of magnetoelectric composites.

    PubMed

    Lage, Enno; Kirchhof, Christine; Hrkac, Viktor; Kienle, Lorenz; Jahns, Robert; Knöchel, Reinhard; Quandt, Eckhard; Meyners, Dirk

    2012-06-01

    Magnetoelectric composite materials are promising candidates for highly sensitive magnetic-field sensors. However, the composites showing the highest reported magnetoelectric coefficients require the presence of external d.c. magnetic bias fields, which is detrimental to their use as sensitive high-resolution magnetic-field sensors. Here, we report magnetoelectric composite materials that instead rely on intrinsic magnetic fields arising from exchange bias in the device. Thin-film magnetoelectric two-two composites were fabricated by magnetron sputtering on silicon-cantilever substrates. The composites consist of piezoelectric AlN and multilayers with the sequence Ta/Cu/Mn(70)Ir(30)/Fe(50)Co(50) or Ta/Cu/Mn(70)Ir(30)/Fe(70.2)Co(7.8)Si(12)B(10) serving as the magnetostrictive component. The thickness of the ferromagnetic layers and angle dependency of the exchange bias field are used to adjust the shift of the magnetostriction curve in such a way that the maximum piezomagnetic coefficient occurs at zero magnetic bias field. These self-biased composites show high sensitivity to a.c. magnetic fields with a maximum magnetoelectric coefficient of 96 V cm(-1) Oe(-1) at mechanical resonance. PMID:22522594

  13. Microchips for DNA sequencing

    NASA Astrophysics Data System (ADS)

    Mastrangelo, Carlos H.; Palaniappan, S.; Man, Piu Francis; Burns, Mark A.; Burke, David T.

    1999-08-01

    Genetic information is vital for understanding features and response of an organism. In humans, genetic errors are linked to the development of major diseases such as cancer and diabetes. In order to maximally exploit this information it is necessary to develop miniature sequencing assays that are rapid and inexpensive. In this paper we show how this could be attained with microfluidic chips that contain integrated assays. To date simple silicon/glass chips aimed for sequencing purpose have been realized; but these chips are not yet practical. Some of the solutions that are used to bring these devices closer to commercial applications are discussed.

  14. Ranking and Sequencing Model

    Energy Science and Technology Software Center (ESTSC)

    2009-08-13

    This database application (commonly called the Supermodel) provides a repository for managing critical facility/project information, allows the user to subjectively an objectively assess key criteria , quantify project risks, develop ROM cost estimates, determine facility/project end states, ultimately performing risk-based modeling to rank facilities/project based on risk, sequencing project schedules and provides an optimized recommended sequencing/scheduling of these projects which maximize the S&M cost savings to perform closure projects which benefit all stakeholders.

  15. The Linus sequence Paul Balister

    E-print Network

    Stephan, Frank

    The Linus sequence Paul Balister Steve Kalikow Amites Sarkar May 7, 2007 Abstract Define the Linus these sequences, such as exponential decay of the frequency of highly periodic subwords of the Linus sequence, zero entropy of any stationary process obtained as a limit of word frequencies in the Linus sequence

  16. The Linus sequence Paul Balister

    E-print Network

    Sarkar, Amites

    The Linus sequence Paul Balister Steve Kalikow Amites Sarkar June 1, 2008 Abstract Define the Linus of the Linus sequence, zero entropy of any stationary process obtained as a limit of word frequencies in the Linus sequence, and infinite average value of the Sally sequence. In addition we make a number

  17. Complete Nucleotide Sequence and Analysis of Two Conjugative Broad Host Range Plasmids from a Marine Microbial Biofilm

    PubMed Central

    Norberg, Peter; Bergström, Maria; Hermansson, Malte

    2014-01-01

    The complete nucleotide sequence of plasmids pMCBF1 and pMCBF6 was determined and analyzed. pMCBF1 and pMCBF6 form a novel clade within the IncP-1 plasmid family designated IncP-1 ?. The plasmids were exogenously isolated earlier from a marine biofilm. pMCBF1 (62 689 base pairs; bp) and pMCBF6 (66 729 bp) have identical backbones, but differ in their mercury resistance transposons. pMCBF1 carries Tn5053 and pMCBF6 carries Tn5058. Both are flanked by 5 bp direct repeats, typical of replicative transposition. Both insertions are in the vicinity of a resolvase gene in the backbone, supporting the idea that both transposons are “res-site hunters” that preferably insert close to and use external resolvase functions. The similarity of the backbones indicates recent insertion of the two transposons and the ongoing dynamics of plasmid evolution in marine biofilms. Both plasmids also carry the insertion sequence ISPst1, albeit without flanking repeats. ISPs1is located in an unusual site within the control region of the plasmid. In contrast to most known IncP-1 plasmids the pMCBF1/pMCBF6 backbone has no insert between the replication initiation gene (trfA) and the vegetative replication origin (oriV). One pMCBF1/pMCBF6 block of about 2.5 kilo bases (kb) has no similarity with known sequences in the databases. Furthermore, insertion of three genes with similarity to the multidrug efflux pump operon mexEF and a gene from the NodT family of the tripartite multi-drug resistance-nodulation-division (RND) system in Pseudomonas aeruginosa was found. They do not seem to confer antibiotic resistance to the hosts of pMCBF1/pMCBF6, but the presence of RND on promiscuous plasmids may have serious implications for the spread of antibiotic multi-resistance. PMID:24647540

