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Sample records for 3-5 fold higher

  1. Adenosine 3':5'-cyclic monophosphate in higher plants: Isolation and characterization of adenosine 3':5'-cyclic monophosphate from Kalanchoe and Agave.

    PubMed

    Ashton, A R; Polya, G M

    1977-07-01

    1.3':5'-Cyclic AMP was extensively purified from Kalanchoe daigremontiana and Agave americana by neutral alumina and anion- and cation-exchange column chromatography. Inclusion of 3':5'-cyclic [8-3H]AMP from the point of tissue extraction permitted calculation of yields. The purification procedure removed contaminating material that was shown to interfere with the 3':5'-cyclic AMP estimation and characterization procedures. 2. The partially purified 3':5'-cyclic AMP was quantified by means of a radiochemical saturation assay using an ox heart 3':5'-cyclic AMP-binding protein and by an assay involving activation of a mammalian protein kinase. 3. The plant 3':5'-cyclic AMP co-migrated with 3':5'-cyclic [8-3H]AMP on cellulose chromatography, poly(ethyleneimine)-cellulose chromatography and silica-gel t.l.c. developed with several solvent systems. 4. The plant 3':5'-cyclic AMP was degraded by ox heart 3':5'-cyclic nucleotide phosphodiesterase at the same rates as authentic 3':5'-cyclic AMP. 1-Methyl-3-isobutylxanthine (1 mM), a specific inhibitor of the 3':5'-cyclic nucleotide phosphodieterase, completely inhibited such degradation. 5. The concentrations of 3':5'-cyclic AMP satisfying the above criteria in Kalanchoe and Agave were 2-6 and 1 pmol/g fresh wt. respectively. Possible bacterial contribution to these analyses was estimated to be less than 0.002pmol/g fresh wt. Evidence for the occurrence of 3':5'-cyclic AMP in plants is discussed.

  2. Attempts to detect cyclic adenosine 3':5'-monophosphate in higher plants by three assay methods.

    PubMed

    Bressan, R A; Ross, C W

    1976-01-01

    Endogenous levels of cyclic adenosine-3':5'-monophosphate in coleoptile first leaf segments of oat (Avena sativa L.), potato (Solanum tuberosum L.) tubers, tobacco (Nicotiana tabacum L.) callus, and germinating seeds of lettuce (Lactuca sativa L.) were measured with a modified Gilman binding assay and a protein kinase activation assay. The incorporation of adenosine-8-(14)C into compounds with properties similar to those of cyclic AMP was also measured in studies with germinating lettuce seeds. The binding assay proved reliable for mouse and rat liver analyses, but was nonspecific for plant tissues. It responded to various components from lettuce and potato tissues chromatographically similar to but not identical with cyclic AMP. The protein kinase activation assay was much more specific, but it also exhibited positive responses in the presence of compounds not chromatographically identical to cyclic AMP. The concentrations of cyclic AMP in the plant tissues tested were at the lower limits of detection and characterization obtainable with these assays. The estimates of maximal levels were much lower than reported in many previous studies. PMID:16659419

  3. A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 Å resolution

    PubMed Central

    Zhang, Xing; Guo, Huatao; Jin, Lei; Czornyj, Elizabeth; Hodes, Asher; Hui, Wong H; Nieh, Angela W; Miller, Jeff F; Zhou, Z Hong

    2013-01-01

    Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering efforts are hampered without atomic structures. Here, we report a cryo electron microscopy structure of the BPP-1 head at 3.5 Å resolution. Our atomic model shows two of the three protein folds representing major viral lineages: jellyroll for its cement protein (CP) and HK97-like (‘Johnson’) for its major capsid protein (MCP). Strikingly, the fold topology of MCP is permuted non-circularly from the Johnson fold topology previously seen in viral and cellular proteins. We illustrate that the new topology is likely the only feasible alternative of the old topology. β-sheet augmentation and electrostatic interactions contribute to the formation of non-covalent chainmail in BPP-1, unlike covalent inter-protein linkages of the HK97 chainmail. Despite these complex interactions, the termini of both CP and MCP are ideally positioned for DGR-based phage-display engineering. DOI: http://dx.doi.org/10.7554/eLife.01299.001 PMID:24347545

  4. Folding paper-based lithium-ion batteries for higher areal energy densities.

    PubMed

    Cheng, Qian; Song, Zeming; Ma, Teng; Smith, Bethany B; Tang, Rui; Yu, Hongyu; Jiang, Hanqing; Chan, Candace K

    2013-10-01

    Paper folding techniques are used in order to compact a Li-ion battery and increase its energy per footprint area. Full cells were prepared using Li4Ti5O12 and LiCoO2 powders deposited onto current collectors consisting of paper coated with carbon nanotubes. Folded cells showed higher areal capacities compared to the planar versions with a 5 × 5 cell folded using the Miura-ori pattern displaying a ~14× increase in areal energy density.

  5. Effects of 3,5-Dibromo-4-Hydroxybenzonitrile (Bromoxynil) on Bioenergetics of Higher Plant Mitochondria (Pisum sativum).

    PubMed Central

    Zottini, M.; Scoccianti, V.; Zannoni, D.

    1994-01-01

    The herbicide bromoxynil (3,5-dibromo-4-hydroxybenzonitrile) was tested on mitochondria from etiolated pea (Pisum sativum L. cv Alaska) stems. This compound when used at micromolar concentrations ([almost equal to]20 [mu]M) inhibited malate- and succinate-dependent respiration by intact mitochondria but not oxidation of exogenously added NADH. Bromoxynil did not affect the activities of the succinic and the internal NADH dehydrogenases. Analyses of the effects induced by this herbicide on the membrane potential, [delta]pH, matrix Ca2+ movements, and dicarboxylate transport demonstrated that bromoxynil is likely to act as an inhibitor of the dicarboxylate carrier. In addition, bromoxynil caused a mild membrane uncoupling at concentrations [greater than or equal to]20 [mu]M. No effect on the ATPase activity was observed. PMID:12232423

  6. Creative Responses to Changing Realities: A Conference for Northwest Postsecondary and Higher Education (Portland, Oregon, November 3-5, 1981).

    ERIC Educational Resources Information Center

    Highline Community Coll., Midway, WA. Northwest Program Development and Coordination Center.

    Proceedings of the 1981 Creative Responses Conference, which explored approaches to the rapidly changing realities of postsecondary and higher education, are presented. The following major addresses and authors are included: "Hard Times: Constraints or Opportunities," Dale Parnell; "Leadership in the Challenge of Global Competition," George B.…

  7. Human type 3 5α-reductase is expressed in peripheral tissues at higher levels than types 1 and 2 and its activity is potently inhibited by finasteride and dutasteride.

    PubMed

    Yamana, Kazutoshi; Labrie, Fernand; Luu-The, Van

    2010-08-01

    5α-Reductases are crucial enzymes involved in the biosynthesis of dihydrotestosterone, the most potent natural androgen. To date, three types of 5α-reductases, chronologically named types 1, 2 and 3 5α-reductases (SRD5a-1, 2 and 3) have been described. In the present paper, we characterized the activity and compared the mRNA expression levels of SRD5a-3 with those of SRD5a-1 and 2 in various human tissues, and determined its sensitivity to finasteride and dutasteride. We have established HEK-293 cell line that stably expressed SRD5a-3 for studying its activity and the inhibitory effect of finasteride, using [14C]labeled steroids. mRNA expression levels were quantified using real-time PCR in many male and female human tissues including the prostate, adipose tissue, mammary gland, as well as breast and prostate cancer cell lines. Incubation of HEK-SRD5a-3 cells with [14C]4-androstenedione and [14C]testosterone allowed us to show that SRD5a-3 can catalyze very efficiently both substrates 4-androstenedione and testosterone into 5α-androstanedione and dihydrotestosterone, respectively. We observed that the affinity of the enzyme for 4-androstenedione is higher than for testosterone. The activity of SRD5a-3 and SRD5a-2 are similarly sensitive to finasteride, whereas dutasteride is a much more potent inhibitor of SRD5a-3 than SRD5a-2. Tissue distribution analysis shows that SRD5a-3 mRNA expression levels are higher than those of SRD5a-1 and SRD5a-2 in 20 analyzed tissues. In particular, it is highly expressed in the skin, brain, mammary gland and breast cancer cell lines, thus suggesting that SRD5a-3 could play an important role in the production of androgens in these and other peripheral tissues. PMID:25961201

  8. Folding Beauties

    ERIC Educational Resources Information Center

    Berman, Leah Wrenn

    2006-01-01

    This article has its genesis in an MAA mini-course on origami, where a way to get a parabola by folding paper was presented. This article discusses the methods and mathematics of other curves obtained by paper-folding.

  9. Extreme Folding

    NASA Astrophysics Data System (ADS)

    Demaine, Erik

    2012-02-01

    Our understanding of the mathematics and algorithms behind paper folding, and geometric folding in general, has increased dramatically over the past several years. These developments have found a surprisingly broad range of applications. In the art of origami, it has helped spur the technical origami revolution. In engineering and science, it has helped solve problems in areas such as manufacturing, robotics, graphics, and protein folding. On the recreational side, it has led to new kinds of folding puzzles and magic. I will give an overview of the mathematics and algorithms of folding, with a focus on new mathematics and sculpture.

  10. The Long-term Risk of Upper-extremity Lymphedema is Two-fold Higher in Breast Cancer Patients than in Melanoma Patients

    PubMed Central

    Voss, Rachel K.; Cromwell, Kate D.; Chiang, Yi-Ju; Armer, Jane M.; Ross, Merrick I.; Lee, Jeffrey E.; Gershenwald, Jeffrey E.; Stewart, Bob R.; Shaitelman, Simona F.; Cormier, Janice N.

    2015-01-01

    Background and Objectives We assessed the cumulative incidence, symptoms, and risk factors for upper-extremity lymphedema in breast cancer and melanoma patients undergoing sentinel lymph node biopsy or axillary lymph node dissection. Methods Patients were recruited preoperatively (time 0) and assessed at 6, 12, and 18 months postoperatively. Limb volume change (LVC) was measured by perometry. Lymphedema was categorized as none, mild (LVC 5–9.9%), or moderate/severe (LVC≥10%). Symptoms were assessed with a validated lymphedema instrument. Longitudinal logistic regression analyses were conducted to identify risk factors associated with moderate/severe lymphedema. Results Among 205 breast cancer and 144 melanoma patients, the cumulative incidence of moderate/severe lymphedema at 18 months was 36.5% and 35.0, respectively. However, in adjusted analyses, factors associated with moderate/severe lymphedema were breast cancer (OR 2.0, p=0.03), body mass index ≥30 kg/m2 (OR 1.6, p=0.04), greater number of lymph nodes removed (OR 1.05, p<0.01), and longer interval since surgery (OR 2.33 at 18 months, p<0.01). Conclusions: Lymphedema incidence increased over time in both cohorts. However, the adjusted risk of moderate/severe lymphedema was two-fold higher in breast cancer patients. These results may be attributed to surgical treatment of the primary tumor in the breast and more frequent use of radiation. PMID:26477877

  11. 1,3,5-Trinitrobenzene

    Integrated Risk Information System (IRIS)

    1,3,5 - Trinitrobenzene ; CASRN 99 - 35 - 4 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcino

  12. Physical experiments of transpressional folding

    NASA Astrophysics Data System (ADS)

    Tikoff, Basil; Peterson, Karl

    1998-06-01

    In order to understand the process of folding in obliquely convergent settings, we formed folds within a shear box capable of creating homogeneous transpressional deformations. Folds were created in a single layer of stiff mixed plasticine and silicone that overlay a Newtonian silicone, for a variety of plate convergence angles. As small amplitude folds became visible, they were parallel to the long axis of the horizontal finite strain ellipse. With increasing deformation, the fold hinges rotated parallel with the long axis of the horizontal finite strain ellipse for all angles of convergence. This parallelism indicates that fold hinges, once formed, rotate with the horizontal strain ellipse rather than as material lines. The experiments highlight several interesting effects of transpression dynamics. The fold hinges initiate parallel to either ṡ1 or ṡ2 and are parallel to either S1 or S2 with increasing deformation. Neither infinitesimal strain (stress) nor finite strain is resolvable solely from fold geometry. Further, the net amount of contraction determined by folding across the zone was overestimated in all cases except pure contraction. This effect is obvious for the case of wrenching, where folding implies that the zone contracts if elongation parallel to the fold hinge is not considered. Therefore, attempts to balance cross-sections in transpressional zones will tend to overestimate contraction unless the wrench component of deformation is addressed. This result is validated by applying the modeling results in folding in central California adjacent to the San Andreas fault, where cross-section balancing indicates higher amounts of contraction than predicted by plate motion.

  13. Multidimensional theory of protein folding

    NASA Astrophysics Data System (ADS)

    Itoh, Kazuhito; Sasai, Masaki

    2009-04-01

    Theory of multidimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in terms of cooperativity within individual regions and interactions among multiple regions and thus obtained classification is used to analyze the folding process of several example proteins. Ribosomal protein S6, src-SH3 domain, CheY, barnase, and BBL domain are analyzed with the two-dimensional representation by using a structure-based Hamiltonian model. The extension to the higher dimensional representation leads to the finer description of the folding process. Barnase, NtrC, and an ankyrin repeat protein are examined with the three-dimensional representation. The multidimensional representation allows us to directly address questions on folding pathways, intermediates, and transition states.

  14. Structural Bridges through Fold Space

    PubMed Central

    Edwards, Hannah; Deane, Charlotte M.

    2015-01-01

    Several protein structure classification schemes exist that partition the protein universe into structural units called folds. Yet these schemes do not discuss how these units sit relative to each other in a global structure space. In this paper we construct networks that describe such global relationships between folds in the form of structural bridges. We generate these networks using four different structural alignment methods across multiple score thresholds. The networks constructed using the different methods remain a similar distance apart regardless of the probability threshold defining a structural bridge. This suggests that at least some structural bridges are method specific and that any attempt to build a picture of structural space should not be reliant on a single structural superposition method. Despite these differences all representations agree on an organisation of fold space into five principal community structures: all-α, all-β sandwiches, all-β barrels, α/β and α + β. We project estimated fold ages onto the networks and find that not only are the pairings of unconnected folds associated with higher age differences than bridged folds, but this difference increases with the number of networks displaying an edge. We also examine different centrality measures for folds within the networks and how these relate to fold age. While these measures interpret the central core of fold space in varied ways they all identify the disposition of ancestral folds to fall within this core and that of the more recently evolved structures to provide the peripheral landscape. These findings suggest that evolutionary information is encoded along these structural bridges. Finally, we identify four highly central pivotal folds representing dominant topological features which act as key attractors within our landscapes. PMID:26372166

  15. Structural Bridges through Fold Space.

    PubMed

    Edwards, Hannah; Deane, Charlotte M

    2015-09-01

    Several protein structure classification schemes exist that partition the protein universe into structural units called folds. Yet these schemes do not discuss how these units sit relative to each other in a global structure space. In this paper we construct networks that describe such global relationships between folds in the form of structural bridges. We generate these networks using four different structural alignment methods across multiple score thresholds. The networks constructed using the different methods remain a similar distance apart regardless of the probability threshold defining a structural bridge. This suggests that at least some structural bridges are method specific and that any attempt to build a picture of structural space should not be reliant on a single structural superposition method. Despite these differences all representations agree on an organisation of fold space into five principal community structures: all-α, all-β sandwiches, all-β barrels, α/β and α + β. We project estimated fold ages onto the networks and find that not only are the pairings of unconnected folds associated with higher age differences than bridged folds, but this difference increases with the number of networks displaying an edge. We also examine different centrality measures for folds within the networks and how these relate to fold age. While these measures interpret the central core of fold space in varied ways they all identify the disposition of ancestral folds to fall within this core and that of the more recently evolved structures to provide the peripheral landscape. These findings suggest that evolutionary information is encoded along these structural bridges. Finally, we identify four highly central pivotal folds representing dominant topological features which act as key attractors within our landscapes.

  16. Progress in fold recognition.

    PubMed

    Flöckner, H; Braxenthaler, M; Lackner, P; Jaritz, M; Ortner, M; Sippl, M J

    1995-11-01

    The prediction experiment reveals that fold recognition has become a powerful tool in structural biology. We applied our fold recognition technique to 13 target sequences. In two cases, replication terminating protein and prosequence of subtilisin, the predicted structures are very similar to the experimentally determined folds. For the first time, in a public blind test, the unknown structures of proteins have been predicted ahead of experiment to an accuracy approaching molecular detail. In two other cases the approximate folds have been predicted correctly. According to the assessors there were 12 recognizable folds among the target proteins. In our postprediction analysis we find that in 7 cases our fold recognition technique is successful. In several of the remaining cases the predicted folds have interesting features in common with the experimental results. We present our procedure, discuss the results, and comment on several fundamental and technical problems encountered in fold recognition.

  17. Let Them Fold

    ERIC Educational Resources Information Center

    Grant, Nicholas; Tobin, Alexander

    1972-01-01

    Directions are given for seven activities involving the folding of paper strips to illustrate geometric concepts. Properties of pentagons, triangles, hexagons, and Mobius bands resulting from the various foldings are discussed. (DT)

  18. 32 CFR 3.5 - Appropriate use.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... CONTRACTS, GRANTS, OR COOPERATIVE AGREEMENTS FOR PROTOTYPE PROJECTS § 3.5 Appropriate use. In accordance... is participating to a significant extent in the prototype project; or (b) No nontraditional Defense contractor is participating to a significant extent in the prototype project, but at least one of...

  19. 32 CFR 3.5 - Appropriate use.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... CONTRACTS, GRANTS, OR COOPERATIVE AGREEMENTS FOR PROTOTYPE PROJECTS § 3.5 Appropriate use. In accordance... is participating to a significant extent in the prototype project; or (b) No nontraditional Defense contractor is participating to a significant extent in the prototype project, but at least one of...

  20. 32 CFR 3.5 - Appropriate use.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... CONTRACTS, GRANTS, OR COOPERATIVE AGREEMENTS FOR PROTOTYPE PROJECTS § 3.5 Appropriate use. In accordance... is participating to a significant extent in the prototype project; or (b) No nontraditional Defense contractor is participating to a significant extent in the prototype project, but at least one of...

  1. 32 CFR 3.5 - Appropriate use.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... CONTRACTS, GRANTS, OR COOPERATIVE AGREEMENTS FOR PROTOTYPE PROJECTS § 3.5 Appropriate use. In accordance... is participating to a significant extent in the prototype project; or (b) No nontraditional Defense contractor is participating to a significant extent in the prototype project, but at least one of...

  2. 32 CFR 3.5 - Appropriate use.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... CONTRACTS, GRANTS, OR COOPERATIVE AGREEMENTS FOR PROTOTYPE PROJECTS § 3.5 Appropriate use. In accordance... is participating to a significant extent in the prototype project; or (b) No nontraditional Defense contractor is participating to a significant extent in the prototype project, but at least one of...

  3. Water Sourcebook. Grades 3-5.

    ERIC Educational Resources Information Center

    Tennessee Valley Authority, Knoxville.

    The goal of this supplemental activity guide for elementary students in grades 3-5 is to develop awareness, knowledge, and skills for sound water use decisions. Materials developed for the program are compatible with existing curriculum standards established by State Boards of Education throughout the United States and teach concepts included in…

  4. Protein folding by motion planning

    NASA Astrophysics Data System (ADS)

    Thomas, Shawna; Song, Guang; Amato, Nancy M.

    2005-12-01

    We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMs). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structures, assuming we know the native fold. A feature of our PRM-based framework is that the large sets of folding pathways in the roadmaps it produces, in just a few hours on a desktop PC, provide global information about the protein's energy landscape. This is an advantage over other simulation methods such as molecular dynamics or Monte Carlo methods which require more computation and produce only a single trajectory in each run. In our initial studies, we obtained encouraging results for several small proteins. In this paper, we investigate more sophisticated techniques for analyzing the folding pathways in our roadmaps. In addition to more formally revalidating our previous results, we present a case study showing that our technique captures known folding differences between the structurally similar proteins G and L. This research was supported in part by NSF CAREER Award CCR-9624315, NSF Grants ACI-9872126, EIA-9975018, EIA-0103742, EIA-9805823, ACR-0113971, CCR-0113974, EIA-9810937, EIA-0079874 and the Texas Higher Education Coordinating Board grant ATP-000512-0261-2001. ST was supported in part by an NSF Graduate Research Fellowship. GS was supported in part by an IBM PhD Fellowship.

  5. Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)

    Integrated Risk Information System (IRIS)

    Hexahydro - 1,3,5 - trinitro - 1,3,5 - triazine ( RDX ) ; CASRN 121 - 82 - 4 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health

  6. Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)

    Integrated Risk Information System (IRIS)

    Octahydro - 1,3,5,7 - tetranitro - 1,3,5,7 - tetr . . . ( HMX ) ; CASRN 2691 - 41 - 0 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I

  7. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2012-10-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold distribution procedure. The fold distribution provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of change in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Distribution, Proposal 12778, as Cycle 19.

  8. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2010-09-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Analysis {11863} during Cycle 17.

  9. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2009-07-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Analysis {10035} during Cycle 12.

  10. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2013-10-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold distribution procedure. The fold distribution provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of change in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Distribution, Proposal 13149, as Cycle 20.

  11. STIS MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2011-10-01

    The performance of MAMA microchannel plates can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the STIS MAMA Fold Analysis, Proposal 12416, as Cycle 18.

  12. Fast protein folding kinetics

    PubMed Central

    Gelman, Hannah; Gruebele, Martin

    2014-01-01

    Fast folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast folding proteins has provided insight into the mechanisms which allow some proteins to find their native conformation well less than 1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even “slow” folding processes: fast folders are small, relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast folding proteins and provides an overview of the major findings of fast folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general as well as some work that is left to do. PMID:24641816

  13. A galaxy of folds.

    PubMed

    Alva, Vikram; Remmert, Michael; Biegert, Andreas; Lupas, Andrei N; Söding, Johannes

    2010-01-01

    Many protein classification systems capture homologous relationships by grouping domains into families and superfamilies on the basis of sequence similarity. Superfamilies with similar 3D structures are further grouped into folds. In the absence of discernable sequence similarity, these structural similarities were long thought to have originated independently, by convergent evolution. However, the growth of databases and advances in sequence comparison methods have led to the discovery of many distant evolutionary relationships that transcend the boundaries of superfamilies and folds. To investigate the contributions of convergent versus divergent evolution in the origin of protein folds, we clustered representative domains of known structure by their sequence similarity, treating them as point masses in a virtual 2D space which attract or repel each other depending on their pairwise sequence similarities. As expected, families in the same superfamily form tight clusters. But often, superfamilies of the same fold are linked with each other, suggesting that the entire fold evolved from an ancient prototype. Strikingly, some links connect superfamilies with different folds. They arise from modular peptide fragments of between 20 and 40 residues that co-occur in the connected folds in disparate structural contexts. These may be descendants of an ancestral pool of peptide modules that evolved as cofactors in the RNA world and from which the first folded proteins arose by amplification and recombination. Our galaxy of folds summarizes, in a single image, most known and many yet undescribed homologous relationships between protein superfamilies, providing new insights into the evolution of protein domains. PMID:19937658

  14. Biodegradation of Hexahydro-1,3,5-Trinitro-1,3,5-Triazine

    PubMed Central

    McCormick, N. G.; Cornell, J. H.; Kaplan, A. M.

    1981-01-01

    Biodegradation of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) occurs under anaerobic conditions, yielding a number of products, including: hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine, hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine, hexahydro-1,3,5-trinitroso-1,3,5-triazine, hydrazine, 1,1-dimethyl-hydrazine, 1,2-dimethylhydrazine, formaldehyde, and methanol. A scheme for the biodegradation of RDX is proposed which proceeds via successive reduction of the nitro groups to a point where destabilization and fragmentation of the ring occurs. The noncyclic degradation products arise via subsequent reduction and rearrangement reactions of the fragments. The scheme suggests the presence of several additional compounds, not yet identified. Several of the products are mutagenic or carcinogenic or both. Anaerobic treatment of RDX wastewaters, which also contain high nitrate levels, would permit the denitrification to occur, with concurrent degradation of RDX ultimately to a mixture of hydrazines and methanol. The feasibility of using an aerobic mode in the further degradation of these products is discussed. PMID:16345884

  15. Mathematics Through Paper Folding.

    ERIC Educational Resources Information Center

    Olson, Alton T.

    This booklet is a revised edition of Donovan Johnson's "Paper Folding for the Mathematics Class" (ED 077 711). It begins with directions for folding basic constructions such as as a straight line, the line perpendicular to a given line passing through a given point, and the bisector of an angle. Subsequent chapters cover concepts related to…

  16. Folding by Design

    NASA Astrophysics Data System (ADS)

    Dodd, Paul; Damasceno, Pablo; Glotzer, Sharon

    2014-03-01

    A form of self-assembly, ``self-folding'' presents an alternative approach to the creation of reconfigurable, responsive materials with applications ranging from robotics to drug design. However, the complexity of interactions present in biological and engineered systems that undergo folding makes it challenging to isolate the main factors controlling their assembly and dis-assembly. Here we use computer simulations of simple, minimalistic self-foldable structures and investigate their stochastic folding process. By dynamically accessing all the states that lead to, or inhibit, successful folding, we show that the mechanisms by which general stochastic systems can achieve their ``native'' structures can be identified and used to design rules for optimized folding propensity. Research supported by the National Science Foundation, Emerging Frontiers in Research and Innovation Award # EFRI-1240264.

  17. Distinguishing between sequential and nonsequentially folded proteins: implications for folding and misfolding.

    PubMed Central

    Tsai, C. J.; Maizel, J. V.; Nussinov, R.

    1999-01-01

    We describe here an algorithm for distinguishing sequential from nonsequentially folding proteins. Several experiments have recently suggested that most of the proteins that are synthesized in the eukaryotic cell may fold sequentially. This proposed folding mechanism in vivo is particularly advantageous to the organism. In the absence of chaperones, the probability that a sequentially folding protein will misfold is reduced significantly. The problem we address here is devising a procedure that would differentiate between the two types of folding patterns. Footprints of sequential folding may be found in structures where consecutive fragments of the chain interact with each other. In such cases, the folding complexity may be viewed as being lower. On the other hand, higher folding complexity suggests that at least a portion of the polypeptide backbone folds back upon itself to form three-dimensional (3D) interactions with noncontiguous portion(s) of the chain. Hence, we look at the mechanism of folding of the molecule via analysis of its complexity, that is, through the 3D interactions formed by contiguous segments on the polypeptide chain. To computationally splice the structure into consecutively interacting fragments, we either cut it into compact hydrophobic folding units or into a set of hypothetical, transient, highly populated, contiguous fragments ("building blocks" of the structure). In sequential folding, successive building blocks interact with each other from the amino to the carboxy terminus of the polypeptide chain. Consequently, the results of the parsing differentiate between sequentially vs. nonsequentially folded chains. The automated assessment of the folding complexity provides insight into both the likelihood of misfolding and the kinetic folding rate of the given protein. In terms of the funnel free energy landscape theory, a protein that truly follows the mechanism of sequential folding, in principle, encounters smoother free energy barriers

  18. Six-fold coordinated carbon dioxide VI.

    PubMed

    Iota, Valentin; Yoo, Choong-Shik; Klepeis, Jae-Hyun; Jenei, Zsolt; Evans, William; Cynn, Hyunchae

    2007-01-01

    Under standard conditions, carbon dioxide (CO2) is a simple molecular gas and an important atmospheric constituent, whereas silicon dioxide (SiO2) is a covalent solid, and one of the fundamental minerals of the planet. The remarkable dissimilarity between these two group IV oxides is diminished at higher pressures and temperatures as CO2 transforms to a series of solid phases, from simple molecular to a fully covalent extended-solid V, structurally analogous to SiO2 tridymite. Here, we present the discovery of an extended-solid phase of CO2: a six-fold coordinated stishovite-like phase VI, obtained by isothermal compression of associated CO2-II (refs 1,2) above 50 GPa at 530-650 K. Together with the previously reported CO2-V (refs 3-5) and a-carbonia, this extended phase indicates a fundamental similarity between CO2 (a prototypical molecular solid) and SiO2 (one of Earth's fundamental building blocks). We present a phase diagram with a limited stability domain for molecular CO2-I, and suggest that the conversion to extended-network solids above 40-50 GPa occurs via intermediate phases II (refs 1,2), III (refs 7,8) and IV (refs 9,10). The crystal structure of phase VI suggests strong disorder along the c axis in stishovite-like P42/mnm, with carbon atoms manifesting an average six-fold coordination within the framework of sp3 hybridization. PMID:17160005

  19. NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2009-07-01

    The performance of MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS SMOV as proposal 13555 {visit 5}.

  20. Hexahydro-1,3,5-trinitro-1,3,5-triazine translocation in poplar trees

    SciTech Connect

    Thompson, P.L.; Ramer, L.A.; Schnoor, J.L.

    1999-02-01

    This article evaluates the translocation of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in hybrid poplar trees (Populus deltoides x nigra, DN34) grown in hydroponic solutions. Mass balances with [U-{sup 14}C]RDX were used to assess RDX translocation. Up to 60% of the RDX uptaken by the tree accumulated in leaf tissues. Analysis of plant extracts by high-performance liquid chromatography equipped with radiochemical detection indicated that RDX was not significantly transformed during exposure periods of up to 7 d. The bioaccumulation of RDX may be an important concern for phytoremediation efforts.

  1. 1,3,5-Hydroxybenzene structures in mosses

    USGS Publications Warehouse

    Wilson, M.A.; Sawyer, J.; Hatcher, P.G.; Lerch, H. E.

    1989-01-01

    A number of mosses from widely different families have been studied by cross polarization solid state 13C NMR spectroscopy. Although polysaccharide-type materials dominate the NMR spectra, significant amounts of aromatic carbons are observed in some mosses. Some of this material can be removed by ultrasonic bath treatment, and is lignin derived, probably from impurities from fine root material from associated higher plants. However other material is truly moss-derived and appears to be from 1,3,5-hydroxybenzene structures. This is inconsistent with lignin as being a component of mosses, and suggests a tannin or hydroxybenzofuran polymer is responsible for moss rigidity. ?? 1989.

  2. Protein Folding Stages and Universal Exponents

    NASA Astrophysics Data System (ADS)

    Huang, Kerson

    We propose three stages in protein folding, based on physical arguements involving the interplay between the hydrophobic effect and hydrogen bonding, and computer simulations using the CSAW (conditioned self-avoiding walk) model. These stages are characterized by universal exponents ν = 3/5, 3/7, 2/5 in the power law R ~ Nν, where R is the radius of gyration and N is the number of residues. They correspond to the experimentally observed stages: unfolded, preglobule, molten globule.

  3. Protein Folding Stages and Universal Exponents

    NASA Astrophysics Data System (ADS)

    Huang, Kerson

    2011-11-01

    We propose three stages in protein folding, based on physical arguements involving the interplay between the hydrophobic effect and hydrogen bonding, and computer simulations using the CSAW (conditioned self-avoiding walk) model. These stages are characterized by universal exponents ν = 3/5, 3/7, 2/5 in the power law R ˜ Nν, where R is the radius of gyration and N is the number of residues. They correspond to the experimentally observed stages: unfolded, preglobule, molten globule.

  4. Stress and strain evolution of folding rocks

    NASA Astrophysics Data System (ADS)

    Llorens, Maria-Gema; Griera, Albert; Bons, Paul; Gomez-Rivas, Enrique; Weikusat, Ilka

    2015-04-01

    One of the main objectives of structural geology is to unravel rock deformation histories. Fold shapes can be used to estimate the orientation and amount of strain associated with folding. However, much more information on rheology and kinematics can potentially be extracted from fold geometries (Llorens et al., 2013a). We can study the development of folds, quantify the relationships between the different parameters that determine their geometries and estimate their mechanical evolution. This approach allows us to better understand and predict not only rock but also ice deformation. One of the main parameters in fold development is the viscosity contrast between the folding layer and the matrix in which it is embedded (m), since it determines the initial fold wavelength and the amplification rate of the developing folds. Moreover, non-linear viscous rheology influences fold geometry too (Llorens et al., 2013b). We present a series of 2-dimensional simulations of folding of viscous single layers in pure and simple shear. We vary different parameters in order to compare and determine their influence on the resulting fold patterns and the associated mechanical response of the material. To perform these simulations we use the software platform ELLE (www.elle.ws) with the non-linear viscous finite element code BASIL. The results show that layers thicken at the beginning of deformation in all simulations, and visible folds start earlier or later depending on the viscosity contrast. When folds start to nucleate the layer maximum shear strain decreases, moving away from the theoretical trend for homogeneous strain (no folding). This allows the accurate determination of the onset of folding. Maximum deviatoric stresses are higher in power-law than in linear-viscosity materials, and it is initially double in pure shear than in simple shear conditions. Therefore, folding a competent layer requires less work in simple than in pure shear. The maximum deviatoric stress

  5. Folding without charges

    PubMed Central

    Kurnik, Martin; Hedberg, Linda; Danielsson, Jens; Oliveberg, Mikael

    2012-01-01

    Surface charges of proteins have in several cases been found to function as “structural gatekeepers,” which avoid unwanted interactions by negative design, for example, in the control of protein aggregation and binding. The question is then if side-chain charges, due to their desolvation penalties, play a corresponding role in protein folding by avoiding competing, misfolded traps? To find out, we removed all 32 side-chain charges from the 101-residue protein S6 from Thermus thermophilus. The results show that the charge-depleted S6 variant not only retains its native structure and cooperative folding transition, but folds also faster than the wild-type protein. In addition, charge removal unleashes pronounced aggregation on longer timescales. S6 provides thus an example where the bias toward native contacts of a naturally evolved protein sequence is independent of charges, and point at a fundamental difference in the codes for folding and intermolecular interaction: specificity in folding is governed primarily by hydrophobic packing and hydrogen bonding, whereas solubility and binding relies critically on the interplay of side-chain charges. PMID:22454493

  6. Folds and Etudes

    ERIC Educational Resources Information Center

    Bean, Robert

    2007-01-01

    In this article, the author talks about "Folds" and "Etudes" which are images derived from anonymous typing exercises that he found in a used copy of "Touch Typing Made Simple". "Etudes" refers to the musical tradition of studies for a solo instrument, which is a typewriter. Typing exercises are repetitive attempts to type words and phrases…

  7. Modelling of lateral fold growth and fold linkage: Applications to fold-and-thrust belt tectonics

    NASA Astrophysics Data System (ADS)

    Grasemann, Bernhard; Schmalholz, Stefan

    2013-04-01

    We use a finite element model to investigate the three-dimensional fold growth and interference of two initially isolated fold segments. The most critical parameter, which controls the fold linkage mode, is the phase difference between the laterally growing fold hinge lines: 1) "Linear-linkage" yields a sub-cylindrical fold with a saddle at the location where the two initial folds linked. 2) "Oblique-linkage" produces a curved fold resembling a Type II refold structure. 3) "Oblique-no-linkage" results in two curved folds with fold axes plunging in opposite directions. 4) "Linear-no-linkage" yields a fold train of two separate sub-cylindrical folds with fold axes plunging in opposite directions. The transition from linkage to no-linkage occurs when the fold separation between the initially isolated folds is slightly larger than one half of the low-amplitude fold wavelength. The model results compare well with previously published plasticine analogue models and can be directly applied to the investigation of fold growth history in fold-and-thust belts. An excellent natural example of lateral fold linkage is described from the Zagros fold-and-thrust belt in the Kurdistan Region of Iraq. The fold growth in this region is not controlled by major thrust faults but the shortening of the Paleozoic to Cenozoic passive margin sediments of the Arabian plate occurred mainly by detachment folding. The sub-cylindrical anticlines with hinge-parallel lengths of more than 50 km have not developed from single sub-cylindrical embryonic folds but they have merged from different fold segments that joined laterally during fold amplification and lateral fold growth. Linkage points are marked by geomorphological saddle points which are structurally the lowermost points of antiforms and points of principal curvatures with opposite sign. Linkage points can significantly influence the migration of mineral-rich fluids and hydrocarbons and are therefore of great economic importance.

  8. Oxidative folding: recent developments.

    PubMed

    Szarka, András; Bánhegyi, Gábor

    2011-10-01

    Disulfide bond formation in proteins is an effective tool of both structure stabilization and redox regulation. The prokaryotic periplasm and the endoplasmic reticulum of eukaryotes were long considered as the only compartments for enzyme mediated formation of stable disulfide bonds. Recently, the mitochondrial intermembrane space has emerged as the third protein-oxidizing compartment. The classic view on the mechanism of oxidative folding in the endoplasmic reticulum has also been reshaped by new observations. Moreover, besides the structure stabilizing function, reversible disulfide bridge formation in some proteins of the endoplasmic reticulum, seems to play a regulatory role. This review briefly summarizes the present knowledge of the redox systems supporting oxidative folding, emphasizing recent developments. PMID:25962043

  9. The protein folding network

    NASA Astrophysics Data System (ADS)

    Rao, Francesco; Caflisch, Amedeo

    2004-03-01

    Networks are everywhere. The conformation space of a 20-residue antiparallel beta-sheet peptide [1], sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. As previously found for the World-Wide Web as well as for social and biological networks , the conformation space contains highly connected hubs like the native state which is the most populated free energy basin. Furthermore, the network shows a hierarchical modularity [2] which is consistent with the funnel mechanism of folding [3] and is not observed for a random heteropolymer lacking a native state. Here we show that the conformation space network describes the free energy landscape without requiring projections into arbitrarily chosen reaction coordinates. The network analysis provides a basis for understanding the heterogeneity of the folding transition state and the existence of multiple pathways. [1] P. Ferrara and A. Caflisch, Folding simulations of a three-stranded antiparallel beta-sheet peptide, PNAS 97, 10780-10785 (2000). [2] Ravasz, E. and Barabási, A. L. Hierarchical organization in complex networks. Phys. Rev. E 67, 026112 (2003). [3] Dill, K. and Chan, H From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10-19 (1997)

  10. Folded waveguide coupler

    DOEpatents

    Owens, Thomas L.

    1988-03-01

    A resonant cavity waveguide coupler for ICRH of a magnetically confined plasma. The coupler consists of a series of inter-leaved metallic vanes disposed withn an enclosure analogous to a very wide, simple rectangular waveguide that has been "folded" several times. At the mouth of the coupler, a polarizing plate is provided which has coupling apertures aligned with selected folds of the waveguide through which rf waves are launched with magnetic fields of the waves aligned in parallel with the magnetic fields confining the plasma being heated to provide coupling to the fast magnetosonic wave within the plasma in the frequency usage of from about 50-200 mHz. A shorting plate terminates the back of the cavity at a distance approximately equal to one-half the guide wavelength from the mouth of the coupler to ensure that the electric field of the waves launched through the polarizing plate apertures are small while the magnetic field is near a maximum. Power is fed into the coupler folded cavity by means of an input coaxial line feed arrangement at a point which provides an impedance match between the cavity and the coaxial input line.

  11. Ab initio RNA folding

    NASA Astrophysics Data System (ADS)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-01

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  12. Water quality criteria for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).

    PubMed

    Etnier, E L

    1989-04-01

    The occurrence of the munitions compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in groundwater surrounding Army ammunition plants may result in contamination of local drinking water supplies. RDX exerts its primary toxic effect in humans on the central nervous system, but also involves gastrointestinal and renal effects. Symptomatic effects following acute exposure include hyperirritability, nausea, vomiting, generalized epileptiform seizures, and prolonged postictal confusion and amnesia. Health effects data were analyzed for RDX, and although no controlled human studies exist concerning the acute or chronic toxic effects of exposure to RDX, sufficient animal toxicity data are available to derive an ambient water quality criterion for the protection of human health. This paper summarizes the available literature on metabolism of RDX and human and animal toxicity. Based on noncarcinogenic mammalian toxicity data, and following the methodologies of the U.S. Environmental Protection Agency, an ambient water quality criterion for the protection of human health of 103 micrograms/liter is proposed for ingestion of drinking water and aquatic foodstuffs. A criterion of 105 micrograms/liter is proposed for ingestion of drinking water alone.

  13. Water quality criteria for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)

    SciTech Connect

    Etnier, E.L.

    1989-04-01

    The occurrence of the munitions compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in groundwater surrounding Army ammunition plants may result in contamination of local drinking water supplies. RDX exerts its primary toxic effect in humans on the central nervous system, but also involves gastrointestinal and renal effects. Symptomatic effects following acute exposure include hyperirritability, nausea, vomiting, generalized epileptiform seizures, and prolonged postictal confusion and amnesia. Health effects data were analyzed for RDX, and although no controlled human studies exist concerning the acute or chronic toxic effects of exposure to RDX, sufficient animal toxicity data are available to derive an ambient water quality criterion for the protection of human health. This paper summarizes the available literature on metabolism of RDX and human and animal toxicity. Based on noncarcinogenic mammalian toxicity data, and following the methodologies of the U.S. Environmental Protection Agency, an ambient water quality criterion for the protection of human health of 103 micrograms/liter is proposed for ingestion of drinking water and aquatic foodstuffs. A criterion of 105 micrograms/liter is proposed for ingestion of drinking water alone.54 references.

  14. Purification and characterization of DNase VII, a 3'. -->. 5'-directed exonuclease from human placenta

    SciTech Connect

    Hollis, G.F.; Grossman, L.

    1981-01-01

    An exonuclease, DNase VII, has been purified 6000-fold from human placenta. The enzyme has an apparent molecular weight of 43,000, requires Mg/sup 2 +/ for activity, and has a pH optimum of 7.8. The enzyme hydrolyzes single-stranded and nicked duplex DNA at the same rate proceeding in a 3' ..-->.. 5' direction liberating 5'-mononucleotides. It does not measurably hydrolyze polyribonucleotides.

  15. Preparation of 1,3,5-triamino-2,4,6-trinitrobenzene from 3,5-dichloroanisole

    SciTech Connect

    Ott, Donald G.; Benziger, Theodore M.

    1991-01-01

    Preparation of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) from 3,5-dichloroanisole. Nitration of 3,5-dichloroanisole under relatively mild conditions gave 3,5-dichloro-2,4,6-trinitroanisole in high yield and purity. Ammonolysis of this latter compound gave the desired TATB. Another route to TATB was through the treatment of the 3,5-dichloro-2,4,6-trinitroanisole with thionyl chloride and dimethylformamide to yield 1,3,5-trichloro-2,4,6-trinitrobenzene. Ammonolysis of this product produced TATB.

  16. Preparation of 1,3,5-triamino-2,4,6-trinitrobenzene from 3,5-dichloroanisole

    SciTech Connect

    Ott, D.G.; Benziger, T.M.

    1991-03-05

    Preparation of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) from 3,5-dichloroanisole is described. Nitration of 3,5-dichloroanisole under relatively mild conditions gave 3,5-dichloro-2,4,6-trinitroanisole in high yield and purity. Ammonolysis of this latter compound gave the desired TATB. Another route to TATB was through the treatment of the 3,5-dichloro-2,4,6-trinitroanisole with thionyl chloride and dimethylformamide to yield 1,3,5-trichloro-2,4,6-trinitrobenzene. Ammonolysis of this product produced TATB. 8 figures.

  17. Preparation of 1,3,5-triamino-2,4,6-trinitrobenzene from 3,5-dichloranisole

    SciTech Connect

    Ott, Donald G.; Benziger, Theodore M.

    1990-01-01

    Preparation of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) from 3,5-dichloroanisole. Nitration of 3,5-dichloroanisole under relatively mild conditions gave 3,5-dichloro-2,4,6-trinitroanisole in high yield and purity. Ammonolysis of this latter compound gave the desired TATB. Another route to TATB was through the treatment of the 3,5-dichloro-2,4,6-trinitroanisole with thionyl chloride and dimethylformamide to yield 1,3,5-trichloro-2,4,6-trinitrobenzene. Ammonolysis of this product produced TATB.

  18. Molecular dynamics characterization of void defects in crystalline (1,3,5-trinitro-1,3,5-triazacyclohexane).

    PubMed

    Boyd, Sylke; Murray, Jane S; Politzer, Peter

    2009-11-28

    In the context of a continuing investigation of factors that affect the sensitivities of energetic materials to detonation initiation, we have carried out a molecular dynamics characterization of void defects in crystalline (1,3,5-trinitro-1,3,5-triazacyclo-hexane). An empirical force field that is capable of handling flexible molecules in a pliable crystal was used. Voids ranging in size from 2 to 30 adjacent vacated sites were created in model lattices of 216 or 512 molecules. Energetic and geometric ground state properties were determined. The void formation energy per molecule removed was found to decrease from 50 kcal/mol for a single vacancy to about 23+/-2 kcal/mol for voids larger than one unit cell (8 molecules). Analysis of the local binding energies in the vicinity of a void reveals not only the expected decrease for molecules directly on the void surface but also a wide spread of values in the first 5-10 A away from the surface; this includes some molecules with local binding energies significantly higher than in the defect-free lattice. Molecular conformational changes and reorientations begin to be found in the vicinities of voids larger than one unit cell. Thermal behavior investigated includes void and molecular diffusion coefficients and fluctuations in void size. PMID:19947705

  19. Folding of Pollen Grains

    NASA Astrophysics Data System (ADS)

    Katifori, Eleni; Alben, Silas; Cerda, Enrique; Nelson, David; Dumais, Jacques

    2008-03-01

    At dehiscence, which occurs when the anther reaches maturity and opens, pollen grains dehydrate and their volume is reduced. The pollen wall deforms to accommodate the volume loss, and the deformation pathway depends on the initial turgid pollen grain geometry and the mechanical properties of the pollen wall. We demonstrate, using both experimental and theoretical approaches, that the design of the apertures (areas on the pollen wall where the stretching and the bending modulus are reduced) is critical for controlling the folding pattern, and ensures the pollen grain viability. An excellent fit to the experiments is obtained using a discretized version of the theory of thin elastic shells.

  20. Thermodynamic characterization of an equilibrium folding intermediate of staphylococcal nuclease.

    PubMed Central

    Xie, D.; Fox, R.; Freire, E.

    1994-01-01

    High-sensitivity differential scanning calorimetry and CD spectroscopy have been used to probe the structural stability and measure the folding/unfolding thermodynamics of a Pro117-->Gly variant of staphylococcal nuclease. It is shown that at neutral pH the thermal denaturation of this protein is well accounted for by a 2-state mechanism and that the thermally denatured state is a fully hydrated unfolded polypeptide. At pH 3.5, thermal denaturation results in a compact denatured state in which most, if not all, of the helical structure is missing and the beta subdomain apparently remains largely intact. At pH 3.0, no thermal transition is observed and the molecule exists in the compact denatured state within the 0-100 degrees C temperature interval. At high salt concentration and pH 3.5, the thermal unfolding transition exhibits 2 cooperative peaks in the heat capacity function, the first one corresponding to the transition from the native to the intermediate state and the second one to the transition from the intermediate to the unfolded state. As is the case with other proteins, the enthalpy of the intermediate is higher than that of the unfolded state at low temperatures, indicating that, under those conditions, its stabilization must be of an entropic origin. The folding intermediate has been modeled by structural thermodynamic calculations. Structure-based thermodynamic calculations also predict that the most probable intermediate is one in which the beta subdomain is essentially intact and the rest of the molecule unfolded, in agreement with the experimental data. The structural features of the equilibrium intermediate are similar to those of a kinetic intermediate previously characterized by hydrogen exchange and NMR spectroscopy. PMID:7756977

  1. Structural Characteristics of Novel Protein Folds

    PubMed Central

    Fernandez-Fuentes, Narcis; Dybas, Joseph M.; Fiser, Andras

    2010-01-01

    Folds are the basic building blocks of protein structures. Understanding the emergence of novel protein folds is an important step towards understanding the rules governing the evolution of protein structure and function and for developing tools for protein structure modeling and design. We explored the frequency of occurrences of an exhaustively classified library of supersecondary structural elements (Smotifs), in protein structures, in order to identify features that would define a fold as novel compared to previously known structures. We found that a surprisingly small set of Smotifs is sufficient to describe all known folds. Furthermore, novel folds do not require novel Smotifs, but rather are a new combination of existing ones. Novel folds can be typified by the inclusion of a relatively higher number of rarely occurring Smotifs in their structures and, to a lesser extent, by a novel topological combination of commonly occurring Smotifs. When investigating the structural features of Smotifs, we found that the top 10% of most frequent ones have a higher fraction of internal contacts, while some of the most rare motifs are larger, and contain a longer loop region. PMID:20421995

  2. Protein photo-folding and quantum folding theory.

    PubMed

    Luo, Liaofu

    2012-06-01

    The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from quantum folding theory by use of a field-theoretical method. All protein photo-folding processes are compared with common protein folding without the interaction of photons (non-radiative folding). It is demonstrated that there exists a common factor (thermo-averaged overlap integral of the vibration wave function, TAOI) for protein folding and protein photo-folding. Based on this finding it is predicted that (i) the stimulated photo-folding rates and the photon-protein resonance Raman scattering sections show the same temperature dependence as protein folding; (ii) the spectral line of the electronic transition is broadened to a band that includes an abundant vibration spectrum without and with conformational transitions, and the width of each vibration spectral line is largely reduced. The particular form of the folding rate-temperature relation and the abundant spectral structure imply the existence of quantum tunneling between protein conformations in folding and photo-folding that demonstrates the quantum nature of the motion of the conformational-electronic system.

  3. Preparation of 1,3,5-triamino-2,4,6-trinitrobenzene from 3,5-dichloranisole

    SciTech Connect

    Oh, D.G.; Benziger, T.M.

    1990-08-28

    This patent describes the preparation of 1,3,5-triamino-2,4,6- trinitrobenzene (TATB) from 2,5-dichloroanisole. Nitration of 3,5- dichloroanisole under relatively mild conditions gave 3,5-dichloro-2,4,6- trinitroanisole in high yield and purity. Ammonolysis of this latter compound gave the desired TATB. Another route to TATB was through the treatment of the 3,5-dichloro-2,4,6-trinitroanisole with thionyl chloride and dimethylformamide to yield 1,3,5-trichloro-2,4,6- trinitrobenzene. Ammonolysis of this product produced TATB.

  4. Folded pendulum tiltmeter

    NASA Astrophysics Data System (ADS)

    Wu, Shuchao; Fan, Shuhua; Luo, Jun; Hsu, Houtse

    2002-05-01

    The application of the folded pendulum (FP) as a tiltmeter is proposed and some features of it have been studied both theoretically and experimentally. First, FP could have a quite low resonance frequency due to its mechanical structure. The period of our prototype FP is 6.2 s and the amplification factor is about 100. Second, FP is not sensitive to the environmental temperature variation but seriously affected by the temperature gradient. The experiment with a temperature gradient modulation shows that the static equilibrium position of the FP will change by 2.5 μrad if the temperature difference between the horizontal platform and the base of the FP is 0.1 °C. With a prototype FP, we have observed obvious tilt tides, and the calibration result shows that the resolution of the FP is about 1.2 nrad.

  5. Cellular folding pathway of a metastable serpin.

    PubMed

    Chandrasekhar, Kshama; Ke, Haiping; Wang, Ning; Goodwin, Theresa; Gierasch, Lila M; Gershenson, Anne; Hebert, Daniel N

    2016-06-01

    Although proteins generally fold to their thermodynamically most stable state, some metastable proteins populate higher free energy states. Conformational changes from metastable higher free energy states to lower free energy states with greater stability can then generate the work required to perform physiologically important functions. However, how metastable proteins fold to these higher free energy states in the cell and avoid more stable but inactive conformations is poorly understood. The serpin family of metastable protease inhibitors uses large conformational changes that are downhill in free energy to inhibit target proteases by pulling apart the protease active site. The serpin antithrombin III (ATIII) targets thrombin and other proteases involved in blood coagulation, and ATIII misfolding can thus lead to thrombosis and other diseases. ATIII has three disulfide bonds, two near the N terminus and one near the C terminus. Our studies of ATIII in-cell folding reveal a surprising, biased order of disulfide bond formation, with early formation of the C-terminal disulfide, before formation of the N-terminal disulfides, critical for folding to the active, metastable state. Early folding of the predominantly β-sheet ATIII domain in this two-domain protein constrains the reactive center loop (RCL), which contains the protease-binding site, ensuring that the RCL remains accessible. N-linked glycans and carbohydrate-binding molecular chaperones contribute to the efficient folding and secretion of functional ATIII. The inability of a number of disease-associated ATIII variants to navigate the folding reaction helps to explain their disease phenotypes. PMID:27222580

  6. 39 CFR 3.5 - Delegation of authority by Board.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 39 Postal Service 1 2014-07-01 2014-07-01 false Delegation of authority by Board. 3.5 Section 3.5 Postal Service UNITED STATES POSTAL SERVICE THE BOARD OF GOVERNORS OF THE U.S. POSTAL SERVICE BOARD OF GOVERNORS (ARTICLE III) § 3.5 Delegation of authority by Board. As authorized by 39 U.S.C. 402, these bylaws delegate to the Postmaster General...

  7. How the genome folds

    NASA Astrophysics Data System (ADS)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  8. Protein folding in the ER.

    SciTech Connect

    Stevens, F. J.; Argon, Y.; Biosciences Division; Univ. of Chicago

    1999-10-01

    The endoplasmic reticulum (ER) is a major protein folding compartment for secreted, plasma membrane and organelle proteins. Each of these newly-synthesized polypeptides folds in a deterministic process, affected by the unique conditions that exist in the ER. An understanding of protein folding in the ER is a fundamental biomolecular challenge at two levels. The first level addresses how the amino acid sequence programs that polypeptide to efficiently arrive at a particular fold out of a multitude of alternatives, and how different sequences obtain similar folds. At the second level are the issues introduced by folding not in the cytosol, but in the ER, including the risk of aggregation in a molecularly crowded environment, accommodation of post-translational modifications and the compatibility with subsequent intracellular trafficking. This review discusses both the physicochemical and cell biological constraints of folding, which are the challenges that the ER molecular chaperones help overcome.

  9. Administration of 3,5-diiodothyronine (3,5-T2) causes central hypothyroidism and stimulates thyroid-sensitive tissues.

    PubMed

    Padron, Alvaro Souto; Neto, Ruy Andrade Louzada; Pantaleão, Thiago Urgal; de Souza dos Santos, Maria Carolina; Araujo, Renata Lopes; de Andrade, Bruno Moulin; da Silva Leandro, Monique; de Castro, João Pedro Saar Werneck; Ferreira, Andrea Claudia Freitas; de Carvalho, Denise Pires

    2014-06-01

    In general, 3,5-diiodothyronine (3,5-T2) increases the resting metabolic rate and oxygen consumption, exerting short-term beneficial metabolic effects on rats subjected to a high-fat diet. Our aim was to evaluate the effects of chronic 3,5-T2 administration on the hypothalamus-pituitary-thyroid axis, body mass gain, adipose tissue mass, and body oxygen consumption in Wistar rats from 3 to 6 months of age. The rats were treated daily with 3,5-T2 (25, 50, or 75 μg/100 g body weight, s.c.) for 90 days between the ages of 3 and 6 months. The administration of 3,5-T2 suppressed thyroid function, reducing not only thyroid iodide uptake but also thyroperoxidase, NADPH oxidase 4 (NOX4), and thyroid type 1 iodothyronine deiodinase (D1 (DIO1)) activities and expression levels, whereas the expression of the TSH receptor and dual oxidase (DUOX) were increased. Serum TSH, 3,3',5-triiodothyronine, and thyroxine were reduced in a 3,5-T2 dose-dependent manner, whereas oxygen consumption increased in these animals, indicating the direct action of 3,5-T2 on this physiological variable. Type 2 deiodinase activity increased in both the hypothalamus and the pituitary, and D1 activities in the liver and kidney were also increased in groups treated with 3,5-T2. Moreover, after 3 months of 3,5-T2 administration, body mass and retroperitoneal fat pad mass were significantly reduced, whereas the heart rate and mass were unchanged. Thus, 3,5-T2 acts as a direct stimulator of energy expenditure and reduces body mass gain; however, TSH suppression may develop secondary to 3,5-T2 administration.

  10. Bioavailability of Hexahydro-1,3,5-Trinitro-1,3,5-Triazine (RDX) to the Praire Vole (Microtus ochrogaster).

    SciTech Connect

    Fellows, Robert J.; Driver, Crystal J.; Cataldo, Dominic A.; Harvey, Scott D.

    2006-07-01

    Estimating risk to wildlife requires that measures of exposure be equivalent to that of the laboratory studies from which toxic responses were observed. Exposure measures are often based on modeled estimates of uptake through the food web. These modeled estimates use largely untested assumptions that can lead to inaccurate, uncertain, and unreliable estimates of exposure. Recently, concerns have been raised over the potential bioavailability and biotransfer of munitions or energetics materials such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). RDX is more recalcitrant in the soil, may remain as the parent compound for extended periods of time, and is rapidly taken up by the roots of higher plants and partitioned predominantly into the above ground, herbivore-accessible tissues. This study assessed plant incorporated [14C]-RDX and plant derived [14C]-RDX-metabolites ingestion by a representative hindgut herbivore, the prairie vole (Microtus ochrogaster). The animals were fed the labeled chow (≤10 g/ day max) for five or seven days followed by a six or four day chase period with the control chow prior to final weighing and sacrifice. Animal excreta including feces, urine, and respired CO2 were collected and measured. Greater than 95% of all label presented to the voles was recovered in the summed excreta. Seventy-four percent of the label in the total excreta was found in the fecal non-absorbed bulk. This means that greater than 20% of the presented 14C-RDX and plant-derived 14C-RDX-metabolites were absorbed by the animal’s digestive tracts over the time course of the experiment and modified prior to release. These materials were either metabolized to 14CO2 (8 to 10% of the total label) or removed as nitrogenous waste through the kidneys (10 to 14%). The feeding regimes were followed by a rapid, 2 to 3 day, clearing of label from the bulk feces with the cessation of exposure. Both 14C-urine and 14CO2 excretion continued after the feces cleared indicating

  11. 43 CFR 9269.3-5 - Timber management.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false Timber management. 9269.3-5 Section 9269.3-5 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT... Timber management. (a) Sales of forest products; general. (b) Non-sale disposals;...

  12. 43 CFR 9269.3-5 - Timber management.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false Timber management. 9269.3-5 Section 9269.3-5 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT... Timber management. (a) Sales of forest products; general. (b) Non-sale disposals;...

  13. 43 CFR 9269.3-5 - Timber management.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 2 2012-10-01 2012-10-01 false Timber management. 9269.3-5 Section 9269.3-5 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT... Timber management. (a) Sales of forest products; general. (b) Non-sale disposals;...

  14. 40 CFR 721.1055 - Benzeneamine, 3,5-difluoro-.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances § 721.1055 Benzeneamine, 3,5-difluoro-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as benzeneamine, 3,5-difluoro- (PMN P-97-648; CAS No....

  15. Rethinking the biological relationships of the thyroid hormones, l-thyroxine and 3,5,3'-triiodothyronine.

    PubMed

    Maher, Stacey K; Wojnarowicz, Pola; Ichu, Taka-Aki; Veldhoen, Nik; Lu, Linghong; Lesperance, Mary; Propper, Catherine R; Helbing, Caren C

    2016-06-01

    Thyroid hormones (THs), l-thyroxine (T4) and 3,5,3'-triiodothyronine (T3), are essential for vertebrate growth and development. Classically, T4 is 5'-deiodinated to the active hormone, T3, in target tissues which then binds nuclear TH receptors (TRs) and regulates gene transcription. However, it is possible that T4 acts directly on target tissues. Frog metamorphosis is a powerful TR-dependent model for studying TH action. Premetamorphic Rana (Lithobates) catesbeiana tadpoles were injected with 0.1-50 T3 or 0.5-250T4pmol/gbodyweight to account for their 5-fold difference in biological activity and the mRNA profiles in six tissues from well-characterized TH-responsive genes were evaluated after 48h using quantitative real time polymerase chain reaction. 5'-deiodinase-poor tissues should produce superimposable dose-response curves if T4 does not require conversion to T3. This was the case in lung and tail fin; the latter tissue recapitulating these responses in organ culture. 5'-deiodinase-rich tissues should convert T4 to T3. Because T3 has a higher affinity to TRs, a 5-fold higher T4 dose compared to T3 should produce greater transcript induction. This was observed in the brain and for most intestinal transcripts. However, some gene transcripts in the intestine and all transcripts in the back skin produced superimposable response curves suggesting that a direct mode of T4 action is plausible in these tissues. While the liver showed results consistent with its 5'-deiodinase-poor status, we found evidence of an alternate, non-genomic mechanism for two gene transcripts. Therefore, mechanisms not requiring T4 conversion to T3 may play a far greater role than previously thought. PMID:27085304

  16. Evolutionary optimization of protein folding.

    PubMed

    Debès, Cédric; Wang, Minglei; Caetano-Anollés, Gustavo; Gräter, Frauke

    2013-01-01

    Nature has shaped the make up of proteins since their appearance, [Formula: see text]3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last [Formula: see text]1.5 billion years that began during the "big bang" of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions. PMID:23341762

  17. 3D fold growth rates in transpressional tectonic settings

    NASA Astrophysics Data System (ADS)

    Frehner, Marcel

    2015-04-01

    Geological folds are inherently three-dimensional (3D) structures; hence, they also grow in 3D. In this study, fold growth in all three dimensions is quantified numerically using a finite-element algorithm for simulating deformation of Newtonian media in 3D. The presented study is an extension and generalization of the work presented in Frehner (2014), which only considered unidirectional layer-parallel compression. In contrast, the full range from strike slip settings (i.e., simple shear) to unidirectional layer-parallel compression is considered here by varying the convergence angle of the boundary conditions; hence the results are applicable to general transpressional tectonic settings. Only upright symmetrical single-layer fold structures are considered. The horizontal higher-viscous layer exhibits an initial point-like perturbation. Due to the mixed pure- and simple shear boundary conditions a mechanical buckling instability grows from this perturbation in all three dimensions, described by: Fold amplification (vertical growth): Fold amplification describes the growth from a fold shape with low limb-dip angle to a shape with higher limb-dip angle. Fold elongation (growth parallel to fold axis): Fold elongation describes the growth from a dome-shaped (3D) structure to a more cylindrical fold (2D). Sequential fold growth (growth perpendicular to fold axial plane): Sequential fold growth describes the growth of secondary (and further) folds adjacent to the initial isolated fold. The term 'lateral fold growth' is used as an umbrella term for both fold elongation and sequential fold growth. In addition, the orientation of the fold axis is tracked as a function of the convergence angle. Even though the absolute values of all three growth rates are markedly reduced with increasing simple-shear component at the boundaries, the general pattern of the quantified fold growth under the studied general-shear boundary conditions is surprisingly similar to the end

  18. Identification of ovine ruminal microbes capable of biotransforming hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bioremediation is of great interest in the detoxification of soil contaminated with residues from explosives such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Although there are numerous forms of in situ and ex situ bioremediation, ruminants would provide the option of an in situ bioreactor tha...

  19. IRIS Toxicological Review of Hexahydro-1,3,5-Trinitro-1,3,5-Triazine (Rdx) (Interagency Science Consultation Draft)

    EPA Science Inventory

    On March 10, 2016, the public comment draft Toxicological Review of Hexahydro-1,3,5-trinitro-1,3,5-triazine and the draft charge to external peer reviewers were released for public review and comment. The Toxicological Review and charge were reviewed internally by EPA and by othe...

  20. IRIS Toxicological Review of Hexahydro-1,3,5-Trinitro-1,3,5-Triazine (Rdx) (Public Comment Draft)

    EPA Science Inventory

    EPA is developing an Integrated Risk Information System (IRIS) assessment of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and has released the draft assessment for public comment. When final, the assessment will appear on the IRIS database.

  1. IRIS Toxicological Review of Hexahydro-1,3,5-Trinitro-1,3,5-Triazine (Rdx) (External Review Draft)

    EPA Science Inventory

    The IRIS Toxicological Review of Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) was released for external peer review in September 2016. The EPA’s Science Advisory Board’s (SAB) Chemical Assessment Advisory Committee (CAAC) will conduct a peer review of the scientific basis suppor...

  2. Early Events in RNA Folding

    NASA Astrophysics Data System (ADS)

    Thirumalai, D.; Lee, Namkyung; Woodson, Sarah A.; Klimov, Dk

    2001-10-01

    We describe a conceptual framework for understanding the way large RNA molecules fold based on the notion that their free-energy landscape is rugged. A key prediction of our theory is that RNA folding can be described by the kinetic partitioning mechanism (KPM). According to KPM a small fraction of molecules folds rapidly to the native state whereas the remaining fraction is kinetically trapped in a low free-energy non-native state. This model provides a unified description of the way RNA and proteins fold. Single-molecule experiments on Tetrahymena ribozyme, which directly validate our theory, are analyzed using KPM. We also describe the earliest events that occur on microsecond time scales in RNA folding. These must involve collapse of RNA molecules that are mediated by counterion-condensation. Estimates of time scales for the initial events in RNA folding are provided for the Tetrahymena ribozyme.

  3. Kinetic Intermediates in RNA Folding

    NASA Astrophysics Data System (ADS)

    Zarrinkar, Patrick P.; Williamson, James R.

    1994-08-01

    The folding pathways of large, highly structured RNA molecules are largely unexplored. Insight into both the kinetics of folding and the presence of intermediates was provided in a study of the Mg2+-induced folding of the Tetrahymena ribozyme by hybridization of complementary oligodeoxynucleotide probes. This RNA folds via a complex mechanism involving both Mg2+-dependent and Mg2+-independent steps. A hierarchical model for the folding pathway is proposed in which formation of one helical domain (P4-P6) precedes that of a second helical domain (P3-P7). The overall rate-limiting step is formation of P3-P7, and takes place with an observed rate constant of 0.72 ± 0.14 minute-1. The folding mechanism of large RNAs appears similar to that of many multidomain proteins in that formation of independently stable substructures precedes their association into the final conformation.

  4. Graphene folding on flat substrates

    SciTech Connect

    Chen, Xiaoming; Zhao, Yadong; Ke, Changhong; Zhang, Liuyang; Wang, Xianqiao

    2014-10-28

    We present a combined experimental-theoretical study of graphene folding on flat substrates. The structure and deformation of the folded graphene sheet are experimentally characterized by atomic force microscopy. The local graphene folding behaviors are interpreted based on nonlinear continuum mechanics modeling and molecular dynamics simulations. Our study on self-folding of a trilayer graphene sheet reports a bending stiffness of about 6.57 eV, which is about four times the reported values for monolayer graphene. Our results reveal that an intriguing free sliding phenomenon occurs at the interlayer van der Waals interfaces during the graphene folding process. This work demonstrates that it is a plausible venue to quantify the bending stiffness of graphene based on its self-folding conformation on flat substrates. The findings reported in this work are useful to a better understanding of the mechanical properties of graphene and in the pursuit of its applications.

  5. COS NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2010-09-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS MAMA Fold Analysis {11891} during Cycle 17.

  6. COS NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2012-10-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS MAMA Fold Analysis {12723} during Cycle 19.

  7. Compact intermediates in RNA folding

    SciTech Connect

    Woodson, S.A.

    2011-12-14

    Large noncoding RNAs fold into their biologically functional structures via compact yet disordered intermediates, which couple the stable secondary structure of the RNA with the emerging tertiary fold. The specificity of the collapse transition, which coincides with the assembly of helical domains, depends on RNA sequence and counterions. It determines the specificity of the folding pathways and the magnitude of the free energy barriers to the ensuing search for the native conformation. By coupling helix assembly with nascent tertiary interactions, compact folding intermediates in RNA also play a crucial role in ligand binding and RNA-protein recognition.

  8. Folding superfunnel to describe cooperative folding of interacting proteins.

    PubMed

    Smeller, László

    2016-07-01

    This paper proposes a generalization of the well-known folding funnel concept of proteins. In the funnel model the polypeptide chain is treated as an individual object not interacting with other proteins. Since biological systems are considerably crowded, protein-protein interaction is a fundamental feature during the life cycle of proteins. The folding superfunnel proposed here describes the folding process of interacting proteins in various situations. The first example discussed is the folding of the freshly synthesized protein with the aid of chaperones. Another important aspect of protein-protein interactions is the folding of the recently characterized intrinsically disordered proteins, where binding to target proteins plays a crucial role in the completion of the folding process. The third scenario where the folding superfunnel is used is the formation of aggregates from destabilized proteins, which is an important factor in case of several conformational diseases. The folding superfunnel constructed here with the minimal assumption about the interaction potential explains all three cases mentioned above. Proteins 2016; 84:1009-1016. © 2016 Wiley Periodicals, Inc.

  9. Polar switching in trialkylbenzene-1,3,5-tricarboxamides.

    PubMed

    Fitié, Carel F C; Roelofs, W S Christian; Magusin, Pieter C M M; Wübbenhorst, Michael; Kemerink, Martijn; Sijbesma, Rint P

    2012-04-01

    The hydrogen-bonded hexagonal columnar LC (Col(hd)) phases formed by benzene-1,3,5-tricarboxamide (BTA) derivatives can be aligned uniformly by an electric field and display switching behavior with a high remnant polarization. The polar switching in three symmetrically substituted BTAs with alkyl chains varying in length between 6 and 18 carbon atoms (C6, C10, and C18) was investigated by electro-optical switching experiments, dielectric relaxation spectroscopy (DRS), and solid-state NMR. The goal was to characterize ferroelectric properties of BTA-based columnar LCs, which display a macroscopic axial dipole moment due to the head-to-tail stacking of hydrogen-bonded amides. The Col(hd) phase of all three BTAs can be aligned uniformly by a dc field ∼30 V/μm. Moreover, C10 and C18 display extrinsic polar switching characterized by a remnant polarization and coercive field of 1-2 μC/cm(2) and 20-30 V/μm, respectively. In the absence of an external field, the polarization is lost in 1-1000 s, depending on device details and temperature. DRS revealed a columnar glass transition in the low-temperature region of the LC phase related to collective vibrations in the hydrogen-bonded columns that freeze out below 41-54 °C. At higher temperatures, a relaxation process is present originating from the collective reorientation of amide groups along the column axis (inversion of the macrodipole). Matching activation energies suggest that the molecular mechanism underlying the polar switching and the R-processes is identical. These results illustrate that LC phases based on BTAs offer the unique possibility to integrate polarization with other functionalities in a single nanostructured material.

  10. Flexural shear in a periclinal fold from the Irish Variscides

    NASA Astrophysics Data System (ADS)

    Bamford, Maurice L. F.; Ford, Mary

    Periclinal folds occur in a structural culmination in the centre of the Irish Variscan fold belt. The culmination marks a zone of enhanced shortening which is associated with a locally attenuated stratigraphy and an anomalous deformation sequence with respect to the remainder of the orogen. Originally vertical burrows have been used, along with cleavage-fold relations, to study both the three-dimensional evolution of the periclinal folding and the temporal relationship between folding and cleavage. As well as cleavage-forming flattening strains, the burrows record along-strike shear related to the propagation of the periclinal folds. A comparison with strain measurements made outside the culmination zone shows that the Galley Head area suffered higher strains. Integration of field data with published analyses of plasticine modelling of periclinal folds yields models for the propagation of a pericline and for the geometry of its lateral terminations.

  11. Pseudoknots in RNA folding landscapes

    PubMed Central

    Kucharík, Marcel; Hofacker, Ivo L.; Stadler, Peter F.; Qin, Jing

    2016-01-01

    Motivation: The function of an RNA molecule is not only linked to its native structure, which is usually taken to be the ground state of its folding landscape, but also in many cases crucially depends on the details of the folding pathways such as stable folding intermediates or the timing of the folding process itself. To model and understand these processes, it is necessary to go beyond ground state structures. The study of rugged RNA folding landscapes holds the key to answer these questions. Efficient coarse-graining methods are required to reduce the intractably vast energy landscapes into condensed representations such as barrier trees or basin hopping graphs (BHG) that convey an approximate but comprehensive picture of the folding kinetics. So far, exact and heuristic coarse-graining methods have been mostly restricted to the pseudoknot-free secondary structures. Pseudoknots, which are common motifs and have been repeatedly hypothesized to play an important role in guiding folding trajectories, were usually excluded. Results: We generalize the BHG framework to include pseudoknotted RNA structures and systematically study the differences in predicted folding behavior depending on whether pseudoknotted structures are allowed to occur as folding intermediates or not. We observe that RNAs with pseudoknotted ground state structures tend to have more pseudoknotted folding intermediates than RNAs with pseudoknot-free ground state structures. The occurrence and influence of pseudoknotted intermediates on the folding pathway, however, appear to depend very strongly on the individual RNAs so that no general rule can be inferred. Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and Supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html. Contact: qin@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID

  12. Phosphatidylinositol 3,5-bisphosphate: metabolism and cellular functions.

    PubMed

    Michell, Robert H; Heath, Victoria L; Lemmon, Mark A; Dove, Stephen K

    2006-01-01

    Polyphosphoinositides (PPIn) are low-abundance membrane phospholipids that each bind to a distinctive set of effector proteins and, thereby, regulate a characteristic suite of cellular processes. Major functions of phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P(2)] are in membrane and protein trafficking, and in pH control in the endosome-lysosome axis. Recently identified PtdIns(3,5)P(2) effectors include a family of novel beta-propeller proteins, for which we propose the name PROPPINs [for beta-propeller(s) that binds PPIn], and possibly proteins of the epsin and CHMP (charged multi-vesicular body proteins) families. All eukaryotes, with the exception of some pathogenic protists and microsporidians, possess proteins needed for the formation, metabolism and functions of PtdIns(3,5)P(2). The importance of PtdIns(3,5)P(2) for normal cell function is underscored by recent evidence for its involvement in mammalian cell responses to insulin and for PtdIns(3,5)P(2) dysfunction in the human genetic conditions X-linked myotubular myopathy, Type-4B Charcot-Marie-Tooth disease and fleck corneal dystrophy.

  13. Kinetics of the {beta} {yields} {delta} Solid-Solid Transition of HMX, Octahydro-1,3,5,7-Tetranitro-1,3,5,7-Tetrazocine

    SciTech Connect

    Weese, R K; Maienschein, J L; Perrino, C T

    2001-09-05

    We apply Differential Scanning Calorimetry, DSC, to measure the kinetics of the {beta} {yields} {delta} solid-solid phase transition of Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocinet HMX. Integration of the DSC signal gives a direct measurement of degree of conversion. We apply 1st order kinetics, the Ozawa method, and isoconversional analysis to show that the phase transition is not a simple one-step reaction, but instead is a complex combination of steps. The range of activation energies found in this work, centering around 500 kJ/mol, is higher than previously reported values. We discuss possible reasons for the higher activation energies measured here.

  14. Shear properties of vocal fold mucosal tissues and their effect on vocal fold oscillation

    NASA Astrophysics Data System (ADS)

    Chan, Roger Wai Kai

    Viscoelastic shear properties of vocal fold mucosal tissues and phonosurgical biomaterials were measured with a parallel-plate rotational rheometer. Elastic, viscous and damping properties were quantified as a function of frequency (0.01 Hz to 15 Hz) for human vocal fold mucosal tissues (N = 15), implantable biomaterials commonly used in the treatment of vocal fold paralysis (Teflon, gelatin, and collagen) (the non-mucosal group), and biomaterials currently or potentially useful in the treatment of vocal fold mucosal defects (adipose tissue or fat, hyaluronic acid, and fibronectin) (the mucosal group). It was found that intersubject differences as large as an order of magnitude were often observed for the shear properties of vocal fold mucosal tissues, part of which may be age- and gender-related. Shear properties of the non-mucosal group biomaterials were often much higher than those of the mucosal group biomaterials, which were relatively close to the shear properties of mucosal tissues. Viscoelastic and rheological modeling showed that shear properties of human vocal fold mucosa may be described by a quasi-linear viscoelastic theory and a statistical network theory, based upon which extrapolations to audio frequencies were possible. A theory of small-amplitude vocal fold oscillation was revisited to describe the effects of tissue shear properties on vocal fold oscillation and phonation threshold pressure, a measure of the 'ease' of phonation and an objective indication of vocal function. It was found that phonation threshold pressure is directly related to the viscous shear modulus or the 'effective damping modulus', a concept proposed to quantify the effective amount of damping in vocal fold oscillation. The mucosal group biomaterials were incorporated into the artificial vocal fold mucosa of a physical model in order to empirically assess their effects on phonation threshold pressure. Results showed that higher threshold pressures were consistently observed

  15. Extraction, purification, identification and metabolism of 3',5'-cyclic UMP, 3',5'-cyclic IMP and 3',5'-cyclic dTMP from rat tissues.

    PubMed Central

    Newton, R P; Kingston, E E; Hakeem, N A; Salih, S G; Beynon, J H; Moyse, C D

    1986-01-01

    The large-scale extraction and partial purification of endogenous 3',5'-cyclic UMP, 3',5'-cyclic IMP and 3',5'-cyclic dTMP are described. Rat liver, kidney, heart, spleen and lung tissues were subjected to a sequential purification procedure involving freeze-clamping, perchlorate extraction, alumina and Sephadex ion-exchange chromatography and preparative electrophoresis. The samples thus obtained co-chromatographed with authentic cyclic UMP, cyclic IMP and cyclic dTMP on t.l.c. and h.p.l.c. and the u.v. spectra of the extracted samples were identical with those of the standards. Fast atom bombardment of the three cyclic nucleotide standards yielded mass spectra containing a molecular protonated ion in each case; mass-analysed ion kinetic-energy spectrometry ('m.i.k.e.s') of these ions produced a spectrum unique to the parent cyclic nucleotide. The extracted putative cyclic UMP, cyclic IMP and cyclic dTMP each produced a m.i.k.e.s. identical with that obtained with the corresponding cyclic nucleotide standard. Rat liver, heart, kidney, brain, intestine, spleen, testis and lung protein preparations were each found capable of the synthesis of cyclic UMP, cyclic IMP and cyclic dTMP from the corresponding nucleoside triphosphate, of the hydrolysis of these cyclic nucleotides and of their binding, with the exception that cyclic dTMP was not synthesized by the kidney preparation. PMID:3019316

  16. Relative contributions of collagen and elastin to elasticity of the vocal fold under tension.

    PubMed

    Chan, Roger W; Fu, Min; Young, Lindsay; Tirunagari, Neeraj

    2007-08-01

    This study examined the contributions of collagen and elastin to the tensile elastic properties of the vocal fold lamina propria. Uniaxial stress-strain responses of vocal fold cover and vocal ligament specimens from 20 human larynges (12 males, 8 females) were quantified with sinusoidal stretch-release deformation in vitro. Mid-coronal sections of 12 specimens were examined histologically with Masson's trichrome and elastin van Gieson stain to quantify the relative densities of collagen and elastin fibers. Results showed that significantly higher levels of collagen were found in the male vocal fold than female, for both the cover and the ligament. For male there was a significantly higher level of elastin in the cover than in the ligament. On average, the elastic modulus of the male cover was about twice that of the female at high-tensile strain (35-40%), whereas the male ligament was 3-5 times stiffer than the female in the same range. The ligament was stiffer than the cover for male, but the opposite was observed for female. These findings suggested that collagen and elastin could contribute differentially to elasticity of the cover and the ligament. The data may provide guidance for surgical reconstruction and tissue engineering of different lamina propria layers.

  17. Novel sequences propel familiar folds.

    PubMed

    Jawad, Zahra; Paoli, Massimo

    2002-04-01

    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  18. Problem Solving through Paper Folding

    ERIC Educational Resources Information Center

    Wares, Arsalan

    2014-01-01

    The purpose of this article is to describe a couple of challenging mathematical problems that involve paper folding. These problem-solving tasks can be used to foster geometric and algebraic thinking among students. The context of paper folding makes some of the abstract mathematical ideas involved relatively concrete. When implemented…

  19. COS NUV MAMA Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, Thomas

    2013-10-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as Cycle 20 proposal 13128.

  20. Periodic folding of viscous sheets

    NASA Astrophysics Data System (ADS)

    Ribe, Neil M.

    2003-09-01

    The periodic folding of a sheet of viscous fluid falling upon a rigid surface is a common fluid mechanical instability that occurs in contexts ranging from food processing to geophysics. Asymptotic thin-layer equations for the combined stretching-bending deformation of a two-dimensional sheet are solved numerically to determine the folding frequency as a function of the sheet’s initial thickness, the pouring speed, the height of fall, and the fluid properties. As the buoyancy increases, the system bifurcates from “forced” folding driven kinematically by fluid extrusion to “free” folding in which viscous resistance to bending is balanced by buoyancy. The systematics of the numerically predicted folding frequency are in good agreement with laboratory experiments.

  1. Colour variation in red grapevines (Vitis vinifera L.): genomic organisation, expression of flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase genes and related metabolite profiling of red cyanidin-/blue delphinidin-based anthocyanins in berry skin

    PubMed Central

    Castellarin, Simone D; Di Gaspero, Gabriele; Marconi, Raffaella; Nonis, Alberto; Peterlunger, Enrico; Paillard, Sophie; Adam-Blondon, Anne-Francoise; Testolin, Raffaele

    2006-01-01

    Background Structural genes of the phenyl-propanoid pathway which encode flavonoid 3'- and 3',5'-hydroxylases (F3'H and F3'5'H) have long been invoked to explain the biosynthesis of cyanidin- and delphinidin-based anthocyanin pigments in the so-called red cultivars of grapevine. The relative proportion of the two types of anthocyanins is largely under genetic control and determines the colour variation among red/purple/blue berry grape varieties and their corresponding wines. Results Gene fragments of VvF3'H and VvF3'5'H, that were isolated from Vitis vinifera 'Cabernet Sauvignon' using degenerate primers designed on plant homologous genes, translated into 313 and 239 amino acid protein fragments, respectively, with up to 76% and 82% identity to plant CYP75 cytochrome P450 monooxygenases. Putative function was assigned on the basis of sequence homology, expression profiling and its correlation with metabolite accumulation at ten different ripening stages. At the onset of colour transition, transcriptional induction of VvF3'H and VvF3'5'H was temporally coordinated with the beginning of anthocyanin biosynthesis, the expression being 2-fold and 50-fold higher, respectively, in red berries versus green berries. The peak of VvF3'5'H expression was observed two weeks later concomitantly with the increase of the ratio of delphinidin-/cyanidin-derivatives. The analysis of structural genomics revealed that two copies of VvF3'H are physically linked on linkage group no. 17 and several copies of VvF3'5'H are tightly clustered and embedded into a segmental duplication on linkage group no. 6, unveiling a high complexity when compared to other plant flavonoid hydroxylase genes known so far, mostly in ornamentals. Conclusion We have shown that genes encoding flavonoid 3'- and 3',5'-hydroxylases are expressed in any tissues of the grape plant that accumulate flavonoids and, particularly, in skin of ripening red berries that synthesise mostly anthocyanins. The correlation between

  2. Degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by Stenotrophomonas maltophilia PB1.

    PubMed Central

    Binks, P R; Nicklin, S; Bruce, N C

    1995-01-01

    A mixed microbial culture capable of metabolizing the explosive RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) was obtained from soil enrichments under aerobic and nitrogen-limiting conditions. A bacterium, Stenotrophomonas maltophilia PB1, isolated from the culture used RDX as a sole source of nitrogen for growth. Three moles of nitrogen was used per mole of RDX, yielding a metabolite identified by mass spectroscopy and 1H nuclear magnetic resonance analysis as methylene-N-(hydroxymethyl)-hydroxylamine-N'-(hydroxymethyl)nitroamin e. The bacterium also used s-triazine as a sole source of nitrogen but not the structurally similar compounds octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine, cyanuric acid, and melamine. An inducible RDX-degrading activity was present in crude cell extracts. PMID:7747953

  3. Poly[(μ-3,5-dinitro-benzoato)(μ-3,5-dinitro-benzoic acid)rubidium].

    PubMed

    Miao, Yanqing; Fan, Tao

    2011-08-01

    The asymmetric unit of the title compound, [Rb(C(7)H(3)N(2)O(6))(C(7)H(4)N(2)O(6))](n), comprises an Rb(+) cation, a 3,5-dinitro-benzoate anion and a 3,5-dinitro-benzoic acid ligand. The Rb(+) cation is nine-coordinated by O atoms from four 3,5-dinitro-benzoate anions and three neutral 3,5-dinitro-benzoic acid ligands. The metal atom is firstly linked by four bridging carboxyl groups, forming a binuclear motif, which is further linked by the nitro groups into a two-dimensional framework along the [110] direction. A short O-H⋯O hydrogen bond between two adjacent carboxy/carboxylate groups occurs. PMID:22090832

  4. Hexahydro-1,3,5-trinitro-1,3,5-triazine mineralization by zerovalent iron and mixed anaerobic cultures.

    PubMed

    Oh, B T; Just, C L; Alvarez, P J

    2001-11-01

    Soil microcosms were used to evaluate the potential benefits of an integrated microbial-Fe0 system to treat groundwater contamination by RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine). Microcosms amended with both Fe0 filings and municipal anaerobic sludge mineralized RDX faster and to a greater extent than separate treatments, with up to 51% 14CO2 recovery after 77 d. The nitroso byproducts 1,3-dinitro-5-nitroso-1,3,5-triazacyclohexane (MNX), 1,3-dinitroso-5-nitro-1,3,5-triazacyclohexane (DNX), and 1,3,5-trinitroso-1,3,5-triazacyclohexane (TNX) were detected in all microcosms, although these compounds never accumulated above 5% of the added RDX on a molar basis. A soluble intermediate that was tentatively identified as methylenedinitramine [(O2NNH)2CH2] was relatively persistent, although it accumulated to a much lower extent in combined-treatment reactors than in sets with Fe0 or sludge alone. Some of the radiolabel was bound to soil and Fe0 and could not be extracted with CH3CN. This fraction, which was recovered by combustion with a biological oxidizer, was also found at lower concentrations in combined-treatment reactors. This work suggests that permeable reactive Fe0 barriers might be an effective approach to intercept and degrade RDX plumes and that treatment efficiency might be enhanced by biogeochemical interactions through bioaugmentation.

  5. Fast events in protein folding

    SciTech Connect

    Woodruff, W.; Callender, R.; Causgrove, T.; Dyer, R.; Williams, S.

    1996-04-01

    The primary objective of this work was to develop a molecular understanding of how proteins achieve their native three-dimensional (folded) structures. This requires the identification and characterization of intermediates in the protein folding process on all relevant timescales, from picoseconds to seconds. The short timescale events in protein folding have been entirely unknown. Prior to this work, state-of-the-art experimental approaches were limited to milliseconds or longer, when much of the folding process is already over. The gap between theory and experiment is enormous: current theoretical and computational methods cannot realistically model folding processes with lifetimes longer than one nanosecond. This unique approach to employ laser pump-probe techniques that combine novel methods of laser flash photolysis with time-resolved vibrational spectroscopic probes of protein transients. In this scheme, a short (picosecond to nanosecond) laser photolysis pulse was used to produce an instantaneous pH or temperature jump, thereby initiating a protein folding or unfolding reaction. Structure-specific, time-resolved vibrational probes were then used to identify and characterize protein folding intermediates.

  6. Effects of Knots on Protein Folding Properties

    PubMed Central

    Soler, Miguel A.; Faísca, Patrícia F. N.

    2013-01-01

    This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism) via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may affect key aspects of folding kinetics. In this regard, we found clear evidence for a functional advantage of knots: knots enhance kinetic stability because a knotted protein unfolds at a distinctively slower rate than its unknotted counterpart. However, an increase in knot deepness does not necessarily lead to more effective changes in folding properties. In this regard, a terminus with a non-trivial conformation (e.g. hairpin) can have a more dramatic effect in enhancing kinetic stability than knot depth. Nevertheless, our results suggest that the probability of the denatured ensemble to keep knotted is higher for proteins with deeper knots, indicating that knot depth plays a role in determining the topology of the denatured state. Refolding simulations starting from denatured knotted conformations show that not every knot is able to nucleate folding and further indicate that the formation of the knotting loop is a key event in the folding of knotted trefoils. They also show that there are specific native contacts within the knotted core that are crucial to keep a native knotting loop in denatured conformations which otherwise have no detectable structure. The study of the knotting mechanism reveals that the threading of the knotting loop generally occurs towards late folding in conformations that exhibit a significant degree of structural consolidation. PMID:24023962

  7. Radioimmunoassay for 3,5-diiodothyronine and evidence for dependence on conversion from 3,5,3'-triiodothyronine

    SciTech Connect

    Pangaro, L.; Burman, K.D.; Wartofsky, L.; Cahnmann, H.J.; Smallridge, R.C.; O'Brian, J.T.; Wright, F.D.; Latham, K.

    1980-06-01

    The present report describes a RIA for 3,5-diiodothyronine (3,5T/sub 2/) which uses inner ring-labeled 3,5-(/sup 125/I)T/sub 2/ as the ligand and has a lower limit of detectability of 0.5 ng/dl. Cross-reaction was 0.14% with T/sub 3/, less than 0.001% with T/sub 4/, 1.2% with 3,3',5-triiodothyroacetic acid, and 6.1% with 3,5-diiodothyroacetic acid. No cross-reaction was detectable for iodothyronines within their physiological ranges. Intraassay variation ranged from 2.2 to 7.8%, and interassay variation ranged from 12.7 to 14%. The mean (+-SE) serum 3.5T/sub 2/ concentration in 70 normal subjects was 4.3 +- 0.2 ng/dl. The mean (+-SE) 3.5T/sub 2/ in 14 hyperthyroid patients was increased to 18.4 +- 2.3 ng/dl (P < 0.001), and all but 1 patient had an elevated level. In 10 hypothyroid patients the mean (+-SE) 3,5T/sub 2/ level was decreased to 1.4 +- 0.3 ng/dl (P < 0.001). In 4 patients, levels overlapped with the normal range. In 4 hypothyroid subjects treated with L-T/sub 1/, 3,5T/sub 2/ levels were normal, suggesting that the majority of 3,5T/sub 2/ originates from extrathyroidal conversion from T/sub 3/. Studies in fasting obese subjects demonstrated that serum 3,5T/sub 2/ (mean +- SE) levels fell from 3.4 +- 0.3 to 2.5 +- 0.7 ng/dl during fasting. This fall was significant (P < 0.001) and in parallel with the fall in T/sub 3/ levels of 182 +- 20 to 126 +- 12 ng/dl. In fasting subjects given 100 ..mu..g oral L-T/sub 3//day T/sub 3/ levels rose from 138 +- 11 to 362 +- 26 ng/dl. 3,5T/sub 2/ levels (corrected for cross-reaction and for contamination of oral T/sub 3/ with 3,5T/sub 2/) rose from 2.2 +- 0.7 to 6.4 +- 1.0 ng/dl. In fasting subjects given 25 ..mu..g oral L-T/sub 3//day, T/sub 3/ levels fell from 165 +- 5.1 to 139 +- 6.9 ng/dl. Corrected 3,5T/sub 2/ levels changed from 3.7 +- 0.4 to 2.5 +- 0.3 ng/dl. Neither change were significant.

  8. 3,5-Dichlorophenol Removal From Wastewater Using Alternative Adsorbents

    NASA Astrophysics Data System (ADS)

    Kobetičová, Hana; Lipovský, Marek; Wachter, Igor; Soldán, Maroš

    2015-06-01

    The main objective of this paper is to evaluate the efficiency of 3,5-dichlorophenol removal from wastewater by using alternative low cost adsorbents. Waste from the production and processing of metals (black nickel mud, red mud) and a biosorbent (Lemna minor) were used for this research. Initial concentration of the contaminant was 4 mmol L-1, the contact time of sorbent and waste water was 0 - 48 hrs and the temperature during experiment was 25 ± 0.2 °C. The results show that the highest removal efficiency of 3,5 - dichlorophenol (58.18 %) was reached by the red mud in 48 hours.

  9. What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs.

    PubMed

    Dellus-Gur, Eynat; Toth-Petroczy, Agnes; Elias, Mikael; Tawfik, Dan S

    2013-07-24

    Protein evolvability includes two elements--robustness (or neutrality, mutations having no effect) and innovability (mutations readily inducing new functions). How are these two conflicting demands bridged? Does the ability to bridge them relate to the observation that certain folds, such as TIM barrels, accommodate numerous functions, whereas other folds support only one? Here, we hypothesize that the key to innovability is polarity--an active site composed of flexible, loosely packed loops alongside a well-separated, highly ordered scaffold. We show that highly stabilized variants of TEM-1 β-lactamase exhibit selective rigidification of the enzyme's scaffold while the active-site loops maintained their conformational plasticity. Polarity therefore results in stabilizing, compensatory mutations not trading off, but instead promoting the acquisition of new activities. Indeed, computational analysis indicates that in folds that accommodate only one function throughout evolution, for example, dihydrofolate reductase, ≥ 60% of the active-site residues belong to the scaffold. In contrast, folds associated with multiple functions such as the TIM barrel show high scaffold-active-site polarity (~20% of the active site comprises scaffold residues) and >2-fold higher rates of sequence divergence at active-site positions. Our work suggests structural measures of fold polarity that appear to be correlated with innovability, thereby providing new insights regarding protein evolution, design, and engineering.

  10. ProFold: Protein Fold Classification with Additional Structural Features and a Novel Ensemble Classifier

    PubMed Central

    2016-01-01

    Protein fold classification plays an important role in both protein functional analysis and drug design. The number of proteins in PDB is very large, but only a very small part is categorized and stored in the SCOPe database. Therefore, it is necessary to develop an efficient method for protein fold classification. In recent years, a variety of classification methods have been used in many protein fold classification studies. In this study, we propose a novel classification method called proFold. We import protein tertiary structure in the period of feature extraction and employ a novel ensemble strategy in the period of classifier training. Compared with existing similar ensemble classifiers using the same widely used dataset (DD-dataset), proFold achieves 76.2% overall accuracy. Another two commonly used datasets, EDD-dataset and TG-dataset, are also tested, of which the accuracies are 93.2% and 94.3%, higher than the existing methods. ProFold is available to the public as a web-server.

  11. ProFold: Protein Fold Classification with Additional Structural Features and a Novel Ensemble Classifier

    PubMed Central

    2016-01-01

    Protein fold classification plays an important role in both protein functional analysis and drug design. The number of proteins in PDB is very large, but only a very small part is categorized and stored in the SCOPe database. Therefore, it is necessary to develop an efficient method for protein fold classification. In recent years, a variety of classification methods have been used in many protein fold classification studies. In this study, we propose a novel classification method called proFold. We import protein tertiary structure in the period of feature extraction and employ a novel ensemble strategy in the period of classifier training. Compared with existing similar ensemble classifiers using the same widely used dataset (DD-dataset), proFold achieves 76.2% overall accuracy. Another two commonly used datasets, EDD-dataset and TG-dataset, are also tested, of which the accuracies are 93.2% and 94.3%, higher than the existing methods. ProFold is available to the public as a web-server. PMID:27660761

  12. Fog spontaneously folds mosquito wings

    NASA Astrophysics Data System (ADS)

    Dickerson, Andrew K.; Liu, Xing; Zhu, Ting; Hu, David L.

    2015-02-01

    The flexibility of insect wings confers aerodynamic benefits, but can also present a hazard if exposed to fog or dew. Fog can cause water to accumulate on wings, bending them into tight taco shapes and rendering them useless for flight. In this combined experimental and theoretical study, we use high-speed video to film the spontaneous folding of isolated mosquito wings due to the evaporation of a water drop. We predict shapes of the deformed wing using two-dimensional elastica theory, considering both surface tension and Laplace pressure. We also recommend fold-resistant geometries for the wings of flapping micro-aerial vehicles. Our work reveals the mechanism of insect wing folding and provides a framework for further study of capillarity-driven folding in both natural and biomimetic systems at small scales.

  13. How do metal ions direct ribozyme folding?

    NASA Astrophysics Data System (ADS)

    Denesyuk, Natalia A.; Thirumalai, D.

    2015-10-01

    Ribozymes, which carry out phosphoryl-transfer reactions, often require Mg2+ ions for catalytic activity. The correct folding of the active site and ribozyme tertiary structure is also regulated by metal ions in a manner that is not fully understood. Here we employ coarse-grained molecular simulations to show that individual structural elements of the group I ribozyme from the bacterium Azoarcus form spontaneously in the unfolded ribozyme even at very low Mg2+ concentrations, and are transiently stabilized by the coordination of Mg2+ ions to specific nucleotides. However, competition for scarce Mg2+ and topological constraints that arise from chain connectivity prevent the complete folding of the ribozyme. A much higher Mg2+ concentration is required for complete folding of the ribozyme and stabilization of the active site. When Mg2+ is replaced by Ca2+ the ribozyme folds, but the active site remains unstable. Our results suggest that group I ribozymes utilize the same interactions with specific metal ligands for both structural stability and chemical activity.

  14. Electrochemistry of folded graphene edges.

    PubMed

    Ambrosi, Adriano; Bonanni, Alessandra; Pumera, Martin

    2011-05-01

    There is enormous interest in the investigation of electron transfer rates at the edges of graphene due to possible energy storage and sensing applications. While electrochemistry at the edges and the basal plane of graphene has been studied in the past, the new frontier is the electrochemistry of folded graphene edges. Here we describe the electrochemistry of folded graphene edges and compare it to that of open graphene edges. The materials were characterized in detail by high-resolution transmission electron microscopy, Raman spectroscopy, high-resolution X-ray photoelectron spectroscopy, electrochemical impedance spectroscopy and cyclic voltammetry. We found that the heterogeneous electron transfer rate is significantly lower on folded graphene edges compared to open edge sites for ferro/ferricyanide, and that electrochemical properties of open edges offer lower potential detection of biomarkers than the folded ones. It is apparent, therefore, that for sensing and biosensing applications the folded edges are less active than open edges, which should then be preferred for such applications. As folded edges are the product of thermal treatment of multilayer graphene, such thermal procedures should be avoided when fabricating graphene for electrochemical applications.

  15. Wee Recyclers. An Activity Guide for Ages 3-5.

    ERIC Educational Resources Information Center

    Wisconsin State Dept. of Natural Resources, Madison.

    Recycling and reusing are skills that can be developed in early child care programs. This activity guide is intended to help teach children (ages 3-5) about recycling using simple, hands-on activities. Teacher-directed activities involve setting up a recycling center, sorting recyclable items, landfills, litter, a recycling alphabet, and ways that…

  16. 9 CFR 3.5 - Mobile or traveling housing facilities.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Transportation of Dogs and Cats 1 Facilities and Operating Standards § 3.5 Mobile or traveling housing facilities. (a) Heating, cooling, and temperature. Mobile or traveling housing facilities for dogs and cats must be sufficiently heated and cooled when necessary to protect the dogs and cats from temperature...

  17. 9 CFR 3.5 - Mobile or traveling housing facilities.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... Transportation of Dogs and Cats 1 Facilities and Operating Standards § 3.5 Mobile or traveling housing facilities. (a) Heating, cooling, and temperature. Mobile or traveling housing facilities for dogs and cats must be sufficiently heated and cooled when necessary to protect the dogs and cats from temperature...

  18. 9 CFR 3.5 - Mobile or traveling housing facilities.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Transportation of Dogs and Cats 1 Facilities and Operating Standards § 3.5 Mobile or traveling housing facilities. (a) Heating, cooling, and temperature. Mobile or traveling housing facilities for dogs and cats must be sufficiently heated and cooled when necessary to protect the dogs and cats from temperature...

  19. 45 CFR 1210.3-5 - Preparation for appeal.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... SERVICE VISTA TRAINEE DESELECTION AND VOLUNTEER EARLY TERMINATION PROCEDURES VISTA Volunteer Early Termination § 1210.3-5 Preparation for appeal. (a) Entitlement to Representation. A Volunteer may be accompanied, represented and advised by a representative of the Volunteer's own choice at any stage of...

  20. 45 CFR 1210.3-5 - Preparation for appeal.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... SERVICE VISTA TRAINEE DESELECTION AND VOLUNTEER EARLY TERMINATION PROCEDURES VISTA Volunteer Early Termination § 1210.3-5 Preparation for appeal. (a) Entitlement to Representation. A Volunteer may be accompanied, represented and advised by a representative of the Volunteer's own choice at any stage of...

  1. 45 CFR 1210.3-5 - Preparation for appeal.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... SERVICE VISTA TRAINEE DESELECTION AND VOLUNTEER EARLY TERMINATION PROCEDURES VISTA Volunteer Early Termination § 1210.3-5 Preparation for appeal. (a) Entitlement to Representation. A Volunteer may be accompanied, represented and advised by a representative of the Volunteer's own choice at any stage of...

  2. 9 CFR 3.5 - Mobile or traveling housing facilities.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Transportation of Dogs and Cats 1 Facilities and Operating Standards § 3.5 Mobile or traveling housing facilities. (a) Heating, cooling, and temperature. Mobile or traveling housing facilities for dogs and cats must be sufficiently heated and cooled when necessary to protect the dogs and cats from temperature...

  3. Differentiating Instruction with Menus Grades 3-5: Math

    ERIC Educational Resources Information Center

    Westphal, Laurie E.

    2007-01-01

    "Differentiating Instruction With Menus Grades 3-5" offers teachers everything they need to create a student-centered learning environment based on choice. Addressing the four main subject areas (language arts, math, science, and social studies) and the major concepts taught within these areas, these books provide a number of different types of…

  4. Synthesis and biological evaluation of 3,5-dimethoxystilbene analogs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In our continuing effort to discover natural product-based pest management agents, derivatives of 3,5-dimethoxystilbene were synthesized yielding 27 new and 6 known compounds. Of these, compounds 11 and 12 showed strong Aedes aegypti larvicidal activity (LC50 14.7 and 16.2 ppm, respectively). In fur...

  5. Science in Action Series: AGATE ( pt 3/5 )

    NASA Technical Reports Server (NTRS)

    1997-01-01

    This show was made for the Office of Education at NASA Langley. The objective is to make math and science appealing to a middle school audience. This clip (pt 3/5 ) tells us more about the plane. How much will it cost to run, and how will we learn to fly?

  6. 43 CFR 9269.3-5 - Timber management.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Timber management. 9269.3-5 Section 9269.3... Timber management. (a) Sales of forest products; general. (b) Non-sale disposals; general—(1) Unauthorized cutting of timber-mineral and non-mineral lands. (i) The cutting or removing of the...

  7. Differentiating Instruction with Menus Grades 3-5: Science

    ERIC Educational Resources Information Center

    Westphal, Laurie E.

    2007-01-01

    "Differentiating Instruction With Menus Grades 3-5" offers teachers everything they need to create a student-centered learning environment based on choice. Addressing the four main subject areas (language arts, math, science, and social studies) and the major concepts taught within these areas, these books provide a number of different types of…

  8. Differentiating Instruction with Menus Grades 3-5: Language Arts

    ERIC Educational Resources Information Center

    Westphal, Laurie E.

    2007-01-01

    "Differentiating Instruction With Menus Grades 3-5" offers teachers everything they need to create a student-centered learning environment based on choice. Addressing the four main subject areas (language arts, math, science, and social studies) and the major concepts taught within these areas, these books provide a number of different types of…

  9. Differentiating Instruction with Menus Grades 3-5: Social Studies

    ERIC Educational Resources Information Center

    Westphal, Laurie E.

    2007-01-01

    "Differentiating Instruction With Menus Grades 3-5" offers teachers everything they need to create a student-centered learning environment based on choice. Addressing the four main subject areas (language arts, math, science, and social studies) and the major concepts taught within these areas, these books provide a number of different types of…

  10. 9 CFR 3.5 - Mobile or traveling housing facilities.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Transportation of Dogs and Cats 1 Facilities and Operating Standards § 3.5 Mobile or traveling housing facilities. (a) Heating, cooling, and temperature. Mobile or traveling housing facilities for dogs and cats must be sufficiently heated and cooled when necessary to protect the dogs and cats from temperature...

  11. Distonic biradical anions. Synthesis and characterization of the 3,5-dehydrophenyl and 1,3,5-trimethylenebenzene negative ions

    SciTech Connect

    Hu, J.; Squires, R.R.

    1996-06-19

    We recently described a new method for producing intense beams of structurally-defined biradical negative ions (`distonic radical anions`) in the gas phase based on reactions between trimethylsilyl-substituted carbanions and molecular fluorine. We now wish to report the extension of this procedure to the rational synthesis of negative ions of triradicals, i.e., `distonic biradical anions.` The significance of these species is manifold. Polyradicals and their associated ions are the central focus of current efforts to produce synthetic organic ferromagnets. In this report, we describe the gas-phase synthesis and characterization of 3,5-dehydrophenyl anion, 1, and 1,3,5-trimethylenebenzene negative ion, 2. Ion 1 corresponds to the negative ion of the ({sigma},{sigma},{sigma}) triradical 1,3,5-benzenetriyl, and it can also be viewed as a deprotonated m-benzyne. 29 refs.

  12. Abiotic transformation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by green rusts.

    PubMed

    Larese-Casanova, Philip; Scherer, Michelle M

    2008-06-01

    The rate and extent of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) transformation was measured in the presence of carbonate and sulfate green rust suspended in solutions containing common groundwater anions. Formaldehyde (HCHO), nitrous oxide gas (N2O(g)), and ammonium (NH4+) were the major end products, accounting for about 70% of the carbon mass balance and about half of the nitrogen mass balance. Results from experiments with both 14C-RDX and LC-MS analysis indicate that the remaining carbon products are soluble and most likely small (< 50 Da). The transient appearance of 1,3-dinitro-5-nitroso-1,3,5-triazacyclohexane (MNX), 1,3-dinitroso-5-nitro-1,3,5-triazacyclohexane (DNX), and 1,3,5-trinitroso-1,3,5-triazacyclohexane (TNX) indicate that some nitro-group reduction occurred. The kinetics of RDX transformation was rapid with a half-life of less than an hour in a pH 7.0 KBr solution. Little difference in rates of RDX transformation or product distribution was observed between carbonate and sulfate green rust, and an apparent reaction order of 1.0 was measured with respect to Fe(II) in both green rusts. Phosphate anions completely inhibited RDX reduction, and carbonate and sulfate anions resulted in slower kinetics, and in some cases, an initial lag period, compared to bromide and chloride. Our results suggest that green rusts may contribute to abiotic natural attenuation of RDX in Fe-rich subsurface environments, but that it will be important to consider groundwater composition when assessing rates of attenuation.

  13. Foreland basins and fold belts

    SciTech Connect

    Macqueen, R.W.; Leckie, D.A. )

    1992-01-01

    The papers in this book describe six foreland basins and fold belts in terms of their regional setting, stratigraphy, tectonics, and structure, and their oil and gas systems. All of the basins show general similarities, but each differs significantly in detail from the others, posing something of a problem in terms of arriving at a 'typical' foreland basin and fold belt. Some are major hydrocarbon producers; others are not. The major characteristics of the six foreland basins and fold belts are summarized in Tables 1 through 5, which provide a convenient means of comparing and contrasting these basins and their hydrocarbon resources. The Western Canada foreland basin and fold belt serves as the type example for several reasons. These include: its setting and clear relationship to a major orogene of Mesozoic-Cenozoic age; the fact that it is uncomplicated by later overprinting, segmentation, or cover rocks unlike the Ouachita, Eastern Venezuela, and U.S. Rocky Mountain foreland basins and fold belts); the fact that there is a large volume of publicly available data on the basin and an active exploration and research community; and the fact that it has reasonable oil and gas reserves in a well-defined stratigraphic framework.

  14. Synthetic routes to 3(5)-phosphonylated pyrazoles

    NASA Astrophysics Data System (ADS)

    Goulioukina, N. S.; Makukhin, N. N.; Beletskaya, I. P.

    2016-07-01

    This review comprehensively covers the currently available synthetic routes to 3(5)-phosphonylated pyrazoles. There are demonstrated significant advances in this field over the last 10–15 years caused by the use of the Bestmann–Ohira reagent [as well as (diazomethyl)phosphonates and phosphonylated hydrazonoyl halides] in reactions with diverse dipolarophiles. 1,3-Dipolar cycloaddition of diazo compounds to α,β-unsaturated phosphonates as well as intramolecular heterocyclization of (1-diazoallyl)phosphonates and (3--diazo-1-propenyl)phosphonates are discussed. Synthetic potential of cyclocondensation of organophosphorus 1,3-dielectrophilic compounds with hydrazines is shown. Ways to introduce a phosphonate group into the pyrazole ring are considered. Examples of chemical transformations of 3(5)-phosphonylated pyrazoles are reported. The bibliography includes 88 references.

  15. Synthetic routes to 3(5)-phosphonylated pyrazoles

    NASA Astrophysics Data System (ADS)

    Goulioukina, N. S.; Makukhin, N. N.; Beletskaya, I. P.

    2016-07-01

    This review comprehensively covers the currently available synthetic routes to 3(5)-phosphonylated pyrazoles. There are demonstrated significant advances in this field over the last 10-15 years caused by the use of the Bestmann-Ohira reagent [as well as (diazomethyl)phosphonates and phosphonylated hydrazonoyl halides] in reactions with diverse dipolarophiles. 1,3-Dipolar cycloaddition of diazo compounds to α,β-unsaturated phosphonates as well as intramolecular heterocyclization of (1-diazoallyl)phosphonates and (3--diazo-1-propenyl)phosphonates are discussed. Synthetic potential of cyclocondensation of organophosphorus 1,3-dielectrophilic compounds with hydrazines is shown. Ways to introduce a phosphonate group into the pyrazole ring are considered. Examples of chemical transformations of 3(5)-phosphonylated pyrazoles are reported. The bibliography includes 88 references.

  16. Dendrimers Based on [1,3,5]-Triazines

    PubMed Central

    STEFFENSEN, MACKAY B.; HOLLINK, EMILY; KUSCHEL, FRANK; BAUER, MONIKA; SIMANEK, ERIC E.

    2009-01-01

    A comprehensive and chronological account of dendrimers based on [1,3,5]-triazines is provided. Synthetic strategies to install the triazine through cycloaddition, cyclotrimerization, and nucleophilic aromatic substitution of cyanuric chloride are discussed. Motivations and applications of these architectures are surveyed, including the preparation of supra-molecular assemblies in the solution and solid states and their use in medicines, advanced materials, and separations when anchored to solid supports. PMID:19953202

  17. Practical auxiliary basis implementation of Rung 3.5 functionals

    SciTech Connect

    Janesko, Benjamin G.; Scalmani, Giovanni; Frisch, Michael J.

    2014-07-21

    Approximate exchange-correlation functionals for Kohn-Sham density functional theory often benefit from incorporating exact exchange. Exact exchange is constructed from the noninteracting reference system's nonlocal one-particle density matrix γ(r{sup -vector},r{sup -vector}′). Rung 3.5 functionals attempt to balance the strengths and limitations of exact exchange using a new ingredient, a projection of γ(r{sup -vector},r{sup -vector} ′) onto a semilocal model density matrix γ{sub SL}(ρ(r{sup -vector}),∇ρ(r{sup -vector}),r{sup -vector}−r{sup -vector} ′). γ{sub SL} depends on the electron density ρ(r{sup -vector}) at reference point r{sup -vector}, and is closely related to semilocal model exchange holes. We present a practical implementation of Rung 3.5 functionals, expanding the r{sup -vector}−r{sup -vector} ′ dependence of γ{sub SL} in an auxiliary basis set. Energies and energy derivatives are obtained from 3D numerical integration as in standard semilocal functionals. We also present numerical tests of a range of properties, including molecular thermochemistry and kinetics, geometries and vibrational frequencies, and bandgaps and excitation energies. Rung 3.5 functionals typically provide accuracy intermediate between semilocal and hybrid approximations. Nonlocal potential contributions from γ{sub SL} yield interesting successes and failures for band structures and excitation energies. The results enable and motivate continued exploration of Rung 3.5 functional forms.

  18. Removing 3,5-Dichlorophenol from Wastewater by Alternative Adsorbents

    NASA Astrophysics Data System (ADS)

    Kobetičová, Hana; Galbičková, Blanka; Ševčíková, Janka; Soldán, Maroš

    2014-12-01

    The main objective of this paper is to evaluate an efficiency of 3,5 - dichlorophenol removal from wastewater by using alternative adsorbents. Chlorophenols are organic compounds consisting of a benzene ring, OH groups and also atoms of chlorine. Chlorophenols may have a huge isomere variety that means there are differences in their chemical and physical properties. Due to their toxicity it is necessary to remove them from waste water and in this paper an alternative way of such process is described.

  19. Rapid compaction during RNA folding

    NASA Astrophysics Data System (ADS)

    Russell, Rick; Millett, Ian S.; Tate, Mark W.; Kwok, Lisa W.; Nakatani, Bradley; Gruner, Sol M.; Mochrie, Simon G. J.; Pande, Vijay; Doniach, Sebastian; Herschlag, Daniel; Pollack, Lois

    2002-04-01

    We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide a time-resolved picture of the global folding process of the Tetrahymena group I RNA over a time window of more than five orders of magnitude. A substantial phase of compaction is observed on the low millisecond timescale, and the overall compaction and global shape changes are largely complete within one second, earlier than any known tertiary contacts are formed. This finding indicates that the RNA forms a nonspecifically collapsed intermediate and then searches for its tertiary contacts within a highly restricted subset of conformational space. The collapsed intermediate early in folding of this RNA is grossly akin to molten globule intermediates in protein folding.

  20. A novel imaging method revealed phosphatidylinositol 3,5-bisphosphate-rich domains in the endosome/lysosome membrane

    PubMed Central

    Takatori, Sho; Fujimoto, Toyoshi

    2016-01-01

    ABSTRACT We developed a new method to observe distribution of phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P2] using electron microscopy. In freeze-fracture replicas of quick-frozen samples, PtdIns(3,5)P2 was labeled specifically using recombinant ATG18 tagged with glutathione S-transferase and 4×FLAG, which was mixed with an excess of recombinant PX domain to suppress binding of ATG18 to phosphatidylinositol 3-phosphate. Using this method, PtdIns(3,5)P2 was found to be enriched in limited domains in the yeast vacuole and mammalian endosomes. In the yeast vacuole exposed to hyperosmolar stress, PtdIns(3,5)P2 was distributed at a significantly higher density in the intramembrane particle (IMP)-deficient liquid-ordered domains than in the surrounding IMP-rich domains. In mammalian cells, PtdIns(3,5)P2 was observed in endosomes of tubulo-vesicular morphology labeled for RAB5 or RAB7. Notably, distribution density of PtdIns(3,5)P2 in the endosome was significantly higher in the vesicular portion than in the tubular portion. The nano-scale distribution of PtdIns(3,5)P2 revealed in the present study is important to understand its functional roles in the vacuole and endosomes. PMID:27195064

  1. NoFold: RNA structure clustering without folding or alignment.

    PubMed

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures.

  2. Hearings on the Reauthorization of the Higher Education Act. Hearings before the Subcommittee on Postsecondary Education of the Committee on Education and Labor. House of Representatives, Ninety-Eighth Congress, Second Session on H.R. 5240. (Washington, DC, March 27-29, April 3-5, and April 10-12; St. Louis, Missouri, March 30; Flushing, New York, April 2; Winona, Minnesota, April 6, and Eau Claire, Wisconsin, April 7, 1984).

    ERIC Educational Resources Information Center

    Congress of the U.S., Washington, DC. House Committee on Education and Labor.

    Hearings on a bill to reauthorize the Higher Education Act of 1965 are presented, with attention to policy formulations of the Higher Education Act Amendments of 1984 and the Administration's fiscal year (FY) 1985 budget and legislative proposals. Consideration is given to the appropriate federal role in higher education, the proper focus of…

  3. Effect of mycorrhizal fungi on the phytoremediation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).

    PubMed

    Thompson, Phillip L; Polebitski, Austin S

    2010-02-01

    The objective of this research was to decrease the bioaccumulation of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) in the leaves of switchgrass (Panicum virgatum) and hybrid poplar trees (Populus deltoides x nigra, DN34) by exploiting the symbiotic relationship between these plants and mycorrhizal fungi. Prior to dosing with uniformly labeled (14)C-RDX, plants were grown for three months to establish the symbiosis. Results showed that the presence of mycorrhizal fungi does not significantly decrease the concentration of RDX in leaf tissues for experimental periods of 30 days. Results also indicated that a radiolabeled volatile organic compound was emitted by both plant species. This is the first evidence that a whole plant can facilitate the transformation of RDX to a volatile organic chemical.

  4. Electrochemical reduction of hexahydro-1,3,5-trinitro-1,3,5-triazine in aqueous solutions.

    PubMed

    Bonin, Pascale M L; Bejan, Dorin; Schutt, Leah; Hawari, Jalal; Bunce, Nigel J

    2004-03-01

    Electrochemical reduction of RDX, hexahydro-1,3,5-trinitro-1,3,5-triazine, a commercial and military explosive, was examined as a possible remediation technology for treating RDX-contaminated groundwater. A cascade of divided flow-through cells was used, with reticulated vitreous carbon cathodes and IrO2/Ti dimensionally stable anodes, initially using acetonitrile/water solutions to increase the solubility of RDX. The major degradation pathway involved reduction of RDX to the corresponding mononitroso compound, followed by ring cleavage to yield formaldehyde and methylenedinitramine. The reaction intermediates underwent further reduction and/or hydrolysis, the net result being the complete transformation of RDX to small molecules. The rate of degradation increased with current density, but the current efficiency was highest at low current densities. The technique was extended successfully both to 100% aqueous solutions of RDX and to an undivided electrochemical cell.

  5. Quantum theory on protein folding

    NASA Astrophysics Data System (ADS)

    Luo, LiaoFu

    2014-03-01

    The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds and stretching-bending vibrations the molecular torsion has the lowest energy and can be looked as the slow variable of the system. Simultaneously, from the multi-minima property of torsion potential the local conformational states are well defined. Following the idea that the slow variables slave the fast ones and using the nonadiabaticity operator method we deduce the Hamiltonian describing conformational change. It is shown that the influence of fast variables on the macromolecule can fully be taken into account through a phase transformation of slow variable wave function. Starting from the conformation-transition Hamiltonian the nonradiative matrix element was calculated and a general formulas for protein folding rate was deduced. The analytical form of the formula was utilized to study the temperature dependence of protein folding rate and the curious non-Arrhenius temperature relation was interpreted. By using temperature dependence data the multi-torsion correlation was studied. The decoherence time of quantum torsion state is estimated. The proposed folding rate formula gives a unifying approach for the study of a large class problems of biological conformational change.

  6. Semiempirical prediction of protein folds

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel; Colubri, Andrés; Appignanesi, Gustavo

    2001-08-01

    We introduce a semiempirical approach to predict ab initio expeditious pathways and native backbone geometries of proteins that fold under in vitro renaturation conditions. The algorithm is engineered to incorporate a discrete codification of local steric hindrances that constrain the movements of the peptide backbone throughout the folding process. Thus, the torsional state of the chain is assumed to be conditioned by the fact that hopping from one basin of attraction to another in the Ramachandran map (local potential energy surface) of each residue is energetically more costly than the search for a specific (Φ, Ψ) torsional state within a single basin. A combinatorial procedure is introduced to evaluate coarsely defined torsional states of the chain defined ``modulo basins'' and translate them into meaningful patterns of long range interactions. Thus, an algorithm for structure prediction is designed based on the fact that local contributions to the potential energy may be subsumed into time-evolving conformational constraints defining sets of restricted backbone geometries whereupon the patterns of nonbonded interactions are constructed. The predictive power of the algorithm is assessed by (a) computing ab initio folding pathways for mammalian ubiquitin that ultimately yield a stable structural pattern reproducing all of its native features, (b) determining the nucleating event that triggers the hydrophobic collapse of the chain, and (c) comparing coarse predictions of the stable folds of moderately large proteins (N~100) with structural information extracted from the protein data bank.

  7. Delayed myelosuppression with acute exposure to hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and environmental degradation product hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX) in rats

    SciTech Connect

    Jaligama, Sridhar; Kale, Vijay M.; Wilbanks, Mitchell S.; Perkins, Edward J.; Meyer, Sharon A.

    2013-02-01

    Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), a widely used munitions compound, and hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX), its N-nitroso product of anaerobic microbial nitroreduction, are contaminants of military sites. Previous studies have shown MNX to be the most acutely toxic among the nitroreduced degradation products of RDX and to cause mild anemia at high dose. The present study compares hematotoxicity with acute oral exposure to MNX with parent RDX. Both RDX and MNX caused a modest decrease in blood hemoglobin and ∼ 50% loss of granulocytes (NOAELs = 47 mg/kg) in female Sprague–Dawley rats observed 14 days post-exposure. We explored the possibility that blood cell loss observed after 14 days was delayed in onset because of toxicity to bone marrow (BM) progenitors. RDX and MNX decreased granulocyte/macrophage-colony forming cells (GM-CFCs) at 14, but not 7, days (NOAELs = 24 mg/kg). The earliest observed time at which MNX decreased GM-CFCs was 10 days post-exposure. RDX and MNX likewise decreased BM burst-forming units-erythroid (BFU-Es) at 14, but not 7, days. Granulocyte–erythrocyte–monocyte–megakaryocyte (GEMM)-CFCs were unaffected by RDX and MNX at 7 days suggesting precursor depletion did not account for GM-CFC and BFU-E loss. MNX added to the culture media was without effect on GM-CFC formation indicating no direct inhibition. Flow cytometry showed no differential loss of BM multilineage progenitors (Thy1.1{sup +}) or erythroid (CD71{sup +}) precursors with MNX suggesting myeloid and erythroid lineages were comparably affected. Collectively, these data indicate that acute exposure to both RDX and MNX caused delayed suppression of myelo- and erythropoiesis with subsequent decrease of peripheral granulocytes and erythrocytes. Highlights: ► Acute oral exposure to munitions RDX causes myelosuppression. ► Environmental degradation product MNX is comparable in effect. ► RDX and MNX are cytotoxic to both myeloid and erythroid

  8. The WIN 3.5 meter telescope project

    NASA Astrophysics Data System (ADS)

    Johns, Matt; Pilachowski, Caty

    1990-07-01

    The University of Wisconsin-Indiana University-National Optical Astronomy Observatories ('WIN') 3.5-m aperture telescope project's design concepts and development status are assessed. The WIN telescope employs a wide field of view in order to take advantage of recent advancements in multiobject fiber-optic spectroscopy. A novel support system is under development for the borosilicate honeycomb primary mirror blank which acts solely on the mirror's rear surface; mirror temperature will be actively controlled. The WIN telescope's control system will use a distributed, easily expanded and upgraded network of microprocessors connected to a master computer via serial bus.

  9. Is Protein Folding Sub-Diffusive?

    PubMed Central

    Krivov, Sergei V.

    2010-01-01

    Protein folding dynamics is often described as diffusion on a free energy surface considered as a function of one or few reaction coordinates. However, a growing number of experiments and models show that, when projected onto a reaction coordinate, protein dynamics is sub-diffusive. This raises the question as to whether the conventionally used diffusive description of the dynamics is adequate. Here, we numerically construct the optimum reaction coordinate for a long equilibrium folding trajectory of a Go model of a -repressor protein. The trajectory projected onto this coordinate exhibits diffusive dynamics, while the dynamics of the same trajectory projected onto a sub-optimal reaction coordinate is sub-diffusive. We show that the higher the (cut-based) free energy profile for the putative reaction coordinate, the more diffusive the dynamics become when projected on this coordinate. The results suggest that whether the projected dynamics is diffusive or sub-diffusive depends on the chosen reaction coordinate. Protein folding can be described as diffusion on the free energy surface as function of the optimum reaction coordinate. And conversely, the conventional reaction coordinates, even though they might be based on physical intuition, are often sub-optimal and, hence, show sub-diffusive dynamics. PMID:20862361

  10. Sequential Injection/Electrochemical Immunoassay for Quantifying the Pesticide Metabolite 3, 5, 6-Trichloro-2-Pyridinol

    SciTech Connect

    Liu, Guodong; Riechers, Shawn L.; Timchalk, Chuck; Lin, Yuehe

    2005-12-04

    An automated and sensitive sequential injection electrochemical immunoassay was developed to monitor a potential insecticide biomarker, 3, 5, 6-trichloro-2-pyridinol. The current method involved a sequential injection analysis (SIA) system equipped with a thin-layer electrochemical flow cell and permanent magnet, which was used to fix 3,5,6-trichloro-2-pyridinol (TCP) antibody coated magnetic beads (TCP-Ab-MBs) in the reaction zone. After competitive immunoreactions among TCP-Ab-MBs, TCP analyte, and horseradish peroxidase (HRP) labeled TCP, a 3, 3?, 5, 5?-tetramethylbenzidine dihydrochloride and hydrogen peroxide (TMB-H2O2) substrate solution was injected to produce an electroactive enzymatic product. The activity of HRP tracers was monitored by a square wave voltammetric scanning electroactive enzymatic product in the thin-layer flow cell. The voltammetric characteristics of the substrate and the enzymatic product were investigated under batch conditions, and the parameters of the immunoassay were optimized in the SIA system. Under the optimal conditions, the system was used to measure as low as 6 ng L-1 (ppt) TCP, which is around 50-fold lower than the value indicated by the manufacturer of the TCP RaPID Assay? kit (0.25 ug/L, colorimetric detection). The performance of the developed immunoassay system was successfully evaluated on tap water and river water samples spiked with TCP. This technique could be readily used for detecting other environmental contaminants by developing specific antibodies against contaminants and is expected to open new opportunities for environmental and biological monitoring.

  11. A more than one-hundred-fold higher per capita rate of authorship of five democratic nations versus their relatively undemocratic neighboring nations among 6,437 articles in 14 medical journals: does democracy and civil liberties promote intellectual creativity and medical research?

    PubMed

    Cappell, Mitchell S

    2009-08-01

    The aim of this work is to compare medical research productivity between democratic countries and their relatively undemocratic neighbors to identify mechanisms to promote medical research. Country of authorship was determined manually for articles published in 14 medical journals in 2005, and compared pairwise for democracies vs. relatively undemocratic nations: Israel vs. the rest of the Middle East; Japan vs. Russia; South Korea vs. North Korea; and Taiwan or Hong Kong vs. Mainland China. Democracies were quantitatively defined according to the Freedom House Index and the Economist's Index of Democracy. The frequency of publication of Israeli authors of unsolicited articles (excludes editorials) was found to be 1.08%, while its percentage of the world population is only .11% (OR = 9.97, 95%-ORCI: 4.30-23.1, P < 0.0001). This increase was invariant for more prestigious original articles (investigations) vs. less prestigious review articles or case reports, and for more prestigious high-impact factor journals vs. less prestigious low-impact factor journals. This increase was apparently not due to political favoritism: the relative frequency (RF) of Israeli authors of unsolicited articles was significantly higher than the RF of Israeli authors of solicited articles (i.e., invited editorials) (1.08% vs. 0.13%, OR = 8.38, 95%-ORCI = 1.46-48.1, P = 0.007); and was significantly higher than the RF of Israeli editorial board members (1.08% vs. 0.08%, OR = 13.0, 95%-ORCI = 2.27-74.7, P < 0.0001). Contrariwise, the frequency of publication of authors from the Middle East excluding Israel was 0.30%, while its percentage of the world population is 4.04% (OR = 0.071, 95%-ORCI = 0.04-0.12, P < 0.0001). The OR of Israeli authorship was incredibly 140.4-fold higher than the OR of the MEEI! The OR of authors of other democratic countries was also more than 100-fold the OR of authors of their undemocratic neighbors: Japan (OR = 4.93, 95%-ORCI = 3.82-6.36, P < 0.0001) vs. Russia

  12. Folded supersymmetry with a twist

    DOE PAGES

    Cohen, Timothy; Craig, Nathaniel; Lou, Hou Keong; Pinner, David

    2016-03-30

    Folded supersymmetry (f-SUSY) stabilizes the weak scale against radiative corrections from the top sector via scalar partners whose gauge quantum numbers differ from their Standard Model counterparts. This non-trivial pairing of states can be realized in extra-dimensional theories with appropriate supersymmetry-breaking boundary conditions. We present a class of calculable f-SUSY models that are parametrized by a non-trivial twist in 5D boundary conditions and can accommodate the observed Higgs mass and couplings. Although the distinctive phenomenology associated with the novel folded states should provide strong evidence for this mechanism, the most stringent constraints are currently placed by conventional supersymmetry searches. Asmore » a result, these models remain minimally fine-tuned in light of LHC8 data and provide a range of both standard and exotic signatures accessible at LHC13.« less

  13. The dynamics of interacting folds under biaxial compressive stresses.

    PubMed

    Shin, Hyunjae; Dixit, Atray C; Stone, Howard A; Abkarian, Manouk; Kim, Pilnam

    2016-04-21

    The gradual in-plane compression of a solid film bonded to a soft substrate can lead to surface wrinkling and even to the formation of a network of folds for sufficiently high strain. An understanding of how these folds initiate, propagate, and interact with each other is still lacking. In a previous study, we developed an experimental system to observe the wrinkle-to-fold transition of layered elastic materials under biaxial compressive stresses. Here we focus on the dynamic interaction of a pair of propagating folds under biaxial compression. We find experimentally that their behavior is mediated through their tips and depends on the separation of the tips and their angle of interception. When the angle is lower than 45°, the two folds either form a unique fold by the coalescence of their tips when close enough, or bend their trajectories to intersect each other and form a lenticular region in analogy with cracks. When the angle is higher then 45°, the folds simply intersect and form a T-like junction. We rationalize this behavior by conducting numerical simulations to visualize the stress field around the two tips and find that the initial geometric position of the tips primarily determines the final state of the folds. PMID:27021924

  14. Steric constraints as folding coadjuvant

    NASA Astrophysics Data System (ADS)

    Tarragó, M. E.; Rocha, Luiz F.; Dasilva, R. A.; Caliri, A.

    2003-03-01

    Through the analyses of the Miyazawa-Jernigan matrix it has been shown that the hydrophobic effect generates the dominant driving force for protein folding. By using both lattice and off-lattice models, it is shown that hydrophobic-type potentials are indeed efficient in inducing the chain through nativelike configurations, but they fail to provide sufficient stability so as to keep the chain in the native state. However, through comparative Monte Carlo simulations, it is shown that hydrophobic potentials and steric constraints are two basic ingredients for the folding process. Specifically, it is shown that suitable pairwise steric constraints introduce strong changes on the configurational activity, whose main consequence is a huge increase in the overall stability condition of the native state; detailed analysis of the effects of steric constraints on the heat capacity and configurational activity are provided. The present results support the view that the folding problem of globular proteins can be approached as a process in which the mechanism to reach the native conformation and the requirements for the globule stability are uncoupled.

  15. Beam assisted fabrication of 3-5/Si monolithic devices

    NASA Astrophysics Data System (ADS)

    Robinson, Gary Y.; Collins, George J.; Solanki, Raj

    1989-05-01

    The results of a two-year project to explore new methods for deposition of 3-5 semiconducting film on silicon substrates are summarized. Gas-source molecular beam epitaxy was used for the first time to achieve heteroepitaxy of InP on Si. The InP films contain low concentrations of impurities (less than 400 ppb), luminescence under optical excitation, and exhibit high structural quality. Laser-assisted epitaxy was used for selective area growth of GaP and InP on Si using a new phosphorous precursor, and in situ removal of oxide on Si was achieved photochemically. Plasma-assisted chemical vapor deposition of AlN films has been carried out at low substrate temperatures using an electron beam to excite a remote plasma.

  16. Dissociative electron attachment to the nitroamine HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine).

    PubMed

    Postler, Johannes; Goulart, Marcelo M; Matias, Carolina; Mauracher, Andreas; Ferreira da Silva, Filipe; Scheier, Paul; Limão-Vieira, Paulo; Denifl, Stephan

    2013-05-01

    In the present study, dissociative electron attachment (DEA) measurements with gas phase HMX, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine, C4H8N8O8, have been performed by means of a crossed electron-molecular beam experiment. The most intense signals are observed at 46 and 176 u and assigned to NO2(-) and C3H6N5O4(-), respectively. Anion efficiency curves for 15 negatively charged fragments have been measured in the electron energy region from about 0-20 eV with an energy resolution of ~0.7 eV. Product anions are observed mainly in the low energy region, near 0 eV, arising from surprisingly complex reactions associated with multiple bond cleavages and structural and electronic rearrangement. The remarkable instability of HMX towards electron attachment with virtually zero kinetic energy reflects the highly explosive nature of this compound. Substantially different intensity ratios of resonances for common fragment anions allow distinguishing the nitroamines HMX and royal demolition explosive molecule (RDX) in negative ion mass spectrometry based on free electron capture.

  17. Microbially Mediated Biodegradation of Hexahydro-1,3,5-Trinitro-1,3,5- Triazine by Extracellular Electron Shuttling Compounds

    PubMed Central

    Kwon, Man Jae; Finneran, Kevin T.

    2006-01-01

    The potential for humic substances to stimulate the reduction of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) was investigated. This study describes a novel approach for the remediation of RDX-contaminated environments using microbially mediated electron shuttling. Incubations without cells demonstrated that reduced AQDS transfers electrons directly to RDX, which was reduced without significant accumulation of the nitroso intermediates. Three times as much reduced AQDS (molar basis) was needed to completely reduce RDX. The rate and extent of RDX reduction differed greatly among electron shuttle/acceptor amendments for resting cell suspensions of Geobacter metallireducens and G. sulfurreducens with acetate as the sole electron donor. AQDS and purified humic substances stimulated the fastest rate of RDX reduction. The nitroso metabolites did not significantly accumulate in the presence of AQDS or humic substances. RDX reduction in the presence of poorly crystalline Fe(III) was relatively slow and metabolites transiently accumulated. However, adding humic substances or AQDS to Fe(III)-containing incubations increased the reduction rates. Cells of G. metallireducens alone reduced RDX; however, the rate of RDX reduction was slow relative to AQDS-amended incubations. These data suggest that extracellular electron shuttle-mediated RDX transformation is not organism specific but rather is catalyzed by multiple Fe(III)- and humic-reducing species. Electron shuttle-mediated RDX reduction may eventually become a rapid and effective cleanup strategy in both Fe(III)-rich and Fe(III)-poor environments. PMID:16957213

  18. Toxicity of the explosives 2,4,6-trinitrotoluene, hexahydro-1,3,5-trinitro-1,3,5-triazine, and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine in sediments to Chironomus tentans and Hyalella azteca: low-dose hormesis and high-dose mortality.

    PubMed

    Steevens, Jeffery A; Duke, B Maurice; Lotufo, Guilherme R; Bridges, Todd S

    2002-07-01

    The toxicity of the explosives 2,4,6-trinitrotoluene (TNT); hexahydro-1,3,5-trinitro-1,3,5-triazine (royal demolition explosive [RDX]); and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (high-melting explosive [HMX]), was evaluated in spiked sediment with two freshwater invertebrates. The midge Chironomus tentans and the amphipod Hyalella azteca demonstrated significant toxic effects after exposure to TNT and its degradation products, 1,3,5-trinitrobenzene (TNB) and 2,4-diamino-6-nitrotoluene (2,4-DANT). Significant reductions in survival of C. tentans exposed to TNT, TNB, and 2,4-DANT were observed at nominal sediment concentrations as low as 200 mg/kg. Hyalella azteca was more sensitive to TNT, TNB, and 2,4-DANT than the midge, where significant reductions in survival were observed at nominal concentrations of 50, 100, and 200 mg/kg, respectively. Survival of the midge and the amphipod was unaffected after exposure to RDX or HMX at the highest concentrations of 1,000 and 400 mg/kg, respectively. Growth of the midge, measured as total weight, was significantly reduced by 2,4-DANT. However, significantly increased growth was observed after exposure to sublethal concentrations of RDX and HMX. Although significant reductions in amphipod survival were observed at high concentrations of TNB, growth was significantly increased at sublethal concentrations. The results of the current investigation suggest that organisms exposed to explosives at contaminated sites may be affected at concentrations less than 25 mg/kg through hormetic growth enhancement and at higher concentrations through increased mortality.

  19. Ventricular-Fold Dynamics in Human Phonation

    ERIC Educational Resources Information Center

    Bailly, Lucie; Bernardoni, Nathalie Henrich; Müller, Frank; Rohlfs, Anna-Katharina; Hess, Markus

    2014-01-01

    Purpose: In this study, the authors aimed (a) to provide a classification of the ventricular-fold dynamics during voicing, (b) to study the aerodynamic impact of these motions on vocal-fold vibrations, and (c) to assess whether ventricular-fold oscillations could be sustained by aerodynamic coupling with the vocal folds. Method: A 72-sample…

  20. Folding of a Cyclin Box

    PubMed Central

    Chemes, Lucía B.; Noval, María G.; Sánchez, Ignacio E.; de Prat-Gay, Gonzalo

    2013-01-01

    The retinoblastoma tumor suppressor (Rb) controls the proliferation, differentiation, and survival of cells in most eukaryotes with a role in the fate of stem cells. Its inactivation by mutation or oncogenic viruses is required for cellular transformation and eventually carcinogenesis. The high conservation of the Rb cyclin fold prompted us to investigate the link between conformational stability and ligand binding properties of the RbAB pocket domain. RbAB unfolding presents a three-state transition involving cooperative secondary and tertiary structure changes and a partially folded intermediate that can oligomerize. The first transition corresponds to unfolding of the metastable B subdomain containing the binding site for the LXCXE motif present in cellular and viral targets, and the second transition corresponds to the stable A subdomain. The low thermodynamic stability of RbAB translates into a propensity to rapidly oligomerize and aggregate at 37 °C (T50 = 28 min) that is suppressed by human papillomavirus E7 and E2F peptide ligands, suggesting that Rb is likely stabilized in vivo through binding to target proteins. We propose that marginal stability and associated oligomerization may be conserved for function as a “hub” protein, allowing the formation of multiprotein complexes, which could constitute a robust mechanism to retain its cell cycle regulatory role throughout evolution. Decreased stability and oligomerization are shared with the p53 tumor suppressor, suggesting a link between folding and function in these two essential cell regulators that are inactivated in most cancers and operate within multitarget signaling pathways. PMID:23632018

  1. Toxicity of hexahydro-1,3,5-trinitro-1,3,5-triazine to larval zebrafish (Danio rerio)

    USGS Publications Warehouse

    Mukhi, S.; Pan, X.; Cobb, G.P.; Patino, R.

    2005-01-01

    Hexahydro-1,3,5-trinitro-1,3,5-triazine, a cyclonitramine commonly known as RDX, is used in the production of military munitions. Contamination of soil, sediment, and ground and surface waters with RDX has been reported in different places around the world. Acute and subacute toxicities of RDX have been relatively well documented in terrestrial vertebrates, but among aquatic vertebrates the information available is limited. The objective of this study was to characterize the acute toxicity of RDX to larval zebrafish. Mortality (LC50) and incidence of vertebral column deformities (EC50) were two of the end points measured in this study. The 96-h LC50 was estimated at 22.98 and 25.64 mg l-1 in two different tests. The estimated no-observed-effective- concentration (NOEC) values of RDX on lethality were 13.27 ?? 0.05 and 15.32 ?? 0.30 mg l-1; and the lowest-observed-effective- concentration (LOEC) values were 16.52 ?? 0.05 and 19.09 ?? 0.23 mg l-1 in these two tests, respectively. The 96-h EC50 for vertebral deformities on survivors from one of the acute lethality tests was estimated at 20.84 mg l-1, with NOEC and LOEC of 9.75 ?? 0.34 and 12.84 ?? 0.34 mg l-1, respectively. Behavioral aberrations were also noted in this acute toxicity study, including the occurrence of whirling movement and lethargic behavior. The acute effects of RDX on survival, incidence of deformities, and behavior of larval zebrafish occurred at the high end of the most frequently reported concentrations of RDX in aquatic environments. The chronic effects of RDX in aquatic vertebrates need to be determined for an adequate assessment of the ecological risk of environmental RDX. ?? 2005 Elsevier Ltd. All rights reserved.

  2. Toxicity of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in three vertebrate species.

    PubMed

    Johnson, Mark S; McFarland, Craig A; Bazar, Matthew A; Quinn, Michael J; LaFiandra, Emily May; Talent, Larry G

    2010-04-01

    The explosive, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine or high-melting explosive (HMX), has been found in soils in areas used for testing and training by the military. Many of these areas contain habitat for valued wildlife species. In an effort to better understand the environmental consequences from exposure, a reptilian (western fence lizard [Sceloporus occidentalis]), an amphibian (red-backed salamander [Plethodon cinereus]), and a mammalian species (rabbit [Oryctolagus cuniculus]) were exposed to HMX under controlled laboratory conditions. Lizards and rabbits were exposed to HMX by way of corn oil through gavage, and salamanders were exposed to HMX in soil. Two deaths occurred from acute oral exposures to lizards to 5000 mg HMX/kg BW. Histological and gross pathologic assessment suggested gut impaction as a possible cause of death. Salamanders exposed to concentrations of HMX in soil < or = 1970 mg HMX/kg soil for 10 days did not show adverse effects. Rabbits, however, showed neurologic effects manifested as hyperkinetic events with convulsions at > 24 h after oral exposures. An LD(50) for rabbits was calculated as 93 mg/kg (95% confidence interval 76-117). A subacute 14-day testing regime found a lowest observed effect level of 10 mg/kg-d and a no observed adverse effect level of 5 mg/kg-d based on hyperkinesia and seizure incidence, although changes suggesting functional hepatic alterations were also found. These data suggest that physiologic differences between species, particularly in gastrointestinal structure and function, can affect the absorption of HMX and hence lead to marked differences in toxicity from exposure to the same compound. PMID:20012743

  3. Toxicity of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in three vertebrate species.

    PubMed

    Johnson, Mark S; McFarland, Craig A; Bazar, Matthew A; Quinn, Michael J; LaFiandra, Emily May; Talent, Larry G

    2010-04-01

    The explosive, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine or high-melting explosive (HMX), has been found in soils in areas used for testing and training by the military. Many of these areas contain habitat for valued wildlife species. In an effort to better understand the environmental consequences from exposure, a reptilian (western fence lizard [Sceloporus occidentalis]), an amphibian (red-backed salamander [Plethodon cinereus]), and a mammalian species (rabbit [Oryctolagus cuniculus]) were exposed to HMX under controlled laboratory conditions. Lizards and rabbits were exposed to HMX by way of corn oil through gavage, and salamanders were exposed to HMX in soil. Two deaths occurred from acute oral exposures to lizards to 5000 mg HMX/kg BW. Histological and gross pathologic assessment suggested gut impaction as a possible cause of death. Salamanders exposed to concentrations of HMX in soil < or = 1970 mg HMX/kg soil for 10 days did not show adverse effects. Rabbits, however, showed neurologic effects manifested as hyperkinetic events with convulsions at > 24 h after oral exposures. An LD(50) for rabbits was calculated as 93 mg/kg (95% confidence interval 76-117). A subacute 14-day testing regime found a lowest observed effect level of 10 mg/kg-d and a no observed adverse effect level of 5 mg/kg-d based on hyperkinesia and seizure incidence, although changes suggesting functional hepatic alterations were also found. These data suggest that physiologic differences between species, particularly in gastrointestinal structure and function, can affect the absorption of HMX and hence lead to marked differences in toxicity from exposure to the same compound.

  4. Elevated root retention of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in coniferous trees.

    PubMed

    Schoenmuth, Bernd; Mueller, Jakob O; Scharnhorst, Tanja; Schenke, Detlef; Büttner, Carmen; Pestemer, Wilfried

    2014-03-01

    For decades, the explosive RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) has been used for military and industrial applications. Residues of RDX pollute soils in large areas globally and the persistence and high soil mobility of these residues can lead to leaching into groundwater. Dendroremediation, i.e. the long-term use of trees to clean up polluted soils, is gaining acceptance as a green and sustainable strategy. Although the coniferous tree species Norway spruce and Scots pine cover large areas of military land in Central Europe, the potential of any coniferous tree for dendroremediation of RDX is still unknown. In this study, uptake experiments with a (14)C-labelled RDX solution (30 mg L(-1)) revealed that RDX was predominantly retained in the roots of 6-year-old coniferous trees. Only 23 % (pine) to 34 % (spruce) of RDX equivalents (RDXeq) taken up by the roots were translocated to aboveground tree compartments. This finding contrasts with the high aerial accumulation of RDXeq (up to 95 %) in the mass balances of all other plant species. Belowground retention of RDXeq is relatively stable in fine root fractions, since water leaching from tissue homogenates was less than 5 %. However, remobilisation from milled coarse roots and tree stubs reached up to 53 %. Leaching from homogenised aerial tree material was found to reach 64 % for needles, 58 % for stems and twigs and 40 % for spring sprouts. Leaching of RDX by precipitation increases the risk for undesired re-entry into the soil. However, it also opens the opportunity for microbial mineralisation in the litter layer or in the rhizosphere of coniferous forests and offers a chance for repeated uptake of RDX by the tree roots. PMID:24281674

  5. Chaperonin-mediated Protein Folding

    PubMed Central

    Horwich, Arthur L.

    2013-01-01

    We have been studying chaperonins these past twenty years through an initial discovery of an action in protein folding, analysis of structure, and elucidation of mechanism. Some of the highlights of these studies were presented recently upon sharing the honor of the 2013 Herbert Tabor Award with my early collaborator, Ulrich Hartl, at the annual meeting of the American Society for Biochemistry and Molecular Biology in Boston. Here, some of the major findings are recounted, particularly recognizing my collaborators, describing how I met them and how our great times together propelled our thinking and experiments. PMID:23803606

  6. Atomic-level description of ubiquitin folding

    PubMed Central

    Piana, Stefano; Lindorff-Larsen, Kresten; Shaw, David E.

    2013-01-01

    Equilibrium molecular dynamics simulations, in which proteins spontaneously and repeatedly fold and unfold, have recently been used to help elucidate the mechanistic principles that underlie the folding of fast-folding proteins. The extent to which the conclusions drawn from the analysis of such proteins, which fold on the microsecond timescale, apply to the millisecond or slower folding of naturally occurring proteins is, however, unclear. As a first attempt to address this outstanding issue, we examine here the folding of ubiquitin, a 76-residue-long protein found in all eukaryotes that is known experimentally to fold on a millisecond timescale. Ubiquitin folding has been the subject of many experimental studies, but its slow folding rate has made it difficult to observe and characterize the folding process through all-atom molecular dynamics simulations. Here we determine the mechanism, thermodynamics, and kinetics of ubiquitin folding through equilibrium atomistic simulations. The picture emerging from the simulations is in agreement with a view of ubiquitin folding suggested from previous experiments. Our findings related to the folding of ubiquitin are also consistent, for the most part, with the folding principles derived from the simulation of fast-folding proteins, suggesting that these principles may be applicable to a wider range of proteins. PMID:23503848

  7. Photosynthesis 3.5 thousand million years ago.

    PubMed

    Olson, J M; Pierson, B K

    1986-01-01

    The recent discovery of stromatolites and microfossils in 3.5-Ga-old sedimentary rock formations is evidence for the existence of phototrophic prokaryotes at that time. Values of δ(13)C for sedimentary organic carbon strongly suggest autotrophic CO2 fixation, and the existence of large deposits of sedimentary sulfate is consistent with a photosynthesis dependent on reduced sulfur compounds for reducing power. The ancient photoautotrophs are though to have contained only one kind of reaction center with either chlorophyll a or bacteriochlorophyll a as primary electron donor and with one or more iron-sulfur centers as secondary electron acceptors. Light-harvesting pigments might have been chlorophyll a, bacteriochlorophyll a, or possibly bacteriochlorophyll c.A new proposal is made to explain how these organisms could have survived an intense UV flux at the earth's surface in the absence of an ozone layer. Photochemically produced ferric iron was abundant in sediments, and the UV-absorption of this ferric iron would have been sufficient to shield those organisms living below the watersediment interface.

  8. Improving protein fold recognition by random forest

    PubMed Central

    2014-01-01

    Background Recognizing the correct structural fold among known template protein structures for a target protein (i.e. fold recognition) is essential for template-based protein structure modeling. Since the fold recognition problem can be defined as a binary classification problem of predicting whether or not the unknown fold of a target protein is similar to an already known template protein structure in a library, machine learning methods have been effectively applied to tackle this problem. In our work, we developed RF-Fold that uses random forest - one of the most powerful and scalable machine learning classification methods - to recognize protein folds. Results RF-Fold consists of hundreds of decision trees that can be trained efficiently on very large datasets to make accurate predictions on a highly imbalanced dataset. We evaluated RF-Fold on the standard Lindahl's benchmark dataset comprised of 976 × 975 target-template protein pairs through cross-validation. Compared with 17 different fold recognition methods, the performance of RF-Fold is generally comparable to the best performance in fold recognition of different difficulty ranging from the easiest family level, the medium-hard superfamily level, and to the hardest fold level. Based on the top-one template protein ranked by RF-Fold, the correct recognition rate is 84.5%, 63.4%, and 40.8% at family, superfamily, and fold levels, respectively. Based on the top-five template protein folds ranked by RF-Fold, the correct recognition rate increases to 91.5%, 79.3% and 58.3% at family, superfamily, and fold levels. Conclusions The good performance achieved by the RF-Fold demonstrates the random forest's effectiveness for protein fold recognition. PMID:25350499

  9. Learning Protein Folding Energy Functions

    PubMed Central

    Guan, Wei; Ozakin, Arkadas; Gray, Alexander; Borreguero, Jose; Pandit, Shashi; Jagielska, Anna; Wroblewska, Liliana; Skolnick, Jeffrey

    2014-01-01

    A critical open problem in ab initio protein folding is protein energy function design, which pertains to defining the energy of protein conformations in a way that makes folding most efficient and reliable. In this paper, we address this issue as a weight optimization problem and utilize a machine learning approach, learning-to-rank, to solve this problem. We investigate the ranking-via-classification approach, especially the RankingSVM method and compare it with the state-of-the-art approach to the problem using the MINUIT optimization package. To maintain the physicality of the results, we impose non-negativity constraints on the weights. For this we develop two efficient non-negative support vector machine (NNSVM) methods, derived from L2-norm SVM and L1-norm SVMs, respectively. We demonstrate an energy function which maintains the correct ordering with respect to structure dissimilarity to the native state more often, is more efficient and reliable for learning on large protein sets, and is qualitatively superior to the current state-of-the-art energy function. PMID:25311546

  10. All-or-none folding of a polymer in confinement

    NASA Astrophysics Data System (ADS)

    Taylor, Mark

    A flexible homopolymer chain with sufficiently short-range interactions undergoes a discontinuous transition from an expanded coil to a compact crystallite analogous to the all-or-none folding transition exhibited by fast-folding proteins. One anticipates that geometric confinement will reduce the entropy of the unfolded chain, thereby stabilizing the folded state and shifting the transition to higher temperature. In this work we study a flexible square-well N-mer chain (monomer diameter d) located between two hard walls forming a slit-like pore (width W) with the chain end-tethered to one wall. We carry out Monte simulations with Wang-Landau sampling to construct the single-chain density of states and use both microcanonical and canonical analyses to characterize phase transitions. When the slit width is similar to the size of the folded chain we observe a modest stabilization effect. Further reduction of the slit width geometrically prohibits the chain from folding into the free-chain ground state. However, a discontinuous all-or-none folding transition still occurs to a flattened crystallite that spans the pore. All-or-none folding persists even to the limit of a very narrow pore (W d) where the ground-state structure is a quasi-two-dimensional crystal. Funding: NSF DMR-1204747.

  11. Thermal oxidation of 3-5 compound semiconductors

    NASA Astrophysics Data System (ADS)

    Monteironeto, Othon Derego

    1988-11-01

    Thermal oxidation of 3-5 compound semiconductors has been studied in the temperature range of 300 to 600 C. Two members of this class of materials, namely InP and GaAs, were the object of the experimental work carried out here. The main analytical tools used were transmission electron microscopy (TEM) and secondary ion mass spectroscopy (SIMS). TEM was employed to access microstructural changes and SIMS to access the composition redistribution that takes place as a consequence of the oxidation reaction. Below 400 C oxidation of both materials led to the formation of amorphous scales, which consisted of a mixture of gallium and arsenic oxides in the case of GaAs, and indium phosphate and oxide in the case of InP. The oxidation kinetics of InP was found to be slower than that of GaAs. In the high temperature regime, i.e., above 400 C, the oxidation of both materials resulted in crystalline products. Precipitation of the group 5 element at the scale/semiconductor interface took place during oxidation. At the GaAs/Ga2O3interface, As precipitates were formed with a truncated square pyramid shape bound by (111) sub GaAs planes. The precipitates found at the InPO4/InP interface were either a phosphorus rich phase or red phosphorus. Strong vaporization under the electron beam prohibited a more accurate determination. The morphology of those precipitates were very similar to the As ones in GaAs.

  12. Tuning the formations of metal-1,3,5-benzenetricarboxylate frameworks via the assistance of amino acids

    SciTech Connect

    Lei, Xiao-Ping; Lian, Ting-Ting; Chen, Shu-Mei; Zhang, Jian

    2015-03-15

    Seven new metal-1,3,5-benzenetricarboxylate coordination polymers have been synthesized by modification of auxiliary components during the assembly reactions. Their structures have been determined by single-crystal X-ray diffraction analyses and further characterized by XRD and TGA. Interestingly, they show fascinating topological structures. Compounds 1 and 2 possess the undulating layer structure with 3-connected hcb network and (3,6)-connected kgd network. Compound 3 possesses three-dimensional (3D) pillared-layer structure with 3-connected 2-fold interpenetrating srs net. Compound 4 also has the 3D 2-fold interpenetrating pillared-layer structure; however, it has (3,5)-connected hms topology because the Cd(II) center is 5-connected. Compound 5 possess 3D structure through hydrogen bonding interactions between ladder-like layers. Compounds 6 and 7 have the similar 3D frameworks with 4-connected umc net and (3,7)-connected (3.4.5)(3{sup 2}.4{sup 6}.5{sup 5}.6{sup 8}) topology, respectively. The photoluminescent properties of compounds 2–7 were also investigated. - Graphical abstract: Presented here are seven new metal-1,3,5-benzenetricarboxylate coordination polymers with diverse structures from 2D layers to 3D open frameworks. The synthesis and structural diversity of these compounds are determined by the additional amino acids as unusual buffering agents. - Highlights: • Structural diversity of metal-1,3,5-benzenetricarboxylate frameworks. • Tuning structural topologies of MOFs via the assistance of amino acids. • Amino acids as unusual buffering agents for the synthesis of MOFs.

  13. Six-fold coordinated carbon dioxide VI

    SciTech Connect

    Iota, Valentin; Yoo, Choong-Shik; Klepeis, Jae-Hyun; Jenei, Zsolt; Evans, William; Cynn, Hyunchae

    2008-06-16

    Under standard conditions, carbon dioxide (CO{sub 2}) is a simple molecular gas and an important atmospheric constituent, whereas silicon dioxide (SiO{sub 2}) is a covalent solid, and one of the fundamental minerals of the planet. The remarkable dissimilarity between these two group IV oxides is diminished at higher pressures and temperatures as CO{sub 2} transforms to a series of solid phases, from simple molecular to a fully covalent extended-solid V, structurally analogous to SiO{sub 2} tridymite. Here, we present the discovery of an extended-solid phase of CO{sub 2}: a six-fold coordinated stishovite-like phase VI, obtained by isothermal compression of associated CO{sub 2}-II above 50 GPa at 530-650 K. Together with the previously reported CO{sub 2}-V and a-carbonia, this extended phase indicates a fundamental similarity between CO{sub 2} (a prototypical molecular solid) and SiO{sub 2} (one of Earth's fundamental building blocks). We present a phase diagram with a limited stability domain for molecular CO{sub 2}-I, and suggest that the conversion to extended-network solids above 40-50 GPa occurs via intermediate phases II, III and IV. The crystal structure of phase VI suggests strong disorder along the c axis in stishovite-like P4{sub 2}/mnm, with carbon atoms manifesting an average six-fold coordination within the framework of sp{sup 3} hybridization.

  14. Elastic energy of proteins and the stages of protein folding

    NASA Astrophysics Data System (ADS)

    Lei, J.; Huang, K.

    2009-12-01

    We propose a universal elastic energy for proteins, which depends only on the radius of gyration Rg and the residue number N. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable parameters are fitted to data from the computer simulation of the folding of a set of proteins using the CSAW (conditioned self-avoiding walk) model. The elastic energy gives rise to scaling relations of the form Rg~Nν in different regions. It shows three folding stages characterized by the progression with exponents ν=3/5, 3/7, 2/5, which we identify as the unfolded stage, pre-globule, and molten globule, respectively. The pre-globule goes over to the molten globule via a break in behavior akin to a first-order phase transition, which is initiated by a sudden acceleration of hydrogen bonding.

  15. Homeostasis of Hyaluronic Acid in Normal and Scarred Vocal Folds

    PubMed Central

    Tateya, Ichiro; Tateya, Tomoko; Watanuki, Makoto; Bless, Diane M.

    2015-01-01

    Summary Objectives/Hypothesis Vocal fold scarring is one of the most challenging laryngeal disorders to treat. Hyaluronic acid (HA) is the main component of lamina propria, and it plays an important role in proper vocal fold vibration and is also thought to be important in fetal wound healing without scarring. Although several animal models of vocal fold scarring have been reported, little is known about the way in which HA is maintained in vocal folds. The purpose of this study was to clarify the homeostasis of HA by examining the expression of hyaluronan synthase (Has) and hyaluronidase (Hyal), which produce and digest HA, respectively. Study Design Experimental prospective animal study. Methods Vocal fold stripping was performed on 38 Sprague-Dawley rats. Vocal fold tissue was collected at five time points (3 days–2 months). Expression of HA was examined by immunohistochemistry, and messenger RNA (mRNA) expression of Has and Hyal was examined by real-time polymerase chain reaction and in-situ hybridization. Results In scarred vocal folds, expression of Has1 and Has2 increased at day 3 together with expression of HA and returned to normal at 2 weeks. At 2 months, Has3 and Hyal3 mRNA showed higher expressions than normal. Conclusions Expression patterns of Has and Hyal genes differed between normal, acute-scarred, and chronic-scarred vocal folds, indicating the distinct roles of each enzyme in maintaining HA. Continuous upregulation of Has genes in the acute phase may be necessary to achieve scarless healing of vocal folds. PMID:25499520

  16. Geometry of Miura-folded metamaterials

    PubMed Central

    Schenk, Mark; Guest, Simon D.

    2013-01-01

    This paper describes two folded metamaterials based on the Miura-ori fold pattern. The structural mechanics of these metamaterials are dominated by the kinematics of the folding, which only depends on the geometry and therefore is scale-independent. First, a folded shell structure is introduced, where the fold pattern provides a negative Poisson’s ratio for in-plane deformations and a positive Poisson’s ratio for out-of-plane bending. Second, a cellular metamaterial is described based on a stacking of individual folded layers, where the folding kinematics are compatible between layers. Additional freedom in the design of the metamaterial can be achieved by varying the fold pattern within each layer. PMID:23401549

  17. Paper Folding for the Mathematics Class.

    ERIC Educational Resources Information Center

    Johnson, Donovan A.

    Directions are given for folding paper to show geometric figures and relationships. Topics covered are folding the basic constructions, geometric concepts concerning triangles and quadrilaterals, circle relationships, products and factors, polygon constructions, symmetry, conic sections, and recreations. (DT)

  18. The parallel universe of RNA folding.

    PubMed

    Batey, R T; Doudna, J A

    1998-05-01

    How do large RNA molecules find their active conformations among a universe of possible structures? Two recent studies reveal that RNA folding is a rapid and ordered process, with surprising similarities to protein folding mechanisms.

  19. Extracting Information from Folds in Rocks.

    ERIC Educational Resources Information Center

    Hudleston, Peter John

    1986-01-01

    Describes the three processes of folding in rocks: buckling, bending, and passive folding. Discusses how geometrical properties and strain distributions help to identify which processes produce natural folds, and also provides information about the mechanical properties of rocks, and the sense of shear in shear zones. (TW)

  20. Dynamics of Folds in the Plane

    ERIC Educational Resources Information Center

    Krylov, Nikolai A.; Rogers, Edwin L.

    2011-01-01

    Take a strip of paper and fold a crease intersecting the long edges, creating two angles. Choose one edge and consider the angle with the crease. Fold the opposite edge along the crease, creating a new crease that bisects the angle. Fold again, this time using the newly created crease and the initial edge, creating a new angle along the chosen…

  1. Surgical revision of the upper eyelid fold.

    PubMed

    Cies, W A; Baylis, H I

    1975-12-01

    We performed surgery on 107 patients primarily with blepharoptosis and eyelid fold abnormalities, between 1973 and 1974. Production of an eyelid fold at the time of an initial blepharoptosis procedure should be a primary goal. Lack of a distinct symmetrical upper eyelid fold constituted a cosmetic blemish and necessitated revision.

  2. Accumulation of hexahydro-1,3,5-trinitro-1,3,5-triazine by the earthworm Eisenia andrei in a sandy loam soil.

    PubMed

    Sarrazin, Manon; Dodard, Sabine G; Savard, Kathleen; Lachance, Bernard; Robidoux, Pierre Y; Kuperman, Roman G; Hawari, Jalal; Ampleman, Guy; Thiboutot, Sonia; Sunahara, Geoffrey I

    2009-10-01

    The heterocyclic polynitramine hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a highly energetic compound found as a soil contaminant at some defense installations. Although RDX is not lethal to soil invertebrates at concentrations up to 10,000 mg/kg, it decreases earthworm cocoon formation and juvenile production at environmentally relevant concentrations found at contaminated sites. Very little is known about the uptake of RDX in earthworms and the potential risks for food-chain transfer of RDX in the environment. Toxicokinetic studies were conducted to quantify the bioaccumulation factors (BAFs) using adult earthworms (Eisenia andrei) exposed for up to 14 d to sublethal concentrations of nonlabeled RDX or [14C]RDX in a Sassafras sandy loam soil. High-performance liquid chromatography of acetonitrile extracts of tissue and soil samples indicated that nonlabeled RDX can be accumulated by the earthworm in a concentration- and time-dependent manner. The BAF, expressed as the earthworm tissue to soil concentration ratio, decreased from 6.7 to 0.1 when the nominal soil RDX concentrations were increased from 1 to 10,000 mg/kg. Tissue concentrations were comparable in earthworms exposed to nonlabeled RDX or [14C]RDX. The RDX bioaccumulation also was estimated using the kinetically derived model (BAFK), based on the ratio of the uptake to elimination rate constants. The established BAFK of 3.6 for [14C]RDX uptake was consistent with the results for nonlabeled RDX. Radioactivity also was present in the tissue residues of [14C]RDX-exposed earthworms following acetonitrile extraction, suggesting the formation of nonextractable [14C]RDX metabolites associated with tissue macromolecules. These findings demonstrated a net accumulation of RDX in the earthworm and the potential for food-chain transfer of RDX to higher-trophic-level receptors.

  3. Control and localization of rat adrenal cyclic guanosine 3', 5'-monophosphate. Comparison with adrenal cyclic adenosine 3', 5'-monophosphate.

    PubMed Central

    Whitley, T H; Stowe, N W; Ong, S H; ey, R L; Steiner, A L

    1975-01-01

    Cyclic AMP and cyclic GMP were measured in rat adrenal glands after either hypophysectomy alone or after hypophysectomy and treatment with ACTH. Adrenal cyclic GMP levels rise in acutely hypophysectomized rats to a maximum at 1 h of approximately 200% of control levels; there is a return to base line at 4-12 h after hypophysectomy. In contrast, adrenal cyclic AMP falls immediately to about 50% of control levels after hypophysectomy and remains at approximately 1 pmol per mg tissue. Doses of ACTH beyond the physiological range markedly suppress adrenal cyclic GMP while producing a 50-fold or greater rise in cyclic AMP in hypophysectomized rats. This pattern of adrenal cyclic GMP rise was unchanged in acutely hypophysectomized animals treated with desamethasone. N-6-2'-0 dibutyryl cyclic AMP acted similarly to the effect of ACTH in bringing about a suppression of adrenal cyclic GMP levels. Physiological i.v. pulse doses of ACTH produced a rapid dose related increase in adrenal cyclic GMP. In vitro incubation of quartered adrenal pairs with 500 mU ACTH produced elevated cyclic AMP levels and suppression of cyclic GMP. Whereas adrenal cyclic AMP fell rapidly to 50% of control levels after hypophysectomy and remained at about 1 pmol per mg tissue for 7 days, adrenal cyclic GMP showed a biphasic rhythm in long-term hypophysectomized animals. After an initial peak at 1 h after hypophysectomy, adrenal cyclic GMP declined to baseline at 4-12 h but thereafter progressively rose with time, eventually reaching levels over 1 pmol per mg tissue. Fluorescent immunocytochemical staining of rat adrenal zona fasciculata showed cyclic AMP largely confined to cytoplasmic elements with little fluorescence contained in nuclei. In constant, cyclic GMP was found discretely positioned in nuclei with prominent fluorescence in nucleoli in addition to cytoplasmic localization. It is concluded that in hypophysectomized rats ACTH, either directly or in conjunction with altertion of adrenal

  4. Understanding Protein Non-Folding

    PubMed Central

    Uversky, Vladimir N.; Dunker, A. Keith

    2010-01-01

    This review describes the family of intrinsically disordered proteins, members of which fail to form rigid 3-D structures under physiological conditions, either along their entire lengths or only in localized regions. Instead, these intriguing proteins/regions exist as dynamic ensembles within which atom positions and backbone Ramachandran angles exhibit extreme temporal fluctuations without specific equilibrium values. Many of these intrinsically disordered proteins are known to carry out important biological functions which, in fact, depend on the absence of specific 3-D structure. The existence of such proteins does not fit the prevailing structure-function paradigm, which states that unique 3-D structure is a prerequisite to function. Thus, the protein structure-function paradigm has to be expanded to include intrinsically disordered proteins and alternative relationships among protein sequence, structure, and function. This shift in the paradigm represents a major breakthrough for biochemistry, biophysics and molecular biology, as it opens new levels of understanding with regard to the complex life of proteins. This review will try to answer the following questions: How were intrinsically disordered proteins discovered? Why don't these proteins fold? What is so special about intrinsic disorder? What are the functional advantages of disordered proteins/regions? What is the functional repertoire of these proteins? What are the relationships between intrinsically disordered proteins and human diseases? PMID:20117254

  5. Protein folding in the endoplasmic reticulum: lessons from the human chorionic gonadotropin beta subunit.

    PubMed Central

    Ruddon, R. W.; Sherman, S. A.; Bedows, E.

    1996-01-01

    There have been few studies of protein folding in the endoplasmic reticulum of intact mammalian cells. In the one case where the in vivo and in vitro folding pathways of a mammalian secretory protein have been compared, the folding of the human chorionic gonadotropin beta subunit (hCG-beta), the order of formation of the detected folding intermediates is the same. The rate and efficiency with which multidomain proteins such as hCG-beta fold to native structure in intact cells is higher than in vitro, although intracellular rates of folding of the beta subunit can be approached in vitro in the presence of an optimal redox potential and protein disulfide isomerase. Understanding how proteins fold in vivo may provide a new way to diagnose and treat human illnesses that occur due to folding defects. PMID:8844836

  6. Identification of the molecular basis for the functional difference between flavonoid 3'-hydroxylase and flavonoid 3',5'-hydroxylase.

    PubMed

    Seitz, Christian; Ameres, Stefanie; Forkmann, Gert

    2007-07-24

    Flavonoid 3'-hydroxylase (F3'H) and flavonoid 3',5'-hydroxylase (F3'5'H) are cytochrome P450 enzymes and determine the B-ring hydroxylation pattern of flavonoids by introducing hydroxyl groups at the 3'- or the 3'- and 5'-position, respectively. Sequence identity between F3'H and F3'5'H is generally low since their divergence took place early in the evolution of higher plants. However, in the Asteraceae the family-specific evolution of an F3'5'H from an F3'H precursor occurred, and consequently sequence identity is substantially higher. We used this phenomenon for alignment studies, in order to identify regions which could be involved in determining substrate specificity and functionality. Subsequent construction and expression of chimeric genes indicated that substrate specificity of F3'H and F3'5'H is determined near the N-terminal end and the functional difference between these two enzymes near the C-terminal end. The impact on function of individual amino acids located in substrate recognition site 6 (SRS6) was further tested by site-directed mutagenesis. Most interestingly, a conservative Thr to Ser exchange at position 487 conferred additional 5'-hydroxylation activity to recombinant Gerbera hybrida F3'H, whereas the reverse substitution transformed recombinant Osteospermum hybrida F3'5'H into an F3'H with low remaining 5'-hydroxylation activity. Since the physicochemical properties of Thr and Ser are highly similar, the difference in size appears to be the main factor contributing to functional difference. The results further suggest that relatively few amino acids exchanges were required for the evolutionary extension of 3'- to 3',5'-hydroxylation activity.

  7. Folding of viscous sheets and filaments

    NASA Astrophysics Data System (ADS)

    Skorobogatiy, M.; Mahadevan, L.

    2000-12-01

    We consider the nonlinear folding behavior of a viscous filament or a sheet under the influence of an external force such as gravity. Everyday examples of this phenomenon are provided by the periodic folding of a sheet of honey as it impinges on toast, or the folding of a stream of shampoo as it falls on one's hand. To understand the evolution of a fold, we formulate and solve a free-boundary problem for the phenomenon, give scaling laws for the size of the folds and the frequency with which they are laid out, and verify these experimentally.

  8. The effect of free radicals on hepatic 5'-monodeiodination of thyroxine and 3,3',5'-triiodothyronine.

    PubMed

    Huang, T S; Boado, R J; Chopra, I J; Solomon, D H; Teco, G N

    1987-08-01

    Free radicals have been implicated in many pathological processes, including ischemia, inflammation, and malignancy. Since a reduction in extrathyroidal outer ring monodeiodination of T4 and rT3 occurs in virtually all systemic illnesses, we have studied the effect of free radicals on iodothyronine (T4 and rT3) 5'-monodeiodinating activity (MA) of liver tissue in vitro. Rat liver microsomes or homogenate were preincubated in Tris buffer for 30 min with a free radical-generating system (FRGS) and then incubated with T4 (2.5 microM) or [125I]rT3 (0.4 nM) and dithiothreitol (DTT; 5-20 mM with T4 and 20-150 mM with [125I]rT3) in the same buffer for 10 or 30 min. T3 generated during incubation was quantified by RIA of ethanol extracts of the incubation mixture. 125I generated from [125I]rT3 was quantified after precipitation of the incubation mixture with trichloroacetic acid or by paper chromatography. Free radicals caused 55% or more reduction in hepatic T4 MA and 44% or more reduction in rT3 MA in various experiments. The inhibition of hepatic rT3 MA after incubation with FRGS persisted despite removal of FRGS and washing of microsomes preincubated with FRGS before studying the MA. However, inclusion of DTT (1-60 mM) during preincubation of tissue with FRGS prevented the FRGS-induced inhibition of rT3 MA. Depletion of the iodothyronine substrate did not occur when FRGS inhibited T4 and rT3 5'-monodeiodination. Free radical scavengers, i.e. superoxide dismutase (600 IU/ml), catalase (300 U/ml), tocopherol (10 mg/ml), thiourea (0.15 M), and tert-butanol (0.15 M), all significantly reduced the inhibition of hepatic rT3 MA caused by FRGS. The FRGS-induced inhibition of hepatic T4 MA was reduced by the same doses of tocopherol, thiourea, and tert-butanol, but not by superoxide dismutase or catalase. Since free radicals may effect tissue damage by lipid peroxidation and since the latter results in generation of malondialdehyde (MDA) as a by-product of the reaction, we

  9. Anatomy and Histology of an Epicanthal Fold.

    PubMed

    Park, Jae Woo; Hwang, Kun

    2016-06-01

    The aim of this study is to elucidate the precise anatomical and histological detail of the epicanthal fold.Thirty-two hemifaces of 16 Korean adult cadavers were used in this study (30 hemifaces with an epicanthal fold, 2 without an epicanthal fold). In 2 patients who had an epicanthoplasty, the epicanthal folds were sampled.In a dissection, the periorbital skin and subcutaneous tissues were removed and the epicanthal fold was observed in relation to each part of the orbicularis oculi muscle. Specimens including the epicanthal fold were embeddedin in paraffin, sectioned at 10 um, and stained with Hematoxylin-Eosin. The horizontal section in the level of the paplebral fissure was made and the prepared slides were observed under a light microscope.In the specimens without an epicanthal fold, no connection between the upper preseptal muscle and the lower preseptal muscle was found. In the specimens with an epicanthal fold, a connection of the upper preseptal muscle to the lower preseptal muscle was observed. It was present in all 15 hemifaces (100%). There was no connection between the pretarsal muscles. In a horizontal section, the epicanthal fold was composed of 3 compartments: an outer skin lining, a core structure, and an innerskin lining. The core structure was mainly composed of muscular fibers and fibrotic tissue and they were intermingled.Surgeons should be aware of the anatomical details of an epicanthal fold. In removing or reconstructing an epicanthal fold, the fibromuscular core band should also be removed or reconstructed.

  10. Geomorphology and fold growth, southern Tunisia.

    NASA Astrophysics Data System (ADS)

    Ahamadi, R.; Mercier, E.; Ouali, J.; van Vliet-Lanoë, B.; Mansy, J. L.; Launeau, P.; Rekis, F.

    2003-04-01

    At the northern edge of the Gafsa basin, a fold belt, the Metlaoui chain mostly rised from the Upper Miocene till today [1]. This region, endoreic since the Oligocene, is for lithologic and climate reasons a good laboratory to test various theories concerning fold growth. The origin of the fold belt is link to a main detachment level at the base of the Jurassic series (seismic profiles). The folding is facilitate with few strong calcareous beds by the dominance of soft lithologic series. This enhances the sliding along secondary detachment levels. Geomorphological, hydrological and chronological arguments prove that the folds mostly deformed as a "fault propagation fold" [2]. Furthermore, detailed field observations validate several features first observed by modelling of "fault propagation fold": 1) the stability of the roof of the fold, 2) the propagation of a knock-fold in front of the fold, disturbing the shape of pediments [3] and 3) the backward migration and extent of the backslope of the fold, in association with a backward migration of the depot centre of the syntectonic sedimentation. [1] Outtani, F., B. Addoum, E. Mercier, D. Frizon de Lamotte, J. Andrieux, Tectonophysics, 249, 233-248, 1995. [2] Suppe, J., and D.A. Medwedeff, , Eclogae geol. Helv., 83(3), 409-454, 1990. [3] Rafini S. and E. Mercier (2002). Sedimentary Geology, 146, 75-89

  11. Efficient biocatalytic synthesis of (R)-[3,5-bis(trifluoromethyl)phenyl] ethanol by a newly isolated Trichoderma asperellum ZJPH0810 using dual cosubstrate: ethanol and glycerol.

    PubMed

    Li, Jun; Wang, Pu; He, Jun-Yao; Huang, Jin; Tang, Jun

    2013-08-01

    (R)-[3,5-bis(trifluoromethyl)phenyl] ethanol is a crucial intermediate for the synthesis of Aprepitant. An efficient biocatalytic process for (R)-[3,5-bis(trifluoromethyl)phenyl] ethanol was developed via the asymmetric reduction of 3,5-bis(trifluoromethyl) acetophenone, catalyzed by whole cells of newly isolated Trichoderma asperellum ZJPH0810 using ethanol and glycerol as dual cosubstrate for cofactor recycling. A fungal strain ZJPH0810, showing asymmetric biocatalytic activity of 3,5-bis(trifluoromethyl) acetophenone to its corresponding (R)-[3,5-bis(trifluoromethyl)phenyl] ethanol, was isolated from a soil sample. Based on its morphological and physiological characteristics and internal transcribed spacer sequence, this isolate was identified as T. asperellum ZJPH0810, which afforded an NADH-dependent (R)-stereospecific carbonyl reductase and was a promising biocatalyst for the synthesis of (R)-[3,5-bis(trifluoromethyl)phenyl] ethanol. Some key reaction parameters involved in the bioreduction catalyzed by T. asperellum ZJPH0810 were subsequently optimized. The effectiveness of (R)-[3,5-bis(trifluoromethyl)phenyl] ethanol production was significantly enhanced by employing a novel dual cosubstrate-coupled system for cofactor recycling. The established efficient bioreduction system contained 50 mM of 3,5-bis(trifluoromethyl) acetophenone and 60 g l(-1) of resting cells, employing ethanol (6.0 %, v/v) and glycerol (0.5 %, v/v) as dual cosubstrate. The bioreduction was performed in distilled water medium, at 30 °C and 200 rpm. Under the above conditions, a best yield of 93.4 % was obtained, which is nearly a 3.5-fold increase in contrast to no addition of cosubstrate. The ee value of the product reached above 98 %. This biocatalytic process shows great potential in the production of (R)-[3,5-bis(trifluoromethyl)phenyl] ethanol, a valuable chiral building block in the pharmaceutical industry.

  12. Six-fold Coordinated Carbon Dioxide VI

    SciTech Connect

    Iota, V; Yoo, C; Klepeis, J; Jenei, Z

    2006-03-01

    Under standard conditions, carbon dioxide (CO{sub 2}) is a simple molecular gas and an important atmospheric constituent while silicon dioxide (SiO{sub 2}) is a covalent solid, and represents one of the fundamental minerals of the planet. The remarkable dissimilarity between these two group IV oxides is diminished at higher pressures and temperatures as CO{sub 2} transforms to a series of solid phases, from simple molecular to a fully covalent extended-solid V, structurally analogous to SiO{sub 2} tridymite. Here, we present the discovery of a new extended-solid phase of carbon dioxide (CO{sub 2}): a six-fold coordinated stishovite-like phase VI, obtained by isothermal compression of associated CO{sub 2}-II above 50GPa at 530-650K. Together with the previously reported CO{sub 2}-V and a-carbonia, this new extended phase indicates a fundamental similarity between CO{sub 2}--a prototypical molecular solid, and SiO{sub 2}--one of Earth's fundamental building blocks. The phase diagram suggests a limited stability domain for molecular CO{sub 2}-I, and proposes that the conversion to extended-network solids above 40-50 GPa occurs via intermediate phases II, III, and IV. The crystal structure of phase VI suggests strong disorder along the caxis in stishovite-like P4{sub 2}/mnm, with carbon atoms manifesting an average six-fold coordination within the framework of sp{sup 3} hybridization.

  13. STAT3/5-Dependent IL9 Overexpression Contributes to Neoplastic Cell Survival in Mycosis Fungoides

    PubMed Central

    Vieyra-Garcia, Pablo A.; Wei, Tianling; Naym, David Gram; Fredholm, Simon; Fink-Puches, Regina; Cerroni, Lorenzo; Odum, Niels; O'Malley, John T.; Gniadecki, Robert; Wolf, Peter

    2016-01-01

    Purpose Sustained inflammation is a key feature of mycosis fungoides (MF), the most common form of cutaneous T-cell lymphoma (CTCL). Resident IL9–producing T cells have been found in skin infections and certain inflammatory skin diseases, but their role in MF is currently unknown. Experimental Design We analyzed lesional skin from patients with MF for the expression of IL9 and its regulators. To determine which cells were producing IL9, high-throughput sequencing was used to identify malignant clones and Vb-specific antibodies were employed to visualize malignant cells in histologic preparations. To explore the mechanism of IL9 secretion, we knocked down STAT3/5 and IRF4 by siRNA transfection in CTCL cell lines receiving psoralen+UVA (PUVA) ± anti-IL9 antibody. To further examine the role of IL9 in tumor development, the EL-4 T-cell lymphoma model was used in C57BL/6 mice. Results Malignant and reactive T cells produce IL9 in lesional skin. Expression of the Th9 transcription factor IRF4 in malignant cells was heterogeneous, whereas reactive T cells expressed it uniformly. PUVA or UVB phototherapy diminished the frequencies of IL9- and IL9r-positive cells, as well as STAT3/5a and IRF4 expression in lesional skin. IL9 production was regulated by STAT3/5 and silencing of STAT5 or blockade of IL9 with neutralizing antibodies potentiated cell death after PUVA treatment in vitro. IL9-depleted mice exhibited a reduction of tumor growth, higher frequencies of regulatory T cells, and activated CD4 and CD8 T lymphocytes. Conclusion Our results suggest that IL9 and its regulators are promising new targets for therapy development in mycosis fungoides. PMID:26851186

  14. Reduced alphabet for protein folding prediction.

    PubMed

    Huang, Jitao T; Wang, Titi; Huang, Shanran R; Li, Xin

    2015-04-01

    What are the key building blocks that would have been needed to construct complex protein folds? This is an important issue for understanding protein folding mechanism and guiding de novo protein design. Twenty naturally occurring amino acids and eight secondary structures consist of a 28-letter alphabet to determine folding kinetics and mechanism. Here we predict folding kinetic rates of proteins from many reduced alphabets. We find that a reduced alphabet of 10 letters achieves good correlation with folding rates, close to the one achieved by full 28-letter alphabet. Many other reduced alphabets are not significantly correlated to folding rates. The finding suggests that not all amino acids and secondary structures are equally important for protein folding. The foldable sequence of a protein could be designed using at least 10 folding units, which can either promote or inhibit protein folding. Reducing alphabet cardinality without losing key folding kinetic information opens the door to potentially faster machine learning and data mining applications in protein structure prediction, sequence alignment and protein design.

  15. Some aspects of vocal fold bowing.

    PubMed

    Tanaka, S; Hirano, M; Chijiwa, K

    1994-05-01

    Bowing of the vocal fold frequently occurs in patients with vocal fold paralysis (VFP), those with sulcus vocalis, and those who have had laser surgery. Additionally, there are vocal folds that present bowing with no noticeable organic lesion. For the purpose of investigating the causes and mechanisms of vocal fold bowing, consecutive fiberscopic videorecordings of 127 patients with VFP, 33 with sulcus vocalis, 33 with laser surgery, and 33 with dysphonia having no clinically noticeable organic lesion were reviewed. Sixty-nine percent of the paralyzed vocal folds had bowing, and the occurrence of bowing was significantly related to the activity of the thyroarytenoid muscle as measured by electromyography. The cricothyroid activity had no significant relationship to vocal fold bowing. All vocal folds with sulcus presented with bowing. Thirty-five percent of the vocal folds that had had laser surgery had bowing. The extent of tissue removal was closely related to the occurrence of bowing. Twelve cases with no organic lesion had vocal fold bowing. Of these 12 patients, 8 were male and 9 were older than 60 years. Some aging process in the mucosa was presumed to be the cause of the bowing in this age group of patients without clinically noticeable organic lesions. Causes of vocal fold bowing in the younger group of patients without organic lesions were not determined in this study.

  16. Some aspects of vocal fold bowing.

    PubMed

    Tanaka, S; Hirano, M; Chijiwa, K

    1994-05-01

    Bowing of the vocal fold frequently occurs in patients with vocal fold paralysis (VFP), those with sulcus vocalis, and those who have had laser surgery. Additionally, there are vocal folds that present bowing with no noticeable organic lesion. For the purpose of investigating the causes and mechanisms of vocal fold bowing, consecutive fiberscopic videorecordings of 127 patients with VFP, 33 with sulcus vocalis, 33 with laser surgery, and 33 with dysphonia having no clinically noticeable organic lesion were reviewed. Sixty-nine percent of the paralyzed vocal folds had bowing, and the occurrence of bowing was significantly related to the activity of the thyroarytenoid muscle as measured by electromyography. The cricothyroid activity had no significant relationship to vocal fold bowing. All vocal folds with sulcus presented with bowing. Thirty-five percent of the vocal folds that had had laser surgery had bowing. The extent of tissue removal was closely related to the occurrence of bowing. Twelve cases with no organic lesion had vocal fold bowing. Of these 12 patients, 8 were male and 9 were older than 60 years. Some aging process in the mucosa was presumed to be the cause of the bowing in this age group of patients without clinically noticeable organic lesions. Causes of vocal fold bowing in the younger group of patients without organic lesions were not determined in this study. PMID:8179251

  17. Kinetic partitioning mechanism of HDV ribozyme folding

    SciTech Connect

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  18. Kinetic partitioning mechanism of HDV ribozyme folding

    NASA Astrophysics Data System (ADS)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-01

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  19. Folding of synthetic homogeneous glycoproteins in the presence of a glycoprotein folding sensor enzyme.

    PubMed

    Dedola, Simone; Izumi, Masayuki; Makimura, Yutaka; Seko, Akira; Kanamori, Akiko; Sakono, Masafumi; Ito, Yukishige; Kajihara, Yasuhiro

    2014-03-10

    UDP-glucose:glycoprotein glucosyltransferase (UGGT) plays a key role in recognizing folded and misfolded glycoproteins in the glycoprotein quality control system of the endoplasmic reticulum. UGGT detects misfolded glycoproteins and re-glucosylates them as a tag for misfolded glycoproteins. A flexible model to reproduce in vitro folding of a glycoprotein in the presence of UGGT in a mixture containing correctly folded, folding intermediates, and misfolded glycoproteins is described. The data demonstrates that UGGT can re-glucosylate all intermediates in the in vitro folding experiments, thus indicating that UGGT inspects not only final folded products, but also the glycoprotein folding intermediates.

  20. Protein folding at atomic resolution: analysis of autonomously folding supersecondary structure motifs by nuclear magnetic resonance.

    PubMed

    Sborgi, Lorenzo; Verma, Abhinav; Sadqi, Mourad; de Alba, Eva; Muñoz, Victor

    2013-01-01

    The study of protein folding has been conventionally hampered by the assumption that all single-domain proteins fold by an all-or-none process (two-state folding) that makes it impossible to resolve folding mechanisms experimentally. Here we describe an experimental method for the thermodynamic analysis of protein folding at atomic resolution using nuclear magnetic resonance (NMR). The method is specifically developed for the study of small proteins that fold autonomously into basic supersecondary structure motifs, and that do so in the sub-millisecond timescale (folding archetypes). From the NMR experiments we obtain hundreds of atomic unfolding curves that are subsequently analyzed leading to the determination of the characteristic network of folding interactions. The application of this approach to a comprehensive catalog of elementary folding archetypes holds the promise of becoming the first experimental approach capable of unraveling the basic rules connecting protein structure and folding mechanism. PMID:22987355

  1. Fabrication of ten-fold photonic quasicrystalline structures

    SciTech Connect

    Sun, XiaoHong Wu, YuLong; Liu, Wen; Liu, Wei; Han, Juan; Jiang, Lei

    2015-05-15

    Compared to periodic crystals, quasicrystals have higher point group symmetry and are more favorable in achieving complete band-gaps. In this report, a top-cut prism interferometer is designed to fabricate ten-fold photonic quasicrystalline structures. By optimizing the exposing conditions and material characteristics, appropriate quasicrystals have been obtained in the SU8 photoresist films. Atomic Force Microscopy and laser diffraction are used to characterize the fabricated structures. The measurement results show the consistence between the theoretical design and experiments. This will provide guidance for the large-area and fast production of ten-fold quasicrystalline structures with high quality.

  2. Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-Monophosphate

    DOE PAGES

    Tian, Yuanyuan; Cui, Wenjun; Huang, Manna; Robinson, Howard; Wan, Yiqian; Wang, Yousheng; Ke, Hengming

    2014-08-05

    Cyclic nucleotide phosphodiesterases (PDEs) decompose second messengers cAMP and cGMP that play critical roles in many physiological processes. PDE1 of Saccharomyces cerevisiae has been subcloned and expressed in Escherichia coli. Recombinant yPDE1 has a KM of 110 μM and a kcat of 16.9 s⁻¹ for cAMP and a KM of 105 μM and a kcat of 11.8 s₅⁻¹ for cGMP. Thus, the specificity constant (kcat/KMcAMP)/(kcat/KMcGMP) of 1.4 indicates a dual specificity of yPDE1 for hydrolysis of both cAMP and cGMP. The crystal structures of unliganded yPDE1 and its complex with GMP at 1.31 Å resolution reveal a new structural foldingmore » that is different from those of human PDEs but is partially similar to that of some other metalloenzymes such as metallo-β-lactamase. In spite of their different structures and divalent metals, yPDE1 and human PDEs may share a common mechanism for hydrolysis of cAMP and cGMP.« less

  3. Acoustic characterization of liposome suspensions and Optison® at 3.5 MHz

    NASA Astrophysics Data System (ADS)

    Coussios, Constantin-C.; Holland, Christy K.; Jakubowska, Ludwika; Huang, Shao-Ling; MacDonald, Robert C.; Nagaraj, Ashwin; McPherson, David D.

    2003-04-01

    Liposomes-phospholipid vesicles that can encapsulate both gas and fluid-are currently being developed as contrast agents and vehicles for targeted drug delivery. The backscattering coefficient and attenuation of liposome suspensions were measured at 3.5 MHz as a function of liposome concentration and compared to those of Optison®. The backscattering coefficient of liposomes at concentrations in excess of 1.15×108/ml exceeds that of Optison® at the clinical dose (5.0-8.0×104/ml). On the other hand, the attenuation of ultrasound through liposome suspensions is negligible relative to the attenuation through Optison® (0.25 dB/cm), suggesting that liposomes have a much higher scatter-to-attenuation ratio and could be more efficient as contrast agents. A theoretical model that treats the gas within the liposomes as a free air bubble was used to estimate the backscattering coefficient and correlated well with experimental results. Church's model [J. Acoust. Soc. Am. 97, 1510-1521 (1995)] for Albunex® was also found to provide an accurate estimate of the backscattering coefficient of Optison®. These models suggest that the marked difference in attenuation between the two agents can be attributed to the fact that liposomes are sub-resonant in size at 3.5 MHz, but Optison® microspheres act as resonant scatterers. a)Currently at Boston University.

  4. GENE EXPRESSION CHANGES IN ARABIDOPSIS THALIANA SEEDLING ROOTS EXPOSED TO THE MUNITION HEXAHYDRO-1,3,5-TRINITRO-1,3,5-TRIAZINE

    EPA Science Inventory

    Arabidopsis thaliana root transcriptome responses to the munition, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), were assessed using serial analysis of gene expression (SAGE). Comparison of the transcriptional profile for the RDX response to a profile previously described for Ar...

  5. On the universe of protein folds.

    PubMed

    Kolodny, Rachel; Pereyaslavets, Leonid; Samson, Abraham O; Levitt, Michael

    2013-01-01

    In the fifty years since the first atomic structure of a protein was revealed, tens of thousands of additional structures have been solved. Like all objects in biology, proteins structures show common patterns that seem to define family relationships. Classification of proteins structures, which started in the 1970s with about a dozen structures, has continued with increasing enthusiasm, leading to two main fold classifications, SCOP and CATH, as well as many additional databases. Classification is complicated by deciding what constitutes a domain, the fundamental unit of structure. Also difficult is deciding when two given structures are similar. Like all of biology, fold classification is beset by exceptions to all rules. Thus, the perspectives of protein fold space that the fold classifications offer differ from each other. In spite of these ambiguities, fold classifications are useful for prediction of structure and function. Studying the characteristics of fold space can shed light on protein evolution and the physical laws that govern protein behavior.

  6. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect

    Zheng, Zhongzhou; Sosnick, Tobin R.

    2010-05-25

    Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here, we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu {yields} Glu{sup -}) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the {beta}5-strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high-energy states.

  7. Protein vivisection reveals elusive intermediates in folding.

    PubMed

    Zheng, Zhongzhou; Sosnick, Tobin R

    2010-04-01

    Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here, we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu-->Glu(-)) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the beta5-strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high-energy states.

  8. Seasonal and diurnal dependence of Pc 3-5 magnetic pulsation power at geomagnetically conjugate stations in the auroral zones

    SciTech Connect

    Saito, Hiroaki National Institute of Polar Research, Tokyo ); Sato, Natsuo ); Tonegawa, Yutaka ); Yoshino, Takeo ); Saemundsson, T. )

    1989-06-01

    Seasonal and diurnal variations of Pc 3-5 magnetic pulsation powers have been examined using 2 years of magnetic data from geomagnetically conjugate stations, Syowa in Antarctica and Husafell and Tjoernes in Iceland. The magnetic pulsation powers are found to be relatively higher at the winter hemisphere station than at the summer station. The pulsations observed during equinox show a diurnal dependence, i.e., that the power density is higher in the geomagnetic morning at the stations in Iceland than at Syowa, and this relationship is reversed in the afternoon. The power density ratio of Pc 3 pulsations between the conjugate stations, which is associated with the seasons and with local time, is higher than that of Pc 5. These characteristics can be attributed to the effects of sunlight in the ionosphere, i.e., Pc 3-5 pulsations are shielded when the waves propagate from the magnetosphere to the ground through the sunlit ionosphere.

  9. Acquired retinal folds in the cat.

    PubMed

    MacMillan, A D

    1976-06-01

    Retinal folds were found in 5 cats. The apparent cause of the folding was varied: in 1 cat the folds appeared after a localized retinal detachment; in 2 cats the condition accompanied other intraocular abnormalities associated with feline infectious peritonitis; 1 cat had active keratitis, and the retinal changes were thought to have been injury related; and 1 cat, bilaterally affected, had chronic glomerulonephritis. PMID:945253

  10. 1H NMR for quantifying sulfide trapping efficiency by using 1,3,5-tris(2-hydroxyethyl)-1,3,5-triazinane.

    PubMed

    Canuto, André V S; Echevarria, Aurea

    2014-07-01

    Hydrogen sulfide (H2S) is an extremely toxic colourless gas; it is corrosive and denser than air. It usually happens in oil and natural gas fields, refineries, coal mines, and in some industrial effluent treatment systems. This work presents an alternative method of monitoring and quantifying H2S trapping efficiency by using 1,3,5-tris(2-hydroxyethyl)-1,3,5-triazinane as a sequestering agent, and sodium sulfide as a source of sulfide ion, through (1)H NMR spectroscopy. The results proved that the reaction occurs very quickly at 20 °C at pH 7 and 10. 3,5-di(2-hydroxyethyl)-1,3,5-thiodiazinane and 5-(2-hydroxyethyl)-1,3,5-dithiozinane were observed and quantified; it was evidenced that (1)H NMR spectroscopy can be applied as a fast and effective method to quantify H2S trapping efficiency. PMID:24723368

  11. COS Side 2 NUV MAMA Fold Test

    NASA Astrophysics Data System (ADS)

    Bacinski, John

    2013-10-01

    The performance of the MAMA microchannel plate can be monitored using a MAMA fold analysis procedure. The fold analysis provides a measurement of the distribution of charge cloud sizes incident upon the anode giving some measure of changes in the pulse-height distribution of the MCP and, therefore, MCP gain. This proposal executes the same steps as the COS MAMA Fold Analysis {13128} during Cycle 20.This proposal is an exact duplication of nominal COS MAMA Fold Analysis {proposal 13128, Cycle 20}. Any changes 13128 or subsequent cycle submissions should be reflected in this proposal and vice versa.

  12. Assessment of optimized Markov models in protein fold classification.

    PubMed

    Lampros, Christos; Simos, Thomas; Exarchos, Themis P; Exarchos, Konstantinos P; Papaloukas, Costas; Fotiadis, Dimitrios I

    2014-08-01

    Protein fold classification is a challenging task strongly associated with the determination of proteins' structure. In this work, we tested an optimization strategy on a Markov chain and a recently introduced Hidden Markov Model (HMM) with reduced state-space topology. The proteins with unknown structure were scored against both these models. Then the derived scores were optimized following a local optimization method. The Protein Data Bank (PDB) and the annotation of the Structural Classification of Proteins (SCOP) database were used for the evaluation of the proposed methodology. The results demonstrated that the fold classification accuracy of the optimized HMM was substantially higher compared to that of the Markov chain or the reduced state-space HMM approaches. The proposed methodology achieved an accuracy of 41.4% on fold classification, while Sequence Alignment and Modeling (SAM), which was used for comparison, reached an accuracy of 38%. PMID:25152041

  13. Microwave-enhanced folding and denaturation of globular proteins

    NASA Astrophysics Data System (ADS)

    Bohr, Henrik; Bohr, Jakob

    2000-04-01

    It is shown that microwave irradiation can affect the kinetics of the folding process of some globular proteins, especially β-lactoglobulin. At low temperature the folding from the cold denatured phase of the protein is enhanced, while at a higher temperature the denaturation of the protein from its folded state is enhanced. In the latter case, a negative temperature gradient is needed for the denaturation process, suggesting that the effects of the microwaves are nonthermal. This supports the notion that coherent topological excitations can exist in proteins. The application of microwaves hold promises for a wide range of biotechnological applications, such as protein synthesis, protein aggregation, etc., and may have implications for biological systems as well.

  14. Aromatic fluorine compounds. I. The synthesis of 2,5- and 3,5-difluorobenzotrifluorides

    USGS Publications Warehouse

    Finger, G.C.; Reed, F.H.

    1944-01-01

    The preparation of 2,5- and 3,5-difluorobenzotrifluoride and some of their intermediates is described. 3,5-Dinitrobenzotrifluoride was prepared from 3-nitrobenzotrifluoride with a fuming nitric-sulfuric acid mixture.

  15. In Search of Enzymes with a Role in 3', 5'-Cyclic Guanosine Monophosphate Metabolism in Plants.

    PubMed

    Gross, Inonge; Durner, Jörg

    2016-01-01

    In plants, nitric oxide (NO)-mediated 3', 5'-cyclic guanosine monophosphate (cGMP) synthesis plays an important role during pathogenic stress response, stomata closure upon osmotic stress, the development of adventitious roots and transcript regulation. The NO-cGMP dependent pathway is well characterized in mammals. The binding of NO to soluble guanylate cyclase enzymes (GCs) initiates the synthesis of cGMP from guanosine triphosphate. The produced cGMP alters various cellular responses, such as the function of protein kinase activity, cyclic nucleotide gated ion channels and cGMP-regulated phosphodiesterases. The signal generated by the second messenger is terminated by 3', 5'-cyclic nucleotide phosphodiesterase (PDEs) enzymes that hydrolyze cGMP to a non-cyclic 5'-guanosine monophosphate. To date, no homologues of mammalian cGMP-synthesizing and degrading enzymes have been found in higher plants. In the last decade, six receptor proteins from Arabidopsis thaliana have been reported to have guanylate cyclase activity in vitro. Of the six receptors, one was shown to be a NO dependent guanylate cyclase enzyme (NOGC1). However, the role of these proteins in planta remains to be elucidated. Enzymes involved in the degradation of cGMP remain elusive, albeit, PDE activity has been detected in crude protein extracts from various plants. Additionally, several research groups have partially purified and characterized PDE enzymatic activity from crude protein extracts. In this review, we focus on presenting advances toward the identification of enzymes involved in the cGMP metabolism pathway in higher plants. PMID:27200049

  16. Guiding the folding pathway of DNA origami

    NASA Astrophysics Data System (ADS)

    Dunn, Katherine E.; Dannenberg, Frits; Ouldridge, Thomas E.; Kwiatkowska, Marta; Turberfield, Andrew J.; Bath, Jonathan

    2015-09-01

    DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short `staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its

  17. Retinal and Choroidal Folds in Papilledema

    PubMed Central

    Sibony, Patrick A.; Kupersmith, Mark J.; Feldon, Steven E.; Wang, Jui-Kai; Garvin, Mona

    2015-01-01

    Purpose To determine the frequency, patterns, associations, and biomechanical implications of retinal and choroidal folds in papilledema due to idiopathic intracranial hypertension (IIH). Methods Retinal and choroidal folds were studied in patients enrolled in the IIH Treatment Trial using fundus photography (n = 165 study eyes) and spectral-domain optical coherence tomography (SD-OCT; n = 125). We examined the association between folds and peripapillary shape, retinal nerve fiber layer (RNFL) thickness, disc volume, Frisén grade, acuity, perimetric mean deviation, intraocular pressure, intracranial pressure, and refractive error. Results We identified three types of folds in IIH patients with papilledema: peripapillary wrinkles (PPW), retinal folds (RF), and choroidal folds (CF). Frequency, with photos, was 26%, 19%, and 1%, respectively; SD-OCT frequency was 46%, 47%, and 10%. At least one type of fold was present in 41% of patients with photos and 73% with SD-OCT. Spectral-domain OCT was more sensitive. Structural parameters related to the severity of papilledema were associated with PPW and RF, whereas anterior deformation of the peripapillary RPE/basement membrane layer was associated with CF and RF. Folds were not associated with vision loss at baseline. Conclusions Folds in papilledema are biomechanical signs of stress/strain on the optic nerve head and load-bearing structures induced by intracranial hypertension. Folds are best imaged with SD-OCT. The patterns of retinal and choroidal folds are the products of a complex interplay between the degree of papilledema and anterior deformation of the load-bearing structures (sclera and possibly the lamina cribrosa), both modulated by structural geometry and material properties of the optic nerve head. (ClinicalTrials.gov number, NCT01003639.) PMID:26335066

  18. A 3.5 year diary study: Remembering and life story importance are predicted by different event characteristics.

    PubMed

    Thomsen, Dorthe Kirkegaard; Jensen, Thomas; Holm, Tine; Olesen, Martin Hammershøj; Schnieber, Anette; Tønnesvang, Jan

    2015-11-01

    Forty-five participants described and rated two events each week during their first term at university. After 3.5 years, we examined whether event characteristics rated in the diary predicted remembering, reliving, and life story importance at the follow-up. In addition, we examined whether ratings of life story importance were consistent across a three year interval. Approximately 60% of events were remembered, but only 20% of these were considered above medium importance to life stories. Higher unusualness, rehearsal, and planning predicted whether an event was remembered 3.5 years later. Higher goal-relevance, importance, emotional intensity, and planning predicted life story importance 3.5 years later. There was a moderate correlation between life story importance rated three months after the diary and rated at the 3.5 year follow-up. The results suggest that autobiographical memory and life stories are governed by different mechanisms and that life story memories are characterized by some degree of stability.

  19. 41 CFR 102-3.5 - What does this subpart cover and how does it apply?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What does this subpart cover and how does it apply? 102-3.5 Section 102-3.5 Public Contracts and Property Management Federal...? § 102-3.5 What does this subpart cover and how does it apply? This subpart provides the policy...

  20. 40 CFR 721.4265 - Hydrazinecarboxamide, N-(3,5-difluorophenyl-).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Hydrazinecarboxamide, N-(3,5... Specific Chemical Substances § 721.4265 Hydrazinecarboxamide, N-(3,5-difluorophenyl-). (a) Chemical... hydrazinecarboxamide, N-(3,5-difluorophenyl-) (PMN P-97-649; CAS No. 167412-23-9) is subject to reporting under...

  1. 40 CFR 721.4265 - Hydrazinecarboxamide, N-(3,5-difluorophenyl-).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Hydrazinecarboxamide, N-(3,5... Specific Chemical Substances § 721.4265 Hydrazinecarboxamide, N-(3,5-difluorophenyl-). (a) Chemical... hydrazinecarboxamide, N-(3,5-difluorophenyl-) (PMN P-97-649; CAS No. 167412-23-9) is subject to reporting under...

  2. 41 CFR 102-3.5 - What does this subpart cover and how does it apply?

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 41 Public Contracts and Property Management 3 2012-01-01 2012-01-01 false What does this subpart cover and how does it apply? 102-3.5 Section 102-3.5 Public Contracts and Property Management Federal...? § 102-3.5 What does this subpart cover and how does it apply? This subpart provides the policy...

  3. 41 CFR 102-3.5 - What does this subpart cover and how does it apply?

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false What does this subpart cover and how does it apply? 102-3.5 Section 102-3.5 Public Contracts and Property Management Federal...? § 102-3.5 What does this subpart cover and how does it apply? This subpart provides the policy...

  4. 41 CFR 102-3.5 - What does this subpart cover and how does it apply?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 41 Public Contracts and Property Management 3 2013-07-01 2013-07-01 false What does this subpart cover and how does it apply? 102-3.5 Section 102-3.5 Public Contracts and Property Management Federal...? § 102-3.5 What does this subpart cover and how does it apply? This subpart provides the policy...

  5. 41 CFR 102-3.5 - What does this subpart cover and how does it apply?

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 41 Public Contracts and Property Management 3 2014-01-01 2014-01-01 false What does this subpart cover and how does it apply? 102-3.5 Section 102-3.5 Public Contracts and Property Management Federal...? § 102-3.5 What does this subpart cover and how does it apply? This subpart provides the policy...

  6. Folded Supersymmetry and the LDP Paradox

    SciTech Connect

    Burdman, Gustavo; Chacko, Z.; Goh, Hock-Seng; Harnik, Roni

    2006-09-21

    We present a new class of models that stabilize the weak scale against radiative corrections up to scales of order 5 TeV without large corrections to precision electroweak observables. In these ''folded supersymmetric'' theories the one loop quadratic divergences of the Standard Model Higgs field are canceled by opposite spin partners, but the gauge quantum numbers of these new particles are in general different from those of the conventional superpartners. This class of models is built around the correspondence that exists in the large N limit between the correlation functions of supersymmetric theories and those of their non-supersymmetric orbifold daughters. By identifying the mechanism which underlies the cancellation of one loop quadratic divergences in these theories, we are able to construct simple extensions of the Standard Model which are radiatively stable at one loop. Ultraviolet completions of these theories can be obtained by imposing suitable boundary conditions on an appropriate supersymmetric higher dimensional theory compactified down to four dimensions. We construct a specific model based on these ideas which stabilizes the weak scale up to about 20 TeV and where the states which cancel the top loop are scalars not charged under Standard Model color. Its collider signatures are distinct from conventional supersymmetric theories and include characteristic events with hard leptons and missing energy.

  7. Simultaneous Alignment and Folding of Protein Sequences

    PubMed Central

    Waldispühl, Jérôme; O'Donnell, Charles W.; Will, Sebastian; Devadas, Srinivas; Backofen, Rolf

    2014-01-01

    Abstract Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm's complexity is polynomial in time and space. Algorithmically, partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments, partiFold-Align significantly outperforms state-of-the-art pairwise and multiple sequence alignment tools in the most difficult low-sequence homology case. It also improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families (partiFold-Align is available at http://partifold.csail.mit.edu/). PMID:24766258

  8. Local vs global motions in protein folding

    PubMed Central

    Maisuradze, Gia G.; Liwo, Adam; Senet, Patrick; Scheraga, Harold A.

    2013-01-01

    It is of interest to know whether local fluctuations in a polypeptide chain play any role in the mechanism by which the chain folds to the native structure of a protein. This question is addressed by analyzing folding and non-folding trajectories of a protein; as an example, the analysis is applied to the 37-residue triple β-strand WW domain from the Formin binding protein 28 (FBP28) (PDB ID: 1E0L). Molecular dynamics (MD) trajectories were generated with the coarse-grained united-residue force field, and one- and two-dimensional free-energy landscapes (FELs) along the backbone virtual-bond angle θ and backbone virtual-bond-dihedral angle γ of each residue, and principal components, respectively, were analyzed. The key residues involved in the folding of the FBP28 WW domain are elucidated by this analysis. The correlations between local and global motions are found. It is shown that most of the residues in the folding trajectories of the system studied here move in a concerted fashion, following the dynamics of the whole system. This demonstrates how the choice of a pathway has to involve concerted movements in order for this protein to fold. This finding also sheds light on the effectiveness of principal component analysis (PCA) for the description of the folding dynamics of the system studied. It is demonstrated that the FEL along the PCs, computed by considering only several critically-placed residues, can correctly describe the folding dynamics. PMID:23914144

  9. Protein folding: When ribosomes pick the structure

    NASA Astrophysics Data System (ADS)

    Sivertsson, Elin M.; Itzhaki, Laura S.

    2014-05-01

    Anfinsen's principle tells us that the folded structure of a protein is determined solely by its sequence. Now, it has been shown that the rate at which a polypeptide chain is synthesized in the cell can affect which of two alternative folded structures it adopts.

  10. Folding Polyominoes from One Level to Two

    ERIC Educational Resources Information Center

    Frederickson, Greg N.

    2011-01-01

    For any given polyomino, is it possible to cut it into pieces and then hinge the pieces, so that the polyomino folds up into a similar version of itself but two levels thick? While we don't know how to do this for every polyomino, the article does show how to cut, hinge, and fold polyominoes from several infinite classes, providing an…

  11. Similarities between protein folding and granular jamming

    PubMed Central

    Jose, Prasanth P; Andricioaei, Ioan

    2012-01-01

    Grains and glasses, widely different materials, arrest their motions upon decreasing temperature and external load, respectively, in common ways, leading to a universal jamming phase diagram conjecture. However, unified theories are lacking, mainly because of the disparate nature of the particle interactions. Here we demonstrate that folded proteins exhibit signatures common to both glassiness and jamming by using temperature- and force-unfolding molecular dynamics simulations. Upon folding, proteins develop a peak in the interatomic force distributions that falls on a universal curve with experimentally measured forces on jammed grains and droplets. Dynamical signatures are found as a dramatic slowdown of stress relaxation upon folding. Together with granular similarities, folding is tied not just to the jamming transition, but a more nuanced picture of anisotropy, preparation protocol and internal interactions emerges. Results have implications for designing stable polymers and can open avenues to link protein folding to jamming theory. PMID:23093180

  12. Geometry and wetting of capillary folding.

    PubMed

    Péraud, Jean-Philippe; Lauga, Eric

    2014-04-01

    Capillary forces are involved in a variety of natural phenomena, ranging from droplet breakup to the physics of clouds. The forces from surface tension can also be exploited in industrial applications provided the length scales involved are small enough. Recent experimental investigations showed how to take advantage of capillarity to fold planar structures into three-dimensional configurations by selectively melting polymeric hinges joining otherwise rigid shapes. In this paper we use theoretical calculations to quantify the role of geometry and fluid wetting on the final folded state. Considering folding in two and three dimensions, studying both hydrophilic and hydrophobic situations with possible contact-angle hysteresis, and addressing the shapes to be folded to be successively infinite, finite, curved, kinked, and elastic, we are able to derive an overview of the geometrical parameter space available for capillary folding.

  13. Prediction of sound from human vocal folds

    NASA Astrophysics Data System (ADS)

    Bodony, Daniel; Luo, Haoxiang; Mittal, Rajat

    2007-11-01

    The creation of voiced sounds in humans depends on the flow-induced vibration of the vocal folds within the larynx. The vocal folds, which are a complex structural system of cartilage and tissue, create an oscillatory ``glottal jet'' whose harmonic content partially determines the tone of the speech. In this work we will discuss the process of sound generation in the laynx by combining a fully coupled two-dimensional fluid-structure simulation of the incompressible flow field in the vicinity of the vocal folds to an acoustic analogy description of the sound field. The structural dynamics of the vocal folds are based on physically realistic properties and are coupled to the motion of the fluid via an immersed boundary method. Relationships between the sound produced and the vocal fold dynamics will be discussed.

  14. Visualizing chaperone-assisted protein folding.

    PubMed

    Horowitz, Scott; Salmon, Loïc; Koldewey, Philipp; Ahlstrom, Logan S; Martin, Raoul; Quan, Shu; Afonine, Pavel V; van den Bedem, Henry; Wang, Lili; Xu, Qingping; Trievel, Raymond C; Brooks, Charles L; Bardwell, James C A

    2016-07-01

    Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone. PMID:27239796

  15. Fan-fold shielded electrical leads

    DOEpatents

    Rohatgi, Rajeev R.; Cowan, Thomas E.

    1996-01-01

    Fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate.

  16. Fan-fold shielded electrical leads

    DOEpatents

    Rohatgi, R.R.; Cowan, T.E.

    1996-06-11

    Disclosed are fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate. 3 figs.

  17. Folding and Finding RNA Secondary Structure

    PubMed Central

    Mathews, David H.; Moss, Walter N.; Turner, Douglas H.

    2010-01-01

    SUMMARY Optimal exploitation of the expanding database of sequences requires rapid finding and folding of RNAs. Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison. New functional noncoding RNAs in genome sequences can be found by combining sequence comparison with the assumption that functional noncoding RNAs will have more favorable folding free energies than other RNAs. When a new RNA is discovered, experiments and sequence comparison can restrict folding space so that secondary structure can be rapidly determined with the help of predicted free energies. In turn, secondary structure restricts folding in three dimensions, which allows modeling of three-dimensional structure. An example from a domain of a retrotransposon is described. Discovery of new RNAs and their structures will provide insights into evolution, biology, and design of therapeutics. Applications to studies of evolution are also reviewed. PMID:20685845

  18. The robustness and innovability of protein folds.

    PubMed

    Tóth-Petróczy, Agnes; Tawfik, Dan S

    2014-06-01

    Assignment of protein folds to functions indicates that >60% of folds carry out one or two enzymatic functions, while few folds, for example, the TIM-barrel and Rossmann folds, exhibit hundreds. Are there structural features that make a fold amenable to functional innovation (innovability)? Do these features relate to robustness--the ability to readily accumulate sequence changes? We discuss several hypotheses regarding the relationship between the architecture of a protein and its evolutionary potential. We describe how, in a seemingly paradoxical manner, opposite properties, such as high stability and rigidity versus conformational plasticity and structural order versus disorder, promote robustness and/or innovability. We hypothesize that polarity--differentiation and low connectivity between a protein's scaffold and its active-site--is a key prerequisite for innovability.

  19. A Canonical Biomechanical Vocal Fold Model

    PubMed Central

    Bhattacharya, Pinaki; Siegmund, Thomas H.

    2012-01-01

    Summary The present article aimed at constructing a canonical geometry of the human vocal fold (VF) from subject-specific image slice data. A computer-aided design approach automated the model construction. A subject-specific geometry available in literature, three abstractions (which successively diminished in geometric detail) derived from it, and a widely used quasi two-dimensional VF model geometry were used to create computational models. The first three natural frequencies of the models were used to characterize their mechanical response. These frequencies were determined for a representative range of tissue biomechanical properties, accounting for underlying VF histology. Compared with the subject-specific geometry model (baseline), a higher degree of abstraction was found to always correspond to a larger deviation in model frequency (up to 50% in the relevant range of tissue biomechanical properties). The model we deemed canonical was optimally abstracted, in that it significantly simplified the VF geometry compared with the baseline geometry but can be recalibrated in a consistent manner to match the baseline response. Models providing only a marginally higher degree of abstraction were found to have significant deviation in predicted frequency response. The quasi two-dimensional model presented an extreme situation: it could not be recalibrated for its frequency response to match the subject-specific model. This deficiency was attributed to complex support conditions at anterior-posterior extremities of the VFs, accentuated by further issues introduced through the tissue biomechanical properties. In creating canonical models by leveraging advances in clinical imaging techniques, the automated design procedure makes VF modeling based on subject-specific geometry more realizable. PMID:22209063

  20. Vocal Fold Fibroblasts Immunoregulate Activated Macrophage Phenotype

    PubMed Central

    King, Suzanne N.; Chen, Fei; Jetté, Marie E.; Thibeault, Susan L.

    2012-01-01

    Recent evidence suggests that fibroblasts play a critical role in regulating inflammation during wound healing because they express several inflammatory mediators in response to bacteria. The objective of this study was to analyze the effects of lipopolysaccaride (LPS) on the immunomodulatory properties of vocal fold fibroblasts (VFF) derived from polyps, scar and normal tissue co-cultured with macrophages, to provide insight into their interactions during the inflammatory process. Fibroblasts were co-cultured with CD14+ monocytes and after 7 days, wells were treated with LPS for 24 and 72 hours. Culture supernatants were collected and concentrations of TNF-α, IL-6, IL-8, IL-10, IL-12, IL-1β, and MCP-1 were quantified by ELISA. Normal VFF and CD14+ monocultures were used as controls. Twenty-four hours after LPS activation, macrophages co-cultured with polyp VFF had significantly increased expression of TNF-α, IL-1β, IL-12, and IL-10 compared to controls (p<0.0001). In contrast, macrophages co-cultured with scar VFF had significantly lower expression of TNF-α, IL-1β and IL-12 with significantly higher IL-10 compared to control (p<0.0001). After 72 hours, macrophages co-cultured with polyp VFF increased expression of TNF-α, IL-1β, IL-10, IL-6, IL-8, MCP-1 and TGF-β (p<0.01) and macrophages co-cultured with scar VFF significantly decreased their expression of IL-1β and IL-12 compared to control (p<0.0001). Scar VFF at both time points produced significantly lower levels of IL-8, MCP-1, IL-6 and TGF-β compared to controls (p<0.05). Based on our findings, VFF and macrophages secrete several inflammatory mediators that modify their diverse functions. Polyp and scar VFF may play a role in regulating abnormal inflammatory responses, which could result in excessive ECM deposition that disrupts the function of the vocal folds. PMID:23123198

  1. Isolation of three hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading species of the family Enterobacteriaceae from nitramine explosive-contaminated soil.

    PubMed Central

    Kitts, C L; Cunningham, D P; Unkefer, P J

    1994-01-01

    Three species of the family Enterobacteriaceae that biochemically reduced hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) were isolated from nitramine explosive-contaminated soil. Two isolates, identified as Morganella morganii and Providencia rettgeri, completely transformed both RDX and the nitroso-RDX reduction intermediates. The third isolate, identified as Citrobacter freundii, partially transformed RDX and generated high concentrations of nitroso-RDX intermediates. All three isolates produced 14CO2 from labeled RDX under O2-depleted culture conditions. While all three isolates transformed HMX, only M. morganii transformed HMX in the presence of RDX. PMID:7811097

  2. Isolation of three hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading species of the family Enterobacteriaceae from nitramine explosive-contaminated soil.

    PubMed

    Kitts, C L; Cunningham, D P; Unkefer, P J

    1994-12-01

    Three species of the family Enterobacteriaceae that biochemically reduced hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) were isolated from nitramine explosive-contaminated soil. Two isolates, identified as Morganella morganii and Providencia rettgeri, completely transformed both RDX and the nitroso-RDX reduction intermediates. The third isolate, identified as Citrobacter freundii, partially transformed RDX and generated high concentrations of nitroso-RDX intermediates. All three isolates produced 14CO2 from labeled RDX under O2-depleted culture conditions. While all three isolates transformed HMX, only M. morganii transformed HMX in the presence of RDX.

  3. Role of nitrogen limitation in transformation of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) by Gordonia sp. strain KTR9.

    PubMed

    Indest, Karl J; Hancock, Dawn E; Jung, Carina M; Eberly, Jed O; Mohn, William W; Eltis, Lindsay D; Crocker, Fiona H

    2013-03-01

    The transcriptome of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine)-degrading strain Gordonia sp. strain KTR9 and its glnR mutant were studied as a function of nitrogen availability to further investigate the observed ammonium-mediated inhibition of RDX degradation. The results indicate that nitrogen availability is a major determinant of RDX degradation and xplA gene expression in KTR9.

  4. Development of DANDYs, new 3,5-diaryl-7-azaindoles demonstrating potent DYRK1A kinase inhibitory activity.

    PubMed

    Gourdain, Stéphanie; Dairou, Julien; Denhez, Clément; Bui, Linh Chi; Rodrigues-Lima, Fernando; Janel, Nathalie; Delabar, Jean M; Cariou, Kevin; Dodd, Robert H

    2013-12-12

    A series of 3,5-diaryl-1H-pyrrolo[2,3-b]pyridines were synthesized and evaluated for inhibition of DYRKIA kinase in vitro. Derivatives having hydroxy groups on the aryl moieties (2c, 2j-l) demonstrated high inhibitory potencies with Kis in the low nanomolar range. Their methoxy analogues were up to 100 times less active. Docking studies at the ATP binding site suggested that these compounds bind tightly to this site via a network of multiple H-bonds with the peptide backbone. None of the active compounds were cytotoxic to KB cells at 10(-6) M. Kinase profiling revealed that compound 2j showed 2-fold selectivity for DYRK1A with respect to DYRK2 and DYRK3. PMID:24188002

  5. Folding Elastic Thermal Surface - FETS

    NASA Technical Reports Server (NTRS)

    Urquiza, Eugenio; Zhang, Burt X.; Thelen, Michael P.; Rodriquez, Jose I.; Pellegrino, Sergio

    2013-01-01

    the FETS is also self-locking so the panels stay in a rigid and extended configuration after deployment. This unexpected benefit makes the tape-spring hinge design of the FETS a light, simple, reliable, compact, non-outgassing hinge, spring, and latch. While tape-spring hinges are not novel, they have never been used to deploy passive unfolding thermal surfaces (radiator panels, covers, sun shades, or IR thermal shields). Furthermore, because this technology is compact, it has minimal impact on the launch envelope and mass specifications. FETS enhances the performance of hosted payload instruments where the science data is limited by dark noise. Incorporating FETS into a thermal control system increases radiator area, which lowers the optical detector temperature. This results in higher SNR (signal-to-noise ratio) and improved science data.

  6. Dynamics of an Ultrafast Folding Subdomain in the Context of a Larger Protein Fold

    PubMed Central

    Davis, Caitlin M.; Dyer, R. Brian

    2014-01-01

    Small fast folding subdomains with low contact order have been postulated to facilitate the folding of larger proteins. We have tested this idea by determining how the fastest folding linear β-hairpin, CLN025, which folds on the nanosecond time scale, folds within the context of a two-hairpin WW domain system, which folds on the microsecond time scale. The folding of the wild type FBP28 WW domain was compared to constructs in which each of the loops was replaced by CLN025. A combination of FTIR spectroscopy and laser-induced temperature-jump coupled with infrared spectroscopy was used to probe changes in the peptide backbone. The relaxation dynamics of the β-sheets and β-turn were measured independently by probing the corresponding bands assigned in the amide I region. The folding rate of the CLN025 β-hairpin is unchanged within the larger protein. Insertion of the β-hairpin into the second loop results in an overall stabilization of the WW domain and a relaxation lifetime five times faster than the parent WW domain. In both mutants, folding is initiated in the turns and the β-sheets form last. These results demonstrate that fast folding subdomains can be used to speed the folding of more complex proteins, and that the folding dynamics of the subdomain is unchanged within the context of the larger protein. PMID:24320936

  7. Effects of Folding on Metalloprotein Active Sites

    NASA Astrophysics Data System (ADS)

    Winkler, Jay R.; Wittung-Stafshede, Pernilla; Leckner, Johan; Malmstrom, Bo G.; Gray, Harry B.

    1997-04-01

    Experimental data for the unfolding of cytochrome c and azurin by guanidinium chloride (GuHCl) are used to construct free-energy diagrams for the folding of the oxidized and reduced proteins. With cytochrome c, the driving force for folding the reduced protein is larger than that for the oxidized form. Both the oxidized and the reduced folded forms of yeast cytochrome c are less stable than the corresponding states of the horse protein. Due to the covalent attachment of the heme and its fixed tetragonal coordination geometry, cytochrome c folding can be described by a two-state model. A thermodynamic cycle leads to an expression for the difference in self-exchange reorganization energies for the folded and unfolded proteins. The reorganization energy for electron exchange in the folded protein is approximately 0.5 eV smaller than that for a heme in aqueous solution. The finding that reduced azurin unfolds at lower GuHCl concentrations than the oxidized protein suggests that the coordination structure of copper is different in oxidized and reduced unfolded states: it is likely that the geometry of CuI in the unfolded protein is linear or trigonal, whereas CuII prefers to be tetragonal. The evidence indicates that protein folding lowers the azurin reorganization energy by roughly 1.7 eV relative to an aqueous Cu(1,10-phenanthroline)2{}2+/+ reference system.

  8. Quantification of a Helical Origami Fold

    NASA Astrophysics Data System (ADS)

    Dai, Eric; Han, Xiaomin; Chen, Zi

    2015-03-01

    Origami, the Japanese art of paper folding, is traditionally viewed as an amusing pastime and medium of artistic expression. However, in recent years, origami has served as a source of inspiration for innovations in science and engineering. Here, we present the geometric and mechanical properties of a twisting origami fold. The origami structure created by the fold exhibits several interesting properties, including rigid foldibility, local bistability and finely tunable helical coiling, with control over pitch, radius and handedness of the helix. In addition, the pattern generated by the fold closely mimics the twist buckling patterns shown by thin materials, for example, a mobius strip. We use six parameters of the twisting origami pattern to generate a fully tunable graphical model of the fold. Finally, we present a mathematical model of the local bistability of the twisting origami fold. Our study elucidates the mechanisms behind the helical coiling and local bistability of the twisting origami fold, with potential applications in robotics and deployable structures. Acknowledgment to Branco Weiss Fellowship for funding.

  9. Folding pathways of the Tetrahymena ribozyme.

    PubMed

    Mitchell, David; Russell, Rick

    2014-06-12

    Like many structured RNAs, the Tetrahymena group I intron ribozyme folds through multiple pathways and intermediates. Under standard conditions in vitro, a small fraction reaches the native state (N) with kobs ≈ 0.6 min(-1), while the remainder forms a long-lived misfolded conformation (M) thought to differ in topology. These alternative outcomes reflect a pathway that branches late in folding, after disruption of a trapped intermediate (Itrap). Here we use catalytic activity to probe the folding transitions from Itrap to the native and misfolded states. We show that mutations predicted to weaken the core helix P3 do not increase the rate of folding from Itrap but they increase the fraction that reaches the native state rather than forming the misfolded state. Thus, P3 is disrupted during folding to the native state but not to the misfolded state, and P3 disruption occurs after the rate-limiting step. Interestingly, P3-strengthening mutants also increase native folding. Additional experiments show that these mutants are rapidly committed to folding to the native state, although they reach the native state with approximately the same rate constant as the wild-type ribozyme (~1 min(-1)). Thus, the P3-strengthening mutants populate a distinct pathway that includes at least one intermediate but avoids the M state, most likely because P3 and the correct topology are formed early. Our results highlight multiple pathways in RNA folding and illustrate how kinetic competitions between rapid events can have long-lasting effects because the "choice" is enforced by energy barriers that grow larger as folding progresses.

  10. Folding pathways of the Tetrahymena ribozyme

    PubMed Central

    Mitchell, David; Russell, Rick

    2014-01-01

    Like many structured RNAs, the Tetrahymena group I intron ribozyme folds through multiple pathways and intermediates. Under standard conditions in vitro, a small fraction reaches the native state (N) with kobs ≈ 0.6 min–1, while the remainder forms a long-lived misfolded conformation (M) thought to differ in topology. These alternative outcomes reflect a pathway that branches late in folding, after disruption of a trapped intermediate (Itrap). Here, we use catalytic activity to probe the folding transitions from Itrap to the native and misfolded states. We show that mutations predicted to weaken the core helix P3 do not increase the rate of folding from Itrap but they increase the fraction that reaches the native state rather than forming the misfolded state. Thus, P3 is disrupted during folding to the native state but not to the misfolded state, and P3 disruption occurs after the rate-limiting step. Interestingly, P3-strengthening mutants also increase native folding. Additional experiments show that these mutants are rapidly committed to folding to the native state, although they reach the native state with approximately the same rate constant as the wild-type ribozyme (~1 min–1). Thus, the P3-strengthening mutants populate a distinct pathway that includes at least one intermediate but avoids the M state, most likely because P3 and the correct topology are formed early. Our results highlight multiple pathways in RNA folding and illustrate how kinetic competitions between rapid events can have long-lasting effects because the ‘choice’ is enforced by energy barriers that grow larger as folding progresses. PMID:24747051

  11. Network measures for protein folding state discrimination

    PubMed Central

    Menichetti, Giulia; Fariselli, Piero; Remondini, Daniel

    2016-01-01

    Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there is not a first-principle model to explain this different behavior. We exploit the network properties of protein structures by introducing novel observables to address the problem of classifying the different types of folding kinetics. These observables display a plain physical meaning, in terms of vibrational modes, possible configurations compatible with the native protein structure, and folding cooperativity. The relevance of these observables is supported by a classification performance up to 90%, even with simple classifiers such as discriminant analysis. PMID:27464796

  12. Osteochondrodysplasia in three Scottish Fold cats.

    PubMed

    Chang, Jinhwa; Jung, Joohyun; Oh, Sunkyoung; Lee, Sungok; Kim, Gyeongmin; Kim, Haksang; Kweon, Ohkyeong; Yoon, Junghee; Choi, Mincheol

    2007-09-01

    This report explains typical radiographic features of Scottish Fold osteochondrodysplasia. Three Scottish Fold cats suffering from lameness were referred to the Veterinary Medical Teaching Hospital, Seoul National University, Korea. Based on the breed predisposition, history, clinical signs, physical examination, and radiographic findings, Scottish Fold osteochondrodysplasia was confirmed in three cases. Radiographic changes mainly included exostosis and secondary arthritis around affected joint lesions, and defective conformation in the phalanges and caudal vertebrae. The oral chondroprotective agents such as glucosamine and chondroitin sulfate make the patients alleviate their pain without adverse effects. PMID:17679781

  13. Mechanical Models of Fault-Related Folding

    SciTech Connect

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  14. Network measures for protein folding state discrimination.

    PubMed

    Menichetti, Giulia; Fariselli, Piero; Remondini, Daniel

    2016-01-01

    Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there is not a first-principle model to explain this different behavior. We exploit the network properties of protein structures by introducing novel observables to address the problem of classifying the different types of folding kinetics. These observables display a plain physical meaning, in terms of vibrational modes, possible configurations compatible with the native protein structure, and folding cooperativity. The relevance of these observables is supported by a classification performance up to 90%, even with simple classifiers such as discriminant analysis. PMID:27464796

  15. Under-folded proteins: Conformational ensembles and their roles in protein folding, function, and pathogenesis.

    PubMed

    Uversky, Vladimir N

    2013-11-01

    For decades, protein function was intimately linked to the presence of a unique, aperiodic crystal-like structure in a functional protein. The two only places for conformational ensembles of under-folded (or partially folded) protein forms in this picture were either the end points of the protein denaturation processes or transiently populated folding intermediates. Recent years witnessed dramatic change in this perception and conformational ensembles, which the under-folded proteins are, have moved from the shadow. Accumulated to date data suggest that a protein can exist in at least three global forms-functional and folded, functional and intrinsically disordered (nonfolded), and nonfunctional and misfolded/aggregated. Under-folded protein states are crucial for each of these forms, serving as important folding intermediates of ordered proteins, or as functional states of intrinsically disordered proteins (IDPs) and IDP regions (IDPRs), or as pathology triggers of misfolded proteins. Based on these observations, conformational ensembles of under-folded proteins can be classified as transient (folding and misfolding intermediates) and permanent (IDPs and stable misfolded proteins). Permanently under-folded proteins can further be split into intentionally designed (IDPs and IDPRs) and unintentionally designed (misfolded proteins). Although intrinsic flexibility, dynamics, and pliability are crucial for all under-folded proteins, the different categories of under-foldedness are differently encoded in protein amino acid sequences.

  16. Dew-driven folding of insect wings

    NASA Astrophysics Data System (ADS)

    Dickerson, Andrew; Beadles, Sam; Clement, Courtney; Hu, David

    2013-11-01

    Small insect wings fold into tacos when exposed to dewfall or fog for extended times. Such shapes are tightly held together and require great force or long evaporation times for the wings to unfold. In this experimental investigation, we use time-lapse and high-speed videography on a mosquito wing exposed to fog to characterize the folding process from a flat wing to a taco. We observe a taco is formed through a series of processes involving wing bending, unbending, and subsequent tight folding of the wing following the sliding of the drop off the wing. We use a simplified 2D model to determine the forces coalescing drops exert on the wing, and present folding-resistant design suggestions for micro-aerial vehicle wings.

  17. Folded waveguide coupler for ion cyclotron heating

    SciTech Connect

    Owens, T.L.; Chen, G.L.

    1986-01-01

    A new type of waveguide coupler for plasma heating in the ion cyclotron range of frequencies is described. The coupler consists of a series of interleaved metallic vanes within a rectangular enclosure analogous to a wide rectangular waveguide that has been ''folded'' several times. At the mouth of the coupler, a plate is attached which contains coupling apertures in each fold or every other fold of the waveguide, depending upon the wavenumber spectrum desired. This plate serves primarily as a wave field polarizer that converts coupler fields to the polarization of the fast magnetosonic wave within the plasma. Theoretical estimates indicate that the folded waveguide is capable of high-efficiency, multimegawatt operation into a plasma. Bench tests have verified the predicted field structure within the waveguide in preparation for high-power tests on the Radio Frequency Test Facility at the Oak Ridge National Laboratory.

  18. Self-folding miniature elastic electric devices

    NASA Astrophysics Data System (ADS)

    Miyashita, Shuhei; Meeker, Laura; Tolley, Michael T.; Wood, Robert J.; Rus, Daniela

    2014-09-01

    Printing functional materials represents a considerable impact on the access to manufacturing technology. In this paper we present a methodology and validation of print-and-self-fold miniature electric devices. Polyvinyl chloride laminated sheets based on metalized polyester film show reliable self-folding processes under a heat application, and it configures 3D electric devices. We exemplify this technique by fabricating fundamental electric devices, namely a resistor, capacitor, and inductor. Namely, we show the development of a self-folded stretchable resistor, variable resistor, capacitive strain sensor, and an actuation mechanism consisting of a folded contractible solenoid coil. Because of their pre-defined kinematic design, these devices feature elasticity, making them suitable as sensors and actuators in flexible circuits. Finally, an RLC circuit obtained from the integration of developed devices is demonstrated, in which the coil based actuator is controlled by reading a capacitive strain sensor.

  19. Reinke Edema: Watch For Vocal Fold Cysts.

    PubMed

    Tüzüner, Arzu; Demirci, Sule; Yavanoglu, Ahmet; Kurkcuoglu, Melih; Arslan, Necmi

    2015-06-01

    Reinke edema is one of the common cause of dysphonia middle-aged population, and severe thickening of vocal folds require surgical treatment. Smoking plays a major role on etiology. Vocal fold cysts are also benign lesions and vocal trauma blamed for acquired cysts. We would like to present 3 cases with vocal fold cyst related with Reinke edema. First case had a subepidermal epidermoid cyst with Reinke edema, which could be easily observed before surgery during laryngostroboscopy. Second case had a mucous retention cyst into the edematous Reinke tissue, which was detected during surgical intervention, and third case had a epidermoid cyst that occurred 2 months after before microlaryngeal operation regarding Reinke edema reduction. These 3 cases revealed that surgical management of Reinke edema needs a careful dissection and close follow-up after surgery for presence of vocal fold cysts.

  20. Statistical properties of a folded elastic rod

    NASA Astrophysics Data System (ADS)

    Bayart, Elsa; Deboeuf, Stéphanie; Boué, Laurent; Corson, Francis; Boudaoud, Arezki; Adda-Bedia, Mokhtar

    2010-03-01

    A large variety of elastic structures naturally seem to be confined into environments too small to accommodate them; the geometry of folded structures span a wide range of length-scales. The elastic properties of these confined systems are further constrained by self-avoidance as well as by the dimensionality of both structures and container. To mimic crumpled paper, we devised an experimental setup to study the packing of a dimensional elastic object in 2D geometries: an elastic rod is folded at the center of a circular Hele-Shaw cell by a centripetal force. The initial configuration of the rod and the acceleration of the rotating disk allow to span different final folded configurations while the final rotation speed controls the packing intensity. Using image analysis we measure geometrical and mechanical properties of the folded configurations, focusing on length, curvature and energy distributions.

  1. Monster Mash: Protein Folding Gone Wrong

    MedlinePlus

    ... Articles | Inside Life Science Home Page Monster Mash: Protein Folding Gone Wrong By Joseph Piergrossi Posted October 31, 2013 In this image, globs of misfolded proteins called amyloid plaques (blobs) are found outside neurons ( ...

  2. Unexplained Profound Hypoglycemia After Vocal Fold Lipoinjection.

    PubMed

    Modanlou, Shohreh; Marie Giglio, Nicole; Carroll, Thomas; Pancaro, Carlo

    2016-02-01

    Vocal fold injection is used for the management of glottal incompetence from various causes. The procedure is well tolerated and has few reported complications. We present a case of a 66-year-old man with long-lasting hoarseness secondary to vocal fold atrophy, who underwent an uneventful bilateral vocal fold injection with autologous fat. While in the recovery area, he experienced profuse sweating approximately 30 minutes after the surgical procedure. His blood glucose value was measured at 24 mg/dL, and plasmatic insulin level was 246 mU/L. To our knowledge, this is the first reported case of a systemic side effect after vocal fold lipoinjection. PMID:26491839

  3. Topology Explains Why Automobile Sunshades Fold Oddly

    ERIC Educational Resources Information Center

    Feist, Curtis; Naimi, Ramin

    2009-01-01

    Automobile sunshades always fold into an "odd" number of loops. The explanation why involves elementary topology (braid theory and linking number, both explained in detail here with definitions and examples), and an elementary fact from algebra about symmetric group.

  4. Cellular Mechanisms of Membrane Protein Folding

    PubMed Central

    Skach, William R.

    2010-01-01

    The membrane protein folding problem can be articulated by two central questions. How is protein topology established by selective peptide transport to opposite sides of the cellular membrane? And how are transmembrane segments inserted, integrated and folded within the lipid bilayer? In eukaryotes, this process usually takes place in the endoplasmic reticulum (ER) coincident with protein synthesis, and is facilitated by the translating Ribosome and the Sec61 Translocon Complex (RTC). At its core, the RTC forms a dynamic pathway through which the elongating nascent polypeptide moves as it is delivered into cytosolic, lumenal and lipid compartments. This perspective will focus on emerging evidence that the RTC functions as a protein folding machine that restricts conformational space by establishing transmembrane topology and yet provides a permissive environment that enables nascent transmembrane domains to efficiently progress down their folding energy landscape. PMID:19491932

  5. Kinetic Analysis of Protein Folding Lattice Models

    NASA Astrophysics Data System (ADS)

    Chen, Hu; Zhou, Xin; Liaw, Chih Young; Koh, Chan Ghee

    Based on two-dimensional square lattice models of proteins, the relation between folding time and temperature is studied by Monte Carlo simulation. The results can be represented by a kinetic model with three states — random coil, molten globule, and native state. The folding process is composed of nonspecific collapse and final searching for the native state. At high temperature, it is easy to escape from local traps in the folding process. With decreasing temperature, because of the trapping in local traps, the final searching speed decreases. Then the folding shows chevron rollover. Through the analysis of the fitted parameters of the kinetic model, it is found that the main difference between the energy landscapes of the HP model and the Go model is that the number of local minima of the Go model is less than that of the HP model.

  6. Influence of glycosaminoglycan identity on vocal fold fibroblast behavior.

    PubMed

    Jimenez-Vergara, Andrea Carolina; Munoz-Pinto, Dany J; Becerra-Bayona, Silvia; Wang, Bo; Iacob, Alexandra; Hahn, Mariah S

    2011-11-01

    Poly(ethylene glycol) (PEG) hydrogels have recently begun to be studied for the treatment of scarred vocal fold lamina propria due, in part, to their tunable mechanical properties, resistance to fibroblast-mediated contraction, and ability to be polymerized in situ. However, pure PEG gels lack intrinsic biochemical signals to guide cell behavior and generally fail to mimic the frequency-dependent viscoelastic response critical to normal superficial lamina propria function. Recent results suggest that incorporation of viscoelastic bioactive substances, such as glycosaminoglycans (GAGs), into PEG networks may allow these gels to more closely approach the mechanical responses of normal vocal fold lamina propria while also stimulating desired vocal fold fibroblast behaviors. Although a number of vocal fold studies have examined the influence of hyaluronan (HA) on implant mechanics and vocal fold fibroblast responses, the effects of other GAG types have been relatively unexplored. This is significant, since recent studies have suggested that chondroitin sulfate C (CSC) and heparan sulfate (HS) are substantially altered in scarred lamina propria. The present study was therefore designed to evaluate the effects of CSC and HS incorporation on the mechanical response of PEG gels and vocal fold fibroblast behavior relative to HA. As with PEG-HA, the viscoelasticity of PEG-CSC and PEG-HS gels more closely approached that of the normal vocal fold lamina propria than pure PEG hydrogels. In addition, collagen I deposition and fibronectin production were significantly higher in CSC than in HA gels, and levels of the myofibroblast marker smooth muscle α-actin (SM α-actin) were greater in CSC and HS gels than in HA gels. Since collagen I, fibronectin, and SM α-actin are generally elevated in scarred lamina propria these results suggest that CSC and HS may be undesirable for vocal fold implants relative to HA. Investigation of various signaling intermediates indicated that

  7. Influence of glycosaminoglycan identity on vocal fold fibroblast behavior

    PubMed Central

    Jimenez-Vergara, Andrea Carolina; Munoz-Pinto, Dany J.; Becerra-Bayona, Silvia; Wang, Bo; Iacob, Alexandra; Hahn, Mariah S.

    2011-01-01

    Poly(ethylene glycol) (PEG) hydrogels have recently begun to be explored for the treatment of scarred vocal fold lamina propria due, in part, to their tunable mechanical properties, resistance to fibroblast-mediated contraction, and ability to be polymerized in situ. However, pure PEG gels lack intrinsic biochemical signals to guide cell behavior and generally fail to mimic the frequency-dependent viscoelastic response critical to normal superficial lamina propria function. Recent results suggest that incorporation of viscoelastic, bioactive substances, such as glycosaminoglycans (GAGs), into PEG networks may allow these gels to more closely approach the mechanical responses of normal vocal fold lamina propria while also stimulating desired vocal fold fibroblast behaviors. Although a number of vocal fold studies have examined the influence of hyaluronan (HA) on implant mechanics and vocal fold fibroblast responses, the effects of remaining GAG types have been relatively unexplored. This is significant since recent studies suggest that chondroitin sulfate C (CSC) and heparan sulfate (HS) are substantially altered in lamina propria scar. The present study was therefore designed to evaluate the effects of CSC and HS incorporation on PEG gel mechanical response and vocal fold fibroblast behavior relative to HA. As with PEG-HA, the viscoelasticity of PEG-CSC and PEG-HS gels more closely approached that of the normal vocal fold lamina propria than pure PEG hydrogels. In addition, collagen I deposition and fibronectin production were significantly higher in CSC than in HA gels, and levels myofibroblast marker SM-α-actin were greater in CSC and HS gels than in HA gels. Since collagen I, fibronectin, and SM-α-actin are generally elevated in lamina propria scar, these results suggest that CSC and HS may be undesirable for vocal fold implants relative to HA. Investigation of various signaling intermediates indicated that alterations in NFκB-p50, NFκB-p65, or pERK1

  8. Folding funnels, binding funnels, and protein function.

    PubMed Central

    Tsai, C. J.; Kumar, S.; Ma, B.; Nussinov, R.

    1999-01-01

    Folding funnels have been the focus of considerable attention during the last few years. These have mostly been discussed in the general context of the theory of protein folding. Here we extend the utility of the concept of folding funnels, relating them to biological mechanisms and function. In particular, here we describe the shape of the funnels in light of protein synthesis and folding; flexibility, conformational diversity, and binding mechanisms; and the associated binding funnels, illustrating the multiple routes and the range of complexed conformers. Specifically, the walls of the folding funnels, their crevices, and bumps are related to the complexity of protein folding, and hence to sequential vs. nonsequential folding. Whereas the former is more frequently observed in eukaryotic proteins, where the rate of protein synthesis is slower, the latter is more frequent in prokaryotes, with faster translation rates. The bottoms of the funnels reflect the extent of the flexibility of the proteins. Rugged floors imply a range of conformational isomers, which may be close on the energy landscape. Rather than undergoing an induced fit binding mechanism, the conformational ensembles around the rugged bottoms argue that the conformers, which are most complementary to the ligand, will bind to it with the equilibrium shifting in their favor. Furthermore, depending on the extent of the ruggedness, or of the smoothness with only a few minima, we may infer nonspecific, broad range vs. specific binding. In particular, folding and binding are similar processes, with similar underlying principles. Hence, the shape of the folding funnel of the monomer enables making reasonable guesses regarding the shape of the corresponding binding funnel. Proteins having a broad range of binding, such as proteolytic enzymes or relatively nonspecific endonucleases, may be expected to have not only rugged floors in their folding funnels, but their binding funnels will also behave similarly

  9. The 3'-5' exoribonuclease Dis3 regulates the expression of specific microRNAs in Drosophila wing imaginal discs.

    PubMed

    Towler, Benjamin P; Jones, Christopher I; Viegas, Sandra C; Apura, Patricia; Waldron, Joseph A; Smalley, Sarah K; Arraiano, Cecilia M; Newbury, Sarah F

    2015-01-01

    Dis3 is a highly conserved exoribonuclease which degrades RNAs in the 3'-5' direction. Mutations in Dis3 are associated with a number of human cancers including multiple myeloma and acute myeloid leukemia. In this work, we have assessed the effect of a Dis3 knockdown on Drosophila imaginal disc development and on expression of mature microRNAs. We find that Dis3 knockdown severely disrupts the development of wing imaginal discs in that the flies have a "no wing" phenotype. Use of RNA-seq to quantify the effect of Dis3 knockdown on microRNA expression shows that Dis3 normally regulates a small subset of microRNAs, with only 11 (10.1%) increasing in level ≥ 2-fold and 6 (5.5%) decreasing in level ≥ 2-fold. Of these microRNAs, miR-252-5p is increased 2.1-fold in Dis3-depleted cells compared to controls while the level of the miR-252 precursor is unchanged, suggesting that Dis3 can act in the cytoplasm to specifically degrade this mature miRNA. Furthermore, our experiments suggest that Dis3 normally interacts with the exosomal subunit Rrp40 in the cytoplasm to target miR-252-5p for degradation during normal wing development. Another microRNA, miR-982-5p, is expressed at lower levels in Dis3 knockdown cells, while the miR-982 precursor remains unchanged, indicating that Dis3 is involved in its processing. Our study therefore reveals an unexpected specificity for this ribonuclease toward microRNA regulation, which is likely to be conserved in other eukaryotes and may be relevant to understanding its role in human disease.

  10. The hydrogen exchange core and protein folding.

    PubMed Central

    Li, R.; Woodward, C.

    1999-01-01

    A database of hydrogen-deuterium exchange results has been compiled for proteins for which there are published rates of out-exchange in the native state, protection against exchange during folding, and out-exchange in partially folded forms. The question of whether the slow exchange core is the folding core (Woodward C, 1993, Trends Biochem Sci 18:359-360) is reexamined in a detailed comparison of the specific amide protons (NHs) and the elements of secondary structure on which they are located. For each pulsed exchange or competition experiment, probe NHs are shown explicitly; the large number and broad distribution of probe NHs support the validity of comparing out-exchange with pulsed-exchange/competition experiments. There is a strong tendency for the same elements of secondary structure to carry NHs most protected in the native state, NHs first protected during folding, and NHs most protected in partially folded species. There is not a one-to-one correspondence of individual NHs. Proteins for which there are published data for native state out-exchange and theta values are also reviewed. The elements of secondary structure containing the slowest exchanging NHs in native proteins tend to contain side chains with high theta values or be connected to a turn/loop with high theta values. A definition for a protein core is proposed, and the implications for protein folding are discussed. Apparently, during folding and in the native state, nonlocal interactions between core sequences are favored more than other possible nonlocal interactions. Other studies of partially folded bovine pancreatic trypsin inhibitor (Barbar E, Barany G, Woodward C, 1995, Biochemistry 34:11423-11434; Barber E, Hare M, Daragan V, Barany G, Woodward C, 1998, Biochemistry 37:7822-7833), suggest that developing cores have site-specific energy barriers between microstates, one disordered, and the other(s) more ordered. PMID:10452602

  11. [Surgery of benign vocal fold lesions].

    PubMed

    Olthoff, A

    2016-09-01

    Surgical treatment of benign vocal fold lesions can be indicated for clinical or functional reasons. The principles of phonosurgery have to be maintained in either case. The appropriate phonosurgical technique depends on the type of vocal fold lesion. Depending on the findings, phonosurgery aims to maintain or improve voice quality. The evaluation of clinical and functional results includes indirect laryngoscopy, videostroboscopy, and voice analysis. PMID:27552826

  12. On a smooth quintic 4-fold

    SciTech Connect

    Cheltsov, I A

    2000-10-31

    The birational geometry of an arbitrary smooth quintic 4-fold is studied using the properties of log pairs. As a result, a new proof of its birational rigidity is given and all birational maps of a smooth quintic 4-fold into fibrations with general fibre of Kodaira dimension zero are described. In the Addendum similar results are obtained for all smooth hypersurfaces of degree n in P{sup n} in the case of n equal to 6, 7, or 8.

  13. Characterization of Metabolites during Biodegradation of Hexahydro-1,3,5-Trinitro-1,3,5-Triazine (RDX) with Municipal Anaerobic Sludge†

    PubMed Central

    Hawari, Jalal; Halasz, Annamaria; Sheremata, Tamara; Beaudet, Sylvie; Groom, Carl; Paquet, Louise; Rhofir, Chakib; Ampleman, Guy; Thiboutot, Sonia

    2000-01-01

    The biodegradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in liquid cultures with municipal anaerobic sludge showed that at least two degradation routes were involved in the disappearance of the cyclic nitramine. In one route, RDX was reduced to give the familiar nitroso derivatives hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX) and hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine (DNX). In the second route, two novel metabolites, methylenedinitramine [(O2NNH)2CH2] and bis(hydroxymethyl)nitramine [(HOCH2)2NNO2], formed and were presumed to be ring cleavage products produced by enzymatic hydrolysis of the inner C—N bonds of RDX. None of the above metabolites accumulated in the system, and they disappeared to produce nitrous oxide (N2O) as a nitrogen-containing end product and formaldehyde (HCHO), methanol (MeOH), and formic acid (HCOOH) that in turn disappeared to produce CH4 and CO2 as carbon-containing end products. PMID:10831452

  14. Phosphatidylinositol 3,5-bisphosphate: regulation of cellular events in space and time.

    PubMed

    Jin, Natsuko; Lang, Michael J; Weisman, Lois S

    2016-02-01

    Phosphorylated phosphatidylinositol lipids are crucial for most eukaryotes and have diverse cellular functions. The low-abundance signalling lipid phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2] is critical for cellular homoeostasis and adaptation to stimuli. A large complex of proteins that includes the lipid kinase Fab1-PIKfyve, dynamically regulates the levels of PI(3,5)P2. Deficiencies in PI(3,5)P2 are linked to some human diseases, especially those of the nervous system. Future studies will probably determine new, undiscovered regulatory roles of PI(3,5)P2, as well as uncover mechanistic insights into how PI(3,5)P2 contributes to normal human physiology.

  15. Muscular Anatomy of the Human Ventricular Folds

    PubMed Central

    Moon, Jerald; Alipour, Fariborz

    2013-01-01

    Objective The purpose of this study was to better understand the muscular anatomy of the ventricular folds (VF) to help improve biomechanical modeling of phonation and to better understand the role of these muscles during phonatory and non-phonatory tasks. Method Four human larynges were decalcified and sectioned coronally from the posterior to anterior using a CryoJane tape transfer system, and stained using Massons trichrome. The total and relative area of muscles observed in each section were calculated and used for characterizing muscle distribution within the ventricular folds. Results The ventricular folds of the larynges contained anteriorly coursing thyroarytenoid and ventricularis muscle fibers lying in the lower half of the VF posteriorly, with some ventricularis muscle evident in the upper and lateral portion of the fold more anteriorly. Very little muscle tissue was observed in the medial half of the fold, and the anterior half of the VF was largely devoid of any muscle tissue. All four VF’s contained muscle bundles coursing superiorly and medially through the upper half of the fold toward the lateral margin of the epiglottis. Conclusions While variability in expression was evident, the well-defined thyroarytenoid muscle was readily apparent lateral to the arytenoid cartilage in all specimens. PMID:24224399

  16. Protein Folding and Misfolding on Surfaces

    PubMed Central

    Stefani, Massimo

    2008-01-01

    Protein folding, misfolding and aggregation, as well as the way misfolded and aggregated proteins affects cell viability are emerging as key themes in molecular and structural biology and in molecular medicine. Recent advances in the knowledge of the biophysical basis of protein folding have led to propose the energy landscape theory which provides a consistent framework to better understand how a protein folds rapidly and efficiently to the compact, biologically active structure. The increased knowledge on protein folding has highlighted its strict relation to protein misfolding and aggregation, either process being in close competition with the other, both relying on the same physicochemical basis. The theory has also provided information to better understand the structural and environmental factors affecting protein folding resulting in protein misfolding and aggregation into ordered or disordered polymeric assemblies. Among these, particular importance is given to the effects of surfaces. The latter, in some cases make possible rapid and efficient protein folding but most often recruit proteins/peptides increasing their local concentration thus favouring misfolding and accelerating the rate of nucleation. It is also emerging that surfaces can modify the path of protein misfolding and aggregation generating oligomers and polymers structurally different from those arising in the bulk solution and endowed with different physical properties and cytotoxicities. PMID:19330090

  17. Optimum folding pathways for growing protein chains.

    PubMed

    Senturk, Serife; Baday, Sefer; Arkun, Yaman; Erman, Burak

    2007-11-26

    The folding of a protein is studied as it grows residue by residue from the N-terminus and enters an environment that stabilizes the folded state. This mode of folding of a growing chain is different from refolding where the full chain folds from a disordered initial configuration to the native state. We propose a sequential dynamic optimization method that computes the evolution of optimum folding pathways as amino acid residues are added to the peptide chain one by one. The dynamic optimization formulation is deterministic and uses Newton's equations of motion and a Go-type potential that establishes the native contacts and excluded volume effects. The method predicts the optimal energy-minimizing path among all the alternative feasible pathways. As two examples, the folding of the chicken villin headpiece, a 36-residue protein, and chymotrypsin inhibitor 2 (CI2), a 64-residue protein, are studied. Results on the villin headpiece show significant differences from the refolding of the same chain studied previously. Results on CI2 mostly agree with the results of refolding experiments and computational work.

  18. "Wet" Versus "Dry" Folding of Polyproline

    NASA Astrophysics Data System (ADS)

    Shi, Liuqing; Holliday, Alison E.; Bohrer, Brian C.; Kim, Doyong; Servage, Kelly A.; Russell, David H.; Clemmer, David E.

    2016-06-01

    When the all- cis polyproline-I helix (PPI, favored in 1-propanol) of polyproline-13 is introduced into water, it folds into the all- trans polyproline-II (PPII) helix through at least six intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we show that the solvent-free intermediates refold into the all- cis PPI helix with high (>90%) efficiency. Moreover, in the absence of solvent, each intermediate appears to utilize the same small set of pathways observed for the solution-phase PPII → PPI transition upon immersion of PPIIaq in 1-propanol. That folding in solution (under conditions where water is displaced by propanol) and folding in vacuo (where energy required for folding is provided by collisional activation) occur along the same pathway is remarkable. Implicit in this statement is that 1-propanol mimics a "dry" environment, similar to the gas phase. We note that intermediates with structures that are similar to PPIIaq can form PPII under the most gentle activation conditions—indicating that some transitions observed in water (i.e. , "we t" folding, are accessible (albeit inefficient) in vacuo. Lastly, these "dry" folding experiments show that PPI (all cis) is favored under "dry" conditions, which underscores the role of water as the major factor promoting preference for trans proline.

  19. Folding of non-Euclidean curved shells

    NASA Astrophysics Data System (ADS)

    Bende, Nakul; Evans, Arthur; Innes-Gold, Sarah; Marin, Luis; Cohen, Itai; Santangelo, Christian; Hayward, Ryan

    2015-03-01

    Origami-based folding of 2D sheets has been of recent interest for a variety of applications ranging from deployable structures to self-folding robots. Though folding of planar sheets follows well-established principles, folding of curved shells involves an added level of complexity due to the inherent influence of curvature on mechanics. In this study, we use principles from differential geometry and thin shell mechanics to establish fundamental rules that govern folding of prototypical creased shells. In particular, we show how the normal curvature of a crease line controls whether the deformation is smooth or discontinuous, and investigate the influence of shell thickness and boundary conditions. We show that snap-folding of shells provides a route to rapid actuation on time-scales dictated by the speed of sound. The simple geometric design principles developed can be applied at any length-scale, offering potential for bio-inspired soft actuators for tunable optics, microfluidics, and robotics. This work was funded by the National Science Foundation through EFRI ODISSEI-1240441 with additional support to S.I.-G. through the UMass MRSEC DMR-0820506 REU program.

  20. The first salen-type ligands derived from 3',5'-diamino-3',5'-dideoxythymidine and -dideoxyxylothymidine and their corresponding copper(II) complexes

    PubMed Central

    Koth, Daniel; Gottschaldt, Michael; Görls, Helmar; Pohle, Karolin

    2006-01-01

    Background There are many nucleoside metal complexes known. According to observations made, only very few of them reveal their central ion to be co-ordinated by the sugar part of their molecules. The regio- and stereospecific exchange of the hydroxyl groups at the sugar moiety by chelating units improves its complexation ability and should give access to a new class of chiral ligands. Results In this paper we present the synthesis of 3',5'-diamino substituted thymidines with ribo- as well as xylo-configuration and the preparation of copper(II) complexes derived from their corresponding Schiff bases. Starting from thymidine, the amino derivatives were prepared in a three and four step reaction sequence respectively. The absolute configuration of the ligands was proved by the three-bond 1H-1H spin spin coupling constants 3J obtained by NMR-studies. Condensation of the amino derivatives with salicylic aldehydes resulted in the corresponding diimines, which represent a new class of chiral salen-type ligands. All ligands formed uncharged stable copper(II) complexes. The structure of 3',5'-bis(3,5-di-tert-butylsalicylaldiminato)-3',5'-dideoxyxylothymidine-copper(II) could be determined by single crystal X-ray structure analysis. The copper centre in this complex has distorted tetrahedral coordination geometry. Conclusion For the synthesis of 3',5'-diamino-3',5'-dideoxy thymidines with xylo- as well as ribo-configuration an effective synthesis pathway has been developed. Their corresponding salicylidene imines form stable coordination compounds with copper(II) ions. They represent the first salen type complexes of nucleosides with this substitution pattern. PMID:16934149

  1. Protein kinase C (PKC) phosphorylates human platelet inositol trisphosphate 5/sup +/-/-phosphomonoesterase (IP/sub 3/ 5'-p'tase) increasing phosphatase activity

    SciTech Connect

    Connolly, T.M.; Majerus, P.W.

    1986-05-01

    Phosphoinositide breakdown in response to thrombin stimulation of human platelets generates messenger molecules that activate PKC (diglyceride) and mobilize Ca/sup + +/ (inositol tris-phosphates). The water soluble products of phospholipase C-mediated metabolism of phosphatidylinositol 4,5-diphosphate are inositol 1,4,5 P/sub 3/ (IP/sub 3/) and inositol 1:2-cyclic 4,5 P/sub 3/ (cIP/sub 3/). A specific phosphatase, IP/sub 3/ 5'-p'tase, cleaves the 5 phosphate from IP/sub 3/ or cIP/sub 3/ to form IP/sub 2/ or cIP/sub 2/ and P/sub i/, none of which mobilizes Ca/sup + +/. Thus, the IP/sub 3/ 5'-p'tase may regulate cellular responses to IP/sub 3/ or cIP/sub 3/. The authors find that IP/sub 3/ 5'-p'tase isolated from human platelets is phosphorylated by rat brain PKC, resulting in a 4-fold increase in IP/sub 3/ 5'-p'tase activity. The authors phosphorylated IP/sub 3/ 5'-p'tase using ..gamma.. /sup 32/P-ATP and found that the labeled enzyme comigrated on SDS-PAGE with the previously described 40K protein phosphorylated in response to thrombin stimulation of platelets. The similarity of the PKC-phosphorylated IP/sub 3/ 5'-p'tase observed in vitro and the thrombin-stimulated phosphorylated 40K protein known to be phosphorylated by PKC in vivo, suggests that these proteins may be the same. These results suggest that platelet Ca/sup + +/ mobilization maybe regulated by PKC phosphorylation of the IP/sub 3/ 5'-p'tase and can explain the observation that phorbol ester treatment of intact human platelets results in decreased production of IP/sub 3/ and decreased Ca/sup + +/ mobilization upon subsequent thrombin addition.

  2. 3,5-Diiodo-L-thyronine prevents high-fat-diet-induced insulin resistance in rat skeletal muscle through metabolic and structural adaptations.

    PubMed

    Moreno, Maria; Silvestri, Elena; De Matteis, Rita; de Lange, Pieter; Lombardi, Assunta; Glinni, Daniela; Senese, Rosalba; Cioffi, Federica; Salzano, Anna Maria; Scaloni, Andrea; Lanni, Antonia; Goglia, Fernando

    2011-10-01

    The worldwide prevalence of obesity-associated pathologies, including type 2 diabetes, requires thorough investigation of mechanisms and interventions. Recent studies have highlighted thyroid hormone analogs and derivatives as potential agents able to counteract such pathologies. In this study, in rats receiving a high-fat diet (HFD), we analyzed the effects of a 4-wk daily administration of a naturally occurring iodothyronine, 3,5-diiodo-L-thyronine (T2), on the gastrocnemius muscle metabolic/structural phenotype and insulin signaling. The HFD-induced increases in muscle levels of fatty acid translocase (3-fold; P<0.05) and TGs (2-fold, P<0.05) were prevented by T2 (each; P<0.05 vs. HFD). T2 increased insulin-stimulated Akt phosphorylation levels (∼2.5-fold; P<0.05 vs. HFD). T2 induced these effects while sparing muscle mass and without cardiac hypertrophy. T2 increased the muscle contents of fast/glycolytic fibers (2-fold; P<0.05 vs. HFD) and sarcolemmal glucose transporter 4 (3-fold; P<0.05 vs. HFD). Adipocyte differentiation-related protein was predominantly present within the slow/oxidative fibers in HFD-T2. In T2-treated rats (vs. HFD), glycolytic enzymes and associated components were up-regulated (proteomic analysis, significance limit: 2-fold; P<0.05), as was phosphofructokinase activity (by 1.3-fold; P<0.05), supporting the metabolic shift toward a more glycolytic phenotype. These results highlight T2 as a potential therapeutic approach to the treatment of diet-induced metabolic dysfunctions.

  3. Biotransformation of the explosives 2,4,6-trinitrotoluene and 1,3,5-triaza 1,3,5-trinitrocyclohexane by Clostridium bifermentans

    SciTech Connect

    Regan, K.M.; Crawford, R.L.

    1994-12-31

    A strain of Clostridium bifermentans isolated from a munitions-supplemented enrichment was able to remove both TNT (2,4,6-trinitrotoluene) and RDX (1,3,5-triaza 1,3,5-trinitrocyclohexane) from its growth media. Biotransformations of TNT and RDX by cometabolism in a nutrient rich medium reduced the removal time from several days to a few hours, as compared to a nutrient limited medium. Redox potential (Eh) of the media had important effects on the biological and abiological transformations of the munition compounds.

  4. Folding patterns and shape optimization using SMA-based self-folding laminates

    NASA Astrophysics Data System (ADS)

    Peraza-Hernandez, Edwin A.; Frei, Katherine R.; Hartl, Darren J.; Lagoudas, Dimitris C.

    2014-03-01

    Origami engineering, a discipline encompassing the creation of practical three-dimensional structures from two- dimensional entities via folding operations, has the potential to impact multiple fields of manufacturing and design. In some circumstances, it may be practical to have self-folding capabilities instead of creating folds by external manipulations (as in morphing structures in outer space or on the ocean floor). This paper considers the use of a self-folding laminate composite consisting of two outer layers of thermally actuated shape memory alloy (SMA) wire meshes separated by an inner compliant insulating layer. Methods for designing folding patterns and determining temperature fields to obtain desired shapes and behaviors are proposed. Sheets composed of the self-folding laminate are modeled via finite element analysis (FEA) and the proposed methods are implemented to test their capabilities. One method uses a previously developed and freely available software called Freeform Origami for folding pattern design. The second method entails the use of optimization to determine the localized activation temperatures required to obtain desired shapes or to perform specific functions. The proposed methods are demonstrated to be applicable for the design of folding patterns and determination of activation temperatures for the self-folding laminate by showing successful examples of their implementation. This exploratory study provides new tools that can be integrated into the design framework of self-folding origami structures.

  5. The B gene of pea encodes a defective flavonoid 3',5'-hydroxylase, and confers pink flower color.

    PubMed

    Moreau, Carol; Ambrose, Mike J; Turner, Lynda; Hill, Lionel; Ellis, T H Noel; Hofer, Julie M I

    2012-06-01

    The inheritance of flower color in pea (Pisum sativum) has been studied for more than a century, but many of the genes corresponding to these classical loci remain unidentified. Anthocyanins are the main flower pigments in pea. These are generated via the flavonoid biosynthetic pathway, which has been studied in detail and is well conserved among higher plants. A previous proposal that the Clariroseus (B) gene of pea controls hydroxylation at the 5' position of the B ring of flavonoid precursors of the anthocyanins suggested to us that the gene encoding flavonoid 3',5'-hydroxylase (F3'5'H), the enzyme that hydroxylates the 5' position of the B ring, was a good candidate for B. In order to test this hypothesis, we examined mutants generated by fast neutron bombardment. We found allelic pink-flowered b mutant lines that carried a variety of lesions in an F3'5'H gene, including complete gene deletions. The b mutants lacked glycosylated delphinidin and petunidin, the major pigments present in the progenitor purple-flowered wild-type pea. These results, combined with the finding that the F3'5'H gene cosegregates with b in a genetic mapping population, strongly support our hypothesis that the B gene of pea corresponds to a F3'5'H gene. The molecular characterization of genes involved in pigmentation in pea provides valuable anchor markers for comparative legume genomics and will help to identify differences in anthocyanin biosynthesis that lead to variation in pigmentation among legume species.

  6. Communication: Three-fold covariance imaging of laser-induced Coulomb explosions

    NASA Astrophysics Data System (ADS)

    Pickering, James D.; Amini, Kasra; Brouard, Mark; Burt, Michael; Bush, Ian J.; Christensen, Lauge; Lauer, Alexandra; Nielsen, Jens H.; Slater, Craig S.; Stapelfeldt, Henrik

    2016-04-01

    We apply a three-fold covariance imaging method to analyse previously acquired data [C. S. Slater et al., Phys. Rev. A 89, 011401(R) (2014)] on the femtosecond laser-induced Coulomb explosion of spatially pre-aligned 3,5-dibromo-3',5'-difluoro-4'-cyanobiphenyl molecules. The data were acquired using the "Pixel Imaging Mass Spectrometry" camera. We show how three-fold covariance imaging of ionic photofragment recoil trajectories can be used to provide new information about the parent ion's molecular structure prior to its Coulomb explosion. In particular, we show how the analysis may be used to obtain information about molecular conformation and provide an alternative route for enantiomer determination.

  7. Communication: Three-fold covariance imaging of laser-induced Coulomb explosions.

    PubMed

    Pickering, James D; Amini, Kasra; Brouard, Mark; Burt, Michael; Bush, Ian J; Christensen, Lauge; Lauer, Alexandra; Nielsen, Jens H; Slater, Craig S; Stapelfeldt, Henrik

    2016-04-28

    We apply a three-fold covariance imaging method to analyse previously acquired data [C. S. Slater et al., Phys. Rev. A 89, 011401(R) (2014)] on the femtosecond laser-induced Coulomb explosion of spatially pre-aligned 3,5-dibromo-3',5'-difluoro-4'-cyanobiphenyl molecules. The data were acquired using the "Pixel Imaging Mass Spectrometry" camera. We show how three-fold covariance imaging of ionic photofragment recoil trajectories can be used to provide new information about the parent ion's molecular structure prior to its Coulomb explosion. In particular, we show how the analysis may be used to obtain information about molecular conformation and provide an alternative route for enantiomer determination.

  8. Cross folding in southern Bighorn basin

    SciTech Connect

    Gubbels, T.L.

    1986-08-01

    Analysis of Landsat Thematic Mapper imagery coupled with surface structural investigations of well-exposed folds in the southern Bighorn basin have revealed two northwest-trending folds that have been refolded. The eastern boundary of the Owl Creek Mountains is characterized by a well-defined alignment of folds that extend north-northwest from the Owl Creek thrust front. Bridger monocline, Wildhorse Butte anticline, and Red Hole anticline lie along this trend. Initial Laramide folding, probably during latest Cretaceous time, resulted in a single, continuous, north-northwest-trending anticline with a southwestward vergence. This anticline was progressively unfolded from south to north as the Owl Creek Range was thrust southward over the Wind River basin in earliest Eocene time; scissors-like vertical motion along this flexure rotated the axial surface of the early formed Bridger anticline, resulting in a monocline with a reversed vergence (northeastward). Formation of the Thermopolis/East Warm Springs anticline parallel to the north flank of the range accompanied thrusting and effectively refolded the northern end of the Wildhorse Butte anticline along an east-west axis. Faulting of the oversteepened south limb of the Red Hole cross fold was contemporaneous with folding. Cross-cutting fold axes in this area and the Mud Creek area to the west are best explained by a counterclockwise change in stress direction during the latest phase of the Laramide orogeny. Vertical movement along the eastern side of the Owl Creek Range results from differential motion in the hanging wall of the crystalline thrust sheet.

  9. Spatially confined folding of chromatin in the interphase nucleus

    PubMed Central

    Mateos-Langerak, Julio; Bohn, Manfred; de Leeuw, Wim; Giromus, Osdilly; Manders, Erik M. M.; Verschure, Pernette J.; Indemans, Mireille H. G.; Gierman, Hinco J.; Heermann, Dieter W.; van Driel, Roel; Goetze, Sandra

    2009-01-01

    Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Polymer models have been used to describe chromatin folding. However, none of the proposed models gives a satisfactory explanation of experimental data. In particularly, they ignore that each chromosome occupies a confined space, i.e., the chromosome territory. Here, we present a polymer model that is able to describe key properties of chromatin over length scales ranging from 0.5 to 75 Mb. This random loop (RL) model assumes a self-avoiding random walk folding of the polymer backbone and defines a probability P for 2 monomers to interact, creating loops of a broad size range. Model predictions are compared with systematic measurements of chromatin folding of the q-arms of chromosomes 1 and 11. The RL model can explain our observed data and suggests that on the tens-of-megabases length scale P is small, i.e., 10–30 loops per 100 Mb. This is sufficient to enforce folding inside the confined space of a chromosome territory. On the 0.5- to 3-Mb length scale chromatin compaction differs in different subchromosomal domains. This aspect of chromatin structure is incorporated in the RL model by introducing heterogeneity along the fiber contour length due to different local looping probabilities. The RL model creates a quantitative and predictive framework for the identification of nuclear components that are responsible for chromatin–chromatin interactions and determine the 3-dimensional organization of the chromatin fiber. PMID:19234129

  10. Estimation of vocal fold plane in 3D CT images for diagnosis of vocal fold abnormalities.

    PubMed

    Hewavitharanage, Sajini; Gubbi, Jayavardhana; Thyagarajan, Dominic; Lau, Ken; Palaniswami, Marimuthu

    2015-01-01

    Vocal folds are the key body structures that are responsible for phonation and regulating air movement into and out of lungs. Various vocal fold disorders may seriously impact the quality of life. When diagnosing vocal fold disorders, CT of the neck is the commonly used imaging method. However, vocal folds do not align with the normal axial plane of a neck and the plane containing vocal cords and arytenoids does vary during phonation. It is therefore important to generate an algorithm for detecting the actual plane containing vocal folds. In this paper, we propose a method to automatically estimate the vocal fold plane using vertebral column and anterior commissure localization. Gray-level thresholding, connected component analysis, rule based segmentation and unsupervised k-means clustering were used in the proposed algorithm. The anterior commissure segmentation method achieved an accuracy of 85%, a good estimate of the expert assessment. PMID:26736949

  11. Nanocellulose 3, 5-Dimethylphenylcarbamate Derivative Coated Chiral Stationary Phase: Preparation and Enantioseparation Performance.

    PubMed

    Zhang, Xiaoli; Wang, Litao; Dong, Shuqing; Zhang, Xia; Wu, Qi; Zhao, Liang; Shi, Yanping

    2016-05-01

    Nanocrystalline cellulose (NCC) with high surface area and high ordered crystalline structure was prepared from microcrystalline cellulose (MCC) under the hydrolysis of sodium hypochlorite. NCC was further reacted with 3,5-dimethylphenyl isocyanate to obtain the nanocellulose derivative, and then coated successfully on the surface of silica gel to a prepared NCC-coated chiral stationary phase (CSP) as a new kind of chiral separation material. Similarly, MCC derivative-coated CSP was also prepared as contrast. The chiral separation performance of NCC-based CSP was evaluated and compared with MCC-based CSP by high-performance liquid chromatography. Moreover, the effects of the alcohol modifiers, mobile phase additives, and flow rates on chiral separations were investigated in detail. The results showed that 10 chiral compounds were separated on NCC-based CSP with better peak shape and higher column efficiency than MCC-based CSP, which confirmed that NCC-based CSP was a promising packing material for the resolution of chiral compounds.Chirality 28:376-381, 2016. © 2016 Wiley Periodicals, Inc. PMID:26949227

  12. Nanocellulose 3, 5-Dimethylphenylcarbamate Derivative Coated Chiral Stationary Phase: Preparation and Enantioseparation Performance.

    PubMed

    Zhang, Xiaoli; Wang, Litao; Dong, Shuqing; Zhang, Xia; Wu, Qi; Zhao, Liang; Shi, Yanping

    2016-05-01

    Nanocrystalline cellulose (NCC) with high surface area and high ordered crystalline structure was prepared from microcrystalline cellulose (MCC) under the hydrolysis of sodium hypochlorite. NCC was further reacted with 3,5-dimethylphenyl isocyanate to obtain the nanocellulose derivative, and then coated successfully on the surface of silica gel to a prepared NCC-coated chiral stationary phase (CSP) as a new kind of chiral separation material. Similarly, MCC derivative-coated CSP was also prepared as contrast. The chiral separation performance of NCC-based CSP was evaluated and compared with MCC-based CSP by high-performance liquid chromatography. Moreover, the effects of the alcohol modifiers, mobile phase additives, and flow rates on chiral separations were investigated in detail. The results showed that 10 chiral compounds were separated on NCC-based CSP with better peak shape and higher column efficiency than MCC-based CSP, which confirmed that NCC-based CSP was a promising packing material for the resolution of chiral compounds.Chirality 28:376-381, 2016. © 2016 Wiley Periodicals, Inc.

  13. Corrosion inhibition properties of graphene oxide on mild steel in 3.5% NaCl

    NASA Astrophysics Data System (ADS)

    Anandh Senthilvasan, Prem; Rangarajan, Murali

    2016-09-01

    In this work the corrosion inhibition of mild steel in 3.5% Sodium chloride (NaCl) solution at ambient conditions by Graphene Oxide (GO) has been studied. Graphene oxide was prepared by Modified Hummers Method and characterized by Fourier Transform Infrared spectroscopy (FTIR), UV-Visible spectroscopy (UV-Vis), X-ray Diffraction (XRD), Scanning Electron Microscopy (SEM), and Thermo-Gravimetric Analysis (TGA). The electrochemical corrosion behaviour of mild steel has been studied in the absence and presence of GO coatings by Tafel polarization and impedance analyses. The modified electrode has 44.8mV potential shift in the cathodic direction and reduction in current by 41.9 μA (61%). This indicates the strong protection offered by graphene oxide film. The obtained impedance spectra also clearly show that the charge transfer resistance of graphene oxide film is much higher than that of the uncoated steel electrode, demonstrating the strong protection offered by graphene oxide films for mild steel.

  14. Computational and theoretical methods for protein folding.

    PubMed

    Compiani, Mario; Capriotti, Emidio

    2013-12-01

    A computational approach is essential whenever the complexity of the process under study is such that direct theoretical or experimental approaches are not viable. This is the case for protein folding, for which a significant amount of data are being collected. This paper reports on the essential role of in silico methods and the unprecedented interplay of computational and theoretical approaches, which is a defining point of the interdisciplinary investigations of the protein folding process. Besides giving an overview of the available computational methods and tools, we argue that computation plays not merely an ancillary role but has a more constructive function in that computational work may precede theory and experiments. More precisely, computation can provide the primary conceptual clues to inspire subsequent theoretical and experimental work even in a case where no preexisting evidence or theoretical frameworks are available. This is cogently manifested in the application of machine learning methods to come to grips with the folding dynamics. These close relationships suggested complementing the review of computational methods within the appropriate theoretical context to provide a self-contained outlook of the basic concepts that have converged into a unified description of folding and have grown in a synergic relationship with their computational counterpart. Finally, the advantages and limitations of current computational methodologies are discussed to show how the smart analysis of large amounts of data and the development of more effective algorithms can improve our understanding of protein folding.

  15. Protein Folding and Mechanisms of Proteostasis

    PubMed Central

    Díaz-Villanueva, José Fernando; Díaz-Molina, Raúl; García-González, Victor

    2015-01-01

    Highly sophisticated mechanisms that modulate protein structure and function, which involve synthesis and degradation, have evolved to maintain cellular homeostasis. Perturbations in these mechanisms can lead to protein dysfunction as well as deleterious cell processes. Therefore in recent years the etiology of a great number of diseases has been attributed to failures in mechanisms that modulate protein structure. Interconnections among metabolic and cell signaling pathways are critical for homeostasis to converge on mechanisms associated with protein folding as well as for the preservation of the native structure of proteins. For instance, imbalances in secretory protein synthesis pathways lead to a condition known as endoplasmic reticulum (ER) stress which elicits the adaptive unfolded protein response (UPR). Therefore, taking this into consideration, a key part of this paper is developed around the protein folding phenomenon, and cellular mechanisms which support this pivotal condition. We provide an overview of chaperone protein function, UPR via, spatial compartmentalization of protein folding, proteasome role, autophagy, as well as the intertwining between these processes. Several diseases are known to have a molecular etiology in the malfunction of mechanisms responsible for protein folding and in the shielding of native structure, phenomena which ultimately lead to misfolded protein accumulation. This review centers on our current knowledge about pathways that modulate protein folding, and cell responses involved in protein homeostasis. PMID:26225966

  16. Experimental investigation of protein folding and misfolding.

    PubMed

    Dobson, Christopher M

    2004-09-01

    Newly synthesised proteins need to fold, often to intricate and close-packed structures, in order to function. The underlying mechanism by which this complex process takes place both in vitro and in vivo is now becoming understood, at least in general terms, as a result of the application of a wide range of biophysical and computational methods used in combination with the techniques of biochemistry and protein engineering. It is increasingly apparent, however, that folding is not only crucial for generating biological activity, but that it is also coupled to a wide range of processes within the cell, ranging from the trafficking of proteins to specific organelles to the regulation of cell growth and differentiation. Not surprisingly, therefore, the failure of proteins to fold appropriately, or to remain correctly folded, is associated with a large number of cellular malfunctions that give rise to disease. Misfolding, and its consequences such as aggregation, can be investigated by extending the types of techniques used to study the normal folding process. Application of these techniques is enabling the development of a unified description of the interconversion and regulation of the different conformational states available to proteins in living systems. Such a description proves a generic basis for understanding the fundamental links between protein misfolding and its associated clinical disorders, such as Alzheimer's disease and Type II diabetes, and for exploring novel therapeutic strategies directed at their prevention and treatment on a rational basis.

  17. A sweet code for glycoprotein folding.

    PubMed

    Caramelo, Julio J; Parodi, Armando J

    2015-11-14

    Glycoprotein synthesis is initiated in the endoplasmic reticulum (ER) lumen upon transfer of a glycan (Glc3Man9GlcNAc2) from a lipid derivative to Asn residues (N-glycosylation). N-Glycan-dependent quality control of glycoprotein folding in the ER prevents exit to Golgi of folding intermediates, irreparably misfolded glycoproteins and incompletely assembled multimeric complexes. It also enhances folding efficiency by preventing aggregation and facilitating formation of proper disulfide bonds. The control mechanism essentially involves four components, resident lectin-chaperones (calnexin and calreticulin) that recognize monoglucosylated polymannose protein-linked glycans, lectin-associated oxidoreductase acting on monoglucosylated glycoproteins (ERp57), a glucosyltransferase that creates monoglucosylated epitopes in protein-linked glycans (UGGT) and a glucosidase (GII) that removes the glucose units added by UGGT. This last enzyme is the only mechanism component sensing glycoprotein conformations as it creates monoglucosylated glycans exclusively in not properly folded glycoproteins or in not completely assembled multimeric glycoprotein complexes. Glycoproteins that fail to properly fold are eventually driven to proteasomal degradation in the cytosol following the ER-associated degradation pathway, in which the extent of N-glycan demannosylation by ER mannosidases play a relevant role in the identification of irreparably misfolded glycoproteins.

  18. Petrofabric test of viscous folding theory

    NASA Astrophysics Data System (ADS)

    Onasch, Charles M.

    1984-06-01

    Compression and extension axes are deduced from quartz deformation lamellae in a quartzite and a graywacke folded into an asymetrical syncline. Deformation lamellae fabrics in the two sandstones are distinctly different. In the graywacke, regardless of bedding orientation or position on the fold, compression axes are normal or nearly normal to the axial planar rough cleavage. Extension axes generally lie in the cleavage plane, parallel to dip. In most quartzite samples, compression axes are parallel or subparallel to bedding, at high angles to the fold axis and extension axes are normal to bedding. Two samples from the very base of the formation indicate compression parallel to the fold axis with extension parallel to bedding, at high angles to the fold axis. One of these two shows both patterns. The lamellae fabric geometry in these two samples suggests the presence of a neutral surface in the quartzite. The lamellae-derived compression and extension axes are in good agreement with the buckling behavior of a viscous layer (quartzite) embedded in a less viscous medium (graywacke and shale below and shale and carbonate above).

  19. Nonlinear Models for Protein Folding and Function

    NASA Astrophysics Data System (ADS)

    Cruzeiro, L.

    Earlier a specific kinetic process for reproducible protein folding was proposed according to which the nascent chain is helical and the first step in in vivo protein folding is the bending of the initial helix at specific amino acid sites. Here the theoretical feasibility of this kinetic process is tested. To that end, two proteins, one belonging to the mainly α class and the other belonging to the α/β class, are selected and targeted molecular dynamics is applied to generate folding pathways for those two proteins, starting from two well defined initial conformations: a fully extended and a α-helical conformation. Not only are the native states closer to an initial helical structure for both proteins but also the pathways from the α-helical initial conformation to the native state have lower potential energy than the pathways that start from the fully extended conformation. For the α/β protein, 30% (40%) of the pathways from an initial α-helix (fully extended) structure lead to unentangled native folds, a success rate that can be increased to 85% by the introduction of a putative intermediate structure. These results lend support to the kinetic process proposed and open up a new direction in which to look for a solution to the protein folding problem. The chapter ends with a section that emphasizes the formal similarities between the dynamics quantum vibrational excited states in proteins and electrons in nonlinear lattices.

  20. Towards a systematic classification of protein folds

    NASA Astrophysics Data System (ADS)

    Lindgård, Per-Anker; Bohr, Henrik

    1997-10-01

    A lattice model Hamiltonian is suggested for protein structures that can explain the division into structural fold classes during the folding process. Proteins are described by chains of secondary structure elements, with the hinges in between being the important degrees of freedom. The protein structures are given a unique name, which simultaneously represent a linear string of physical coupling constants describing hinge spin interactions. We have defined a metric and a precise distance measure between the fold classes. An automated procedure is constructed in which any protein structure in the usual protein data base coordinate format can be transformed into the proposed chain representation. Taking into account hydrophobic forces we have found a mechanism for the formation of domains with a unique fold containing predicted magic numbers \\{4,6,9,12,16,18,...\\} of secondary structures and multiples of these domains. It is shown that the same magic numbers are robust and occur as well for packing on other nonclosed packed lattices. We have performed a statistical analysis of available protein structures and found agreement with the predicted preferred abundances of proteins with a predicted magic number of secondary structures. Thermodynamic arguments for the increased abundance and a phase diagram for the folding scenario are given. This includes an intermediate high symmetry phase, the parent structures, between the molten globule and the native states. We have made an exhaustive enumeration of dense lattice animals on a cubic lattice for acceptance number Z=4 and Z=5 up to 36 vertices.

  1. Method of refining 2,2-isopropylidenebis-3,5- dibromophenylene-4-oxydiethanol

    NASA Technical Reports Server (NTRS)

    Kobayashi, T.; Nawata, K.; Hiratsuka, K.

    1982-01-01

    A method of refining 2,2-isopropylidenebis-3,5-dibromophenylene-4-oxydiethanol is described which is characterized by recrystallization of 2,2-isopropylidenebis-3,5-dibromophenylene-4-oxydiethanol using one or more aromatic hydrocarbons such as benzene, xylene, toluene, ethylbenzene or pseudocumene.

  2. AquaSMART: Water & Boating Safety, Grades 3-5. Teacher's Guide.

    ERIC Educational Resources Information Center

    Texas State Dept. of Parks and Wildlife, Austin.

    This teacher's guide accompanies a program designed to teach water and boating safety to students in grades 3-5. The written curriculum accompanies a video, AquaSMART 3-5. The theme of the curriculum is AquaSMART. To become AquaSMART, students must learn 10 basic lessons for water and boating safety. The written curriculum begins with an overview…

  3. 45 CFR 3.5 - Lost and found, and abandoned property.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Section 3.5 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION CONDUCT OF PERSONS AND TRAFFIC ON THE NATIONAL INSTITUTES OF HEALTH FEDERAL ENCLAVE General § 3.5 Lost and found, and... Services Administration regulations (41 CFR part 101-48). Abandoned, or other unclaimed property and,...

  4. 45 CFR 3.5 - Lost and found, and abandoned property.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Section 3.5 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION CONDUCT OF PERSONS AND TRAFFIC ON THE NATIONAL INSTITUTES OF HEALTH FEDERAL ENCLAVE General § 3.5 Lost and found, and... Services Administration regulations (41 CFR part 101-48). Abandoned, or other unclaimed property and,...

  5. IMMUNOASSAY METHODS FOR MEASURING ATRAZINE AND 3,5,6-TRICHLORO-2-PYRIDINOL IN FOODS

    EPA Science Inventory

    This chapter describes the use of enzyme-linked immunosorbent assay (ELISA) methods for the analysis of two potential environmental contaminants in food sample media, atrazine and 3,5,6-trichloro-2-pyridinol (3,5,6-TCP). Two different immunoassay formats are employed: a magnetic...

  6. 14 CFR 3.5 - Statements about products, parts, appliances and materials.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ..., appliances and materials. 3.5 Section 3.5 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT... and materials. (a) Definitions. The following terms will have the stated meanings when used in this.... Product means an aircraft, aircraft engine, or aircraft propeller. Record means any writing, drawing,...

  7. 14 CFR 3.5 - Statements about products, parts, appliances and materials.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ..., appliances and materials. 3.5 Section 3.5 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT... and materials. (a) Definitions. The following terms will have the stated meanings when used in this.... Product means an aircraft, aircraft engine, or aircraft propeller. Record means any writing, drawing,...

  8. 14 CFR 3.5 - Statements about products, parts, appliances and materials.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ..., appliances and materials. 3.5 Section 3.5 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT... and materials. (a) Definitions. The following terms will have the stated meanings when used in this.... Product means an aircraft, aircraft engine, or aircraft propeller. Record means any writing, drawing,...

  9. 14 CFR 3.5 - Statements about products, parts, appliances and materials.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ..., appliances and materials. 3.5 Section 3.5 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT... and materials. (a) Definitions. The following terms will have the stated meanings when used in this.... Product means an aircraft, aircraft engine, or aircraft propeller. Record means any writing, drawing,...

  10. 14 CFR 3.5 - Statements about products, parts, appliances and materials.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ..., appliances and materials. 3.5 Section 3.5 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT... and materials. (a) Definitions. The following terms will have the stated meanings when used in this.... Product means an aircraft, aircraft engine, or aircraft propeller. Record means any writing, drawing,...

  11. Effect of experimental contamination with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine on soil bacterial communities.

    PubMed

    Juck, D; Driscoll, B T; Charles, T C; Greer, C W

    2003-03-01

    The effect of contamination with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) on an indigenous soil bacterial community was examined in two uncontaminated loam soil columns possessing native grasses. One column was spiked twice with RDX crystals for a total RDX load of 1000 mg (kg soil)(-1). The reduced metabolite of RDX degradation, hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine, was observed in the column leachate, suggesting anaerobic degradation of RDX. Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA from both contaminated and uncontaminated columns produced identical banding patterns which were stable over the course of the experimental period. The bacterial diversity remained high in the contaminated column, as determined by restriction fragment length polymorphism and rarefaction analyses of random 16S rDNA clones. These combined results suggested that long-term exposure to 1000 mg RDX (kg soil)(-1) did not produce an observable effect on bacterial diversity or the numerically dominant members of the indigenous soil bacterial community.

  12. Bleaching effect of a 405-nm diode laser irradiation used with titanium dioxide and 3.5% hydrogen peroxide

    NASA Astrophysics Data System (ADS)

    Sakai, K.; Kato, J.; Nakazawa, T.; Hirai, Y.

    2007-09-01

    A 405-nm diode laser has recently been developed for soft tissue problems in dentistry. A new in-office bleaching agent consisting of a titanium dioxide photocatalyst and 3.5% hydrogen peroxide has proven to react well with light irradiated at a wavelength of around 400 nm. In this study, we evaluated the bleaching efficacy of a newly developed 405-nm diode laser on bovine teeth treated with a bleaching agent composed of titanium dioxide and 3.5% hydrogen peroxide. Sixteen bovine incisors were randomly divided into two groups: Group A, irradiated by the 405-nm diode laser at 200 mW; Group B, irradiated by the 405-nm diode laser at 400 mW. The bleaching agent with titanium dioxide and 3.5% hydrogen peroxide was applied to bovine enamel and irradiated for 1 min. The specimens were then washed and dried, and the same procedure was repeated nine more times. After irradiation, we assessed the effects of bleaching on the enamel by measuring the color of the specimens with a spectrophotometer and examining the enamel surfaces with a scanning electron microscope. L* rose to a high score, reaching a significantly higher post-treatment level in comparison to pretreatment. In a comparison of the color difference (Δ E) between Group A and Group B, the specimens in Group B showed significantly higher values after 10 min of irradiation for the post-treatment. No remarkable differences in the enamel surface morphology were found between the unbleached and bleached enamel. The use of a 405-nm diode laser in combination with a bleaching agent of titanium dioxide and 3.5% hydrogen peroxide may be an effective method for bleaching teeth without the risk of tooth damage.

  13. Proteopedia: Rossmann Fold: A Beta-Alpha-Beta Fold at Dinucleotide Binding Sites

    ERIC Educational Resources Information Center

    Hanukoglu, Israel

    2015-01-01

    The Rossmann fold is one of the most common and widely distributed super-secondary structures. It is composed of a series of alternating beta strand (ß) and alpha helical (a) segments wherein the ß-strands are hydrogen bonded forming a ß-sheet. The initial beta-alpha-beta (ßaß) fold is the most conserved segment of Rossmann folds. As this segment…

  14. Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome

    PubMed Central

    Elcock, Adrian H

    2006-01-01

    Although molecular simulation methods have yielded valuable insights into mechanistic aspects of protein refolding in vitro, they have up to now not been used to model the folding of proteins as they are actually synthesized by the ribosome. To address this issue, we report here simulation studies of three model proteins: chymotrypsin inhibitor 2 (CI2), barnase, and Semliki forest virus protein (SFVP), and directly compare their folding during ribosome-mediated synthesis with their refolding from random, denatured conformations. To calibrate the methodology, simulations are first compared with in vitro data on the folding stabilities of N-terminal fragments of CI2 and barnase; the simulations reproduce the fact that both the stability and thermal folding cooperativity increase as fragments increase in length. Coupled simulations of synthesis and folding for the same two proteins are then described, showing that both fold essentially post-translationally, with mechanisms effectively identical to those for refolding. In both cases, confinement of the nascent polypeptide chain within the ribosome tunnel does not appear to promote significant formation of native structure during synthesis; there are however clear indications that the formation of structure within the nascent chain is sensitive to location within the ribosome tunnel, being subject to both gain and loss as the chain lengthens. Interestingly, simulations in which CI2 is artificially stabilized show a pronounced tendency to become trapped within the tunnel in partially folded conformations: non-cooperative folding, therefore, appears in the simulations to exert a detrimental effect on the rate at which fully folded conformations are formed. Finally, simulations of the two-domain protease module of SFVP, which experimentally folds cotranslationally, indicate that for multi-domain proteins, ribosome-mediated folding may follow different pathways from those taken during refolding. Taken together, these

  15. The 3.5 micron light curves of long period variable stars. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Strecker, D. W.

    1973-01-01

    Infrared observations at an effective wavelength of 3.5 microns of a selected group of long period variable (LPV) stars are presented. Mira type and semiregular stars of M, S, and C spectral classifications were monitored throughout the full cycle of variability. Although the variable infrared radiation does not exactly repeat in intensity or time, the regularity is sufficient to produce mean 3.5 micron light curves. The 3.5 micron maximum radiation lags the visual maximum by about one-seventh of a cycle, while the minimum 3.5 micron intensity occurs nearly one-half cycle after infrared maximum. In some stars, there are inflections or humps on the ascending portion of the 3.5 micron light curve which may also be seen in the visual variations.

  16. Hypocrellin B graft on activated carbon and photocatalytic oxidation of 2,3,5-trimethylphenol

    NASA Astrophysics Data System (ADS)

    Liu, Wei; Li, Ying; Zhang, Pei; Zhang, Jucheng; Min, Yong; Yi, Zhongzhou; Zhang, Canbang; Wu, Mingzhu; Chen, Rui

    2008-12-01

    Hypocrellin B, a photosensitizer isolated from Hypocrella Bambuase sacc in Yunnan province, has significant anti-tumor and anti-virus character. In this article, hypocrellin B, which was grafted on activated carbon, was used as photocatalysts to catalytic oxidize 2,3,5-trimethylphenol to 2,3,5-trimethylhydrobenzoquinone because of its high photons efficiency. This study realized nearly 100% selectivity for 2,3,5-trimethylhydrobenzoquinone under visible light irradiation (>400nm) at aerobic atmosphere. The photocatalytic oxidation process has been studied by different parameters like the pretreatment of activated carbon, synthetic mehtod of grafted hypocrellin, and photo-assisted oxidation catalysis of 2,3,5-trimethylphenol to 2,3,5-trimethylhdrobenzoquinone. Compared to the conventional methods, this process could be more eco-friendly.

  17. Non-cylindrical fold growth in the Zagros fold and thrust belt (Kurdistan, NE-Iraq)

    NASA Astrophysics Data System (ADS)

    Bartl, Nikolaus; Bretis, Bernhard; Grasemann, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros mountains extends over 1800 km from Kurdistan in N-Iraq to the Strait of Hormuz in Iran and is one of the world most promising regions for the future hydrocarbon exploration. The Zagros Mountains started to form as a result of the collision between the Eurasian and Arabian Plates, whose convergence began in the Late Cretaceous as part of the Alpine-Himalayan orogenic system. Geodetic and seismological data document that both plates are still converging and that the fold and thrust belt of the Zagros is actively growing. Extensive hydrocarbon exploration mainly focuses on the antiforms of this fold and thrust belt and therefore the growth history of the folds is of great importance. This work investigates by means of structural field work and quantitative geomorphological techniques the progressive fold growth of the Permam, Bana Bawi- and Safeen- Anticlines located in the NE of the city of Erbil in the Kurdistan region of Northern Iraq. This part of the Zagros fold and thrust belt belongs to the so-called Simply Folded Belt, which is dominated by gentle to open folding. Faults or fault related folds have only minor importance. The mechanical anisotropy of the formations consisting of a succession of relatively competent (massive dolomite and limestone) and incompetent (claystone and siltstone) sediments essentially controls the deformation pattern with open to gentle parallel folding of the competent layers and flexural flow folding of the incompetent layers. The characteristic wavelength of the fold trains is around 10 km. Due to faster erosion of the softer rock layers in the folded sequence, the more competent lithologies form sharp ridges with steeply sloping sides along the eroded flanks of the anticlines. Using an ASTER digital elevation model in combination with geological field data we quantified 250 drainage basins along the different limbs of the subcylindrical Permam, Bana Bawi- and Safeen- Anticlines. Geomorphological indices of the drainage

  18. Influence of the ventricular folds on a voice source with specified vocal fold motion1

    PubMed Central

    McGowan, Richard S.; Howe, Michael S.

    2010-01-01

    The unsteady drag on the vocal folds is the major source of sound during voiced speech. The drag force is caused by vortex shedding from the vocal folds. The influence of the ventricular folds (i.e., the “false” vocal folds that protrude into the vocal tract a short distance downstream of the glottis) on the drag and the voice source are examined in this paper by means of a theoretical model involving vortex sheets in a two-dimensional geometry. The effect of the ventricular folds on the output acoustic pressure is found to be small when the movement of the vocal folds is prescribed. It is argued that the effect remains small when fluid-structure interactions account for vocal fold movement. These conclusions can be justified mathematically when the characteristic time scale for change in the velocity of the glottal jet is large compared to the time it takes for a vortex disturbance to be convected through the vocal fold and ventricular fold region. PMID:20329852

  19. Thermal stability of idealized folded carbyne loops

    PubMed Central

    2013-01-01

    Self-unfolding items provide a practical convenience, wherein ring-like frames are contorted into a state of equilibrium and subsequently  pop up’ or deploy when perturbed from a folded structure. Can the same process be exploited at the molecular scale? At the limiting scale is a closed chain of single atoms, used here to investigate the limits of stability of such folded ring structures via full atomistic molecular dynamics. Carbyne is a one-dimensional carbon allotrope composed of sp-hybridized carbon atoms. Here, we explore the stability of idealized carbyne loops as a function of chain length, curvature, and temperature, and delineate an effective phase diagram between folded and unfolded states. We find that while overall curvature is reduced, in addition to torsional and self-adhesive energy barriers, a local increase in curvature results in the largest impedance to unfolding. PMID:24252156

  20. Microbial Manipulation of the Amyloid Fold

    PubMed Central

    DePas, William H.

    2012-01-01

    Microbial biofilms are encased in a protein, DNA and polysaccharide matrix that protects the community, promotes interactions with the environment, and helps cells to adhere together. The protein component of these matrices is often a remarkably stable, β-sheet-rich polymer called amyloid. Amyloids form ordered, self-templating fibers that are highly aggregative, making them a valuable biofilm component. Some eukaryotic proteins inappropriately adopt the amyloid fold and these misfolded protein aggregates disrupt normal cellular proteostasis, which can cause significant cytotoxicity. Indeed, until recently amyloids were considered solely the result of protein misfolding. However, research over the past decade has revealed how various organisms have capitalized on the amyloid fold by developing sophisticated biogenesis pathways that coordinate gene expression, protein folding, and secretion so that amyloid-related toxicities are minimized. How microbes manipulate amyloids, by augmenting their advantageous properties and by reducing their undesirable properties, will be the subject of this review. PMID:23108148

  1. Transversal Clifford gates on folded surface codes

    NASA Astrophysics Data System (ADS)

    Moussa, Jonathan E.

    2016-10-01

    Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and correct errors, while color codes have transversal Clifford gates and better code efficiency in the number of physical qubits needed to achieve a given code distance. A formal equivalence exists between color codes and folded surface codes, but it does not guarantee the transferability of any of these favorable properties. However, the equivalence does imply the existence of constant-depth circuit implementations of logical Clifford gates on folded surface codes. We achieve and improve this result by constructing two families of folded surface codes with transversal Clifford gates. This construction is presented generally for qudits of any dimension. The specific application of these codes to universal quantum computation based on qubit fusion is also discussed.

  2. Kinetics of Peptide Folding in Lipid Membranes

    PubMed Central

    Oh, Kwang-Im; Smith-Dupont, Kathryn B.; Markiewicz, Beatrice N.; Gai, Feng

    2015-01-01

    Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments. PMID:25808575

  3. Stretching and folding in finite time.

    PubMed

    Ma, Tian; Ouellette, Nicholas T; Bollt, Erik M

    2016-02-01

    Complex flows mix efficiently, and this process can be understood by considering the stretching and folding of material volumes. Although many metrics have been devised to characterize stretching, fewer are able to capture folding in a quantitative way in spatiotemporally variable flows. Here, we extend our previous methods based on the finite-time curving of fluid-element trajectories to nonzero scales and show that this finite-scale finite-time curvature contains information about both stretching and folding. We compare this metric to the more commonly used finite-time Lyapunov exponent and illustrate our methods using experimental flow-field data from a quasi-two-dimensional laboratory flow. Our new analysis tools add to the growing set of Lagrangian methods for characterizing mixing in complex, aperiodic fluid flows.

  4. Exact folded-band chaotic oscillator

    NASA Astrophysics Data System (ADS)

    Corron, Ned J.; Blakely, Jonathan N.

    2012-06-01

    An exactly solvable chaotic oscillator with folded-band dynamics is shown. The oscillator is a hybrid dynamical system containing a linear ordinary differential equation and a nonlinear switching condition. Bounded oscillations are provably chaotic, and successive waveform maxima yield a one-dimensional piecewise-linear return map with segments of both positive and negative slopes. Continuous-time dynamics exhibit a folded-band topology similar to Rössler's oscillator. An exact solution is written as a linear convolution of a fixed basis pulse and a discrete binary sequence, from which an equivalent symbolic dynamics is obtained. The folded-band topology is shown to be dependent on the symbol grammar.

  5. Ontogeny of the mouse vocal fold epithelium

    PubMed Central

    Lungova, Vlasta; Verheyden, Jamie M.; Herriges, John; Sun, Xin; Thibeault, Susan L.

    2015-01-01

    This investigation provides the first systematic determination of the cellular and molecular progression of vocal fold (VF) epithelium development in a murine model. We define five principal developmental events that constitute the progression from VF initiation in the embryonic anterior foregut tube to fully differentiated and functional adult tissue. These developmental events include (1) the initiation of the larynx and vocal folds with apposition of the lateral walls of the primitive laryngopharynx (embryonic (E) day 10.5); (2) the establishment of the epithelial lamina with fusion of the lateral walls of the primitive laryngopharynx (E11.5); (3) the epithelial lamina recanalization and separation of VFs (E13.5–18.5); (4) the stratification of the vocal folds (E13.5–18.5); and (5) the maturation of vocal fold epithelium (postnatal stages). The illustration of these morphogenetic events is substantiated by dynamic changes in cell proliferation and apoptosis, as well as the expression pattern of key transcription factors, FOXA2, SOX2 and NKX2-1 that specify and pattern the foregut endoderm. Furthermore, we documented the gradual conversion of VF epithelial cells from simple precursors expressing cytokeratins 8 and 18 in the embryo into mature stratified epithelial cells also expressing cytokeratins 5 and 14 in the adult. Interestingly, in the adult, cytokeratins 5 and 14 appear to be expressed in all cell layers in the VF, in contrast to their preferential localization to the basal cell layer in surrounding epithelium. To begin investigating the role of signaling molecules in vocal fold development, we characterized the expression pattern of SHH pathway genes, and how loss of Shh affects vocal fold development in the mutant. This study defines the cellular and molecular context and serves as the necessary foundation for future functional investigations of VF formation. PMID:25601450

  6. Circular permutant GFP insertion folding reporters

    DOEpatents

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2008-06-24

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  7. Circular permutant GFP insertion folding reporters

    SciTech Connect

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2013-04-16

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  8. Circular permutant GFP insertion folding reporters

    SciTech Connect

    Waldo, Geoffrey S; Cabantous, Stephanie

    2013-02-12

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  9. Circular permutant GFP insertion folding reporters

    SciTech Connect

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2011-06-14

    Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

  10. Efficient enantioselective synthesis of (R)-[3,5-bis(trifluoromethyl)phenyl] ethanol by Leifsonia xyli CCTCC M 2010241 using isopropanol as co-substrate.

    PubMed

    Ouyang, Qi; Wang, Pu; Huang, Jin; Cai, Jinbo; He, Junyao

    2013-03-01

    (R)-[3,5-Bis(trifluoromethyl)phenyl] ethanol is a key chiral intermediate for the synthesis of aprepitant. In this paper, an efficient synthetic process for (R)-[3,5- bis(trifluoromethyl)phenyl] ethanol was developed via the asymmetric reduction of 3,5-bis(trifluoromethyl) acetophenone, catalyzed by Leifsonia xyli CCTCC M 2010241 cells using isopropanol as the co-substrate for cofactor recycling. Firstly, the substrate and product solubility and cell membrane permeability of biocatalysts were evaluated with different co-substrate additions into the reaction system, in which isopropanol manifested as the best hydrogen donor of coupled NADH regeneration during the bioreduction of 3,5-bis(trifluoromethyl) acetophenone. Subsequently, the optimization of parameters for the bioreduction were undertaken to improve the effectiveness of the process. The determined efficient reaction system contained 200 mM of 3,5-bis(trifluoromethyl) acetophenone, 20% (v/v) of isopropanol, and 300 g/l of wet cells. The bioreduction was executed at 30°C and 200 rpm for 30 h, and 91.8% of product yield with 99.9% of enantiometric excess (e.e.) was obtained. The established bioreduction reaction system could tolerate higher substrate concentrations of 3,5- bis(trifluoromethyl) acetophenone, and afforded a satisfactory yield and excellent product e.e. for the desired (R)-chiral alcohol, thus providing an alternative to the chemical synthesis of (R)-[3,5-bis(trifluoromethyl)phenyl] ethanol.

  11. Energetic Salts Based on 3,5-Bis(dinitromethyl)-1,2,4-triazole Monoanion and Dianion: Controllable Preparation, Characterization, and High Performance.

    PubMed

    Zhang, Jiaheng; Dharavath, Srinivas; Mitchell, Lauren A; Parrish, Damon A; Shreeve, Jean'ne M

    2016-06-22

    Molecular modification of known explosives is considered to be an efficient route to design new energetic materials. A new family of energetic salts based on the 3,5-bis(dinitromethyl)-1,2,4-triazole monoanion and dianion were controllably synthesized by using 1-diamino-2,2-dinitroethene as a precursor. X-ray structure determination of monohydrazinium 3,5-bis(dinitromethyl)-1,2,4-triazolate (5) and monoammonium (6) and diammonium 3,5-bis(dinitromethyl)-1,2,4-triazolate hydrate (8·H2O) further confirmed the structures of these anions. In addition, as supported by X-ray data, in the monoanion system, the roving proton on the ring nitrogen rather than on the gem-dinitro carbon results in extensive hydrogen-bonding interactions and higher packing coefficients. Interestingly, 5 and 6 possess the highest calculated crystal densities, 1.965 and 1.957 g cm(-3) at 150 K, for hydrazinium and ammonium energetic salts, respectively. Energetic evaluation indicates that 5 (detonation velocity vD = 9086 m s(-1); detonation pressure P = 38.7 GPa) and 6 (vD, 9271 m s(-1); P = 41.0 GPa) exhibit great detonation properties, superior to those of current highly explosive benchmarks, such as 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX). PMID:27267735

  12. Energetic Salts Based on 3,5-Bis(dinitromethyl)-1,2,4-triazole Monoanion and Dianion: Controllable Preparation, Characterization, and High Performance.

    PubMed

    Zhang, Jiaheng; Dharavath, Srinivas; Mitchell, Lauren A; Parrish, Damon A; Shreeve, Jean'ne M

    2016-06-22

    Molecular modification of known explosives is considered to be an efficient route to design new energetic materials. A new family of energetic salts based on the 3,5-bis(dinitromethyl)-1,2,4-triazole monoanion and dianion were controllably synthesized by using 1-diamino-2,2-dinitroethene as a precursor. X-ray structure determination of monohydrazinium 3,5-bis(dinitromethyl)-1,2,4-triazolate (5) and monoammonium (6) and diammonium 3,5-bis(dinitromethyl)-1,2,4-triazolate hydrate (8·H2O) further confirmed the structures of these anions. In addition, as supported by X-ray data, in the monoanion system, the roving proton on the ring nitrogen rather than on the gem-dinitro carbon results in extensive hydrogen-bonding interactions and higher packing coefficients. Interestingly, 5 and 6 possess the highest calculated crystal densities, 1.965 and 1.957 g cm(-3) at 150 K, for hydrazinium and ammonium energetic salts, respectively. Energetic evaluation indicates that 5 (detonation velocity vD = 9086 m s(-1); detonation pressure P = 38.7 GPa) and 6 (vD, 9271 m s(-1); P = 41.0 GPa) exhibit great detonation properties, superior to those of current highly explosive benchmarks, such as 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX).

  13. Control of folding by gravity and matrix thickness: Implications for large-scale folding

    NASA Astrophysics Data System (ADS)

    Schmalholz, S. M.; Podladchikov, Y. Y.; Burg, J.-P.

    2002-01-01

    We show that folding of a non-Newtonian layer resting on a homogeneous Newtonian matrix with finite thickness under influence of gravity can occur by three modes: (1) matrix-controlled folding, dependent on the effective viscosity contrast between layer and matrix, (2) gravity-controlled folding, dependent on the Argand number (the ratio of the stress caused by gravity to the stress caused by shortening), and (3) detachment folding, dependent on the ratio of matrix thickness to layer thickness. We construct a phase diagram that defines the transitions between each of the three folding modes. Our priority is transparency of the analytical derivations (e.g., thin-plate versus thick-plate approximations), which permits complete classification of the folding modes involving a minimum number of dimensionless parameters. Accuracy and sensitivity of the analytical results to model assumptions are investigated. In particular, depth dependence of matrix rheology is only important for folding over a narrow range of material parameters. In contrast, strong depth dependence of the viscosity of the folding layer limits applicability of ductile rheology and leads to a viscoelastic transition. Our theory is applied to estimate the effective thickness of the folded central Asian upper crust using the ratio of topographic wavelength to Moho depth. Phase diagrams based on geometrical parameters show that gravity does not significantly control folding in the Jura and the Zagros Mountains but does control folding in central Asia. Applicability conditions of viscous and thin sheet models for large-scale lithospheric deformation, derived in terms of the Argand number, have implications for the plate-like style of planetary tectonics.

  14. Competition between surface adsorption and folding of fibril-forming polypeptides

    NASA Astrophysics Data System (ADS)

    Ni, Ran; Kleijn, J. Mieke; Abeln, Sanne; Cohen Stuart, Martien A.; Bolhuis, Peter G.

    2015-02-01

    Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse-grained model, we systematically studied the folding and adsorption behavior of a β -roll forming polypeptide. We find that there are two different folding pathways depending on the temperature: (i) at low temperature, the polypeptide folds in solution into a β -roll before adsorbing onto the attractive surface; (ii) at higher temperature, the polypeptide first adsorbs in a disordered state and folds while on the surface. The folding temperature increases with increasing attraction as the folded β -roll is stabilized by the surface. Surprisingly, further increasing the attraction lowers the folding temperature again, as strong attraction also stabilizes the adsorbed disordered state, which competes with folding of the polypeptide. Our results suggest that to enhance the folding, one should use a weakly attractive surface. They also explain the recent experimental observation of the nonmonotonic effect of charge on the fibril formation on an oppositely charged surface [C. Charbonneau et al., ACS Nano 8, 2328 (2014), 10.1021/nn405799t].

  15. Higher Education or Higher Skilling?

    ERIC Educational Resources Information Center

    Muller, Steven

    1974-01-01

    Higher education may return to education for a minority, an unlikely course; concentrate on higher skilling, the road we are on today; or restore general education, the most attractive possibility, which can be implemented by restoring basic education in literacy, history, human biology, and language. (JH)

  16. SUZUKI-MIYAURA COUPLING REACTIONS OF 3,5-DICHLORO-1,2,4-THIADIAZOLE

    PubMed Central

    Farahat, Abdelbasset A.; Boykin, David W.

    2014-01-01

    3,5-Dichloro-1,2,4-thiadiazole was allowed to react with different arylboronic acids under different Suzuki-Miyaura coupling conditions: at room temperature 5-aryl-3-chloro-1,2,4-thiadiazoles were obtained and at toluene reflux temperature the products were 3,5-diaryl-1,2,4-thiadiazoles. Sequential coupling reactions lead to 3,5-diaryl-1,2,4-thiadiazoles with non-identical aryl groups. The structure of 3-methoxy-5-(4-methoxyphenyl)-1,2,4-thiadiazole was established from X-ray crystallographic data. PMID:24644388

  17. Theoretical study of the thermodynamic properties, phase transition wave, and phase transition velocity for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine

    SciTech Connect

    Long, Yao; Chen, Jun

    2015-09-21

    We develop a phonon-electron free energy model to study the thermodynamic properties and phase transitions of δ-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine. The bulk modulus, thermal expansion coefficient, specific heat, Hugoniot curve, and phase transition curve are calculated in wide temperature and pressure ranges. The results are in agreement with the available experiments at zero pressure, and are reasonable predictions at high pressure for the lack of experiment. Two kinds of phase transition waves are investigated. We find the velocity of shock-induced phase transition wave is between 3400 m/s and 4700 m/s, and the velocity of self-sustaining phase transition wave is between 1300 m/s and 1900 m/s.

  18. Ab initio study of coherent anti-Stokes Raman scattering (CARS) of the 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) explosive

    NASA Astrophysics Data System (ADS)

    Mohammed, Abdelsalam; Ågren, Hans; Thorvaldsen, Andreas J.; Ruud, Kenneth

    2010-01-01

    Coherent anti-Stokes Raman scattering (CARS) of the 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) C 3H 6N 6O 6 molecule is studied by ab initio methods. The results are compared to available experimental observations and against calculations and experimental observations of the conventional non-resonant Raman spectrum for RDX. It is found that all intense bands in the observed CARS spectrum and all Raman differential cross sections are well reproduced by the calculations. The features of the resonant CARS signal vary strongly from the corresponding Raman signal, and are obtained with a considerably larger cross section, a fact that could further facilitate the use of CARS spectroscopy in applications of stand-off detection of gaseous samples at ultra-low concentrations.

  19. Liquid chromatography/electrospray ionization tandem mass spectrometry analysis of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX).

    PubMed

    Pan, Xiaoping; Zhang, Baohong; Tian, Kang; Jones, Lindsey E; Liu, Jun; Anderson, Todd A; Wang, Jia-Sheng; Cobb, George P

    2006-01-01

    A quantitative liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method was developed for the analysis of the explosive, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX). In negative ionization mode, HMX forms an acetate adduct ion [M + CH(3)COO](-), m/z 355, in the presence of a small amount of acetic acid in the mobile phase. The ESI collision-induced dissociation (CID) spectrum of m/z 355 was acquired and the transitions m/z 355 --> 147 and m/z 355 --> 174 were chosen for the determination of HMX in samples. Using this quantification technique, the method detection limit was 1.57 microg/L and good linearity was achieved in the range 5-500 microg/L. This method will help to unambiguously analyze environmentally relevant concentrations of HMX.

  20. Fold in Origami and Unfold Math

    ERIC Educational Resources Information Center

    Georgeson, Joseph

    2011-01-01

    Students enjoy origami and like making everything from paper cranes to footballs out of small, colorful squares of paper. They can invent their own shapes and are intrigued by the polyhedrons that they can construct. Paper folding is fun, but where is the math? Unless teachers develop lessons that address mathematical objectives, origami could be…

  1. Role of cofactors in metalloprotein folding.

    PubMed

    Wilson, Corey J; Apiyo, David; Wittung-Stafshede, Pernilla

    2004-01-01

    Metals are commonly found as natural constituents of proteins. Since many such metals can interact specifically with their corresponding unfolded proteins in vitro , cofactor-binding prior to polypeptide folding may be a biological path to active metalloproteins. By interacting with the unfolded polypeptide, the metal may create local structure that initiates and directs the polypeptide-folding process. Here, we review recent literature that addresses the involvement of metals in protein-folding reactions in vitro . To date, the best characterized systems are simple one such as blue-copper proteins, heme-binding proteins, iron-sulfur-cluster proteins and synthetic metallopeptides. Taken together, the available data demonstrates that metals can play diverse roles: it is clear that many cofactors bind before polypeptide folding and influence the reaction; yet, some do not bind until a well-structured active site is formed. The significance of characterizing the effects of metals on protein conformational changes is underscored by the many human diseases that are directly linked to anomalous protein-metal interactions.

  2. Folded-path optical analysis gas cell

    DOEpatents

    Carangelo, Robert M.; Wright, David D.

    1995-01-01

    A folded-path gas cell employs an elliptical concave mirror in confronting relationship to two substantially spherical concave mirrors. At least one of the spherical mirrors, and usually both, are formed with an added cylindrical component to increase orthogonal focii coincidence and thereby to increase the radiation energy throughput characteristic of the cell.

  3. Hydroxyapatite surface-induced peptide folding.

    PubMed

    Capriotti, Lisa A; Beebe, Thomas P; Schneider, Joel P

    2007-04-25

    Herein, we describe the design and surface-binding characterization of a de novo designed peptide, JAK1, which undergoes surface-induced folding at the hydroxyapatite (HA)-solution interface. JAK1 is designed to be unstructured in buffered saline solution, yet undergo HA-induced folding that is largely governed by the periodic positioning of gamma-carboxyglutamic acid (Gla) residues within the primary sequence of the peptide. Circular dichroism (CD) spectroscopy and analytical ultracentrifugation indicate that the peptide remains unfolded and monomeric in solution under normal physiological conditions; however, CD spectroscopy indicates that in the presence of hydroxyapatite, the peptide avidly binds to the mineral surface adopting a helical structure. Adsorption isotherms indicate nearly quantitative surface coverage and Kd = 310 nM for the peptide-surface binding event. X-ray photoelectron spectroscopy (XPS) coupled with the adsorption isotherm data suggests that JAK1 binds to HA, forming a self-limiting monolayer. This study demonstrates the feasibility of using HA surfaces to trigger the intramolecular folding of designed peptides and represents the initial stages of defining the design rules that allow HA-induced peptide folding.

  4. Folding and faulting of an elastic continuum

    PubMed Central

    Gourgiotis, Panos A.

    2016-01-01

    Folding is a process in which bending is localized at sharp edges separated by almost undeformed elements. This process is rarely encountered in Nature, although some exceptions can be found in unusual layered rock formations (called ‘chevrons’) and seashell patterns (for instance Lopha cristagalli). In mechanics, the bending of a three-dimensional elastic solid is common (for example, in bulk wave propagation), but folding is usually not achieved. In this article, the route leading to folding is shown for an elastic solid obeying the couple-stress theory with an extreme anisotropy. This result is obtained with a perturbation technique, which involves the derivation of new two-dimensional Green's functions for applied concentrated force and moment. While the former perturbation reveals folding, the latter shows that a material in an extreme anisotropic state is also prone to a faulting instability, in which a displacement step of finite size emerges. Another failure mechanism, namely the formation of dilation/compaction bands, is also highlighted. Finally, a geophysical application to the mechanics of chevron formation shows how the proposed approach may explain the formation of natural structures. PMID:27118925

  5. Hydroxyapatite surface-induced peptide folding.

    PubMed

    Capriotti, Lisa A; Beebe, Thomas P; Schneider, Joel P

    2007-04-25

    Herein, we describe the design and surface-binding characterization of a de novo designed peptide, JAK1, which undergoes surface-induced folding at the hydroxyapatite (HA)-solution interface. JAK1 is designed to be unstructured in buffered saline solution, yet undergo HA-induced folding that is largely governed by the periodic positioning of gamma-carboxyglutamic acid (Gla) residues within the primary sequence of the peptide. Circular dichroism (CD) spectroscopy and analytical ultracentrifugation indicate that the peptide remains unfolded and monomeric in solution under normal physiological conditions; however, CD spectroscopy indicates that in the presence of hydroxyapatite, the peptide avidly binds to the mineral surface adopting a helical structure. Adsorption isotherms indicate nearly quantitative surface coverage and Kd = 310 nM for the peptide-surface binding event. X-ray photoelectron spectroscopy (XPS) coupled with the adsorption isotherm data suggests that JAK1 binds to HA, forming a self-limiting monolayer. This study demonstrates the feasibility of using HA surfaces to trigger the intramolecular folding of designed peptides and represents the initial stages of defining the design rules that allow HA-induced peptide folding. PMID:17397165

  6. Folded-path optical analysis gas cell

    DOEpatents

    Carangelo, R.M.; Wright, D.D.

    1995-08-08

    A folded-path gas cell employs an elliptical concave mirror in confronting relationship to two substantially spherical concave mirrors. At least one of the spherical mirrors, and usually both, are formed with an added cylindrical component to increase orthogonal foci coincidence and thereby to increase the radiation energy throughput characteristic of the cell. 10 figs.

  7. Folded cavity design for a ruby resonator

    NASA Technical Reports Server (NTRS)

    Arunkumar, K. A.; Trolinger, James D.

    1988-01-01

    A folded cavity laser resonator operating in the TEM(00) mode has been built and tested. The new oscillator configuration leads to an increase in efficiency and to better line narrowing due to the increased number of passes through the laser rod and tuning elements, respectively. The modification is shown to lead to cavity ruggedization.

  8. Fast phase randomization via two-folds

    PubMed Central

    Jeffrey, M. R.

    2016-01-01

    A two-fold is a singular point on the discontinuity surface of a piecewise-smooth vector field, at which the vector field is tangent to the discontinuity surface on both sides. If an orbit passes through an invisible two-fold (also known as a Teixeira singularity) before settling to regular periodic motion, then the phase of that motion cannot be determined from initial conditions, and, in the presence of small noise, the asymptotic phase of a large number of sample solutions is highly random. In this paper, we show how the probability distribution of the asymptotic phase depends on the global nonlinear dynamics. We also show how the phase of a smooth oscillator can be randomized by applying a simple discontinuous control law that generates an invisible two-fold. We propose that such a control law can be used to desynchronize a collection of oscillators, and that this manner of phase randomization is fast compared with existing methods (which use fixed points as phase singularities), because there is no slowing of the dynamics near a two-fold. PMID:27118901

  9. Global hairpin folding of tau in solution.

    PubMed

    Jeganathan, Sadasivam; von Bergen, Martin; Brutlach, Henrik; Steinhoff, Heinz-Jürgen; Mandelkow, Eckhard

    2006-02-21

    The microtubule-associated protein tau stabilizes microtubules in its physiological role, whereas it forms insoluble aggregates (paired helical filaments) in Alzheimer's disease. Soluble tau is considered a natively unfolded protein whose residual folding and intramolecular interactions are largely undetermined. In this study, we have applied fluorescence resonance energy transfer (FRET) and electron paramagnetic resonance (EPR) to examine the proximity and flexibility of tau domains and the global folding. FRET pairs spanning the tau molecule were created by inserting tryptophans (donor) and cysteines (labeled with IAEDANS as an acceptor) by site-directed mutagenesis. The observed FRET distances were significantly different from those expected for a random coil. Notably, the C-terminal end of tau folds over into the vicinity of the microtubule-binding repeat domain, the N-terminus remains outside the FRET distance of the repeat domain, yet both ends of the molecule approach one another. The interactions between the domains were obliterated by denaturation in GdnHCl. Paramagnetic spin-labels attached in various domains of tau were analyzed by EPR and exhibited a high mobility throughout. The data indicate that tau retains some global folding even in its "natively unfolded" state, combined with the high flexibility of the chain.

  10. Coiling and Folding of Viscoelastic Jets

    NASA Astrophysics Data System (ADS)

    Majmudar, Trushant; Varagnat, Matthieu; McKinley, Gareth

    2007-11-01

    The study of fluid jets impacting on a flat surface has industrial applications in many areas, including processing of foods and consumer goods, bottle filling, and polymer melt processing. Previous studies have focused primarily on purely viscous, Newtonian fluids, which exhibit a number of different dynamical regimes including dripping, steady jetting, folding, and steady coiling. Here we add another dimension to the problem by focusing on mobile (low viscosity) viscoelastic fluids, with the study of two wormlike-micellar fluids, a cetylpyridinum-salicylic acid salt (CPyCl/NaSal) solution, and an industrially relevant shampoo base. We investigate the effects of viscosity and elasticity on the dynamics of axi-symmetric jets. The viscoelasticity of the fluids is systematically controlled by varying the concentration of salt counterions. Experimental methods include shear and extensional rheology measurements to characterize the fluids, and high-speed digital video imaging. In addition to the regimes observed in purely viscous systems, we also find a novel regime in which the elastic jet buckles and folds on itself, and alternates between coiling and folding behavior. We suggest phase diagrams and scaling laws for the coiling and folding frequencies through a systematic exploration of the experimental parameter space (height of fall, imposed flow rate, elasticity of the solution).

  11. Self-folding graphene-polymer bilayers

    NASA Astrophysics Data System (ADS)

    Deng, Tao; Yoon, ChangKyu; Jin, Qianru; Li, Mingen; Liu, Zewen; Gracias, David H.

    2015-05-01

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  12. Abstract folding space analysis based on helices

    PubMed Central

    Huang, Jiabin; Backofen, Rolf; Voß, Björn

    2012-01-01

    RNA has many pivotal functions especially in the regulation of gene expression by ncRNAs. Identification of their structure is an important requirement for understanding their function. Structure prediction alone is often insufficient for this task, due to algorithmic problems, parameter inaccuracies, and biological peculiarities. Among the latter, there are base modifications, cotranscriptional folding leading to folding traps, and conformational switching as in the case of riboswitches. All these require more in-depth analysis of the folding space. The major drawback, which all methods have to cope with, is the exponential growth of the folding space. Therefore, methods are often limited in the sequence length they can analyze, or they make use of heuristics, sampling, or abstraction. Our approach adopts the abstraction strategy and remedies some problems of existing methods. We introduce a position-specific abstraction based on helices that we term helix index shapes, or hishapes for short. Utilizing a dynamic programming framework, we have implemented this abstraction in the program RNAHeliCes. Furthermore, we developed two hishape-based methods, one for energy barrier estimation, called HiPath, and one for abstract structure comparison, termed HiTed. We demonstrate the superior performance of HiPath compared to other existing methods and the competitive accuracy of HiTed. RNAHeliCes, together with HiPath and HiTed, are available for download at http://www.cyanolab.de/software/RNAHeliCes.htm. PMID:23104999

  13. Self-folding graphene-polymer bilayers

    SciTech Connect

    Deng, Tao; Yoon, ChangKyu; Jin, Qianru; Li, Mingen; Liu, Zewen; Gracias, David H.

    2015-05-18

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  14. Searching for the 3.5 keV Line in the Stacked Suzaku Observations of Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Bulbul, Esra; Markevitch, Maxim; Foster, Adam; Miller, Eric; Bautz, Mark; Loewenstein, Mike; Randall, Scott W.; Smith, Randall K.

    2016-11-01

    We perform a detailed study of the stacked Suzaku observations of 47 galaxy clusters, spanning a redshift range of 0.01–0.45, to search for the unidentified 3.5 keV line. This sample provides an independent test for the previously detected line. We detect a 2σ -significant spectral feature at 3.5 keV in the spectrum of the full sample. When the sample is divided into two subsamples (cool-core and non-cool core clusters), the cool-core subsample shows no statistically significant positive residuals at the line energy. A very weak (∼ 2σ confidence) spectral feature at 3.5 keV is permitted by the data from the non-cool-core clusters sample. The upper limit on a neutrino decay mixing angle of {\\sin }2(2θ )=6.1× {10}-11 from the full Suzaku sample is consistent with the previous detections in the stacked XMM-Newton sample of galaxy clusters (which had a higher statistical sensitivity to faint lines), M31, and Galactic center, at a 90% confidence level. However, the constraint from the present sample, which does not include the Perseus cluster, is in tension with previously reported line flux observed in the core of the Perseus cluster with XMM-Newton and Suzaku.

  15. sym-Trisubstituted 1,3,5-Triazine Derivatives as Promising Organic Corrosion Inhibitors for Steel in Acidic Solution.

    PubMed

    El-Faham, Ayman; Dahlous, Kholood A; Al Othman, Zeid A; Al-Lohedan, Hamad A; El-Mahdy, Gamal A

    2016-03-31

    Triazine derivatives, namely, 2,4,6-tris(quinolin-8-yloxy)-1,3,5-triazine (T3Q), N²,N⁴,N⁶-tris(pyridin-2-ylmethyl)-1,3,5-triazine-2,4,6-triamine (T3AMPy) and 2,2',2''-[(1,3,5-triazine-2,4,6-triyl)tris(azanediyl)] tris(ethan-1-ol) (T3EA) were synthesized and their inhibition of steel corrosion in hydrochloric acid solution was investigated using electrochemical techniques. The corrosion protection of the prepared compounds increased with increasing concentration and reached up to 98% at 250 ppm. The adsorption of T3Q, T3AMPy, and T3EA on the steel surface was in accordance with the Langmuir adsorption isotherm. The electrochemical results revealed that T3Q, T3AMPy and T3EA act as excellent organic inhibitors and can labeled as mixed type inhibitors. The efficiencies of the tested compounds were affected by the nature of the side chain present in the triazine ring, where T3EA gave the least inhibition while T3Q and T3AMPy gave higher and almost the same inhibition effects. The inhibition efficiencies obtained from the different electrochemical techniques were in good agreement.

  16. THE X-RAY LINE FEATURE AT 3.5 KeV IN GALAXY CLUSTER SPECTRA

    SciTech Connect

    Phillips, K. J. H.; Sylwester, B.; Sylwester, J. E-mail: bs@cbk.pan.wroc.pl

    2015-08-10

    Recent work by Bulbul et al. and Boyarsky et al. has suggested that a line feature at ∼3.5 keV in the X-ray spectra of galaxy clusters and individual galaxies seen with XMM-Newton is due to the decay of sterile neutrinos, a dark matter candidate. This identification has been criticized by Jeltema and Profumo on the grounds that model spectra suggest that atomic transitions in helium-like potassium (K xviii) and chlorine (Cl xvi) are more likely to be the emitters. Here it is pointed out that the K xviii lines have been observed in numerous solar flare spectra at high spectral resolution with the RESIK crystal spectrometer and also appear in Chandra HETG spectra of the coronally active star σ Gem. In addition, the solar flare spectra at least indicate a mean coronal potassium abundance, which is a factor between 9 and 11 higher than the solar photospheric abundance. This fact, together with the low statistical quality of the XMM-Newton spectra, completely account for the ∼3.5 keV feature and there is therefore no need to invoke a sterile neutrino interpretation of the observed line feature at ∼3.5 keV.

  17. sym-Trisubstituted 1,3,5-Triazine Derivatives as Promising Organic Corrosion Inhibitors for Steel in Acidic Solution.

    PubMed

    El-Faham, Ayman; Dahlous, Kholood A; Al Othman, Zeid A; Al-Lohedan, Hamad A; El-Mahdy, Gamal A

    2016-01-01

    Triazine derivatives, namely, 2,4,6-tris(quinolin-8-yloxy)-1,3,5-triazine (T3Q), N²,N⁴,N⁶-tris(pyridin-2-ylmethyl)-1,3,5-triazine-2,4,6-triamine (T3AMPy) and 2,2',2''-[(1,3,5-triazine-2,4,6-triyl)tris(azanediyl)] tris(ethan-1-ol) (T3EA) were synthesized and their inhibition of steel corrosion in hydrochloric acid solution was investigated using electrochemical techniques. The corrosion protection of the prepared compounds increased with increasing concentration and reached up to 98% at 250 ppm. The adsorption of T3Q, T3AMPy, and T3EA on the steel surface was in accordance with the Langmuir adsorption isotherm. The electrochemical results revealed that T3Q, T3AMPy and T3EA act as excellent organic inhibitors and can labeled as mixed type inhibitors. The efficiencies of the tested compounds were affected by the nature of the side chain present in the triazine ring, where T3EA gave the least inhibition while T3Q and T3AMPy gave higher and almost the same inhibition effects. The inhibition efficiencies obtained from the different electrochemical techniques were in good agreement. PMID:27043517

  18. Thermochemistry of uracils. Experimental and computational enthalpies of formation of 5,6-dimethyl-, 1,3,5-trimethyl-, and 1,3,5,6-tetramethyluracils.

    PubMed

    Notario, Rafael; Emel'yanenko, Vladimir N; Roux, María Victoria; Ros, Francisco; Verevkin, Sergey P; Chickos, James S; Liebman, Joel F

    2013-01-10

    We describe in the current paper an experimental and computational study of three methylated uracils, in particular, the 5,6-dimethyl-, 1,3,5-trimethyl-, and 1,3,5,6-tetramethyl derivatives. The values of the standard (p(0) = 0.1 MPa) molar enthalpies of formation in the gas phase at T = 298.15 K have been determined. The energies of combustion were measured by static bomb combustion calorimetry, and from the results obtained, the standard molar enthalpies of formation in the crystalline state at T = 298.15 K were calculated. The enthalpies of sublimation were determined using the transpiration method in a saturated N(2) stream. Values of -(376.2 ± 2.6), -(355.9 ± 3.0), and -(381.7 ± 2.8) kJ·mol(-1) for the gas-phase enthalpies of formation at T = 298.15 K of 5,6-dimethyluracil, 1,3,5-trimethyluracil, and 1,3,5,6-tetramethyluracil, respectively, were obtained from the experimental thermochemical study. An extended theoretical study with the G3 and the G4 quantum-chemical methods has been carried out for all the possible methylated uracils. There is a very good agreement between experimental and calculated enthalpies of formation for the three derivatives studied. A Free-Wilson analysis on G4-calculated enthalpies of formation has been carried out, and the contribution of methylation in the different positions of the uracil ring has been estimated. PMID:23215007

  19. Abundance and diversity of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)-metabolizing bacteria in UXO-contaminated marine sediments.

    PubMed

    Zhao, Jian-Shen; Manno, Dominic; Hawari, Jalal

    2007-03-01

    Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) is a toxic explosive known to be resistant to biodegradation. In this study, we found that sediment collected from two unexploded ordnance (UXO) disposal sites (UXO-3, UXO-5) and one nearby reference site (midref) in Hawaii contained anaerobic bacteria capable of removing HMX. Two groups of HMX-removing bacteria were found in UXO-5: group I contained aerotolerant anaerobes and microaerophiles, and group II contained facultative anaerobes. In UXO-3 and midref sediments, HMX-metabolizing bacteria were strictly anaerobic (group III and group IV). Using 16S rRNA sequencing, group I was assigned to a novel phylogenetic cluster of Clostridiales, and groups II and III were related to Paenibacillus and Tepidibacter of Firmicutes, respectively. Group IV bacteria were identified as Desulfovibrio of Deltaproteobacteria. Using [UL-(14)C]-HMX, group IV isolates were found to mineralize HMX (26.8% in 308 d) as determined by liberated (14)CO(2), but negligible mineralization was observed in groups I-III. Resting cells of isolates metabolized HMX to N(2)O and HCHO via the intermediary formation of 1-nitroso-octahydro-3,5,7-trinitro-1,3,5,7-tetrazocine together with methylenedinitramine. These experimental findings suggest that HMX biotransformation occurred either via initial denitration followed by ring cleavage or via reduction of one or more of the N-NO(2) group(s) to the corresponding N-NO bond(s) prior to ring cleavage.

  20. Description and classification of folds in single surfaces

    NASA Astrophysics Data System (ADS)

    Twiss, Robert J.

    I propose a new three-parameter description of fold style in folded surfaces based on the ratio of the amplitude to the half-wavelength (the aspect ratio P), the maximum angle of relative rotation of opposite limbs of the fold (the folding angle φ), and a measure of the relative curvature at the fold closure (the bluntness b). For symmetric folds, the first two parameters define a trapezoid that circumscribes the fold and provides the primary criterion for the classification of fold style. Within a given trapezoid, fold style variations are defined by the bluntness. Perfect folds in profile are defined to have a single hinge with perfectly straight limbs tangent to hinge zones that are perfect circular arcs. An analytic description of the variation in perfect fold geometry defines the limits for all natural single-hinged folds. The proposed system includes folds with folding angles both less than and greater than isoclinal folds, it applies to both single-hinged and multiple-hinged folds, and it also can be extended to apply to asymmetric folds. Previously proposed two-parameter classification systems can only describe folds that are restricted to a specific surface through the three-parameter fold style space proposed here.

  1. Fault-related folding during extension: Plunging basement-cored folds in the Basin and Range

    USGS Publications Warehouse

    Howard, K.A.; John, Barbara E.

    1997-01-01

    Folds are able to form in highly extended areas where stratified cover rocks respond to basement fault offsets. The response of cover rocks to basement faulting can be studied especially well in plunging structures that expose large structural relief. The southern Basin and Range province contains plunging folds kilometres in amplitude at the corners of domino-like tilt blocks of basement rocks, where initially steep transverse and normal faults propagated upward toward the layered cover rocks. Exposed tilted cross sections, as much as 8 km thick, display transitions from faulted basement to folded cover that validate laboratory models of forced folds. The folded cover masks a deeper extensional style of brittle segmentation and uniform steep tilting.

  2. Oxidative folding of peptides with cystine-knot architectures: kinetic studies and optimization of folding conditions.

    PubMed

    Reinwarth, Michael; Glotzbach, Bernhard; Tomaszowski, Michael; Fabritz, Sebastian; Avrutina, Olga; Kolmar, Harald

    2013-01-01

    Bioactive peptides often contain several disulfide bonds that provide the main contribution to conformational rigidity and structural, thermal, or biological stability. Among them, cystine-knot peptides-commonly named "knottins"-make up a subclass with several thousand natural members. Hence, they are considered promising frameworks for peptide-based pharmaceuticals. Although cystine-knot peptides are available through chemical and recombinant synthetic routes, oxidative folding to afford the bioactive isomers still remains a crucial step. We therefore investigated the oxidative folding of ten protease-inhibiting peptides from two knottin families, as well as that of an HIV entry inhibitor and of aprotinin, under two conventional sets of folding conditions and by a newly developed procedure. Kinetic studies identified folding conditions that resulted in correctly folded miniproteins with high rates of conversion even for highly hydrophobic and aggregation-prone peptides in concentrated solutions. PMID:23229141

  3. 3,5-Bis(3-alkylaminomethyl-4-hydroxybenzylidene)-4-piperidones: A Novel Class of Potent Tumor-Selective Cytotoxins.

    PubMed

    Karki, Subhas S; Das, Umashankar; Umemura, Naoki; Sakagami, Hiroshi; Iwamoto, Shoko; Kawase, Masami; Balzarini, Jan; De Clercq, Erik; Dimmock, Stephen G; Dimmock, Jonathan R

    2016-01-28

    Novel 4-piperidone derivatives 2a-f are disclosed as potent cytotoxins. Many of these compounds are more potent than the reference drug melphalan. The compounds in series 2, 4-7 display selective toxicities toward various neoplasms compared to some normal cells. 2a is one of the promising lead molecules that display >11-fold higher growth inhibiting potency than 5-fluorouracil against human colon cancer cells. 2a induces apoptosis, DNA fragmentation, and cleavage of poly ADP-ribose polymerase. PMID:26727215

  4. Anion-controlled assembly of metal 3,5-bis(benzimidazol-1-ylmethyl) benzoate complexes: Synthesis, characterization and property

    NASA Astrophysics Data System (ADS)

    Kuai, Hai-Wei; Lv, Gao-Chao; Hou, Chao; Sun, Wei-Yin

    2015-03-01

    Hydrothermal reactions of 3,5-bis(benzimidazol-1-ylmethyl)benzoic acid (HL) with Cd(II), Cu(II) and Zn(II) salts provide eight new metal complexes which were characterized by single crystal and powder X-ray diffraction, IR, elemental and thermogravimetric analyses. Two cadmium frameworks [Cd(L)2]·2H2O (1) and [Cd(L)Cl] (2) have 3D structures with (42.65.83)(42.6) and rtl (4.62)2(42.610.83) topologies, respectively. Structural diversity of four copper complexes [Cu3(L)2]·NO3·0.5H2O (3), [Cu2(HL)2(SO4)]·3.5H2O (4), [Cu(L)(bdc)0.5]·1.5H2O (5) and [Cu2(L)(HL)(Hbdc)] (6) (H2bdc=1,4-benzenedicarboxylic acid) is achieved through the alteration of copper salts and addition of auxiliary ligand. As a result, 3 has a 1D ladder structure, 4 is a discrete dinuclear complex, 5 displays a (3,4)-connected 2-nodal 3-fold interpenetrating framework with (42.6.102.12)(42.6) topology, 6 exhibits a 4-connected uninodal 2D sql (44.62) network. Within the zinc series, ZnCl2 and ZnSO4 were used for the syntheses of [Zn(L)Cl] (7) and [Zn(L)(SO4)0.5]·2H2O (8), respectively. 7 shows a 3-connected uninodal 2D hcb network with (63) topology and 8 is a (3,6)-connected 2-nodal 3D framework with (42.6)2(44.62.88.10) topology. The luminescent properties of the Cd(II) and Zn(II) complexes were investigated.

  5. Generation of buckle folds in Naga fold thrust belt, north-east India

    NASA Astrophysics Data System (ADS)

    Saha, B.; Dietl, C.

    2009-04-01

    Naga fold thrust belt (NFTB), India, formed as a result of northward migration of the Indian plate initiated in Eocene and its subsequent collision with the Burmese plate during Oligocene. The NW-SE oriented compression generated a spectrum of structures; among them, we intend to focus on the folds- varying from gentle to tight asymmetric in geometry. Large recumbent folds are often associated with thrusting. Buckle folds forming under shallow crustal conditions are frequently reported from NFTB. Buckle folding occurs mainly within sandstones with intercalated shale layers which are in the study area typical for the Barail, Surma and Tipam Groups. We have tried to explain the controlling factors behind the variation of the buckle fold shapes and their varying wavelengths throughout the fold thrust belt with the aid of analogue (sand box) modelling. It is undoubted that competence contrast along with the layer parallel compressive stress are the major influencing factors in generation of buckle folds. Schmalholz and Podladchikov (1999) and Jeng et al. (2002) have shown that when low strain rate and low temperature are applicable, not only the viscosity contrast, but also the elasticity contrast govern the geometry of the developing buckle folds. Rocks deforming under high temperature and high pressure deform in pure viscous manner, whereas, rocks undergoing less confining stress and less temperature, are subjected to pure elastic deformation. However, they are the end members, and most of the deformations are a combination of these two end members, i.e. of viscoelastic nature. Our models are made up of sieved sand (0.5 mm grain size) and mica layers (1-5 mm) This interlayering imparts a mechanical anisotropy in the model. Mica is not a pure viscous material, rather it displays more elastic behaviour. The mica layers in the model produce bedding parallel slip during shortening through internal reorganization of the individual mica crystals leading to the thickening

  6. A microring resonator sensor for sensitive detection of 1,3,5-trinitrotoluene (TNT).

    PubMed

    Orghici, Rozalia; Lützow, Peter; Burgmeier, Jörg; Koch, Jan; Heidrich, Helmut; Schade, Wolfgang; Welschoff, Nina; Waldvogel, Siegfried

    2010-01-01

    A microring resonator sensor device for sensitive detection of the explosive 1,3,5-trinitrotoluene (TNT) is presented. It is based on the combination of a silicon microring resonator and tailored receptor molecules. PMID:22163576

  7. A microring resonator sensor for sensitive detection of 1,3,5-trinitrotoluene (TNT).

    PubMed

    Orghici, Rozalia; Lützow, Peter; Burgmeier, Jörg; Koch, Jan; Heidrich, Helmut; Schade, Wolfgang; Welschoff, Nina; Waldvogel, Siegfried

    2010-01-01

    A microring resonator sensor device for sensitive detection of the explosive 1,3,5-trinitrotoluene (TNT) is presented. It is based on the combination of a silicon microring resonator and tailored receptor molecules.

  8. A Microring Resonator Sensor for Sensitive Detection of 1,3,5-Trinitrotoluene (TNT)

    PubMed Central

    Orghici, Rozalia; Lützow, Peter; Burgmeier, Jörg; Koch, Jan; Heidrich, Helmut; Schade, Wolfgang; Welschoff, Nina; Waldvogel, Siegfried

    2010-01-01

    A microring resonator sensor device for sensitive detection of the explosive 1,3,5-trinitrotoluene (TNT) is presented. It is based on the combination of a silicon microring resonator and tailored receptor molecules. PMID:22163576

  9. Adenosine 3', 5'-cyclic monophosphate levels in Thermomonospora curvata during cellulase biosynthesis

    SciTech Connect

    Fennington, G.; Neubauer, D.; Stutzenberger, F.

    1983-01-01

    The enzymatic degradation of cellulose requires the synergistic activity of at least three enzymes: exo-beta-1,4-glucanase (EC3.2.1.91), endo-beta-1,4-glucanase (EC3.2.1.4), and beta-glucosidase (EC3.2.1.21). Despite extensive studies on a variety of cellulolytic bacteria and fungi, the mechanism(s) regulating the biosynthesis of this inducible catabolic enzyme complex remains unknown. The intracellular concentrations of cyclic nucleotides such as adenosine 3',5'-cyclic monophosphate (cAMP) have been shown to play a major role in mediating catabolite repression of enzyme biosynthesis. The cAMP acts through a cAMP receptor protein (termed CRP or CAP) which is a dimer having two identical subunits each capable of binding one molecule of cAMP. The N-terminal domain of the CRP binds the cAMP while the C-terminal domain binds to DNA at the promotor region of a cAMP-dependent operon and stimulates transcription by promoting the formation of a preinitiation complex between RNA polymerase and the DNA. Intracellular cAMP levels in E. coli (the prototype organism for such studies) are influenced by the type and availability of carbon source used for growth. High intracellular cAMP levels should lead to higher concentrations of cAMP-CRP complexes which should increase the transcription rates for cAMP-dependent operons (such as the lac operon of beta-galactosidase) and indeed the differential rate of beta-galactosidase biosynthesis correlates to intracellular cAMP levels. In the case of cellulase, catabolite repression by glucose or other readily metabolizable compounds closely controls production in an apparently similar manner and therefore a correlation may exist between enzyme biosynthesis and intracellular cAMP levels. This communication describes the fluctuation in cAMP levels during cellulase induction and repression in the thermophilic actinomycete, Thermomonospora curvata.

  10. An updated set of nutations derived from the reanalysis of 3.5 decades VLBI observations

    NASA Astrophysics Data System (ADS)

    Zhu, Ping; Koot, Laurence; Rivoldini, Attilio; Dehant, Veronique

    2016-04-01

    The global VLBI observation started in the 1979. After that the qualities of the measurements are continuously improving by taking into account various instrumental and environmental effects. The MHB2000 models was introduced in 2002 (Mathews, et.al. 2002, [1]) and it has a good agreement (5 μas) on the short period nutation series (<400 days) with the values derived from 2 decades (1979-2000) VLBI data while a higher uncertainties up to 56 μas for those longer periods (>400 days) nutation series (Herring et.al. 2002). In MHB2000, the forcing frequencies of the nutation series are solved by least-squares fitting to the VLBI data in frequency domain. Koot et al. (2008), have processed another similar set of nutation series by inversing the time series of VLBI data (1984-2005) using a Bayesian approach. In the present work, we will repeat both approaches using the up-to-date 3.5 decades VLBI observations (1980-2014) meanwhile paying more attention on the results of longer period (>400 days). Finally some features of Earth's interior structure will be discussed based on the determined nutation series. [1] Mathews, P.M., Herring, T.A. & Buffett, B.A., 2002. Modeling of nutation and precession: new nutation series for nonrigid Earth and insights into the Earth's interior, J. Geophys. Res., 107, 2068, doi: 10.1029/2001JB000390. [2] Herring, T. A., P. M. Mathews, and B. A. Buffett, Modeling of nutation and precession: Very long baseline interferometry results, J. Geophys. Res., 107, B4, 2069, doi: 10.1029/2001JB000165, 2002 [3] Koot, L., Rivoldini, A., de Viron, O. & Dehant, V., 2008. Estimation of Earth interior parameters from a Bayesian inversion of very long baseline interferometry nutation time series, J. Geophys. Res., 113, 8414, doi: 10.1029/2007JB005409.

  11. De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints.

    PubMed

    Smock, Robert G; Yadid, Itamar; Dym, Orly; Clarke, Jane; Tawfik, Dan S

    2016-01-28

    Molecular evolution has focused on the divergence of molecular functions, yet we know little about how structurally distinct protein folds emerge de novo. We characterized the evolutionary trajectories and selection forces underlying emergence of β-propeller proteins, a globular and symmetric fold group with diverse functions. The identification of short propeller-like motifs (<50 amino acids) in natural genomes indicated that they expanded via tandem duplications to form extant propellers. We phylogenetically reconstructed 47-residue ancestral motifs that form five-bladed lectin propellers via oligomeric assembly. We demonstrate a functional trajectory of tandem duplications of these motifs leading to monomeric lectins. Foldability, i.e., higher efficiency of folding, was the main parameter leading to improved functionality along the entire evolutionary trajectory. However, folding constraints changed along the trajectory: initially, conflicts between monomer folding and oligomer assembly dominated, whereas subsequently, upon tandem duplication, tradeoffs between monomer stability and foldability took precedence. PMID:26806127

  12. De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints.

    PubMed

    Smock, Robert G; Yadid, Itamar; Dym, Orly; Clarke, Jane; Tawfik, Dan S

    2016-01-28

    Molecular evolution has focused on the divergence of molecular functions, yet we know little about how structurally distinct protein folds emerge de novo. We characterized the evolutionary trajectories and selection forces underlying emergence of β-propeller proteins, a globular and symmetric fold group with diverse functions. The identification of short propeller-like motifs (<50 amino acids) in natural genomes indicated that they expanded via tandem duplications to form extant propellers. We phylogenetically reconstructed 47-residue ancestral motifs that form five-bladed lectin propellers via oligomeric assembly. We demonstrate a functional trajectory of tandem duplications of these motifs leading to monomeric lectins. Foldability, i.e., higher efficiency of folding, was the main parameter leading to improved functionality along the entire evolutionary trajectory. However, folding constraints changed along the trajectory: initially, conflicts between monomer folding and oligomer assembly dominated, whereas subsequently, upon tandem duplication, tradeoffs between monomer stability and foldability took precedence.

  13. De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints

    PubMed Central

    Smock, Robert G.; Yadid, Itamar; Dym, Orly; Clarke, Jane; Tawfik, Dan S.

    2016-01-01

    Summary Molecular evolution has focused on the divergence of molecular functions, yet we know little about how structurally distinct protein folds emerge de novo. We characterized the evolutionary trajectories and selection forces underlying emergence of β-propeller proteins, a globular and symmetric fold group with diverse functions. The identification of short propeller-like motifs (<50 amino acids) in natural genomes indicated that they expanded via tandem duplications to form extant propellers. We phylogenetically reconstructed 47-residue ancestral motifs that form five-bladed lectin propellers via oligomeric assembly. We demonstrate a functional trajectory of tandem duplications of these motifs leading to monomeric lectins. Foldability, i.e., higher efficiency of folding, was the main parameter leading to improved functionality along the entire evolutionary trajectory. However, folding constraints changed along the trajectory: initially, conflicts between monomer folding and oligomer assembly dominated, whereas subsequently, upon tandem duplication, tradeoffs between monomer stability and foldability took precedence. PMID:26806127

  14. [Results of treating forearm bone shaft fractures with a 3.5 mm self compressive plate].

    PubMed

    Małecki, P; Kaleta, M; Tokarowski, A; Kusz, D; Wójcik, B

    1997-01-01

    Results of 29 forearm bones shaft fracture treatment with 3.5mm self compressive plate in 26 patients aged 18-64 (mean 33) are presented. Open reduction with 3.5mm self compressive plate fixation has been performed in all cases. Anderson et al criteria were used to assess functional and radiological outcome. Excellent and good functional results were achieved in 25 cases, one was rated fair, no poor results were observed. PMID:9490253

  15. The geometry and topology of natural sheath folds: a new tool for structural analysis

    NASA Astrophysics Data System (ADS)

    Alsop, G. I.; Holdsworth, R. E.

    2004-09-01

    Curvilinear sheath folds are classically depicted as displaying symmetrical geometries about two orthogonal mirror planes centred along the (X-Y) axial surface and the (X-Z) medial (culmination/depression) surface which bisects the fold nose. However, 10,000 geometric analyses of minor folds and fabrics formed during ductile thrusting in the Caledonides of northern Scotland reveals that major dome and basin sheath folds can display distinct and predictable asymmetries across both axial and medial surfaces. The strain is typically heterogeneous so that structural fabrics and younging evidence are preserved within sheath folds at varying stages of development. This allows an analysis of the evolution of such structures from 'tongue' folds to more extreme 'tubular' forms. Geometric relationships between measured orientations of fold hinges, axial planes, extension lineations and foliations are compared on fabric topology plots (FTPs), which provide an effective tool for monitoring planar and linear fabric rotations with increasing progressive non-coaxial deformation. They consistently display systematic variation from regions of lower to higher strain on passing from upper to lower fold limbs across major axial surfaces, and on crossing medial surfaces from short to long hinge-line segments. Axial and medial surfaces effectively therefore divide major sheath folds into quadrants with different amounts, senses and combinations of planar and linear fabric rotation within each domain. Such heterogeneous deformation implies that models of intense non-coaxial deformation uniformly affecting pre-existing folds may overestimate bulk displacement and shear strain. Variable fold hinge-line rotation about medial surfaces also provides an effective mechanism for the closure of major sheaths, which may otherwise project for unfeasible distances in the X direction. Bedding/cleavage intersections are developed at greater angles to the transport direction than fold hinges which they

  16. PI(3,5)P2 biosynthesis regulates oligodendrocyte differentiation by intrinsic and extrinsic mechanisms

    PubMed Central

    Mironova, Yevgeniya A; Lenk, Guy M; Lin, Jing-Ping; Lee, Seung Joon; Twiss, Jeffery L; Vaccari, Ilaria; Bolino, Alessandra; Havton, Leif A; Min, Sang H; Abrams, Charles S; Shrager, Peter; Meisler, Miriam H; Giger, Roman J

    2016-01-01

    Proper development of the CNS axon-glia unit requires bi-directional communication between axons and oligodendrocytes (OLs). We show that the signaling lipid phosphatidylinositol-3,5-bisphosphate [PI(3,5)P2] is required in neurons and in OLs for normal CNS myelination. In mice, mutations of Fig4, Pikfyve or Vac14, encoding key components of the PI(3,5)P2 biosynthetic complex, each lead to impaired OL maturation, severe CNS hypomyelination and delayed propagation of compound action potentials. Primary OLs deficient in Fig4 accumulate large LAMP1+ and Rab7+ vesicular structures and exhibit reduced membrane sheet expansion. PI(3,5)P2 deficiency leads to accumulation of myelin-associated glycoprotein (MAG) in LAMP1+perinuclear vesicles that fail to migrate to the nascent myelin sheet. Live-cell imaging of OLs after genetic or pharmacological inhibition of PI(3,5)P2 synthesis revealed impaired trafficking of plasma membrane-derived MAG through the endolysosomal system in primary cells and brain tissue. Collectively, our studies identify PI(3,5)P2 as a key regulator of myelin membrane trafficking and myelinogenesis. DOI: http://dx.doi.org/10.7554/eLife.13023.001 PMID:27008179

  17. The ML1Nx2 Phosphatidylinositol 3,5-Bisphosphate Probe Shows Poor Selectivity in Cells.

    PubMed

    Hammond, Gerald R V; Takasuga, Shunsuke; Sasaki, Takehiko; Balla, Tamas

    2015-01-01

    Phosphatidylinositol (3,5)-bisphosphate (PtdIns(3,5)P2) is a quantitatively minor phospholipid in eukaryotic cells that plays a fundamental role in regulating endocytic membrane traffic. Despite its clear importance for cellular function and organism physiology, mechanistic details of its biology have so far not been fully elucidated. In part, this is due to a lack of experimental tools that specifically probe for PtdIns(3,5)P2 in cells to unambiguously identify its dynamics and site(s) of action. In this study, we have evaluated a recently reported PtdIns(3,5)P2 biosensor, GFP-ML1Nx2, for its veracity as such a probe. We report that, in live cells, the localization of this biosensor to sub-cellular compartments is largely independent of PtdIns(3,5)P2, as assessed after pharmacological, chemical genetic or genomic interventions that block the lipid's synthesis. We therefore conclude that it is unwise to interpret the localization of ML1Nx2 as a true and unbiased biosensor for PtdIns(3,5)P2.

  18. PI(3,5)P2 biosynthesis regulates oligodendrocyte differentiation by intrinsic and extrinsic mechanisms.

    PubMed

    Mironova, Yevgeniya A; Lenk, Guy M; Lin, Jing-Ping; Lee, Seung Joon; Twiss, Jeffery L; Vaccari, Ilaria; Bolino, Alessandra; Havton, Leif A; Min, Sang H; Abrams, Charles S; Shrager, Peter; Meisler, Miriam H; Giger, Roman J

    2016-01-01

    Proper development of the CNS axon-glia unit requires bi-directional communication between axons and oligodendrocytes (OLs). We show that the signaling lipid phosphatidylinositol-3,5-bisphosphate [PI(3,5)P2] is required in neurons and in OLs for normal CNS myelination. In mice, mutations of Fig4, Pikfyve or Vac14, encoding key components of the PI(3,5)P2 biosynthetic complex, each lead to impaired OL maturation, severe CNS hypomyelination and delayed propagation of compound action potentials. Primary OLs deficient in Fig4 accumulate large LAMP1(+) and Rab7(+) vesicular structures and exhibit reduced membrane sheet expansion. PI(3,5)P2 deficiency leads to accumulation of myelin-associated glycoprotein (MAG) in LAMP1(+)perinuclear vesicles that fail to migrate to the nascent myelin sheet. Live-cell imaging of OLs after genetic or pharmacological inhibition of PI(3,5)P2 synthesis revealed impaired trafficking of plasma membrane-derived MAG through the endolysosomal system in primary cells and brain tissue. Collectively, our studies identify PI(3,5)P2 as a key regulator of myelin membrane trafficking and myelinogenesis. PMID:27008179

  19. Higher Education.

    ERIC Educational Resources Information Center

    Hendrickson, Robert M.

    This eighth chapter of "The Yearbook of School Law, 1986" summarizes and analyzes over 330 state and federal court cases litigated in 1985 in which institutions of higher education were involved. Among the topics examined were relationships between postsecondary institutions and various governmental agencies; discrimination in the employment of…

  20. Higher Education.

    ERIC Educational Resources Information Center

    Hendrickson, Robert M.; Gregory, Dennis E.

    Decisions made by federal and state courts during 1983 concerning higher education are reported in this chapter. Issues of employment and the treatment of students underlay the bulk of the litigation. Specific topics addressed in these and other cases included federal authority to enforce regulations against age discrimination and to revoke an…

  1. Higher Education.

    ERIC Educational Resources Information Center

    Hendrickson, Robert M.

    Litigation in 1987 was very brisk with an increase in the number of higher education cases reviewed. Cases discussed in this chapter are organized under four major topics: (1) intergovernmental relations; (2) employees, involving discrimination claims, tenured and nontenured faculty, collective bargaining and denial of employee benefits; (3)…

  2. Higher Education.

    ERIC Educational Resources Information Center

    Hendrickson, Robert M.; Finnegan, Dorothy E.

    The higher education case law in 1988 is extensive. Cases discussed in this chapter are organized under five major topics: (1) intergovernmental relations; (2) employees, involving discrimination claims, tenured and nontenured faculty, collective bargaining, and denial of employee benefits; (3) students, involving admissions, financial aid, First…

  3. Higher Learning.

    ERIC Educational Resources Information Center

    Bok, Derek

    Factors that distinguish the United States higher education system and its performance are considered, with attention to new developments, propsects for change, undergraduate education, and professional schools (especially law, business, and medicine). The way universities change the methods and content of their teaching in response to new…

  4. Microfluidic Mixers for Studying Protein Folding

    PubMed Central

    Waldauer, Steven A.; Wu, Ling; Yao, Shuhuai; Bakajin, Olgica; Lapidus, Lisa J.

    2012-01-01

    The process by which a protein folds into its native conformation is highly relevant to biology and human health yet still poorly understood. One reason for this is that folding takes place over a wide range of timescales, from nanoseconds to seconds or longer, depending on the protein1. Conventional stopped-flow mixers have allowed measurement of folding kinetics starting at about 1 ms. We have recently developed a microfluidic mixer that dilutes denaturant ~100-fold in ~8 μs2. Unlike a stopped-flow mixer, this mixer operates in the laminar flow regime in which turbulence does not occur. The absence of turbulence allows precise numeric simulation of all flows within the mixer with excellent agreement to experiment3-4. Laminar flow is achieved for Reynolds numbers Re ≤100. For aqueous solutions, this requires micron scale geometries. We use a hard substrate, such as silicon or fused silica, to make channels 5-10 μm wide and 10 μm deep (See Figure 1). The smallest dimensions, at the entrance to the mixing region, are on the order of 1 μm in size. The chip is sealed with a thin glass or fused silica coverslip for optical access. Typical total linear flow rates are ~1 m/s, yielding Re~10, but the protein consumption is only ~0.5 nL/s or 1.8 μL/hr. Protein concentration depends on the detection method: For tryptophan fluorescence the typical concentration is 100 μM (for 1 Trp/protein) and for FRET the typical concentration is ~100 nM. The folding process is initiated by rapid dilution of denaturant from 6 M to 0.06 M guanidine hydrochloride. The protein in high denaturant flows down a central channel and is met on either side at the mixing region by buffer without denaturant moving ~100 times faster (see Figure 2). This geometry causes rapid constriction of the protein flow into a narrow jet ~100 nm wide. Diffusion of the light denaturant molecules is very rapid, while diffusion of the heavy protein molecules is much slower, diffusing less than 1 μm in 1 ms

  5. Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability

    PubMed Central

    Pancsa, Rita; Varadi, Mihaly; Tompa, Peter; Vranken, Wim F.

    2016-01-01

    Proteins fulfil a wide range of tasks in cells; understanding how they fold into complex three-dimensional (3D) structures and how these structures remain stable while retaining sufficient dynamics for functionality is essential for the interpretation of overall protein behaviour. Since the 1950's, solvent exchange-based methods have been the most powerful experimental means to obtain information on the folding and stability of proteins. Considerable expertise and care were required to obtain the resulting datasets, which, despite their importance and intrinsic value, have never been collected, curated and classified. Start2Fold is an openly accessible database (http://start2fold.eu) of carefully curated hydrogen/deuterium exchange (HDX) data extracted from the literature that is open for new submissions from the community. The database entries contain (i) information on the proteins investigated and the underlying experimental procedures and (ii) the classification of the residues based on their exchange protection levels, also allowing for the instant visualization of the relevant residue groups on the 3D structures of the corresponding proteins. By providing a clear hierarchical framework for the easy sharing, comparison and (re-)interpretation of HDX data, Start2Fold intends to promote a better understanding of how the protein sequence encodes folding and structure as well as the development of new computational methods predicting protein folding and stability. PMID:26582925

  6. Vocal fold and ventricular fold vibration in period-doubling phonation: physiological description and aerodynamic modeling.

    PubMed

    Bailly, Lucie; Henrich, Nathalie; Pelorson, Xavier

    2010-05-01

    Occurrences of period-doubling are found in human phonation, in particular for pathological and some singing phonations such as Sardinian A Tenore Bassu vocal performance. The combined vibration of the vocal folds and the ventricular folds has been observed during the production of such low pitch bass-type sound. The present study aims to characterize the physiological correlates of this acoustical production and to provide a better understanding of the physical interaction between ventricular fold vibration and vocal fold self-sustained oscillation. The vibratory properties of the vocal folds and the ventricular folds during phonation produced by a professional singer are analyzed by means of acoustical and electroglottographic signals and by synchronized glottal images obtained by high-speed cinematography. The periodic variation in glottal cycle duration and the effect of ventricular fold closing on glottal closing time are demonstrated. Using the detected glottal and ventricular areas, the aerodynamic behavior of the laryngeal system is simulated using a simplified physical modeling previously validated in vitro using a larynx replica. An estimate of the ventricular aperture extracted from the in vivo data allows a theoretical prediction of the glottal aperture. The in vivo measurements of the glottal aperture are then compared to the simulated estimations. PMID:21117769

  7. 3,5,5-Trimethylhexanoylferrocene induction of heme oxygenase activity in normal hepatocytes.

    PubMed

    Lambrecht, R W; Cable, J W; Pepe, J A; Bonkovsky, H L

    1994-04-29

    Recent work showed that the combination of 50 microM glutethimide plus 50 microM ferric nitrilotriacetate (FeNTA) synergistically induces heme oxygenase (HO) activity in cultured chick embryo liver cells (Cable et al., Biochem Biophys Res Commun 168: 176-181, 1990). This synergistic induction is due to increased heme synthesis, which then acts to increase HO gene transcription. The aim of the current studies was to characterize the effects on hepatic heme metabolism of (3,5,5-trimethylhexanoyl)ferrocene (TMH-ferrocene), which causes hepatic iron-loading in rats. Unlike FeNTA, TMH-ferrocene alone maximally induced HO activity at 5-10 microM TMH-ferrocene. At higher concentrations, HO activities declined, as did total cellular protein synthesis. Induction of HO was maximal after a 12-hr exposure to TMH-ferrocene, similar to induction by glutethimide plus FeNTA. The effect of TMH-ferrocene on HO could not be ascribed to greater cellular uptake of iron, since cell-associated iron levels were higher after FeNTA than after TMH-ferrocene treatment. TMH-ferrocene (up to 20 microM) did not induce delta-aminolevulinic acid synthase activity. Uroporphyrin accumulation in cells treated with TMH-ferrocene was minimal, but the combination of TMH-ferrocene and glutethimide caused a synergistic increase in uroporphyrin accumulation, similar to treatment with glutethimide plus FeNTA. 4,6-Dioxoheptanoic acid, an inhibitor of heme synthesis, blocked the induction of HO caused by glutethimide and FeNTA, but did not decrease the induction of HO by TMH-ferrocene. TMH-ferrocene-mediated induction of HO does not appear to be due to lipid peroxidation, since malondialdehyde formation was greater for ferrocene (a structural analog of TMH-ferrocene that does not induce HO) than for TMH-ferrocene. Furthermore, the anti-oxidant, butylated hydroxyanisole, which prevented lipid peroxidation, decreased HO induced by glutethimide plus FeNTA, but butylated hydroxyanisole did not affect HO induced

  8. [Immunogenicity of additional varicella vaccination 3-5 years after the initial vaccination].

    PubMed

    Ozaki, Takao; Nishimura, Naoko; Gotoh, Kensei; Funahashi, Keiji; Yoshii, Hironori; Okuno, Yoshinobu

    2013-07-01

    additional varicella vaccination 3-5 years after the initial vaccination is thought to have greater immunogenicity and is considered effective.

  9. Zinc Binding Modulates the Entire Folding Free Energy Surface of Human Cu,Zn Superoxide Dismutase

    PubMed Central

    Kayatekin, Can; Zitzewitz, Jill A.; Matthews, C. Robert

    2009-01-01

    Over 100 amino acid replacements in human Cu, Zn superoxide dismutase (SOD) are known to cause amyotrophic lateral sclerosis, a gain-of-function neurodegenerative disease that destroys motor neurons. Supposing that aggregates of partially-folded states are primarily responsible for toxicity, the role of the structurally-important zinc ion in defining the folding free energy surface of dimeric SOD was determined by comparing the thermodynamic and kinetic folding properties of the zinc-free and zinc-bound forms of the protein. The presence of zinc was found to decrease the free energies of a peptide model of the unfolded monomer, a stable variant of the folded monomeric intermediate and the folded dimeric species. The unfolded state binds zinc weakly with a micromolar dissociation constant, and the folded monomeric intermediate and the native dimeric form both bind zinc tightly, with sub-nanomolar dissociation constants. Coupled with the strong driving force for the subunit association reaction, the shift in the populations towards more well-folded states in the presence of zinc decreases the steady-state populations of higher-energy states in SOD under expected in vivo zinc concentrations (∼nanomolar). The significant decrease in the population of partially-folded states is expected to diminish their potential for aggregation and account for the known protective effect of zinc. The ∼100-fold increase in the rate of folding of SOD in the presence of micromolar concentrations of zinc demonstrates a significant role for a pre-organized zinc-binding loop in the transition state ensemble for the rate-limiting monomer folding reaction in this β-barrel protein. PMID:18840448

  10. Calibration and Validation of WRF 3.0-CLM3.5 in Snowpack Simulations

    NASA Astrophysics Data System (ADS)

    Jin, J.; Wen, L.; Subin, Z. M.; Miller, N. L.

    2009-12-01

    The Community Land Model version 3.5 (CLM3.5) developed by the National Center for Atmospheric Research (NCAR) was coupled into the Weather Research and Forecasting (WRF) Model version 3.0. The performance of WRF3.0-CLM3.5 in simulating snowpack was extensively evaluated with in-situ observations from a mountainous site called Col de Porte, located in northern Alps region of France, and the Columbia River Basin, located in the northwestern United States. CLM3.5 was configured with a five-layer snow scheme, and includes snow compaction and liquid water transfer processes, and a sophisticated snow albedo scheme. WRF3.0-CLM3.5 was forced with the National Center for Atmospheric Research/National Centers for Environmental Prediction Reanalysis data to simulate for the 1988-1989 snow season for the Col de Porte site and the 2001-2002 season for the Columbia River Basin, with 60km-20km two-way nested domains. The initial simulations show that WRF3.0-CLM3.5 significantly improves snow simulations when compared to those produced with the WRF3.0 coupled to the Noah land surface scheme at the both study sites. However, WRF3.0-CLM3.5 still tends to underestimate the observed snowpack. Calibration with the observed data from the Col de Porte site indicates that the snow water content bias mainly results from stronger, high elevation incoming solar radiation. An adjustment for the radiation scheme in WRF3.0 was made to reduce the incoming radiation to better fit with the observations. This adjustment improves snow simulations at both Col de Porte site and the Columbia River Basin. Additional offline snow simulations with CLM3.5 driven with observed forcing data were performed at the Col de Porte site. These offline simulations are compared to the results produced with the coupled WRF3.0-CLM3.5. Through this comparison, snow-atmosphere interactions are quantitatively indentified. The improved snow simulations in WRF3.0-CLM3.5 will benefit regional hydro-climate research and

  11. PREFACE Protein folding: lessons learned and new frontiers Protein folding: lessons learned and new frontiers

    NASA Astrophysics Data System (ADS)

    Pappu, Rohit V.; Nussinov, Ruth

    2009-03-01

    In appropriate physiological milieux proteins spontaneously fold into their functional three-dimensional structures. The amino acid sequences of functional proteins contain all the information necessary to specify the folds. This remarkable observation has spawned research aimed at answering two major questions. (1) Of all the conceivable structures that a protein can adopt, why is the ensemble of native-like structures the most favorable? (2) What are the paths by which proteins manage to robustly and reproducibly fold into their native structures? Anfinsen's thermodynamic hypothesis has guided the pursuit of answers to the first question whereas Levinthal's paradox has influenced the development of models for protein folding dynamics. Decades of work have led to significant advances in the folding problem. Mean-field models have been developed to capture our current, coarse grain understanding of the driving forces for protein folding. These models are being used to predict three-dimensional protein structures from sequence and stability profiles as a function of thermodynamic and chemical perturbations. Impressive strides have also been made in the field of protein design, also known as the inverse folding problem, thereby testing our understanding of the determinants of the fold specificities of different sequences. Early work on protein folding pathways focused on the specific sequence of events that could lead to a simplification of the search process. However, unifying principles proved to be elusive. Proteins that show reversible two-state folding-unfolding transitions turned out to be a gift of natural selection. Focusing on these simple systems helped researchers to uncover general principles regarding the origins of cooperativity in protein folding thermodynamics and kinetics. On the theoretical front, concepts borrowed from polymer physics and the physics of spin glasses led to the development of a framework based on energy landscape theories. These

  12. Folded membrane dialyzer with mechanically sealed edges

    DOEpatents

    Markley, Finley W.

    1976-01-01

    A semipermeable membrane is folded in accordion fashion to form a stack of pleats and the edges are sealed so as to isolate the opposite surfaces of the membrane. The stack is contained within a case that provides ports for flow of blood in contact with one surface of the membrane through channels formed by the pleats and also provides ports for flow of a dialysate through channels formed by the pleats in contact with the other surface of the membrane. The serpentine side edges of the membrane are sealed by a solidified plastic material, whereas effective mechanical means are provided to seal the end edges of the folded membrane. The mechanical means include a clamping strip which biases case sealing flanges into a sealed relationship with end portions of the membrane near the end edges, which portions extend from the stack and between the sealing flanges.

  13. Chevron folding patterns and heteroclinic orbits

    NASA Astrophysics Data System (ADS)

    Budd, Christopher J.; Chakhchoukh, Amine N.; Dodwell, Timothy J.; Kuske, Rachel

    2016-09-01

    We present a model of multilayer folding in which layers with bending stiffness EI are separated by a very stiff elastic medium of elasticity k2 and subject to a horizontal load P. By using a dynamical system analysis of the resulting fourth order equation, we show that as the end shortening per unit length E is increased, then if k2 is large there is a smooth transition from small amplitude sinusoidal solutions at moderate values of P to larger amplitude chevron folds, with straight limbs separated by regions of high curvature when P is large. The chevron solutions take the form of near heteroclinic connections in the phase-plane. By means of this analysis, values for P and the slope of the limbs are calculated in terms of E and k2.

  14. Ca-Dependent Folding of Human Calumenin.

    PubMed

    Mazzorana, Marco; Hussain, Rohanah; Sorensen, Thomas

    2016-01-01

    Human calumenin (hCALU) is a six EF-hand protein belonging to the CREC family. As other members of the family, it is localized in the secretory pathway and regulates the activity of SERCA2a and of the ryanodine receptor in the endoplasmic reticulum (ER). We have studied the effects of Ca2+ binding to the protein and found it to attain a more compact structure upon ion binding. Circular Dichroism (CD) measurements suggest a major rearrangement of the protein secondary structure, which reversibly switches from disordered at low Ca2+ concentrations to predominantly alpha-helical when Ca2+ is added. SAXS experiments confirm the transition from an unfolded to a compact structure, which matches the structural prediction of a trilobal fold. Overall our experiments suggest that calumenin is a Ca2+ sensor, which folds into a compact structure, capable of interacting with its molecular partners, when Ca2+ concentration within the ER reaches the millimolar range. PMID:26991433

  15. RNA Hairpin Folding in the Crowded Cell

    PubMed Central

    Gao, Mimi; Gnutt, David; Orban, Axel; Appel, Bettina; Righetti, Francesco; Winter, Roland; Narberhaus, Franz; Müller, Sabine

    2016-01-01

    Abstract Precise secondary and tertiary structure formation is critically important for the cellular functionality of ribonucleic acids (RNAs). RNA folding studies were mainly conducted in vitro, without the possibility of validating these experiments inside cells. Here, we directly resolve the folding stability of a hairpin‐structured RNA inside live mammalian cells. We find that the stability inside the cell is comparable to that in dilute physiological buffer. On the contrary, the addition of in vitro artificial crowding agents, with the exception of high‐molecular‐weight PEG, leads to a destabilization of the hairpin structure through surface interactions and reduction in water activity. We further show that RNA stability is highly variable within cell populations as well as within subcellular regions of the cytosol and nucleus. We conclude that inside cells the RNA is subject to (localized) stabilizing and destabilizing effects that lead to an on average only marginal modulation compared to diluted buffer. PMID:26833452

  16. Fast-Folding Proteins under Stress

    PubMed Central

    Dave, Kapil; Gruebele, Martin

    2015-01-01

    Proteins are subject to a variety of stresses in biological organisms, including pressure and temperature, which are the easiest stresses to simulate by molecular dynamics. We discuss the effect of pressure and thermal stress on very fast folding model proteins, whose in vitro folding can be fully simulated on computers and compared with experiments. We then discuss experiments that can be used to subject proteins to low and high temperature unfolding, as well as low and high pressure unfolding. Pressure and temperature are prototypical perturbations that illustrate how close many proteins are to instability, a property that cells can exploit to control protein function. We conclude by reviewing some recent in-cell experiments, and progress being made in simulating and measuring protein stability and function inside live cells. PMID:26231095

  17. Ca-Dependent Folding of Human Calumenin

    PubMed Central

    Mazzorana, Marco; Hussain, Rohanah; Sorensen, Thomas

    2016-01-01

    Human calumenin (hCALU) is a six EF-hand protein belonging to the CREC family. As other members of the family, it is localized in the secretory pathway and regulates the activity of SERCA2a and of the ryanodine receptor in the endoplasmic reticulum (ER). We have studied the effects of Ca2+ binding to the protein and found it to attain a more compact structure upon ion binding. Circular Dichroism (CD) measurements suggest a major rearrangement of the protein secondary structure, which reversibly switches from disordered at low Ca2+ concentrations to predominantly alpha-helical when Ca2+ is added. SAXS experiments confirm the transition from an unfolded to a compact structure, which matches the structural prediction of a trilobal fold. Overall our experiments suggest that calumenin is a Ca2+ sensor, which folds into a compact structure, capable of interacting with its molecular partners, when Ca2+ concentration within the ER reaches the millimolar range. PMID:26991433

  18. Predictive Computational Modeling of Chromatin Folding

    NASA Astrophysics Data System (ADS)

    di Pierro, Miichele; Zhang, Bin; Wolynes, Peter J.; Onuchic, Jose N.

    In vivo, the human genome folds into well-determined and conserved three-dimensional structures. The mechanism driving the folding process remains unknown. We report a theoretical model (MiChroM) for chromatin derived by using the maximum entropy principle. The proposed model allows Molecular Dynamics simulations of the genome using as input the classification of loci into chromatin types and the presence of binding sites of loop forming protein CTCF. The model was trained to reproduce the Hi-C map of chromosome 10 of human lymphoblastoid cells. With no additional tuning the model was able to predict accurately the Hi-C maps of chromosomes 1-22 for the same cell line. Simulations show unknotted chromosomes, phase separation of chromatin types and a preference of chromatin of type A to sit at the periphery of the chromosomes.

  19. RNA Hairpin Folding in the Crowded Cell.

    PubMed

    Gao, Mimi; Gnutt, David; Orban, Axel; Appel, Bettina; Righetti, Francesco; Winter, Roland; Narberhaus, Franz; Müller, Sabine; Ebbinghaus, Simon

    2016-02-24

    Precise secondary and tertiary structure formation is critically important for the cellular functionality of ribonucleic acids (RNAs). RNA folding studies were mainly conducted in vitro, without the possibility of validating these experiments inside cells. Here, we directly resolve the folding stability of a hairpin-structured RNA inside live mammalian cells. We find that the stability inside the cell is comparable to that in dilute physiological buffer. On the contrary, the addition of in vitro artificial crowding agents, with the exception of high-molecular-weight PEG, leads to a destabilization of the hairpin structure through surface interactions and reduction in water activity. We further show that RNA stability is highly variable within cell populations as well as within subcellular regions of the cytosol and nucleus. We conclude that inside cells the RNA is subject to (localized) stabilizing and destabilizing effects that lead to an on average only marginal modulation compared to diluted buffer.

  20. A rabbit vocal fold laser scarring model for testing lamina propria tissue engineering therapies

    PubMed Central

    Mau, Ted; Du, Mindy; Xu, Chet C.

    2015-01-01

    Objectives/Hypothesis To develop a vocal fold scarring model using an ablative laser in the rabbit as a platform for testing bioengineered therapies for missing or damaged lamina propria. Study Design Prospective controlled animal study. Methods An optimal laser energy level was first determined by assessing the depths of vocal fold injury created by a Holmium:YAG laser at various energy levels on fresh cadaveric rabbit larynges. The selected energy level was then used to create controlled unilateral injuries in vocal folds of New Zealand white rabbits, with the contralateral folds serving as uninjured controls. After 4 weeks, the larynges were harvested and subjected to excised-larynx phonation with high-speed imaging and immunohistochemical staining for collagen types I and III, elastin, and hyaluronic acid (HA) with quantitative histological analysis. Results 1.8 joules produced full-thickness injury of the lamina propria without extensive muscle injury. After 4 weeks, the injured vocal folds vibrated with reduced amplitude (P = 0.036) in excised-larynx phonation compared to normal vocal folds. The injured vocal folds contained a higher relative density of collagen type I (P = 0.004), higher elastin (P = 0.022), and lower HA (P = 0.030) compared to normal controls. Collagen type III was unchanged. Conclusions With its potential for higher precision of injury, this laser vocal fold scarring model may serve as an alternative to scarring produced by cold instruments for studying the effects of vocal fold lamina propria bioengineered therapies. Level of Evidence N/A. PMID:24715695

  1. The phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2)-dependent Tup1 conversion (PIPTC) regulates metabolic reprogramming from glycolysis to gluconeogenesis.

    PubMed

    Han, Bong-Kwan; Emr, Scott D

    2013-07-12

    Glucose/carbon metabolism is a fundamental cellular process in living cells. In response to varying environments, eukaryotic cells reprogram their glucose/carbon metabolism between aerobic or anaerobic glycolysis, oxidative phosphorylation, and/or gluconeogenesis. The distinct type of glucose/carbon metabolism that a cell carries out has significant effects on the cell's proliferation and differentiation. However, it is poorly understood how the reprogramming of glucose/carbon metabolism is regulated. Here, we report a novel endosomal PI(3,5)P2 lipid-dependent regulatory mechanism that is required for metabolic reprogramming from glycolysis to gluconeogenesis in Saccharomyces cerevisiae. Certain gluconeogenesis genes, such as FBP1 (encoding fructose-1,6-bisphosphatase 1) and ICL1 (encoding isocitrate lyase 1) are under control of the Mig1 repressor and Cyc8-Tup1 corepressor complex. We previously identified the PI(3,5)P2-dependent Tup1 conversion (PIPTC), a mechanism to convert Cyc8-Tup1 corepressor to Cti6-Cyc8-Tup1 coactivator. We demonstrate that the PIPTC plays a critical role for transcriptional activation of FBP1 and ICL1. Furthermore, without the PIPTC, the Cat8 and Sip4 transcriptional activators cannot be efficiently recruited to the promoters of FBP1 and ICL1, suggesting a key role for the PIPTC in remodulating the chromatin architecture at the promoters. Our findings expand our understanding of the regulatory mechanisms for metabolic reprogramming in eukaryotes to include key regulation steps outside the nucleus. Given that Tup1 and the metabolic enzymes that control PI(3,5)P2 are highly conserved among eukaryotes, our findings may provide important insights toward understanding glucose/carbon metabolic reprogramming in other eukaryotes, including humans.

  2. Cleavage of carbon-nitrogen bond in 1,3,5-tri-tert-butyl-1,3,5-triazacyclohexane by copper(I) bromide

    NASA Astrophysics Data System (ADS)

    Khatua, Suman; Majumdar, Amit

    2016-09-01

    Reactions of CuCl, CuCl2 and CuBr2 with 1,3,5-tri-tert-butyl-1,3,5-triazacyclohexane (tBu3tach) resulted in the formation of [(tBu3tach-H)+(CuCl2)] (1), [(tBu3tach)(CuCl2)] (2) and [(tBu3tach-H)+(CuBr2)] (3) respectively. Interestingly, CuBr was found to mediate the cleavage of the C-N bonds of tBu3tach in a vast range of solvents, namely, chloroform, dichloromethane, tetrahydrofuran, acetonitrile and methanol to yield [Cu4Br4(tBuNCH2)4] (4) and stands as an example of C-N bond cleavage of 1,3,5-triazacyclohexane rings by copper salts. Compounds 1 and 3 contains amidinium cations and are unstable in solution towards the release of copper. The release of copper from 3 in solution was confirmed by the isolation of the compound, [CuBr(MeCN)] (5). Formation of the amidinium cations [(tBu3tach-H)+] in 1 and 3 may be avoided by the use of PPh3 to yield [(tBu3tach)Cu(PPh3)](PF6) (6), while the coordinated N-tert-butylmethanimine (tBuNCH2) in 4 could be replaced by PPh3 to yield [Cu4Br4(PPh3)4] (7). Complexes 1-7 are characterized by a combination of single crystal X-ray structure determination and/or elemental analysis, NMR, IR, and UV-Vis spectroscopy, and Mass spectrometry.

  3. Chen’s Double Eyelid Fold Ratio

    PubMed Central

    Chen, Chen-Chia; Tai, Hao-Chih

    2016-01-01

    Background: Double eyelidplasty can construct palpebral folds and enhance beauty perception for Asians with single eyelids. A new palpebral parameter for the quantitative interpretation of surgical outcomes is proposed on the basis of a photometric study of the altered proportions of Asian eyes after double eyelid operation. Methods: A total of 100 Asian adults with single upper eyelids who were satisfied with the enlarged eyes by operation were included in the study. A retrospective measurement of palpebral parameters in the frontal profile both preoperatively and 6 months postoperatively was performed. The proportions of various parameters in the eyebrow–eye aesthetic unit were calculated and analyzed. Results: Double eyelidplasty can augment the vertical dimension of palpebral fissure by 27.9% increase on average. The vertical ratio of palpebral fissure to the eyebrow–eye unit is augmented by 34.4% increase. The vertical ratio of the subunit below double eyelid fold peak to the unit is augmented by 82.6% increase. Conclusions: Double eyelidplasty can substantially enlarge the vertical dimensions of the eyes of Asians with single eyelids. The eyes are perceived to be larger because of the visually assimilated illusion of the superimposed eyelid fold and the relative proportions of the eyebrow–eye unit. The authors propose using a vertical ratio of the subunit below double eyelid fold peak in the eyebrow–eye unit to measure the visually perceived proportion of the eye in the unit. This ratio can be applied clinically for a quantitative evaluation of the surgical outcome after double eyelidplasty. PMID:27200243

  4. Probing the cytochrome c' folding landscape.

    PubMed

    Pletneva, Ekaterina V; Zhao, Ziqing; Kimura, Tetsunari; Petrova, Krastina V; Gray, Harry B; Winkler, Jay R

    2007-11-01

    The folding kinetics of R. palustris cytochrome c' (cyt c') have been monitored by heme absorption and native Trp72 fluorescence at pH 5. The Trp72 fluorescence burst signal suggests early compaction of the polypeptide ensemble. Analysis of heme transient absorption spectra reveals deviations from two-state behavior, including a prominent slow phase that is accelerated by the prolyl isomerase cyclophilin. A nonnative proline configuration (Pro21) likely interferes with the formation of the helical bundle surrounding the heme.

  5. Understanding the Folding-Function Tradeoff in Proteins

    PubMed Central

    Gosavi, Shachi

    2013-01-01

    When an amino-acid sequence cannot be optimized for both folding and function, folding can get compromised in favor of function. To understand this tradeoff better, we devise a novel method for extracting the “function-less” folding-motif of a protein fold from a set of structurally similar but functionally diverse proteins. We then obtain the β-trefoil folding-motif, and study its folding using structure-based models and molecular dynamics simulations. CompariA protein sequence serves two purpson with the folding of wild-type β-trefoil proteins shows that function affects folding in two ways: In the slower folding interleukin-1β, binding sites make the fold more complex, increase contact order and slow folding. In the faster folding hisactophilin, residues which could have been part of the folding-motif are used for function. This reduces the density of native contacts in functional regions and increases folding rate. The folding-motif helps identify subtle structural deviations which perturb folding. These may then be used for functional annotation. Further, the folding-motif could potentially be used as a first step in the sequence design of function-less scaffold proteins. Desired function can then be engineered into these scaffolds. PMID:23593437

  6. Non-invasive in vivo measurement of the shear modulus of human vocal fold tissue.

    PubMed

    Kazemirad, Siavash; Bakhshaee, Hani; Mongeau, Luc; Kost, Karen

    2014-03-21

    Voice is the essential part of singing and speech communication. Voice disorders significantly affect the quality of life. The viscoelastic mechanical properties of the vocal fold mucosa determine the characteristics of the vocal folds oscillations, and thereby voice quality. In the present study, a non-invasive method was developed to determine the shear modulus of human vocal fold tissue in vivo via measurements of the mucosal wave propagation speed during phonation. Images of four human subjects' vocal folds were captured using high speed digital imaging (HSDI) and magnetic resonance imaging (MRI) for different phonation pitches, specifically fundamental frequencies between 110 and 440 Hz. The MRI images were used to obtain the morphometric dimensions of each subject's vocal folds in order to determine the pixel size in the high-speed images. The mucosal wave propagation speed was determined for each subject and at each pitch value using an automated image processing algorithm. The transverse shear modulus of the vocal fold mucosa was then calculated from a surface (Rayleigh) wave propagation dispersion equation using the measured wave speeds. It was found that the mucosal wave propagation speed and therefore the shear modulus of the vocal fold tissue were generally greater at higher pitches. The results were in good agreement with those from other studies obtained via in vitro measurements, thereby supporting the validity of the proposed measurement method. This method offers the potential for in vivo clinical assessments of vocal folds viscoelasticity from HSDI.

  7. Multiple-probe analysis of folding and unfolding pathways of human serum albumin. Evidence for a framework mechanism of folding.

    PubMed

    Santra, Manas Kumar; Banerjee, Abhijit; Krishnakumar, Shyam Sundar; Rahaman, Obaidur; Panda, Dulal

    2004-05-01

    The changes in the far-UV CD signal, intrinsic tryptophan fluorescence and bilirubin absorbance showed that the guanidine hydrochloride (GdnHCl)-induced unfolding of a multidomain protein, human serum albumin (HSA), followed a two-state process. However, using environment sensitive Nile red fluorescence, the unfolding and folding pathways of HSA were found to follow a three-state process and an intermediate was detected in the range 0.25-1.5 m GdnHCl. The intermediate state displayed 45% higher fluorescence intensity than that of the native state. The increase in the Nile red fluorescence was found to be due to an increase in the quantum yield of the HSA-bound Nile red. Low concentrations of GdnHCl neither altered the binding affinity of Nile red to HSA nor induced the aggregation of HSA. In addition, the secondary structure of HSA was not perturbed during the first unfolding transition (<1.5 m GdnHCl); however, the secondary structure was completely lost during the second transition. The data together showed that the half maximal loss of the tertiary structure occurred at a lower GdnHCl concentration than the loss of the secondary structure. Further kinetic studies of the refolding process of HSA using multiple spectroscopic techniques showed that the folding occurred in two phases, a burst phase followed by a slow phase. An intermediate with native-like secondary structure but only a partial tertiary structure was found to form in the burst phase of refolding. Then, the intermediate slowly folded into the native state. An analysis of the refolding data suggested that the folding of HSA could be best explained by the framework model.

  8. Resummation of semiclassical short folded string

    NASA Astrophysics Data System (ADS)

    Beccaria, Matteo; Macorini, Guido

    2012-02-01

    We reconsider semiclassical quantization of folded string spinning in AdS3 part of AdS5 × S5 using integrability-based (algebraic curve) method. We focus on the "short string" (small spin S) limit with the angular momentum J in S 5 scaled down according to {mathcal J} = ρ sqrt {S} in terms of the variables {mathcal J} = J/ sqrt {λ } , S = S/ sqrt {λ } . The semi-classical string energy in this particular scaling limit admits the double expansion E = {sum {_{{n = 0}}^{infty }sum {_{{p = 0}}^{infty }left( {sqrt {λ } } right)} }^{{1 - n}}}{a_{{n,p}}}left( ρ right){S^{{P + 1/2}}} . It behaves smoothly as J → 0 and partially resums recent results by Gromov and Valatka. We explicitly compute various one-loop coefficients a1, p ( ρ) by summing over the fluctuation frequencies for integrable perturbations around the classical solution. For the simple folded string, the result agrees with what could be derived exploiting a recent conjecture of Basso. However, the method can be extended to more general situations. As an example, we consider the m-folded string where Basso's conjecture fails. For this classical solution, we present the exact values of a 1,0( ρ) and a 1,1( ρ) for m = 2, 3, 4, 5 and explain how to work out the general case.

  9. Folding pathways of prion and doppel.

    PubMed Central

    Settanni, Giovanni; Hoang, Trinh Xuan; Micheletti, Cristian; Maritan, Amos

    2002-01-01

    The relevance of various residue positions for the stability and the folding characteristics of the prion protein in its normal cellular form are investigated by using molecular dynamics simulations of models exploiting the topology of the native state. These models allow for reproducing the experimentally validated two-state behavior of the normal prion isoform. Highly significant correlations are found between the most topologically relevant sites in our analysis and the single point mutations known to be associated with the arousal of the genetic forms of prion disease. Insight into the conformational change is provided by comparing the folding process of cellular prion and doppel that share a similar native state topology: the folding pathways of the former can be grouped in two main classes according to which tertiary structure contacts are formed first enroute to the native state. For the latter a single class of pathways leads to the native state again through a two-state process. Our results are consistent and supportive of the recent experimental findings that doppel lacks the scrapie isoform and that such remarkably different behavior involves residues in the region containing the two beta-strands and the intervening helix. PMID:12496120

  10. Simulating protein folding in different environmental conditions.

    PubMed

    Homouz, Dirar

    2014-01-01

    Molecular dynamics simulations have become an invaluable tool in investigating the dynamics of protein folding. However, most computational studies of protein folding assume dilute aqueous simulation conditions in order to reduce the complexity of the system under study and enhance the efficiency. Nowadays, it is evident that environmental conditions encountered in vivo (or even in vitro) play a major role in regulating the dynamics of protein folding especially when one considers the highly condensed environment in the cellular cytoplasm. In order to factor in these conditions, we can utilize the high efficiency of well-designed low resolution (coarse-grained) simulation models to reduce the complexity of these added protein-milieu interactions involving different time and length scales. The goal of this chapter is to describe some recently developed coarse-grained simulation techniques that are specifically designed to go beyond traditional aqueous solvent conditions. The chapter also gives the reader a flavor of the things that we can study using such "smart" low resolution models.

  11. Computing the conformational entropy for RNA folds

    NASA Astrophysics Data System (ADS)

    Liu, Liang; Chen, Shi-Jie

    2010-06-01

    We develop a polymer physics-based method to compute the conformational entropy for RNA tertiary folds, namely, conformations consisting of multiple helices connected through (cross-linked) loops. The theory is based on a virtual bond conformational model for the nucleotide chain. A key issue in the calculation of the entropy is how to treat the excluded volume interactions. The weak excluded volume interference between the different loops leads to the decomposition of the whole structure into a number of three-body building blocks, each consisting of a loop and two helices connected to the two ends of the loop. The simple construct of the three-body system allows an accurate computation for the conformational entropy for each building block. The assembly of the building blocks gives the entropy of the whole structure. This approach enables treatment of molten globule-like folds (partially unfolded tertiary structures) for RNAs. Extensive tests against experiments and exact computer enumerations indicate that the method can give accurate results for the entropy. The method developed here provides a solid first step toward a systematic development of a theory for the entropy and free energy landscape for complex tertiary folds for RNAs and proteins.

  12. RNA folding pathways in stop motion.

    PubMed

    Bottaro, Sandro; Gil-Ley, Alejandro; Bussi, Giovanni

    2016-07-01

    We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal structures are heterogeneous enough to describe metastable as well as intermediate states. These ensembles are first validated by performing a quantitative comparison against available solution nuclear magnetic resonance (NMR) data of a set of RNA tetranucleotides. Notably, the agreement is better with respect to the one obtained by comparing NMR with extensive all-atom molecular dynamics simulations. We then propose a procedure based on diffusion maps and Markov models that makes it possible to obtain reaction pathways and their relative probabilities from fragment ensembles. This approach is applied to study the helix-to-loop folding pathway of all the tetraloops from the GNRA and UNCG families. The results give detailed insights into the folding mechanism that are compatible with available experimental data and clarify the role of intermediate states observed in previous simulation studies. The method is computationally inexpensive and can be used to study arbitrary conformational transitions. PMID:27091499

  13. Macrocyclization of Folded Diamines in Cavitands.

    PubMed

    Shi, Qixun; Masseroni, Daniele; Rebek, Julius

    2016-08-31

    Synthetic access to water-soluble cavitands and capsules has moved recognition events from organic solvents into aqueous media. Here we report the binding and reactivity of long-chain α,ω-diamines (C11 to C18) in cavitand hosts. The containers bind the diamines in folded conformations that bury the hydrocarbon chains and expose the amino groups to the aqueous medium. Their acylation with succinic anhydride results in improved yields of monofunctionalized products. The cavitand-bound amino acid products were cyclized to the corresponding macrocyclic dilactams in D2O using water-soluble carbodiimide. Direct reaction of the folded diamines in the cavitand with activated diesters of succinic acid and glutaric acids resulted in 54-96% yields of the 17- to 25-membered dilactams. These cavitand-chaperoned reactions provided 3- to 10-fold improvements over the yields obtained in bulk solution and offer an alternative to high dilution methods. The cavitand induces unlikely conformations in flexible guests and channels their reactivity along otherwise improbable paths. PMID:27529442

  14. RNA folding pathways in stop motion

    PubMed Central

    Bottaro, Sandro; Gil-Ley, Alejandro; Bussi, Giovanni

    2016-01-01

    We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal structures are heterogeneous enough to describe metastable as well as intermediate states. These ensembles are first validated by performing a quantitative comparison against available solution nuclear magnetic resonance (NMR) data of a set of RNA tetranucleotides. Notably, the agreement is better with respect to the one obtained by comparing NMR with extensive all-atom molecular dynamics simulations. We then propose a procedure based on diffusion maps and Markov models that makes it possible to obtain reaction pathways and their relative probabilities from fragment ensembles. This approach is applied to study the helix-to-loop folding pathway of all the tetraloops from the GNRA and UNCG families. The results give detailed insights into the folding mechanism that are compatible with available experimental data and clarify the role of intermediate states observed in previous simulation studies. The method is computationally inexpensive and can be used to study arbitrary conformational transitions. PMID:27091499

  15. Self-Folding Single Cell Grippers

    PubMed Central

    2015-01-01

    Given the heterogeneous nature of cultures, tumors, and tissues, the ability to capture, contain, and analyze single cells is important for genomics, proteomics, diagnostics, therapeutics, and surgery. Moreover, for surgical applications in small conduits in the body such as in the cardiovascular system, there is a need for tiny tools that approach the size of the single red blood cells that traverse the blood vessels and capillaries. We describe the fabrication of arrayed or untethered single cell grippers composed of biocompatible and bioresorbable silicon monoxide and silicon dioxide. The energy required to actuate these grippers is derived from the release of residual stress in 3–27 nm thick films, did not require any wires, tethers, or batteries, and resulted in folding angles over 100° with folding radii as small as 765 nm. We developed and applied a finite element model to predict these folding angles. Finally, we demonstrated the capture of live mouse fibroblast cells in an array of grippers and individual red blood cells in untethered grippers which could be released from the substrate to illustrate the potential utility for in vivo operations. PMID:24937214

  16. BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum

    PubMed Central

    Robinson, Anne S.; Petzold, Linda

    2014-01-01

    The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, experimental evidence revealed the spatial heterogeneity of BiP within the nuclear and peripheral ER of S. cerevisiae (commonly referred to as ‘clusters’). Here, we developed a model to evaluate the potential advantages of accounting for multiple BiP molecules binding to peptides, while proposing that BiP's spatial heterogeneity may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness of binding multiple chaperone molecules to peptides. Using two metrics: folding efficiency and chaperone cost, we determined that the single binding site model achieves a higher efficiency than models characterized by multiple binding sites, in the absence of cooperativity. Due to entropic pulling, however, multiple chaperones perform in concert to facilitate the resolubilization and ultimate yield of folded proteins. As a result of cooperativity, multiple binding site models used fewer BiP molecules and maintained a higher folding efficiency than the single binding site model. These insilico investigations reveal that clusters of BiP molecules bound to unfolded proteins may enhance folding efficiency through cooperative action via entropic pulling. PMID:24991821

  17. BiP clustering facilitates protein folding in the endoplasmic reticulum.

    PubMed

    Griesemer, Marc; Young, Carissa; Robinson, Anne S; Petzold, Linda

    2014-07-01

    The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, experimental evidence revealed the spatial heterogeneity of BiP within the nuclear and peripheral ER of S. cerevisiae (commonly referred to as 'clusters'). Here, we developed a model to evaluate the potential advantages of accounting for multiple BiP molecules binding to peptides, while proposing that BiP's spatial heterogeneity may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness of binding multiple chaperone molecules to peptides. Using two metrics: folding efficiency and chaperone cost, we determined that the single binding site model achieves a higher efficiency than models characterized by multiple binding sites, in the absence of cooperativity. Due to entropic pulling, however, multiple chaperones perform in concert to facilitate the resolubilization and ultimate yield of folded proteins. As a result of cooperativity, multiple binding site models used fewer BiP molecules and maintained a higher folding efficiency than the single binding site model. These insilico investigations reveal that clusters of BiP molecules bound to unfolded proteins may enhance folding efficiency through cooperative action via entropic pulling. PMID:24991821

  18. BiP clustering facilitates protein folding in the endoplasmic reticulum.

    PubMed

    Griesemer, Marc; Young, Carissa; Robinson, Anne S; Petzold, Linda

    2014-07-01

    The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER): translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, experimental evidence revealed the spatial heterogeneity of BiP within the nuclear and peripheral ER of S. cerevisiae (commonly referred to as 'clusters'). Here, we developed a model to evaluate the potential advantages of accounting for multiple BiP molecules binding to peptides, while proposing that BiP's spatial heterogeneity may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness of binding multiple chaperone molecules to peptides. Using two metrics: folding efficiency and chaperone cost, we determined that the single binding site model achieves a higher efficiency than models characterized by multiple binding sites, in the absence of cooperativity. Due to entropic pulling, however, multiple chaperones perform in concert to facilitate the resolubilization and ultimate yield of folded proteins. As a result of cooperativity, multiple binding site models used fewer BiP molecules and maintained a higher folding efficiency than the single binding site model. These insilico investigations reveal that clusters of BiP molecules bound to unfolded proteins may enhance folding efficiency through cooperative action via entropic pulling.

  19. Procollagen triple helix assembly: an unconventional chaperone-assisted folding paradigm.

    PubMed

    Makareeva, Elena; Leikin, Sergey

    2007-10-10

    Fibers composed of type I collagen triple helices form the organic scaffold of bone and many other tissues, yet the energetically preferred conformation of type I collagen at body temperature is a random coil. In fibers, the triple helix is stabilized by neighbors, but how does it fold? The observations reported here reveal surprising features that may represent a new paradigm for folding of marginally stable proteins. We find that human procollagen triple helix spontaneously folds into its native conformation at 30-34 degrees C but not at higher temperatures, even in an environment emulating Endoplasmic Reticulum (ER). ER-like molecular crowding by nonspecific proteins does not affect triple helix folding or aggregation of unfolded chains. Common ER chaperones may prevent aggregation and misfolding of procollagen C-propeptide in their traditional role of binding unfolded polypeptide chains. However, such binding only further destabilizes the triple helix. We argue that folding of the triple helix requires stabilization by preferential binding of chaperones to its folded, native conformation. Based on the triple helix folding temperature measured here and published binding constants, we deduce that HSP47 is likely to do just that. It takes over 20 HSP47 molecules to stabilize a single triple helix at body temperature. The required 50-200 microM concentration of free HSP47 is not unusual for heat-shock chaperones in ER, but it is 100 times higher than used in reported in vitro experiments, which did not reveal such stabilization.

  20. Saddle Mountains: the evolution of an anticline in the Yakima Fold Belt

    SciTech Connect

    Reidel, S.P.

    1984-10-01

    Thickness variations record paleostructural relief and thus provide a method of calculating the growth rate of the Saddle Mountains. These calculations indicate the uplift was growing at about 250 m/my during Grande Ronde time but slowed to less than 40 m/my by the end of the Miocene. Thickness variations and amount of uplift of suprabasalt sediments indicate this low average rate persisted at least until 3.5 Ma. This low average rate of uplift, projected to the present time, accounts for the present structural relief of the Saddle Mountains. Estimates of the rate of shortening are of the same order of magnitude as that of uplift. Studies of other folds in the province show a similar pattern of evolution suggesting that the age, timing, and growth rate of the Saddle Mountains provide a model for anticlinal folds of the Yakima Fold Belt. The close correlation of growth rate of the folds with rate of magma supply of the Columbia River Basalt Group suggests that the Yakima Fold Belt resulted from the same tectonic processes that produced eruption of the Columbia River basalt.

  1. Effect of Zn and Sb Additions on the Impression Creep Behavior of Lead-Free Sn-3.5Ag Solder Alloy

    NASA Astrophysics Data System (ADS)

    Pourmajidian, M.; Mahmudi, R.; Geranmayeh, A. R.; Hashemizadeh, S.; Gorgannejad, S.

    2016-01-01

    The effect of separate additions of 1.5 wt.% Zn and 1.5 wt.% Sb on the creep behavior of Sn-3.5 wt.% Ag lead-free solder alloy was investigated by impression testing. The tests were carried out under constant punching stresses in the range of 60-120 MPa and at temperatures in the range of 298-370 K. Both of the ternary alloys showed creep resistances higher than that of the eutectic binary Sn-3.5Ag alloy. The superior creep resistance of the ternary Sn-3.5Ag-1.5Sb alloy is attributed to the strong solid solutioning effect of antimony in the tin matrix, while the formation of AgZn particles and refinement of the Ag3Sn precipitates account for the higher creep resistance of the Sn-3.5Ag-1.5Zn alloy. The average stress exponents of 8.2, 8.5, and 8.6 and activation energies of 47.4 kJ mol-1, 45.3 kJ mol-1, , and 43.3 kJ mol-1 were obtained for Sn-3.5Ag, Sn-3.5Ag-1.5Zn, and Sn-3.5Ag-1.5Sb, respectively. These activation energies are close to 46 kJ mol-1 for dislocation pipe diffusion of tin. This, together with the stress exponents of 8.2-8.6, suggests that dislocation climb controlled by dislocation pipe diffusion is the predominant creep mechanism in these alloys.

  2. Formation, structure and magnetism of the metastable defect fluorite phases AVO{sub 3.5+x} (A=In, Sc)

    SciTech Connect

    Shafi, Shahid P.; Lundgren, Rylan J.; Cranswick, Lachlan M.D.; Bieringer, Mario

    2007-12-15

    We report the preparation and stability of ScVO{sub 3.5+x} and the novel phase InVO{sub 3.5+x}. AVO{sub 3.5+x} (A=Sc, In) defect fluorite structures are formed as metastable intermediates during the topotactic oxidation of AVO{sub 3} bixbyites. The oxidation pathway has been studied in detail by means of thermogravimetric/differential thermal analysis and in-situ powder X-ray diffraction. The oxidation of the bixbyite phase follows a topotactic pathway at temperatures between 300 and 400 deg. C in air/carbon dioxide. The range of accessible oxygen stoichiometries for the AVO{sub 3.5+x} structures following this pathway are 0.00{<=}x{<=}0.22. Rietveld refinements against powder X-ray and neutron data revealed that InVO{sub 3.54} and ScVO{sub 3.70} crystallize in the defect fluorite structure in space group Fm-3 m (227) with a=4.9863(5) and 4.9697(3)A, respectively with A{sup 3+}/V{sup 4+} disorder on the (4a) cation site. Powder neutron diffraction experiments indicate clustering of oxide defects in all samples. Bulk magnetic measurements showed the presence of V{sup 4+} and the absence of magnetic ordering at low temperatures. Powder neutron diffraction experiments confirmed the absence of a long range ordered magnetic ground state. - Graphical abstract: Topotactic oxidation of AVO{sub 3} bixbyite to AVO{sub 3.5} defect fluorite structure followed by in-situ powder X-ray diffraction. The upper structural diagram shows a six coordinated (A/V)-O{sub 6} fragment in bixbyite, the lower structure illustrates the same seven-fold coordinated (A/V)-O{sub 7} cubic environment in the defect fluorite structure.

  3. Electron shuttle-mediated biotransformation of hexahydro-1,3,5-trinitro-1,3,5-triazine adsorbed to granular activated carbon.

    PubMed

    Millerick, Kayleigh; Drew, Scott R; Finneran, Kevin T

    2013-08-01

    Granular activated carbon (GAC) effectively removes hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) from groundwater but generates RDX-laden GAC that must be disposed of or regenerated. Batch reactors containing GAC to which RDX was preadsorbed were used in experiments to test the potential for adsorbed RDX reduction and daughter product formation using (i) chemically reduced anthrahydroquinone-2,6-disulfonate (AH2QDS), (ii) resting Geobacter metallireducens strain GS-15, and (iii) a combined system containing AQDS and GS-15. Approximately 97.0% of the adsorbed RDX was transformed in each of these experimental systems by 90 h. Chemically reduced AQDS (AH2QDS) transformed 99.2% of adsorbed RDX; formaldehyde was produced rapidly and was stoichiometric (3 mol HCHO per mol RDX). Geobacter metallireducens also reduced RDX with and without AQDS present. This is the first study to demonstrate biological transformation of RDX adsorbed to GAC. Formaldehyde increased and then decreased in biological systems, suggesting a previously unreported capacity for G. metallireducens to oxidize formaldehyde, which was confirmed with resting cell suspensions. These data suggest the masses of GAC waste currently produced by activated carbon at RDX remediation sites can be minimized, decreasing the carbon footprint of the treatment technology. Alternatively, this strategy may be used to develop a Bio-GAC system for ex situ RDX treatment. PMID:23837558

  4. Fate of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in soil and bioaccumulation in bush bean hydroponic plants

    SciTech Connect

    Harvey, S.D.; Fellows, R.J.; Cataldo, D.A.; Bean, R.M. )

    1991-01-01

    Soils amended with [[sup 14]C]hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) were sampled over 60 d and subjected to exhaustive Soxhlet extraction followed by HPLC analysis. RDX was the only radiolabeled compound observed in soil extracts. Emission of volatile organics and [sup 14]CO[sub 2] from soil accounted for only 0.31 % of the amended radiolabel. Mass balance for RDX-amended soil was better than 84% throughout the two-month study. The analytical method developed for plants involved acid hydrolysis, solvent extraction, fractionation on Florisil adsorbent and separation by HPLC. The described methodology allowed for RDX recovery of 86 [+-] 3% from fortified bush bean leaf tissue. Further experiments were conducted with bush bean plants maintained on RDX-containing hydroponic solutions. Hydroponic plants did not emit detectable amounts of [sup 14]CO[sub 2] or radiolabeled volatile organics. Analysis of the plant tissue indicated bioaccumulation of RDX in the aerial tissues of hydroponic plants exposed for either 1 or 7 d. Metabolism of RDX to polar metabolites was observed in plants exposed for 7 d.

  5. Growth changes of eighteen herbaceous angiosperms induced by Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in soil.

    PubMed

    Hagan, Frank L; Koeser, Andrew K; Dawson, Jeffrey O

    2016-01-01

    Study objectives were to describe and quantify growth responses (tolerance as shoot and root biomass accumulation) to soil-applied Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) treatments of eighteen terrestrial, herbaceous, angiospermous species and also; to determine how much of RDX, RDX transformation products, total N and RDX-derived N accumulated in the foliage. RDX altered growth of eighteen plant species or cultivars at levels of 100, 500, and 1,000 mg kg(-1)dry soil in a 75-d greenhouse study. Sixteen species or cultivars exhibited growth inhibition while two were stimulated in growth by RDX. A maximum amount of foliar RDX in a subset of three plant species was 36.0 mg per plant in Coronilla varia. Foliar concentrations of transformation products of RDX were low relative to RDX in the subset of three species. The proportion of RDX-N with respect to total N was constant, suggesting that foliar RDX transformation did not explain differences in tolerance. There was a δ (15)N shift towards that of synthetic RDX in foliage of the three species at a level of 1,000 mg kg(-1) RDX, proportional in magnitude to uptake of N from RDX and tolerance ranking.Reddened leaf margins for treated Sida spinosa indicate the potential of this species as a biosensor for RDX.

  6. Toxicologic and histopathologic response of the terrestrial salamander Plethodon cinereus to soil exposures of 1,3,5-trinitrohexahydro-1,3,5-triazine.

    PubMed

    Johnson, M S; Paulus, H I; Salice, C J; Checkai, R T; Simini, M

    2004-11-01

    Red-backed salamanders (Plethodon cinereus) were exposed to four different concentrations of 1,3,5-trinitrohexahydro-1,3,5-triazine (RDX) in soil under controlled laboratory conditions for 28 days. Wild-caught P. cinereus (N = 20/treatment) were exposed to target concentrations of 5,000, 1000, 100, 10, and 0 mg RDX/kg soil (dry wt) using a microcosm design. Animals were fed 5 to 10 uncontaminated mutant Drosophila flies every 3 days and monitored daily. Animals were weighed 1 day before being placed in treatment and weekly thereafter. RDX concentrations in soil were analytically determined after the compound was added and mixed at the beginning, the midpoint, and the end of exposure. RDX soil concentrations were relatively stable throughout the exposure period. Signs of overt toxicity were observed primarily in the highest exposure group. Salamanders exposed to 5,000 mg RDX/kg soil exhibited signs of neuromuscular effects (lethargy, gaping, hypersensitivity, tremors) and exhibited significant weight loss. A single moribund animal from this group lost >20% of its original body weight and was killed. Animals in this exposure group also lost weight relative to animals in other treatments. Histopathologic evaluations, including an evaluation of melanomacrophage parameters, indicated no strong treatment-related findings. This study provided information regarding the effects from subchronic dermal exposure of a terrestrial amphibian species to RDX in soil and provides a microcosm approach to the evaluation of toxicity of contaminants in soil to a terrestrial vertebrate.

  7. On the low pressure shock initiation of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine based plastic bonded explosives

    NASA Astrophysics Data System (ADS)

    Vandersall, Kevin S.; Tarver, Craig M.; Garcia, Frank; Chidester, Steven K.

    2010-05-01

    In large explosive and propellant charges, relatively low shock pressures on the order of 1-2 GPa impacting large volumes and lasting tens of microseconds can cause shock initiation of detonation. The pressure buildup process requires several centimeters of shock propagation before shock to detonation transition occurs. In this paper, experimentally measured run distances to detonation for lower input shock pressures are shown to be much longer than predicted by extrapolation of high shock pressure data. Run distance to detonation and embedded manganin gauge pressure histories are measured using large diameter charges of six octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) based plastic bonded explosives (PBX's): PBX 9404; LX-04; LX-07; LX-10; PBX 9501; and EDC37. The embedded gauge records show that the lower shock pressures create fewer and less energetic "hot spot" reaction sites, which consume the surrounding explosive particles at reduced reaction rates and cause longer distances to detonation. The experimental data is analyzed using the ignition and growth reactive flow model of shock initiation in solid explosives. Using minimum values of the degrees of compression required to ignite hot spot reactions, the previously determined high shock pressure ignition and growth model parameters for the six explosives accurately simulate the much longer run distances to detonation and much slower growths of pressure behind the shock fronts measured during the shock initiation of HMX PBX's at several low shock pressures.

  8. RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) biodegradation in aquifer sediments under manganese-reducing conditions

    USGS Publications Warehouse

    Bradley, Paul M.; Dinicola, Richard S.

    2005-01-01

    A shallow, RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine)–contaminated aquifer at Naval Submarine Base Bangor has been characterized as predominantly manganese-reducing, anoxic with local pockets of oxic conditions. The potential contribution of microbial RDX degradation to localized decreases observed in aquifer RDX concentrations was assessed in sediment microcosms amended with [U-14C] RDX. Greater than 85% mineralization of14C-RDX to 14CO2 was observed in aquifer sediment microcosms under native, manganese-reducing, anoxic conditions. Significant increases in the mineralization of 14C-RDX to 14CO2 were observed in anoxic microcosms under NO3-amended or Mn(IV)-amended conditions. No evidence of 14C-RDX biodegradation was observed under oxic conditions. These results indicate that microbial degradation of RDX may contribute to natural attenuation of RDX in manganese-reducing aquifer systems.

  9. Anaerobic transformation of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) by ovine rumen microorganisms.

    PubMed

    Perumbakkam, Sudeep; Craig, A M

    2012-01-01

    Explosives such as octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) provide a challenge in terms of bioremediation. In the present study, sheep rumen was studied for its potential to detoxify HMX using analytical chemistry and molecular microbial ecology tools. Results indicated significant loss (p < 0.05) of HMX at 8 h post-incubation and complete disappearance of the parent molecule after 16 h. Qualitative LC-MS/MS analysis provided evidence for the formation of 1-NO-HMX and MEDINA metabolites. A total of 1006 16S rRNA-V3 clones were sequenced and the Classifier tool of the RDPII database was used to sort the sequences at their phylum level. Most sequences were associated with either the phylum Bacteroidetes or Firmicutes. Significant differences at the phylum level (p < 0.001) were found between 0 h and 8 h HMX treatments. Using LibCompare analysis, 8 h HMX treatment showed enrichment of clones (p < 0.01) belonging to the genus Prevotella. From these results, it could be concluded that members of the genus Prevotella are enriched in the rumen and are capable of detoxifying HMX.

  10. Synthesis, structural and computational characterization of 2-amino-3,5-diiodobenzoic acid and 2-amino-3,5-dibromobenzoic acid

    NASA Astrophysics Data System (ADS)

    Yıldırım, M. Hakkı; Paşaoğlu, Hümeyra; Odabaşoğlu, Hakkı Yasin; Odabaşoğlu, Mustafa; Yıldırım, Arzu Özek

    2015-07-01

    The benzoic acid compounds 2-amino-3,5-dibromobenzoic acid (2A35Br) and 2-amino-3,5-diiodobenzoic (2A35I) acid have been synthesized and characterized by single-crystal X-ray diffraction, FT-IR spectroscopy, UV-Vis spectroscopy and computational methods. Molecular geometry, intra- and inter-molecular interactions have been investigated by using X-ray diffraction technique. Fundamental vibrational bands of the title compounds were founded by FT-IR and UV-Vis method was used to obtain electronic bands. Geometry optimizations and the calculation of IR frequencies were performed both Gaussian type orbitals at Gaussian 09W and Slater type orbitals at ADF2009.01 software. The calculations are compatible with the experiment results. In addition, geometrical parameters, energies, HOMO-LUMO gaps and electrophilicity indexes have been calculated for thirty possible positional isomers of 2A35Br and 2A35I. Calculations show that 2A35Br and 2A35I isomers have the lowest energy, the narrowest HOMO-LUMO gap and the highest electrophilicity index values. Molecular electrostatic potential maps, Fukui indices, natural bond orbital analysis, thermodynamic parameters and non-linear optical properties of the 2A35Br and 2A35I were also investigated by theoretical calculations.

  11. Comparative neurotoxicity of two energetic compounds, hexanitrohexaazaisowurtzitane and hexahydro-1,3,5-trinitro-1,3,5-triazine, in the earthworm Eisenia fetida.

    PubMed

    Gong, Ping; Inouye, Laura S; Perkins, Edward J

    2007-05-01

    Hexanitrohexaazaisowurtzitane (CL-20) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), both energetic compounds, share some degree of structural similarity. A noninvasive electrophysiological technique was employed to assess the impacts of acute sublethal exposures on impulse conduction in medial (MGF) and lateral (LGF) giant nerve fiber pathways of the earthworm Eisenia fetida and to evaluate the reversibility of neurotoxic effects. Earthworms were exposed to either 0.02 to 2.15 microg/cm2 of CL-20 or 0.04 to 5.35 microg/cm2 of RDX, for 1 to 14 d, on moistened filter paper. Conduction velocities of MGF and LGF were recorded on a digital oscilloscope before and after exposure. Results indicate that at exposure levels as low as 0.02 microg/cm2 of CL-20 or 0.21 microg/cm2 of RDX, worms exhibited physiological impacts such as retardation, stiffness, and body shrink. Both MGF and LGF conduction velocities were negatively correlated with increasing doses of CL-20 or RDX. However, such neurotoxic effects were alleviated or even eliminated within a few days after exposed worms were transferred to an uncontaminated environment, indicating that the neurotoxicity is reversible even after 6-d exposure. The CL-20 is more potent than RDX, which is consistent with previous studies on lethality, growth, and reproduction endpoints in soil oligochaetes.

  12. Density functional study of 1,3,5-trinitro-1,3,5-triazine molecular crystal with van der Waals interactions.

    PubMed

    Shimojo, Fuyuki; Wu, Zhongqing; Nakano, Aiichiro; Kalia, Rajiv K; Vashishta, Priya

    2010-03-01

    Volume dependence of the total energy and vibrational properties of crystalline l,3,5-trinitro-l,3,5-triazine (RDX) are calculated using the density functional theory (DFT). For this molecular crystal, properties calculated with a generalized gradient approximation to the exchange-correlation energy differ drastically from experimental values. This discrepancy arises from the inadequacy in treating weak van der Waals (vdW) interactions between molecules in the crystal, and an empirical vdW correction to DFT (DFT-D approach by Grimme) is shown to account for the dispersion effects accurately for the RDX crystal, while incurring little computational overhead. The nonempirical van der Waals density-functional (vdW-DF) method also provides an accurate description of the vdW corrections but with orders-of-magnitude more computation. We find that the vibrational properties of RDX are affected in a nontrivial manner by the vdW correction due to its dual role--reduction of the equilibrium volume and additional atomic forces.

  13. In Silico Alkaline Hydrolysis of Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine: Density Functional Theory Investigation.

    PubMed

    Sviatenko, Liudmyla K; Gorb, Leonid; Hill, Frances C; Leszczynska, Danuta; Shukla, Manoj K; Okovytyy, Sergiy I; Hovorun, Dmytro; Leszczynski, Jerzy

    2016-09-20

    HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), an energetic material used in military applications, may be released to the environment during manufacturing, transportation, storage, training, and disposal. A detailed investigation of a possible mechanism of alkaline hydrolysis, as one of the most promising methods for HMX remediation, was performed by computational study at PCM(Pauling)/M06-2X/6-311++G(d,p) level. Obtained results suggest that HMX hydrolysis at pH 10 represents a highly exothermic multistep process involving initial deprotonation and nitrite elimination, hydroxide attachment accompanied by cycle cleavage, and further decomposition of cycle-opened intermediate to the products caused by a series of C-N bond ruptures, hydroxide attachments, and proton transfers. Computationally predicted products of HMX hydrolysis such as nitrite, 4-nitro-2,4-diazabutanal, formaldehyde, nitrous oxide, formate, and ammonia correspond to experimentally observed species. Based on computed reaction pathways for HMX decomposition by alkaline hydrolysis, the kinetics of the entire process was modeled. Very low efficiency of this reaction at pH 10 was observed. Computations predict significant increases (orders of magnitude) of the hydrolysis rate for hydrolysis reactions undertaken at pH 11, 12, and 13. PMID:27523798

  14. Dissolution and sorption of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and 2,4,6-trinitrotoluene (TNT) residues from detonated mineral surfaces.

    PubMed

    Jaramillo, Ashley M; Douglas, Thomas A; Walsh, Marianne E; Trainor, Thomas P

    2011-08-01

    Composition B (Comp B) is a commonly used military formulation composed of the toxic explosive compounds 2,4,6-trinitrotoluene (TNT), and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Numerous studies of the temporal fate of explosive compounds in soils, surface water and laboratory batch reactors have been conducted. However, most of these investigations relied on the application of explosive compounds to the media via aqueous addition and thus these studies do not provide information on the real world loading of explosive residues during detonation events. To address this we investigated the dissolution and sorption of TNT and RDX from Comp B residues loaded to pure mineral phases through controlled detonation. Mineral phases included nontronite, vermiculite, biotite and Ottawa sand (quartz with minor calcite). High Performance Liquid Chromatography and Attenuated Total Reflectance Fourier Transform Infrared spectroscopy were used to investigate the dissolution and sorption of TNT and RDX residues loaded onto the mineral surfaces. Detonation resulted in heterogeneous loading of TNT and RDX onto the mineral surfaces. Explosive compound residues dissolved rapidly (within 9 h) in all samples but maximum concentrations for TNT and RDX were not consistent over time due to precipitation from solution, sorption onto mineral surfaces, and/or chemical reactions between explosive compounds and mineral surfaces. We provide a conceptual model of the physical and chemical processes governing the fate of explosive compound residues in soil minerals controlled by sorption-desorption processes. PMID:21601233

  15. Biotransformation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by a prospective consortium and its most effective isolate Serratia marcescens

    SciTech Connect

    Young, D.M.; Ogden, K.L.; Unkefer, P.J.

    1997-03-05

    The biotransformation of hexahydro-1,3,5-trinitro-1,3,5 triazine (RDX) has been observed in liquid culture by a consortium of bacteria found in horse manure. Five types of bacteria were found to predominate in the consortium and were isolated. The most effective of these isolates at transforming RDX was Serratia marcescens. The biotransformation of RDX by all of these bacteria was found to occur only in the anoxic stationary phase. The process of bacterial growth and RDX biotransformation was quantified for the purpose of developing a predictive type model. Cell growth was assumed to follow Monod kinetics. All of the aerobic and anoxid growth parameters were determined: {mu}{sub max}, K{sub s}, and Y{sub x/s}. RDX was found to competitively inhibit cell growth in both atmospheres. Degradation of RDX by Serratia marcescens was found to proceed through the stepwise reduction of the three nitro groups to nitroso groups. Each of these reductions was found to be first order in both component and cell concentrations. The degradation rate constant for the first step in this reduction process by the consortium was 0.022 L/g cells {center_dot} h compared to 0.033 L/g cells {center_dot} h for the most efficient isolate.

  16. The effect of p,p'-dichlorodiphenyltrichloroethane on levels of guanosine 3',5'-cyclic monophosphate and adenosine 3',5'-cyclic monophosphate in two species of insects.

    PubMed

    Bodnaryk, R P

    1976-11-01

    Within 1 h after topical application of a convulsive dose (4 mug per fly, 47 mg/kg) of p,p'-dichlorodiphenyltrichloroethane (DDT) to the adult male of Sarcophaga bullata Parker, guanosine 3',5'-cyclic monophosphate (cyclic GMP) levels rose by 71.5% (P less than 0.05) in the head, 159.5% (P less than 0.01) in the thorax, and 23.4% (P greater than 0.05) in the abdomen compared to controls. Adenosine 3',5'-cyclic monophosphate (cyclic AMP) levels were not significantly affected by the DDT treatment. A convulsive dose (100 mug per larva, 250 mg/kg) of DDT applied to larvae of Mamestra configurata Wlk. caused the whole body level of cyclic GMP to rise by 81.6% (P less than 0.01) after 1 h, and by 95.9% (P less than 0.01) after 3 h. Levels of cyclic AMP were not affected. A hypothesis is advanced suggesting that an abnormally high rate of discharge of acetylcholine (and in the later stages of poisoning, its actual accumulation) at central cholinergic synapses causes cyclic GMP levels to rise, perhaps in post-synaptic cells. The elevated cyclic GMP-cyclic AMP ratio found in DDT-poisoned insects may be of fundamental importance in the complex sequence of events leading to tremor, hyperexcitability, paralysis, and death.

  17. Characterization of polymorphic states in energetic samples of 1,3,5-trinitro-1,3,5-triazine (RDX) fabricated using drop-on-demand inkjet technology.

    PubMed

    Emmons, Erik D; Farrell, Mikella E; Holthoff, Ellen L; Tripathi, Ashish; Green, Norman; Moon, Raphael P; Guicheteau, Jason A; Christesen, Steven D; Pellegrino, Paul M; Fountain, Augustus W

    2012-06-01

    The United States Army and the first responder community are evaluating optical detection systems for the trace detection of hazardous energetic materials. Fielded detection systems must be evaluated with the appropriate material concentrations to accurately identify the residue in theater. Trace levels of energetic materials have been observed in mutable polymorphic phases and, therefore, the systems being evaluated must be able to detect and accurately identify variant sample phases observed in spectral data. In this work, we report on the novel application of drop-on-demand technology for the fabrication of standardized trace 1,3,5-trinitro-1,3,5-triazine (RDX) samples. The drop-on-demand sample fabrication technique is compared both visually and spectrally to the more commonly used drop-and-dry technique. As the drop-on-demand technique allows for the fabrication of trace level hazard materials, concerted efforts focused on characterization of the polymorphic phase changes observed with low concentrations of RDX commonly used in drop-on-demand processing. This information is important when evaluating optical detection technologies using samples prepared with a drop-on-demand inkjet system, as the technology may be "trained" to detect the common bulk α phase of the explosive based on its spectral features but fall short in positively detecting a trace quantity of RDX (β-phase). We report the polymorphic shifts observed between α- and β-phases of this energetic material and discuss the conditions leading to the favoring of one phase over the other.

  18. Effects of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) exposure on reproduction and hatchling development in Northern bobwhite quail.

    PubMed

    Brunjes, Kristina J; Severt, Scott A; Liu, Jun; Pan, Xiaoping; Brausch, John; Cox, Stephen A; Cobb, George P; McMurry, Scott T; Kendall, Ronald J; Smith, Philip N

    2007-04-15

    Adult Northern bobwhite quail (Colinus virginianus) were exposed via food to octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), an energetic compound found in soils at military training installations. Depuration of HMX into eggs was examined in an initial study, and effects on egg production, hatching, growth, development, and survival of chicks were examined in a follow-up study. HMX was readily and rapidly transferred from female quail into eggs. Marked weight loss was observed in quail exposed to 125 and 250 mg/kg HMX in food, likely due to reductions in food intake rather than a toxic mechanism. In the second study, significant alterations in body mass occurred among quail at concentrations >52.5 +/- 9.3 mg/kg but not at 12.3 +/- 1.1 mg/kg in food. Treatment-related reductions in food consumption and decreases in egg laying rates were observed. No HMX-related effects were found in chick growth or survival. Quail inhabiting HMX-contaminated sites could possibly be exposed to HMX and therefore deposition of HMX into eggs is also possible. However, results of these studies further suggest that the potential for reproductive toxicity of HMX to birds is low.

  19. Chronic toxicity of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in soil determined using the earthworm (Eisenia andrei) reproduction test.

    PubMed

    Robidoux, P Y; Hawari, J; Thiboutot, S; Ampleman, G; Sunahara, G I

    2001-01-01

    The sublethal and chronic effects of the environmental contaminant and explosive octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in artificial soil were assessed using the earthworm (Eisenia andrei). Based on various reproduction parameters (total and hatched number of cocoons, number of juveniles and their biomass), fecundity was reduced at the different concentrations of HMX tested (from 280.0 +/- 12.3 to 2502.9 +/- 230.0 mg kg-1 dry soil) in spiked artificial soil (LOEC: 280.0 +/- 12.3 mg kg-1 dry soil). The growth of adult E. andrei was also reduced at the different concentrations tested, though no mortality occurred, even at the highest tested concentrations. The number of juveniles produced was correlated with the number of total and hatched cocoons, and the biomass of juveniles was correlated with the number of cocoons. Pooled results of these and earlier studies on explosives (TNT, RDX) using the E. andrei reproduction test confirm that effects of HMX on cocoon production are indicative of some reproductive consequences (number of juvenile and their biomass), whereas adult growth, in general, does not correlate strongly with change in reproduction capacity.

  20. Performance of mesophilic anaerobic granules for removal of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) from aqueous solution.

    PubMed

    An, Chun-jiang; He, Yan-ling; Huang, Guo-he; Liu, Yong-hong

    2010-07-15

    The performance of mesophilic anaerobic granules to degrade octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) was investigated under various conditions. The results of batch experiments showed that anaerobic granules were capable of removing HMX from aqueous solution with high efficiency. Both biotic and abiotic mechanisms contributed to the removal of HMX by anaerobic granules under mesophilic conditions. Adsorption appeared to play a significant role in the abiotic process. Furthermore, HMX could be biodegraded by anaerobic granules as the sole substrate. After 16 days of incubation, 99.04% and 96.42% of total HMX could be removed by 1g VSS/L acclimated and unacclimated granules, respectively. Vancomycin, an inhibitor of acetogenic bacteria, caused a significant inhibition of HMX biotransformation, while 2-bromoethanesulfonic acid, an inhibitor of methanogenic bacteria, only resulted in a slight decrease of metabolic activity. The presence of the glucose, as a suitable electron donor and carbon source, was found to enhance the degradation of HMX by anaerobic granules. Our study showed that sulfate had little adverse effects on biotransformation of HMX by anaerobic granules. However, nitrate had significant inhibitory effect on the extent of HMX removal especially in the initial period. This study offered good prospects of using high-rate anaerobic technology in the treatment of munition wastewater.

  1. Food avoidance behavior to dietary octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) exposure in the northern bobwhite (Colinusvirginianus).

    PubMed

    Johnson, Mark S; Gogal, Robert M; Larsen, Calvert T

    2005-08-13

    High-melting explosive (HMX; octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) is a widely utilized explosive component of munitions used by the military. Consequently, production and use through testing and training at military installations has resulted in deposition of HMX in soil. Since these areas are often used by birds, the oral toxicity of HMX exposure to northern bobwhite (Colinus virginianus) was evaluated. Attempts to determine the acute lethal dose were unsuccessful. Initially, 8 birds (1 male/1 female per dose group) were orally dosed at levels ranging from 125 to 2125 mg HMX/kg body weight. A single death at the midrange resulted in subsequent trials of oral doses up to 10,760 mg/kg body weight. Only a single death occurred at 7173 mg/kg. A subsequent 28-d feeding study was then conducted to evaluate the potential for toxicity resulting from repetitive oral exposures. Northern bobwhite were exposed to concentrations of HMX in feed of either 10000, 1000, 100, or 0 mg/kg. These exposures resulted in a clear concentration-related reduction in feed consumption and body mass. Reductions in egg production in females were correlated with changes in body mass and feed consumption. Other physiological indicators were consistent with a considerable reduction in feed intake. These results suggest that HMX concentration is responsible for intense feed aversion behavior and thus not likely a factor that would appreciably contribute to risk for wild birds at military ranges.

  2. Cloning, Sequencing, and Characterization of the Hexahydro-1,3,5-Trinitro-1,3,5-Triazine Degradation Gene Cluster from Rhodococcus rhodochrous

    PubMed Central

    Seth-Smith, Helena M. B.; Rosser, Susan J.; Basran, Amrik; Travis, Emma R.; Dabbs, Eric R.; Nicklin, Steve; Bruce, Neil C.

    2002-01-01

    Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a high explosive which presents an environmental hazard as a major land and groundwater contaminant. Rhodococcus rhodochrous strain 11Y was isolated from explosive contaminated land and is capable of degrading RDX when provided as the sole source of nitrogen for growth. Products of RDX degradation in resting-cell incubations were analyzed and found to include nitrite, formaldehyde, and formate. No ammonium was excreted into the medium, and no dead-end metabolites were observed. The gene responsible for the degradation of RDX in strain 11Y is a constitutively expressed cytochrome P450-like gene, xplA, which is found in a gene cluster with an adrenodoxin reductase homologue, xplB. The cytochrome P450 also has a flavodoxin domain at the N terminus. This study is the first to present a gene which has been identified as being responsible for RDX biodegradation. The mechanism of action of XplA on RDX is thought to involve initial denitration followed by spontaneous ring cleavage and mineralization. PMID:12324318

  3. Electron shuttle-mediated biotransformation of hexahydro-1,3,5-trinitro-1,3,5-triazine adsorbed to granular activated carbon.

    PubMed

    Millerick, Kayleigh; Drew, Scott R; Finneran, Kevin T

    2013-08-01

    Granular activated carbon (GAC) effectively removes hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) from groundwater but generates RDX-laden GAC that must be disposed of or regenerated. Batch reactors containing GAC to which RDX was preadsorbed were used in experiments to test the potential for adsorbed RDX reduction and daughter product formation using (i) chemically reduced anthrahydroquinone-2,6-disulfonate (AH2QDS), (ii) resting Geobacter metallireducens strain GS-15, and (iii) a combined system containing AQDS and GS-15. Approximately 97.0% of the adsorbed RDX was transformed in each of these experimental systems by 90 h. Chemically reduced AQDS (AH2QDS) transformed 99.2% of adsorbed RDX; formaldehyde was produced rapidly and was stoichiometric (3 mol HCHO per mol RDX). Geobacter metallireducens also reduced RDX with and without AQDS present. This is the first study to demonstrate biological transformation of RDX adsorbed to GAC. Formaldehyde increased and then decreased in biological systems, suggesting a previously unreported capacity for G. metallireducens to oxidize formaldehyde, which was confirmed with resting cell suspensions. These data suggest the masses of GAC waste currently produced by activated carbon at RDX remediation sites can be minimized, decreasing the carbon footprint of the treatment technology. Alternatively, this strategy may be used to develop a Bio-GAC system for ex situ RDX treatment.

  4. Towards ten-watt-level 3-5 µm Raman lasers using tellurite fiber.

    PubMed

    Zhu, Gongwen; Geng, Lixiang; Zhu, Xiushan; Li, Li; Chen, Qian; Norwood, R A; Manzur, T; Peyghambarian, N

    2015-03-23

    Raman lasers based on mid-infrared fibers operating at 3-5 µm atmospheric transparency window are attractive sources for several applications. Compared to fluoride and chalcogenide fibers, tellurite fibers are more advantageous for high power Raman fiber laser sources at 3-5 µm because of their broader Raman gain bandwidth, much larger Raman shift and better physical and chemical properties. Here we report on our simulations for the development of 10-watt-level 3-5 µm Raman lasers using tellurite fibers as the nonlinear gain medium and readily available continuous-wave (cw) and Q-switched erbium-doped fluoride fiber lasers at 2.8 µm as the pump sources. Our results show that a watt-level or even ten-watt-level fiber laser source in the 3-5 µm atmospheric transparency window can be achieved by utilizing the 1st- and 2nd-order Raman scattering in the tellurite fiber. The presented numerical study provides valuable guidance for future 3-5 um Raman fiber laser development. PMID:25837094

  5. Synthesis and Thermal Decomposition Mechanism of the Energetic Compound 3,5-Dinitro-4-nitroxypyrazole

    NASA Astrophysics Data System (ADS)

    Feng, Xiao-Qin; Cao, Duan-Lin; Cui, Jian-Lan

    2016-07-01

    A novel energetic material, 3,5-dinitro-4-nitroxypyrazole (DNNP), was synthesized via nitration and nucleophilic substitution reaction using 4-chloropyrazole as raw material. The structure of DNNP was characterized by Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR), and elemental analysis. Its detonation properties were calculated and compared with those of other commonly used energetic compounds. The thermal decomposition mechanism of DNNP was studied by means of thermogravimetry and differential scanning calorimetry coupled with a mass spectrometry (DSC-MS). The results show that the detonation properties of DNNP were better than those of TNT and comparable to those of 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX). In addition, the thermal decomposition mechanism of DNNP was supposed. Initially, the O-NO2 bond was broken, thereby producing a nitropyrazole oxygen radical. Subsequently, the nitropyrazole oxygen radical was decomposed by free radical cleavage of nitro or isomerized to nitritepyrazole and subsequently decomposed by free radical cleavage of the nitroso group. Finally, pyrazole ring fission occurred and produced N2, NO, N2O, and CO2.

  6. Induction of phosphodiesterase by cyclic adenosine 3':5'-monophosphate in differentiating Dictyostelium discoideum amoebae.

    PubMed

    Klein, C

    1975-09-25

    Cyclic adenosine 3':5'-monophosphate added to the starvation media of Dictyostelium discoideum amoebae induces both intracellular and extracellular phosphodiesterase activities of these cells. The induced enzyme activity appears several hours earlier than that in starved cells which have not been induced with cyclic nucleotide. In both cases, the appearance of enzyme is inhibited by cycloheximide, and actinomycin D, and daunomycin. The KmS for the extracellular enzyme(s) of nucleotide-induced and uninduced control cells are identical. The induction of enzyme activity seems specific for cyclic adenosine 3':5'-monophosphate since cyclic guanosine 3':5'-monophosphate, as well as other nucleotides, have no effect. No differences in the activity or excretion of either N-acetylglucosaminidase or the inhibitory of the extracellular phosphodiesterase are observed between cyclic adenosine 3':5'-monophosphate-induced and control cells. A direct activation of phosphodiesterase by cyclic adenosine 3':5'-monophosphate can be excluded, since the addition of this nucleotide to cell lysates has no effect on the enzyme activity. PMID:170256

  7. Folding of β-barrel membrane proteins in lipid bilayers - Unassisted and assisted folding and insertion.

    PubMed

    Kleinschmidt, Jörg H

    2015-09-01

    In cells, β-barrel membrane proteins are transported in unfolded form to an outer membrane into which they fold and insert. Model systems have been established to investigate the mechanisms of insertion and folding of these versatile proteins into detergent micelles, lipid bilayers and even synthetic amphipathic polymers. In these experiments, insertion into lipid membranes is initiated from unfolded forms that do not display residual β-sheet secondary structure. These studies therefore have allowed the investigation of membrane protein folding and insertion in great detail. Folding of β-barrel membrane proteins into lipid bilayers has been monitored from unfolded forms by dilution of chaotropic denaturants that keep the protein unfolded as well as from unfolded forms present in complexes with molecular chaperones from cells. This review is aimed to provide an overview of the principles and mechanisms observed for the folding of β-barrel transmembrane proteins into lipid bilayers, the importance of lipid-protein interactions and the function of molecular chaperones and folding assistants. This article is part of a Special Issue entitled: Lipid-protein interactions.

  8. A Rat Excised Larynx Model of Vocal Fold Scar

    ERIC Educational Resources Information Center

    Welham, Nathan V.; Montequin, Douglas W.; Tateya, Ichiro; Tateya, Tomoko; Choi, Seong Hee; Bless, Diane M.

    2009-01-01

    Purpose: To develop and evaluate a rat excised larynx model for the measurement of acoustic, aerodynamic, and vocal fold vibratory changes resulting from vocal fold scar. Method: Twenty-four 4-month-old male Sprague-Dawley rats were assigned to 1 of 4 experimental groups: chronic vocal fold scar, chronic vocal fold scar treated with 100-ng basic…

  9. Iontophoresis across the proximal nail fold to target drugs to the nail matrix.

    PubMed

    Manda, Prashanth; Sammeta, Srinivasa M; Repka, Michael A; Murthy, S Narasimha

    2012-07-01

    The main objective of the present study was to investigate the plausibility of iontophoretic delivery of drugs to the nail matrix via proximal nail fold. The in vitro drug transport studies were performed in Franz diffusion cells across folded epidermis, which is used as a model for the proximal nail fold. The amount of drug transported into the receiver compartment following iontophoresis for 3 h at 0.5 mA/cm(2) was 150-fold higher than the control (0.008 ± 0.002 μg/cm(2)). The amount of drug present in the skin after iontophoresis (0.45 ± 0.12 μg/mg) was approximately fivefold higher as compared with that of the control (0.08 ± 0.01 μg/mg). Iontophoresis of terbinafine across the proximal nail fold was assessed using excised cadaver toe model as well. A custom-designed foam-pad-type patch system was used for iontophoresis in cadaver toes. The amount of the drug delivered into the nail matrix following iontophoresis for 3 h was significantly higher than the minimum inhibition concentration of terbinafine. However, on the contrary, passive delivery for about 24 h did not result in any detectable drug levels in the nail matrix. Iontophoresis across the proximal nail fold could be developed as a potential method to target drugs to nail matrix. PMID:22487899

  10. Iontophoresis across the proximal nail fold to target drugs to the nail matrix.

    PubMed

    Manda, Prashanth; Sammeta, Srinivasa M; Repka, Michael A; Murthy, S Narasimha

    2012-07-01

    The main objective of the present study was to investigate the plausibility of iontophoretic delivery of drugs to the nail matrix via proximal nail fold. The in vitro drug transport studies were performed in Franz diffusion cells across folded epidermis, which is used as a model for the proximal nail fold. The amount of drug transported into the receiver compartment following iontophoresis for 3 h at 0.5 mA/cm(2) was 150-fold higher than the control (0.008 ± 0.002 μg/cm(2)). The amount of drug present in the skin after iontophoresis (0.45 ± 0.12 μg/mg) was approximately fivefold higher as compared with that of the control (0.08 ± 0.01 μg/mg). Iontophoresis of terbinafine across the proximal nail fold was assessed using excised cadaver toe model as well. A custom-designed foam-pad-type patch system was used for iontophoresis in cadaver toes. The amount of the drug delivered into the nail matrix following iontophoresis for 3 h was significantly higher than the minimum inhibition concentration of terbinafine. However, on the contrary, passive delivery for about 24 h did not result in any detectable drug levels in the nail matrix. Iontophoresis across the proximal nail fold could be developed as a potential method to target drugs to nail matrix.

  11. Experimental folding and boudinage under pure constrictional conditions

    NASA Astrophysics Data System (ADS)

    Kobberger, Gustav

    1995-07-01

    Constrictional folds are characterized by true fold-axis parallel extension if the rock-volume does not vary during deformation. Studies of such folds in experiments, using plasticine layers of different apparent viscosity and power-law exponent, clearly indicate that fold-axis parallel stretch may be accompanied by plastic elongation as well as boudinage of the competent layer. Characteristic aspects of the experimentally folded competent layers are: (1) coeval development of folds and boudins; (2) layer thickness not changing during deformation; (3) layer-parallel shortening in sections perpendicular to the fold (stretching) axis; (4) enlargement of the initial thickness of the competent layer results in increasing fold wavelength and decreasing number of boudins. The ratio of dominant wavelength to layer thickness of the constrictional folds can be described mathematically approximately by the equation developed for plane strain folding of power-law materials

  12. Sensitivity of 2,6-Diamino-3, 5-Dinitropyrazine-1-Oxide

    SciTech Connect

    Tarver, C M; Urtiew, P A; Tran, T D

    2005-01-20

    The thermal and shock sensitivities of plastic bonded explosive formations based on 2,6-diamino-3,5-dinitropyrazine-1-oxide (commonly called LLM-105 for Lawrence Livermore Molecule No.105) are reported. The One Dimensional Time to Explosion (ODTX) apparatus was used to generate times to thermal explosion at various initial temperatures. A four-reaction chemical decomposition model was developed to calculate the time to thermal explosion versus inverse temperature curve. Three embedded manganin pressure gauge experiments were fired at different initial pressures to measure the pressure buildup and the distance required for transition to detonation. An Ignition and Growth reactive model was calibrated to this shock initiation data. LLM-105 exhibited thermal and shock sensitivities intermediate between those of triaminotrinitrobenzene (TATB) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazine (HMX).

  13. Poly[(μ(5)-3,5-dinitro-benzoato)rubidium].

    PubMed

    Miao, Yanqing; Zhang, Xiaoqing; Liu, Chunye

    2011-07-01

    The asymmetric unit of the title compound, [Rb(C(7)H(3)N(2)O(6))](n), comprises an Rb cation and a 3,5-dinitro-benzoate anion. The Rb cation is eight-coordinated by O atoms from five 3,5-dinitro-benzoate anions. On the other hand, each 3,5-dinitro-benzoate anion links five Rb cations with the carboxyl-ate groups as μ(3)-bridging. The metal atom is firstly linked by the carboxyl-ate groups into a chain along the c-axis direction, which is further linked by bonds between the Rb and nitro O atoms, giving a three-dimensional framework. PMID:21836829

  14. Synthesis and structural characterization of 3,5-dinitro-1,2,4-triazolates.

    PubMed

    Haiges, R; Bélanger-Chabot, G; Kaplan, S M; Christe, K O

    2015-02-21

    Salts of 3,5-dinitro-1H-1,2,4-triazole, a building block for energetic materials, have been prepared and fully characterized. Most of the studied salts exhibit high thermal stability and very low shock and friction sensitivities. 3,5-Dinitro-1,2,4-triazolates with the nitrogen-rich ammonium, guanidinium, aminoguanidinium, and aminotetrazolium cations are energetic and have potential for energetic material applications. Salts containing alkali, alkali earth metal, and silver cations exhibit coloured emissions upon combustion while salts with large organic cations such as PPh4(+) and (Ph3P)2N(+) are highly insensitive and can be easily crystallized.

  15. Access to Pyrazolidin-3,5-diones through Anodic N-N Bond Formation.

    PubMed

    Gieshoff, Tile; Schollmeyer, Dieter; Waldvogel, Siegfried R

    2016-08-01

    Pyrazolidin-3,5-diones are important motifs in heterocyclic chemistry and are of high interest for pharmaceutical applications. In classic organic synthesis, the hydrazinic moiety is installed through condensation using the corresponding hydrazine building blocks. However, most N,N'-diaryl hydrazines are toxic and require upstream preparation owing to their low commercial availability. We present an alternative and sustainable synthetic approach to pyrazolidin-3,5-diones that employs readily accessible dianilides as precursors, which are anodically converted to furnish the N-N bond. The electroconversion is conducted in a simple undivided cell under constant-current conditions. PMID:27392318

  16. The role of ascorbate in protein folding.

    PubMed

    Szarka, András; Lőrincz, Tamás

    2014-05-01

    Ascorbate was linked to protein folding a long time ago. At the first level of this connection, it had been shown that ascorbate functions as an essential cofactor in the hydroxylation enzymes involved in collagen synthesis. Although the hydroxylation reactions catalyzed by the members of the prolyl 4-hydroxylase family are considered to be ascorbate dependent, the hydroxylation of proline alone does not need ascorbate. Prolyl 4-hydroxylases participate in two catalytic reactions: one in which proline residues are hydroxylated, while 2-oxoglutarate is decarboxylated and molecular oxygen is consumed. This reaction is ascorbate independent. However, in another reaction, prolyl 4-hydroxylases catalyze the decarboxylation of 2-oxoglutarate uncoupled from proline hydroxylation but still needing molecular oxygen. At this time, ferrous iron is oxidized and the protein is rendered catalytically inactive until reduced by ascorbate. At the second level of the connection, the oxidation and the oxidized form of ascorbate, dehydroascorbate, is involved in the formation of disulfide bonds of secretory proteins. The significance of the dehydroascorbate reductase activity of protein disulfide isomerase was debated because protein disulfide isomerase as a dehydroascorbate reductase was found to be too slow to be the major route for the reduction of dehydroascorbate (and formation of disulfides) in the endoplasmic reticulum lumen. However, very recently, low tissue ascorbate levels and a noncanonical scurvy were observed in endoplasmic reticulum thiol oxidase- and peroxiredoxin 4-compromised mice. This novel observation implies that ascorbate may be involved in oxidative protein folding and creates a link between the disulfide bond formation (oxidative protein folding) and hydroxylation. PMID:24150425

  17. Energy landscape in protein folding and unfolding

    PubMed Central

    Mallamace, Francesco; Corsaro, Carmelo; Mallamace, Domenico; Vasi, Sebastiano; Vasi, Cirino; Baglioni, Piero; Buldyrev, Sergey V.; Chen, Sow-Hsin; Stanley, H. Eugene

    2016-01-01

    We use 1H NMR to probe the energy landscape in the protein folding and unfolding process. Using the scheme ⇄ reversible unfolded (intermediate) → irreversible unfolded (denatured) state, we study the thermal denaturation of hydrated lysozyme that occurs when the temperature is increased. Using thermal cycles in the range 295

  18. Energy landscape in protein folding and unfolding.

    PubMed

    Mallamace, Francesco; Corsaro, Carmelo; Mallamace, Domenico; Vasi, Sebastiano; Vasi, Cirino; Baglioni, Piero; Buldyrev, Sergey V; Chen, Sow-Hsin; Stanley, H Eugene

    2016-03-22

    We use (1)H NMR to probe the energy landscape in the protein folding and unfolding process. Using the scheme ⇄ reversible unfolded (intermediate) → irreversible unfolded (denatured) state, we study the thermal denaturation of hydrated lysozyme that occurs when the temperature is increased. Using thermal cycles in the range 295 < T < 365 K and following different trajectories along the protein energy surface, we observe that the hydrophilic (the amide NH) and hydrophobic (methyl CH3 and methine CH) peptide groups evolve and exhibit different behaviors. We also discuss the role of water and hydrogen bonding in the protein configurational stability.

  19. Foldons as independently folding units of proteins

    NASA Astrophysics Data System (ADS)

    Panchenko, Anna R.; Luthey-Schulten, Zaida; Wolynes, Peter G.

    1997-02-01

    Independently folding units of proteins, foldons, have been identified by maxima in a scan of the ratio of an energetic stability gap to the energy variance of that segment's molten globule states, reflecting the requirement of minimal frustration. Foldon boundaries, unlike structural domains, depend on the sequence of the protein. Therefore, domains defined by purely structural criteria and the foldons of a given protein may differ in size and structure. The predicted foldons have been compared to the exons and structural modules. Statistical analysis indicates a strong correlation between the energetically determined foldons and Go's geometrically defined structural modules. There is only a weak correlation of foldons to exons.

  20. Communication Between RNA Folding Domains Revealed by Folding of Circularly Permuted Ribozymes

    SciTech Connect

    Lease,R.; Adilakshmi, T.; Heilman-Miller, S.; Woodson, S.

    2007-01-01

    To study the role of sequence and topology in RNA folding, we determined the kinetic folding pathways of two circularly permuted variants of the Tetrahymena group I ribozyme, using time-resolved hydroxyl radical footprinting. Circular permutation changes the distance between interacting residues in the primary sequence, without changing the native structure of the RNA. In the natural ribozyme, tertiary interactions in the P4-P6 domain form in 1 s, while interactions in the P3-P9 form in 1-3 min at 42 C. Permutation of the 5' end to G111 in the P4 helix allowed the stable P4-P6 domain to fold in 200 ms at 30 C, five times faster than in the wild-type RNA, while the other domains folded five times more slowly (5-8 min). By contrast, circular permutation of the 5' end to G303 in J8/7 decreased the folding rate of the P4-P6 domain. In this permuted RNA, regions joining P2, P3 and P4 were protected in 500 ms, while the P3-P9 domain was 60-80% folded within 30 s. RNase T1 digestion and FMN photocleavage showed that circular permutation of the RNA sequence alters the initial ensemble of secondary structures, thereby changing the tertiary folding pathways. Our results show that the natural 5'-to-3' order of the structural domains in group I ribozymes optimizes structural communication between tertiary domains and promotes self-assembly of the catalytic center.

  1. Fault-related fold styles and progressions in fold-thrust belts: Insights from sandbox modeling

    NASA Astrophysics Data System (ADS)

    Yan, Dan-Ping; Xu, Yan-Bo; Dong, Zhou-Bin; Qiu, Liang; Zhang, Sen; Wells, Michael

    2016-03-01

    Fault-related folds of variable structural styles and assemblages commonly coexist in orogenic belts with competent-incompetent interlayered sequences. Despite their commonality, the kinematic evolution of these structural styles and assemblages are often loosely constrained because multiple solutions exist in their structural progression during tectonic restoration. We use a sandbox modeling instrument with a particle image velocimetry monitor to test four designed sandbox models with multilayer competent-incompetent materials. Test results reveal that decollement folds initiate along selected incompetent layers with decreasing velocity difference and constant vorticity difference between the hanging wall and footwall of the initial fault tips. The decollement folds are progressively converted to fault-propagation folds and fault-bend folds through development of fault ramps breaking across competent layers and are followed by propagation into fault flats within an upper incompetent layer. Thick-skinned thrust is produced by initiating a decollement fault within the metamorphic basement. Progressive thrusting and uplifting of the thick-skinned thrust trigger initiation of the uppermost incompetent decollement with formation of a decollement fold and subsequent converting to fault-propagation and fault-bend folds, which combine together to form imbricate thrust. Breakouts at the base of the early formed fault ramps along the lowest incompetent layers, which may correspond to basement-cover contacts, domes the upmost decollement and imbricate thrusts to form passive roof duplexes and constitute the thin-skinned thrust belt. Structural styles and assemblages in each of tectonic stages are similar to that in the representative orogenic belts in the South China, Southern Appalachians, and Alpine orogenic belts.

  2. The little-studied cluster Berkeley 90. I. LS III +46 11: a very massive O3.5 If* + O3.5 If* binary

    NASA Astrophysics Data System (ADS)

    Maíz Apellániz, J.; Negueruela, I.; Barbá, R. H.; Walborn, N. R.; Pellerin, A.; Simón-Díaz, S.; Sota, A.; Marco, A.; Alonso-Santiago, J.; Sanchez Bermudez, J.; Gamen, R. C.; Lorenzo, J.

    2015-07-01

    Context. It appears that most (if not all) massive stars are born in multiple systems. At the same time, the most massive binaries are hard to find owing to their low numbers throughout the Galaxy and the implied large distances and extinctions. Aims: We want to study LS III +46 11, identified in this paper as a very massive binary; another nearby massive system, LS III +46 12; and the surrounding stellar cluster, Berkeley 90. Methods: Most of the data used in this paper are multi-epoch high S/N optical spectra, although we also use Lucky Imaging and archival photometry. The spectra are reduced with dedicated pipelines and processed with our own software, such as a spectroscopic-orbit code, CHORIZOS, and MGB. Results: LS III +46 11 is identified as a new very early O-type spectroscopic binary [O3.5 If* + O3.5 If*] and LS III +46 12 as another early O-type system [O4.5 V((f))]. We measure a 97.2-day period for LS III +46 11 and derive minimum masses of 38.80 ± 0.83 M⊙ and 35.60 ± 0.77 M⊙ for its two stars. We measure the extinction to both stars, estimate the distance, search for optical companions, and study the surrounding cluster. In doing so, a variable extinction is found as well as discrepant results for the distance. We discuss possible explanations and suggest that LS III +46 12 may be a hidden binary system where the companion is currently undetected.

  3. Toxic effects of oral hexahydro-1,3,5-trinitro-1,3,5-triazine in the western fence lizard (Sceloporus occidentalis).

    PubMed

    McFarland, Craig A; Quinn, Michael J; Bazar, Matthew A; Talent, Larry G; Johnson, Mark S

    2009-05-01

    Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has been widely used as an explosive in munition formulations, resulting in contamination of wildlife habitat on military installations. To estimate health effects for reptilian species, acute, subacute, and subchronic oral toxicity studies were conducted using the Western fence lizard (Sceloporus occidentalis). Estimated oral median lethal doses were 72 (95% confidence interval [CI], 49-106) mg/kg body weight (slope, 3.754) for males and 88 (95% CI, 65-119) mg/kg (slope, 4.525) for females. Toxicity from RDX suggested the neurological system as the critical target tissue. A 14-d subacute study followed with males dosed orally with RDX (corn oil) at 0, 10, 20, 25, 30, 45, and 60 mg/kg/d. Signs of toxicity frequently included a characteristic body posture. A significant dose-survival relationship was seen over the range of doses, with a significant decrease in survival at 20 mg/kg/d. Males in the 60-d subchronic study were dosed at 0, 1, 2.5, 5, 8, and 11 mg/kg/d, and signs of toxicity included lethargy, cachexia, and anorexia. Survival was decreased at 8 and 11 mg/kg/d. Reduced growth rate and food consumption occurred at 5 mg/kg/d. Brain tissue was assayed for RDX when seizures were observed at a residue concentration of at least 18 microg/g. No abnormalities were observed in the hematologic indices, whereas plasma proteins were reduced. Hepatic enlargement and decreased testes mass occurred at 8 and 11 mg/kg/d. Plasma testosterone concentrations, sperm counts, and motility measures were variable for all treatment levels. Based on survival, growth rate, food intake, and testes to brain weight ratios, these data suggest a lowest-observed-adverse effect level of 5 mg/kg/d and a no-observed-adverse effect level of 2.5 mg/kg/d. PMID:19102580

  4. Identification of hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading microorganisms via 15N-stable isotope probing.

    PubMed

    Roh, Hyungkeun; Yu, Chang-Ping; Fuller, Mark E; Chu, Kung-Hui

    2009-04-01

    This study reported the application of 15N-stable isotope probing (SIP) to identify active hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)-utilizing microorganisms in groundwater microcosms. Fifteen 16S rRNA gene sequences were derived from the 15N-DNA fraction (contributed from active microorganisms capable of using RDX as a nitrogen source) of microcosms receiving cheese whey. The 16S rRNA gene sequences belonged to Actinobacteria (two clones), alpha-Proteobacteria (seven clones), and gamma-Proteobacteria (six clones). Except for five sequences with high similarity to two known RDX degraders (Enterobacter cloacae and Pseudomonas fluorescens I-C), our results suggested that phylogenetically diverse microorganisms were capable of using RDX as a nitrogen source. Six sequences of the xplA gene (a known RDX-degrading catabolic gene) were detected from the 15N-DNA fraction. The xplA gene sequences were 96-99% similar to the xplA gene of Rhodococcus sp. DN22(a known RDX utilizer), suggesting that other RDX utilizers might contain xplA-like genes. Twenty-five 16S rRNA gene sequences recovered from the unenriched, RDX-contaminated groundwater clustered differently from those obtained from the 15N-DNA fraction of the cheese-whey-amended microcosm. Our results suggested that active RDX utilizers can be stimulated by nutrient source additions even if they are present at low densities, and that use of 15N-SIP can identifythese functional members of the microbial community.

  5. Evaluation of Biostimulation and Bioaugmentation To Stimulate Hexahydro-1,3,5-trinitro-1,3,5,-triazine Degradation in an Aerobic Groundwater Aquifer.

    PubMed

    Michalsen, Mandy M; King, Aaron S; Rule, Rebecca A; Fuller, Mark E; Hatzinger, Paul B; Condee, Charles W; Crocker, Fiona H; Indest, Karl J; Jung, Carina M; Istok, Jack D

    2016-07-19

    Hexahydro-1,3,5-trinitro-1,3,5,-triazine (RDX) is a toxic and mobile groundwater contaminant common to military sites. This study compared in situ RDX degradation rates following bioaugmentation with Gordonia sp. strain KTR9 (henceforth KTR9) to rates under biostimulation conditions in an RDX-contaminated aquifer in Umatilla, OR. Bioaugmentation was achieved by injecting site groundwater (6000 L) amended with KTR9 cells (10(8) cells mL(-1)) and low carbon substrate concentrations (<1 mM fructose) into site wells. Biostimulation (no added cells) was performed by injecting groundwater amended with low (<1 mM fructose) or high (>15 mM fructose) carbon substrate concentrations in an effort to stimulate aerobic or anaerobic microbial activity, respectively. Single-well push-pull tests were conducted to measure RDX degradation rates for each treatment. Average rate coefficients were 1.2 day(-1) for bioaugmentation and 0.7 day(-1) for high carbon biostimulation; rate coefficients for low carbon biostimulation were not significantly different from zero (p values ≥0.060). Our results suggest that bioaugmentation with KTR9 is a feasible strategy for in situ biodegradation of RDX and, at this site, is capable of achieving RDX concentration reductions comparable to those obtained by high carbon biostimulation while requiring ~97% less fructose. Bioaugmentation has potential to minimize substrate quantities and associated costs, as well as secondary groundwater quality impacts associated with anaerobic biostimulation processes (e.g., hydrogen sulfide, methane production) during full-scale RDX remediation.

  6. Analysis of the xplAB-Containing Gene Cluster Involved in the Bacterial Degradation of the Explosive Hexahydro-1,3,5-Trinitro-1,3,5-Triazine

    PubMed Central

    Chong, Chun Shiong; Sabir, Dana Khdr; Lorenz, Astrid; Bontemps, Cyril; Andeer, Peter; Stahl, David A.; Strand, Stuart E.; Rylott, Elizabeth L.

    2014-01-01

    Repeated use of the explosive compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) on military land has resulted in significant soil and groundwater pollution. Rates of degradation of RDX in the environment are low, and accumulated RDX, which the U.S. Environmental Protection Agency has determined is a possible human carcinogen, is now threatening drinking water supplies. RDX-degrading microorganisms have been isolated from RDX-contaminated land; however, despite the presence of these species in contaminated soils, RDX pollution persists. To further understand this problem, we studied RDX-degrading species belonging to four different genera (Rhodococcus, Microbacterium, Gordonia, and Williamsia) isolated from geographically distinct locations and established that the xplA and xplB (xplAB) genes, which encode a cytochrome P450 and a flavodoxin redox partner, respectively, are nearly identical in all these species. Together, the xplAB system catalyzes the reductive denitration of RDX and subsequent ring cleavage under aerobic and anaerobic conditions. In addition to xplAB, the Rhodococcus species studied here share a 14-kb region flanking xplAB; thus, it appears likely that the RDX-metabolizing ability was transferred as a genomic island within a transposable element. The conservation and transfer of xplAB-flanking genes suggest a role in RDX metabolism. We therefore independently knocked out genes within this cluster in the RDX-degrading species Rhodococcus rhodochrous 11Y. Analysis of the resulting mutants revealed that XplA is essential for RDX degradation and that XplB is not the sole contributor of reducing equivalents to XplA. While XplA expression is induced under nitrogen-limiting conditions and further enhanced by the presence of RDX, MarR is not regulated by RDX. PMID:25128343

  7. Evaluation of Biostimulation and Bioaugmentation To Stimulate Hexahydro-1,3,5-trinitro-1,3,5,-triazine Degradation in an Aerobic Groundwater Aquifer.

    PubMed

    Michalsen, Mandy M; King, Aaron S; Rule, Rebecca A; Fuller, Mark E; Hatzinger, Paul B; Condee, Charles W; Crocker, Fiona H; Indest, Karl J; Jung, Carina M; Istok, Jack D

    2016-07-19

    Hexahydro-1,3,5-trinitro-1,3,5,-triazine (RDX) is a toxic and mobile groundwater contaminant common to military sites. This study compared in situ RDX degradation rates following bioaugmentation with Gordonia sp. strain KTR9 (henceforth KTR9) to rates under biostimulation conditions in an RDX-contaminated aquifer in Umatilla, OR. Bioaugmentation was achieved by injecting site groundwater (6000 L) amended with KTR9 cells (10(8) cells mL(-1)) and low carbon substrate concentrations (<1 mM fructose) into site wells. Biostimulation (no added cells) was performed by injecting groundwater amended with low (<1 mM fructose) or high (>15 mM fructose) carbon substrate concentrations in an effort to stimulate aerobic or anaerobic microbial activity, respectively. Single-well push-pull tests were conducted to measure RDX degradation rates for each treatment. Average rate coefficients were 1.2 day(-1) for bioaugmentation and 0.7 day(-1) for high carbon biostimulation; rate coefficients for low carbon biostimulation were not significantly different from zero (p values ≥0.060). Our results suggest that bioaugmentation with KTR9 is a feasible strategy for in situ biodegradation of RDX and, at this site, is capable of achieving RDX concentration reductions comparable to those obtained by high carbon biostimulation while requiring ~97% less fructose. Bioaugmentation has potential to minimize substrate quantities and associated costs, as well as secondary groundwater quality impacts associated with anaerobic biostimulation processes (e.g., hydrogen sulfide, methane production) during full-scale RDX remediation. PMID:27301804

  8. Analysis of the key intermediates of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) in groundwater: occurrence, stability and preservation.

    PubMed

    Paquet, Louise; Monteil-Rivera, Fanny; Hatzinger, Paul B; Fuller, Mark E; Hawari, Jalal

    2011-08-01

    Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a widely used explosive that is present in soils at a number of military sites, including training and testing ranges. Because of its relatively weak adsorption to soil, RDX frequently migrates through the unsaturated zone and causes groundwater contamination. In the environment, RDX can transform to produce mono-, di-, and tri-nitroso derivatives (MNX, DNX, and TNX) and the ring cleavage products methylenedinitramine (MEDINA) and 4-nitro-2,4-diazabutanal (NDAB). The present study was undertaken to analyze RDX and its products in groundwater samples taken from various US military sites. The stability of some of the common transformation intermediates of RDX, including the nitroso derivatives, NDAB and MEDINA, under typical conditions in a groundwater aquifer is not well understood, and appropriate preservation methods for these compounds have not been established. Therefore, we studied the inherent stability of these compounds in deionized water and in groundwater, and evaluated various preservation techniques, including adjustment of pH, temperature, and salinity. NDAB and nitroso derivatives were stable under typical ambient environmental conditions, but MEDINA was highly unstable. The addition of sea salts (10% w/v) was found to stabilize MEDINA when the samples were stored at 4 °C. Using appropriate preservation techniques, we detected nitroso derivatives and NDAB, but no MEDINA, at some of the sites investigated. Stabilizing RDX intermediate products in field samples to allow detection is important because the presence of any of these chemicals can indicate past contamination by RDX and provide insight into the occurrence of in situ natural attenuation. PMID:21734991

  9. Analysis of the key intermediates of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) in groundwater: occurrence, stability and preservation.

    PubMed

    Paquet, Louise; Monteil-Rivera, Fanny; Hatzinger, Paul B; Fuller, Mark E; Hawari, Jalal

    2011-08-01

    Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a widely used explosive that is present in soils at a number of military sites, including training and testing ranges. Because of its relatively weak adsorption to soil, RDX frequently migrates through the unsaturated zone and causes groundwater contamination. In the environment, RDX can transform to produce mono-, di-, and tri-nitroso derivatives (MNX, DNX, and TNX) and the ring cleavage products methylenedinitramine (MEDINA) and 4-nitro-2,4-diazabutanal (NDAB). The present study was undertaken to analyze RDX and its products in groundwater samples taken from various US military sites. The stability of some of the common transformation intermediates of RDX, including the nitroso derivatives, NDAB and MEDINA, under typical conditions in a groundwater aquifer is not well understood, and appropriate preservation methods for these compounds have not been established. Therefore, we studied the inherent stability of these compounds in deionized water and in groundwater, and evaluated various preservation techniques, including adjustment of pH, temperature, and salinity. NDAB and nitroso derivatives were stable under typical ambient environmental conditions, but MEDINA was highly unstable. The addition of sea salts (10% w/v) was found to stabilize MEDINA when the samples were stored at 4 °C. Using appropriate preservation techniques, we detected nitroso derivatives and NDAB, but no MEDINA, at some of the sites investigated. Stabilizing RDX intermediate products in field samples to allow detection is important because the presence of any of these chemicals can indicate past contamination by RDX and provide insight into the occurrence of in situ natural attenuation.

  10. Flame spread through cracks of PBX 9501 (a composite octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine-based explosive)

    NASA Astrophysics Data System (ADS)

    Berghout, H. Laine; Son, Steven F.; Hill, Larry G.; Asay, Blaine W.

    2006-06-01

    Recent experiments involving combustion of PBX 9501 [a plastic-bonded high explosive composed of 95% octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) by weight in a plasticized, estane-based binder] under confined conditions underscore the importance of cracks and flaws in reaction violence. The presence of a small void space or alternative escape path for combustion gases at the closed end of a crack drastically alters combustion violence. In the case of a true closed-ended crack, where gases can only escape by exiting the open end of the crack, luminous combustion spreads through the closed crack at relatively low rates in the range of a few meters per second, regardless of the pressure external to the slot. Hence, external pressure determines whether reaction can progress into the restricted dimensions of the slot, but it does not necessarily determine the dynamics of the flame's progress in the slot. When an alternative combustion-gas escape path is available at the closed end of the slot, luminous combustion spreads through the crack at hundreds of meters per second. Additionally, combustion in cracks of confined PBX 9501 materials exhibits oscillatory behavior with a frequency of about 1000 Hz for the experimental configuration used. This oscillatory behavior resembles combustion instabilities observed in rocket motors and may arise from similar processes. We also report on preliminary experiments involving 19.1 cm long slots in confined PBX 9501, which have produced very high flame-propagation rates of 1500 m/s.

  11. Adsorption-desorption of 2,4,6-trinitrotoluene and hexahydro-1,3,5-trinitro-1,3,5-triazine in soils

    SciTech Connect

    Xue, S.K.; Selim, H.M.; Iskandar, I.K.

    1995-11-01

    This study studied the adsorption-desorption behavior of TNT (2, 4, 6-trinitrotoluene) and RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) in a bentonite/sand reference material (Swy-1 montmorillonite clay mixed with acid-washed sand) and two selected soils (Norwood and Kolin). Release of TNT,RDX, and other compounds from a contaminated soil obtained from the Louisiana Army Ammunition Plant (AAP) site was also investigated. The kinetics of TNT and RDX retention were measured using batch methods for a range of input concentrations. For RDX, the adsorption isotherms were distinctly linear. The TNT adsorption isotherm for bentonite/sand mixture appeared linear and was described equally well using linear, Freundlich, Langmuir, and a modified Langmuir model. For the Norwood and Kolin soils, TNT adsorption isotherms exhibited distinct nonlinearity and the Freundlich model provided the best fit. As indicated by the K{sub d} values, TNT exhibited stronger retention or affinity to all soils and the bentonite/sand mixture than for RDX. The RDX retention data indicated little time-dependent behavior. The TNT retention data indicated a continued decrease in TNT concentration with time in the Norwood and Kolin soils. This was possibly caused by the formation and subsequent adsorption of transformation products because transformation products, such as amino nitro toluene compounds, were identified during batch experiments. For the bentonite/sand mixture, TNT retention was rapid initially and reached apparent equilibrium within 1 day. Unlike Kolin and Norwood soils, there was no hysteretic behavior of TNT adsorption-desorption by the bentonite/sand mixture and a mass balance suggested fully reversible retention mechanisms. 15 refs., 13 figs., 2 tabs.

  12. Transport of 2,4,6-trinitrotoluene and hexahydro-1,3,5-trinitro-1,3,5-triazine in soils

    SciTech Connect

    Selim, H.M.; Xue, S.K.; Iskandar, I.K.

    1995-11-01

    This study investigated the fate and transport of explosives in soils. Transport experiments were conducted to describe the mobility of 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in a SWy-1 reference clay (bentonite mixed with sand) and two selected soils (Norwood and Kolin). Miscible displacement experiments in packed soil columns under steady flow were used. For the bentonite/sand column, TNT was highly mobile and fully reversible when methanol was used as the background solution. In contrast the TNT pulse was strongly retarded with as much as 50% of that applied remaining within the bentonite/sand, Norwood, or Kolin columns. Products of the transformation of TNT to 4-Am-DNT and other compound were identified in the effluent solution. A 7-day flow interruption during the TNT pulse application resulted in decreased TNT levels in the effluent solution. This decrease corresponded to a sudden increase in the 4-Am-DNT concentration in the effluent. For RDX only limited retention was observed. These findings are consistent with results from adsorption-desorption batch experiments. The TNT and RDX transport results were successfully described by a nonlinear multireaction and transport model (MRTM), which accounted for equilibrium and kinetic (reversible and irreversible) retention mechanisms. However, efforts to describe RDX transport were more successful than efforts to describe TNT when independently determined (batch) parameters were used. The mobility of TNT, RDX, and other compounds from a contaminated soil obtained from a Louisiana Army Ammunition Plant (AAP) site was also investigated. A gradual release and subsequent movement of various contaminants, including HMX, TNT, RDX, TNG, 2-Am-DNT, and 4-Am-DNT, was observed. The leaching patterns were consistent with results from uncontaminated Kolin soil columns and reflected the affinity of contaminants during leaching in the AAP soil. 18 refs., 9 figs., 1 tab.

  13. Accumulation and effects of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) exposure in the green anole (Anolis carolinensis).

    PubMed

    McMurry, S T; Jones, L E; Smith, P N; Cobb, G P; Anderson, T A; Lovern, M B; Cox, S; Pan, X

    2012-03-01

    Environmental contamination by energetic compounds is an increasing international concern, although little is known of their accumulation in and affect on wildlife. Reptiles are often good models for contaminants studies due to natural history traits that increase their potential for exposure. We report a study to assess accumulation and effects of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX, High Melting Explosive) in green anoles (Anolis carolinensis). Acute oral toxicity (LD(50)) was estimated to exceed 2000 mg/kg body weight in adult male and female anoles using a standard up-and-down method. Accumulation of HMX was assessed in adult females via dietary exposure and into eggs by two routes (directly from the soil and via maternal transfer). HMX readily accumulated into adult females in a dose-dependent manner and into eggs following both exposure pathways. However, total HMX in soil-exposed eggs was up to 40-times greater than those exposed via maternal transfer. Although there was a suggestion of an HMX-induced reduction in body weight in adult females, overall there were no effects observed over the 12 week exposure period. The only significant effect on eggs was a 50% reduction in hatching success for eggs exposed to 2000 mg/kg HMX in the soil during incubation. Growth and survival of hatchlings was not affected by HMX exposure. Our results demonstrate that HMX accumulates through the food chain and into eggs from the soil, but likely poses minimal threat to lizards except to hatching success in eggs incubated in soils with HMX levels near maximum environmental concentrations.

  14. Drosophila TRPML Forms PI(3,5)P2-activated Cation Channels in Both Endolysosomes and Plasma Membrane*

    PubMed Central

    Feng, Xinghua; Huang, Yu; Lu, Yungang; Xiong, Jian; Wong, Ching-On; Yang, Pu; Xia, Jintang; Chen, De; Du, Guangwei; Venkatachalam, Kartik; Xia, Xuefeng; Zhu, Michael X.

    2014-01-01

    Transient Receptor Potential mucolipin (TRPML) channels are implicated in endolysosomal trafficking, lysosomal Ca2+ and Fe2+ release, lysosomal biogenesis, and autophagy. Mutations in human TRPML1 cause the lysosome storage disease, mucolipidosis type IV (MLIV). Unlike vertebrates, which express three TRPML genes, TRPML1–3, the Drosophila genome encodes a single trpml gene. Although the trpml-deficient flies exhibit cellular defects similar to those in mammalian TRPML1 mutants, the biophysical properties of Drosophila TRPML channel remained uncharacterized. Here, we show that transgenic expression of human TRPML1 in the neurons of Drosophila trpml mutants partially suppressed the pupal lethality phenotype. When expressed in HEK293 cells, Drosophila TRPML was localized in both endolysosomes and plasma membrane and was activated by phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) applied to the cytoplasmic side in whole lysosomes and inside-out patches excised from plasma membrane. The PI(3,5)P2-evoked currents were blocked by phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), but not other phosphoinositides. Using TRPML A487P, which mimics the varitint-waddler (Va) mutant of mouse TRPML3 with constitutive whole-cell currents, we show that TRPML is biphasically regulated by extracytosolic pH, with an optimal pH about 0.6 pH unit higher than that of human TRPML1. In addition to monovalent cations, TRPML exhibits high permeability to Ca2+, Mn2+, and Fe2+, but not Fe3+. The TRPML currents were inhibited by trivalent cations Fe3+, La3+, and Gd3+. These features resemble more closely to mammalian TRPML1 than TRPML2 and TRPML3, but with some obvious differences. Together, our data support the use of Drosophila for assessing functional significance of TRPML1 in cell physiology. PMID:24375408

  15. Supramolecular isomerism, framework flexibility, unsaturated metal center, and porous property of Ag(I)/Cu(I) 3,3',5,5'-tetrametyl-4,4'-bipyrazolate.

    PubMed

    Zhang, Jie-Peng; Kitagawa, Susumu

    2008-01-23

    Template-controlled reactions of 3,3',5,5'-tetramethyl-4,4'-bipyrazole (H2bpz) with [Ag(NH3)2]+ or [Cu(NH3)2]+ give binary metal bipyrazolates [M2(bpz)] (M = Ag, Cu) as two supramolecular isomers (1 and 2). Isomer 1 possesses four-fold interpenetrated (10,3)-a coordination networks, two-fold interpenetrated (10,3)-a channel networks, and guest-accessible coordinatively unsaturated metal clusters. Isomer 2 possesses eight-fold interpenetrated (6(2) x 10)(6 x 10(2)) coordination networks and isolated, small pores. These metal bipyrazolates are chemically stable and thermally stable up to 300-500 degrees C. Their exceptional framework flexibilities have been demonstrated by adsorption measurements and single-crystal diffraction analyses. The guest-accessible Ag(I)/Cu(I) UMC clusters have also been demonstrated to facilitate the accommodation of unsaturated hydrocarbons such as benzene, toluene, mesitylene, and acetylene via weak metal...pi interactions.

  16. Classification for animal vocal fold surgery: Resection margins impact histological outcomes of vocal fold injury

    PubMed Central

    Imaizumi, Mitsuyoshi; Thibeault, Susan L.; Leydon, Ciara

    2014-01-01

    Objective Extent of vocal fold injury impacts the nature and timing of wound healing, and voice outcomes. However, depth and extent of the lesion created to study wound healing in animal models vary across studies, likely contributing to different outcomes. Our goal was to create a surgery classification system to enable comparison of postoperative outcomes across animal vocal fold wound healing studies. Study design Prospective, controlled animal study. Methods Rats underwent one of three types of unilateral vocal fold surgeries classified by depth and length of resection. The surgeries were a subepithelial injury, resection of epithelium and superficial layer of the lamina propria at the midmembranous portion of the vocal fold; transmucosal injury, resection of epithelium and lamina propria; and transmuscular injury, resection of epithelium, lamina propria and superficial portion of the vocalis muscle Wound healing was evaluated histologically at various time points up to 35 days post-injury. Results Complete healing occurred by 14 days post-surgery for subepithelial injury and by day 35 for transmucosal injury. Injury remained present at day 35 for transmuscular injury. Conclusions Timing and completeness of healing varied by extent and depth of resection. Scarless healing occurred rapidly following subepithelial injury, while scarring was observed at five weeks after transmuscular injury. The proposed classification system may facilitate comparison of surgical outcomes across vocal fold wound healing studies. PMID:24965969

  17. Fungal infections of the folds (intertriginous areas).

    PubMed

    Metin, Ahmet; Dilek, Nursel; Demirseven, Duriye Deniz

    2015-01-01

    Superficial fungal infections are widespread, regardless of age and gender, in populations all around the world and may affect the skin and skin appendages. Although there are thousands of fungal infections from various genera and families in nature, those that are pathogenic for humans and nesting in skin folds are limited in number. The prevalence and distribution of these fungi vary according to the patients and certain environmental factors. Because the areas including the lids, external auditory canal, behind the ears, navel, inguinal region, and axillae, also called flexures, are underventilated and moist areas exposed to friction, they are especially sensitive to fungal infections. Fungi can both directly invade the skin, leading to infections, and indirectly stimulate immune mechanisms due to tissue interaction and their antigenic character and contribute to the development or exacerbation of secondary bacterial infections, seborrheic dermatitis, atopic dermatitis, and psoriasis. Superficial fungal infections can be classified and studied as dermatophyte infections, candidal infections, Malassezia infections, and other superficial infections independently from the involved skin fold areas. PMID:26051058

  18. The folding landscape of the epigenome

    NASA Astrophysics Data System (ADS)

    Olarte-Plata, Juan D.; Haddad, Noelle; Vaillant, Cédric; Jost, Daniel

    2016-04-01

    The role of the spatial organization of chromatin in gene regulation is a long-standing but still open question. Experimentally it has been shown that the genome is segmented into epigenomic chromatin domains that are organized into hierarchical sub-nuclear spatial compartments. However, whether this non-random spatial organization only reflects or indeed contributes—and how—to the regulation of genome function remains to be elucidated. To address this question, we recently proposed a quantitative description of the folding properties of the fly genome as a function of its epigenomic landscape using a polymer model with epigenomic-driven attractions. We propose in this article, to characterize more deeply the physical properties of the 3D epigenome folding. Using an efficient lattice version of the original block copolymer model, we study the structural and dynamical properties of chromatin and show that the size of epigenomic domains and asymmetries in sizes and in interaction strengths play a critical role in the chromatin organization. Finally, we discuss the biological implications of our findings. In particular, our predictions are quantitatively compatible with experimental data and suggest a different mean of self-interaction in euchromatin versus heterochromatin domains.

  19. Mesozoic folds, fossil fields, and future finds ( )

    SciTech Connect

    Newman, G.W.; Witter, G.G.

    1988-02-01

    Drilling and surface geologic mapping have shown that pre-Tertiary, post-Triassic folds and upthrusted anticlines in an eastern Nevada fold-belt have accumulated major oil columns. This Mesozoic foldbelt involves a Cambrian through Triassic section, which has hundreds of feet of porosity in Ordovician sandstones, Silurian and Devonian carbonates, and Mississippian sandstones. In addition to the Devonian Pilot and Mississippian Chainman shales, source rocks are found in Cambrian and Ordovician shales and in some Paleozoic carbonates. The occurrence of live and dead oil shows in hundreds of vertical feet of porosity in wells drilled on several of these Mesozoic structures is interpreted as evidence that these structures were giant oil fields prior to being breached by Tertiary Basin and Range extensional faulting, which allowed vertical hydrocarbon leakage. Noting that undrilled Mesozoic structures still exist in the foldbelt and noting that natural processes are seldom 100% efficient - including, probably, the disruptive effects of Basin and range extensional faulting - the authors suggest that there is a very good chance of finding one or more giant fields in the remaining structures of this foldbelt.

  20. Fold-A-Board communication device.

    PubMed

    Sokolowski, Joanna; Maher, Aedan; Jaycox, Katie; Siegler, Kevin

    2011-01-01

    Aphasia is an impairment of language resulting from stroke that can affect a person's ability to use and comprehend words. People who have aphasia often keep a writing device handy to write down information that they have trouble communicating verbally. Device options include expensive keyboard devices or more commonly small inexpensive notebooks. Neither of these options fits the needs of someone with communication problems and the use of only one hand. Our goal was to design a device that would allow persons with aphasia and use of one hand to be able to communicate more easily with others on a daily basis. The information gathered from the interviews and observations gave us direction in our design process. We determined that the device should be accessible with one hand, be small in size, have an erasable surface, and have a professional appearance. Our final design is the Fold-A-Board communication device. The Fold-A-Board communication device meets all the requirements for an easy-to-use writing device.

  1. FOURTEEN-DAY TOXICITY STUDY OF 1,3,5-TRINITROBENZENE IN FISCHER 344 RATS

    EPA Science Inventory

    Toxic effects of 1,3,5-trinitrobenzene (TNB) in male and female rats were evaluated by feeding powdered certified laboratory chow diet supplemented with varied concentrations of TNB (0,50,200,400,800 and 1200 mg kg-1 diet) for 14 days. Food intake by female rats in 400,800 and 12...

  2. DETERMINATION OF 3,5,6-TRICHLORO-2-PYRIDINOL (TCP) BY ELISA

    EPA Science Inventory

    A sensitive, competitive enzyme-linked immunosorbent assay (ELISA) for 3,5,6-trichloro-2pyridinol (TCP) has been developed to quantitate parts per billion (ppb) amounts of the analyte in urine. TCP is a major metabolite and environmental degradation product of the insecticide c...

  3. Evaluation of GALAXY Classroom Science for Grades 3-5. Final Report. Executive Summary.

    ERIC Educational Resources Information Center

    Guth, Gloria J. A.; Austin, Susan; DeLong, Bo; Pasta, David J.; Block, Clifford

    The GALAXY Classroom is a package of integrated curricular and instructional approaches, supported by the first U.S. interactive satellite communications network designed to facilitate the introduction of innovative curricula to improve student learning in elementary schools. GALAXY Classroom Science for grades 3-5 features the organization of…

  4. A Multiple-Data Analysis of the 3.5-Year Development of EFL Student Writers

    ERIC Educational Resources Information Center

    Sasaki, Miyuki

    2004-01-01

    The present study investigated the changes in Japanese students English writing behaviors over a 3.5-year period using multiple data sources including written texts, videotaped writing behaviors, and stimulated-recall protocols. Data from student interviews supplemented the analyses. Because 6 (henceforth, English as a second language [ESL]…

  5. Regioselective Glycosylation of 3-, 5-, 6-, and 7-Hydroxyflavones by Cultured Plant Cells.

    PubMed

    Shimoda, Kei; Kubota, Naoji; Uesugi, Daisuke; Fujitaka, Yuuya; Okada, Shouta; Tanigawa, Masato; Hamada, Hiroki

    2015-06-01

    Regioselective glycosylation of 3-, 5-, 6-, and 7-hydroxyflavones was investigated using cultured plant cells of Eucalyptus perriniana and Phytolacca americana as biocatalysts. 3- and 7-Hydroxyflavones were practically glycosylated into the corresponding β-D-glucosides by E. perriniana and P. americana.

  6. No Time for Tea (Grade Level: Elementary Grades, 3-5)

    ERIC Educational Resources Information Center

    Social Education, 2005

    2005-01-01

    Designed for Grades 3-5, this lesson plan aims to let the students learn how the Constitution of the United States provided the framework for the country's democratic form of government. Students will learn how the Constitution provided for representation within the government. A short story about the Boston Tea Party gives the background related…

  7. Spectral Properties of Clouds from 2.5 microto 3.5 micro.

    PubMed

    Blau, H H; Espinola, R P

    1968-10-01

    On the basis of simple models, the observed spectral reflectance properties of sunlit high altitude clouds in the 2.5-3.5-micro region are related, in decreasing order of importance, to the scattering properties of water droplets and ice crystals, absorption by ir active gases entrained within the cloud, and atmospheric transmission over the sun-cloud path.

  8. Smart Spending and Saving: Personal Finance Economics 3-5. Teacher Resource Manual. EconomicsAmerica.

    ERIC Educational Resources Information Center

    Haskell, Diana C.; Haskell, Douglas A.

    This book is designed to help students in grades 3-5 make better decisions as spenders, savers, borrowers, and managers of money. The learning experiences focus on personal finance and money management. The 10 lessons are divided into 4 units focusing on children making spending decisions, saving decisions, borrowing decisions, and money…

  9. Supporting English Language Learners in Math Class, Grades 3-5

    ERIC Educational Resources Information Center

    Bresser, Rusty; Melanese, Kathy; Sphar, Christine

    2009-01-01

    More than 10 percent of the students in our nation's public schools are English language learners, and this number grows each year. Many of these students are falling behind in math. "Supporting English Language Learners in Math Class, Grades 3-5" outlines the challenges ELL students face when learning math and provides a wealth of specific…

  10. A Fast Liquid Chromatography Tandem Mass Spectrometric Analysis of PETN (Pentaerythritol Tetranitrate), RDX (3,5-Trinitro-1,3,5-triazacyclohexane) and HMX (Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) in Soil, Utilizing a Simple Ultrasonic-Assisted Extraction with Minimum Solvent.

    PubMed

    Anilanmert, Beril; Aydin, Muhammet; Apak, Resat; Avci, Gülfidan Yenel; Cengiz, Salih

    2016-01-01

    Direct analyses of explosives in soil using liquid chromatography tandem mass spectrometry (LC-MS/MS) methods are very limited in the literature and require complex procedures or relatively high amount of solvent. A simple and rapid method was developed for the determination of pentaerythritol tetranitrate (PETN), 3,5-trinitro-1,3,5-triazacyclohexane (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), which are among the explosives used in terrorist attacks. A one-step extraction method for 1.00 g soil with 2.00 mL acetonitrile, and a 8-min LC-MS/MS method was developed. The detection limits for PETN, RDX and HMX were 5.2, 8.5 and 3.4 ng/g and quantitation limits were 10.0, 24.5, 6.0 ng/g. The intermediate precisions and Horwitz Ratio's were between 4.10 - 13.26% and 0.24 - 0.98, in order. This method was applied to a model post-blast debris collected from an artificial explosion and real samples collected after a terrorist attack in Istanbul. The method is easy and fast and requires less solvent use than other methods. PMID:27302580

  11. SUBCHRONIC TOXICITY OF 1,3,5-TRINITROBENZENE IN FISCHER 344 RATS

    EPA Science Inventory

    The subchronic toxicity of 1,3,5-trinitrobenzene (TNB) in male and female Fischer 344 rats was evaluated by feeding a powdered certified laboratory diet containing 0, 66.7, 400 and 800 mg TNB/kg diet for 90 days. The calculated average TNB intake was 4.29, 24.70, and 49.28 mg/kg...

  12. Earthwatch: Designing Environmental Education into the Curriculum. Volume I, Grades 3-5.

    ERIC Educational Resources Information Center

    Schaefer, Larry, Ed.; Hungerford, Nancy, Ed.

    This environmental education activities package for grades 3-5 contains activities in the following curriculum areas: (1) social science; (2) science; (3) language arts; and (4) mathematics. The activities are divided into seven sections based on seven environmental topics: (1) ecosystems; (2) population; (3) energy and resources; (4) economics,…

  13. Algebraic Reasoning: Professor Arbegla Introduces Variables and Functions. GEMS Teacher's Guide for Grades 3-5.

    ERIC Educational Resources Information Center

    Kopp, Jaine; Bergman, Lincoln

    This teacher guide helps build a solid foundation in algebra for students in grades 3-5 in which students gain essential understanding of properties of numbers, variables, functions, equations, and formulas. Throughout the problem solving activities, students use computational skills and gain a deeper understanding of the number system. Students…

  14. CHRONIC TOXICITY OF 1,3,5-TRINITROBENZENE IN FISCHER 344 RATS

    EPA Science Inventory

    The chronic toxicity of 1,3,5-trinitrobenzene (TNB) in male and female Fischer 344 (F344) rats was evaluated by feeding a diet containing 0, 5, 60 and 300 ppm of TNB for 2 years. The calculated average TNB intake over 2 years for males and females was 0.22, 2.64, 13.44 and 0.23,...

  15. Identification of distinct biological functions for four 3'-5' RNA polymerases.

    PubMed

    Long, Yicheng; Abad, Maria G; Olson, Erik D; Carrillo, Elisabeth Y; Jackman, Jane E

    2016-09-30

    The superfamily of 3'-5' polymerases synthesize RNA in the opposite direction to all other DNA/RNA polymerases, and its members include eukaryotic tRNA(His) guanylyltransferase (Thg1), as well as Thg1-like proteins (TLPs) of unknown function that are broadly distributed, with family members in all three domains of life. Dictyostelium discoideum encodes one Thg1 and three TLPs (DdiTLP2, DdiTLP3 and DdiTLP4). Here, we demonstrate that depletion of each of the genes results in a significant growth defect, and that each protein catalyzes a unique biological reaction, taking advantage of specialized biochemical properties. DdiTLP2 catalyzes a mitochondria-specific tRNA(His) maturation reaction, which is distinct from the tRNA(His) maturation reaction typically catalyzed by Thg1 enzymes on cytosolic tRNA. DdiTLP3 catalyzes tRNA repair during mitochondrial tRNA 5'-editing in vivo and in vitro, establishing template-dependent 3'-5' polymerase activity of TLPs as a bona fide biological activity for the first time since its unexpected discovery more than a decade ago. DdiTLP4 is cytosolic and, surprisingly, catalyzes robust 3'-5' polymerase activity on non-tRNA substrates, strongly implying further roles for TLP 3'-5' polymerases in eukaryotes.

  16. 3-Chlorotyrosine and 3,5-Dichlorotyrosine as biomarkers of respiratory tract exposure to chlorine gas

    EPA Science Inventory

    Modification of tyrosine by reactive chlorine can produce both 3-chlorotyrosine (CY) and 3,5-dichlorotyrosine (dCY). Both of these amino acids have proven to be promising biomarkers for assessing the extent of myeloperoxidase-catalyzed chlorine stress in a number of adverse physi...

  17. The Self-Assembly Properties of a Benzene-1,3,5-tricarboxamide Derivative

    ERIC Educational Resources Information Center

    Stals, Patrick J. M.; Haveman, Jan F.; Palmans, Anja R. A.; Schenning, Albertus P. H. J.

    2009-01-01

    A series of experiments involving the synthesis and characterization of a benzene-1,3,5-tricarboxamide derivative and its self-assembly properties are reported. These laboratory experiments combine organic synthesis, self-assembly, and physical characterization and are designed for upper-level undergraduate students to introduce the topic of…

  18. Investigation of Unexpected Reaction Intermediates in the Alkaline Hydrolysis of Methyl 3,5-Dinitrobenzoate

    ERIC Educational Resources Information Center

    Silva, Clesia C.; Silva, Ricardo O.; Navarro, Daniela M. A. F.; Navarro, Marcelo

    2009-01-01

    An experimental project aimed at identifying stable reaction intermediates is described. Initially, the studied reaction appears to involve the simple hydrolysis, by aqueous sodium hydroxide, of methyl 3,5-dinitrobenzoate dissolved in dimethyl sulfoxide. On mixing the substrates, however, the reaction mixture unexpectedly turns an intense red in…

  19. Preparation of 1,3,5-triamo-2,4,6-trinitrobenzene of submicron particle size

    DOEpatents

    Rigdon, Lester P.; Moody, Gordon L.; McGuire, Raymond R.

    2001-05-01

    A method is disclosed for the preparation of very small particle size, relatively pure 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Particles of TATB prepared according to the disclosed method are of submicron size and have a surface area in the range from about 3.8 to 27 square meters per gram.

  20. Preparation of 1,3,5-triamino-2,4,6-trinitrobenzene of submicron particle size

    DOEpatents

    Rigdon, Lester P.; Moody, Gordon L.; McGuire, Raymond R.

    2001-01-01

    A method is disclosed for the preparation of very small particle size, relatively pure 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Particles of TATB prepared according to the disclosed method are of submicron size and have a surface area in the range from about 3.8 to 27 square meters per gram.