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Sample records for 3-5 fold higher

  1. Polyketide folding in higher plants: biosynthesis of the phenylanthraquinone knipholone.

    PubMed

    Bringmann, Gerhard; Noll, Torsten F; Gulder, Tanja; Dreyer, Michael; Grüne, Matthias; Moskau, Detlef

    2007-04-27

    The biosynthesis of knipholone, as an axially chiral phenylanthraquinone, in higher plants was examined by feeding experiments with [13C2]-labeled precursors. [13C2]-Acetate and advanced synthetic intermediates were fed to sterile cultures of Kniphofia pumila (Asphodelaceae), with subsequent NMR analysis on the isolated natural product involving 2D INADEQUATE and SELINQUATE experiments. Due to its uneven number of carbon atoms, and because of its uncertain decarboxylation site, the "northern" part of the molecule (i.e., the chrysophanol portion) might originate from four different cyclization modes. According to the labeling pattern of the product isolated after incorporation, this anthraquinone part of knipholone is formed by the so-called F folding mode (originally established for fungi). The acetophenone part of the molecule, which does not undergo a decarboxylation reaction, originates from four acetate units. The surprising lack of randomization of the intact [13C2] units in this "southern" part reveals the absence of a free symmetric intermediate as initially anticipated. This is in agreement with the intact incorporation of the "authentic" southern molecular portion, 4,6-dihydroxy-2-methoxyacetophenone, while the corresponding symmetrical candidate trihydroxyacetophenone was clearly not incorporated, showing that the O-methylation of the freshly cyclized tetraketide is the step that prevents symmetrization of the acetophenone.

  2. 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.

  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. Periodic Folded Wave Patterns for (2+1)-Dimensional Higher-Order Broer Kaup Equation

    NASA Astrophysics Data System (ADS)

    Huang, Wen-Hua

    2008-10-01

    A general solution including three arbitrary functions is obtained for the (2+1)-dimensional higher-order Broer Kaup equation by means of WTC truncation method. Introducing proper multiple valued functions and Jacobi elliptic functions in the seed solution, special types of periodic folded waves are derived. In long wave limit these periodic folded wave patterns may degenerate into single localized folded solitary wave excitations. The interactions of the periodic folded waves and their degenerated single folded solitary waves are investigated graphically and are found to be completely elastic.

  5. 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

    2013-10-09

    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.

  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. MENT, a heterochromatin protein that mediates higher order chromatin folding, is a new serpin family member.

    PubMed

    Grigoryev, S A; Bednar, J; Woodcock, C L

    1999-02-26

    Terminal cell differentiation is correlated with the extensive sequestering of previously active genes into compact transcriptionally inert heterochromatin. In vertebrate blood cells, these changes can be traced to the accumulation of a developmentally regulated heterochromatin protein, MENT. Cryoelectron microscopy of chicken granulocyte chromatin, which is highly enriched with MENT, reveals exceptionally compact polynucleosomes, which maintain a level of higher order folding above that imposed by linker histones. The amino acid sequence of MENT reveals a close structural relationship with serpins, a large family of proteins known for their ability to undergo dramatic conformational transitions. Conservation of the "hinge region" consensus in MENT indicates that this ability is retained by the protein. MENT is distinguished from the other serpins by being a basic protein, containing several positively charged surface clusters, which are likely to be involved in ionic interactions with DNA. One of the positively charged domains bears a significant similarity to the chromatin binding region of nuclear lamina proteins and with the A.T-rich DNA-binding motif, which may account for the targeting of MENT to peripheral heterochromatin. MENT ectopically expressed in a mammalian cell line is transported into nuclei and is associated with intranuclear foci of condensed chromatin.

  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. Nucleosomes, Linker DNA, and Linker Histone form a Unique Structural Motif that Directs the Higher-Order Folding and Compaction of Chromatin

    NASA Astrophysics Data System (ADS)

    Bednar, Jan; Horowitz, Rachel A.; Grigoryev, Sergei A.; Carruthers, Lenny M.; Hansen, Jeffrey C.; Koster, Abraham J.; Woodcock, Christopher L.

    1998-11-01

    The compaction level of arrays of nucleosomes may be understood in terms of the balance between the self-repulsion of DNA (principally linker DNA) and countering factors including the ionic strength and composition of the medium, the highly basic N termini of the core histones, and linker histones. However, the structural principles that come into play during the transition from a loose chain of nucleosomes to a compact 30-nm chromatin fiber have been difficult to establish, and the arrangement of nucleosomes and linker DNA in condensed chromatin fibers has never been fully resolved. Based on images of the solution conformation of native chromatin and fully defined chromatin arrays obtained by electron cryomicroscopy, we report a linker histone-dependent architectural motif beyond the level of the nucleosome core particle that takes the form of a stem-like organization of the entering and exiting linker DNA segments. DNA completes ≈ 1.7 turns on the histone octamer in the presence and absence of linker histone. When linker histone is present, the two linker DNA segments become juxtaposed ≈ 8 nm from the nucleosome center and remain apposed for 3-5 nm before diverging. We propose that this stem motif directs the arrangement of nucleosomes and linker DNA within the chromatin fiber, establishing a unique three-dimensional zigzag folding pattern that is conserved during compaction. Such an arrangement with peripherally arranged nucleosomes and internal linker DNA segments is fully consistent with observations in intact nuclei and also allows dramatic changes in compaction level to occur without a concomitant change in topology.

  11. High sensitivity of an Ha-RAS transgenic model of superficial bladder cancer to metformin is associated with ~ 240-fold higher drug concentration in urine than serum

    PubMed Central

    Liu, Zhongbo; Yokoyama, Noriko N.; Blair, Chris A.; Li, Xuesen; Avizonis, Daina; Wu, Xue-Ru; Uchio, Edward; Youssef, Ramy; McClelland, Michael; Pollak, Michael; Zi, Xiaolin

    2016-01-01

    While pharmacoepidemiologic and laboratory studies have supported the hypothesis that the anti-diabetic drug metformin may be useful in treating or preventing cancer, there is limited evidence to suggest which specific cancer sites may be particularly sensitive. Sensitivity likely is determined both by features of tumor pathophysiology and by pharmacokinetic factors. We used UPII mutant Ha-ras transgenic mice that develop hyperplasia and low-grade, papillary urothelial cell carcinoma to determine if metformin has activity in a model of superficial bladder cancer. Metformin significantly improved survival, reduced urinary tract obstruction, reduced bladder weight (a surrogate for tumor volume) and led to clear activation of AMP α kinase and inhibition of mTOR signaling in neoplastic tissue. We investigated the basis of the unusual sensitivity of this model to metformin, and observed that following oral dosing, urothelium is exposed to drug concentrations via the urine that are ~ 240 fold higher than those in the circulation. In addition, we observed that bladder cancer cell lines (RT4, UMUC-3 and J82) with homozygous deletion of either TSC1 or PTEN are more sensitive to metformin than those (TEU2, TCCSUP and HT1376) with wild-type TSC1 and PTEN genes. Our findings provide a strong rationale for clinical trials of oral metformin in treatment of superficial bladder cancer. PMID:26921394

  12. 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

  13. Folding of apominimyoglobin.

    PubMed Central

    De Sanctis, G; Ascoli, F; Brunori, M

    1994-01-01

    The acid unfolding pathway of apominimyoglobin (apo-mini-Mb), a 108-aa fragment (aa 32-139) of horse heart apomyoglobin has been studied by means of circular dichroism, in comparison with the native apoprotein. Similar to sperm whale apomyoglobin [Hughson, F. M., Wright, P. E. & Baldwin, R. L. (1990) Science 249, 1544-1548], a partly folded intermediate (alpha-helical content approximately 35%) is populated at pH 4.2 for horse heart apomyoglobin. For this intermediate, Hughson et al. proposed a structural model with a compact subdomain involving tertiary interactions between the folded A, G, and H helices, with the remainder of the protein essentially unfolded. As described in this paper, a folding intermediate with an alpha-helical content of approximately 33% is populated at pH 4.3-5.0 also in apo-mini-Mb. The acid unfolding pathway is similarly affected in both the native and the mini apoprotein by 15% trifluoroethanol, a helix-stabilizing compound. Thus, the folding of the apo-mini-Mb intermediate is similar to that observed for the native apoprotein, in spite of the absence in the miniprotein of the A helix and of a large part of the H helix, which are crucial for the stability of apo-Mb intermediate. Our results suggest that acquisition of a folded state in apo-mini-Mb occurs through an alternative pathway, which may or may not be shared also by apo-Mb. PMID:7972092

  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. 12 CFR 3.5 - Applicability.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... written agreement or a temporary or final order pursuant to 12 U.S.C. 1818 (b) or (c), or as a condition... 12 Banks and Banking 1 2011-01-01 2011-01-01 false Applicability. 3.5 Section 3.5 Banks and... Office determines, pursuant to the procedures set forth in subpart C, that different minimum...

  16. 12 CFR 3.5 - Applicability.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... written agreement or a temporary or final order pursuant to 12 U.S.C. 1818 (b) or (c), or as a condition... 12 Banks and Banking 1 2013-01-01 2013-01-01 false Applicability. 3.5 Section 3.5 Banks and... Office determines, pursuant to the procedures set forth in subpart C, that different minimum...

  17. Your Child's Development: 3-5 Days

    MedlinePlus

    ... Feeding Your 1- to 2-Year-Old Your Child’s Development: 3-5 Days KidsHealth > For Parents > Your Child’s Development: 3-5 Days A A A Though only ... the sole of the foot Social and Emotional Development soothed by a ... When to Talk to Your Doctor Every child develops at his or her own pace, but ...

  18. Your Child's Development: 3-5 Days

    MedlinePlus

    ... Feeding Your 1- to 2-Year-Old Your Child’s Development: 3-5 Days KidsHealth > For Parents > Your Child’s Development: 3-5 Days Print A A A en ... the sole of the foot Social and Emotional Development soothed by a ... When to Talk to Your Doctor Every child develops at his or her own pace, but ...

  19. Mechanics of Curved Folds

    NASA Astrophysics Data System (ADS)

    Dias, Marcelo A.; Santangelo, Christian D.

    2011-03-01

    Despite an almost two thousand year history, origami, the art of folding paper, remains a challenge both artistically and scientifically. Traditionally, origami is practiced by folding along straight creases. A whole new set of shapes can be explored, however, if, instead of straight creases, one folds along arbitrary curves. We present a mechanical model for curved fold origami in which the energy of a plastically-deformed crease is balanced by the bending energy of developable regions on either side of the crease. Though geometry requires that a sheet buckle when folded along a closed curve, its shape depends on the elasticity of the sheet. NSF DMR-0846582.

  20. 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.

  1. Synthesis of deoxyribonucleotidyl(3'5')arabinonucleosides

    SciTech Connect

    Gray, S.H.; Ainsworth, C.F.; Bell, C.L.; Danyluk, S.S.; MacCoss, M.

    1983-01-01

    Two different synthetic routes using phosphotriester methodology have been utilized to prepare deoxyribonucleotidyl(3'-5)arabinonucleosides containing 9-..beta..-D-arabinofuranosyladenine (ara-A vidarabine) and 1-..beta..-D-arabinofuranosylcytosine (ara-C, cytarabine) at the 3'-terminus in amounts and purity (greater than 95%) suitable for NMR analysis.

  2. 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…

  3. 12 CFR 3.5 - Applicability.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY MINIMUM CAPITAL RATIOS; ISSUANCE OF DIRECTIVES Minimum Capital Ratios § 3.5 Applicability. This subpart is applicable to all banks unless the... ratios are appropriate for an individual bank based upon its particular circumstances, or...

  4. 12 CFR 3.5 - Applicability.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY MINIMUM CAPITAL RATIOS; ISSUANCE OF DIRECTIVES Minimum Capital Ratios § 3.5 Applicability. This subpart is applicable to all banks unless the... ratios are appropriate for an individual bank based upon its particular circumstances, or...

  5. Elbow Synovial Fold Syndrome

    DTIC Science & Technology

    2007-12-01

    Density MR with arrows The clinical differential diagnosis of plica syndrome includes lateral epicondylitis (aka tennis elbow ), loose bodies... Elbow Synovial Fold Syndrome Radiology Corner Elbow Synovial Fold Syndrome Guarantor: CPT Amit Sanghi, USA, MC FS Contributors: CPT Amit...the case of a 17 year old female with elbow synovial fold syndrome (aka plica synovialis). The etiology is thought to be related to repetitive

  6. 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

  7. A galaxy of folds

    PubMed Central

    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

  8. 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.

  9. 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

  10. 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

  11. Dermal Sensitization of 1-Acetyloctahydro-3,5,7-Trinitro-1,3,5,7-Tetrazocine.

    DTIC Science & Technology

    1984-08-08

    tetrazocine (SEX) in guinea pigs MATERIALS Test Substance Chemical name: 1-Acetyloctahydro-3,5,7-Trinitro-I,3,5,7- Tetrazocine (SEX) Chemical Abstract Service...exist as a contaminant in P.DX/HMX manufacturing process. The characteristics of SEX are as follows: Chemical Abstract Service Registry No.: 13980-00-2

  12. 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

  13. Biodegradation of hexahydro-1,3,5-trinitro-1,3,5-triazine

    SciTech Connect

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

    1981-11-01

    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-dimethylhydrazine, 1,2-dimethylhydrazine, formaldehyde, and methanol. A scheme for the biodegradation of RDX is poposed 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.

  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. [Effects of 3,5-dimethylpyrazole phosphate (DMPZP) on soil nitrification].

    PubMed

    Shi, Yun-feng; Wu, Zhi-jie; Chen, Li-jun; Sun, Zhi-mei

    2007-05-01

    With aerobic incubation test, this paper studied the effects of 3,5-dimethylpyrazole phosphate (DMPZP) on soil nitrification, taking dicyandiamide (DCD) as reference. The results indicated that when the dosage was 1.0% of applied N, DMPZP could significantly inhibit the oxidation of soil ammonium, increase soil NH4+ -N concentration, and decrease soil NO3- -N concentration. The inhibitory effect of DMPZP increased with its increasing dosage. DCD showed a higher efficacy when its dosage was the same with DMPZP, but a lower efficacy when the DMPZP was applied two-fold. However, the efficacy of equimolar DMPZP was significantly higher than that of DCD, because of the smaller molecular weight of DCD. The highest inhibitory effect of DMPZP was observed during the period of 7-14 days after its application, with an inhibition rate higher than 30%. Compared with the control, the apparent inhibition rate was decreased by 29.3% and 41.7% on the 7th day, and by 18.6% and 34.3% on the 14th day when the application rate of DMPZP was 1.0% and 2.0% of applied N, respectively. DMPZP could also slow down the falling rate of soil pH, but no significant difference was observed between the treatments of applying DMPZP and DCD.

  16. Folding of polyglutamine chains

    NASA Astrophysics Data System (ADS)

    Chopra, Manan; Reddy, Allam S.; Abbott, N. L.; de Pablo, J. J.

    2008-10-01

    Long polyglutamine chains have been associated with a number of neurodegenerative diseases. These include Huntington's disease, where expanded polyglutamine (PolyQ) sequences longer than 36 residues are correlated with the onset of symptoms. In this paper we study the folding pathway of a 54-residue PolyQ chain into a β-helical structure. Transition path sampling Monte Carlo simulations are used to generate unbiased reactive pathways between unfolded configurations and the folded β-helical structure of the polyglutamine chain. The folding process is examined in both explicit water and an implicit solvent. Both models reveal that the formation of a few critical contacts is necessary and sufficient for the molecule to fold. Once the primary contacts are formed, the fate of the protein is sealed and it is largely committed to fold. We find that, consistent with emerging hypotheses about PolyQ aggregation, a stable β-helical structure could serve as the nucleus for subsequent polymerization of amyloid fibrils. Our results indicate that PolyQ sequences shorter than 36 residues cannot form that nucleus, and it is also shown that specific mutations inferred from an analysis of the simulated folding pathway exacerbate its stability.

  17. Structural features of protein folding nuclei.

    PubMed

    Garbuzynskiy, S O; Kondratova, M S

    2008-03-05

    A crucial event of protein folding is the formation of a folding nucleus. We demonstrate the presence of a considerable coincidence between the location of folding nuclei and the location of so-called "root structural motifs", which have unique overall folds and handedness. In the case of proteins with a single root structural motif, the involvement in the formation of a folding nucleus is in average significantly higher for amino acids residues that are in root structural motifs, compared to residues in other parts of the protein. The tests carried out revealed that the observed difference is statistically reliable. Thus, a structural feature that corresponds to the protein folding nucleus is now found.

  18. Programmable matter by folding

    PubMed Central

    Hawkes, E.; An, B.; Benbernou, N. M.; Tanaka, H.; Kim, S.; Demaine, E. D.; Rus, D.; Wood, R. J.

    2010-01-01

    Programmable matter is a material whose properties can be programmed to achieve specific shapes or stiffnesses upon command. This concept requires constituent elements to interact and rearrange intelligently in order to meet the goal. This paper considers achieving programmable sheets that can form themselves in different shapes autonomously by folding. Past approaches to creating transforming machines have been limited by the small feature sizes, the large number of components, and the associated complexity of communication among the units. We seek to mitigate these difficulties through the unique concept of self-folding origami with universal crease patterns. This approach exploits a single sheet composed of interconnected triangular sections. The sheet is able to fold into a set of predetermined shapes using embedded actuation. To implement this self-folding origami concept, we have developed a scalable end-to-end planning and fabrication process. Given a set of desired objects, the system computes an optimized design for a single sheet and multiple controllers to achieve each of the desired objects. The material, called programmable matter by folding, is an example of a system capable of achieving multiple shapes for multiple functions. PMID:20616049

  19. The longstanding challenge of the nanocrystallization of 1,3,5-trinitroperhydro-1,3,5-triazine (RDX)

    PubMed Central

    Spitzer, Denis

    2017-01-01

    Research efforts for realizing safer and higher performance energetic materials are continuing unabated all over the globe. While the thermites – pyrotechnic compositions of an oxide and a metal – have been finely tailored thanks to progress in other sectors, organic high explosives are still stagnating. The most symptomatic example is the longstanding challenge of the nanocrystallization of 1,3,5-trinitroperhydro-1,3,5-triazine (RDX). Recent advances in crystallization processes and milling technology mark the beginning of a new area which will hopefully lead the pyroelectric industry to finally embrace nanotechnology. This work reviews the previous and current techniques used to crystallize RDX at a submicrometer scale or smaller. Several key points are highlighted then discussed, such as the smallest particle size and its morphology, and the scale-up capacity and the versatility of the process. PMID:28326236

  20. 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

  1. IRIS Toxicological Review of Hexahydro-1,3,5-Trinitro-1,3,5 ...

    EPA Pesticide Factsheets

    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 supporting the RDX assessment and release a final report of their review. Information regarding the peer review can be found on the SAB website. EPA is undertaking an update of the Integrated Risk Information System (IRIS) health assessment for RDX. The outcome of this project is an updated Toxicological Review and IRIS Summary for RDX that will be entered into the IRIS database.

  2. 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.

  3. 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…

  4. Biodegradation of 1,3,5-trinitro-1,3,5-triazine (RDX).

    PubMed

    Lee, Sheng-Yih; Brodman, Bruce W

    2004-01-01

    Two bacteria were isolated from 1,3,5-trinitro-1,3,5-triazine (RDX) contaminated soil at Picatinny Arsenal, New Jersey. These organisms were subsequently identified as Rhiziobium rhizogenes BL and Burkholderia sp.BL by the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ, German Collection of Microorganisms and Cell Cultures). In addition a fungus, identified as Cladosporium cladosporioides by DSMZ, was found to be growing on water wet RDX. All of these organisms were found to degrade RDX. The two bacteria were found to represent new species that have not been reported before. It was found that these organisms along with an added carbon source could degrade RDX to simple gaseous products. Data are presented that elucidate the mechanisms of RDX biodegradation for these organisms.

  5. 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.

  6. 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.

  7. 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)

  8. 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.

  9. Ab initio RNA folding.

    PubMed

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-17

    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.

  10. Geometric formalism for DNA quadruplex folding.

    PubMed

    Webba da Silva, Mateus

    2007-01-01

    Understanding the control of self-assembly and stereochemical properties of DNA higher order architectural folds is of fundamental importance in biology as well as biochemical technological applications. Guanine-rich DNA sequences can form tetrahelical architectures termed quadruplexes. A formalism is presented describing the interdependency of a set of structural descriptors as a geometric basis for folding of unimolecular quadruplex topologies. It represents a standard for interpretation of structural characteristics of quadruplexes, and is comprehensive in explicitly harmonizing the results of published literature with a unified language. The formalism is a fundamental step towards prediction of unimolecular quadruplex folding topologies from primary sequence.

  11. 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.

  12. 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.

  13. Information from folds: A review

    NASA Astrophysics Data System (ADS)

    Hudleston, Peter J.; Treagus, Susan H.

    2010-12-01

    Folds are spectacular geological structures that are seen in layered rock on many different scales. To mark 30 years of the Journal of Structural Geology, we review the information that can be gained from studies of folds in theory, experiment and nature. We first review theoretical considerations and modeling, from classical approaches to current developments. The subject is dominated by single-layer fold theory, with the assumption of perfect layer-parallel shortening, but we also review multilayer fold theory and modeling, and folding of layers that are oblique to principal stresses and strains. This work demonstrates that viscosity ratio, degree of non-linearity of the flow law, anisotropy, and the thickness and spacing distribution of layers of different competence are all important in determining the nature and strength of the folding instability. Theory and modeling provide the basis for obtaining rheological information from natural folds, through analysis of wavelength/thickness ratios of single layer folds, and fold shapes. They also provide a basis for estimating the bulk strain from folded layers. Information about folding mechanisms can be obtained by analysis of cleavage and fabric patterns in folded rocks, and the history of deformation can be revealed by understanding how asymmetry can develop in folds, by how folds develop in shear zones, and how folds develop in more complex three-dimensional deformations.

  14. Folding above faults, Rocky Mountains

    SciTech Connect

    McConnell, D.A. . Dept. of Geology)

    1992-01-01

    Asymmetric folds formed above basement faults can be observed throughout the Rocky Mountains. Several previous interpretations of the folding process made the implicit assumption that one or both fold hinges migrated or rolled'' through the steep forelimb of the fold as the structure evolved (rolling hinge model). Results of mapping in the Bighorn and Seminoe Mountains, WY, and Sangre de Cristo Range, CO, do not support this hypothesis. An alternative interpretation is presented in which fold hinges remained fixed in position during folding (fixed hinge model). Mapped folds share common characteristics: (1) axial traces of the folds intersect faults at or near the basement/cover interface, and diverge from faults upsection; (2) fold hinges are narrow and interlimb angles cluster around 80--100[degree] regardless of fold location; (3) fold shape is typically angular, despite published cross sections that show concentric folds; and, (4) beds within the folds show thickening and/or thinning, most commonly adjacent to fold hinges. The rolling hinge model requires that rocks in the fold forelimbs bend through narrow fold hinges as deformation progressed. Examination of massive, competent rock units such as the Ord. Bighorn Dolomite, Miss. Madison Limestone, and, Penn. Tensleep Sandstone reveals no evidence of the extensive internal deformation that would be expected if hinges rolled through rocks of the forelimb. The hinges of some folds (e.g. Golf Creek anticline, Bighorn Mountains) are offset by secondary faults, effectively preventing the passage of rocks from backlimb to forelimb. The fixed hinge model proposes that the fold hinges were defined early in fold evolution, and beds were progressively rotated and steepened as the structure grew.

  15. 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.

  16. Folds on Europa

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This image, acquired by NASA's Galileo spacecraft on September 26, 1998, shows features on the surface of Jupiter's moon Europa that a scientific report published today interprets as signs of compressive folding.

    The imaged area is in the Astypalaea Linea region of Europa's southern hemisphere, seen with low-angle sunshine coming from the upper right. North is toward the top.

    Astypalaea Linea is the smooth, gray area that stretches from north to south across the image mosaic. It is thought to have formed by a combination of pulling apart and sliding of the icy surface. The telltale fold features are within the smoother portions of the surface between the more dominant ridges, which are attributed to upwelling of material through surface ice. In the smooth areas, the surface has gentle swells and dips, which show most clearly in the version on the right, processed to accentuate broader-scale shapes. For example, a dip about 15 kilometers (about 10 miles) wide cuts diagonally across the northern half of the largest smooth area, and a rise runs parallel to that in the southern half of the smooth area. closeup detail

    Louise M. Prockter, at Johns Hopkins University, and Robert T. Pappalardo, at Brown University, report in the journal Science today that those rises, or anticlines, and dips, or synclines, appear to be the result of compression causing the crust to fold.

    Additional evidence comes from smaller features more visible in the version on the left, covering the same area. At the crest of the gentle rise in the largest smooth area are small fractures that could be caused by the stretching stress of bending the surface layer upwards. Similarly, at the bottom of the adjacent dip are small, wrinkle-like ridges that could be caused by stress from bending the surface layer downwards.

    The Jet Propulsion Laboratory, Pasadena, Calif., manages the Galileo mission for NASA's Office of Space Science, Washington, D.C. JPL is a division of the California

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

    DOEpatents

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

    DOEpatents

    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.

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

    DOEpatents

    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.

  20. Separation of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane and 1,3,5-trinitro-1,3,5- triazacyclohexane by molecularly imprinted solid-phase extraction.

    PubMed

    Wang, Jian; Meng, Zi-Hui; Xue, Min; Qiu, Li-Li; Zhang, Chen-Fan

    2017-03-01

    Synthesis of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane and 1,3,5-trinitro-1,3,5-triazacyclohexane by the Bachmann process leads to a mixture of both. The separation of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane and 1,3,5-trinitro-1,3,5-triazacyclohexane from their mixture is difficult because the sizes and physical properties of these homologous compounds are similar. For this purpose, seven molecularly imprinted polymers have been synthesized for each explosive, and a selective solid-phase extraction procedure has been developed. A molecularly imprinted polymer, synthesized with 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane as the template, methacrylic acid as the monomer and trimethylolpropane trimethacrylate as the cross-linking agent in a molar ratio of 1:8:8 showed the best separation capability. A packed cartridge containing this polymer can be reused for 23 solid-phase extraction cycles without repacking, and the total separation capability toward 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane reached 6.81 mg per gram of polymer. 1,3,5-Trinitro-1,3,5-triazacyclohexane was not detected in the separated 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane by high-performance liquid chromatography and vice versa. This newly developed method had the advantages of high recovery (100%) and purity, environmental friendliness, and room temperature operability. This study showed that some molecularly imprinted polymers that cannot absorb target analytes well in the solvent in which the polymers were polymerized might have high-binding capacity for the analytes and show imprinting effects in other solvents.

  1. 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

  2. 45 CFR 1210.3-5 - Preparation for appeal.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false Preparation for appeal. 1210.3-5 Section 1210.3-5... Termination § 1210.3-5 Preparation for appeal. (a) Entitlement to Representation. A Volunteer may be... because of conflict of position. (b) Time for Preparation and Presentation. (1) A...

  3. 45 CFR 1210.3-5 - Preparation for appeal.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 4 2012-10-01 2012-10-01 false Preparation for appeal. 1210.3-5 Section 1210.3-5... Termination § 1210.3-5 Preparation for appeal. (a) Entitlement to Representation. A Volunteer may be... because of conflict of position. (b) Time for Preparation and Presentation. (1) A...

  4. 45 CFR 1210.3-5 - Preparation for appeal.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 4 2013-10-01 2013-10-01 false Preparation for appeal. 1210.3-5 Section 1210.3-5... Termination § 1210.3-5 Preparation for appeal. (a) Entitlement to Representation. A Volunteer may be... because of conflict of position. (b) Time for Preparation and Presentation. (1) A...

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

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 4 2011-10-01 2011-10-01 false Preparation for appeal. 1210.3-5 Section 1210.3-5 Public Welfare Regulations Relating to Public Welfare (Continued) CORPORATION FOR NATIONAL AND COMMUNITY SERVICE VISTA TRAINEE DESELECTION AND VOLUNTEER EARLY TERMINATION PROCEDURES VISTA Volunteer Early Termination § 1210.3-5 Preparation for...

  6. 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.

  7. Cosubstrate independent mineralization of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by a Desulfovibrio species under anaerobic conditions.

    PubMed

    Arnett, Clint M; Adrian, Neal R

    2009-02-01

    Past handling practices associated with the manufacturing and processing of the high explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has resulted in extensive environmental contamination. In-situ biodegradation is a promising technology for remediating RDX contaminated sites but often relies on the addition of a cosubstrate. A sulfate-reducing bacterium isolated from an RDX-degrading enrichment culture was studied for its ability to grow on RDX as a sole source of carbon and nitrogen and for its ability to mineralize RDX in the absence of a cosubstrate. The results showed the isolate degraded 140 muM RDX in 63 days when grown on RDX as a carbon source. Biomass within the carbon limited culture increased 9-fold compared to the RDX unamended controls. When the isolate was incubated with RDX as sole source of nitrogen it degraded 160 muM RDX in 41 days and exhibited a 4-fold increase in biomass compared to RDX unamended controls. Radiolabeled studies under carbon limiting conditions with (14)C-hexahydro-1,3,5-trinitro-1,3,5-triazine confirmed mineralization of the cyclic nitramine. After 60 days incubation 26% of the radiolabel was recovered as (14)CO(2), while in the control bottles less than 1% of the radiolabel was recovered as (14)CO(2). Additionally, approximately 2% of the radiolabeled carbon was found to be associated with the biomass. The 16S rDNA gene was sequenced and identified the isolate as a novel species of Desulfovibrio, having a 95.1% sequence similarity to Desulfovibrio desulfuricans. This is the first known anaerobic bacterium capable of mineralizing RDX when using it as a carbon and energy source for growth.

  8. Folded dielectric elastomer actuators

    NASA Astrophysics Data System (ADS)

    Carpi, Federico; Salaris, Claudio; DeRossi, Danilo

    2007-04-01

    Polymer-based linear actuators with contractile ability are currently demanded for several types of applications. Within the class of dielectric elastomer actuators, two basic configurations are available today for such a purpose: the multi-layer stack and the helical structure. The first consists of several layers of elementary planar actuators stacked in series mechanically and parallel electrically. The second configuration relies on a couple of helical compliant electrodes alternated with a couple of helical dielectrics. The fabrication of both these configurations presents some specific drawbacks today, arising from the peculiarity of each structure. Accordingly, the availability of simpler solutions may boost the short-term use of contractile actuators in practical applications. For this purpose, a new configuration is here described. It consists of a monolithic structure made of an electroded sheet, which is folded up and compacted. The resulting device is functionally equivalent to a multi-layer stack with interdigitated electrodes. However, with respect to a stack the new configuration is advantageously not discontinuous and can be manufactured in one single phase, avoiding layer-by-layer multi-step procedures. The development and preliminary testing of prototype samples of this new actuator made of a silicone elastomer are presented here.

  9. 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.

  10. Cortical Folding Patterns and Predicting Cytoarchitecture

    PubMed Central

    Rajendran, Niranjini; Busa, Evelina; Augustinack, Jean; Hinds, Oliver; Yeo, B.T. Thomas; Mohlberg, Hartmut; Amunts, Katrin; Zilles, Karl

    2008-01-01

    The human cerebral cortex is made up of a mosaic of structural areas, frequently referred to as Brodmann areas (BAs). Despite the widespread use of cortical folding patterns to perform ad hoc estimations of the locations of the BAs, little is understood regarding 1) how variable the position of a given BA is with respect to the folds, 2) whether the location of some BAs is more variable than others, and 3) whether the variability is related to the level of a BA in a putative cortical hierarchy. We use whole-brain histology of 10 postmortem human brains and surface-based analysis to test how well the folds predict the locations of the BAs. We show that higher order cortical areas exhibit more variability than primary and secondary areas and that the folds are much better predictors of the BAs than had been previously thought. These results further highlight the significance of cortical folding patterns and suggest a common mechanism for the development of the folds and the cytoarchitectonic fields. PMID:18079129

  11. Predicting protein folds with fold-specific PSSM libraries.

    PubMed

    Hong, Yoojin; Chintapalli, Sree Vamsee; Ko, Kyung Dae; Bhardwaj, Gaurav; Zhang, Zhenhai; van Rossum, Damian; Patterson, Randen L

    2011-01-01

    Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies. Herein, we outline an effective method for fold recognition using sets of PSSMs, each of which is constructed for different protein folds. Our analyses demonstrate that FSL (Fold-specific Position Specific Scoring Matrix Libraries) can predict/relate structures given only their amino acid sequences of highly divergent proteins. This ability to detect distant relationships is dependent on low-identity sequence alignments obtained from FSL. Results from our experiments demonstrate that FSL perform well in recognizing folds from the "twilight-zone" SABmark dataset. Further, this method is capable of accurate fold prediction in newly determined structures. We suggest that by building complete PSSM libraries for all unique folds within the Protein Database (PDB), FSL can be used to rapidly and reliably annotate a large subset of protein folds at proteomic level. The related programs and fold-specific PSSMs for our FSL are publicly available at: http://ccp.psu.edu/download/FSLv1.0/.

  12. Evolutionary Optimization of Protein Folding

    PubMed Central

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

    2013-01-01

    Nature has shaped the make up of proteins since their appearance, 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 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

  13. Computational analysis of hydrogenated graphyne folding

    NASA Astrophysics Data System (ADS)

    Lenear, Christopher; Becton, Matthew; Wang, Xianqiao

    2016-02-01

    This letter employs molecular mechanics simulations to analyze the geometric changes of foreign-atom-doped graphyne. Simulation results show that higher the density of dopant and the greater area covered by the dopant correlates to a greater folding angle of the graphyne sheet. Compared to graphene, graphyne folding could prove to be more effective for various nanodevices based on its unique band gap, especially when doped, and its tunable interactions with and absorption of foreign molecules. Therefore, our findings may offer unique perspectives into the development of novel graphyne-based nanodevices and stimulate the community's research interest in graphene-related origami.

  14. Detachment folding, fold amplification, and diapirism in thrust wedge experiments

    NASA Astrophysics Data System (ADS)

    Bonini, Marco

    2003-12-01

    The relations between detachment folding, fold amplification, and salt diapirism in contractional settings have been investigated by means of scaled analogue models. The viscosity of the silicone layer simulating salt in nature and the shortening rates were combined in order to reproduce weak (type 1 models) and strong (type 2 models) décollements. Deformation patterns in the roof sequence exhibited two contrasting styles, (1) outward propagation of detachment folding along the décollement (OFP mode) and (2) passive roof duplex (PRD mode). In type 2 models, detachment folding propagated away from the most external thrust in the floor sequence, while in type 1 models, long-lived detachment folds almost invariably localized amplified above a floor thrust tip as a result of strain localization. A silicone wall intruded occasionally into the crestal graben of detachment folds in type 1 and OFP models. Best fitting of transition models data points indicates nonlinear relations with regression curves close to the equilateral hyperbola equation for both OFP-PRD and amplified detachment folds-box folds transitions. A quantitative comparison of model results with nature has been attempted by plotting salt-based fold-and-thrust belts data points on the scaled transition curves obtained from the modeling. Such a comparison relates shear stress products and ratios to the conditions favoring the amplification of detachment folds and the potential emplacement of ductile diapirs in their core. By reducing the roof sequence strength, pore fluid pressure λb is inferred to shift the equilibrium of fold-and-thrust belts toward the field of OFP and diapirism.

  15. 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.

  16. 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.

  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. 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

  19. 43 CFR 4120.3-5 - Assignment of range improvements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false Assignment of range improvements. 4120.3-5... MANAGEMENT, DEPARTMENT OF THE INTERIOR RANGE MANAGEMENT (4000) GRAZING ADMINISTRATION-EXCLUSIVE OF ALASKA Grazing Management § 4120.3-5 Assignment of range improvements. The authorized officer shall not...

  20. 43 CFR 4120.3-5 - Assignment of range improvements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Assignment of range improvements. 4120.3-5... MANAGEMENT, DEPARTMENT OF THE INTERIOR RANGE MANAGEMENT (4000) GRAZING ADMINISTRATION-EXCLUSIVE OF ALASKA Grazing Management § 4120.3-5 Assignment of range improvements. The authorized officer shall not...

  1. 43 CFR 4120.3-5 - Assignment of range improvements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 2 2012-10-01 2012-10-01 false Assignment of range improvements. 4120.3-5... MANAGEMENT, DEPARTMENT OF THE INTERIOR RANGE MANAGEMENT (4000) GRAZING ADMINISTRATION-EXCLUSIVE OF ALASKA Grazing Management § 4120.3-5 Assignment of range improvements. The authorized officer shall not...

  2. 43 CFR 4120.3-5 - Assignment of range improvements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false Assignment of range improvements. 4120.3-5... MANAGEMENT, DEPARTMENT OF THE INTERIOR RANGE MANAGEMENT (4000) GRAZING ADMINISTRATION-EXCLUSIVE OF ALASKA Grazing Management § 4120.3-5 Assignment of range improvements. The authorized officer shall not...

  3. 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 9269.3-5 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;...

  4. 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;...

  5. 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;...

  6. 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;...

  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. Changes of protein stiffness during folding detect protein folding intermediates.

    PubMed

    Małek, Katarzyna E; Szoszkiewicz, Robert

    2014-01-01

    Single-molecule force-quench atomic force microscopy (FQ-AFM) is used to detect folding intermediates of a simple protein by detecting changes of molecular stiffness of the protein during its folding process. Those stiffness changes are obtained from shape and peaks of an autocorrelation of fluctuations in end-to-end length of the folding molecule. The results are supported by predictions of the equipartition theorem and agree with existing Langevin dynamics simulations of a simplified model of a protein folding. In the light of the Langevin simulations the experimental data probe an ensemble of random-coiled collapsed states of the protein, which are present both in the force-quench and thermal-quench folding pathways.

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

    PubMed Central

    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

    2014-01-01

    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. PMID:24692290

  10. 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

  11. How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway.

    PubMed

    Dyson, H Jane; Wright, Peter E

    2017-01-17

    Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (∼2 s) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ∼ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the

  12. 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.

  13. 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...

  14. 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...

  15. 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...

  16. 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…

  17. How do chaperonins fold protein?

    PubMed Central

    Motojima, Fumihiro

    2015-01-01

    Protein folding is a biological process that is essential for the proper functioning of proteins in all living organisms. In cells, many proteins require the assistance of molecular chaperones for their folding. Chaperonins belong to a class of molecular chaperones that have been extensively studied. However, the mechanism by which a chaperonin mediates the folding of proteins is still controversial. Denatured proteins are folded in the closed chaperonin cage, leading to the assumption that denatured proteins are completely encapsulated inside the chaperonin cage. In contrast to the assumption, we recently found that denatured protein interacts with hydrophobic residues at the subunit interfaces of the chaperonin, and partially protrude out of the cage. In this review, we will explain our recent results and introduce our model for the mechanism by which chaperonins accelerate protein folding, in view of recent findings. PMID:27493521

  18. Enhanced extraction of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in the presence of sodium dodecyl sulphate and its application to environmental samples.

    PubMed

    Guarav; Malik, Ashok Kumar; Rai, Pramod Kumar

    2008-08-01

    A method for enhanced extraction of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) from environmental samples is developed with the assistance of sodium dodecyl sulphate (SDS) surfactant. In this study, the concentration of SDS surfactant and other analytical parameters are optimized on a high-performance liquid chromatography-UV system. An isocratic flow of 1.0 mL/min with mobile phase acetonitrile-water; 70:30 (v/v) at 230 nm wavelength on a reverse-phase amide column is used for baseline separation of explosives and making calibration curves. The amount of recovered explosives from spiked soil and water samples are calculated. The limits of detection obtained for HMX and RDX standards are 1.5 and 3.8 ppb (S/N=3), respectively, which are much better than obtained by the Environmental Protection Agency method 8330. The recoveries are found to be enhanced by 1.7 and 1.6-fold with SDS solution as compared to water for HMX and RDX, respectively, from soil samples.

  19. Inframammary fold: a histologic reappraisal.

    PubMed

    Muntan, C D; Sundine, M J; Rink, R D; Acland, R D

    2000-02-01

    The inframammary fold is a defining element in the shape and structure of the female breast. It should be preserved whenever possible in ablative procedures and recreated accurately when the breast is reconstructed after mastectomy. To date, no accurate anatomic description of this essential structure exists. Previous studies have suggested that the fold is produced by a supporting ligament running from the dermis in the fold region to a variety of locations on the rib cage. This clinic's experience with mastectomy, augmentation mammaplasty, and breast reconstruction does not support the existence of a ligamentous structure. To define the structure of the inframammary fold, 10 female and 2 male cadavers were studied. The anterior chest wall was removed en bloc and frozen in orthostatic position. Parasagittal sections were made of the inframammary fold with the chest wall intact. After decalcification of the ribs and routine histologic preparation, thin sections were stained with Gomori's trichrome. On light microscopic examination, no demonstrable ligamentous structure of dense regular connective tissue could be identified in the fold region in any of the 12 specimens. Superficial and deep fascial layers were uniformly observed anterior to the pectoralis major and serratus anterior muscles. The superficial fascia was connected to the dermis in the fold region in a variety of configurations. In some cases, the deep fascia fused with the superficial fascia and dermis at the fold level. In other cases, bundles of collagen fibers arising from the superficial fascial layer were found to insert into the dermis at the inframammary fold, slightly inferior to it, or both. These bundles were observed consistently in sections from the sternum to the middle axillary line. They were distinct from Cooper's suspensory ligaments, which are seen more superiorly in the glandular tissue.

  20. Protein folding by distributed computing and the denatured state ensemble.

    PubMed

    Marianayagam, Neelan J; Fawzi, Nicolas L; Head-Gordon, Teresa

    2005-11-15

    The distributed computing (DC) paradigm in conjunction with the folding@home (FH) client server has been used to study the folding kinetics of small peptides and proteins, giving excellent agreement with experimentally measured folding rates, although pathways sampled in these simulations are not always consistent with the folding mechanism. In this study, we use a coarse-grain model of protein L, whose two-state kinetics have been characterized in detail by using long-time equilibrium simulations, to rigorously test a FH protocol using approximately 10,000 short-time, uncoupled folding simulations starting from an extended state of the protein. We show that the FH results give non-Poisson distributions and early folding events that are unphysical, whereas longer folding events experience a correct barrier to folding but are not representative of the equilibrium folding ensemble. Using short-time, uncoupled folding simulations started from an equilibrated denatured state ensemble (DSE), we also do not get agreement with the equilibrium two-state kinetics because of overrepresented folding events arising from higher energy subpopulations in the DSE. The DC approach using uncoupled short trajectories can make contact with traditionally measured experimental rates and folding mechanism when starting from an equilibrated DSE, when the simulation time is long enough to sample the lowest energy states of the unfolded basin and the simulated free-energy surface is correct. However, the DC paradigm, together with faster time-resolved and single-molecule experiments, can also reveal the breakdown in the two-state approximation due to observation of folding events from higher energy subpopulations in the DSE.

  1. Primary Dermal Irritation of 1-Acetyloctahydro-3,5,7-Trinitro-1,3,5,7-Tetrazine.

    DTIC Science & Technology

    1983-06-01

    Tetrazine Chemical Abstract 3ervice F ;istry V" 139800-00-2 Lewis--2 Structural formula: C-CH3 H C N-NO2 02 N-N H2 H4X-N Empirical formula: C6H11N7...CHEMICAL DATA Chemical name: 1-Acetyloctahydro-3,5,7-Trinitro-1,3,5,7-Tetrazine Chemical Abstract Service Registry No.: 139800-00-2 Structural formula

  2. 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

  3. 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.

  4. Folding gravitational-wave interferometers

    NASA Astrophysics Data System (ADS)

    Sanders, J. R.; Ballmer, Stefan W.

    2017-01-01

    The sensitivity of kilometer-scale terrestrial gravitational wave interferometers is limited by mirror coating thermal noise. Alternative interferometer topologies can mitigate the impact of thermal noise on interferometer noise curves. In this work, we explore the impact of introducing a single folding mirror into the arm cavities of dual-recycled Fabry–Perot interferometers. While simple folding alone does not reduce the mirror coating thermal noise, it makes the folding mirror the critical mirror, opening up a variety of design and upgrade options. Improvements to the folding mirror thermal noise through crystalline coatings or cryogenic cooling can increase interferometer range by as much as a factor of two over the Advanced LIGO reference design.

  5. 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.

  6. Electrostatics of folded and unfolded bovine β-lactoglobulin.

    PubMed

    Eberini, Ivano; Sensi, Cristina; Barbiroli, Alberto; Bonomi, Franco; Iametti, Stefania; Galliano, Monica; Gianazza, Elisabetta

    2012-05-01

    We report on electrophoretic, spectroscopic, and computational studies aimed at clarifying, at atomic resolution, the electrostatics of folded and unfolded bovine β-lactoglobulin (BLG) with a detailed characterization of the specific aminoacids involved. The procedures we used involved denaturant gradient gel electrophoresis, isoelectric focusing, electrophoretic titration curves, circular dichroism and fluorescence spectra in the presence of increasing concentrations of urea (up to 8 M), electrostatics computations and low-mode molecular dynamics. Discrepancy between electrophoretic and spectroscopic evidence suggests that changes in mobility induced by urea are not just the result of changes in gyration radius upon unfolding. Electrophoretic titration curves run across a pH range of 3.5-9 in the presence of urea suggest that more than one aminoacid residue may have anomalous pKa value in native BLG. Detailed computational studies indicate a shift in pKa of Glu44, Glu89, and Glu114, mainly due to changes in global and local desolvation. For His161, the formation of hydrogen bond(s) could add up to desolvation contributions. However, since His161 is at the C terminus, the end-effect associated to the solvated form strongly influences its pKa value with extreme variation between crystal structures on one side and NMR or low-mode molecular dynamics structures on the other. The urea concentration effective in BLG unfolding depends on pH, with higher stability of the protein at lower pH.

  7. 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.

  8. Non-Enzymatic Oligomerization of 3', 5' Cyclic AMP.

    PubMed

    Costanzo, Giovanna; Pino, Samanta; Timperio, Anna Maria; Šponer, Judit E; Šponer, Jiří; Nováková, Olga; Šedo, Ondrej; Zdráhal, Zbyněk; Di Mauro, Ernesto

    2016-01-01

    Recent studies illustrate that short oligonucleotide sequences can be easily produced from nucleotide precursors in a template-free non-enzymatic way under dehydrating conditions, i.e. using essentially dry materials. Here we report that 3',5' cyclic AMP may also serve as a substrate of the reaction, which proceeds under moderate conditions yet with a lower efficiency than the previously reported oligomerization of 3',5' cyclic GMP. Optimally the oligomerization requires (i) a temperature of 80°C, (ii) a neutral to alkaline environment and (iii) a time on the order of weeks. Differences in the yield and required reaction conditions of the oligomerizations utilizing 3',5' cGMP and cAMP are discussed in terms of the crystal structures of the compounds. Polymerization of 3',5' cyclic nucleotides, whose paramount relevance in a prebiotic chemistry context has been widely accepted for decades, supports the possibility that the origin of extant genetic materials might have followed a direct uninterrupted path since its very beginning, starting from non-elaborately pre-activated monomer compounds and simple reactions.

  9. 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…

  10. 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…

  11. 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…

  12. 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…

  13. 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?

  14. 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...

  15. [3,5-dimethoxyfenol--marker intoxication with Taxus baccata].

    PubMed

    Stríbrný, J; Dogosi, M; Snupárek, Z; Toupalík, P; Baláz, P; Bartos, P

    2010-07-01

    Autopsy findings of fatal intoxication with yew (Taxus baccata) are nonspecific. A presence of plant residues in the digestive tract can signalize yew intoxication. If yew decoction is consumed, plant residues are not found. In such a case the intoxication can be signalized by the presence of 3,5-dimethoxyphenol in biological material. Authors of this article describe the proof and quantification of the 3,5-dimethoxyphenol in two cases of fatal intoxication with yew. In both cases the liquid/liquid extraction and solid phase extraction was used. Extracts obtained from the acidic and basic environment were analysed. Extracts from the acidic environment were methylated and the extracts from the basic environment were acetylated. The analyses were carried out by gas chromatography/mass spectrometry. In the blood of both intoxicated persons the presence of 3,5-dimethoxyphenol was proved and its concentration 82 ng/ml and 417 ng/ml was quantificated. In both cases the presence of 3,5-dimethoxyphenol was also proved in the gastric contents and urine.

  16. Examining Core Curricula in Writing for Grades 3-5

    ERIC Educational Resources Information Center

    Holtz, Jill; McCurdy, Merilee; Roehling, Julia V.

    2015-01-01

    Within a Response to Intervention (RtI) framework, Tier 1 instruction requires the selection of research-based core curricula. However, many educators and administrators are not aware of high-quality core writing curricula. The authors assembled a rubric to assist schools in evaluating core writing curricula for Grades 3-5. Rubric components…

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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…

  3. The Geometry of Almost Einstein (2, 3, 5) Distributions

    NASA Astrophysics Data System (ADS)

    Sagerschnig, Katja; Willse, Travis

    2017-01-01

    We analyze the classic problem of existence of Einstein metrics in a given conformal structure for the class of conformal structures inducedf Nurowski's construction by (oriented) (2, 3, 5) distributions. We characterize in two ways such conformal structures that admit an almost Einstein scale: First, they are precisely the oriented conformal structures c that are induced by at least two distinct oriented (2, 3, 5) distributions; in this case there is a 1-parameter family of such distributions that induce c. Second, they are characterized by the existence of a holonomy reduction to SU(1, 2), SL(3, R), or a particular semidirect product SL(2, R) ltimes Q_+, according to the sign of the Einstein constant of the corresponding metric. Via the curved orbit decomposition formalism such a reduction partitions the underlying manifold into several submanifolds and endows each ith a geometric structure. This establishes novel links between (2, 3, 5) distributions and many other geometries - several classical geometries among them - including: Sasaki-Einstein geometry and its paracomplex and null-complex analogues in dimension 5; Kähler-Einstein geometry and its paracomplex and null-complex analogues, Fefferman Lorentzian conformal structures, and para-Fefferman neutral conformal structures in dimension 4; CR geometry and the point geometry of second-order ordinary differential equations in dimension 3; and projective geometry in dimension 2. We describe a generalized Fefferman construction that builds from a 4-dimensional Kähler-Einstein or para-Kähler-Einstein structure a family of (2, 3, 5) distributions that induce the same (Einstein) conformal structure. We exploit some of these links to construct new examples, establishing the existence of nonflat almost Einstein (2, 3, 5) conformal structures for which the Einstein constant is positive and negative.

  4. Turbulent phenomena in protein folding.

    PubMed

    Kalgin, Igor V; Chekmarev, Sergei F

    2011-01-01

    Protein folding and hydrodynamic turbulence are two long-standing challenges, in molecular biophysics and fluid dynamics, respectively. The theories of these phenomena have been developed independently and used different formalisms. Here we show that the protein folding flows can be surprisingly similar to turbulent fluid flows. Studying a benchmark model protein (an SH3 domain), we have found that the flows for the slow folding trajectories of the protein, in which a partly formed N- and C-terminal β sheet hinders the RT loop from attaching to the protein core, have many properties of turbulent flows of a fluid. The flows are analyzed in a three-dimensional (3D) space of collective variables, which are the numbers of native contacts between the terminal β strands, between the RT loop and the protein core, and the rest of the native contacts. We have found that the flows have fractal nature and are filled with 3D eddies; the latter contain strange attractors, at which the tracer flow paths behave as saddle trajectories. Two regions of the space increment have been observed, in which the flux variations are self-similar with the scaling exponent h=1/3, in surprising agreement with the Kolmogorov inertial range theory of turbulence. In one region, the cascade of protein rearrangements is directed from larger to smaller scales (net folding), and in the other, it is oppositely directed (net unfolding). Folding flows for the fast trajectories are essentially "laminar" and do not have the property of self-similarity. Based on the results of our study, we infer, and support this inference by simulations, that the origin of the similarity between the protein folding and turbulent motion of a fluid is in a cascade mechanism of structural transformations in the systems that underlies these phenomena.

  5. 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.

  6. NoFold: RNA structure clustering without folding or alignment

    PubMed Central

    Middleton, Sarah A.

    2014-01-01

    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. PMID:25234928

  7. Folded orthogonal frequency division multiplexing.

    PubMed

    Corcoran, Bill; Zhu, Chen; Song, Binhuang; Lowery, Arthur J

    2016-12-26

    We propose and demonstrate a new sub-carrier multiplexing scheme, utilizing orthogonal, periodic-sinc-shaped sub-carrier spectra. This 'folded' OFDM allows for multi-carrier bands to be generated with the precise, rectangular frequency definition of Nyquist WDM. We show that this scheme can be implemented with 10 GHz sub-bands, showing a 0.5-dB implementation penalty and successful transmission over 4160-km. We further investigate 40-GHz bands in an add/drop multiplexing scenario on a 50-GHz WDM grid, and show that folded OFDM can provided advantages over conventional OFDM in bandwidth-limited systems.

  8. Mesoscale Modeling of Chromatin Folding

    NASA Astrophysics Data System (ADS)

    Schlick, Tamar

    2009-03-01

    Eukaryotic chromatin is the fundamental protein/nucleic acid unit that stores the genetic material. Understanding how chromatin fibers fold and unfold in physiological conditions is important for interpreting fundamental biological processes like DNA replication and transcription regulation. Using a mesoscopic model of oligonucleosome chains and tailored sampling protocols, we elucidate the energetics of oligonucleosome folding/unfolding and the role of each histone tail, linker histones, and divalent ions in regulating chromatin structure. The resulting compact topologies reconcile features of the zigzag model with straight linker DNAs with the solenoid model with bent linker DNAs for optimal fiber organization and reveal dynamic and energetic aspects involved.

  9. Biodegradation of the nitramine explosives hexahydro-1,3,5-trinitro-1,3,5-triazine and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine in cold marine sediment under anaerobic and oligotrophic conditions.

    PubMed

    Zhao, Jian-Shen; Greer, Charles W; Thiboutot, Sonia; Ampleman, Guy; Hawari, Jalal

    2004-02-01

    The in situ degradation of the two nitramine explosives, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), was evaluated using a mixture of RDX and HMX, incubated anaerobically at 10 degrees C with marine sediment from a previous military dumping site of unexploded ordnance (UXO) in Halifax Harbor, Nova Scotia, Canada. The RDX concentration (14.7 mg.L-1) in the aqueous phase was reduced by half in 4 days, while reduction of HMX concentration (1.2 mg.L-1) by half required 50 days. Supplementation with the carbon sources glucose, acetate, or citrate did not affect the removal rate of RDX but improved removal of HMX. Optimal mineralization of RDX and HMX was obtained in the presence of glucose. Using universally labeled (UL)-[14C]RDX, we obtained a carbon mass balance distributed as follows: CO2, 48%-58%; water soluble products, 27%-31%; acetonitrile extractable products, 2.0%-3.4%; and products covalently bound to the sediments and biomass, 8.9% (in the presence of glucose). The disappearance of RDX was accompanied by the formation of the mononitroso derivative hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX) and formaldehyde (HCHO) that subsequently disappeared. In the case of HMX, mineralization reached only 13%-27% after 115 days of incubation in the presence or absence of the carbon sources. The disappearance of HMX was also accompanied by the formation of the mononitroso derivative. The total population of psychrotrophic anaerobes that grew at 10 degrees C was 2.6 x 10(3) colony-forming units.(g sediment dry mass)-1, and some psychrotrophic sediment isolates were capable of degrading RDX under conditions similar to those used for sediments. Based on the distribution of products, we suggest that the sediment microorganisms degrade RDX and HMX via an initial reduction to the corresponding mononitroso derivative, followed by denitration and ring cleavage.

  10. Protein folding in the cell

    NASA Astrophysics Data System (ADS)

    Gething, Mary-Jane; Sambrook, Joseph

    1992-01-01

    In the cell, as in vitro, the final conformation of a protein is determined by its amino-acid sequence. But whereas some isolated proteins can be denatured and refolded in vitro in the absence of other macromolecular cellular components, folding and assembly of polypeptides in vivo involves other proteins, many of which belong to families that have been highly conserved during evolution.

  11. Use of Protein Folding Reagents.

    PubMed

    2016-04-01

    The reagents and methods for purification and use of the most commonly used denaturants, guanidine hydrochloride (guanidine-HCl) and urea, are described. Other protein denaturants and reagents used to fold proteins are briefly mentioned. Sulfhydryl reagents (reducing agents) and "oxido-shuffling" (or oxidative regeneration) systems are also described.

  12. 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.

  13. 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.

  14. 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

  15. Seeing experiments with the WIYN 3.5-m Telescope

    NASA Astrophysics Data System (ADS)

    Blanco, Daniel R.; Corson, Charles; Sawyer, David G.

    2000-08-01

    The WIYN 3.5 meter telescope uses active thermal control of the primary mirror and both active and passive ventilation of the observatory enclosure. These features have proven effective for delivering consistently excellent images, and make the WIYN facility an ideal test bed for quantitative measurements of the effects of temperature and ventilation on mirror and dome seeing. We describe the results of seeing experiments conducted over the first four years of operations at the WIYN Observatory.

  16. 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

  17. Quantitative Morphology of Epithelial Folds

    PubMed Central

    Štorgel, Nick; Krajnc, Matej; Mrak, Polona; Štrus, Jasna; Ziherl, Primož

    2016-01-01

    The shape of spatially modulated epithelial morphologies such as villi and crypts is usually associated with the epithelium-stroma area mismatch leading to buckling. We propose an alternative mechanical model based on intraepithelial stresses generated by differential tensions of apical, lateral, and basal sides of cells as well as on the elasticity of the basement membrane. We use it to theoretically study longitudinal folds in simple epithelia and we identify four types of corrugated morphologies: compact, invaginated, evaginated, and wavy. The obtained tissue contours and thickness profiles are compared to epithelial folds observed in invertebrates and vertebrates, and for most samples, the agreement is within the estimated experimental error. Our model establishes the groove-crest modulation of tissue thickness as a morphometric parameter that can, together with the curvature profile, be used to estimate the relative differential apicobasal tension in the epithelium. PMID:26745429

  18. Folded supersymmetry with a twist

    DOE PAGES

    Cohen, Timothy; Craig, Nathaniel; Lou, Hou Keong; ...

    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

  19. Folded supersymmetry with a twist

    SciTech Connect

    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. As 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.

  20. 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

  1. 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

  2. 3.5 D temperature model of a coal stockpile

    SciTech Connect

    Ozdeniz, A.H.; Corumluoglu, O.; Kalayci, I.; Sensogut, C.

    2008-07-01

    Overproduced coal mines that are not sold should remain in coal stock sites. If these coal stockpiles remain at the stock yards over a certain period of time, a spontaneous combustion can be started. Coal stocks under combustion threat can cost too much economically to coal companies. Therefore, it is important to take some precautions for saving the stockpiles from the spontaneous combustion. In this research, a coal stock which was 5 m wide, 10 m long, and 3 m in height, with a weight of 120 tons, was monitored to observe internal temperature changes with respect to time under normal atmospheric conditions. Internal temperature measurements were obtained at 20 points distributed all over the two layers in the stockpile. Temperatures measured by a specially designed mechanism were then stored into a computer every 3 h for a period of 3 months. Afterward, this dataset was used to delineate 3.5 D temporal temperature distribution models for these two levels, and they were used to analyze and interpret what was seen in these models to derive some conclusions. It was openly seen, followed, and analyzed that internal temperature changes in the stockpile went up to 31{sup o}C by 3.5 D models created for this research.

  3. Choristoneura fumiferana nucleopolyhedrovirus encodes a functional 3'-5' exonuclease.

    PubMed

    Yang, Dan-Hui; de Jong, Jondavid G; Makhmoudova, Amina; Arif, Basil M; Krell, Peter J

    2004-12-01

    The Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) encodes an ORF homologous to type III 3'-5' exonucleases. The CfMNPV v-trex ORF was cloned into the Bac-to-Bac baculovirus expression-vector system, expressed in insect Sf21 cells with an N-terminal His tag and purified to homogeneity by using Ni-NTA affinity chromatography. Biochemical characterization of the purified V-TREX confirmed that this viral protein is a functional 3'-5' exonuclease that cleaves oligonucleotides from the 3' end in a stepwise, distributive manner, suggesting a role in proofreading during viral DNA replication and DNA repair. Enhanced degradation of a 5'-digoxigenin- or 5'-(32)P-labelled oligo(dT)(30) substrate was observed at increasing incubation times or increased amounts of V-TREX. The 3'-excision activity of V-TREX was maximal at alkaline pH (9.5) in the presence of 5 mM MgCl(2), 2 mM dithiothreitol and 0.1 mg BSA ml(-1).

  4. Global search for minimum energy (H2O)n clusters, n = 3-5.

    PubMed

    Day, Mary Beth; Kirschner, Karl N; Shields, George C

    2005-08-04

    The Gaussian-3 (G3) model chemistry method has been used to calculate the relative deltaG(o) values for all possible conformers of neutral clusters of water, (H2O)n, where n = 3-5. A complete 12-fold conformational search around each hydrogen bond produced 144, 1728, and 20,736 initial starting structures of the water trimer, tetramer, and pentamer. These structures were optimized with PM3, followed by HF/6-31G* optimization, and then with the G3 model chemistry. Only two trimers are present on the G3 potential energy hypersurface. We identified 5 tetramers and 10 pentamers on the potential energy and free-energy hypersurfaces at 298 K. None of these 17 structures were linear; all linear starting models folded into cyclic or three-dimensional structures. The cyclic pentamer is the most stable isomer at 298 K. On the basis of this and previous studies, we expect the cyclic tetramers and pentamers to be the most significant cyclic water clusters in the atmosphere.

  5. NMR and computational studies of chiral discrimination by amylose tris(3,5-dimethylphenylcarbamate).

    PubMed

    Ye, Yun K; Bai, Shi; Vyas, Shyam; Wirth, Mary J

    2007-02-08

    Proton NMR and simulations were combined to study the origin of chiral selectivity by a polysaccharide used in a commercial chromatographic stationary phase: amylose tris(3,5-dimethylphenylcarbamate). This material has unusually high enantioselectivity for p-O-tert-butyltyrosine allyl ester, which is activated by the presence of an acid. Proton NMR spectra agreed with the HPLC in showing that the l-enantiomer interacts much more strongly with the polysaccharide and that acidity switches on the selectivity. 2D NOESY spectra revealed which protons of each enantiomer and the polysaccharide were in proximity, and these spectra revealed folding of the l-enantiomer. Computations generated energy-minimized structures for the polysaccharide-enantiomer complexes, independently predicting folding of the l-enantiomer. Molecular dynamics simulations 2 ns in duration, repeated for three different energy-minimized structures, generated pair distribution functions that are in excellent agreement with the 2D NOESY spectra. The modeling studies revealed why acidity switches on chiral selectivity and minimally affects the chromatographic retention time of the unfavored d-enantiomer. The results comprise the first case of a chiral separation by a commercial polysaccharide stationary phase being explained using a combination of 2D NOESY and simulations, providing excellent agreement between experiment and computation and lending detailed molecular insight into enantioselectivity for this system.

  6. Immunogenicity of Infanrix™ hexa administered at 3, 5 and 11 months of age.

    PubMed

    Van Der Meeren, Olivier; Kuriyakose, Sherine; Kolhe, Devayani; Hardt, Karin

    2012-04-05

    A pooled analysis of data from four vaccination studies conducted in Europe was undertaken to assess the immunogenicity of Infanrix™ hexa (DTPa-HBV-IPV/Hib, GlaxoSmithKline Biologicals) when administered in a total of 702 healthy infants at 3, 5 and 11-12 months of age. One month after dose 2, between 96.3% and 100% of subjects had seroprotective antibodies against diphtheria, tetanus, hepatitis B and poliovirus types 1, 2 and 3; 91.7% against Hib and ≥99.0% were seropositive for each pertussis antigen. One month after the third dose, 98.9-100% of subjects were seroprotected/seropositive for all vaccine antigens. Geometric mean antibody concentrations/titres for each vaccine antigen increased by 6.7-52.9 fold after the third vaccine dose. No serious adverse events in DTPa-HBV-IPV/Hib recipients were vaccine related. Infanrix™ hexa induces an adequate immune response after 2-dose primary plus booster doses when administered according to a 3, 5 and 11 months schedule.

  7. 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…

  8. 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.

  9. ANIMO 3.5: User`s guide for the ANIMO version 3.5 nutrient leaching model

    SciTech Connect

    Kroes, J.; Roelsma, J.

    1998-12-31

    This document presents a description of the use of the nutrient leaching model ANIMO (Agricultural Nutrient Model) version 3.5 with special emphasis for input instructions. Each input parameter is characterized by its unit, range, data type, variable name in computer code and symbol in theoretical description, Program outputs and program execution are briefly given. An example is presented with values of input parameters and model results. A technical program description is given as a brief description of program structure, nomenclature, and source code.

  10. Folded MEMS approach to NMRG

    NASA Astrophysics Data System (ADS)

    Gundeti, Venu Madhav

    Atomic gyroscopes have a potential for good performance advantages and several attempts are being made to miniaturize them. This thesis describes the efforts made in implementing a Folded MEMS based NMRG. The micro implementations of all the essential components for NMRG (Nuclear Magnetic Resonance Gyroscope) are described in detail in regards to their design, fabrication, and characterization. A set of micro-scale Helmholtz coils are described and the homogeneity of the generated magnetic field is analyzed for different designs of heaters. The dielectric mirrors and metallic mirrors are compared in terms of reflectivity and polarization change up on reflection. A pyramid shaped folded backbone structure is designed, fabricated, and assembled along with all the required components. A novel double-folded structure 1/4th the size of original version is fabricated and assembled. Design and modeling details of a 5 layered shield with shielding factor > 106 and total volume of around 90 cc are also presented. A table top setup for characterization of atomic vapor cell is described in detail. A micro vapor cell based Rb magnetometer with a sensitivity of 108 pT/√Hz is demonstrated. The challenges due to DC heating are addressed and mitigated using an AC heater. Several experiments related to measuring the relaxation time of Xe are provided along with results. For Xe131, relaxation times of T1 = 23.78 sec, T2 = 18.06 sec and for Xe129, T1 = 21.65 sec and T2 = 20.45 sec are reported.

  11. 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

  12. 3'-5' tRNAHis Guanylyltransferase in Bacteria

    PubMed Central

    Heinemann, Ilka; Randau, Lennart; Tomko, Robert J.; Söll, Dieter

    2010-01-01

    The identity of the histidine specific transfer RNA (tRNAHis) is largely determined by a unique guanosine residue at position −1. In eukaryotes and archaea, the tRNAHis guanylyltransferase (Thg1) catalyzes 3'-5' addition of G to the 5'-terminus of tRNAHis. Here, we show that Thg1 also occurs in bacteria. We demonstrate in vitro Thg1 activity for recombinant enzymes from the two bacteria Bacillus thuringiensis and Myxococcus xanthus and provide a closer investigation of several archaeal Thg1. The reaction mechanism of prokaryotic Thg1 differs from eukaryotic enzymes, as it does not require ATP. Complementation of a yeast thg1 knockout strain with bacterial Thg1 verified in vivo activity and suggests a relaxed recognition of the discriminator base in bacteria. PMID:20650272

  13. Alkaline hydrolysis of hexahydro-1,3,5-trinitro-1,3,5-triazine: M06-2X investigation.

    PubMed

    Sviatenko, Liudmyla K; Gorb, Leonid; Hill, Frances C; Leszczynska, Danuta; Okovytyy, Sergiy I; Leszczynski, Jerzy

    2015-09-01

    Alkaline hydrolysis mechanism of possible environmental contaminant RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) was investigated computationally at the PCM(Pauling)/M06-2X/6-311++G(d,p) level of theory. Results obtained show that the initial deprotonation of RDX by hydroxide leads to nitrite elimination and formation of a denitrated cyclohexene intermediate. Further nucleophilic attack by hydroxide onto cyclic CN double bond results in ring opening. It was shown that the presence of hydroxide is crucial for this stage of the reaction. The dominant decomposition pathway leading to a ring-opened intermediate was found to be formation of 4-nitro-2,4-diazabutanal. Hydrolytic transformation of its byproduct (methylene nitramine) leads to end products such as formaldehyde and nitrous oxide. Computational results are in a good agreement with experimental data on hydrolysis of RDX, suggesting that 4-nitro-2,4-diazabutanal, nitrite, formaldehyde, and nitrous oxide are main products for early stages of RDX decomposition under alkaline conditions.

  14. 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

  15. 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

  16. 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.

  17. [Interaction of adenosin-3',5'-cyclosulfate with adenosine-3'5'-cyclophosphate dependent protein kinase and phosphodiesterase].

    PubMed

    Severin, E S; Tkachuk, V A; Guliaev, N N

    1976-02-01

    Interaction of adenosine-3',5'-cyclosulphate (cAMS) cAMP analogue, having sulphur atom instead of phosphorus in a six-term cyclic system with pig brain proteinkinase and rabbit skeletal muscle phosphodiesterase is studied. The affinity of proteinkinase to cAMS was found to be in 25000 times lower than the affinity of cAMP, the affinity of cAMS to the active site of phosphodiesterase being high enough. It is suggested that in the regulatory subunit of proteinkinase positive kationic group participates in nucleotide binding by interacting with negative oxygen atom of six-term cyclophosphate system. There is no such a group in the active site of phospodiesterase, because the absence of negative charge in case of cAMS only slightly affects the constant of cAMS binding by phosphodiesterase.

  18. 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.

  19. Electron attachment to hydrated oligonucleotide dimers: guanylyl-3',5'-cytidine and cytidylyl-3',5'-guanosine.

    PubMed

    Gu, Jiande; Xie, Yaoming; Schaefer, Henry F

    2010-05-03

    The dinucleoside phosphate deoxycytidylyl-3',5'-deoxyguanosine (dCpdG) and deoxyguanylyl-3',5'-deoxycytidine (dGpdC) systems are among the largest to be studied by reliable theoretical methods. Exploring electron attachment to these subunits of DNA single strands provides significant progress toward definitive predictions of the electron affinities of DNA single strands. The adiabatic electron affinities of the oligonucleotides are found to be sequence dependent. Deoxycytidine (dC) on the 5' end, dCpdG, has larger adiabatic electron affinity (AEA, 0.90 eV) than dC on the 3' end of the oligomer (dGpdC, 0.66 eV). The geometric features, molecular orbital analyses, and charge distribution studies for the radical anions of the cytidine-containing oligonucleotides demonstrate that the excess electron in these anionic systems is dominantly located on the cytosine nucleobase moiety. The pi-stacking interaction between nucleobases G and C seems unlikely to improve the electron-capturing ability of the oligonucleotide dimers. The influence of the neighboring base on the electron-capturing ability of cytosine should be attributed to the intensified proton accepting-donating interaction between the bases. The present investigation demonstrates that the vertical detachment energies (VDEs) of the radical anions of the oligonucleotides dGpdC and dCpdG are significantly larger than those of the corresponding nucleotides. Consequently, reactions with low activation barriers, such as those for O-C sigma bond and N-glycosidic bond breakage, might be expected for the radical anions of the guanosine-cytosine mixed oligonucleotides.

  20. Evaluation of the Community Land Model 3.5 with carbon and nitrogen cycles (CLM3.5CN) at a Tibetan grassland site

    NASA Astrophysics Data System (ADS)

    Lee, Young-Hee; Lim, Hee-Jeong; Ichii, Kazuhito; Li, Yingnian

    2013-11-01

    The Tibetan plateau plays an important role in energy and carbon cycles by providing an elevated heat source and by storing a large amount of soil carbon due to low temperature. The main vegetation of the plateau is alpine grassland. This study evaluates performance of Community Land Model 3.5 with carbon and nitrogen cycles (CLM3.5CN) over a alpine grassland in the Tibetan plateau in terms of energy and carbon fluxes in conditions of reasonable phenology and initial carbon pool comparable to observations. Comparison between model and observation shows following features. The model captures the magnitude of maximum leaf area index (LAI) but underestimats leaf mass. Net ecosystem exchange (NEE) is significantly underestimated during the growing season and soil temperature is also underestimated throughout a year with higher negative bias in winter than in other seasons. In order to examine the cause of the model deficiencies, we design four sensitivity tests: seasonal mulch; shallow rooting depth; reduction of critical soil moisture to limit the decomposition rate; smaller specific leaf area (SLA). Considering seasonal mulch improves the negative bias of soil temperature during dormant season has little effect on the NEE during the growing seasson. Underestimation of NEE during the growing season is partly due to underestimated decomposition rate which results from underestimated soil temperature and deep root placement in the soil column. Underestimation of latent heat flux during summer is partly due to use of large SLA in the model. Other deficiencies are also discussed.

  1. Cyclic adenosine 3',5'-monophosphate levels and activities of adenylate cyclase and cyclic adenosine 3',5'-monophosphate phosphodiesterase in Pseudomonas and Bacteroides.

    PubMed Central

    Siegel, L S; Hylemon, P B; Phibbs, P V

    1977-01-01

    A modified Gilman assay was used to determine the concentrations of cyclic adenosine 3',5'-monophosphate (cAMP) in rapidly filtered cells and in the culture filtrates of Pseudomonas aeruginosa, Escherichia coli K-12, and Bacteroides fragilis. In P. aeruginosa cultures, levels of cAMP in the filtrate increased with the culture absorbance (3.5 to 19.8 X 10(-9) M) but did not vary significantly with the carbon source used to support growth. Intracellular concentrations (0.8 to 3.2 X 10(-5) M) were substantially higher and did not vary appreciably during growth or with carbon source. Sodium cAMP (5 mM) failed to reverse the catabolite repression of inducible glucose-6-phosphate dehydrogenase (EC 1.1.1.49) synthesis caused by the addition of 10 mM succinate. Exogenous cAMP also had no discernible effect on the catabolite repression control of inducible mannitol dehydrogenase (EC 1.1.1.67). P. aeruginosa was found to contain both soluble cAMP phosphodiesterase (EC 3.1.4.17) and membrane-associated adenylate cyclase (EC 4.6.1.1) activity, and these were compared to the activities detected in crude extracts of E. coli. B. fragilis crude cell extracts contain neither of these enzyme activities, and little or no cAMP was detected in cells or culture filtrates of this anaerobic bacterium. PMID:187575

  2. Kinematics and thermodynamics of a folding heteropolymer.

    PubMed Central

    Fukugita, M; Lancaster, D; Mitchard, M G

    1993-01-01

    In order to elucidate the folding dynamics of protein, we have carried out numerical simulations of a heteropolymer model of self-interacting random chains. We find that folding propensity depends strongly on sequence and that both folding and nonfolding sequences exist. Furthermore we show that folding is a two-step process: the transition from coil state to unique folded state takes place through a globule phase. In addition to the continuous coil-globule transition, there exists an abrupt transition that separates the unique folded state from the globule state and ensures the stability of the native state. PMID:8327518

  3. Probing RNA folding by hydroxyl radical footprinting.

    PubMed

    Costa, Maria; Monachello, Dario

    2014-01-01

    In recent years RNA molecules have emerged as central players in the regulation of gene expression. Many of these noncoding RNAs possess well-defined, complex, three-dimensional structures which are essential for their biological function. In this context, much effort has been devoted to develop computational and experimental techniques for RNA structure determination. Among available experimental tools to investigate the higher-order folding of structured RNAs, hydroxyl radical probing stands as one of the most informative and reliable ones. Hydroxyl radicals are oxidative species that cleave the nucleic acid backbone solely according to the solvent accessibility of individual phosphodiester bonds, with no sequence or secondary structure specificity. Therefore, the cleavage pattern obtained directly reflects the degree of protection/exposure to the solvent of each section of the molecule under inspection, providing valuable information about how these different sections interact together to form the final three-dimensional architecture. In this chapter we describe a robust, accurate and very sensitive hydroxyl radical probing method that can be applied to any structured RNA molecule and is suitable to investigate RNA folding and RNA conformational changes induced by binding of a ligand.

  4. Generating technique for U(1){sup 3} 5D supergravity

    SciTech Connect

    Gal'tsov, Dmitri V.; Scherbluk, Nikolai G.

    2008-09-15

    We develop a generating technique for solutions of U(1){sup 3} 5D supergravity via dimensional reduction to three dimensions. This theory, which recently attracted attention in connection with black rings, can be viewed as a consistent truncation of the T{sup 6} compactification of the 11-dimensional supergravity. Its further reduction to three dimensions accompanied by dualization of the vector fields leads to a 3D gravity coupled sigma model on the homogeneous space SO(4,4)/SO(4)xSO(4) or SO(4,4)/SO(2,2)xSO(2,2) depending on the signature of the three-space. We construct a 8x8 matrix representation of these cosets in terms of lower-dimensional blocks. Using it we express a solution generating transformations in terms of potentials and identify those preserving asymptotic conditions relevant to black holes and black rings. As an application we derive the doubly rotating black hole solution with three independent charges. A suitable contraction of the above cosets is used to construct a new representation of the coset G{sub 2(2)}/(SL(2,R)xSL(2,R)) relevant for minimal five-dimensional supergravity.

  5. Staphylococcus epidermidis Csm1 is a 3'-5' exonuclease.

    PubMed

    Ramia, Nancy F; Tang, Li; Cocozaki, Alexis I; Li, Hong

    2014-01-01

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) offer an adaptive immune system that protects bacteria and archaea from nucleic acid invaders through an RNA-mediated nucleic acid cleavage mechanism. Our knowledge of nucleic acid cleavage mechanisms is limited to three examples of widely different ribonucleoprotein particles that target either DNA or RNA. Staphylococcus epidermidis belongs to the Type III-A CRISPR system and has been shown to interfere with invading DNA in vivo. The Type III-A CRISPR system is characterized by the presence of Csm1, a member of Cas10 family of proteins, that has a permuted histidine-aspartate domain and a nucleotidyl cyclase-like domain, both of which contain sequence features characteristic of nucleases. In this work, we show in vitro that a recombinant S. epidermidis Csm1 cleaves single-stranded DNA and RNA exonucleolytically in the 3'-5' direction. We further showed that both cleavage activities are divalent-metal-dependent and reside in the GGDD motif of the cyclase-like domain. Our data suggest that Csm1 may work in the context of an effector complex to degrade invading DNA and participate in CRISPR RNA maturation.

  6. 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

  7. Folding tools for flat conductor cable harnesses

    NASA Technical Reports Server (NTRS)

    Loggins, R.

    1971-01-01

    Vise grip pliers have detachable metal gripping plates which are changed to accommodate cables from 1 to 3 in. wide and to form any desired fold angle. A second tool squeezes cable along crease to complete the fold.

  8. Vibrational spectra of 3,5-dimethylpyrazole and deuterated derivatives.

    PubMed

    Orza, J M; García, M V; Alkorta, I; Elguero, J

    2000-07-01

    The infrared (IR) and Raman spectra of 3,5-dimethylpyrazole have been recorded in the vapor, liquid (melt and solution) and solid states. Two deuterated derivatives, C5H7N-ND and C5D7N-NH, were also studied in solid state and in solutions. Instrumental resolution was relatively low, 2.0 cm(-1) in the IR and approximately 2.7 cm(-1) in the Raman spectra. The solids are made of cyclic hydrogen-bonded trimers. These trimers, present also in chloroform and acetone solutions, give rise to characteristic high absorption IR spectra in the 3200-2500 cm(-1) region, related to Fermi resonance involving nu(NH) vibrations. Bands from trimers are not present in water solutions but these solutions show spectral features similar in several ways to those of the trimer, attributable to solvent-bonded complexes. Evidence of H-bonding interactions with the other solvents is also visible in the high-frequency region. The two very intense bands in the Raman spectra of the solids appearing at 115 and 82 cm(-1) in the parent compound are also connected with a trimer formation. To interpret the experimental data, ab initio computations of the harmonic vibrational frequencies and IR and Raman intensities were carried out using the Gaussian 94 program package after full optimization at the RHF/6-31G* level for the three monomeric compounds as well as for three models of the trimer, with C3h, C3 and C1 symmetry. The combined use of experiments and computations allow a firm assignment of most of the observed bands for all the systems. In general, the agreement between theory and experiment is very good, with the exception of the IR and Raman intensities of some transitions. Particularly noticeable is the failure of the theoretical calculation in accounting for the high intensity of the Raman bands of the solid about 115 and 82 cm(-1).

  9. 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)

  10. 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…

  11. 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.

  12. Synthesis, antimalarial activity and molecular docking of hybrid 4-aminoquinoline-1,3,5-triazine derivatives.

    PubMed

    Bhat, Hans Raj; Singh, Udaya Pratap; Thakur, Anjali; Kumar Ghosh, Surajit; Gogoi, Kabita; Prakash, Anil; Singh, Ramendra K

    2015-10-01

    A series of novel hybrid 4-aminoquinoline 1,3,5-triazine derivatives was synthesized in a five-steps reaction and evaluated for their in vitro antimalarial activity against chloroquine-sensitive (3D7) and chloroquine-resistant (RKL-2) strains of Plasmodium falciparum. Entire synthetic derivatives showed higher antimalarial activity on the sensitive strain while two compounds, viz., 9a and 9c displayed good activity against both the strains of P. falciparum. The observed activity was further substantiated by docking study on both wild and qradruple mutant type P. falciparum dihydrofolate reductase-thymidylate synthase (pf-DHFR-TS).

  13. APE2 Zf-GRF facilitates 3'-5' resection of DNA damage following oxidative stress

    SciTech Connect

    Wallace, Bret D.; Berman, Zachary; Mueller, Geoffrey A.; Lin, Yunfeng; Chang, Timothy; Andres, Sara N.; Wojtaszek, Jessica L.; DeRose, Eugene F.; Appel, C. Denise; London, Robert E.; Yan, Shan; Williams, R. Scott

    2016-12-27

    The Xenopus laevis APE2 (apurinic/apyrimidinic endonuclease 2) nuclease participates in 3'-5' nucleolytic resection of oxidative DNA damage and activation of the ATR-Chk1 DNA damage response (DDR) pathway via ill-defined mechanisms. Here we report that APE2 resection activity is regulated by DNA interactions in its Zf-GRF domain, a region sharing high homology with DDR proteins Topoisomerase 3α (TOP3α) and NEIL3 (Nei-like DNA glycosylase 3), as well as transcription and RNA regulatory proteins, such as TTF2 (transcription termination factor 2), TFIIS, and RPB9. Biochemical and NMR results establish the nucleic acid-binding activity of the Zf-GRF domain. Moreover, an APE2 Zf-GRF X-ray structure and small-angle X-ray scattering analyses show that the Zf-GRF fold is typified by a crescent-shaped ssDNA binding claw that is flexibly appended to an APE2 endonuclease/exonuclease/phosphatase (EEP) catalytic core. Structure-guided Zf-GRF mutations impact APE2 DNA binding and 3'-5' exonuclease processing, and also prevent efficient APE2-dependent RPA recruitment to damaged chromatin and activation of the ATR-Chk1 DDR pathway in response to oxidative stress in Xenopus egg extracts. Collectively, our data unveil the APE2 Zf-GRF domain as a nucleic acid interaction module in the regulation of a key single-strand break resection function of APE2, and also reveal topologic similarity of the Zf-GRF to the zinc ribbon domains of TFIIS and RPB9.

  14. 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

  15. 0.4-3.5-micrometer Observations of 4179 Toutatis

    NASA Astrophysics Data System (ADS)

    Howell, E. S.; Britt, D. T.; Bell, J. F.; Binzel, R. P.; Lebofsky, L. A.

    1993-07-01

    We obtained nearly simultaneous observations of 4179 Toutatis over a 0.3-3.5 micrometer wavelength range on 4 January 1993 UT. Howell obtained a 1.2-2.5 micrometer spectrophotometry using the Multiple Mirror Telescope in Arizona. Britt and Bell obtained narrowband photometry in the 3-micrometer region as well as broadband JHK photometry from the Infrared Telescope Facility in Hawaii. Binzel measured the visible spectrum using a CCD spectrograph at the McGraw-Hill Observatory in Arizona. Using V photometry reported by Pravec in the Czech Republic on adjacent nights [1], we were able to combine all these spectral regions. The rotation period of this object is approximately 10 days, so the time differences between the measurements of different spectral regions are negligible. Tholen has classified 4179 Toutatis as an S-type asteroid based on visible photometry. We measure a pyroxene absorption band near 2 micrometers, present in most S-type asteroid spectra. Unfortunately, a gap in spectral coverage prevents us from determining the characteristics of the 1-micrometer absorption band accurately. The spectral slope as measured from 1.25 to 2.2 micrometers is 6-10%, which is modest compared to other S-type asteroids. The spectrum of this asteroid is similar to other near-Earth S-type asteroids that have been observed in the near-infrared wavelength region. On 4 January 1993, 4179 Toutatis was 0.182 AU from the Earth, and 1.158 AU from the Sun. At this solar distance, the thermal emission contributes substantially to the flux at 3 micrometers. The determination of thermal emission is complicated by the slow rotation rate and the irregular shape of this object that was revealed by radar observations [2]. Preliminary results suggest that no 3-micrometer absorption feature is present, indicating that this object is anhydrous. Using these spectral data, we will compare 4179 Toutatis to other S-type asteroids, both in the main belt and the near-Earth environment. References

  16. 3D fold growth in transpression

    NASA Astrophysics Data System (ADS)

    Frehner, Marcel

    2016-12-01

    Geological folds in transpression are inherently 3D structures; hence their growth and rotation behavior is studied using 3D numerical finite-element simulations. Upright single-layer buckle folds in Newtonian materials are considered, which grow from an initial point-like perturbation due to a combination of in-plane shortening and shearing (i.e., transpression). The resulting fold growth exhibits three components: (1) fold amplification (vertical), (2) fold elongation (parallel to fold axis), and (3) sequential fold growth (perpendicular to axial plane) of new anti- and synforms adjacent to the initial fold. Generally, the fold growth rates are smaller for shearing-dominated than for shortening-dominated transpression. In spite of the growth rate, the folding behavior is very similar for the different convergence angles. The two lateral directions always exhibit similar growth rates implying that the bulk fold structure occupies an increasing roughly circular area. Fold axes are always parallel to the major horizontal principal strain axis (λ→max, i.e., long axis of the horizontal finite strain ellipse), which is initially also parallel to the major horizontal instantaneous stretching axis (ISA→max). After initiation, the fold axes rotate together with λ→max. Sequential folds appearing later do not initiate parallel to ISA→max, but parallel to λ→max, i.e. parallel to the already existing folds, and also rotate with λ→max. Therefore, fold axes do not correspond to passive material lines and hinge migration takes place as a consequence. The fold axis orientation parallel to λ→max is independent of convergence angle and viscosity ratio. Therefore, a triangular relationship between convergence angle, amount of shortening, and fold axis orientation exists. If two of these values are known, the third can be determined. This relationship is applied to the Zagros fold-and-thrust-belt to estimate the degree of strain partitioning between the Simply

  17. 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.

  18. 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.

  19. Controlled Folding of Single Crystal Graphene.

    PubMed

    Wang, Bin; Huang, Ming; Kim, Na Yeon; Cunning, Benjamin V; Huang, Yuan; Qu, Deshun; Chen, Xianjue; Jin, Sunghwan; Biswal, Mandakini; Zhang, Xu; Lee, Sun Hwa; Lim, Hyunseob; Yoo, Won Jong; Lee, Zonghoon; Ruoff, Rodney S

    2017-03-08

    Folded graphene in which two layers are stacked with a twist angle between them has been predicted to exhibit unique electronic, thermal, and magnetic properties. We report the folding of a single crystal monolayer graphene film grown on a Cu(111) substrate by using a tailored substrate having a hydrophobic region and a hydrophilic region. Controlled film delamination from the hydrophilic region was used to prepare macroscopic folded graphene with good uniformity on the millimeter scale. This process was used to create many folded sheets each with a defined twist angle between the two sheets. By identifying the original lattice orientation of the monolayer graphene on Cu foil, or establishing the relation between the fold angle and twist angle, this folding technique allows for the preparation of twisted bilayer graphene films with defined stacking orientations and may also be extended to create folded structures of other two-dimensional nanomaterials.

  20. The Role of Biotransformation and Oxidative Stress in 3,5-Dichloroaniline (3,5-DCA) Induced Nephrotoxicity in Isolated Renal Cortical Cells from Male Fischer 344 Rats

    PubMed Central

    Racine, Christopher R.; Ferguson, Travis; Preston, Debbie; Ward, Dakota; Ball, John; Anestis, Dianne; Valentovic, Monica; Rankin, Gary O.

    2016-01-01

    Among the mono- and dichloroanilines, 3,5-Dichloroaniline (3,5-DCA) is the most potent nephrotoxicant in vivo and in vitro. However, the role of renal biotransformation in 3,5-DCA induced nephrotoxicity is unknown. The current study was designed to determine the in vitro nephrotoxic potential of 3,5-DCA in isolated renal cortical cells (IRCC) obtained from male Fischer 344 rats, and the role of renal bioactivation and oxidative stress in 3,5-DCA nephrotoxicity. IRCC (~4 million cells/ml) from male rats were exposed to 3,5-DCA (0-1.0 mM) for up to 120 min. In IRCC, 3,5-DCA was cytotoxic at 1.0 mM by 60 min as evidenced by the increased release of lactate dehydrogenase (LDH), but 120 min was required for 3,5-DCA 0.5 mM to increase LDH release. In subsequent studies, IRCC were exposed to a pretreatment (antioxidant or enzyme inhibitor) prior to exposure to 3,5-DCA (1.0 mM) for 90 min. Cytotoxicity induced by 3,5-DCA was attenuated by pretreatment with inhibitors of flavin-containing monooxygenase (FMO; methimazole, N-octylamine), cytochrome P450 (CYP; piperonyl butoxide, metyrapone), or peroxidase (indomethacin, mercaptosuccinate) enzymes. Use of more selective CYP inhibitors suggested that the CYP 2C family contributed to 3,5-DCA bioactivation. Antioxidants (glutathione, N-acetyl-L-cysteine, α-tocopherol, ascorbate, pyruvate) also attenuated 3,5-DCA nephrotoxicity, but oxidized glutathione levels and the oxidized/reduced glutathione ratios were not increased. These results indicate that 3,5-DCA may be activated via several renal enzyme systems to toxic metabolites, and that free radicals, but not oxidative stress, contribute to 3,5-DCA induced nephrotoxicity in vitro. PMID:26808022

  1. Mononuclear copper(II) complexes with 3,5-substituted-4-salicylidene-amino-3,5-dimethyl-1,2,4-triazole: synthesis, structure and potent inhibition of protein tyrosine phosphatases.

    PubMed

    Ma, Ling; Lu, Liping; Zhu, Miaoli; Wang, Qingming; Li, Ying; Xing, Shu; Fu, Xueqi; Gao, Zengqiang; Dong, Yuhui

    2011-06-28

    Six copper complexes of Schiff base ligands containing 3,5-substituted-4-salicylideneamino-3,5-dimethyl-1,2,4-triazole have been synthesized and well characterized. The structures of complexes 1 and 2 were determined by X-ray crystal analysis. Fluorescence and potentiometric study indicated that in the physiological pH range, one ligand was dissociated from the complexes to form 1:1 mononucleus copper complexes. The complexes potently inhibit protein tyrosine phosphatase 1B (PTP1B), T-cell protein tyrosine phosphatase (TCPTP), megakaryocyte protein tyrosine phosphatase 2 (PTP-MEG2) and Src homology phosphatase 1 (SHP-1) with 3-4 fold selectivity against PTP1B over TCPTP and PTP-MEG2, and 3-9 fold over SHP-1, but display almost no inhibition against Src homology phosphatase 2 (SHP-2). Complex 1 inhibits PTP1B with a competitive model with K(i) of 30 nM. Substitution with small groups at the phenyl of the ligand does not obviously influence the inhibitory ability of the complexes.

  2. Trace level analysis of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and its biodegradation intermediates in liquid media by solid-phase extraction and high-pressure liquid chromatography analysis.

    PubMed

    Chow, Teresa M; Wilcoxon, Monte R; Piwoni, Marvin D; Adrian, Neal R

    2004-10-01

    The use of solid-phase extraction for the analysis of liquid media containing low microg/L levels of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), mononitroso-RDX (MNX), dinitroso-RDX (DNX), and trinitroso-RDX (TNX) is examined. Aqueous samples (100 mL) consisting of water and a microbiological basal medium are spiked with known concentrations of RDX, MNX, DNX, and TNX. The compounds are extracted from the liquid media using a Porapak RDX cartridge and then eluted from the cartridge with 5 mL of acetonitrile. The eluent is concentrated to 1 mL before analysis by high-pressure liquid chromatography (HPLC). The method detection limits for RDX are 0.1 microg/L in water and 0.5 microg/L in the basal medium after a 100-fold concentration. For MNX, DNX, and TNX, the method detection limits are approximately 0.5 microg/L in water and approximately 1 microg/L in the basal medium after a 100-fold concentration. Interferences in the basal medium and a contaminant in the standard made quantitation for MNX and TNX, respectively, is less accurate below the 1 microg/L level. Solid-phase extraction of the liquid media gave good recoveries of nitramines and nitroso intermediates from a microbiological basal medium, allowing HPLC detection of RDX and the nitroso intermediates in the low microg/L (ppb) range.

  3. 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.

  4. 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.

  5. Novel dinuclear dimethylamido-3,5-dimethylpyrazolato and tetranuclear dimethylamido-3,5-dimethylpyrazolato-polyoxo zirconium(IV) complexes. Synthesis and structural characterisation.

    PubMed

    Sanz, Martial; Mosquera, Marta E G; Cuenca, Tomás

    2009-04-14

    The dinuclear dimethylamido-tris(3,5-dimethylpyrazolato)-zirconium(IV) complex [Zr(3,5-Me2Pz)3(NMe2)]2 1 is prepared by treatment of [Zr(NMe2)4] with 3 equivalents of 3,5-dimethylpyrazole (3,5-Me2PzH) with elimination of dimethylamine. When [Zr(NMe2)4] reacted with 2 equivalents of 3,5-Me2PzH, the bis(dimethylamido)-bis(3,5-dimethylpyrazolato)zirconium(IV) compound [Zr(3,5-Me2Pz)2(NMe2)2]2 2 is obtained. Hydrolysis of [Zr(3,5-Me2Pz)3(NMe2)]2 in wet toluene affords the tetranuclear oxo compound [Zr4(eta2-3,5-Me2Pz)4(NMe2)2(mu3-O)2(mu2-3,5-Me2Pz)4(mu2-NMe2)2] . All synthesised compounds are characterised by NMR spectroscopic and analytical methods. Single crystal X-ray diffraction analysis has established the molecular structures of 1 and 4.

  6. Kinetic partitioning mechanism of HDV ribozyme folding.

    PubMed

    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.

  7. 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.

  8. 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.

  9. Asymmetric hindwing foldings in rove beetles.

    PubMed

    Saito, Kazuya; Yamamoto, Shuhei; Maruyama, Munetoshi; Okabe, Yoji

    2014-11-18

    Foldable wings of insects are the ultimate deployable structures and have attracted the interest of aerospace engineering scientists as well as entomologists. Rove beetles are known to fold their wings in the most sophisticated ways that have right-left asymmetric patterns. However, the specific folding process and the reason for this asymmetry remain unclear. This study reveals how these asymmetric patterns emerge as a result of the folding process of rove beetles. A high-speed camera was used to reveal the details of the wing-folding movement. The results show that these characteristic asymmetrical patterns emerge as a result of simultaneous folding of overlapped wings. The revealed folding mechanisms can achieve not only highly compact wing storage but also immediate deployment. In addition, the right and left crease patterns are interchangeable, and thus each wing internalizes two crease patterns and can be folded in two different ways. This two-way folding gives freedom of choice for the folding direction to a rove beetle. The use of asymmetric patterns and the capability of two-way folding are unique features not found in artificial structures. These features have great potential to extend the design possibilities for all deployable structures, from space structures to articles of daily use.

  10. Viscoelastic properties of the false vocal fold

    NASA Astrophysics Data System (ADS)

    Chan, Roger W.

    2004-05-01

    The biomechanical properties of vocal fold tissues have been the focus of many previous studies, as vocal fold viscoelasticity critically dictates the acoustics and biomechanics of phonation. However, not much is known about the viscoelastic response of the ventricular fold or false vocal fold. It has been shown both clinically and in computer simulations that the false vocal fold may contribute significantly to the aerodynamics and sound generation processes of human voice production, with or without flow-induced oscillation of the false fold. To better understand the potential role of the false fold in phonation, this paper reports some preliminary measurements on the linear and nonlinear viscoelastic behavior of false vocal fold tissues. Linear viscoelastic shear properties of human false fold tissue samples were measured by a high-frequency controlled-strain rheometer as a function of frequency, and passive uniaxial tensile stress-strain response of the tissue samples was measured by a muscle lever system as a function of strain and loading rate. Elastic moduli (Young's modulus and shear modulus) of the false fold tissues were calculated from the measured data. [Work supported by NIH.

  11. 0. 35-3. 5 micron photometry of blazars

    SciTech Connect

    Sitko, M.L.; Sitko, A.K. Cincinnati Observatory, OH )

    1991-02-01

    Thirty-one blazars were observed photometrically in the near-infrared, with additional observations in the optical for many of them. A few of them exhibit spectral behavior indicative of multiple emission components or emission processes. Six objects were also analyzed for any possible correlation between spectral steepness and luminosity. In one object, 0735 + 178, the spectral index alpha is correlated with the flux level with 99.9 pct confidence. Two other objects, 0846 + 513 and 0851 + 202, showed similar correlations at the 98 and 90 pct confidence levels, respectively. In all three cases the spectrum became flatter at higher flux levels. the data are consistent with expectations of models of inhomogeneous synchrotron models. In some cases, the self-Compton component may contribute significantly to the optical flux. 27 refs.

  12. 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.

  13. 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.

  14. Optical methods for measuring DNA folding

    NASA Astrophysics Data System (ADS)

    Smith, Adam D.; Ukogu, Obinna A.; Devenica, Luka M.; White, Elizabeth D.; Carter, Ashley R.

    2017-03-01

    One of the most important biological processes is the dynamic folding and unfolding of deoxyribonucleic acid (DNA). The folding process is crucial for DNA to fit within the boundaries of the cell, while the unfolding process is essential for DNA replication and transcription. To accommodate both processes, the cell employs a highly active folding mechanism that has been the subject of intense study over the last few decades. Still, many open questions remain. What are the pathways for folding or unfolding? How does the folding equilibrium shift? And, what is the energy landscape for a particular process? Here, we review these emerging questions and the in vitro, optical methods that have provided answers, introducing the topic for those physicists seeking to step into biology. Specifically, we discuss two iconic experiments for DNA folding, the tethered particle motion (TPM) experiment and the optical tweezers experiment.

  15. Implicit modeling of folds and overprinting deformation

    NASA Astrophysics Data System (ADS)

    Laurent, Gautier; Ailleres, Laurent; Grose, Lachlan; Caumon, Guillaume; Jessell, Mark; Armit, Robin

    2016-12-01

    Three-dimensional structural modeling is gaining importance for a broad range of quantitative geoscientific applications. However, existing approaches are still limited by the type of structural data they are able to use and by their lack of structural meaning. Most techniques heavily rely on spatial data for modeling folded layers, but are unable to completely use cleavage and lineation information for constraining the shape of modeled folds. This lack of structural control is generally compensated by expert knowledge introduced in the form of additional interpretive data such as cross-sections and maps. With this approach, folds are explicitly designed by the user instead of being derived from data. This makes the resulting structures subjective and deterministic. This paper introduces a numerical framework for modeling folds and associated foliations from typical field data. In this framework, a parametric description of fold geometry is incorporated into the interpolation algorithm. This way the folded geometry is implicitly derived from observed data, while being controlled through structural parameters such as fold wavelength, amplitude and tightness. A fold coordinate system is used to support the numerical description of fold geometry and to modify the behavior of classical structural interpolators. This fold frame is constructed from fold-related structural elements such as axial foliations, intersection lineations, and vergence. Poly-deformed terranes are progressively modeled by successively modeling each folding event going backward through time. The proposed framework introduces a new modeling paradigm, which enables the building of three-dimensional geological models of complex poly-deformed terranes. It follows a process based on the structural geologist approach and is able to produce geomodels that honor both structural data and geological knowledge.

  16. 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; ...

    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

  17. Deterministic Folding in Stiff Elastic Membranes

    NASA Astrophysics Data System (ADS)

    Tallinen, T.; Åström, J. A.; Timonen, J.

    2008-09-01

    Crumpled membranes have been found to be characterized by complex patterns of spatially seemingly random facets separated by narrow ridges of high elastic energy. We demonstrate by numerical simulations that compression of stiff elastic membranes with small randomness in their initial configurations leads to either random ridge configurations (high entropy) or nearly deterministic folds (low elastic energy). For folding with symmetric ridge configurations to appear in part of the crumpling processes, the crumpling rate must be slow enough. Folding stops when the thickness of the folded structure becomes important, and crumpling continues thereafter as a random process.

  18. Protein Folding and Self-Organized Criticality

    NASA Astrophysics Data System (ADS)

    Bajracharya, Arun; Murray, Joelle

    Proteins are known to fold into tertiary structures that determine their functionality in living organisms. However, the complex dynamics of protein folding and the way they consistently fold into the same structures is not fully understood. Self-organized criticality (SOC) has provided a framework for understanding complex systems in various systems (earthquakes, forest fires, financial markets, and epidemics) through scale invariance and the associated power law behavior. In this research, we use a simple hydrophobic-polar lattice-bound computational model to investigate self-organized criticality as a possible mechanism for generating complexity in protein folding.

  19. Oxidation of hydroquinone, 2,3-dimethylhydroquinone and 2,3,5-trimethylhydroquinone by human myeloperoxidase.

    PubMed

    Burner, U; Krapfenbauer, G; Furtmüller, P G; Regelsberger, G; Obinger, C

    2000-01-01

    Myeloperoxidase is very susceptible to reducing radicals because the reduction potential of the ferric/ferrous redox couple is much higher compared with other peroxidases. Semiquinone radicals are known to reduce heme proteins. Therefore, the kinetics and spectra of the reactions of p-hydroquinone, 2,3-dimethylhydroquinone and 2,3,5-trimethylhydroquinone with compounds I and II were investigated using both sequential-mixing stopped-flow techniques and conventional spectrophotometric measurements. At pH 7 and 15 degrees C the rate constants for compound I reacting with p-hydroquinone, 2,3-dimethylhydroquinone and 2,3,5-trimethylhydroquinone were determined to be 5.6+/-0.4 x 10(7) M(-1)s(-1), 1.3+/-0.1 x 10(6) M(-1)s(-1) and 3.1+/-0.3 x 10(6) M(-1)s(-1), respectively. The corresponding reaction rates for compound II reduction were calculated to be 4.5+/-0.3 x 10(6) M(-1)s(-1), 1.9+/-0.1 x 10(5) M(-1)s(-1) and 4.5+/-0.2 x 10(4) M(-1)s(-1), respectively. Semiquinone radicals, produced by compounds I and II in the classical peroxidation cycle, promote compound III (oxymyeloperoxidase) formation. We could monitor formation of ferrous myeloperoxidase as well as its direct transition to compound II by addition of molecular oxygen. Formation of ferrous myeloperoxidase is shown to depend strongly on the reduction potential of the corresponding redox couple benzoquinone/semiquinone. With 2,3-dimethylhydroquinone and 2,3,5-trimethylhydroquinone as substrate, myeloperoxidase is extremely quickly trapped as compound III. These MPO-typical features could have potential in designing specific drugs which inhibit the production of hypochlorous acid and consequently attenuate inflammatory tissue damage.

  20. Gross Motor Development in Children Aged 3-5 Years, United States 2012.

    PubMed

    Kit, Brian K; Akinbami, Lara J; Isfahani, Neda Sarafrazi; Ulrich, Dale A

    2017-02-14

    Objective Gross motor development in early childhood is important in fostering greater interaction with the environment. The purpose of this study is to describe gross motor skills among US children aged 3-5 years using the Test of Gross Motor Development (TGMD-2). Methods We used 2012 NHANES National Youth Fitness Survey (NNYFS) data, which included TGMD-2 scores obtained according to an established protocol. Outcome measures included locomotor and object control raw and age-standardized scores. Means and standard errors were calculated for demographic and weight status with SUDAAN using sample weights to calculate nationally representative estimates, and survey design variables to account for the complex sampling methods. Results The sample included 339 children aged 3-5 years. As expected, locomotor and object control raw scores increased with age. Overall mean standardized scores for locomotor and object control were similar to the mean value previously determined using a normative sample. Girls had a higher mean locomotor, but not mean object control, standardized score than boys (p < 0.05). However, the mean locomotor standardized scores for both boys and girls fell into the range categorized as "average." There were no other differences by age, race/Hispanic origin, weight status, or income in either of the subtest standardized scores (p > 0.05). Conclusions In a nationally representative sample of US children aged 3-5 years, TGMD-2 mean locomotor and object control standardized scores were similar to the established mean. These results suggest that standardized gross motor development among young children generally did not differ by demographic or weight status.

  1. 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

  2. Hierarchical classification of protein folds using a novel ensemble classifier.

    PubMed

    Lin, Chen; Zou, Ying; Qin, Ji; Liu, Xiangrong; Jiang, Yi; Ke, Caihuan; Zou, Quan

    2013-01-01

    The analysis of biological information from protein sequences is important for the study of cellular functions and interactions, and protein fold recognition plays a key role in the prediction of protein structures. Unfortunately, the prediction of protein fold patterns is challenging due to the existence of compound protein structures. Here, we processed the latest release of the Structural Classification of Proteins (SCOP, version 1.75) database and exploited novel techniques to impressively increase the accuracy of protein fold classification. The techniques proposed in this paper include ensemble classifying and a hierarchical framework, in the first layer of which similar or redundant sequences were deleted in two manners; a set of base classifiers, fused by various selection strategies, divides the input into seven classes; in the second layer of which, an analogous ensemble method is adopted to predict all protein folds. To our knowledge, it is the first time all protein folds can be intelligently detected hierarchically. Compared with prior studies, our experimental results demonstrated the efficiency and effectiveness of our proposed method, which achieved a success rate of 74.21%, which is much higher than results obtained with previous methods (ranging from 45.6% to 70.5%). When applied to the second layer of classification, the prediction accuracy was in the range between 23.13% and 46.05%. This value, which may not be remarkably high, is scientifically admirable and encouraging as compared to the relatively low counts of proteins from most fold recognition programs. The web server Hierarchical Protein Fold Prediction (HPFP) is available at http://datamining.xmu.edu.cn/software/hpfp.

  3. Hierarchical Classification of Protein Folds Using a Novel Ensemble Classifier

    PubMed Central

    Qin, Ji; Liu, Xiangrong; Jiang, Yi; Ke, Caihuan; Zou, Quan

    2013-01-01

    The analysis of biological information from protein sequences is important for the study of cellular functions and interactions, and protein fold recognition plays a key role in the prediction of protein structures. Unfortunately, the prediction of protein fold patterns is challenging due to the existence of compound protein structures. Here, we processed the latest release of the Structural Classification of Proteins (SCOP, version 1.75) database and exploited novel techniques to impressively increase the accuracy of protein fold classification. The techniques proposed in this paper include ensemble classifying and a hierarchical framework, in the first layer of which similar or redundant sequences were deleted in two manners; a set of base classifiers, fused by various selection strategies, divides the input into seven classes; in the second layer of which, an analogous ensemble method is adopted to predict all protein folds. To our knowledge, it is the first time all protein folds can be intelligently detected hierarchically. Compared with prior studies, our experimental results demonstrated the efficiency and effectiveness of our proposed method, which achieved a success rate of 74.21%, which is much higher than results obtained with previous methods (ranging from 45.6% to 70.5%). When applied to the second layer of classification, the prediction accuracy was in the range between 23.13% and 46.05%. This value, which may not be remarkably high, is scientifically admirable and encouraging as compared to the relatively low counts of proteins from most fold recognition programs. The web server Hierarchical Protein Fold Prediction (HPFP) is available at http://datamining.xmu.edu.cn/software/hpfp. PMID:23437146

  4. 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

  5. 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

  6. 75 FR 55327 - Tetrahydro-3,5-dimethyl-2H-1,3,5-thiadiazine-2-thione (Dazomet); Notice of Receipt of Request to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-10

    ... withdraws its request. If this request is granted, any sale, distribution, or use of products listed in this... voluntarily amend two tetrahydro-3,5-dimethyl-2H-1,3,5-thiadiazine-2-thione product registrations to terminate...- thione products registered for use in the United States. EPA intends to grant this request at the...

  7. Trinuclear rare earth metal complexes based on 1,3,5-triamino-1,3,5-trideoxy-cis inositol as catalysts for the hydrolysis of phosphodiesters.

    PubMed

    Ramadan, Ahmed M; Calatayud Sala, José Miguel; Parac-Vogt, Tatjana N

    2011-02-14

    Trinuclear rare-earth metal complexes [M₃(taciH₋₃)₂](3+) (M = La(3+), Y(3+)), based on a rigid polyamino-polyalcohol ligand 1,3,5-triamino-1,3,5-trideoxy-cis-inositol (taci), are proven to be efficient catalysts for the hydrolysis of 2-hydroxypropyl-4-nitrophenyl phophate (HPNP), a commonly used RNA model system.

  8. 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...

  9. Acute Oral Toxicity of 1-Acetyloctahydro-3,5,7-Trinitro-1,3,5,7-Tetrazocine (Sex) in Male and Female Rats.

    DTIC Science & Technology

    1984-05-01

    flame proof cabinet at room temperature. %.. White--2 Chemical name: 1-Acetyloctahydro-3,5,7-Trinitro-1,3,5,7-Tetrazocine Chemical Abstract Service...Trinitrocyclotetramethylenetetramine Chemical Abstract Service Registry No.: 13980-00-2 Structural formula: 0 11 C-CH 0 2 N-N CH2 HC-N NO 2 , Empirical formula: C6H1

  10. The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family.

    PubMed

    Ferreiro, Diego U; Cho, Samuel S; Komives, Elizabeth A; Wolynes, Peter G

    2005-12-02

    Proteins consisting of repeating amino acid motifs are abundant in all kingdoms of life, especially in higher eukaryotes. Repeat-containing proteins self-organize into elongated non-globular structures. Do the same general underlying principles that dictate the folding of globular domains apply also to these extended topologies? Using a simplified structure-based model capturing a perfectly funneled energy landscape, we surveyed the predicted mechanism of folding for ankyrin repeat containing proteins. The ankyrin family is one of the most extensively studied classes of non-globular folds. The model based only on native contacts reproduces most of the experimental observations on the folding of these proteins, including a folding mechanism that is reminiscent of a nucleation propagation growth. The confluence of simulation and experimental results suggests that the folding of non-globular proteins is accurately described by a funneled energy landscape, in which topology plays a determinant role in the folding mechanism.

  11. A Computational Model of Cerebral Cortex Folding

    PubMed Central

    Nie, Jingxin; Guo, Lei; Li, Gang; Faraco, Carlos; Miller, L Stephen; Liu, Tianming

    2010-01-01

    The geometric complexity and variability of the human cerebral cortex has long intrigued the scientific community. As a result, quantitative description of cortical folding patterns and the understanding of underlying folding mechanisms have emerged as important research goals. This paper presents a computational 3-dimensional geometric model of cerebral cortex folding initialized by MRI data of a human fetal brain and deformed under the governance of a partial differential equation modeling cortical growth. By applying different simulation parameters, our model is able to generate folding convolutions and shape dynamics of the cerebral cortex. The simulations of this 3D geometric model provide computational experimental support to the following hypotheses: 1) Mechanical constraints of the skull regulate the cortical folding process. 2) The cortical folding pattern is dependent on the global cell growth rate of the whole cortex. 3) The cortical folding pattern is dependent on relative rates of cell growth in different cortical areas. 4) The cortical folding pattern is dependent on the initial geometry of the cortex. PMID:20167224

  12. Fractures Sets Associated to Buckle Folds

    NASA Astrophysics Data System (ADS)

    Liu, X.; Eckert, A.; Connolly, P. T.

    2014-12-01

    Buckle folds of single and multilayered sedimentary strata in the literature are commonly associated to a variety of different fracture sets, both shear and tensile. Amongst the most noticeable fractures are tensile fractures occurring in the outer hinges of the fold crest and shear fractures in the bottom of fold hinge zones. These fractures are well explained and understood by the extensional and compressional strain/stress pattern in the fold hinge. However, tensile fractures parallel to the fold axis, tensile fractures cutting through the limb, normal faults on the fold hinge, and shear fractures of different orientations in the fold limb cannot intuitively be linked to the stress regime occurring during the buckling process. This study utilizes a 2D and 3D finite element modeling approach using Maxwell visco-elastic rheology to study the stress conditions during single and multilayer buckling for each fracture set to occur. The numerical simulations include sensitivity analyses on material parameters such as permeability, viscosity and overburden thickness. For fracture sets not likely to occur during the buckling process pre- and post folding processes such as initial overpressure, extensional unfolding, and erosional unloading are studied.

  13. Microsecond subdomain folding in dihydrofolate reductase.

    PubMed

    Arai, Munehito; Iwakura, Masahiro; Matthews, C Robert; Bilsel, Osman

    2011-07-08

    The characterization of microsecond dynamics in the folding of multisubdomain proteins has been a major challenge in understanding their often complex folding mechanisms. Using a continuous-flow mixing device coupled with fluorescence lifetime detection, we report the microsecond folding dynamics of dihydrofolate reductase (DHFR), a two-subdomain α/β/α sandwich protein known to begin folding in this time range. The global dimensions of early intermediates were monitored by Förster resonance energy transfer, and the dynamic properties of the local Trp environments were monitored by fluorescence lifetime detection. We found that substantial collapse occurs in both the locally connected adenosine binding subdomain and the discontinuous loop subdomain within 35 μs of initiation of folding from the urea unfolded state. During the fastest observable ∼550 μs phase, the discontinuous loop subdomain further contracts, concomitant with the burial of Trp residue(s), as both subdomains achieve a similar degree of compactness. Taken together with previous studies in the millisecond time range, a hierarchical assembly of DHFR--in which each subdomain independently folds, subsequently docks, and then anneals into the native conformation after an initial heterogeneous global collapse--emerges. The progressive acquisition of structure, beginning with a continuously connected subdomain and spreading to distal regions, shows that chain entropy is a significant organizing principle in the folding of multisubdomain proteins and single-domain proteins. Subdomain folding also provides a rationale for the complex kinetics often observed.

  14. Stochastic Resonance in Protein Folding Dynamics.

    PubMed

    Davtyan, Aram; Platkov, Max; Gruebele, Martin; Papoian, Garegin A

    2016-05-04

    Although protein folding reactions are usually studied under static external conditions, it is likely that proteins fold in a locally fluctuating cellular environment in vivo. To mimic such behavior in in vitro experiments, the local temperature of the solvent can be modulated either harmonically or using correlated noise. In this study, coarse-grained molecular simulations are used to investigate these possibilities, and it is found that both periodic and correlated random fluctuations of the environment can indeed accelerate folding kinetics if the characteristic frequencies of the applied fluctuations are commensurate with the internal timescale of the folding reaction; this is consistent with the phenomenon of stochastic resonance observed in many other condensed-matter processes. To test this theoretical prediction, the folding dynamics of phosphoglycerate kinase under harmonic temperature fluctuations are experimentally probed using Förster resonance energy transfer fluorescence measurements. To analyze these experiments, a combination of theoretical approaches is developed, including stochastic simulations of folding kinetics and an analytical mean-field kinetic theory. The experimental observations are consistent with the theoretical predictions of stochastic resonance in phosphoglycerate kinase folding. When combined with an alternative experiment on the protein VlsE using a power spectrum analysis, elaborated in Dave et al., ChemPhysChem 2016, 10.1002/cphc.201501041, the overall data overwhelmingly point to the experimental confirmation of stochastic resonance in protein folding dynamics.

  15. 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.

  16. 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

  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. 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.

  19. Cooperative Tertiary Interaction Network Guides RNA Folding

    SciTech Connect

    Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan; Briber, R.M.; Woodson, Sarah A.

    2013-04-08

    Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.

  20. 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.

  1. The origami of thioredoxin-like folds

    PubMed Central

    Pan, Jonathan L.; Bardwell, James C.A.

    2006-01-01

    Origami is the Japanese art of folding a piece of paper into complex shapes and forms. Much like origami of paper, Nature has used conserved protein folds to engineer proteins for a particular task. An example of a protein family, which has been used by Nature numerous times, is the thioredoxin superfamily. Proteins in the thioredoxin superfamily are all structured with a β-sheet core surrounded with α-helices, and most contain a canonical CXXC motif. The remarkable feature of these proteins is that the link between them is the fold; however, their reactivity is different for each member due to small variations in this general fold as well as their active site. This review attempts to unravel the minute differences within this protein family, and it also demonstrates the ingenuity of Nature to use a conserved fold to generate a diverse collection of proteins to perform a number of different biochemical tasks. PMID:17008712

  2. 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

  3. 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.

  4. 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.

  5. DiO-C/sub 3/-(5) and diS-C/sub 3/-(5): interactions with RBC, ghosts and phospholipid vesicles

    SciTech Connect

    Guillet, E.G.; Kimmich, G.A.

    1981-01-01

    The experiments presented below compare the interaction of diO-C/sub 3/-(5) and diS-C/sub 3/-(5) with erythrocytes, erythrocyte ghosts and phospholipid vesicles derived from erythrocyte membranes. The results confirm earlier reports of diS-C/sub 3/-(5) dimerization in the presence of hemoglobin and of dye aggregate formation in erythrocyte suspensions. DiO-C/sub 3/-(5), on the other hand, binds to vesicles and ghosts freed of hemoglobin in a potential-dependent manner but without forming dye aggregates. The two dyes bind to the different preparations in similar proportions, but diS-C/sub 3/-(5) is bound in amounts 3-40 times greater depending in the degree of polarization. The results show that a mechanism other than binding to hemoglobin must occur in order to explain the potential-dependent binding of both dyes to ghosts and vesicles. A primary interaction must exist between the dye molecule and the lipid bilayer in a biologicl membrane, and this would be expected to occur in the presence of hemoglobin or other cytosolic components. DiO-C/sub 3/-(5) is a better dye to use than diS-C/sub 3/-(5) for mechanistic studies, in order to avoid problems associated with formation of complex aggregates of the latter dye, especially in hyperpolarized membrane suspensions.

  6. DiO-C3-(5) and DiS-C3-(5): Interactions with RBC, ghosts and phospholipid vesicles.

    PubMed

    Guillet, E G; Kimmich, G A

    1981-03-15

    The experiments presented below compare the interaction of diO-C3-(5) and diS-C3-(5) with erythrocytes, erythrocyte ghosts and phospholipid vesicles derived from erythrocyte membranes. The results confirm earlier reports of diS-C3-(5) dimerization in the presence of hemoglobin and of dye aggregate formation in erythrocyte suspensions. DiO-C3-(5), on the other hand, binds to vesicles and ghosts freed of hemoglobin in a potential-dependent manner but without forming dye aggregates. The two dyes bind to the different preparations in similar proportions, but diS-C3-(5) is bound in amounts 3-40 times greater depending on the degree of polarization. The results show that mechanism other than binding to hemoglobin must occur in order to explain the potential-dependent binding of both dyes to ghosts and vesicles. A primary interaction must exist between the dye molecule and the lipid bilayer in a biological membrane, and this would be expected to occur in the presence of hemoglobin or other cytosolic components. DiO-C3-(5) is a better dye to use than diS-C3-(5) for mechanistic studies, in order to avoid problems associated with formation of complex aggregates of the latter dye, especially in hyperpolarized membrane suspensions.

  7. 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.

  8. 45 CFR 3.5 - Lost and found, and abandoned property.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Lost and found, and abandoned property. 3.5 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,...

  9. 45 CFR 3.5 - Lost and found, and abandoned property.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 1 2014-10-01 2014-10-01 false Lost and found, and abandoned property. 3.5 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,...

  10. 45 CFR 3.5 - Lost and found, and abandoned property.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 1 2013-10-01 2013-10-01 false Lost and found, and abandoned property. 3.5 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,...

  11. 45 CFR 3.5 - Lost and found, and abandoned property.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 1 2011-10-01 2011-10-01 false Lost and found, and abandoned property. 3.5 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,...

  12. 45 CFR 3.5 - Lost and found, and abandoned property.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 1 2012-10-01 2012-10-01 false Lost and found, and abandoned property. 3.5 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,...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 14 CFR 3.5 - Statements about products, parts, appliances and materials.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 14 Aeronautics and Space 1 2014-01-01 2014-01-01 false Statements about products, parts, appliances and materials. 3.5 Section 3.5 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION DEFINITIONS GENERAL REQUIREMENTS § 3.5 Statements about products, parts,...

  19. 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...

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

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 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, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 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. 40 CFR 721.4265 - Hydrazinecarboxamide, N-(3,5-difluorophenyl-).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 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...

  3. 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 OF TRANSPORTATION DEFINITIONS GENERAL REQUIREMENTS § 3.5 Statements about products, parts, appliances... product, part, appliance or material. (b) Prohibition against fraudulent and intentionally...

  4. 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 OF TRANSPORTATION DEFINITIONS GENERAL REQUIREMENTS § 3.5 Statements about products, parts, appliances... product, part, appliance or material. (b) Prohibition against fraudulent and intentionally...

  5. 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 OF TRANSPORTATION DEFINITIONS GENERAL REQUIREMENTS § 3.5 Statements about products, parts, appliances... product, part, appliance or material. (b) Prohibition against fraudulent and intentionally...

  6. 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 OF TRANSPORTATION DEFINITIONS GENERAL REQUIREMENTS § 3.5 Statements about products, parts, appliances... product, part, appliance or material. (b) Prohibition against fraudulent and intentionally...

  7. 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...

  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. GroEL-mediated protein folding.

    PubMed Central

    Fenton, W. A.; Horwich, A. L.

    1997-01-01

    I. Architecture of GroEL and GroES and the reaction pathway A. Architecture of the chaperonins B. Reaction pathway of GroEL-GroES-mediated folding II. Polypeptide binding A. A parallel network of chaperones binding polypeptides in vivo B. Polypeptide binding in vitro 1. Role of hydrophobicity in recognition 2. Homologous proteins with differing recognition-differences in primary structure versus effects on folding pathway 3. Conformations recognized by GroEL a. Refolding studies b. Binding of metastable intermediates c. Conformations while stably bound at GroEL 4. Binding constants and rates of association 5. Conformational changes in the substrate protein associated with binding by GroEL a. Observations b. Kinetic versus thermodynamic action of GroEL in mediating unfolding c. Crossing the energy landscape in the presence of GroEL III. ATP binding and hydrolysis-driving the reaction cycle IV. GroEL-GroES-polypeptide ternary complexes-the folding-active cis complex A. Cis and trans ternary complexes B. Symmetric complexes C. The folding-active intermediate of a chaperonin reaction-cis ternary complex D. The role of the cis space in the folding reaction E. Folding governed by a "timer" mechanism F. Release of nonnative polypeptides during the GroEL-GroES reaction G. Release of both native and nonnative forms under physiologic conditions H. A role for ATP binding, as well as hydrolysis, in the folding cycle V. Concluding remarks. PMID:9098884

  10. Excited State Processes for Aqueous Rh(NH3)5Cl(2+) and Rh(NH3)5Br(2+).

    DTIC Science & Technology

    1981-04-10

    white precipitate of Rh(NH3)5(H20)) Br3 was collected and dried overnight at 110-0 C. The resulting yellow product was recrystallized from water/HClO4 to...aquation. In all cases, product concentrations were corrected for the usually small degree of dark or thermal reaction. Pulsed Laser Experiments. The...direct photochemical production . According to Palmer and Harris [16] the reaction Rh(NH 3)5(OH) 2+ + C02(aq) = Rh(NH 3)5(Co3) + + H+ occurs with a rate

  11. Cooperativity and modularity in protein folding

    PubMed Central

    Sasai, Masaki; Chikenji, George; Terada, Tomoki P.

    2016-01-01

    A simple statistical mechanical model proposed by Wako and Saitô has explained the aspects of protein folding surprisingly well. This model was systematically applied to multiple proteins by Muñoz and Eaton and has since been referred to as the Wako-Saitô-Muñoz-Eaton (WSME) model. The success of the WSME model in explaining the folding of many proteins has verified the hypothesis that the folding is dominated by native interactions, which makes the energy landscape globally biased toward native conformation. Using the WSME and other related models, Saitô emphasized the importance of the hierarchical pathway in protein folding; folding starts with the creation of contiguous segments having a native-like configuration and proceeds as growth and coalescence of these segments. The Φ-values calculated for barnase with the WSME model suggested that segments contributing to the folding nucleus are similar to the structural modules defined by the pattern of native atomic contacts. The WSME model was extended to explain folding of multi-domain proteins having a complex topology, which opened the way to comprehensively understanding the folding process of multi-domain proteins. The WSME model was also extended to describe allosteric transitions, indicating that the allosteric structural movement does not occur as a deterministic sequential change between two conformations but as a stochastic diffusive motion over the dynamically changing energy landscape. Statistical mechanical viewpoint on folding, as highlighted by the WSME model, has been renovated in the context of modern methods and ideas, and will continue to provide insights on equilibrium and dynamical features of proteins.

  12. 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

  13. Kinetics of chain motions within a protein-folding intermediate

    PubMed Central

    Neuweiler, Hannes; Banachewicz, Wiktor; Fersht, Alan R.

    2010-01-01

    Small proteins can fold remarkably rapidly, even in μs. What limits their rate of folding? The Engrailed homeodomain is a particularly well-characterized example, which folds ultrafast via an intermediate, I, of solved structure. It is a puzzle that the helix2-turn-helix3 motif of the 3-helix bundle forms in approximately 2 μs, but the final docking of preformed helix1 in I requires approximately 20 μs. Simulation and structural data suggest that nonnative interactions may slow down helix docking. Here we report the direct measurement of chain motions in I by using photoinduced electron transfer fluorescence-quenching correlation spectroscopy (PET-FCS). We use a mutant that traps I at physiological ionic strength but refolds at higher ionic strength. A single Trp in helix3 quenches the fluorescence of an extrinsic label on contact with it. We placed the label along the sequence to probe segmental chain motions. At high ionic strength, we found two relaxations for all probed positions on the 2- and 20-μs time scale, corresponding to the known folding processes, and a 200-ns phase attributable to loop closure kinetics in the unfolded state. At low ionic strength, we found only the 2-μs and 200-ns phase for labels in the helix2-turn-helix3 motif of I, because the native state is not significantly populated. But for labels in helix1 we observed an additional approximately 10-μs phase showing that it was moving slowly, with a rate constant similar to that for overall folding under native conditions. Folding was rate-limited by chain motions on a rough energy surface where nonnative interactions constrain motion. PMID:21135210

  14. A bidirectional shape memory alloy folding actuator

    NASA Astrophysics Data System (ADS)

    Paik, Jamie K.; Wood, Robert J.

    2012-06-01

    This paper presents a low-profile bidirectional folding actuator based on annealed shape memory alloy sheets applicable for meso- and microscale systems. Despite the advantages of shape memory alloys—high strain, silent operation, and mechanical simplicity—their application is often limited to unidirectional operation. We present a bidirectional folding actuator that produces two opposing 180° motions. A laser-patterned nickel alloy (Inconel 600) heater localizes actuation to the folding sections. The actuator has a thin ( < 1 mm) profile, making it appropriate for use in robotic origami. Various design parameters and fabrication variants are described and experimentally explored in the actuator prototype.

  15. 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

  16. 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).

  17. Comparison of the folded stripline and stacked stripline concepts to the folded waveguide launcher

    SciTech Connect

    Gardner, W.L.; Caughman, J.B.O.; Hoffman, D.J.; Probert, P.H.

    1993-12-31

    Two new concepts are being developed as possible upgrades to the folded waveguide launcher. The folded stripline is a folded waveguide with an additional conductor positioned inside. The term stripline refers to the resemblance of the design to microwave microstrip line. The conductor provides support for TEM mode propagation, which eliminates cutoff and the nonlinear frequency dependence of the waveguide impedance and phase velocity. A natural extension to the folded stripline is the stacked stripline, which comprises several stacked, independent TEM waveguides. Initial measurements indicate that both concepts have better magnetic flux coupling than the folded waveguide.

  18. Comparison of the folded stripline and stacked stripline concepts to the folded waveguide launcher

    SciTech Connect

    Gardner, W.L.; Caughman, J.B.O.; Hoffman, D.J. ); Probert, P.H. )

    1994-10-15

    Two new concepts are being developed as possible upgrades to the folded waveguide launcher. The folded stripline is a folded waveguide with an additional conductor positioned inside. The term [ital stripline] refers to the resemblance of the design to microwave microstrip line. The conductor provides support for TEM mode propagation, which eliminates cutoff and the nonlinear frequency dependence of the waveguide impedance and phase velocity. A natural extension to the folded stripline is the stacked stripline, which comprises several stacked, independent TEM waveguides. Initial measurements indicate that both concepts have better magnetic flux coupling than the folded waveguide.

  19. Vibrational properties, phonon spectrum and related thermal parameters of β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine: a theoretical study.

    PubMed

    Qian, Wen; Zhang, Weibin; Zong, Hehou; Gao, Guofang; Zhou, Yang; Zhang, Chaoyang

    2016-01-01

    The vibrational spectrum, phonon dispersion curve, and phonon density of states (DOS) of β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (β-HMX) crystal were obtained by molecular simulation and calculations. As results, it was found that the peaks at low frequency (0-2.5 THz) are comparable with the experimental Terahertz absorption and the molecular vibrational modes are in agreement with previous reports. Thermodynamic properties including Gibbs free energy, enthalpy, and heat capacity as functions of temperature were obtained based on the calculated phonon spectrum. The heat capacity at normal temperature was calculated using linear fitting method, with a result consistent with experiments. Graphical Abstract Phonon spectrum and heat capacity of β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine from DFT calculation.

  20. Aeroelastic and Flight Dynamics Analysis of Folding Wing Systems

    NASA Astrophysics Data System (ADS)

    Wang, Ivan

    This dissertation explores the aeroelastic stability of a folding wing using both theoretical and experimental methods. The theoretical model is based on the existing clamped-wing aeroelastic model that uses beam theory structural dynamics and strip theory aerodynamics. A higher-fidelity theoretical model was created by adding several improvements to the existing model, namely a structural model that uses ANSYS for individual wing segment modes and an unsteady vortex lattice aerodynamic model. The comparison with the lower-fidelity model shows that the higher-fidelity model typical provides better agreement between theory and experiment, but the predicted system behavior in general does not change, reinforcing the effectiveness of the low-fidelity model for preliminary design of folding wings. The present work also conducted more detailed aeroelastic analyses of three-segment folding wings, and in particular considers the Lockheed-type configurations to understand the existence of sudden changes in predicted aeroelastic behavior with varying fold angle for certain configurations. These phenomena were observed in carefully conducted experiments, and nonlinearities---structural and geometry---were shown to suppress the phenomena. Next, new experimental models with better manufacturing tolerances are designed to be tested in the Duke University Wind Tunnel. The testing focused on various configurations of three-segment folding wings in order to obtain higher quality data. Next, the theoretical model was further improved by adding aircraft longitudinal degrees of freedom such that the aeroelastic model may predict the instabilities for the entire aircraft and not just a clamped wing. The theoretical results show that the flutter instabilities typically occur at a higher air speed due to greater frequency separation between modes for the aircraft system than a clamped wing system, but the divergence instabilities occur at a lower air speed. Lastly, additional

  1. 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.

  2. Cycle 22 COS/NUV Fold Distribution

    NASA Astrophysics Data System (ADS)

    Wheeler, T.; Welty, A.

    2016-09-01

    We summarize the Cycle 22 COS/NUV Fold Distribution for the Cosmic Origins Spectrograph's (COS) MAMA detector on the Hubble Space Telescope. The detector micro-channel plate's health state is determined and the results are presented.

  3. Folded Resonant Horns for Power Ultrasonic Applications

    NASA Technical Reports Server (NTRS)

    Sherrit, Stewart; Askins, Stephen; Gradziel, Michael; Bao, Xiaoqi; Chang, Zensheu; Dolgin, Benjamin; Bar-Cohen, Yoseph; Peterson, Tom

    2003-01-01

    Folded horns have been conceived as alternatives to straight horns used as resonators and strain amplifiers in power ultrasonic systems. Such systems are used for cleaning, welding, soldering, cutting, and drilling in a variety of industries. In addition, several previous NASA Tech Briefs articles have described instrumented drilling, coring, and burrowing machines that utilize combinations of sonic and ultrasonic vibrational actuation. The main advantage of a folded horn, relative to a straight horn of the same resonance frequency, is that the folded horn can be made shorter (that is, its greatest linear dimension measured from the outside can be made smaller). Alternatively, for a given length, the resonance frequency can be reduced. Hence, the folded-horn concept affords an additional degree of design freedom for reducing the length of an ultrasonic power system that includes a horn.

  4. Folding, Binding, Misfolding and Aggregation with AWSEM

    NASA Astrophysics Data System (ADS)

    Schafer, Nicholas P.

    This thesis discusses our recent results using the Associative-memory, Water-mediated, Structure and Energy Model (AWSEM), an optimized, coarse-grained molecular dynamics protein folding model, to fold, bind, and predict the misfolding behavior of proteins. AWSEM is capable of performing de novo structure prediction on small alpha-helical protein domains and predict the binding interfaces of homo- and hetero-dimers. More recent work demonstrates how the misfolding behavior of tandem constructs in AWSEM is consistent with crucial aspects of ensemble and single molecule experiments on the aggregation and misfolding of these constructs. The first chapter is a review of the energy landscape theory of protein folding as it applies to the problem of protein structure prediction, and more specifically how energy landscape theory and the principle of minimal frustration can be used to optimize parameters of coarse-grained protein folding simulation models. The subsequent four chapters are reports of novel research performed with one such model.

  5. 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.

  6. Origami: Paper Folding--The Algorithmic Way.

    ERIC Educational Resources Information Center

    Heukerott, Pamela Beth

    1988-01-01

    Describes origami, the oriental art of paper folding as an activity to teach upper elementary students concepts and skills in geometry involving polygons, angles, measurement, symmetry, and congruence. (PK)

  7. Frustration in Condensed Matter and Protein Folding

    NASA Astrophysics Data System (ADS)

    Li, Z.; Tanner, S.; Conroy, B.; Owens, F.; Tran, M. M.; Boekema, C.

    2014-03-01

    By means of computer modeling, we are studying frustration in condensed matter and protein folding, including the influence of temperature and Thomson-figure formation. Frustration is due to competing interactions in a disordered state. The key issue is how the particles interact to reach the lowest frustration. The relaxation for frustration is mostly a power function (randomly assigned pattern) or an exponential function (regular patterns like Thomson figures). For the atomic Thomson model, frustration is predicted to decrease with the formation of Thomson figures at zero kelvin. We attempt to apply our frustration modeling to protein folding and dynamics. We investigate the homogeneous protein frustration that would cause the speed of the protein folding to increase. Increase of protein frustration (where frustration and hydrophobicity interplay with protein folding) may lead to a protein mutation. Research is supported by WiSE@SJSU and AFC San Jose.

  8. The Ribosome Modulates Nascent Protein Folding

    PubMed Central

    Kaiser, Christian M.; Goldman, Daniel H.; Chodera, John D.; Tinoco, Ignacio; Bustamante, Carlos

    2014-01-01

    Proteins are synthesized by the ribosome and generally must fold to become functionally active. Although it is commonly assumed that the ribosome affects the folding process, this idea has been extremely difficult to demonstrate. We have developed an experimental system to investigate the folding of single ribosome-bound stalled nascent polypeptides with optical tweezers. In T4 lysozyme, synthesized in a reconstituted in vitro translation system, the ribosome slows the formation of stable tertiary interactions and the attainment of the native state relative to the free protein. Incomplete T4 lysozyme polypeptides misfold and aggregate when free in solution, but they remain folding-competent near the ribosomal surface. Altogether, our results suggest that the ribosome not only decodes the genetic information and synthesizes polypeptides, but also promotes efficient de novo attainment of the native state. PMID:22194581

  9. 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.

  10. Synthesis, characterization and anticancer evaluation of novel tri-arm star shaped 1,3,5-triazine hydrazones

    NASA Astrophysics Data System (ADS)

    Machakanur, Shrinath S.; Patil, Basavaraj R.; Badiger, Dayananda S.; Bakale, Raghavendra P.; Gudasi, Kalagouda B.; Annie Bligh, S. W.

    2012-03-01

    A series of novel trisubstituted triazine hydrazones [N3C3(sbnd OC6H4-p-CHdbnd Nsbnd NHsbnd C(O)sbnd C6H4-p-X)3] (X = H, Br, Cl, F, OH, OCH3, CH3, NO2, NH2) were prepared by a three-fold condensation reaction of 2,4,6-tris(4-formylphenoxy)-1,3,5-triazine with p-substituted benzoic acid hydrazides [NH2sbnd NHsbnd C(O)sbnd C6H4-p-X] with excellent yields. The structures were confirmed by elemental analysis, FT-IR, 1H, 13C, 2D-HSQC NMR and mass spectrometry (MALDI-TOF). These derivatives bearing hydrolysable hydrazone linkages were evaluated for their invitro antiproliferative activity against the human liver carcinoma cell line (HepG2) and human cervix carcinoma cell line (HeLa).

  11. 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.

  12. FOLD PROFILER: A MATLAB ®—based program for fold shape classification

    NASA Astrophysics Data System (ADS)

    Lisle, R. J.; Fernández Martínez, J. L.; Bobillo-Ares, N.; Menéndez, O.; Aller, J.; Bastida, F.

    2006-02-01

    FOLD PROFILER is a MATLAB code for classifying the shapes of profiles of folded surfaces. The classification is based on the comparison of the natural fold profile with curves representing mathematical functions. The user is offered a choice of four methods, each based on a different type of function: cubic Bezier curves, conic sections, power functions and superellipses. The comparison is carried out by the visual matching of the fold profile displayed on-screen from an imported digital image and computed theoretical curves which are superimposed on the image of the fold. To improve the fit with the real fold shape, the parameters of the theoretical curves are changed by simple mouse actions. The parameters of the mathematical function that best fits the real folds are used to classify the fold shape. FOLD PROFILER allows the rapid implementation of four existing methods for fold shape analysis. The attractiveness of this analytical tool lies in the way it gives an instant visual appreciation of the effect of changing the parameters that are used to classify fold geometry.

  13. 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

  14. 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

  15. [Congenital retinal folds in different clinical cases].

    PubMed

    Munteanu, M

    2005-01-01

    We present 12 clinical cases of congenital retinal folds with different etiologies: posterior primitive vitreous persistency and hyperplasia (7 cases),retinocytoma (1 case). retinopathy of prematurity (1 case), astrocytoma of the retina (1 case), retinal vasculitis (1 case), Goldmann-Favre syndrome (1 case). Etiopathogenic and nosological aspects are discussed; the congenital retinal folds are interpreted as a symptom in a context of a congenital or acquired vitreo-retinal pathology.

  16. Geometric Folding Algorithms: Bridging Theory to Practice

    DTIC Science & Technology

    2009-11-03

    Proved that any orthogonal polyhedron can be folded from a single, universal crease pattern (box pleating). 1.2 Origami Design • Developed...mathematical theory for what happens in paper between creases, in partic- ular for the case of circular creases. • Circular crease origami on permanent...sheet of paper. • Developing mathematical theory of Robert Lang’s TreeMaker framework for efficiently folding tree-shaped origami "bases

  17. Protein folding and misfolding: mechanism and principles.

    PubMed

    Englander, S Walter; Mayne, Leland; Krishna, Mallela M G

    2007-11-01

    Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors

  18. 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.

  19. "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.

  20. 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.

  1. Dual folding pathways of an α /β protein from all-atom ab initio folding simulations

    NASA Astrophysics Data System (ADS)

    Lei, Hongxing; Wang, Zhi-Xiang; Wu, Chun; Duan, Yong

    2009-10-01

    Successful ab initio folding of proteins with both α-helix and β-sheet requires a delicate balance among a variety of forces in the simulation model, which may explain that the successful folding of any α /β proteins to within experimental error has yet to be reported. Here we demonstrate that it is an achievable goal to fold α /β proteins with a force field emphasizing the balance between the two major secondary structures. Using our newly developed force field, we conducted extensive ab initio folding simulations on an α /β protein full sequence design (FSD) employing both conventional molecular dynamics and replica exchange molecular dynamics in combination with a generalized-Born solvation model. In these simulations, the folding of FSD to the native state with high population (>64.2%) and high fidelity (Cα-Root Mean Square Deviation of 1.29 Å for the most sampled conformation when compared to the experimental structure) was achieved. The folding of FSD was found to follow two pathways. In the major pathway, the folding started from the formation of the helix. In the minor pathway, however, folding of the β-hairpin started first. Further examination revealed that the helix initiated from the C-terminus and propagated toward the N-terminus. The formation of the hydrophobic contacts coincided with the global folding. Therefore the hydrophobic force does not appear to be the driving force of the folding of this protein.

  2. 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.

  3. The nature of protein folding pathways

    PubMed Central

    Englander, S. Walter; Mayne, Leland

    2014-01-01

    How do proteins fold, and why do they fold in that way? This Perspective integrates earlier and more recent advances over the 50-y history of the protein folding problem, emphasizing unambiguously clear structural information. Experimental results show that, contrary to prior belief, proteins are multistate rather than two-state objects. They are composed of separately cooperative foldon building blocks that can be seen to repeatedly unfold and refold as units even under native conditions. Similarly, foldons are lost as units when proteins are destabilized to produce partially unfolded equilibrium molten globules. In kinetic folding, the inherently cooperative nature of foldons predisposes the thermally driven amino acid-level search to form an initial foldon and subsequent foldons in later assisted searches. The small size of foldon units, ∼20 residues, resolves the Levinthal time-scale search problem. These microscopic-level search processes can be identified with the disordered multitrack search envisioned in the “new view” model for protein folding. Emergent macroscopic foldon–foldon interactions then collectively provide the structural guidance and free energy bias for the ordered addition of foldons in a stepwise pathway that sequentially builds the native protein. These conclusions reconcile the seemingly opposed new view and defined pathway models; the two models account for different stages of the protein folding process. Additionally, these observations answer the “how” and the “why” questions. The protein folding pathway depends on the same foldon units and foldon–foldon interactions that construct the native structure. PMID:25326421

  4. Probing possible downhill folding: native contact topology likely places a significant constraint on the folding cooperativity of proteins with approximately 40 residues.

    PubMed

    Badasyan, Artem; Liu, Zhirong; Chan, Hue Sun

    2008-12-12

    Experiments point to appreciable variations in folding cooperativity among natural proteins with approximately 40 residues, indicating that the behaviors of these proteins are valuable for delineating the contributing factors to cooperative folding. To explore the role of native topology in a protein's propensity to fold cooperatively and how native topology might constrain the degree of cooperativity achievable by a given set of physical interactions, we compared folding/unfolding kinetics simulated using three classes of native-centric C(alpha) chain models with different interaction schemes. The approach was applied to two homologous 45-residue fragments from the peripheral subunit-binding domain family and a 39-residue fragment of the N-terminal domain of ribosomal protein L9. Free-energy profiles as functions of native contact number were computed to assess the heights of thermodynamic barriers to folding. In addition, chevron plots of folding/unfolding rates were constructed as functions of native stability to facilitate comparison with available experimental data. Although common Gō-like models with pairwise Lennard-Jones-type interactions generally fold less cooperatively than real proteins, the rank ordering of cooperativity predicted by these models is consistent with experiment for the proteins investigated, showing increasing folding cooperativity with increasing nonlocality of a protein's native contacts. Models that account for water-expulsion (desolvation) barriers and models with many-body (nonadditive) interactions generally entail higher degrees of folding cooperativity indicated by more linear model chevron plots, but the rank ordering of cooperativity remains unchanged. A robust, experimentally valid rank ordering of model folding cooperativity independent of the multiple native-centric interaction schemes tested here argues that native topology places significant constraints on how cooperatively a protein can fold.

  5. 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

  6. Folding at the birth of the nascent chain: coordinating translation with co-translational folding.

    PubMed

    Zhang, Gong; Ignatova, Zoya

    2011-02-01

    In the living cells, the folding of many proteins is largely believed to begin co-translationally, during their biosynthesis at the ribosomes. In the ribosomal tunnel, the nascent peptide may establish local interactions and stabilize α-helical structures. Long-range contacts are more likely outside the ribosomes after release of larger segments of the nascent chain. Examples suggest that domains can attain native-like structure on the ribosome with and without population of folding intermediates. The co-translational folding is limited by the speed of the gradual extrusion of the nascent peptide which imposes conformational restraints on its folding landscape. Recent experimental and in silico modeling studies indicate that translation kinetics fine-tunes co-translational folding by providing a time delay for sequential folding of distinct portions of the nascent chain.

  7. 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).

  8. Computational and theoretical methods for protein folding.

    PubMed

    Compiani, Mario; Capriotti, Emidio

    2013-12-03

    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.

  9. Visualizing chaperone-assisted protein folding

    PubMed Central

    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 CA

    2016-01-01

    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, where 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 novel 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 E. coli chaperone Spy. This study resulted in a series of snapshots depicting the various folding states of Im7 while bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded and native-like states, and reveals how a substrate can explore its folding landscape while bound to a chaperone. PMID:27239796

  10. 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

  11. 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.

  12. 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…

  13. Palaeomagnetic analysis of plunging fold structures: Errors and a simple fold test

    NASA Astrophysics Data System (ADS)

    Stewart, Simon A.

    1995-02-01

    The conventional corrections for bedding dip in palaeomagnetic studies involve either untilting about strike or about some inclined axis—the choice is usually governed by the perceived fold hinge orientation. While it has been recognised that untilting bedding about strike can be erroneous if the beds lie within plunging fold structures, there are several types of fold which have plunging hinges, but whose limbs have rotated about horizontal axes. Examples are interference structures and forced folds; restoration about inclined axes may be incorrect in these cases. The angular errors imposed upon palaeomagnetic lineation data via the wrong choice of rotation axis during unfolding are calculated here and presented for lineations in any orientation which could be associated with an upright, symmetrical fold. This extends to palaeomagnetic data previous analyses which were relevant to bedding-parallel lineations. This numerical analysis highlights the influence of various parameters which describe fold geometry and relative lineation orientation upon the angular error imparted to lineation data by the wrong unfolding method. The effect of each parameter is described, and the interaction of the parameters in producing the final error is discussed. Structural and palaeomagnetic data are cited from two field examples of fold structures which illustrate the alternative kinematic histories. Both are from thin-skinned thrust belts, but the data show that one is a true plunging fold, formed by rotation about its inclined hinge, whereas the other is an interference structure produced by rotation of the limbs about non-parallel horizontal axes. Since the angle between the palaeomagnetic lineations and the inclined fold hinge is equal on both limbs in the former type of structure, but varies from limb to limb in the latter, a simple test can be defined which uses palaeomagnetic lineation data to identify rotation axes and hence fold type. This test can use pre- or syn-folding

  14. Osmolyte-induced folding of an intrinsically disordered protein: folding mechanism in the absence of ligand.

    PubMed

    Chang, Yu-Chu; Oas, Terrence G

    2010-06-29

    Understanding the interconversion between thermodynamically distinguishable states present in a protein folding pathway provides not only the kinetics and energetics of protein folding but also insights into the functional roles of these states in biological systems. The protein component of the bacterial RNase P holoenzyme from Bacillus subtilis (P protein) was previously shown to be unfolded in the absence of its cognate RNA or other anionic ligands. P protein was used in this study as a model system to explore general features of intrinsically disordered protein (IDP) folding mechanisms. The use of trimethylamine N-oxide (TMAO), an osmolyte that stabilizes the unliganded folded form of the protein, enabled us to study the folding process of P protein in the absence of ligand. Transient stopped-flow kinetic traces at various final TMAO concentrations exhibited multiphasic kinetics. Equilibrium "cotitration" experiments were performed using both TMAO and urea during the titration to produce a urea-TMAO titration surface of P protein. Both kinetic and equilibrium studies show evidence of a previously undetected intermediate state in the P protein folding process. The intermediate state is significantly populated, and the folding rate constants are relatively slow compared to those of intrinsically folded proteins similar in size and topology. The experiments and analysis described serve as a useful example for mechanistic folding studies of other IDPs.

  15. 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

  16. Gas-phase folding and unfolding of cytochrome c cations.

    PubMed Central

    Wood, T D; Chorush, R A; Wampler, F M; Little, D P; O'Connor, P B; McLafferty, F W

    1995-01-01

    Water is thought to play a dominant role in protein folding, yet gaseous multiply protonated proteins from which the water has been completely removed show hydrogen/deuterium (H/D) exchange behavior similar to that used to identify conformations in solution. Indicative of the gas-phase accessibility to D2O, multiply-charged (6+ to 17+) cytochrome c cations exchange at six (or more) distinct levels of 64 to 173 out of 198 exchangeable H atoms, with the 132 H level found at charge values 8+ to 17+. Infrared laser heating and fast collisions can apparently induce ions to unfold to exchange at a higher distinct level, while charge-stripping ions to lower charge values yields apparent folding as well as unfolding. PMID:7708663

  17. Transversal Clifford gates on folded surface codes

    SciTech Connect

    Moussa, Jonathan E.

    2016-10-12

    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. Lastly, the specific application of these codes to universal quantum computation based on qubit fusion is also discussed.

  18. Transversal Clifford gates on folded surface codes

    DOE PAGES

    Moussa, Jonathan E.

    2016-10-12

    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 surfacemore » 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. Lastly, the specific application of these codes to universal quantum computation based on qubit fusion is also discussed.« less

  19. Exact folded-band chaotic oscillator.

    PubMed

    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.

  20. 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

  1. The early folding kinetics of apomyoglobin.

    PubMed Central

    Pappu, R. V.; Weaver, D. L.

    1998-01-01

    The folding pathway of apomyoglobin has been experimentally shown to have early kinetic intermediates involving the A, B, G, and H helices. The earliest detected kinetic events occur on a ns to micros time scale. We show that the early folding kinetics of apomyoglobin may be understood as the association of nascent helices through a network of diffusion-collision-coalescence steps G + H <--> GH + A <--> AGH + B <--> ABGH obtained by solving the diffusion-collision model in a chemical kinetics approximation. Our reproduction of the experimental results indicates that the model is a useful way to analyze folding data. One prediction from our fit is that the nascent A and H helices should be relatively more helix-like before coalescence than the other apomyoglobin helices. PMID:9521125

  2. 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.

  3. 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

  4. Desorption of 1,3,5-Trichlorobenzene from Multi-Walled Carbon Nanotubes: Impact of Solution Chemistry and Surface Chemistry

    PubMed Central

    Ma, Xingmao; Uddin, Sheikh

    2013-01-01

    The strong affinity of carbon nanotubes (CNTs) to environmental contaminants has raised serious concern that CNTs may function as a carrier of environmental pollutants and lead to contamination in places where the environmental pollutants are not expected. However, this concern will not be realized until the contaminants are desorbed from CNTs. It is well recognized that the desorption of environmental pollutants from pre-laden CNTs varies with the environmental conditions, such as the solution pH and ionic strength. However, comprehensive investigation on the influence of solution chemistry on the desorption process has not been carried out, even though numerous investigations have been conducted to investigate the impact of solution chemistry on the adsorption of environmental pollutants on CNTs. The main objective of this study was to determine the influence of solution chemistry (e.g., pH, ionic strength) and surface functionalization on the desorption of preloaded 1,3,5-trichlorobenzene (1,3,5-TCB) from multi-walled carbon nanotubes (MWNTs). The results suggested that higher pH, ionic strength and natural organic matter in solution generally led to higher desorption of 1,3,5-TCB from MWNTs. However, the extent of change varied at different values of the tested parameters (e.g., pH < 7 vs. pH > 7). In addition, the impact of these parameters varied with MWNTs possessing different surface functional groups, suggesting that surface functionalization could considerably alter the environmental behaviors and impact of MWNTs.

  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. FOLD LENS FLUX ANOMALIES: A GEOMETRIC APPROACH

    SciTech Connect

    Goldberg, David M.; Chessey, Mary K.; Harris, Wendy B.; Richards, Gordon T.

    2010-06-01

    We develop a new approach for studying flux anomalies in quadruply imaged fold lens systems. We show that in the absence of substructure, microlensing, or differential absorption, the expected flux ratios of a fold pair can be tightly constrained using only geometric arguments. We apply this technique to 11 known quadruple lens systems in the radio and infrared and compare our estimates to the Monte Carlo based results of Keeton et al. We show that a robust estimate for a flux ratio from a smoothly varying potential can be found, and at long wavelengths those lenses deviating from this ratio almost certainly contain significant substructure.

  7. Fold Lens Flux Anomalies: A Geometric Approach

    NASA Astrophysics Data System (ADS)

    Goldberg, David M.; Chessey, Mary K.; Harris, Wendy B.; Richards, Gordon T.

    2010-06-01

    We develop a new approach for studying flux anomalies in quadruply imaged fold lens systems. We show that in the absence of substructure, microlensing, or differential absorption, the expected flux ratios of a fold pair can be tightly constrained using only geometric arguments. We apply this technique to 11 known quadruple lens systems in the radio and infrared and compare our estimates to the Monte Carlo based results of Keeton et al. We show that a robust estimate for a flux ratio from a smoothly varying potential can be found, and at long wavelengths those lenses deviating from this ratio almost certainly contain significant substructure.

  8. 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.

  9. 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.

  10. Circular permutant GFP insertion folding reporters

    DOEpatents

    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.

  11. Circular permutant GFP insertion folding reporters

    DOEpatents

    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.

  12. 3.5 Year Monitoring of 225 GHz Opacity at the Summit of Greenland

    NASA Astrophysics Data System (ADS)

    Matsushita, Satoki; Asada, Keiichi; Martin-Cocher, Pierre L.; Chen, Ming-Tang; Ho, Paul T. P.; Inoue, Makoto; Koch, Patrick M.; Paine, Scott N.; Turner, David D.

    2017-02-01

    We present the 3.5 years monitoring results of 225 GHz opacity at the summit of the Greenland ice sheet (Greenland Summit Camp) at an altitude of 3200 m using a tipping radiometer. We chose this site as our submillimeter telescope (Greenland Telescope) site, because conditions are expected to have low submillimeter opacity and because its location offers favorable baselines to existing submillimeter telescopes for global-scale Very Long Baseline Interferometry. The site shows a clear seasonal variation with the average opacity lower by a factor of two during winter. The 25%, 50%, and 75% quartiles of the 225 GHz opacity during the winter months of November through April are 0.046, 0.060, and 0.080, respectively. For the winter quartiles of 25% and 50%, the Greenland site is about 10%-30% worse than the Atacama Large Millimeter/submillimeter Array (ALMA) or the South Pole sites. Estimated atmospheric transmission spectra in winter season are similar to the ALMA site at lower frequencies (\\lt 450 GHz), which are transparent enough to perform astronomical observations almost all of the winter time with opacities \\lt 0.5, but 10%-25% higher opacities at higher frequencies (\\gt 450 GHz) than those at the ALMA site. This is due to the lower altitude of the Greenland site and the resulting higher line wing opacity from pressure-broadened saturated water lines in addition to higher dry air continuum absorption at higher frequencies. Nevertheless, half of the winter time at the Greenland Summit Camp can be used for astronomical observations at frequencies between 450 GHz and 1000 GHz with opacities \\lt 1.2, and 10% of the time show \\gt 10 % transmittance in the THz (1035 GHz, 1350 GHz, and 1500 GHz) windows. Summer season is good for observations at frequencies lower than 380 GHz. One major advantage of the Greenland Summit Camp site in winter is that there is no diurnal variation due to the polar night condition, and therefore the durations of low-opacity conditions

  13. Backscatter from a limestone seafloor at 2-3.5 kHz: measurements and modeling.

    PubMed

    Soukup, Raymond J; Gragg, Robert F

    2003-05-01

    Physics-based interface scattering models for the seafloor [H.-H. Essen, J. Acoust. Soc. Am. 95, 1299-1310 (1994); Gragg et al., ibid. 110, 2878-2901 (2001)] exhibit features in their predicted grazing angle dependence. These features have a strong dependence on the assumed composition and roughness of the bottom. Verifying such predictions requires data that cover a wide range of grazing angles and involve minimal sub-bottom penetration. Such measurements were performed in the frequency band 2-3.5 kHz over an exposed limestone bottom off the Carolina coast during the second Littoral Warfare Advanced Development Focused Technology Experiment of 1996 (LWAD FTE 96-2). Direct-path bottom scattering strengths were obtained in shallow water (198-310 m deep) for grazing angles from 8 degrees to 75 degrees using data fusion from multiple experimental geometries coupled with careful signal processing. The processing included corrections for the surface-reflected path, other multipaths, and characteristics of the reverberation decay observed over the pulse duration at higher grazing angles. The resulting frequency and grazing-angle dependences exhibit trends consistent with theoretical predictions, and geoacoustic parameters obtained by inversion are consistent with values expected for limestone.

  14. Doping of Cn (N = 1, 3, 5, 8) cluster ion tracks in polyimide

    NASA Astrophysics Data System (ADS)

    Fink, D.; Klett, R.; Chung, W. H.; Grünwald, R.; Döbeli, M.; Ames, F.; Chadderton, L. T.; Vacik, J.; Hnatowicz, V.

    Cn+ cluster ions (n = 1, 3, 5, and 8) are implanted at 1 MeV/carbon atom and at fluences of 1010 to 1014 cluster ions/cm2 into thin polyimide foils. The ion-induced radiochemical changes are examined by infrared spectroscopy. The samples are then doped with either aqueous LiCl, or methylene blue dye solutions. The dopant uptake is determined by UV-Vis spectrometry in the first, and by NDP (neutron depth profiling) in the latter case. NDP examinations additionally give information about the depth distributions of the incorporated Li+ ions. Remarkable changes in the infrared signals and in the dopant uptake are found only at fluences when ion track overlapping sets in. For the same fluence, clusters with larger size show more efficient destruction than smaller ones. Also the dopant uptake capability is higher in cluster-irradiated polymers than in single-atomic C+ ion irradiated samples. The depth distribution of the incorporated dopant usually consists of both a pronounced surface-near, and a bulk dopant-enriched region. The surface-near dopant profile increases in height and width with increasing cluster size and fluence. The depth profile shape of the bulk component follows the one of the ion's energy transfer to the target via nuclear collisions. A rule of thumb to describe the action of such a cluster ion onto polymers is given.

  15. 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.

  16. 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.

  17. Untemplated nonenzymatic polymerization of 3',5'cGMP: a plausible route to 3',5'-linked oligonucleotides in primordia.

    PubMed

    Šponer, Judit E; Šponer, Jiří; Giorgi, Alessandra; Di Mauro, Ernesto; Pino, Samanta; Costanzo, Giovanna

    2015-02-19

    The high-energy 3',5' phosphodiester linkages conserved in 3',5' cyclic GMPs offer a genuine solution for monomer activation required by the transphosphorylation reactions that could lead to the emergence of the first simple oligonucleotide sequences on the early Earth. In this work we provide an in-depth characterization of the effect of the reaction conditions on the yield of the polymerization reaction of 3',5' cyclic GMPs both in aqueous environment as well as under dehydrating conditions. We show that the threshold temperature of the polymerization is about 30 °C lower under dehydrating conditions than in solution. In addition, we present a plausible exergonic reaction pathway for the polymerization reaction, which involves transient formation of anionic centers at the O3' positions of the participating riboses. We suggest that excess Na(+) cations inhibit the polymerization reaction because they block the anionic mechanism via neutralizing the negatively charged O3'. Our experimental findings are compatible with a prebiotic scenario, where gradual desiccation of the environment could induce polymerization of 3',5' cyclic GMPs synthesized in liquid.

  18. Intramolecular C-arylation of 2,3,5-tri-O-benzyl- and 2,3,5-tri-O-(3-methylbenzyl)-pentofuranose derivatives.

    PubMed

    Martin, O R

    1987-12-31

    Upon treatment with tin(IV) chloride, 1-O-acetyl-2,3,5-tri-O-benzyl- and 1-O-acetyl-2,3,5-tri-O-(3-methylbenzyl)pentofuranose (D-ribo, L-arabino) undergo intramolecular Friedel-Crafts alkylation of the aromatic substituent at O-2 to give unusual internal C-glycosyl compounds (isochroman derivatives) in high yield. The final products are also partially debenzylated at O-3 or O-5 (up to 25%) under these conditions. By contrast, the corresponding methyl glycosides are poor substrates for the intramolecular C-arylation reaction, as methyl 2,3,5-tri-O-(3-methylbenzyl)-beta-D-ribofuranoside was found to give preponderantly methyl 3,5-di-O-(3-methylbenzyl)-alpha-D-ribofuranoside (11) (49%), and the C-arylation product in 30% yield only in the presence of the same Lewis acid. The competitive formation of 11 is thought to be due to the anomerization of the substrate leading to a tin(IV) complex coordinated with O-1 and O-2, which promoted the cleavage of the benzyl group at O-2. These reactions provide a novel and efficient C-arylation method and suggest a new approach to selectively protected D-ribofuranose derivatives. Evidence for the uncommon C-arylated structure of the new products was gained from their 1H- and 13C(APT)-n.m.r. spectra.

  19. 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...

  20. 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…

  1. 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].

  2. 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.

  3. Understanding the role of the topology in protein folding by computational inverse folding experiments.

    PubMed

    Mucherino, Antonio; Costantini, Susan; di Serafino, Daniela; D'Apuzzo, Marco; Facchiano, Angelo; Colonna, Giovanni

    2008-08-01

    Recent studies suggest that protein folding should be revisited as the emergent property of a complex system and that the nature allows only a very limited number of folds that seem to be strongly influenced by geometrical properties. In this work we explore the principles underlying this new view and show how helical protein conformations can be obtained starting from simple geometric considerations. We generated a large data set of C-alpha traces made of 65 points, by computationally solving a backbone model that takes into account only topological features of the all-alpha proteins; then, we built corresponding tertiary structures, by using the sequences associated to the crystallographic structures of four small globular all-alpha proteins from PDB, and analysed them in terms of structural and energetic properties. In this way we obtained four poorly populated sets of structures that are reasonably similar to the conformational states typical of the experimental PDB structures. These results show that our computational approach can capture the native topology of all-alpha proteins; furthermore, it generates backbone folds without the influence of the side chains and uses the protein sequence to select a specific fold among the generated folds. This agrees with the recent view that the backbone plays an important role in the protein folding process and that the amino acid sequence chooses its own fold within a limited total number of folds.

  4. 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.

  5. Protein folded states are kinetic hubs

    PubMed Central

    Bowman, Gregory R.; Pande, Vijay S.

    2010-01-01

    Understanding molecular kinetics, and particularly protein folding, is a classic grand challenge in molecular biophysics. Network models, such as Markov state models (MSMs), are one potential solution to this problem. MSMs have recently yielded quantitative agreement with experimentally derived structures and folding rates for specific systems, leaving them positioned to potentially provide a deeper understanding of molecular kinetics that can lead to experimentally testable hypotheses. Here we use existing MSMs for the villin headpiece and NTL9, which were constructed from atomistic simulations, to accomplish this goal. In addition, we provide simpler, humanly comprehensible networks that capture the essence of molecular kinetics and reproduce qualitative phenomena like the apparent two-state folding often seen in experiments. Together, these models show that protein dynamics are dominated by stochastic jumps between numerous metastable states and that proteins have heterogeneous unfolded states (many unfolded basins that interconvert more rapidly with the native state than with one another) yet often still appear two-state. Most importantly, we find that protein native states are hubs that can be reached quickly from any other state. However, metastability and a web of nonnative states slow the average folding rate. Experimental tests for these findings and their implications for other fields, like protein design, are also discussed. PMID:20534497

  6. Sequential self-folding of polymer sheets

    PubMed Central

    Liu, Ying; Shaw, Brandi; Dickey, Michael D.; Genzer, Jan

    2017-01-01

    Shape plays an important role in defining the function of materials, particularly those found in nature. Several strategies exist to program materials to change from one shape to another; however, few can temporally and spatially control the shape. Programming the sequence of shape transformation with temporal control has been driven by the desire to generate complex shapes with high yield and to create multiple shapes from the same starting material. This paper demonstrates a markedly simple strategy for programmed self-folding of two-dimensional (2D) polymer sheets into 3D objects in a sequential manner using external light. Printed ink on the surface of the polymer sheets discriminately absorbs light on the basis of the wavelength of the light and the color of the ink that defines the hinge about which the sheet folds. The absorbed light gradually heats the underlying polymer across the thickness of the sheet, which causes relief of strain to induce folding. These color patterns can be designed to absorb only specific wavelengths of light (or to absorb differently at the same wavelength using color hues), thereby providing control of sheet folding with respect to time and space. This type of shape programming may have numerous applications, including reconfigurable electronics, actuators, sensors, implantable devices, smart packaging, and deployable structures. PMID:28275736

  7. Adaptive Origami for Efficiently Folded Structures

    DTIC Science & Technology

    2016-02-01

    4 3.2 Design of 2D-to- 3D Actuating Mechanisms...printing, lithography) to convert surface patterns on substrates into stable 3D objects. The design and fabrication of structures based on folding...Nafion, where prescribed 3D geometric information can be encoded as a spatially patterned composite of discrete shape-memory and locked-shape-memory

  8. 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…

  9. 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).

  10. Clinical evaluation of vocal fold paralysis.

    PubMed

    Richardson, Brent E; Bastian, Robert W

    2004-02-01

    Vocal fold paralysis is regarded as a sign of other pathologic findings until investigation has proven that there is no lesion to explain the paralysis. We have outlined a cost-effective and time- and labor-efficient method for the clinical evaluation of vocal fold paralysis, including a focused history; vocal capability assessment to find deficits in the function of palate,pharynx, and larynx: and, finally, an intense examination under topical anesthesia to demonstrate these deficits. In essence, it is the endoscopic version of a radiographic study from the skull base through the aortic arch. This method is streamlined as compared with prior protocols for evaluation of vocal fold paralysis, because it directs the necessary further workup according to the likely site of the lesion as indicated by the extended physical examination and can be conducted entirely in the physician's office. Radiographic workup should include CT of the skull base through the upper mediastinum if solely a recurrent nerve paralysis is present; it should include MRI of the skull base if high vagal signs and symptoms are present. If MRI is negative, CT may also be needed for complete evaluation. Neurologic signs that are not all ipsilateral require MRI of the brain and consultation with a neurologist. Esophageal obstruction combined with vocal fold paralysis mandates evaluation via esophagoscopy or an esophagram.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. Fast phase randomization via two-folds.

    PubMed

    Simpson, D J W; Jeffrey, M R

    2016-02-01

    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.

  16. 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.

  17. 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.

  18. Parent-progeny sequencing indicates higher mutation rates in heterozygotes.

    PubMed

    Yang, Sihai; Wang, Long; Huang, Ju; Zhang, Xiaohui; Yuan, Yang; Chen, Jian-Qun; Hurst, Laurence D; Tian, Dacheng

    2015-07-23

    Mutation rates vary within genomes, but the causes of this remain unclear. As many prior inferences rely on methods that assume an absence of selection, potentially leading to artefactual results, we call mutation events directly using a parent-offspring sequencing strategy focusing on Arabidopsis and using rice and honey bee for replication. Here we show that mutation rates are higher in heterozygotes and in proximity to crossover events. A correlation between recombination rate and intraspecific diversity is in part owing to a higher mutation rate in domains of high recombination/diversity. Implicating diversity per se as a cause, we find an ∼3.5-fold higher mutation rate in heterozygotes than in homozygotes, with mutations occurring in closer proximity to heterozygous sites than expected by chance. In a genome that is a patchwork of heterozygous and homozygous domains, mutations occur disproportionately more often in the heterozygous domains. If segregating mutations predispose to a higher local mutation rate, clusters of genes dominantly under purifying selection (more commonly homozygous) and under balancing selection (more commonly heterozygous), might have low and high mutation rates, respectively. Our results are consistent with this, there being a ten times higher mutation rate in pathogen resistance genes, expected to be under positive or balancing selection. Consequently, we do not necessarily need to evoke extremely weak selection on the mutation rate to explain why mutational hot and cold spots might correspond to regions under positive/balancing and purifying selection, respectively.

  19. 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.

  20. 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

    2013-01-02

    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.

  1. Congenital hypothyroidism mutations affect common folding and trafficking in the α/β-hydrolase fold proteins.

    PubMed

    De Jaco, Antonella; Dubi, Noga; Camp, Shelley; Taylor, Palmer

    2012-12-01

    The α/β-hydrolase fold superfamily of proteins is composed of structurally related members that, despite great diversity in their catalytic, recognition, adhesion and chaperone functions, share a common fold governed by homologous residues and conserved disulfide bridges. Non-synonymous single nucleotide polymorphisms within the α/β-hydrolase fold domain in various family members have been found for congenital endocrine, metabolic and nervous system disorders. By examining the amino acid sequence from the various proteins, mutations were found to be prevalent in conserved residues within the α/β-hydrolase fold of the homologous proteins. This is the case for the thyroglobulin mutations linked to congenital hypothyroidism. To address whether correct folding of the common domain is required for protein export, we inserted the thyroglobulin mutations at homologous positions in two correlated but simpler α/β-hydrolase fold proteins known to be exported to the cell surface: neuroligin3 and acetylcholinesterase. Here we show that these mutations in the cholinesterase homologous region alter the folding properties of the α/β-hydrolase fold domain, which are reflected in defects in protein trafficking, folding and function, and ultimately result in retention of the partially processed proteins in the endoplasmic reticulum. Accordingly, mutations at conserved residues may be transferred amongst homologous proteins to produce common processing defects despite disparate functions, protein complexity and tissue-specific expression of the homologous proteins. More importantly, a similar assembly of the α/β-hydrolase fold domain tertiary structure among homologous members of the superfamily is required for correct trafficking of the proteins to their final destination.

  2. Nomenclature proposal to describe vocal fold motion impairment.

    PubMed

    Rosen, Clark A; Mau, Ted; Remacle, Marc; Hess, Markus; Eckel, Hans E; Young, VyVy N; Hantzakos, Anastasios; Yung, Katherine C; Dikkers, Frederik G

    2016-08-01

    The terms used to describe vocal fold motion impairment are confusing and not standardized. This results in a failure to communicate accurately and to major limitations of interpreting research studies involving vocal fold impairment. We propose standard nomenclature for reporting vocal fold impairment. Overarching terms of vocal fold immobility and hypomobility are rigorously defined. This includes assessment techniques and inclusion and exclusion criteria for determining vocal fold immobility and hypomobility. In addition, criteria for use of the following terms have been outlined in detail: vocal fold paralysis, vocal fold paresis, vocal fold immobility/hypomobility associated with mechanical impairment of the crico-arytenoid joint and vocal fold immobility/hypomobility related to laryngeal malignant disease. This represents the first rigorously defined vocal fold motion impairment nomenclature system. This provides detailed definitions to the terms vocal fold paralysis and vocal fold paresis.

  3. [4 anthroposcopic markers in the Northern Greece population: hand folding, arm folding, tongue rolling and tongue folding].

    PubMed

    Pentzos-Daponte, A

    1986-03-01

    Four anthroposcopic traits, namely hand clasping, arm folding, tongue rolling and tongue curling have been studied in a total of 7763 individuals from Thessaloniki and its surroundings, representing a sample of the population of Northern Greece. The statistical analysis of the data indicates significant sex differences only concerning tongue rolling. The frequencies obtained for the four traits under study are compared with data from the literature.

  4. Protein GB1 Folding and Assembly from Structural Elements

    PubMed Central

    Bauer, Mikael C.; Xue, Wei-Feng; Linse, Sara

    2009-01-01

    Folding of the Protein G B1 domain (PGB1) shifts with increasing salt concentration from a cooperative assembly of inherently unstructured subdomains to an assembly of partly pre-folded structures. The salt-dependence of pre-folding contributes to the stability minimum observed at physiological salt conditions. Our conclusions are based on a study in which the reconstitution of PGB1 from two fragments was studied as a function of salt concentrations and temperature using circular dichroism spectroscopy. Salt was found to induce an increase in β-hairpin structure for the C-terminal fragment (residues 41 – 56), whereas no major salt effect on structure was observed for the isolated N-terminal fragment (residues 1 – 41). In line with the increasing evidence on the interrelation between fragment complementation and stability of the corresponding intact protein, we also find that salt effects on reconstitution can be predicted from salt dependence of the stability of the intact protein. Our data show that our variant (which has the mutations T2Q, N8D, N37D and reconstitutes in a manner similar to the wild type) displays the lowest equilibrium association constant around physiological salt concentration, with higher affinity observed both at lower and higher salt concentration. This corroborates the salt effects on the stability towards denaturation of the intact protein, for which the stability at physiological salt is lower compared to both lower and higher salt concentrations. Hence we conclude that reconstitution reports on molecular factors that govern the native states of proteins. PMID:19468325

  5. Physiological and Pharmacological Influences on Thyroxine to 3,5,3′-Triiodothyronine Conversion and Nuclear 3,5,3′-Triiodothyronine Binding in Rat Anterior Pituitary

    PubMed Central

    Cheron, R. G.; Kaplan, M. M.; Larsen, P. R.

    1979-01-01

    Our recent in vivo studies have suggested that intrapituitary l-thyroxine (T4) to 3,5,3′-triiodo-l-thyronine (T3) conversion with subsequent nuclear binding of T3 is an important pathway by which circulating T4 can inhibit thyrotropin release. The present studies were performed to evaluate various physiological and pharmacological influences on these two processes in rat anterior pituitary tissue. Intact pituitary fragments were incubated in buffer—1% bovine serum albumin containing 0.14 ng/ml [131I]T3 and 3.8 ng/ml [125I]T4. Nuclei were isolated after 3 h of incubation and the bound iodothyronines identified by paper chromatography. There was 0.3-1% [125I]T3 contaminating the medium [125I]T4, and this did not change during incubation. Nuclear [125I]T4 was not decreased by 650-fold excesses of medium T3 or T4, suggesting that it was nonspecifically bound. The ratio of nuclear to medium [131I]- and [125I]T3 were expressed as nuclear counts per minute per milligram wet weight of tissue:counts per minute per microliter medium. Intrapituitary T4 to T3 conversion was evidenced by the fact that the nuclear:medium (N:M) ratio for [131I]T3 was 0.45±0.21, whereas that for [125I]T3 was 2.23±1.28 (mean±SD, n = 51). A ratio (R), the N:M [125I]T3 divided by the N:M [131I]T3, was used as an index of intrapituitary T4 to T3 conversion. Increasing medium T3 concentrations up to 50 ng/ml caused a progressive decrease in the N:M ratio for both T3 isotopes, but no change in the value for R, indicating that both competed for the same limited-capacity nuclear receptors. Increasing concentrations of medium T4 caused no change in the N:M [131I]T3 but did cause a significant decrease in R in three of four experiments. These results suggest saturation of T4-5′-monodeiodination occurred at lower T4 concentrations than saturation of nuclear T3 binding sites. In hypothyroid rats, the N:M ratios for both [131I]T3 and [125I]T3 were increased (P < 0.005), but R was three-fold higher

  6. The shape and mechanics of curved-fold origami structures

    NASA Astrophysics Data System (ADS)

    Dias, Marcelo A.; Santangelo, Christian D.