  18. Broad-Host-Range Plasmids from Agricultural Soils Have IncP-1 Backbones with Diverse Accessory Genes?

    PubMed Central

    Sen, Diya; Van der Auwera, Geraldine A.; Rogers, Linda M.; Thomas, Christopher M.; Brown, Celeste J.; Top, Eva M.

    2011-01-01

    Broad-host-range plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to antibiotics and heavy metals or degradation of pollutants. Although some broad-host-range plasmids have been extensively studied, their evolutionary history and genetic diversity remain largely unknown. The goal of this study was to analyze and compare the genomes of 12 broad-host-range plasmids that were previously isolated from Norwegian soils by exogenous plasmid isolation and that encode mercury resistance. Complete nucleotide sequencing followed by phylogenetic analyses based on the relaxase gene traI showed that all the plasmids belong to one of two subgroups (? and ?) of the well-studied incompatibility group IncP-1. A diverse array of accessory genes was found to be involved in resistance to antimicrobials (streptomycin, spectinomycin, and sulfonamides), degradation of herbicides (2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenoxypropionic acid), and a putative new catabolic pathway. Intramolecular transposition of insertion sequences followed by deletion was found to contribute to the diversity of some of these plasmids. The previous observation that the insertion sites of a Tn501-related element are identical in four IncP-1? plasmids (pJP4, pB10, R906, and R772) was further extended to three more IncP-1? plasmids (pAKD15, pAKD18, and pAKD29). We proposed a hypothesis for the evolution of these Tn501-bearing IncP-1? plasmids that predicts recent diversification followed by worldwide spread. Our study increases the available collection of complete IncP-1 plasmid genome sequences by 50% and will aid future studies to enhance our understanding of the evolution and function of this important plasmid family. PMID:21948829

  19. Rational design of a cytotoxic dinuclear Cu2 complex that binds by molecular recognition at two neighboring phosphates of the DNA backbone.

    PubMed

    Jany, Thomas; Moreth, Alexander; Gruschka, Claudia; Sischka, Andy; Spiering, Andre; Dieding, Mareike; Wang, Ying; Samo, Susan Haji; Stammler, Anja; Bögge, Hartmut; Fischer von Mollard, Gabriele; Anselmetti, Dario; Glaser, Thorsten

    2015-03-16

    The mechanism of the cytotoxic function of cisplatin and related anticancer drugs is based on their binding to the nucleobases of DNA. The development of new classes of anticancer drugs requires establishing other binding modes. Therefore, we performed a rational design for complexes that target two neighboring phosphates of the DNA backbone by molecular recognition resulting in a family of dinuclear complexes based on 2,7-disubstituted 1,8-naphthalenediol. This rigid backbone preorganizes the two metal ions for molecular recognition at the distance of two neighboring phosphates in DNA of 6-7 Å. Additionally, bulky chelating pendant arms in the 2,7-position impede nucleobase complexation by steric hindrance. We successfully synthesized the Cu(II)2 complex of the designed family of dinuclear complexes and studied its binding to dsDNA by independent ensemble and single-molecule methods like gel electrophoresis, precipitation, and titration experiments followed by UV-vis spectroscopy, atomic force microscopy (AFM), as well as optical tweezers (OT) and magnetic tweezers (MT) DNA stretching. The observed irreversible binding of our dinuclear Cu(II)2 complex to dsDNA leads to a blocking of DNA synthesis as studied by polymerase chain reactions and cytotoxicity for human cancer cells. PMID:25650993

  20. Molecular Data for a Biochemical Model of DNA Radiation Damage: Electron Impact Ionization and Dissociative Ionization of DNA Bases and Sugar-Phosphate Backbone

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher E.; Fletcher, Graham D.

    2004-01-01

    As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is 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%. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-Hl)(+), with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 17.1 eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage.