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Sample records for novo design synthesis

  1. De Novo Glutamine Synthesis

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    Qiao He MD

    2016-04-01

    Full Text Available Purpose: The aim of this study was to investigate the role of de novo glutamine (Gln synthesis in the proliferation of C6 glioma cells and its detection with 13N-ammonia. Methods: Chronic Gln-deprived C6 glioma (0.06C6 cells were established. The proliferation rates of C6 and 0.06C6 cells were measured under the conditions of Gln deprivation along with or without the addition of ammonia or glutamine synthetase (GS inhibitor. 13N-ammonia uptake was assessed in C6 cells by gamma counting and in rats with C6 and 0.06C6 xenografts by micro–positron emission tomography (PET scanning. The expression of GS in C6 cells and xenografts was assessed by Western blotting and immunohistochemistry, respectively. Results: The Gln-deprived C6 cells showed decreased proliferation ability but had a significant increase in GS expression. Furthermore, we found that low concentration of ammonia was sufficient to maintain the proliferation of Gln-deprived C6 cells, and 13N-ammonia uptake in C6 cells showed Gln-dependent decrease, whereas inhibition of GS markedly reduced the proliferation of C6 cells as well as the uptake of 13N-ammoina. Additionally, microPET/computed tomography exhibited that subcutaneous 0.06C6 xenografts had higher 13N-ammonia uptake and GS expression in contrast to C6 xenografts. Conclusion: De novo Gln synthesis through ammonia–glutamate reaction plays an important role in the proliferation of C6 cells. 13N-ammonia can be a potential metabolic PET tracer for Gln-dependent tumors.

  2. De novo design and synthesis of ultra-short peptidomimetic antibiotics having dual antimicrobial and anti-inflammatory activities.

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    Ravichandran N Murugan

    Full Text Available BACKGROUND: Much attention has been focused on the design and synthesis of potent, cationic antimicrobial peptides (AMPs that possess both antimicrobial and anti-inflammatory activities. However, their development into therapeutic agents has been limited mainly due to their large size (12 to 50 residues in length and poor protease stability. METHODOLOGY/PRINCIPAL FINDINGS: In an attempt to overcome the issues described above, a set of ultra-short, His-derived antimicrobial peptides (HDAMPs has been developed for the first time. Through systematic tuning of pendant hydrophobic alkyl tails at the N(π- and N(τ-positions on His, and the positive charge of Arg, much higher prokaryotic selectivity was achieved, compared to human AMP LL-37. Additionally, the most potent HDAMPs showed promising dual antimicrobial and anti-inflammatory activities, as well as anti-methicillin-resistant Staphylococcus aureus (MRSA activity and proteolytic resistance. Our results from transmission electron microscopy, membrane depolarization, confocal laser-scanning microscopy, and calcein-dye leakage experiments propose that HDAMP-1 kills microbial cells via dissipation of the membrane potential by forming pore/ion channels on bacterial cell membranes. CONCLUSION/SIGNIFICANCE: The combination of the ultra-short size, high-prokaryotic selectivity, potent anti-MRSA activity, anti-inflammatory activity, and proteolytic resistance of the designed HDAMP-1, -3, -5, and -6 makes these molecules promising candidates for future antimicrobial therapeutics.

  3. de novo design and synthesis of Candida antarctica lipase B gene and α-factor leads to high-level expression in Pichia pastoris.

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    Yang, Jiang-Ke; Liu, Li-Ying; Dai, Jiang-Hong; Li, Qin

    2013-01-01

    Candida antarctica lipase B (CALB) is one of the most widely used and studied enzymes in the world. In order to achieve the high-level expression of CALB in Pichia, we optimized the codons of CALB gene and α-factor by using a de novo design and synthesis strategy. Through comparative analysis of a series of recombinants with different expression components, we found that the methanol-inducible expression recombinant carrying the codon-optimized α-factor and mature CALB gene (pPIC9KαM-CalBM) has the highest lipase production capacity. After fermentation parameters optimization, the lipase activity and protein content of the recombinant pPIC9KαM-CalBM reached 6,100 U/mL and 3.0 g/L, respectively, in a 5-L fermentor. We believe this strategy could be of special interest due to its capacity to improve the expression level of target gene, and the Pichia transformants carrying the codon-optimized gene had great potential for the industrial-scale production of CALB lipase.

  4. de novo design and synthesis of Candida antarctica lipase B gene and α-factor leads to high-level expression in Pichia pastoris.

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    Jiang-Ke Yang

    Full Text Available Candida antarctica lipase B (CALB is one of the most widely used and studied enzymes in the world. In order to achieve the high-level expression of CALB in Pichia, we optimized the codons of CALB gene and α-factor by using a de novo design and synthesis strategy. Through comparative analysis of a series of recombinants with different expression components, we found that the methanol-inducible expression recombinant carrying the codon-optimized α-factor and mature CALB gene (pPIC9KαM-CalBM has the highest lipase production capacity. After fermentation parameters optimization, the lipase activity and protein content of the recombinant pPIC9KαM-CalBM reached 6,100 U/mL and 3.0 g/L, respectively, in a 5-L fermentor. We believe this strategy could be of special interest due to its capacity to improve the expression level of target gene, and the Pichia transformants carrying the codon-optimized gene had great potential for the industrial-scale production of CALB lipase.