    2012-12-01

    We develop recursion equations to describe the three-dimensional shape of a sheet upon which a series of concentric curved folds have been inscribed. In the case of no stretching outside the fold, the three-dimensional shape of a single fold prescribes the shape of the entire origami structure. To better explore these structures, we derive continuum equations, valid in the limit of vanishing spacing between folds, to describe the smooth surface intersecting all the mountain folds. We find that this surface has negative Gaussian curvature with magnitude equal to the square of the fold's torsion. A series of open folds with constant fold angle generate a helicoid.

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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 of 14C-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.

  12. 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.

  13. 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.

  14. 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

    NASA Astrophysics Data System (ADS)

    Long, Yao; Chen, Jun

    2015-09-01

    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.

  15. Environmentally assisted cracking of 3.5NiCrMoV low alloy steel under cyclic straining

    SciTech Connect

    Kondo, Yoshiyuki; Bodai, Masaru; Takei, Mao; Sugita, Yuji; Inagaki, Hironobu

    1997-12-01

    Environmentally assisted cracking of 3.5NiCrMoV low alloy steel under cyclic straining was investigated in water environments at 60 C. Effects of strain range, strain rate, strain hold tie and impurities in the water on the crack initiation life were investigated. The effects of long strain hold time up to 100 hours were studied and found to be especially significant. Lower strain rate, longer strain hold time and higher electric conductivity resulted in shorter crack initiation life. The corrosion current from the strained metal was measured in a simulated electrochemical system to clarify the root cause of the life reduction. Test results showed that higher strain range, lower strain rate, longer strain hold time and higher electric conductivity caused increased charge transfer, which caused shorter crack initiation life. A prediction model for the crack initiation life was proposed based on the charge transfer.

  16. Synthesis of novel triplet drugs with 1,3,5-trioxazatriquinane skeletons and their pharmacologies. 1: Synthesis of triplet drugs with morphinan skeletons.

    PubMed

    Nagase, Hiroshi; Watanabe, Akio; Nemoto, Toru; Nakajima, Mayumi; Hasebe, Ko; Mochizuki, Hidenori; Fujii, Hideaki

    2011-07-01

    We synthesized symmetrical and nonsymmetrical triplet drugs with 1,3,5-trioxazatriquinane skeletons. The isolation of key intermediates, oxazoline dimers, made it possible to effectively produce nonsymmetrical triplets. Among the synthesized triplets, KNT-93, composed of three identical opioid μ receptor agonists, showed dose-dependent antinociception via the μ receptor. The effect was 56-fold more potent than that of morphine, a representative μ agonist. The profound analgesic effect induced by KNT-93 might result from simultaneous occupation of three μ opioid receptors.

  17. Initiation of GnRH agonist treatment on 3-5 days postoperatively in endometriosis patients: a randomized controlled trial.

    PubMed

    Gong, Lili; Zhang, Shaofen; Han, Yi; Long, Qiqi; Zou, Shien; Cao, Yuankui

    2015-08-01

    Seventy patients with stage III or IV endometriosis were randomly assigned to 2 groups after conservative surgery. Group O (n = 35) received 3 cycles of a 28-day gonadotropin-releasing hormone agonist (GnRH-a) treatment (goserelin, 3.6 mg) starting 3-5 days postoperatively. Group M (n = 35) received the same treatment starting on days 1-5 of menstruation. Groups were further subdivided according to add-back treatment. Pre- and posttreated levels of estradiol (E2 ), follicle stimulating hormone (FSH), and luteinizing hormone (LH) and visual analog scale (VAS), Kupperman menopausal index (KMI), and bone mineral density (BMD) scores were recorded. The incidence of uterine bleeding was assessed. In both groups, serum levels of E2 , FSH, and LH and VAS scores decreased significantly after treatment. Spotting was the most frequent bleeding pattern. During cycle 1, the bleeding time in group M was much longer that than that in group O (P =.001), and the bleeding rate in group M was significantly higher than that in group O (P =.024, RR = 1.185). In patients with stage III or IV endometriosis, the efficacy of GnRH-a initiated 3-5 days postoperatively was equivalent to that of GnRH-a initiated on days 1-5 of menstruation. Female patients who initiated GnRH-a treatment 3-5 days postoperatively experienced less uterine bleeding during the first cycle of treatment.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. Convoluted accommodation structures in folded rocks

    NASA Astrophysics Data System (ADS)

    Dodwell, T. J.; Hunt, G. W.

    2012-10-01

    A simplified variational model for the formation of convoluted accommodation structures, as seen in the hinge zones of larger-scale geological folds, is presented. The model encapsulates some important and intriguing nonlinear features, notably: infinite critical loads, formation of plastic hinges, and buckling on different length-scales. An inextensible elastic beam is forced by uniform overburden pressure and axial load into a V-shaped geometry dictated by formation of a plastic hinge. Using variational methods developed by Dodwell et al., upon which this paper leans heavily, energy minimisation leads to representation as a fourth-order nonlinear differential equation with free boundary conditions. Equilibrium solutions are found using numerical shooting techniques. Under the Maxwell stability criterion, it is recognised that global energy minimisers can exist with convoluted physical shapes. For such solutions, parallels can be drawn with some of the accommodation structures seen in exposed escarpments of real geological folds.

  4. 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.

  5. Vocal fold mobility alteration reversed after thyroidectomy

    PubMed Central

    Miazaki, Aline Paterno; Araújo-Filho, Vergilius José Furtado; Brandão, Lenine Garcia; de Araujo-Neto, Vergilius José Furtado; Cernea, Claudio Roberto

    2016-01-01

    The involvement of the inferior or recurrent laryngeal nerve (RLN) in mobility derangement of the vocal folds occurs more frequently due to thyroid malignancy invasion. Although uncommon, the same derangement, which is caused by benign thyroid entities, is also described and reverts to normality after a thyroidectomy in up to 89% of cases. In these cases, the pathogenesis of the vocal cord mobility disturbance is attributed to the direct compression of the RLN by massive thyroid enlargement. The authors describe three cases of patients presenting unilateral vocal cord palsy, which, before surgery, was diagnosed by laryngoscopy concomitantly with large and compressive goiter. Vocal fold mobility became normal after the thyroidectomy in all three cases. Therefore, it is noteworthy that these alterations may present reversibility after appropriate surgical treatment. An early surgical approach is recommended to reduce the nerve injury as much as possible; to preserve the integrity of both RLNs since the nerve function will be restored in some patients. PMID:27818960

  6. 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.

  7. Ubiquitylation Directly Induces Fold Destabilization of Proteins

    PubMed Central

    Morimoto, Daichi; Walinda, Erik; Fukada, Harumi; Sugase, Kenji; Shirakawa, Masahiro

    2016-01-01

    Ubiquitin is a common post-translational modifier and its conjugation is a key signal for proteolysis by the proteasome. Because the molecular mass of ubiquitin is larger than that of other modifiers such as phosphate, acetyl, or methyl groups, ubiquitylation not only influences biochemical signaling, but also may exert physical effects on its substrate proteins by increasing molecular volume and altering shape anisotropy. Here we show that ubiquitylation destabilizes the fold of two proteins, FKBP12 and FABP4, and that elongation of the conjugated ubiquitin chains further enhances this destabilization effect. Moreover, NMR relaxation analysis shows that ubiquitylation induces characteristic structural fluctuations in the backbone of both proteins. These results suggest that the ubiquitylation-driven structural fluctuations lead to fold destabilization of its substrate proteins. Thus, physical destabilization by ubiquitylation may facilitate protein degradation by the proteasome. PMID:27991582

  8. 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

  9. Heat capacity change for ribonuclease A folding.

    PubMed Central

    Pace, C. N.; Grimsley, G. R.; Thomas, S. T.; Makhatadze, G. I.

    1999-01-01

    The change in heat capacity deltaCp for the folding of ribonuclease A was determined using differential scanning calorimetry and thermal denaturation curves. The methods gave equivalent results, deltaCp = 1.15+/-0.08 kcal mol(-1) K(-1). Estimates of the conformational stability of ribonuclease A based on these results from thermal unfolding are in good agreement with estimates from urea unfolding analyzed using the linear extrapolation method. PMID:10422839

  10. Calnexin, calreticulin and the folding of glycoproteins.

    PubMed

    1997-05-01

    Calnexin and calreticulin are molecular chaperones in the endoplasmic reticulum (ERJ. They are lectins that interact with newly synthesized glycoproteins that have undergone partial trimming of their core N-linked oligosaccharides. Together with the enzymes responsible for glucose removal and a glucosyltransferase that re-glucosylates already-trimmed glycoproteins, they provide a novel mechanism for promoting folding, oligomeric assembly and quality control in the ER.

  11. 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

  12. 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.

  13. Unhydrolyzable analogues of adenosine 3':5'-monophosphate demonstrating growth inhibition and differentiation in human cancer cells.

    PubMed

    Yokozaki, H; Tortora, G; Pepe, S; Maronde, E; Genieser, H G; Jastorff, B; Cho-Chung, Y S

    1992-05-01

    A set of adenosine 3':5'-monophosphate (cAMP) analogues that combine exocyclic sulfur substitutions in the equatorial (Rp) or the axial (Sp) position of the cyclophosphate ring with modifications in the adenine base of cAMP were tested for their effect on the growth of HL-60 human promyelocytic leukemia cells and LS-174T human colon carcinoma cells. Both diasteromeres of the phosphorothioate derivatives were growth inhibitory, exhibiting a concentration inhibiting 50% of cell proliferation of 3-100 microM. Among the analogues tested, Rp-8-Cl-cAMPS and Sp-8-Br-cAMPS were the two most potent. Rp-8-Cl-cAMPS was 5- to 10-fold less potent than 8-Cl-cAMP while Sp-8-Br-cAMPS was approximately 6-fold more potent than 8-Br-cAMP. The growth inhibition was not due to a block in a specific phase of the cell cycle or due to cytotoxicity. Rp-8-Cl-cAMPS enhanced its growth-inhibitory effect when added together with 8-Cl-cAMP and increased differentiation in combination with N6-benzyl-cAMP. The binding kinetics data showed that these Sp and Rp modifications brought about a greater decrease in affinity for Site B than for Site A of RI (the regulatory subunit of type I cAMP-dependent protein kinase) and a substantial decrease of affinity for Site A of RII (the regulatory subunit of type II protein kinase) but only a small decrease in affinity for Site B of RII, indicating the importance of the Site B binding of RII in the growth-inhibitory effect. These results show that the phosphorothioate analogues of cAMP are useful tools to investigate the mechanism of action of cAMP in growth control and differentiation and may have practical implication in the suppression of malignancy.

  14. Understanding the folding-function tradeoff in proteins.

    PubMed

    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.

  15. 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.

  16. 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

  17. Photochemical carbonylation of adamantanes; simple synthesis of 1,3,5,7-tetranitroadamantane

    SciTech Connect

    Bashir-Hashemi, A.; Li, J.; Gelber, N.

    1995-12-01

    1,3,5,7-Tetranitroadamantane (2) was obtained from the irradiation of a mixture of 1-adamantanecarboxylic acid (1) and oxalylchloride followed by conversion of chlorocarbonyl functions to nitro groups using the method of Eaton et. al.

  18. 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…

  19. 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)…

  20. 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…

  1. Higher Education.

    ERIC Educational Resources Information Center

    Knowles, Laurence W.; Wedlock, Eldon D., Jr.

    Courts have been consistently reluctant to interfere with governing boards' powers to control the administration of institutions of higher education. This deference seems to be based on the belief that board expertise makes it significantly more qualified than are the courts to make the necessary administrative decisions. Uncritical deference by…

  2. 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.

  3. 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.

  4. Orthogonal self-assembly in folding block copolymers.

    PubMed

    Hosono, Nobuhiko; Gillissen, Martijn A J; Li, Yuanchao; Sheiko, Sergei S; Palmans, Anja R A; Meijer, E W

    2013-01-09

    We herein report the synthesis and characterization of ABA triblock copolymers that contain two complementary association motifs and fold into single-chain polymeric nanoparticles (SCPNs) via orthogonal self-assembly. The copolymers were prepared using atom-transfer radical polymerization (ATRP) and possess different pendant functional groups in the A and B blocks (alcohols in the A block and acetylenes in the B block). After postfunctionalization, the A block contains o-nitrobenzyl-protected 2-ureidopyrimidinone (UPy) moieties and the B block benzene-1,3,5-tricarboxamide (BTA) moieties. While the protected UPy groups dimerize after photoinduced deprotection of the o-nitrobenzyl group, the BTA moieties self-assemble into helical aggregates when temperature is reduced. In a two-step thermal/photoirradiation treatment under dilute conditions, the ABA block copolymer forms both BTA-based helical aggregates and UPy dimers intramolecularly. The sequential association of the two self-assembling motifs results in single-chain folding of the polymer, affording nanometer-sized particles with a compartmentalized interior. Variable-temperature NMR studies showed that the BTA and UPy self-assembly steps take place orthogonally (i.e., without mutual interference) in dilute solution. In addition, monitoring of the intramolecular self-assembly of BTA moieties into helical aggregates by circular dichroism spectroscopy showed that the stability of the aggregates is almost independent of UPy dimerization. Size-exclusion chromatography (SEC) and small-angle X-ray scattering analysis provided evidence of significant reductions in the hydrodynamic volume and radius of gyration, respectively, after photoinduced deprotection of the UPy groups; a 30-60% reduction in the size of the polymer chains was observed using SEC in CHCl(3). Molecular imaging by atomic force microscopy (AFM) corroborated significant contraction of individual polymer chains due to intramolecular association of the

  5. Are turns required for the folding of ribonuclease T1?

    PubMed Central

    Garrett, J. B.; Mullins, L. S.; Raushel, F. M.

    1996-01-01

    Ribonuclease T1 (RNase T1) is a small, globular protein of 104 amino acids for which extensive thermodynamic and structural information is known. To assess the specific influence of variations in amino acid sequence on the mechanism for protein folding, circularly permuted variants of RNase T1 were constructed and characterized in terms of catalytic activity and thermodynamic stability. The disulfide bond connecting Cys-2 and Cys-10 was removed by mutation of these residues to alanine (C2, 10A) to avoid potential steric problems imposed by the circular permutations. The original amino-terminus and carboxyl-terminus of the mutant (C2, 10A) were subsequently joined with a tripeptide linker to accommodate a reverse turn and new termini were introduced throughout the primary sequence in regions of solvent-exposed loops at Ser-35 (cp35S1), Asp-49 (cp49D1), Gly-70 (cp70G1), and Ser-96 (cp96S1). These circularly permuted RNase T1 mutants retained 35-100% of the original catalytic activity for the hydrolysis of guanylyl(3'-->5')cytidine, suggesting that the overall tertiary fold of these mutants is very similar to that of wild-type protein. Chemical denaturation curves indicated thermodynamic stabilities at pH 5.0 of 5.7, 2.9, 2.6, and 4.6 kcal/mol for cp35S1, cp49D1, cp70G1, and cp96S1, respectively, compared to a value of 10.1 kcal/mol for wild-type RNase T1 and 6.4 kcal/mol for (C2, 10A) T1. A fifth set of circularly permuted variants was attempted with new termini positioned in a tight beta-turn between Glu-82 and Gln-85. New termini were inserted at Asn-83 (cp83N1), Asn-84 (cp84N1), and Gln-85 (cp85Q1). No detectable amount of protein was ever produced for any of the mutations in this region, suggesting that this turn may be critical for the proper folding and/or thermodynamic stability of RNase T1. PMID:8745397

  6. G3.5 PAMAM Dendrimers Enhance Transepithelial Transport of SN38 while minimizing Gastrointestinal Toxicity

    PubMed Central

    Goldberg, Deborah S.; Vijayalakshmi, Nirmalkumar; Swaan, Peter W.; Ghandehari, Hamidreza

    2011-01-01

    Poly(amido amine) (PAMAM) dendrimers have shown promise in oral drug delivery. Conjugation of SN38 to PAMAM dendrimers has the potential to improve its oral absorption while minimizing gastrointestinal toxicity. In this work we evaluated G3.5 PAMAM dendrimer-SN38 conjugates with ester-linked glycine and β-alanine spacers for their suitability in oral therapy of hepatic colorectal cancer metastases. G3.5-βAlanine-SN38 was mostly stable while G3.5-Glycine-SN38 showed 10%, 20%, and 56% SN38 release in simulated gastric, intestinal and liver environments for up to 6, 24 and 48 hours, respectively. Short-term treatment of Caco-2 cells with G3.5-SN38 conjugates did not reduce cell viability, while comparable concentrations of SN38 caused significant cytotoxicity. G3.5-Glycine-SN38 and G3.5-βAlanine-SN38 showed IC50 values of 0.60 and 3.59 μM, respectively, in HT-29 cells treated for 48 hours, indicating the efficacy of the drug delivery system in colorectal cancer cells with longer incubation time. Both conjugates increased SN38 transepithelial transport compared to the free drug. Transport of G3.5-Glycine-SN38 was highly concentration-dependent whereas transport of G3.5-βAlanine-SN38 was concentration-independent, highlighting the influence of drug loading and spacer chemistry on transport mechanism. Together these results show that PAMAM dendrimers have the potential to improve the oral bioavailability of potent anti-cancer drugs. PMID:21115079

  7. 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.

  8. 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.

  9. 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

  10. Reversal of Trimethyltin-Induced Learning and Memory Deficits by 3,5-Dicaffeoylquinic Acid

    PubMed Central

    Kang, Jin Yong; Park, Seon Kyeong; Guo, Tian Jiao; Ha, Jeong Su; Lee, Du Sang; Kim, Jong Min; Lee, Uk; Kim, Dae Ok

    2016-01-01

    The antiamnesic effect of 3,5-dicaffeoylquinic acid (3,5-diCQA) as the main phenolic compound in Artemisia argyi H. extract on cognitive dysfunction induced by trimethyltin (TMT) (7.1 μg/kg of body weight; intraperitoneal injection) was investigated in order to assess its ameliorating function in mice. In several behavioral tests, namely, the Y-maze, passive avoidance, and Morris water maze (MWM) test, 3,5-diCQA significantly ameliorated learning and memory deficits. After the behavioral tests, brain tissues from the mice were analyzed to characterize the basis of the neuroprotective effect. Acetylcholine (ACh) levels increased, whereas the activity of acetylcholinesterase (AChE) decreased upon administration of 3,5-diCQA. In addition, 3,5-diCQA effectively protected against an increase in malondialdehyde (MDA) content, an increase in the oxidized glutathione (GSH) ratio, and a decline of total superoxide dismutase (SOD) level. 3,5-diCQA may prevent neuronal apoptosis through the protection of mitochondrial activities and the repression of apoptotic signaling molecules such as p-Akt, BAX, and p-tau (Ser 404). PMID:28105250

  11. Folding mechanism of a multiple independently-folding domain protein: double B domain of protein A.

    PubMed

    Arora, Pooja; Hammes, Gordon G; Oas, Terrence G

    2006-10-10

    The antibody binding properties of staphylococcal protein A (SpA) can be attributed to the presence of five highly homologous domains (E, D, A, B, and C). Although the folding of the B domain of protein A (BdpA) is well-characterized, the folding behavior of this domain in the context of full-length SpA in the cell remains unexplored. The sequence of the B domain is 89 and 91% identical to those of domains A and C, respectively. We have fused B domain sequences (BBdpA) as a close approximation of the A-B or B-C portion of SpA. Circular dichroism and fluorescence-detected denaturation curves of BBdpA are experimentally indistinguishable from those of BdpA. The rate constants for folding and unfolding from NMR line shape analysis for the single- and double-domain proteins are the same within experimental uncertainties (+/-20%). These results support the designation of SpA as a multiple independently-folding domain (MIFD) protein. We develop a mathematical model that describes the folding thermodynamics and kinetics of MIFD proteins. The model depicts MIFD protein folding and unfolding as a parallel network and explicitly calculates the flux through all parallel pathways. These fluxes are combined to give a complete description of the global thermodynamics and kinetics of the folding and unfolding of MIFD proteins. The global rates for complete folding and unfolding of a MIFD protein and those of the individual domains depend on the stability of the protein. We show that the global unfolding rate of a MIFD protein may be many orders of magnitude slower than that of the constituent domains.

  12. Folding of a detachment and fault - Modified detachment folding along a lateral ramp, southwestern Montana, USA

    NASA Astrophysics Data System (ADS)

    Schmidt, Christopher; Whisner, S. Christopher; Whisner, Jennifer B.

    2014-12-01

    The inversion of the Middle Proterozoic Belt sedimentary basin during Late Cretaceous thrusting in Montana produced a large eastwardly-convex salient, the southern boundary of which is a 200 km-long oblique to lateral ramp subtended by a detachment between the Belt rocks and Archean basement. A 10 km-long lateral ramp segment exposes the upper levels of the detachment where hanging wall Belt rocks have moved out over the Paleozoic and Mesozoic section. The hanging wall structure consists of a train of high amplitude, faulted, asymmetrical detachment folds. Initial west-east shortening produced layer parallel shortening fabrics and dominantly strike slip faulting followed by symmetrical detachment folding. 'Lock-up' of movement on the detachment surface produced regional simple shear and caused the detachment folds to become asymmetrical and faulted. Folding of the detachment surface after lock-up modified the easternmost detachment folds further into a southeast-verging, overturned fold pair with a ramp-related fault along the base of the stretched mutual limb.

  13. 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…

  14. Infrared study of the stability and folding kinetics of a series of β-hairpin peptides with a common NPDG turn.

    PubMed

    Xu, Yao; Du, Deguo; Oyola, Rolando

    2011-12-29

    The thermal stability and folding kinetics of a series of 15-residue β-hairpins with a common Type I [3:5] NPDG turn were studied using Fourier transform infrared spectroscopy (FTIR) and laser-induced temperature jump (T-jump) with infrared detection, respectively. Mutations at positions 3, 5, or 13 in the peptide sequence SEXYXNPDGTWTXTE, where X represents the position of mutation, were performed to study the roles of hydrophobic interactions in determining the thermodynamic and kinetic properties of β-hairpin folding. The thermal stability studies show a broad thermal folding/unfolding transition for all the peptides. T-jump studies indicate that these β-hairpin peptides fold in less than 2 μs. In addition, both folding and unfolding rate constants decrease with increasing strength of hydrophobic interactions. Kinetically, the hydrophobic interactions have more significant influence on the unfolding rate than the folding rate. Φ-value analysis indicates that the hydrophobic interactions between the side chains are mainly formed at the latter part of the transition-state region during the folding process. In summary, the results suggest that the formation of the native structure of these β-hairpins depends on the correct topology of the hydrophobic cluster. Besides the formation of the turn region as a key process for folding as suggested by previous studies, a hydrophobic collapse process may also play a crucial role during β-hairpin folding.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Statistically Derived Rules for RNA Folding

    NASA Astrophysics Data System (ADS)

    Zuker, Michael

    2004-03-01

    What I am not going to talk about, although I could improvise, is predicting RNA folding by energy minimization. Peter Schuster certainly talked about it, although he didn't present any algorithms, etc. If I had been trained as a physicist or a chemist instead of a mathematician, and if my chemical colleagues had cared about statistics or Boltzmann distributions, I think I would have come up with the McCaskill algorithm for computing partition functions earlier, because no one ever told me that that was a problem needing to be solved. I think there's a good potential for combining the two approaches ...

  20. Polarization aberrations of crossed folding mirrors

    NASA Astrophysics Data System (ADS)

    Crandall, David G.; Chipman, Russell A.

    1995-08-01

    Polarization aberrations due to varying polarization state across the field of view (FOV) are investigated for crossed folding mirrors. We define crossed mirrors as oriented in space such that s-polarized light incident on the first mirror is p-polarized at the second mirror. This completely compensates for polarization state changes at one point in the field of view. The resulting polarization aberrations are explored across the FOV using the example of aluminum mirrors overcoated with a 12 layer, highly reflective, dielectric stack. The polarization aberration is very low along a band across the field of view. For arbitrary points in the FOV, the retardance and diattenuation are slightly elliptical.

  1. 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

  2. Computational Solutions to the Protein Folding Problem,

    DTIC Science & Technology

    1994-05-19

    A TRIDENT SCHOLAR oN PROJECT REPORT 0 NO. 223 "Computational Solutions to the Protein Folding Problem" L T -’ ’r i SEP 2 7 1994 ýV UNITED STATES...potential energy function (Chapter II), 25 1 2 2 U = X• k( l 1 -lo) 2+ X.ko (8,-8o) 2+X.-[1l + cos (Pip + )] Equation 4.1 xei (C ¶±~12.4 a where ri, is...iterative process, a set of k >_ 2"t+ l distinct local minima are computed. This can be done with rela- tive ease by using an efficient unconstrained

  3. Modelling RNA folding under mechanical tension

    PubMed Central

    VIEREGG, JEFFREY R.; TINOCO, IGNACIO

    2006-01-01

    We investigate the thermodynamics and kinetics of RNA unfolding and refolding under mechanical tension. The hierarchical nature of RNA structure and the existence of thermodynamic parameters for base pair formation based on nearest-neighbour interactions allows modelling of sequence-dependent folding dynamics for any secondary structure. We calculate experimental observables such as the transition force for unfolding, the end-to-end distribution function and its variance, as well as kinetic information, for a representative RNA sequence and for a sequence containing two homopolymer segments: A.U and G.C. PMID:16969426

  4. Antibody-detected folding: kinetics of surface epitope formation are distinct from other folding phases.

    PubMed Central

    Raman, C. S.; Jemmerson, R.; Nall, B. T.

    2000-01-01

    The rate of macromolecular surface formation in yeast iso-2 cytochrome c and its site-specific mutant, N52I iso-2, has been studied using a monoclonal antibody that recognizes a tertiary epitope including K58 and H39. The results indicate that epitope refolding occurs after fast folding but prior to slow folding, in contrast to horse cytochrome c where surface formation occurs early. The antibody-detected (ad) kinetic phase accompanying epitope formation has k(ad) = 0.2 s(-1) and is approximately 40-fold slower than the fastest detectable event in the folding of yeast iso-2 cytochrome c (k2f approximately 8 s(-1)), but occurs prior to the absorbance- and fluorescence-detected slow folding steps (k1a approximately 0.06 s(-1); k1b approximately 0.09 s(-1)). N5I iso-2 cytochrome c exhibits similar kinetic behavior with respect to epitope formation. A detailed dissection of the mechanistic differences between the folding pathways of horse and yeast cytochromes c identifies possible reasons for the slow surface formation in the latter. Our results suggest that non-native ligation involving H33 or H39 during refolding may slow down the formation of the tertiary epitope in iso-2 cytochrome c. This study illustrates that surface formation can be coupled to early events in protein folding. Thus, the rate of macromolecular surface formation is fine tuned by the residues that make up the surface and the interactions they entertain during refolding. PMID:10739255

  5. Communication between RNA folding domains revealed by folding of circularly permuted ribozymes.

    PubMed

    Lease, Richard A; Adilakshmi, Tadepalli; Heilman-Miller, Susan; Woodson, Sarah A

    2007-10-12

    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 degrees 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 degrees 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 T(1) 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.

  6. The Numba ductile deformation zone (northwest Cameroon): A geometric analysis of folds based on the Fold Profiler method

    NASA Astrophysics Data System (ADS)

    Njanko, T.; Chatué, C. Njiki; Kwékam, M.; Nké, B. E. Bella; Sandjo, A. F. Yakeu; Fozing, E. M.

    2017-03-01

    The Numba ductile deformation zone (NDDZ) is characterised by folds recorded during the three deformation phases that affected the banded amphibole gneiss. Fold-shape analyses using the program Fold Profiler with the aim to show the importance of folding events in the structural analysis of the NDDZ and its contribution to the Pan-African orogeny in central Africa have been made. Classical field method, conic sections method and Ramsay's fold classification method were applied to (i) have the general orientation of folds, (ii) analyze the fold shapes and (iii) classify the geometry of the folded bands. Fold axes in banded amphibole gneiss plunge moderately (<15°) towards the NNE or SSW. The morphology of F1, F2 and F3 folds in the study area clearly points to (i) Z-shape folds with SE vergence and (ii) a dextral sense of shear motion. Conic section method reveals two dominant families: F1 and F3 folds belong to parabolic shape folds, while F2 folds belong to parabolic shape and hyperbolic shape folds. Ramsay's scheme emphasizes class 1C (for F1, F2 and F3 folds) and class 3 (for F2 folds) as main fold classes. The co-existence of the various fold shapes can be explained by (i) the structuration of the banded gneiss, (ii) the folding mechanisms that associate shear with a non-least compressive or flattening component in a ductile shear zone and (iii) the change in rheological properties of the band during the period of fold formation. These data allow us to conclude that the Numba region underwent ductile dextral shear and can be integrated (i) in a correlation model with the Central Cameroon Shear Zone (CCSZ) and associated syn-kinematic intrusions and (ii) into the tectonic model of Pan-African belt of central Africa in Cameroon.

  7. 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.

  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. 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.

  10. 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.

  11. Structure and mechanical properties of thin films deposited from 1,3,5-trimethyl-1,3,5-trivinylcyclotrisiloxane and water

    NASA Astrophysics Data System (ADS)

    Burkey, Daniel D.; Gleason, Karen K.

    2003-05-01

    Pulsed-plasma chemical vapor deposition of 1,3,5-trimethyl-1,3,5-trivinylcyclotrisiloxane (V3D3) and water produced thin films with significant Si-OH content. Subsequent annealing of the films resulted in condensation of proximal Si-OH groups, further generating a Si-O-Si network and strengthening the film. Fourier-transform infrared spectroscopy analysis showed increasing OH content with increasing plasma duty cycle, and nanoindentation results confirmed increasing hardness with duty cycle, with the 10-40 duty cycle annealed sample having a hardness value of 0.527 GPa. These results were explained within the context of the continuous random network theory and percolation of rigidity arguments. Thermal stability was excellent, with a best-case thickness retention of 99.25% after a 2 h anneal at 400 °C under N2. Dielectric constants for the annealed films ranged between 2.55 and 2.9. The moderate power involved (200 W peak) is amenable to inclusion of a porogen species, opening the possibility of using this methodology to generate a porous thin film with adequate mechanical properties via chemical vapor deposition.

  12. Molecular dynamics simulations of hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using a combined Sorescu-Rice-Thompson AMBER force field.

    PubMed

    Agrawal, Paras M; Rice, Betsy M; Zheng, Lianqing; Thompson, Donald L

    2006-12-28

    We present the results of molecular dynamics simulations of crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using the SRT-AMBER force field (P. M. Agrawal et al., J. Phys. Chem. B 2006, 110, 5721), which combines the rigid-molecule force field developed by Sorescu-Rice-Thompson (D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 1997, 101, 798) with the intramolecular interactions obtained from the Generalized AMBER Force Field (Wang et al., J. Comput. Chem. 2004, 25, 1157). The calculated crystal density at room conditions is about 10% lower than the measured value, while the lattice parameters and thermodynamic melting point are within about 5% at ambient pressure. The chair and inverted chair conformation, bond lengths, and bond angles of the RDX molecule are accurately predicted; however, there are some inaccuracies in the calculated orientations of the NO2 groups. The SRT-AMBER force field predicts overall reasonable results, but modifications, probably in the torsional parameters, are needed for a more accurate force field.

  13. 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

    2013-08-06

    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.

  14. Mechanical restoration of large-scale folded multilayers using the finite element method: Application to the Zagros Simply Folded Belt, N-Iraq

    NASA Astrophysics Data System (ADS)

    Frehner, Marcel; Reif, Daniel; Grasemann, Bernhard

    2010-05-01

    and digital elevation models using the dip-domain method for balancing the cross-section. The lithology consists of Cretaceous to Cenozoic sediments. Massive carbonate rock units act as the competent layers compared to the incompetent behavior of siltstone, claystone and marl layers. We show the first results of the mechanical restoration of the Zagros cross-section and we discuss advantages and disadvantages, as well as some technical aspects of the applied method. First results indicate that a shortening of at least 50% was necessary to create the present-day folded cross-section. This value is higher than estimates of the amount of shortening solely based on kinematic or geometric restoration. One particular problem that is discussed is the presence of (unnaturally) sharp edges in a balanced cross-section produced using the dip-domain method, which need to be eliminated for mechanical restoration calculations to get reasonable results.

  15. 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.

  16. Solvent induced reactivity of 3,5-dimethylpyrazole towards zinc (II) carboxylates.

    PubMed

    Sarma, Rupam; Kalita, Dipjyoti; Baruah, Jubaraj B

    2009-09-28

    The reactions of 3,5-dimethylpyrazole with zinc(II)acetate dihydrate and varieties of aromatic carboxylic acids led to formation of mono-nuclear zinc complexes of composition [Zn(HDMP)2(RCO2)2] (R = C6H5, p-CH3-C6H4, p-NO2-C6H4 etc. HDMP = 3,5-dimethylpyrazole) in methanol, whereas the same reactants in dimethylformamide (DMF) gave binuclear 3,5-dimethylpyrazolato bridged zinc carboxylate complexes containing monodentate 3,5-dimethylpyraozole ligands with composition [Zn2(mu-DMP)2(HDMP)2(RCO2)2]. The mononuclear complexes can be converted to the corresponding binuclear complexes by simply dissolving in DMF. The reaction of zinc(II)acetate dihydrate with p-nitrobenzoic acid and 3,5-dimethylpyrazole in different solvents gave solvated mononuclear complexes of the corresponding solvent. All these solvated complexes having the core [Zn(HDMP)2(p-NO2-C6H4CO2)2] contain two structurally independent molecules in the asymmetric unit (Z' = 2).

  17. 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.

  18. 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.

  19. Numerical modeling of fold-and-thrust belts: Applications to Kuqa foreland fold belt, China

    NASA Astrophysics Data System (ADS)

    Yin, H.; Morgan, J. K.; Zhang, J.; Wang, Z.

    2009-12-01

    We constructed discrete element models to simulate the evolution of fold-and-thrust belts. The impact of rock competence and decollement strength on the geometric pattern and deformation mechanics of fold-and-thrust belts has been investigated. The models reproduced some characteristic features of fold-and-thrust belts, such as faulted detachment folds, pop-ups, far-traveled thrust sheets, passive-roof duplexes, and back thrusts. In general, deformation propagates farther above a weak decollement than above a strong decollement. Our model results confirm that fold-and-thrust belts with strong frictional decollements develop relatively steep and narrow wedges formed by closely spaced imbricate thrust slices, whereas fold belts with weak decollements form wide low-taper wedges composed of faulted detachment folds, pop-ups, and back thrusts. Far-traveled thrust sheets and passive-roof duplexes are observed in the model with a strong lower decollement and a weak upper detachment. Model results also indicate that the thickness of the weak layer is critical. If it is thick enough, it acts as a ductile layer that is able to flow under differential stress, which helps to partition deformation above and below it. The discrete element modeling results were used to interpret the evolution of Kuqa Cenozoic fold-and-thrust belt along northern Tarim basin, China. Seismic and well data show that the widely distributed Paleogene rock salt has a significant impact on the deformation in this area. Structures beneath salt are closely spaced imbricate thrust and passive-roof duplex systems. Deformation above salt propagates much farther than below the salt. Faults above salt are relatively wide spaced. A huge controversy over the Kuqa fold-and-thrust belt is whether it is thin-skinned or thick-skinned. With the insights from DEM results, we suggest that Kuqa structures are mostly thin-skinned with Paleogene salt as decollement, except for the rear part near the backstop, where the

  20. 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.

  1. 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.