  5. De novo DESIGN AND SYNTHESIS OF AN ICE-BINDING, DENDRIMERIC, POLYPEPTIDE BASED ON INSECT ANTIFREEZE PROTEINS

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    Ricardo Vera Bravo

    2011-12-01

    Full Text Available A new strategy is presented for the designand synthesis of peptides that exhibitice-binding and antifreeze activity. Apennant-type dendrimer polypeptidescaffold combining an α-helical backbonewith four short β-strand branches wassynthesized in solid phase using Fmocchemistry in a divergent approach. The51-residue dendrimer was characterizedby reverse phase high performance liquidchromatography, mass spectrometry andcircular dichroism. Each β-strand branchcontained three overlapping TXT aminoacid repeats, an ice-binding motif foundin the ice-binding face of the sprucebudworm (Choristoneura fumiferanaand beetle (Tenebrio molitor antifreezeproteins. Ice crystals in the presence ofthe polypeptide monomer displayed flat,hexagonal plate morphology, similar tothat produced by weakly active antifreezeproteins. An oxidized dimeric form of thedendrimer polypeptide also produced flathexagonal ice crystals and was capableof inhibiting ice crystal growth upontemperature reduction, a phenomenontermed thermal hysteresis, a definingproperty of antifreeze proteins. Linkageof the pennant-type dendrimer to a trifunctionalcascade-type polypeptideproduced a trimeric macromolecule thatgave flat hexagonal ice crystals withhigher thermal hysteresis activity thanthe dimer or monomer and an ice crystal burst pattern similar to that producedby samples containing insect antifreezeproteins. This macromolecule was alsocapable of inhibiting ice recrystallization.

  6. De novo computer-aided design of novel antiviral agents.

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    Massarotti, Alberto; Coluccia, Antonio; Sorba, Giovanni; Silvestri, Romano; Brancale, Andrea

    2012-01-01

    Computer-aided drug design techniques have become an integral part of the drug discovery process. In particular, de novo methodologies can be useful to identify putative ligands for a specific target relying only on the structural information of the target itself. Here we discuss the basic de novo approaches available and their application in antiviral drug design.:

  7. Monosaccharide templates for de novo designed 4-alpha-helix bundle proteins: template effects in carboproteins

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    Brask, Jesper; Dideriksen, J.M.; Nielsen, John;

    2003-01-01

    De novo design and total chemical synthesis of proteins provide powerful approaches to critically test our understanding of protein folding, structure, and stability. The 4-alpha-helix bundle is a frequently studied structure in which four amphiphilic alpha-helical peptide strands form a hydropho......)) and melting points in chemical and thermal denaturation experiments....

  8. Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis.

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    Christen, Matthias; Deutsch, Samuel; Christen, Beat

    2015-08-21

    Recent advances in synthetic biology have resulted in an increasing demand for the de novo synthesis of large-scale DNA constructs. Any process improvement that enables fast and cost-effective streamlining of digitized genetic information into fabricable DNA sequences holds great promise to study, mine, and engineer genomes. Here, we present Genome Calligrapher, a computer-aided design web tool intended for whole genome refactoring of bacterial chromosomes for de novo DNA synthesis. By applying a neutral recoding algorithm, Genome Calligrapher optimizes GC content and removes obstructive DNA features known to interfere with the synthesis of double-stranded DNA and the higher order assembly into large DNA constructs. Subsequent bioinformatics analysis revealed that synthesis constraints are prevalent among bacterial genomes. However, a low level of codon replacement is sufficient for refactoring bacterial genomes into easy-to-synthesize DNA sequences. To test the algorithm, 168 kb of synthetic DNA comprising approximately 20 percent of the synthetic essential genome of the cell-cycle bacterium Caulobacter crescentus was streamlined and then ordered from a commercial supplier of low-cost de novo DNA synthesis. The successful assembly into eight 20 kb segments indicates that Genome Calligrapher algorithm can be efficiently used to refactor difficult-to-synthesize DNA. Genome Calligrapher is broadly applicable to recode biosynthetic pathways, DNA sequences, and whole bacterial genomes, thus offering new opportunities to use synthetic biology tools to explore the functionality of microbial diversity. The Genome Calligrapher web tool can be accessed at https://christenlab.ethz.ch/GenomeCalligrapher  .

  9. Herpes simplex virus 1 induces de novo phospholipid synthesis

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    Sutter, Esther [Electron Microscopy, Institute of Veterinary Anatomy, University of Zuerich (Switzerland); Oliveira, Anna Paula de; Tobler, Kurt [Electron microscopy, Institute of Virology, University of Zuerich (Switzerland); Schraner, Elisabeth M. [Electron Microscopy, Institute of Veterinary Anatomy, University of Zuerich (Switzerland); Sonda, Sabrina [Institute of Parasitology, University of Zuerich (Switzerland); Kaech, Andres [Center for Microscopy and Image Analysis, University of Zuerich (Switzerland); Lucas, Miriam S. [Electron Microscopy ETH Zuerich (EMEZ), Swiss Federal Institute of Technology, Zuerich (Switzerland); Ackermann, Mathias [Electron microscopy, Institute of Virology, University of Zuerich (Switzerland); Wild, Peter, E-mail: pewild@access.uzh.ch [Electron Microscopy, Institute of Veterinary Anatomy, University of Zuerich (Switzerland)

    2012-08-01

    Herpes simplex virus type 1 capsids bud at nuclear membranes and Golgi membranes acquiring an envelope composed of phospholipids. Hence, we measured incorporation of phospholipid precursors into these membranes, and quantified changes in size of cellular compartments by morphometric analysis. Incorporation of [{sup 3}H]-choline into both nuclear and cytoplasmic membranes was significantly enhanced upon infection. [{sup 3}H]-choline was also part of isolated virions even grown in the presence of brefeldin A. Nuclei expanded early in infection. The Golgi complex and vacuoles increased substantially whereas the endoplasmic reticulum enlarged only temporarily. The data suggest that HSV-1 stimulates phospholipid synthesis, and that de novo synthesized phospholipids are inserted into nuclear and cytoplasmic membranes to i) maintain membrane integrity in the course of nuclear and cellular expansion, ii) to supply membrane constituents for envelopment of capsids by budding at nuclear membranes and Golgi membranes, and iii) to provide membranes for formation of transport vacuoles.

  10. De novo design of synthetic prion domains.

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    Toombs, James A; Petri, Michelina; Paul, Kacy R; Kan, Grace Y; Ben-Hur, Asa; Ross, Eric D

    2012-04-24

    Prions are important disease agents and epigenetic regulatory elements. Prion formation involves the structural conversion of proteins from a soluble form into an insoluble amyloid form. In many cases, this structural conversion is driven by a glutamine/asparagine (Q/N)-rich prion-forming domain. However, our understanding of the sequence requirements for prion formation and propagation by Q/N-rich domains has been insufficient for accurate prion propensity prediction or prion domain design. By focusing exclusively on amino acid composition, we have developed a prion aggregation prediction algorithm (PAPA), specifically designed to predict prion propensity of Q/N-rich proteins. Here, we show not only that this algorithm is far more effective than traditional amyloid prediction algorithms at predicting prion propensity of Q/N-rich proteins, but remarkably, also that PAPA is capable of rationally designing protein domains that function as prions in vivo.

  11. Bio-inspired Composites, a de novo Approach to the Conceptualization, Design and Synthesis of Tough Mesoscale Structures with Simple Building Blocks

    Science.gov (United States)

    2013-02-01

    H. Song, M. C. Boyce, and C. Ortiz, Materials design principles of ancient fish armour. Nat Mater, 2008, 7, 9. [23] J. D. Currey, Materials science...Polyelectrolytes on Charged Surfaces. Thin Solid Films, 1992, 210, 1-2. [38] W. Tan and T. A. Desai, Layer-by-layer microfluidics for biomimetic three...and architecture. Bioinspir Biomim, 2012, 7, 1. [132] A. W. Lang, P. Motta, P. Hidalgo, and M. Westcott, Bristled shark skin : a microgeometry for

  12. Revisiting de novo drug design: receptor based pharmacophore screening.

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    Amaravadhi, Harikishore; Baek, Kwanghee; Yoon, Ho Sup

    2014-01-01

    De novo drug design methods such as receptor or protein based pharmacophore modeling present a unique opportunity to generate novel ligands by employing the potential binding sites even when no explicit ligand information is known for a particular target. Recent developments in molecular modeling programs have enhanced the ability of early programs such as LUDI or Pocket that not only identify the key interactions or hot spots at the suspected binding site, but also and convert these hot spots into three-dimensional search queries and virtual screening of the property filtered synthetic libraries. Together with molecular docking studies and consensus scoring schemes they would enrich the lead identification processes. In this review, we discuss the ligand and receptor based de novo drug design approaches with selected examples.

  13. Design Methodology - Design Synthesis

    DEFF Research Database (Denmark)

    Andreasen, Mogens Myrup

    2003-01-01

    ABSTRACT Design Methodology shall be seen as our understanding of how to design; it is an early (emerging late 60ies) and original articulation of teachable and learnable methodics. The insight is based upon two sources: the nature of the designed artefacts and the nature of human designing. Today...... Design Methodology is part of our practice and our knowledge about designing, and it has been strongly supported by the establishing and work of a design research community. The aim of this article is to broaden the reader¿s view of designing and Design Methodology. This is done by sketching...... the development of Design Methodology through time and sketching some important approaches and methods. The development is mainly forced by changing industrial condition, by the growth of IT support for designing, but also by the growth of insight into designing created by design researchers....