  2. Analysis of folded pulse forming line operation.

    PubMed

    Domonkos, M T; Watrous, J; Parker, J V; Cavazos, T; Slenes, K; Heidger, S; Brown, D; Wilson, D

    2014-09-01

    A compact pulse forming line (CPFL) concept based on a folded transmission line and high-breakdown strength dielectric was explored through an effort combining proof-of-principle experiments with electromagnetic modeling. A small-scale folded CPFL was fabricated using surface-mount ceramic multilayer capacitors. The line consisted of 150 capacitors close-packed in parallel and delivered a 300 ns flat-top pulse. The concept was carried to a 10 kV class device using a polymer-ceramic nanocomposite dielectric with a permittivity of 37.6. The line was designed for a 161 ns FWHM length pulse into a matched load. The line delivered a 110 ns FWHM pulse, and the pulse peak amplitude exceeded the matched load ideal. Transient electromagnetic analysis using the particle-in-cell code ICEPIC was conducted to examine the nature of the unexpected pulse shortening and distortion. Two-dimensional analysis failed to capture the anomalous behavior. Three-dimensional analysis replicated the pulse shape and revealed that the bends were largely responsible for the pulse shortening. The bends not only create the expected reflection of the incident TEM wave but also produce a non-zero component of the Poynting vector perpendicular to the propagation direction of the dominant electromagnetic wave, resulting in power flow largely external to the PFL. This analysis explains both the pulse shortening and the amplitude of the pulse.

  3. Fold Lens Flux Anomalies: A Geometric Approach

    NASA Astrophysics Data System (ADS)

    Harris, Wendy B.; Chessey, M. K.; Goldberg, D. M.; Richards, G. T.

    2010-01-01

    Strong gravitational lensing of quasars is a powerful tool to learn about the distribution of dark matter in lensing galaxies. Multiply imaged quasar systems have symmetries which allow for an understanding of the lensing galaxy without detailed mass reconstructions. Keeton et al. (2005) defined a useful expression for the flux anomaly of "fold'' lenses, which we might naively expect to have the same flux: Rfold=(fA-fB)/(fA+fB), where "A'' and "B'' represent the positive and negative parity images straddling a critical curve. We show that the geometric configuration of the images greatly constrains the possible flux anomalies allowable from a smooth galaxy potential. Using gravlens, we create a number of simple galaxies from various mass models to put our solution to the test, and find that simulated flux anomalies are reproduced to an accuracy of |δ R| < 0.04. We then apply our approach to a radio sample of 9 well-studied fold lenses and quickly identify those with significant substructure.

  4. Structure of a Folding Intermediate Reveals the Interplay Between Core and Peripheral Elements in RNA Folding

    SciTech Connect

    Baird, Nathan J.; Westhof, Eric; Qin, Hong; Pan, Tao; Sosnick, Tobin R.

    2010-07-13

    Though the molecular architecture of many native RNA structures has been characterized, the structures of folding intermediates are poorly defined. Here, we present a nucleotide-level model of a highly structured equilibrium folding intermediate of the specificity domain of the Bacillus subtilis RNase P RNA, obtained using chemical and nuclease mapping, circular dichroism spectroscopy, small-angle X-ray scattering and molecular modeling. The crystal structure indicates that the 154 nucleotide specificity domain is composed of several secondary and tertiary structural modules. The structure of the intermediate contains modules composed of secondary structures and short-range tertiary interactions, implying a sequential order of tertiary structure formation during folding. The intermediate lacks the native core and several long-range interactions among peripheral regions, such as a GAAA tetraloop and its receptor. Folding to the native structure requires the local rearrangement of a T-loop in the core in concert with the formation of the GAAA tetraloop-receptor interaction. The interplay of core and peripheral structure formation rationalizes the high degree of cooperativity observed in the folding transition leading to the native structure.

  5. Folding of the hammerhead ribozyme: Pyrrolo-cytosine fluorescence separates core folding from global folding and reveals a pH-dependent conformational change

    PubMed Central

    Buskiewicz, Iwona A.; Burke, John M.

    2012-01-01

    The catalytic activity of the hammerhead ribozyme is limited by its ability to fold into the native tertiary structure. Analysis of folding has been hampered by a lack of assays that can independently monitor the environment of nucleobases throughout the ribozyme–substrate complex in real time. Here, we report the development and application of a new folding assay in which we use pyrrolo-cytosine (pyC) fluorescence to (1) probe active-site formation, (2) examine the ability of peripheral ribozyme domains to support native folding, (3) identify a pH-dependent conformational change within the ribozyme, and (4) explore its influence on the equilibrium between the folded and unfolded core of the hammerhead ribozyme. We conclude that the natural ribozyme folds in two distinct noncooperative steps and the pH-dependent correlation between core folding and activity is linked to formation of the G8-C3 base pair. PMID:22274955

  6. 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).

  7. On the kinetics and energetics of one-electron oxidation of 1,3,5-triazines.

    PubMed

    Azenha, M E D G; Burrows, H D; Canle, M; Coimbra, R; Fernández, M I; García, M V; Rodrigues, A E; Santaballa, J A; Steenken, S

    2003-01-07

    One-electron oxidation of 1,3,5-triazines is observed with both excited uranyl ion (*UO2(2+)) and sulfate radical anion (SO4.-) in aqueous solution, but not with Tl2+, indicating that the standard reduction potentials E degree of 1,3,5-triazine radical cations are = 2.3 +/- 0.1 V vs. NHE, consistent with theoretical calculations; this suggests that if triazines inhibit electron transfer during photosynthesis, they would need to act on the reductive part of the electron transport chain.

  8. 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.

  9. Bis(3,5-dimethylpyrazole-kappaN2)silver(I) nitrate.

    PubMed

    Mohamed, Ahmed A; Fackler, John P

    2002-04-01

    The two independent bis(3,5-dimethylpyrazole)silver(I) cations in crystalline [Ag(C(5)H(7)N(2))(2)]NO(3) display N-Ag-N angles of 175.51 (14) and 174.44 (13) degrees, and an average Ag-N distance of 2.124 (5) A. The nitrate anion is situated between [Ag(C(5)H(7)N(2))(2)]+ units and interacts via hydrogen bonds with the NH groups. The two 3,5-dimethylpyrazole ligands are trans about the silver center. Only a small deviation from linearity is observed in the coordination around silver.

  10. Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways

    PubMed Central

    Mohazab, Ali R.; Plotkin, Steven S.

    2013-01-01

    We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost chain, and calculating the minimal uncrossing cost that would have been required to avoid such events. A depth-first tree search algorithm is applied to find minimal transformations to fold , , , and knotted proteins. In all cases, the extra uncrossing/non-crossing distance is a small fraction of the total distance travelled by a ghost chain. Different structural classes may be distinguished by the amount of extra uncrossing distance, and the effectiveness of such discrimination is compared with other order parameters. It was seen that non-crossing distance over chain length provided the best discrimination between structural and kinetic classes. The scaling of non-crossing distance with chain length implies an inevitable crossover to entanglement-dominated folding mechanisms for sufficiently long chains. We further quantify the minimal folding pathways by collecting the sequence of uncrossing moves, which generally involve leg, loop, and elbow-like uncrossing moves, and rendering the collection of these moves over the unfolded ensemble as a multiple-transformation “alignment”. The consensus minimal pathway is constructed and shown schematically for representative cases of an , , and knotted protein. An overlap parameter is defined between pathways; we find that proteins have minimal overlap indicating diverse folding pathways, knotted proteins are highly constrained to follow a dominant pathway, and proteins are somewhere in between. Thus we have shown how topological chain constraints can induce dominant pathway mechanisms in protein folding. PMID:23365638

  11. An essential role of SVZ progenitors in cortical folding in gyrencephalic mammals

    PubMed Central

    Toda, Tomohisa; Shinmyo, Yohei; Dinh Duong, Tung Anh; Masuda, Kosuke; Kawasaki, Hiroshi

    2016-01-01

    Because folding of the cerebral cortex in the mammalian brain is believed to be crucial for higher brain functions, the mechanisms underlying its formation during development and evolution are of great interest. Although it has been proposed that increased neural progenitors in the subventricular zone (SVZ) are responsible for making cortical folds, their roles in cortical folding are still largely unclear, mainly because genetic methods for gyrencephalic mammals had been poorly available. Here, by taking an advantage of our newly developed in utero electroporation technique for the gyrencephalic brain of ferrets, we investigated the role of SVZ progenitors in cortical folding. We found regional differences in the abundance of SVZ progenitors in the developing ferret brain even before cortical folds began to be formed. When Tbr2 transcription factor was inhibited, intermediate progenitor cells were markedly reduced in the ferret cerebral cortex. Interestingly, outer radial glial cells were also reduced by inhibiting Tbr2. We uncovered that reduced numbers of SVZ progenitors resulted in impaired cortical folding. When Tbr2 was inhibited, upper cortical layers were preferentially reduced in gyri compared to those in sulci. Our findings indicate the biological importance of SVZ progenitors in cortical folding in the gyrencephalic brain. PMID:27403992

  12. 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.

  13. Overestimation of nitrate and nitrite concentrations in water samples due to the presence of nitroglycerin or hexahydro-1,3,5-trinitro-1,3,5-triazine.

    PubMed

    Bordeleau, Geneviève; Martel, Richard; Lévesque, Richard; Ampleman, Guy; Thiboutot, Sonia; Marois, André

    2012-08-24

    A large number of laboratory studies have reported nitrite (NO(2)(-)) and nitrate (NO(3)(-)) to be among the most common degradation products of the high explosives nitroglycerin (NG) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Additionally, several field studies have reported the presence of RDX or NG along with NO(3)(-) in groundwater near production plants. Most studies, however, did not specify whether their NO(2)(-) and NO(3)(-) analyses were performed on samples which also contained RDX or NG. Inconsistent NO(2)(-)/NO(3)(-) results obtained in our laboratory suggested that the presence of RDX or NG in water samples caused an overestimation of NO(2)(-) and NO(3)(-) concentrations when using two of the most common analytical methods, namely ionic chromatography and automated colorimetry. This could have important implications for mass balance calculations and for environmental decisions. This paper focused on quantifying the overestimation of NO(2)(-)/NO(3)(-) due to the presence of RDX and NG, and finding a method for extracting RDX and NG from water samples without affecting NO(2)(-)/NO(3)(-). Results showed that the overestimation can be predicted using regression coefficients; however the margin of error at the 95% confidence level was between 5 and 15%. Alternatively, a cartridge was found which retains both RDX and NG without affecting NO(2)(-)/NO(3)(-). The cartridge can be used for concentrating the RDX or NG in dilute environmental samples, while removing RDX/NG from solution to allow the interference-free analysis of NO(2)(-)/NO(3)(-). Additionally, if recovery of RDX/NG from the cartridges is not desired, the cartridges could be used for the extraction of more than one sample, thus reducing the costs.

  14. Validation of a novel extraction method for studying hexahydro-1,3,5-trinitro-1,3,5 triazine (RDX) biodegradation by ruminal microbiota.

    PubMed

    Giarrizzo, J G; Murty, L; Tanaree, D; Walker, K; Craig, A M

    2013-04-15

    A simple, fast liquid-liquid extraction method was developed for studying hexahydro-1,3,5-trinitro-1,3,5 triazine (RDX) biodegradation using small sample volumes. The method was tested in vitro with anaerobic incubations of RDX with whole rumen fluid (WRF) and a commercial Sporanaerobacter acetigenes strain in methanogenic media for RDX. Additionally, validation experiments were conducted in deionized water in order to show applicability toward various aqueous matrices. Conditions for extraction were as follows: 300 μL of sample were mixed with an equal volume of a 0.34 M ammonium hydroxide solution to reach a basic pH, extracted with a hexane/ethyl acetate 1:1 (v/v) solution (1 mL) and shaken vigorously for 10 s. The resulting organic phase was transferred, then dried under a constant flow of N2 and reconstituted with acetonitrile (300 μL) for HPLC-UV and LC-MS/MS analysis. Percent recovery values were obtained (83-101%) in all matrices for RDX. In WRF (n=3 animals), RDX degradation was observed with almost 100% elimination of RDX after 4 h. The five nitroso and ring cleavage metabolites were observed by mass spectrometry. Liquid cultures of S. acetigenes did not show significant RDX biodegradation activity. RDX extractions from deionized water samples indicated acceptable recoveries with low variability, suggesting suitability of the method for aqueous matrices. Overall, the new method demonstrated acceptable efficiency and reproducibility across three matrices, providing an advantageous alternative for studies where complex matrices and small volume samples are in use.

  15. 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.

  16. 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.

  17. 3,5,3′-Triiodo-L-Thyronine- and 3,5-Diiodo-L-Thyronine- Affected Metabolic Pathways in Liver of LDL Receptor Deficient Mice

    PubMed Central

    Moreno, Maria; Silvestri, Elena; Coppola, Maria; Goldberg, Ira J.; Huang, Li-Shin; Salzano, Anna M.; D'Angelo, Fulvio; Ehrenkranz, Joel R.; Goglia, Fernando

    2016-01-01

    3,5,3′-triiodo-L-thyronine (T3) and 3,5-diiodo-L-thyronine (T2), when administered to a model of familial hypercholesterolemia, i.e., low density lipoprotein receptor (LDLr)-knockout (Ldlr−/−) mice fed with a Western type diet (WTD), dramatically reduce circulating total and very low-density lipoprotein/LDL cholesterol with decreased liver apolipoprotein B (ApoB) production. The aim of the study was to highlight putative molecular mechanisms to manage cholesterol levels in the absence of LDLr. A comprehensive comparative profiling of changes in expression of soluble proteins in livers from Ldlr−/− mice treated with either T3 or T2 was performed. From a total proteome of 450 liver proteins, 25 identified proteins were affected by both T2 and T3, 18 only by T3 and 9 only by T2. Using in silico analyses, an overlap was observed with 11/14 pathways common to both iodothyronines, with T2 and T3 preferentially altering sub-networks centered around hepatocyte nuclear factor 4 α (HNF4α) and peroxisome proliferator-activated receptor α (PPARα), respectively. Both T2 and T3 administration significantly reduced nuclear HNF4α protein content, while T2, but not T3, decreased the expression levels of the HNFα transcriptional coactivator PGC-1α. Lower PPARα levels were found only following T3 treatment while both T3 and T2 lowered liver X receptor α (LXRα) nuclear content. Overall, this study, although it was not meant to investigate the use of T2 and T3 as a therapeutic agent, provides novel insights into the regulation of hepatic metabolic pathways involved in T3- and T2-driven cholesterol reduction in Ldlr−/− mice. PMID:27909409

  18. 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

  19. Accumulation of hexahydro- 1,3,5-trinitro- 1,3,5-triazine in channel catfish (Ictalurus punctatus) and aquatic oligochaetes (Lumbriculus variegatus).

    PubMed

    Belden, Jason B; Lotufo, Guilherme R; Lydy, Michael J

    2005-08-01

    The extensively used military explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has been widely released to the environment during production, usage, and disposal operations. Toxic effects of RDX have been reported in terrestrial and aquatic receptors, but investigations regarding the bioaccumulation potential of RDX in aquatic systems are scarce. The objective of the present study was to describe the toxicokinetics of RDX during aqueous exposure for the channel catfish (Ictalurus punctatus) and aquatic oligochaetes (Lumbriculus variegatus) and to compare the amount of RDX accumulation in juvenile catfish following aqueous exposure only, dietary exposure only, and a combination of dietary and aqueous exposure. The toxicokinetics measurements included bioconcentration factors (BCFs), uptake rates, elimination rates, and biological half-lives. First-order, single-compartment models described the toxicokinetics for both species. Uptake of RDX into oligochaetes was relatively rapid (uptake clearance constant [k(u)] of 5.17 ml/g/h) compared to that in catfish (k(u) = 1.28 ml/g/h). However, elimination also was more rapid in oligochaetes, with biological half-lives of 0.28 and 1.09 h for oligochaetes and catfish, respectively. Thus, both species had very similar estimated BCFs of 2.1 ml/g for oligochaetes and 2.0 ml/g for catfish. Accumulation of RDX in fish that were fed oligochaetes exposed to an exceedingly high water concentration of RDX was minimal. The present investigation indicates that RDX uptake via the aqueous route is the expected dominant uptake pathway, with dietary uptake contributing minimally to the overall body burden in fish inhabiting RDX-contaminated sites. Because of the exceedingly low bioaccumulative potential and low reported toxicity of RDX, the presence of this explosive in aquatic systems is unlikely to pose unacceptable risks to invertebrates and fish.

  20. High power folded waveguide millimeter-wave gyro-TWT

    SciTech Connect

    Choi, J.J.; Ganguly, A.K.; Armstrong, C.M.

    1994-12-31

    Investigations on a periodic TE serpentine waveguide gyro-TWT are underway at NRL. A high power axis-encircling electron beam interacts with a fundamental TE waveguide mode when it passes through an oversized beam tunnel hole in the narrow wall of the H-plane bend rectangular serpentine waveguide. Potential advantages of the circuit configuration include: easy fabrication, fundamental forward space harmonic operation, large beam tunnel suitable for high power application, natural separation of beam and rf, and simplicity of coupling. To avoid bandwidth reduction due to closely spaced stop-bands and large gap detuning angle, a double rigid TE folded waveguide structure is proposed. To utilize the entire bandwidth, it is necessary to suppress gyro-BWO oscillation at the higher space harmonics. Linear theory predicts that oscillation takes place at {approximately} 7 cm near the stop-band frequency. Therefore, a multi-stage configuration is required to saturate the device without oscillations. An experiment is underway at NRL to verify the negative mass instability in both fast and slow wave regions in a transverse folded waveguide structure and to investigate the basic circuit stability characteristics. Design parameters of the amplifier, large signal simulations using a MAGIC code and cold-test results of the circuit components will be presented.

  1. Predictive energy landscapes for folding membrane protein assemblies

    NASA Astrophysics Data System (ADS)

    Truong, Ha H.; Kim, Bobby L.; Schafer, Nicholas P.; Wolynes, Peter G.

    2015-12-01

    We study the energy landscapes for membrane protein oligomerization using the Associative memory, Water mediated, Structure and Energy Model with an implicit membrane potential (AWSEM-membrane), a coarse-grained molecular dynamics model previously optimized under the assumption that the energy landscapes for folding α-helical membrane protein monomers are funneled once their native topology within the membrane is established. In this study we show that the AWSEM-membrane force field is able to sample near native binding interfaces of several oligomeric systems. By predicting candidate structures using simulated annealing, we further show that degeneracies in predicting structures of membrane protein monomers are generally resolved in the folding of the higher order assemblies as is the case in the assemblies of both nicotinic acetylcholine receptor and V-type Na+-ATPase dimers. The physics of the phenomenon resembles domain swapping, which is consistent with the landscape following the principle of minimal frustration. We revisit also the classic Khorana study of the reconstitution of bacteriorhodopsin from its fragments, which is the close analogue of the early Anfinsen experiment on globular proteins. Here, we show the retinal cofactor likely plays a major role in selecting the final functional assembly.

  2. Some physical approaches to protein folding

    NASA Astrophysics Data System (ADS)

    Bascle, J.; Garel, T.; Orland, H.

    1993-02-01

    To understand how a protein folds is a problem which has important biological implications. In this article, we would like to present a physics-oriented point of view, which is twofold. First of all, we introduce simple statistical mechanics models which display, in the thermodynamic limit, folding and related transitions. These models can be divided into (i) crude spin glass-like models (with their Mattis analogs), where one may look for possible correlations between the chain self-interactions and the folded structure, (ii) glass-like models, where one emphasizes the geometrical competition between one- or two-dimensional local order (mimicking α helix or β sheet structures), and the requirement of global compactness. Both models are too simple to predict the spatial organization of a realistic protein, but are useful for the physicist and should have some feedback in other glassy systems (glasses, collapsed polymers .... ). These remarks lead us to the second physical approach, namely a new Monte-Carlo method, where one grows the protein atom-by-atom (or residue-by-residue), using a standard form (CHARMM .... ) for the total energy. A detailed comparison with other Monte-Carlo schemes, or Molecular Dynamics calculations, is then possible; we will sketch such a comparison for poly-alanines. Our twofold approach illustrates some of the difficulties one encounters in the protein folding problem, in particular those associated with the existence of a large number of metastable states. Le repliement des protéines est un problème qui a de nombreuses implications biologiques. Dans cet article, nous présentons, de deux façons différentes, un point de vue de physicien. Nous introduisons tout d'abord des modèles simples de mécanique statistique qui exhibent, à la limite thermodynamique, des transitions de repliement. Ces modèles peuvent être divisés en (i) verres de spin (éventuellement à la Mattis), où l'on peut chercher des corrélations entre les

  3. Exploring the Levinthal limit in protein folding.

    PubMed

    Cruzeiro, Leonor; Degrève, Léo

    2017-03-01

    According to the thermodynamic hypothesis, the native state of proteins is uniquely defined by their amino acid sequence. On the other hand, according to Levinthal, the native state is just a local minimum of the free energy and a given amino acid sequence, in the same thermodynamic conditions, can assume many, very different structures that are as thermodynamically stable as the native state. This is the Levinthal limit explored in this work. Using computer simulations, we compare the interactions that stabilize the native state of four different proteins with those that stabilize three non-native states of each protein and find that the nature of the interactions is very similar for all such 16 conformers. Furthermore, an enhancement of the degree of fluctuation of the non-native conformers can be explained by an insufficient relaxation to their local free energy minimum. These results favor Levinthal's hypothesis that protein folding is a kinetic non-equilibrium process.

  4. Communication: Folding of glycosylated proteins under confinement

    NASA Astrophysics Data System (ADS)

    Shental-Bechor, Dalit; Levy, Yaakov

    2011-10-01

    Conjugating flexible polymers (such as oligosaccharides) to proteins or confining a protein in a restricted volume often increases protein thermal stability. In this communication, we investigate the interplay between conjugation and confinement which is not trivial as the magnitude and the mechanism of stabilization are different in each instance. Using coarse-grained computational approach the folding biophysics is studied when the protein is placed in a sphere of variable radius and is conjugated to 0-6 mono- or penta-saccharides. We observe a synergistic effect on thermal stability when short oligosaccharides are attached and the modified protein is confined in a small cage. However, when large oligosaccharides are added, a conflict between confinement and glycosylation arises as the stabilizing effect of the cage is dramatically reduced and it is almost impossible to further stabilize the protein beyond the mild stabilization induced by the sugars.

  5. Electrotransfection of Polyamine Folded DNA Origami Structures.

    PubMed

    Chopra, Aradhana; Krishnan, Swati; Simmel, Friedrich C

    2016-10-12

    DNA origami structures are artificial molecular nanostructures in which DNA double helices are forced into a closely packed configuration by a multitude of DNA strand crossovers. We show that three different types of origami structures (a flat sheet, a hollow tube, and a compact origami block) can be formed in magnesium-free buffer solutions containing low (<1 mM) concentrations of the condensing agent spermidine. Much like in DNA condensation, the amount of spermidine required for origami folding is proportional to the DNA concentration. At excessive amounts, the structures aggregate and precipitate. In contrast to origami structures formed in conventional buffers, the resulting structures are stable in the presence of high electric field pulses, such as those commonly used for electrotransfection experiments. We demonstrate that spermidine-stabilized structures are stable in cell lysate and can be delivered into mammalian cells via electroporation.

  6. Mesozoic folds, fossil fields, and future finds

    SciTech Connect

    Newman, G.W.; Witter, G.G.

    1988-01-01

    Drilling and surface geologic mapping have shown that pre-Tertiary, post-Triassic folds and upthrusted anticlines in an eastern Nevada foldbelt 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.

  7. How the hydrophobic factor drives protein folding.

    PubMed

    Baldwin, Robert L; Rose, George D

    2016-11-01

    How hydrophobicity (HY) drives protein folding is studied. The 1971 Nozaki-Tanford method of measuring HY is modified to use gases as solutes, not crystals, and this makes the method easy to use. Alkanes are found to be much more hydrophobic than rare gases, and the two different kinds of HY are termed intrinsic (rare gases) and extrinsic (alkanes). The HY values of rare gases are proportional to solvent-accessible surface area (ASA), whereas the HY values of alkanes depend on special hydration shells. Earlier work showed that hydration shells produce the hydration energetics of alkanes. Evidence is given here that the transfer energetics of alkanes to cyclohexane [Wolfenden R, Lewis CA, Jr, Yuan Y, Carter CW, Jr (2015) Proc Natl Acad Sci USA 112(24):7484-7488] measure the release of these shells. Alkane shells are stabilized importantly by van der Waals interactions between alkane carbon and water oxygen atoms. Thus, rare gases cannot form this type of shell. The very short (approximately picoseconds) lifetime of the van der Waals interaction probably explains why NMR efforts to detect alkane hydration shells have failed. The close similarity between the sizes of the opposing energetics for forming or releasing alkane shells confirms the presence of these shells on alkanes and supports Kauzmann's 1959 mechanism of protein folding. A space-filling model is given for the hydration shells on linear alkanes. The model reproduces the n values of Jorgensen et al. [Jorgensen WL, Gao J, Ravimohan C (1985) J Phys Chem 89:3470-3473] for the number of waters in alkane hydration shells.

  8. How the hydrophobic factor drives protein folding

    PubMed Central

    Baldwin, Robert L.; Rose, George D.

    2016-01-01

    How hydrophobicity (HY) drives protein folding is studied. The 1971 Nozaki–Tanford method of measuring HY is modified to use gases as solutes, not crystals, and this makes the method easy to use. Alkanes are found to be much more hydrophobic than rare gases, and the two different kinds of HY are termed intrinsic (rare gases) and extrinsic (alkanes). The HY values of rare gases are proportional to solvent-accessible surface area (ASA), whereas the HY values of alkanes depend on special hydration shells. Earlier work showed that hydration shells produce the hydration energetics of alkanes. Evidence is given here that the transfer energetics of alkanes to cyclohexane [Wolfenden R, Lewis CA, Jr, Yuan Y, Carter CW, Jr (2015) Proc Natl Acad Sci USA 112(24):7484–7488] measure the release of these shells. Alkane shells are stabilized importantly by van der Waals interactions between alkane carbon and water oxygen atoms. Thus, rare gases cannot form this type of shell. The very short (approximately picoseconds) lifetime of the van der Waals interaction probably explains why NMR efforts to detect alkane hydration shells have failed. The close similarity between the sizes of the opposing energetics for forming or releasing alkane shells confirms the presence of these shells on alkanes and supports Kauzmann's 1959 mechanism of protein folding. A space-filling model is given for the hydration shells on linear alkanes. The model reproduces the n values of Jorgensen et al. [Jorgensen WL, Gao J, Ravimohan C (1985) J Phys Chem 89:3470–3473] for the number of waters in alkane hydration shells. PMID:27791131

  9. Developing Essential Understanding of Multiplication and Division for Teaching Mathematics in Grades 3-5

    ERIC Educational Resources Information Center

    Otto, Albert; Caldwell, Janet; Hancock, Sarah Wallus; Zbiek, Rose Mary

    2011-01-01

    This book identifies and examines two big ideas and related essential understandings for teaching multiplication and division in grades 3-5. Big Idea 1 captures the notion that multiplication is usefully defined as a scalar operation. Problem situations modeled by multiplication have an element that represents the scalar and an element that…

  10. 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...

  11. 40 CFR 721.10158 - 2-Pentanone, 3,5-dichloro-.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... reporting. (1) The chemical substance identified as 2-pentanone, 3,5-dichloro- (PMN P-06-16; CAS No. 58371...), (g)(3)(i), (g)(3)(ii), (g)(4) (resulting in receiving stream levels exceeding 0.1 parts per billion... in § 721.125 (a), (b), (c), (d), (e), (f), (g), (h), and (k) are applicable to...

  12. 40 CFR 721.10158 - 2-Pentanone, 3,5-dichloro-.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... reporting. (1) The chemical substance identified as 2-pentanone, 3,5-dichloro- (PMN P-06-16; CAS No. 58371...), (g)(3)(i), (g)(3)(ii), (g)(4) (resulting in receiving stream levels exceeding 0.1 parts per billion... in § 721.125 (a), (b), (c), (d), (e), (f), (g), (h), and (k) are applicable to...

  13. 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…

  14. 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...

  15. 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.

  16. 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.

  17. 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…

  18. 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…

  19. The intensities of methane in the 3-5 mu m region revisited

    NASA Technical Reports Server (NTRS)

    Fejard, L.; Champion, J.; Jouvard, J.; Brown, L.; Pine, A.

    2000-01-01

    The analysis of the linestrengths of the infrared spectrum of methane (12 and 13) in the 3-5 mu m region has been revisited onthe basis of new measurements from Fourier transform spectra recorded at Kitt Peak under various optical densities.

  20. 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…

  1. 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...

  2. 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,...

  3. 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...

  4. Russian/English Interdisciplinary Lessons for General Education and Special Education Students. Grades 3-5.

    ERIC Educational Resources Information Center

    New York City Board of Education, Brooklyn, NY. Office of Bilingual Education.

    The materials consist of four lessons each at grade levels 3-5, designed for use by both Russian bilingual and English-monolingual teachers in general and special education. The lessons are cross-referenced to learning and performance standards established for New York City (New York) public schools. Each unit (group of grade-level lessons)…

  5. Controlling Costs: The 6-3-5 Method - Case Studies at NAVSEA and NATO

    DTIC Science & Technology

    2016-04-30

    Nagy, President/CEO, Catalyst Technologies Morgan Ames, Senior Advisor, Catalyst Technologies Published April 30, 2016 Approved for public...Controlling Costs: The 6-3-5 Method—Case Studies at NAVSEA and NATO Bruce Nagy, President/CEO, Catalyst Technologies Morgan Ames, Senior Advisor... Catalyst Technologies Costing for the Future: Exploring Cost Estimation With Unmanned Autonomous Systems Ricardo Valerdi, Professor, University of

  6. 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.

  7. 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…

  8. Synthesis of 14C-Labelled Octahydor-1,3,5,7-Tetranitro-1,3,5,7-Tetrazocine (HMx0 and 15N-Isotopic Hexahyrro-1,3,5-Trinitro-1,3,5-Triazine (RDX) for use in Microcosm Experiments.

    DTIC Science & Technology

    2000-02-01

    bioremediation process. To synthesize C(14)HMX, acetylation of labelled hexamethylenetetramine (C(14)HMTA) was done yielding 3,7-diacetyl-1,3,5,7... hexamethylenetetramine (N(15)HMTA) was done according to the Hale Process. N(15)HMTA was prepared by reaching cold formaldehyde with isotopic nitrogen-15 ammonium hydroxide.

  9. Haustral fold segmentation with curvature-guided level set evolution.

    PubMed

    Zhu, Hongbin; Barish, Matthew; Pickhardt, Perry; Liang, Zhengrong

    2013-02-01

    Human colon has complex structures mostly because of the haustral folds. The folds are thin flat protrusions on the colon wall, which complicate the shape analysis for computer-aided detection (CAD) of colonic polyps. Fold segmentation may help reduce the structural complexity, and the folds can serve as an anatomic reference for computed tomographic colonography (CTC). Therefore, in this study, based on a model of the haustral fold boundaries, we developed a level-set approach to automatically segment the fold surfaces. To evaluate the developed fold segmentation algorithm, we first established the ground truth of haustral fold boundaries by experts' drawing on 15 patient CTC datasets without severe under/over colon distention from two medical centers. The segmentation algorithm successfully detected 92.7% of the folds in the ground truth. In addition to the sensitivity measure, we further developed a merit of segmented-area ratio (SAR), i.e., the ratio between the area of the intersection and union of the expert-drawn folds and the area of the automatically segmented folds, to measure the segmentation accuracy. The segmentation algorithm reached an average value of SAR = 86.2%, showing a good match with the ground truth on the fold surfaces. We believe the automatically segmented fold surfaces have the potential to benefit many postprocedures in CTC, such as CAD, taenia coli extraction, supine-prone registration, etc.

  10. Improving Protein Fold Recognition by Deep Learning Networks

    NASA Astrophysics Data System (ADS)

    Jo, Taeho; Hou, Jie; Eickholt, Jesse; Cheng, Jianlin

    2015-12-01

    For accurate recognition of protein folds, a deep learning network method (DN-Fold) was developed to predict if a given query-template protein pair belongs to the same structural fold. The input used stemmed from the protein sequence and structural features extracted from the protein pair. We evaluated the performance of DN-Fold along with 18 different methods on Lindahl’s benchmark dataset and on a large benchmark set extracted from SCOP 1.75 consisting of about one million protein pairs, at three different levels of fold recognition (i.e., protein family, superfamily, and fold) depending on the evolutionary distance between protein sequences. The correct recognition rate of ensembled DN-Fold for Top 1 predictions is 84.5%, 61.5%, and 33.6% and for Top 5 is 91.2%, 76.5%, and 60.7% at family, superfamily, and fold levels, respectively. We also evaluated the performance of single DN-Fold (DN-FoldS), which showed the comparable results at the level of family and superfamily, compared to ensemble DN-Fold. Finally, we extended the binary classification problem of fold recognition to real-value regression task, which also show a promising performance. DN-Fold is freely available through a web server at http://iris.rnet.missouri.edu/dnfold.

  11. The folding of an ``average'' beta trefoil protein.

    NASA Astrophysics Data System (ADS)

    Gosavi, Shachi; Jennings, Pat; Onuchic, Jose

    2007-03-01

    The beta-trefoil fold is characterized by twelve beta strands folded into three similar beta-beta-beta-loop-beta (trefoil) units. The overall fold has pseudo-threefold symmetry and consists of a six stranded-barrel, capped by a triangular hairpin triplet. The loops connecting the beta-strands vary in length and structure. It is these loops that give the fold its varied binding capability and the binding sites lie in different parts of the fold. The beta-trefoil proteins have little sequence similarity (sometimes less than 17%) and bind a range of molecules, including other proteins, DNA, membranes and carbohydrates. Protein folding experiments have been performed on four of the beta trefoils, namely, interleukin-1 (IL1B), acidic and basic fibroblast growth factors (FGF-1 and FGF-2) and hisactophilin (HIS). These experiments indicate that the proteins fold by different routes. Folding simulations of the proteins identify the possible folding routes and also show that the shapes of the barriers are different for the different proteins. In this work, we design a model protein which contains only the core fold elements of the beta-trefoil fold. We compare the folding of this ``average'' protein to the folding of His, FGF and IL1B and make some connections with function.

  12. The Fluid Memory of Clays in Faults and Folds

    NASA Astrophysics Data System (ADS)

    van der Pluijm, B.; Fitz-Diaz, E.; Haines, S. H.