  14. A de novo designed monomeric, compact three helix bundle protein on a carbohydrate template

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    Malik, Leila; Nygård, Jesper; Christensen, Niels Johan

    2015-01-01

    De novo design and chemical synthesis of proteins and of other artificial structures, which mimic them, is a central strategy for understanding protein folding and for accessing proteins with novel functions. We have previously described carbohydrates as templates for the assembly of artificial...... proteins, so called carboproteins. The hypothesis is that the template pre-organizes the secondary structure elements and directs the formation of a tertiary structure, thus achieving structural economy in the combination of peptide, linker, and template. We speculate that the structural information from...

  15. Accurate de novo design of hyperstable constrained peptides

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    Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Bahl, Christopher D.; Gilmore, Jason M.; Harvey, Peta J.; Cheneval, Olivier; Buchko, Garry W.; Pulavarti, Surya V. S. R. K.; Kaas, Quentin; Eletsky, Alexander; Huang, Po-Ssu; Johnsen, William A.; Greisen, Per Jr; Rocklin, Gabriel J.; Song, Yifan; Linsky, Thomas W.; Watkins, Andrew; Rettie, Stephen A.; Xu, Xianzhong; Carter, Lauren P.; Bonneau, Richard; Olson, James M.; Coutsias, Evangelos; Correnti, Colin E.; Szyperski, Thomas; Craik, David J.; Baker, David

    2016-09-14

    Covalently-crosslinked peptides present attractive opportunities for developing new therapeutics. Lying between small molecule and protein therapeutics in size, natural crosslinked peptides play critical roles in signaling, virulence and immunity. Engineering novel peptides with precise control over their three-dimensional structures is a significant challenge. Here we describe the development of computational methods for de novo design of conformationally-restricted peptides, and the use of these methods to design hyperstable disulfide-stabilized miniproteins, heterochiral peptides, and N-C cyclic peptides. Experimentally-determined X-ray and NMR structures for 12 of the designs are nearly identical to the computational models. The computational design methods and stable scaffolds provide the basis for a new generation of peptide-based drugs.

  16. De novo synthesis of milk triglycerides in humans

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    Mammary gland (MG) de novo lipogenesis contributes significantly to milk fat in animals but little is known in humans. Objective: To test the hypothesis that the incorporation of 13C carbons from [U-13C]glucose into fatty acids (FA) and glycerol in triglycerides (TG) will be greater: 1) in milk tha...

  17. De-novo design of antimicrobial peptides for plant protection.

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    Benjamin Zeitler

    Full Text Available This work describes the de-novo design of peptides that inhibit a broad range of plant pathogens. Four structurally different groups of peptides were developed that differ in size and position of their charged and hydrophobic clusters and were assayed for their ability to inhibit bacterial growth and fungal spore germination. Several peptides are highly active at concentrations between 0,1 and 1 µg/ml against plant pathogenic bacteria, such as Pseudomonas syringae, Pectobacterium carotovorum, and Xanthomonas vesicatoria. Importantly, no hemolytic activity could be detected for these peptides at concentrations up to 200 µg/ml. Moreover, the peptides are also active after spraying on the plant surface demonstrating a possible way of application. In sum, our designed peptides represent new antimicrobial agents and with the increasing demand for antimicrobial compounds for production of "healthy" food, these peptides might serve as templates for novel antibacterial and antifungal agents.

  18. Accurate de novo design of hyperstable constrained peptides.

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    Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Bahl, Christopher D; Gilmore, Jason M; Harvey, Peta J; Cheneval, Olivier; Buchko, Garry W; Pulavarti, Surya V S R K; Kaas, Quentin; Eletsky, Alexander; Huang, Po-Ssu; Johnsen, William A; Greisen, Per Jr; Rocklin, Gabriel J; Song, Yifan; Linsky, Thomas W; Watkins, Andrew; Rettie, Stephen A; Xu, Xianzhong; Carter, Lauren P; Bonneau, Richard; Olson, James M; Coutsias, Evangelos; Correnti, Colin E; Szyperski, Thomas; Craik, David J; Baker, David

    2016-10-20

    Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes that have evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small-molecule drugs with the specificity of much larger protein therapeutics. The ability to design constrained peptides with precisely specified tertiary structures would enable the design of shape-complementary inhibitors of arbitrary targets. Here we describe the development of computational methods for accurate de novo design of conformationally restricted peptides, and the use of these methods to design 18-47 residue, disulfide-crosslinked peptides, a subset of which are heterochiral and/or N-C backbone-cyclized. Both genetically encodable and non-canonical peptides are exceptionally stable to thermal and chemical denaturation, and 12 experimentally determined X-ray and NMR structures are nearly identical to the computational design models. The computational design methods and stable scaffolds presented here provide the basis for development of a new generation of peptide-based drugs.

  19. De novo synthesis of D- and L-fucosamine containing disaccharides

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    Daniele Leonori

    2013-02-01

    Full Text Available The availability of rare monosaccharides that cannot be isolated from natural sources is currently limiting the access to the synthesis and the biological evaluation of complex bacterial cell-surface glycans. Here, we report the synthesis of D- and L-fucosamine building blocks by a de novo approach from L- and D-Garner aldehydes. These differentially protected monosaccharide building blocks were utilized to prepare disaccharides present on the surface of Pseudomonas aeruginosa bacteria.

  20. Taurine homeostasis requires de novo synthesis via cysteine sulfinic acid decarboxylase during zebrafish early embryogenesis.

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    Chang, Yen-Chia; Ding, Shih-Torng; Lee, Yen-Hua; Wang, Ya-Ching; Huang, Ming-Feng; Liu, I-Hsuan

    2013-02-01

    Cysteine sulfinic acid decarboxylase (Csad) is the rate-limiting enzyme in the de novo biosynthesis of taurine. There are a number of physiological roles of taurine, such as bile salt synthesis, osmoregulation, lipid metabolism, and oxidative stress inhibition. To investigate the role of de novo synthesis of taurine during embryonic development, zebrafish csad was cloned and functionally analyzed. Semi-quantitative RT-PCR showed that csad transcripts are maternally deposited, while whole-mount in situ hybridization demonstrated that csad is expressed in yolk syncytial layer and various embryonic tissues such as notochord, brain, retina, pronephric duct, liver, and pancreas. Knockdown of csad significantly reduced the embryonic taurine level, and the affected embryos had increased early mortality and cardiac anomalies. mRNA coinjection and taurine supplementation rescued the cardiac phenotypes suggesting that taurine originating from the de novo synthesis pathway plays a role in cardiac development. Our findings indicated that the de novo synthesis pathway via Csad plays a critical role in taurine homeostasis and cardiac development in zebrafish early embryos.

  1. De novo formal synthesis of (-)-virginiamycin M2 via the asymmetric hydration of dienoates.

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    Mortensen, Matthew S; Osbourn, Joshua M; O'Doherty, George A

    2007-08-02

    A de novo approach to the formal total synthesis of the macrolide natural product (-)-virginiamycin M2 has been achieved via a convergent approach. The absolute and relative stereochemistry of the nonpeptide portion of (-)-virginiamycin M2 was introduced by two Sharpless asymmetric dihydroxylation reactions.

  2. Exploring amyloid formation by a de novo design.

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    Kammerer, Richard A; Kostrewa, Dirk; Zurdo, Jesús; Detken, Andreas; García-Echeverría, Carlos; Green, Janelle D; Müller, Shirley A; Meier, Beat H; Winkler, Fritz K; Dobson, Christopher M; Steinmetz, Michel O

    2004-03-30

    Protein deposition as amyloid fibrils underlies many debilitating human disorders. The complexity and size of disease-related polypeptides, however, often hinders a detailed rational approach to study effects that contribute to the process of amyloid formation. We report here a simplified peptide sequence successfully designed de novo to fold into a coiled-coil conformation under ambient conditions but to transform into amyloid fibrils at elevated temperatures. We have determined the crystal structure of the coiled-coil form and propose a detailed molecular model for the peptide in its fibrillar state. The relative stabilities of the two structural forms and the kinetics of their interconversion were found to be highly sensitive to small sequence changes. The results reveal the importance of specific packing interactions on the kinetics of amyloid formation and show the potential of this exceptionally favorable system for probing details of the molecular origins of amyloid disease.

  3. De novo design of protein mimics of B-DNA.

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    Yüksel, Deniz; Bianco, Piero R; Kumar, Krishna

    2016-01-01

    Structural mimicry of DNA is utilized in nature as a strategy to evade molecular defences mounted by host organisms. One such example is the protein Ocr - the first translation product to be expressed as the bacteriophage T7 infects E. coli. The structure of Ocr reveals an intricate and deliberate arrangement of negative charges that endows it with the ability to mimic ∼24 base pair stretches of B-DNA. This uncanny resemblance to DNA enables Ocr to compete in binding the type I restriction modification (R/M) system, and neutralizes the threat of hydrolytic cleavage of viral genomic material. Here, we report the de novo design and biophysical characterization of DNA mimicking peptides, and describe the inhibitory action of the designed helical bundles on a type I R/M enzyme, EcoR124I. This work validates the use of charge patterning as a design principle for creation of protein mimics of DNA, and serves as a starting point for development of therapeutic peptide inhibitors against human pathogens that employ molecular camouflage as part of their invasion stratagem.

  4. De novo synthesis and properties of analogues of the self-assembling chlorosomal bacteriochlorophylls

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    Mass, Olga [North Carolina State Univ., Raleigh, NC (United States); Pandithavidana, Dinesh R. [North Carolina State Univ., Raleigh, NC (United States); Ptaszek, Marcin [North Carolina State Univ., Raleigh, NC (United States); Santiago, Koraliz [North Carolina State Univ., Raleigh, NC (United States); Springer, Joseph W. [Washington Univ., St. Louis, MO (United States); Jiao, Jieying [Univ. Of California, Riverside, CA (United States); Tang, Qun [Univ. Of California, Riverside, CA (United States); Kirmaier, Christine [Washington Univ., St. Louis, MO (United States); Bocian, David F. [Univ. Of California, Riverside, CA (United States); Holten, Dewey [Washington Univ., St. Louis, MO (United States); Lindsey, Jonathan S. [North Carolina State Univ., Raleigh, NC (United States)

    2011-01-01

    Natural photosynthetic pigments bacteriochlorophyllsc, d and e in green bacteria undergo self-assembly to create an organized antenna system known as the chlorosome, which collects photons and funnels the resulting excitation energy toward the reaction centers. Mimicry of chlorosome function is a central problem in supramolecular chemistry and artificial photosynthesis, and may have relevance for the design of photosynthesis-inspired solar cells. The main challenge in preparing artificial chlorosomes remains the synthesis of the appropriate pigment (chlorin) equipped with a set of functional groups suitable to direct the assembly and assure efficient energy transfer. Prior approaches have entailed derivatization of porphyrins or semisynthesis beginning with chlorophylls. This paper reports a third approach, the de novo synthesis of macrocycles that contain the same hydrocarbon skeleton as chlorosomal bacteriochlorophylls. The synthesis here of Zn(II) 3-(1-hydroxyethyl)-10-aryl-13¹-oxophorbines (the aryl group consists of phenyl, mesityl, or pentafluorophenyl) entails selective bromination of a 3,13-diacetyl-10-arylchlorin, palladium-catalyzed 13¹-oxophorbine formation, and selective reduction of the 3-acetyl group using BH₃·tBuNH₂. Each macrocycle contains a geminal dimethyl group in the pyrroline ring to provide stability toward adventitious dehydrogenation. A Zn(II) 7-(1-hydroxyethyl)-10-phenyl-17-oxochlorin also has been prepared. Altogether, 30 new hydroporphyrins were synthesized. The UV-Vis absorption spectra of the new chlorosomal bacteriochlorophyll mimics reveal a bathochromic shift of [similar]1800 cm-1 of the Qy band in nonpolar solvent, indicating extensive assembly in solution. The Zn(II) 3-(1-hydroxyethyl)-10-aryl-13¹-oxophorbines differ in the propensity to form assemblies based on the 10-substituent in the following order: mesityl

  5. Engineering Methylobacterium extorquens for de novo synthesis of the sesquiterpenoid α-humulene from methanol.

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    Sonntag, Frank; Kroner, Cora; Lubuta, Patrice; Peyraud, Rémi; Horst, Angelika; Buchhaupt, Markus; Schrader, Jens

    2015-11-01

    Over the last 10 to 15 years, metabolic engineering of microbes has become a versatile tool for high-level de novo synthesis of terpenoids, with the sesquiterpenoids armopha-1,4-diene, farnesene and artemisinic acid as prime examples. However, almost all cell factory approaches towards terpenoids to date have been based on sugar as the raw material, which is mainly used as a food resource and subject to high price volatilities. In this study we present de novo synthesis of the sesquiterpenoid α-humulene from the abundantly available non-food carbon source methanol by metabolically engineered Methylobacterium extorquens AM1. Expression of α-humulene synthase from Zingiber zerumbet in combination with farnesyl pyrophosphate (FPP) synthase from Saccharomyces cerevisiae led to concentrations of up to 18 mg/L α-humulene. Introduction of a prokaryotic mevalonate pathway from Myxococcus xanthus in combination with ribosome binding site optimization of α-humulene and FPP synthases increased product concentration 3-fold. This value was additionally raised by 30% using a carotenoid synthesis deficient mutant strain. Final product concentrations of up to 1.65 g/L were obtained in methanol limited fed-batch cultivations, which is the highest titer of de novo synthesized α-humulene reported to date. This study demonstrates the potential of M. extorquens as a future platform strain for the production of high-value terpenoids from the alternative carbon source methanol.

  6. Carbopeptides: carbohydrates as potential templates for de novo design of protein models.

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    Jensen, K J; Barany, G

    2000-07-01

    De novo design of proteins has evolved into a powerful approach for studying the factors governing protein folding and stability. Among the families of structures frequently studied is the 'four-helix bundle' in which four alpha-helical peptide strands, linked by loops, form a hydrophobic core. Assembly of protein models on a template has been suggested as a way to reduce the entropy of folding. Here we describe the potential use of a carbohydrate as such a template. The monosaccharide D-galactose was per-O-acylated with (Nbeta-Fmoc-betaAla)2O to give a penta-substituted derivative, which was converted to the corresponding glycosyl bromide and used for the glycosylation of 4-hydroxymethylbenzoic acid pentafluorophenyl ester (HMBA-OPfp). The beta-glycosidic carbohydrate template (Nbeta-Fmoc-3Ala)4-beta-D-Galp-(1-O)-MBA-OPfp thus obtained was coupled to a PAL-PEG-PS resin and simultaneously extended at the four arms to yield, after cleavage from the solid support, a carbopeptide with four identical peptide strands. Extension of this concept to, for example, synthesis of novel multiple antigenic peptides (MAPs) and synthesis of carbohydrate clusters can be easily envisioned. The ability to efficiently synthesize such structures sets the stage for further studies to test whether the carbohydrate templates do indeed nucleate folding.

  7. Adaptive Reprogramming of De Novo Pyrimidine Synthesis Is a Metabolic Vulnerability in Triple-Negative Breast Cancer.

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    Brown, Kristin K; Spinelli, Jessica B; Asara, John M; Toker, Alex

    2017-04-01

    Chemotherapy resistance is a major barrier to the treatment of triple-negative breast cancer (TNBC), and strategies to circumvent resistance are required. Using in vitro and in vivo metabolic profiling of TNBC cells, we show that an increase in the abundance of pyrimidine nucleotides occurs in response to chemotherapy exposure. Mechanistically, elevation of pyrimidine nucleotides induced by chemotherapy is dependent on increased activity of the de novo pyrimidine synthesis pathway. Pharmacologic inhibition of de novo pyrimidine synthesis sensitizes TNBC cells to genotoxic chemotherapy agents by exacerbating DNA damage. Moreover, combined treatment with doxorubicin and leflunomide, a clinically approved inhibitor of the de novo pyrimidine synthesis pathway, induces regression of TNBC xenografts. Thus, the increase in pyrimidine nucleotide levels observed following chemotherapy exposure represents a metabolic vulnerability that can be exploited to enhance the efficacy of chemotherapy for the treatment of TNBC.Significance: The prognosis for patients with TNBC with residual disease after chemotherapy is poor. We find that chemotherapy agents induce adaptive reprogramming of de novo pyrimidine synthesis and show that this response can be exploited pharmacologically, using clinically approved inhibitors of de novo pyrimidine synthesis, to sensitize TNBC cells to chemotherapy. Cancer Discov; 7(4); 391-9. ©2017 AACR.See related article by Mathur et al., p. 380This article is highlighted in the In This Issue feature, p. 339.

  8. EvoDesign: De novo protein design based on structural and evolutionary profiles.

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    Mitra, Pralay; Shultis, David; Zhang, Yang

    2013-07-01

    Protein design aims to identify new protein sequences of desirable structure and biological function. Most current de novo protein design methods rely on physics-based force fields to search for low free-energy states following Anfinsen's thermodynamic hypothesis. A major obstacle of such approaches is the inaccuracy of the force field design, which cannot accurately describe the atomic interactions or distinguish correct folds. We developed a new web server, EvoDesign, to design optimal protein sequences of given scaffolds along with multiple sequence and structure-based features to assess the foldability and goodness of the designs. EvoDesign uses an evolution-profile-based Monte Carlo search with the profiles constructed from homologous structure families in the Protein Data Bank. A set of local structure features, including secondary structure, torsion angle and solvation, are predicted by single-sequence neural-network training and used to smooth the sequence motif and accommodate the physicochemical packing. The EvoDesign algorithm has been extensively tested in large-scale protein design experiments, which demonstrate enhanced foldability and structural stability of designed sequences compared with the physics-based designing methods. The EvoDesign server is freely available at http://zhanglab.ccmb.med.umich.edu/EvoDesign.

  9. Specific activation of human interleukin-5 depends on de novo synthesis of an AP-1 complex.

    Science.gov (United States)

    Schwenger, Gretchen T F; Kok, Chee Choy; Arthaningtyas, Estri; Thomas, Marc A; Sanderson, Colin J; Mordvinov, Viatcheslav A

    2002-12-06

    It is clear from the biology of eosinophilia that a specific regulatory mechanism must exist. Because interleukin-5 (IL5) is the key regulatory cytokine, it follows that a gene-specific control of IL5 expression must exist that differs even from closely related cytokines such as IL4. Two features of IL5 induction make it unique compared with other cytokines; first, induction by cyclic adenosine monophosphate (cAMP), which inhibits other T-cell-derived cytokines, and second, sensitivity to protein synthesis inhibitors, which have no effect on other cytokines. This study has utilized the activation of different transcription factors by different stimuli in a human T-cell line to study the role of conserved lymphokine element 0 (CLE0) in the specific induction of IL5. In unstimulated cells the ubiquitous Oct-1 binds to CLE0. Stimulation induces de novo synthesis of the AP-1 members JunD and Fra-2, which bind to CLE0. The amount of IL5 produced correlates with the production of the AP-1 complex, suggesting a key role in IL5 expression. The formation of the AP-1 complex is essential, but the rate-limiting step is the synthesis of AP-1, especially Fra-2. This provides an explanation for the sensitivity of IL5 to protein synthesis inhibitors and a mechanism for the specific induction of IL5 compared with other cytokines.