    2013-12-01

    Constraining fluid sources is key to understanding crustal-scale fluid circulation, rock mechanics, mineral reactions and the origin of economic deposits. The role of meteoric fluids in exhumed fault rocks has been proposed in a few recent studies, notably in mylonites in low-angle normal fault (LANF) systems. However, the extent of meteoric influx and fluid pathways, and a mechanism for infiltration of surface waters up to 10+km depth remains mostly unknown. The occurrence of clay neomineralization in fault rocks and folds has the potential to resolve this question, as clay (trans)formation preserves host fluid information in its isotopic signatures, particularly H. New stable isotope studies of clays in normal faults and folds in the SW US and Mexico show major meteoric input, based on which we propose a mechanism for downward fluid infiltration and upper-crustal circulation. We obtained paired δ18O and δ2H (‰ wrt SMOW) isotopic measurements from neo-formed clays in fault gouge that formed above major LANF detachments in the SW US, which show that clays in brittle fault rocks formed from exchange with pristine to only weakly evolved meteoric fluids. Illite δ18O measurements range from -2.0‰ to +11.5‰, while illite δ2H measurements range from -142‰ to -107‰. Smectite δ18O values are +3.6‰ to 17.9‰, while smectite δ2H measurements are -147‰ to -95‰. The isotopic signature of clays at multiple depths in LANFs indicates that crustal-scale normal fault systems are highly permeable over geologic time scales, and that they are dominated by downward fluid flow of surface waters, instead of buoyancy-driven flow from deeper levels. Clay grain size fractions from folded rocks of the Mexican fold-thrust belt containing chlorite and smectite show very low values in δ2H (-75.9 to -53.9‰), while samples containing illite and kaolinite or pure illite show slightly higher δ2H values (-33.1 to -50.1‰). In these samples the discriminating potential of

  13. RNAiFold: a web server for RNA inverse folding and molecular design.

    PubMed

    Garcia-Martin, Juan Antonio; Clote, Peter; Dotu, Ivan

    2013-07-01

    Synthetic biology and nanotechnology are poised to make revolutionary contributions to the 21st century. In this article, we describe a new web server to support in silico RNA molecular design. Given an input target RNA secondary structure, together with optional constraints, such as requiring GC-content to lie within a certain range, requiring the number of strong (GC), weak (AU) and wobble (GU) base pairs to lie in a certain range, the RNAiFold web server determines one or more RNA sequences, whose minimum free-energy secondary structure is the target structure. RNAiFold provides access to two servers: RNA-CPdesign, which applies constraint programming, and RNA-LNSdesign, which applies the large neighborhood search heuristic; hence, it is suitable for larger input structures. Both servers can also solve the RNA inverse hybridization problem, i.e. given a representation of the desired hybridization structure, RNAiFold returns two sequences, whose minimum free-energy hybridization is the input target structure. The web server is publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold, which provides access to two specialized servers: RNA-CPdesign and RNA-LNSdesign. Source code for the underlying algorithms, implemented in COMET and supported on linux, can be downloaded at the server website.

  14. Multiscale anisotropy controlled by folding: the example of the Chaudrons fold (Corbières, France)

    NASA Astrophysics Data System (ADS)

    Louis, Laurent; Robion, Philippe; David, Christian; Frizon de Lamotte, Dominique

    2006-04-01

    In this paper, anisotropies developed in silicoclastic continental deposits during the building of the Chaudrons anticline (Corbières, France) are studied. A microstructural analysis of the deformational features in three different panels within the fold (crest, hinge, and forelimb, respectively) is reported and compared with early field observations (distribution and orientation of cleavage) and laboratory measurements (estimation of magnetic and acoustic anisotropies). The main finding of this investigation is the preservation of unwelded joints between grains of calcite promoted by the presence of quartz grains. These joints, which appear as discontinuities in a matrix of calcite, are analyzed in orientation and composition. In the three panels of the fold that are investigated, a range of dip angles is observed with at least two major generations of joints, the average orientation of which is found to be consistent with both macroscopic cleavage and magnetic and acoustic fabrics. To account for the multimodal distribution of the joints orientation, we suggest an original scenario in which they are successively generated by sets. Two processes have operated simultaneously during the development of the fold: (1) horizontal rock mass compaction inducing pressure solution and twinning in calcite; (2) preservation of unwelded calcite/calcite grain joints due to stress heterogeneities associated with quartz inclusions. From these results, we suggest that microstructural processes are the same before and during folding, ruling out a passive shearing of cleavage plane formed during a first step of layer parallel shortening.

  15. Mapping the energy landscape for second-stage folding of a single membrane protein

    PubMed Central

    Min, Duyoung; Jefferson, Robert E; Bowie, James U; Yoon, Tae-Young

    2016-01-01

    Membrane proteins are designed to fold and function in a lipid membrane, yet folding experiments within a native membrane environment are challenging to design. Here we show that single-molecule forced unfolding experiments can be adapted to study helical membrane protein folding under native-like bicelle conditions. Applying force using magnetic tweezers, we find that a transmembrane helix protein, Escherichia coli rhomboid protease GlpG, unfolds in a highly cooperative manner, largely unraveling as one physical unit in response to mechanical tension above 25 pN. Considerable hysteresis is observed, with refolding occurring only at forces below 5 pN. Characterizing the energy landscape reveals only modest thermodynamic stability (ΔG = 6.5 kBT) but a large unfolding barrier (21.3 kBT) that can maintain the protein in a folded state for long periods of time (t1/2 ~3.5 h). The observed energy landscape may have evolved to limit the existence of troublesome partially unfolded states and impart rigidity to the structure. PMID:26479439

  16. Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction.

    PubMed

    Shen, Yimin; Maupetit, Julien; Derreumaux, Philippe; Tufféry, Pierre

    2014-10-14

    Peptides and mini proteins have many biological and biomedical implications, which motivates the development of accurate methods, suitable for large-scale experiments, to predict their experimental or native conformations solely from sequences. In this study, we report PEP-FOLD2, an improved coarse grained approach for peptide de novo structure prediction and compare it with PEP-FOLD1 and the state-of-the-art Rosetta program. Using a benchmark of 56 structurally diverse peptides with 25-52 amino acids and a total of 600 simulations for each system, PEP-FOLD2 generates higher quality models than PEP-FOLD1, and PEP-FOLD2 and Rosetta generate near-native or native models for 95% and 88% of the targets, respectively. In the situation where we do not have any experimental structures at hand, PEP-FOLD2 and Rosetta return a near-native or native conformation among the top five best scored models for 80% and 75% of the targets, respectively. While the PEP-FOLD2 prediction rate is better than the ROSETTA prediction rate by 5%, this improvement is non-negligible because PEP-FOLD2 explores a larger conformational space than ROSETTA and consists of a single coarse-grained phase. Our results indicate that if the coarse-grained PEP-FOLD2 method is approaching maturity, we are not at the end of the game of mini-protein structure prediction, but this opens new perspectives for large-scale in silico experiments.

  17. Nitro Derivatives of 1,3,5-Triazepine as Potential High-Energy Materials

    NASA Astrophysics Data System (ADS)

    Singh, Hari Ji; Upadhyay, Manish Kumar

    2013-10-01

    Structure optimization and frequency calculation of six nitro derivatives of 1,3,5-triazepine were performed using a MP2(FULL)/6-311G(d,p) method. In order to obtain reliable energy data, single-point energy and subsequently thermodynamic properties of the species considered were calculated at a fairly high level of theory, CCSD(T)/6-311G(d,p). Solid-phase heats of formation and crystal density were determined using an electrostatic potential (ESP) method utilizing wave function analysis-surface analysis suite (WFA-SAS) code. The result shows that all nitro derivatives possess high positive heats of formation that increase with an increase in the number of nitro groups attached to the ring moiety. The crystal density was found to be in the range of 1.67-1.90 g/cm3. Detonation properties of the compounds were estimated using the Kamlet-Jacobs equation. The results showed that detonation velocity (D) and detonation pressure (P) increased with an increase in the number of nitro groups attached at the ring moiety. It was found that all six nitro derivatives of the title compound had better or comparable performance characteristics than the most widely used commercial explosives, such as TNT, research and development explosives (RDX), and 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX). The trinitro derivative (1,3,5-trinitro-1,3,5-triazepine, F) yielded detonation pressure (P) and detonation velocity (D) of 45.5 GPa and 9.23 km/s, respectively, at a loading density of 1.90 g/cm3, which are superior to the most powerful available explosive HMX (P = 39.00 GPa and D = 9.11 km/s). The results obtained during the present study show that the title compounds can be used as promising futuristic high-energy-density materials (HEDMs).

  18. Surgical Management of Tibial Plateau Fractures With 3.5 mm Simple Plates

    PubMed Central

    Bagherifard, Abolfazl; Jabalameli, Mahmoud; Hadi, Hosseinali; Rahbar, Mohammad; Minator Sajjadi, Mohammadreza; Jahansouz, Ali; Karimi Heris, Hossein

    2016-01-01

    Background Tibial plateau fractures can be successfully fixed utilizing 3.5 mm locking plates. However, there are some disadvantages to using these plates. Objectives In the current prospective study, we investigated the outcome of treating different types of tibial plateau fractures with 3.5 mm simple plates which, to our knowledge, has not been evaluated in previous studies. Materials and Methods Between 2011 and 2013, 32 patients aged 40 ± 0.2 years underwent open reduction and internal fixation for tibial plateau fractures with 3.5 mm simple plates. The patients were followed for 16.14 ± 2.1 months. At each patient’s final visit, the articular surface depression, medial proximal tibial angle, and slope angle were measured and compared with measurements taken early after the operation. The functional outcomes were measured with the WOMAC and Lysholm knee scores. Results The mean union time was 13 ± 1.2 weeks. The mean knee range of motion was 116.8° ± 3.3°. The mean WOMAC and Lysholm scores were 83.5 ± 1.8 and 76.8 ± 1.6, respectively. On the early postoperative and final X-rays, 87.5% and 84% of patients, respectively, had acceptable reduction. Medial proximal tibial and slope angles did not change significantly by the last visit. No patient was found to have complications related to the type of plate. Conclusions In this case series study, the fixation of different types of tibial plateau fractures with 3.5 mm simple non-locking and non-precontoured plates was associated with acceptable clinical, functional, and radiographic outcomes. Based on the advantages and costs of these plates, the authors recommend using 3.5 mm simple plates for different types of tibial plateau fractures. PMID:27626010

  19. Chaperoning osteogenesis: new protein-folding disease paradigms.

    PubMed

    Makareeva, Elena; Aviles, Nydea A; Leikin, Sergey

    2011-03-01

    Recent discoveries of severe bone disorders in patients with deficiencies in several endoplasmic reticulum chaperones are reshaping the discussion of type I collagen folding and related diseases. Type I collagen is the most abundant protein in all vertebrates and a crucial structural molecule for bone and other connective tissues. Its misfolding causes bone fragility, skeletal deformity and other tissue failures. Studies of newly discovered bone disorders indicate that collagen folding, chaperones involved in the folding process, cellular responses to misfolding and related bone pathologies might not follow conventional protein folding paradigms. In this review, we examine the features that distinguish collagen folding from that of other proteins and describe the findings that are beginning to reveal how cells manage collagen folding and misfolding. We discuss implications of these studies for general protein folding paradigms, unfolded protein response in cells and protein folding diseases.

  20. PUFFER (Pop-Up Flat Folding Explorer Robots)

    NASA Astrophysics Data System (ADS)

    Karras, J.; Carpenter, K.; Fuller, C.; Parcheta, C.

    2016-10-01

    PUFFER (Pop-Up Flat Folding Explorer Robots) are origami-inspired folding robots with extreme terrain mobility. PUFFERs are low-volume, low-mass, and low-cost robots for high-reward extreme terrain science.

  1. THE INFLUENCE OF FOLD AND FRACTURE DEVELOPMENT ON RESERVOIR BEHAVIOR OF THE LISBURNE GROUP OF NORTHERN ALASKA

    SciTech Connect

    Wesley K. Wallace; Catherine L. Hanks; Michael T. Whalen; Jerry Jensen; Paul K. Atkinson; Joseph S. Brinton

    2000-05-01

    The Lisburne Group is a major carbonate reservoir unit in northern Alaska. The Lisburne is detachment folded where it is exposed throughout the northeastern Brooks Range, but is relatively undeformed in areas of current production in the subsurface of the North Slope. The objectives of this study are to develop a better understanding of four major aspects of the Lisburne: (1) The geometry and kinematics of detachment folds and their truncation by thrust faults. (2) The influence of folding and lithostratigraphy on fracture patterns. (3) Lithostratigraphy and its influence on folding, faulting, fracturing, and reservoir characteristics. (4) The influence of lithostratigraphy and deformation on fluid flow. The results of field work during the summer of 1999 offer some preliminary insights: The Lisburne Limestone displays a range of symmetrical detachment fold geometries throughout the northeastern Brooks Range. The variation in fold geometry suggests a generalized progression in fold geometry with increasing shortening: Straight-limbed, narrow-crested folds at low shortening, box folds at intermediate shortening, and folds with a large height-to-width ratio and thickened hinges at high shortening. This sequence is interpreted to represent a progressive change in the dominant shortening mechanism from flexural-slip at low shortening to bulk strain at higher shortening. Structural variations in bed thickness occur throughout this progression. Parasitic folding accommodates structural thickening at low shortening and is gradually succeeded by penetrative strain as shortening increases. The amount of structural thickening at low to intermediate shortening may be inversely related to the local amount of structural thickening of the Kayak Shale, the incompetent unit that underlies the Lisburne. The Lisburne Limestone displays a different structural style in the south, across the boundary between the northeastern Brooks Range and the main axis of the Brooks Range fold

  2. Computational prediction of probabilistic ignition threshold of pressed granular Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under shock loading

    NASA Astrophysics Data System (ADS)

    Kim, Seokpum; Miller, Christopher; Horie, Yasuyuki; Molek, Christopher; Welle, Eric; Zhou, Min

    2016-09-01

    The probabilistic ignition thresholds of pressed granular Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine explosives with average grain sizes between 70 μm and 220 μm are computationally predicted. The prediction uses material microstructure and basic constituent properties and does not involve curve fitting with respect to or prior knowledge of the attributes being predicted. The specific thresholds predicted are James-type relations between the energy flux and energy fluence for given probabilities of ignition. Statistically similar microstructure sample sets are computationally generated and used based on the features of micrographs of materials used in actual experiments. The predicted thresholds are in general agreement with measurements from shock experiments in terms of trends. In particular, it is found that grain size significantly affects the ignition sensitivity of the materials, with smaller sizes leading to lower energy thresholds required for ignition. For example, 50% ignition threshold of the material with an average grain size of 220 μm is approximately 1.4-1.6 times that of the material with an average grain size of 70 μm in terms of energy fluence. The simulations account for the controlled loading of thin-flyer shock experiments with flyer velocities between 1.5 and 4.0 km/s, constituent elasto-viscoplasticity, fracture, post-fracture contact and friction along interfaces, bulk inelastic heating, interfacial frictional heating, and heat conduction. The constitutive behavior of the materials is described using a finite deformation elasto-viscoplastic formulation and the Birch-Murnaghan equation of state. The ignition thresholds are determined via an explicit analysis of the size and temperature states of hotspots in the materials and a hotspot-based ignition criterion. The overall ignition threshold analysis and the microstructure-level hotspot analysis also lead to the definition of a macroscopic ignition parameter (J) and a microscopic

  3. Molecular dynamics simulations of melting of perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine

    NASA Astrophysics Data System (ADS)

    Zheng, Lianqing; Thompson, Donald L.

    2006-08-01

    The melting mechanism of superheated perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (α-RDX) has been investigated using molecular dynamics simulations with the fully flexible force field developed by Smith and Bharadwaj [J. Phys. Chem. B 103, 3570 (1999)]. Sequential 50ps equilibration simulations of the constant stress-constant temperature ensemble were performed at 10K intervals over the range of 300-650K, corresponding to a heating rate of 2.0×1011K/s. A solid-solid phase transition is observed between 480 and 490K, followed by melting, which occurs between 500 and 510K. The solid-solid phase transition, both displacive and rotational, is characterized by an abrupt decrease in the lengths of the unit cell edges a and b and an increase of the length of edge c. The molecular conformation in the new phase is AAE, although the axial nitro groups have different changes: one shift is more axial and the other is more equatorial. Phases other than α-RDX have been observed experimentally, however, there are insufficient data for comparisons to ascertain that the new phase observed here corresponds to a real phase. At the high heating rate (2.0×1011K /s) used in the simulations, the melted RDX reaches full orientational disorder at about 540K and translational freedom at around 580K. If the simulation at the melting temperature (510K) is run sufficiently long complete rotational freedom is achieved in a few hundreds of picoseconds, while complete translational freedom requires much longer. These results show that given a sufficiently high heating rate, the system can exist for significant periods of time in a near-liquid state in which the molecules are not as free to rotate and diffuse as in the true liquid state. The bond lengths and bond angles undergo little change upon melting, while there are significant changes in the dihedral angles. The molecular conformation of RDX changes from AAE to EEE upon melting. The ramification of this for formulating

  4. Diagnostic and therapeutic pitfalls in benign vocal fold diseases

    PubMed Central

    Bohlender, Jörg

    2013-01-01

    More than half of patients presenting with hoarseness show benign vocal fold changes. The clinician should be familiar with the anatomy, physiology and functional aspects of voice disorders and also the modern diagnostic and therapeutic possibilities in order to ensure an optimal and patient specific management. This review article focuses on the diagnostic and therapeutic limitations and difficulties of treatment of benign vocal fold tumors, the management and prevention of scarred vocal folds and the issue of unilateral vocal fold paresis. PMID:24403969

  5. Spin glasses and the statistical mechanics of protein folding.

    PubMed Central

    Bryngelson, J D; Wolynes, P G

    1987-01-01

    The theory of spin glasses was used to study a simple model of protein folding. The phase diagram of the model was calculated, and the results of dynamics calculations are briefly reported. The relation of these results to folding experiments, the relation of these hypotheses to previous protein folding theories, and the implication of these hypotheses for protein folding prediction schemes are discussed. PMID:3478708

  6. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

    PubMed

    Buchner, Ginka S; Murphy, Ronan D; Buchete, Nicolae-Viorel; Kubelka, Jan

    2011-08-01

    The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at

  7. Zonal Wave Number 2 Rossby Wave (3.5-day oscillation) Over The Martian Lower Atmosphere

    NASA Astrophysics Data System (ADS)

    Ghosh, P.; Thokuluwa, R. K.

    2013-12-01

    Over the Mars, height (800-50 Pascal pressure coordinate) profiles of temperature (K), measured by radio occultation technique during the MGS (Mars Global Surveyor) mission, obtained for the period of 1-10 January 2006 at the Martian latitude of ~63N in almost all the longitudes are analyzed to study the characteristics of the 3.5-day oscillation. To avoid significant data gaps in a particular longitude sector, we selected a set of 7 Mars longitude regions with ranges of 0-30E, 35-60E, 65-95E, 190-230E, 250-280E, 290-320E, and 325-360E to study the global characteristics of the 3.5-day oscillation. The 3.5-day oscillation is not selected as a-priori but observed as a most significant oscillation during this period of 1-10 January 2006. It is observed that in the longitude of 0-30E, the 3.5-day oscillation shows statistically significant power (above the 95% confidence level white noise) from the lowest height (800 Pascal, 8 hPa) itself and up to the height of 450 Pascal level with the maximum power of ~130 K^2 at the 600 & 650 Pascal levels. It started to grow from the power of ~ 50 K^2 at the lowest height of 800 Pascal level and reached the maximum power in the height of 600-650 Pascal level and then it started to get lessened monotonously up to the height of 450 Pascal level where its power is ~ 20 K^2. Beyond this height and up to the height of 50 Pascal level, the wave amplitude is below the white noise level. As the phase of the wave is almost constant at all the height levels, it seems that the observed 3.5-day oscillation is a stationary wave with respect to the height. In the 35-60 E longitude sector, the vertical structure of the 3.5-day oscillation is similar to what observed for the 0-30 E longitude region but the power is statistically insignificant at all the heights. However in the 65-95E longitude sector, the wave grows from the lowest level (70 K^2) of 800 Pascal to its maximum power of 280 K^2 in the height of 700 Pascal level and then it started

  8. Parasitic folds with wrong vergence: How pre-existing geometrical asymmetries can be inherited during multilayer buckle folding

    NASA Astrophysics Data System (ADS)

    Frehner, Marcel; Schmid, Timothy

    2016-06-01

    Parasitic folds are typical structures in geological multilayer folds; they are characterized by a small wavelength and are situated within folds with larger wavelength. Parasitic folds exhibit a characteristic asymmetry (or vergence) reflecting their structural relationship to the larger-scale fold. Here we investigate if a pre-existing geometrical asymmetry (e.g., from sedimentary structures or folds from a previous tectonic event) can be inherited during buckle folding to form parasitic folds with wrong vergence. We conduct 2D finite-element simulations of multilayer folding using Newtonian materials. The applied model setup comprises a thin layer exhibiting the pre-existing geometrical asymmetry sandwiched between two thicker layers, all intercalated with a lower-viscosity matrix and subjected to layer-parallel shortening. When the two outer thick layers buckle and amplify, two processes work against the asymmetry: layer-perpendicular flattening between the two thick layers and the rotational component of flexural flow folding. Both processes promote de-amplification and unfolding of the pre-existing asymmetry. We discuss how the efficiency of de-amplification is controlled by the larger-scale fold amplification and conclude that pre-existing asymmetries that are open and/or exhibit low amplitude are prone to de-amplification and may disappear during buckling of the multilayer system. Large-amplitude and/or tight to isoclinal folds may be inherited and develop type 3 fold interference patterns.

  9. 77 FR 74513 - Folding Gift Boxes From China

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-14

    ... COMMISSION Folding Gift Boxes From China Determination On the basis of the record \\1\\ developed in the... antidumping duty order on folding gift boxes from China would be likely to lead to continuation or recurrence... Commission are contained in USITC Publication 4365 (November 2012), entitled Folding Gift Boxes from...

  10. Factors that affect coseismic folds in an overburden layer

    NASA Astrophysics Data System (ADS)

    Zeng, Shaogang; Cai, Yongen

    2016-12-01

    Coseismic folds induced by blind thrust faults have been observed in many earthquake zones, and they have received widespread attention from geologists and geophysicists. Numerous studies have been conducted regarding fold kinematics; however, few have studied fold dynamics quantitatively. In this paper, we establish a conceptual model with a thrust fault zone and tectonic stress load to study the factors that affect coseismic folds and their formation mechanisms using the finite element method. The numerical results show that the fault dip angle is a key factor that controls folding. The greater the dip angle is, the steeper the fold slope. The second most important factor is the overburden thickness. The thicker the overburden is, the more gradual the fold. In this case, folds are difficult to identify in field surveys. Therefore, if a fold can be easily identified with the naked eye, the overburden is likely shallow. The least important factors are the mechanical parameters of the overburden. The larger the Young's modulus of the overburden is, the smaller the displacement of the fold and the fold slope. Strong horizontal compression and vertical extension in the overburden near the fault zone are the main mechanisms that form coseismic folds.

  11. Monolithic silica capillary columns with immobilized cellulose tris(3,5-dimethylphenylcarbamate) for enantiomer separations in CEC.

    PubMed

    He, Chiyang; Hendrickx, Ans; Mangelings, Debby; Smeyers-Verbeke, Johanna; Vander Heyden, Yvan

    2009-11-01

    Two types of monolithic silica capillary columns with an immobilized cellulose tris(3,5-dimethylphenylcarbamate) (CDMPC) selector were prepared for enantiomer separations in CEC. The monolithic columns were prepared by a sol-gel process in fused-silica capillaries. CDMPC was then either immobilized on a silica monolith through an intermolecular polycondensation of the cellulose derivative containing a triethoxysilyl group, or on a vinylized silica monolith through radical copolymerization of the cellulose derivative, which also contained a vinyl group. IR spectra confirmed the successful immobilization of CDMPC on both columns. Eleven chiral compounds were used to evaluate the enantioselectivity on both column types. Results indicated that the columns obtained via polycondensation had higher separation ability than those obtained via radical polymerization, and that they showed satisfactory run-to-run repeatability and stability. These new techniques thus provide strategies for preparing immobilized polysaccharide-based chiral silica monolithic capillary columns for chiral separations by means of CEC.

  12. Novel synthesis of silver nanoparticles using 2,3,5,6-tetrakis-(morpholinomethyl) hydroquinone as reducing agent.

    PubMed

    Manivel, P; Balamurugan, A; Ponpandian, N; Mangalaraj, D; Viswanathan, C

    2012-09-01

    2,3,5,6-Tetrakis-(morpholinomethyl) hydroquinone (TMMH) was used as a reducing agent to synthesize spherical shaped silver nanoparticles in water-ethanol medium without using any stabilizing and capping agents. The reducing agent TMMH is prepared by Mannich-type reaction method and (1)H NMR, (13)C NMR and FT-IR spectroscopy techniques were used to characterize the compound (TMMH). The nature of bonding, structural and optical properties of the final product were analyzed using different techniques such as UV-Vis spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM) and Fourier-transform infrared spectroscopy (FTIR). The interaction between silver and reducing agent was confirmed by using FTIR analysis. The final product obtained showed higher crystallinity with cubic structure and an average crystalline size of about 20 nm. The results revealed that it is possible to synthesize crystalline Ag nanoparticles using organic compound as reducing agent.

  13. Novel synthesis of silver nanoparticles using 2,3,5,6-tetrakis-(morpholinomethyl) hydroquinone as reducing agent

    NASA Astrophysics Data System (ADS)

    Manivel, P.; Balamurugan, A.; Ponpandian, N.; Mangalaraj, D.; Viswanathan, C.

    2,3,5,6-Tetrakis-(morpholinomethyl) hydroquinone (TMMH) was used as a reducing agent to synthesize spherical shaped silver nanoparticles in water-ethanol medium without using any stabilizing and capping agents. The reducing agent TMMH is prepared by Mannich-type reaction method and 1H NMR, 13C NMR and FT-IR spectroscopy techniques were used to characterize the compound (TMMH). The nature of bonding, structural and optical properties of the final product were analyzed using different techniques such as UV-Vis spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM) and Fourier-transform infrared spectroscopy (FTIR). The interaction between silver and reducing agent was confirmed by using FTIR analysis. The final product obtained showed higher crystallinity with cubic structure and an average crystalline size of about 20 nm. The results revealed that it is possible to synthesize crystalline Ag nanoparticles using organic compound as reducing agent.

  14. Synthesis, structure and biological activity of 3(5)-trifluoromethyl-1H-pyrazoles derived from hemicurcuminoids

    NASA Astrophysics Data System (ADS)

    Nieto, Carla I.; Cabildo, M. Pilar; Cornago, M. Pilar; Sanz, Dionisia; Claramunt, Rosa M.; Alkorta, Ibon; Elguero, José; García, José A.; López, Ana; Acuña-Castroviejo, Darío

    2015-11-01

    Six new 3(5)-trifluoromethyl-5(3)-substituted-styryl-1H-pyrazoles have been synthesized and their tautomerism studied in solution and in the solid state. The determination of their structures has been based on multinuclear NMR spectroscopy together with GIAO/B3LYP/6-311++G(d,p) theoretical calculations of eight structures for each pyrazole (two tautomers and four conformations). Five out of the six compounds present inhibition percentages of the iNOS isoform higher than 50%. With regard to the nNOS inhibitory activity, only two of the studied compounds show an inhibition of about 50%. Finally, concerning the eNOS, there is a compound presenting a low percentage of inhibition (40.2%) attaining in the other cases 50%.

  15. Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

    NASA Astrophysics Data System (ADS)

    Nissley, Daniel A.; Sharma, Ajeet K.; Ahmed, Nabeel; Friedrich, Ulrike A.; Kramer, Günter; Bukau, Bernd; O'Brien, Edward P.

    2016-02-01

    The rates at which domains fold and codons are translated are important factors in determining whether a nascent protein will co-translationally fold and function or misfold and malfunction. Here we develop a chemical kinetic model that calculates a protein domain's co-translational folding curve during synthesis using only the domain's bulk folding and unfolding rates and codon translation rates. We show that this model accurately predicts the course of co-translational folding measured in vivo for four different protein molecules. We then make predictions for a number of different proteins in yeast and find that synonymous codon substitutions, which change translation-elongation rates, can switch some protein domains from folding post-translationally to folding co-translationally--a result consistent with previous experimental studies. Our approach explains essential features of co-translational folding curves and predicts how varying the translation rate at different codon positions along a transcript's coding sequence affects this self-assembly process.

  16. Elucidate Chromatin Folding at the Mesoscale

    NASA Astrophysics Data System (ADS)

    Qiu, Xiangyun

    Knowledge of the three-dimensional structure of chromatin, an active participant of all gene-directed processes, is required to decode its (epi)genetics-structure-function relationships. Albeit often simplified as ``beads-on-a-string'', chromatin possesses daunting complexity in its intricate intra- and inter-nucleosome interactions, as well as the myriad types of molecules acting on it. On the other hand, the folding of chromatin from an extended chain of nucleosomes is highly constrained, e.g., by rather bulky nucleosomes and semi-rigid linker dsDNAs. Further given the well-defined nucleosome and dsDNA structures at the nanometer scale, this creates an opportunity for low-resolution structural methods such as small angle scattering to obtain mesoscale structures of chromatin, which can be further refined computationally to yield atomistic structures of chromatin. Here we present results from our recent studies of recombinant nucleosome arrays with solution small angle x-ray scattering (SAXS) and ensemble structure modeling.

  17. Bioengineered vocal fold mucosa for voice restoration.

    PubMed

    Ling, Changying; Li, Qiyao; Brown, Matthew E; Kishimoto, Yo; Toya, Yutaka; Devine, Erin E; Choi, Kyeong-Ok; Nishimoto, Kohei; Norman, Ian G; Tsegyal, Tenzin; Jiang, Jack J; Burlingham, William J; Gunasekaran, Sundaram; Smith, Lloyd M; Frey, Brian L; Welham, Nathan V

    2015-11-18

    Patients with voice impairment caused by advanced vocal fold (VF) fibrosis or tissue loss have few treatment options. A transplantable, bioengineered VF mucosa would address the individual and societal costs of voice-related communication loss. Such a tissue must be biomechanically capable of aerodynamic-to-acoustic energy transfer and high-frequency vibration and physiologically capable of maintaining a barrier against the airway lumen. We isolated primary human VF fibroblasts and epithelial cells and cocultured them under organotypic conditions. The resulting engineered mucosae showed morphologic features of native tissue, proteome-level evidence of mucosal morphogenesis and emerging extracellular matrix complexity, and rudimentary barrier function in vitro. When grafted into canine larynges ex vivo, the mucosae generated vibratory behavior and acoustic output that were indistinguishable from those of native VF tissue. When grafted into humanized mice in vivo, the mucosae survived and were well tolerated by the human adaptive immune system. This tissue engineering approach has the potential to restore voice function in patients with otherwise untreatable VF mucosal disease.

  18. Diaper (napkin) dermatitis: A fold (intertriginous) dermatosis.

    PubMed

    Tüzün, Yalçın; Wolf, Ronni; Bağlam, Süleyman; Engin, Burhan

    2015-01-01

    Diaper (napkin) dermatitis is an acutely presenting inflammatory irritant contact dermatitis of the diaper region. It is one of the most common dermatologic diseases in infants and children. In the past, the disease was thought to be caused by ammonia; however, a number of factors, such as friction, wetness, inappropriate skin care, microorganisms, antibiotics, and nutritional defects, are important. Diaper dermatitis commonly affects the lower parts of the abdomen, thighs, and diaper area. Involvement of skin fold regions is typical with diaper dermatitis. At the early stages of the disease, only dryness is observed in the affected area. At later stages, erythematous maceration and edema can be seen. Secondary candidal and bacterial infections can complicate the dermatitis. In the differential diagnosis of the disease, allergic contact dermatitis, intertrigo, psoriasis, atopic and seborrheic dermatitis, and the other diseases should be considered. Causes of the disease should be determined and eliminated primarily. Families need to be informed about the importance of a clean, dry diaper area and the frequency of diaper changes. The use of superabsorbent disposable diapers has decreased the incidence of the disease. Soap and alcohol-containing products should be avoided in cleaning the area. In some cases, corticosteroids and antifungal agents can be administered. If necessary, antibacterial agents and calcineurin inhibitors can also be beneficial.

  19. Displacement of the ventricular fold following cordectomy.

    PubMed

    Fukuda, H; Tsuji, D H; Kawasaki, Y; Kawaida, M; Sakou, T

    1990-01-01

    In order to avoid radiation and its undesirable side effects, we have employed surgical techniques for treatment of early glottic cancer when the lesion is confined to one membranous cord (Fukuda, Saito, Sato, and Kitahara: J. Jpn. Bronchoesophagol. Soc. 30: 7-14, 1979; Fukuda and Saito: Otologica 26: 434-436, 1980; Fukuda, Kawaida, Ohki, Kawasaki, Kita, and Tatehara: J. Jpn. Bronchoesophagaol. Soc. 39: 139-144, 1988). Laser is one of the most popular techniques and it has been accepted as the first choice by many authors (Annyas, Overbeek, Escajadillo, and Hoeksema: Laryngoscope 94: 836-838, 1984; Mcguirt and Koufman: Arch. Otolaryngol. Head Neck Surg. 113: 501-505, 1987; Tsuji, Fukuda, Kawaskai, Kawaida, and Kanzaki: Keio J. Med. 38: 413-418, 1989). However, some cases are difficult to approach by direct laryngoscopy, requiring an external way to expose the lesion. In these cases, cordectomy by laryngofissure is the method of choice, but the function of the glottis could be improved by replacing the excised cord displacing the ventricular fold. This technique, designed by the authors, was carried out in 22 patients and the results from the viewpoint of phonodynamics, voice quality, and cure rate are discussed in this study. The results are encouraging and we believe that this method is a very reasonable alternative to the laser when such equipment is not available. We also believe that late side effects and oncogenic problems associated with radiation are important points to be considered, especially in patients of relatively younger age.

  20. Carbohydrate feeding increases total body and specific tissue 3,5,3'-triiodothyronine neogenesis in the rat

    SciTech Connect

    Gavin, L.A.; Moeller, M.; McMahon, F.A.; Castle, J.N.; Gulli, R.; Cavalieri, R.R.

    1988-08-01

    The glucose-fed rat, in contrast to the chow-fed animal, has a higher serum total T3 concentration and an increase in the hepatic content of T4 5'-deiodinase (type I) activity. The mechanism and significance of these glucose-induced changes in T3 metabolism are elucidated in this study. To focus on extrathyroidal thyroid hormone metabolism the kinetic parameters were determined in thyroidectomized T4-replaced rats (1.25 micrograms T4/100 g BW.day). Kinetics of T4 and T3 were studied separately by infusing labeled hormone to equilibrium. Glucose feeding for 72 h (G) significantly increased both the total and free serum T3 concentrations compared to the respective means in the chow-fed control group (P). The glucose-induced changes in serum T3 reflect the approximate doubling of T3 production to 14.7 +/- 0.6 ng/h.100 g in G rats compared to 7.6 +/- 0.7 ng/h.100 g in P rats. The higher T3 production rate in the G group is due to a significant increase in the fractional total body T4 to T3 conversion (0.33 +/- 0.02) compared to that in the P group (0.19 +/- 0.02). The tissue (liver, kidney, brain, and brown adipose tissue) concentration of T4 (nanograms per g wet wt) was significantly increased in the G group. The increase ranged from 54% in liver to 80% in kidney, brain, and brown adipose tissue. The tissue concentration of T3 (nanograms per g wet wt) was even more dramatically increased by glucose feeding than was T4. The glucose-induced increment in organ T3 ranged from 2.5-fold (kidney, muscle, and brain) to 5-fold (liver and white adipose tissue) to 12-fold (brown adipose tissue). These data indicate that the increase in serum total and free T3 concentrations associated with glucose feeding reflects augmented total body T3 production from T4. The effect of the enhanced T3 neogenesis was generalized, as the T3 content was increased in each organ studied. Thus, glucose feeding has unique effects on T3 metabolism.