  10. De Novo Design of Helical Bundles as Models for Understanding Protein Folding and Function

    OpenAIRE

    Hill, R. Blake; Raleigh, Daniel P.; Lombardi, Angela; DeGrado, William F.

    2000-01-01

    De novo protein design has proven to be a powerful tool for understanding protein folding, structure, and function. In this Account, we highlight aspects of our research on the design of dimeric, four-helix bundles. Dimeric, four-helix bundles are found throughout nature, and the history of their design in our laboratory illustrates our hierarchic approach to protein design. This approach has been successfully applied to create a completely native-like protein. Structural and mutational analy...

  11. Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide

    NARCIS (Netherlands)

    Pagel, K; Seeger, K; Seiwert, B; Villa, Alessandra; Mark, AE; Berger, S; Koksch, B

    2005-01-01

    We report here an advanced approach for the characterization of the folding pattern of a de novo designed antiparallel coiled coil peptide by high-resolution methods. Incorporation of two fluorescence labels at the C- and N-terminus of the peptide chain as well as modi. cation of two hydrophobic cor

  12. Organ-Specific Alterations in Fatty Acid De Novo Synthesis and Desaturation in a Rat Model of Programmed Obesity

    Directory of Open Access Journals (Sweden)

    Desai Mina

    2011-05-01

    Full Text Available Abstract Background Small for gestational age (SGA leads to increased risk of adult obesity and metabolic syndrome. Offspring exposed to 50% maternal food restriction in utero are born smaller than Controls (FR, catch-up in growth by the end of the nursing period, and become obese adults. The objective of the study was to determine stearoyl-CoA desaturase activity (SCD1 and rates of de novo fatty acid synthesis in young FR and Control offspring tissues at the end of the nursing period, as possible contributors to catch-up growth. Methods From gestational day 10 to term, dams fed ad libitum (Control or were 50% food-restricted to produce small FR pups. Control dams nursed all pups. At postnatal day 1 (p1 and p21, offspring body tissues were analyzed by GC/MS, and desaturation indices of palmitoleate/palmitate and oleate/stearate were calculated. SCD1 gene expression was determined by real-time PCR on adipose and liver. Offspring were enriched with deuterium that was given to dams in drinking water during lactation and de novo synthesis of offspring body tissues was determined at p21. Primary adipocyte cell cultures were established at p21 and exposed to U13C-glucose. Results FR offspring exhibited higher desaturation index in p1 and p21 adipose tissue, but decreased desaturation index in liver at p21. SCD1 gene expression at p21 was correspondingly increased in adipose and decreased in liver. FR subcutaneous fat demonstrated increased de novo synthesis at p21. Primary cell cultures exhibited increased de novo synthesis in FR. Conclusions Adipose tissue is the first site to exhibit increased de novo synthesis and desaturase activity in FR. Therefore, abnormal lipogenesis is already present prior to onset of obesity during the period of catch-up growth. These abnormalities may contribute to future obesity development.

  13. Function through synthesis-informed design.

    Science.gov (United States)

    Wender, Paul A; Quiroz, Ryan V; Stevens, Matthew C

    2015-03-17

    In 1996, a snapshot of the field of synthesis was provided by many of its thought leaders in a Chemical Reviews thematic issue on "Frontiers in Organic Synthesis". This Accounts of Chemical Research thematic issue on "Synthesis, Design, and Molecular Function" is intended to provide further perspective now from well into the 21st century. Much has happened in the past few decades. The targets, methods, strategies, reagents, procedures, goals, funding, practices, and practitioners of synthesis have changed, some in dramatic ways as documented in impressive contributions to this issue. However, a constant for most synthesis studies continues to be the goal of achieving function with synthetic economy. Whether in the form of new catalysts, reagents, therapeutic leads, diagnostics, drug delivery systems, imaging agents, sensors, materials, energy generation and storage systems, bioremediation strategies, or molecules that challenge old theories or test new ones, the function of a target has been and continues to be a major and compelling justification for its synthesis. While the targets of synthesis have historically been heavily represented by natural products, increasingly design, often inspired by natural structures, is providing a new source of target structures exhibiting new or natural functions and new or natural synthetic challenges. Complementing isolation and screening approaches to new target identification, design enables one to create targets de novo with an emphasis on sought-after function and synthetic innovation with step-economy. Design provides choice. It allows one to determine how close a synthesis will come to the ideal synthesis and how close a structure will come to the ideal function. In this Account, we address studies in our laboratory on function-oriented synthesis (FOS), a strategy to achieve function by design and with synthetic economy. By starting with function rather than structure, FOS places an initial emphasis on target design

  14. Route of administration (enteral or parenteral) affects the contribution of L-glutamine to de novo L-arginine synthesis in mice: a stable-isotope study.

    Science.gov (United States)

    Boelens, Petra G; Melis, Gerdien C; van Leeuwen, Paul A; ten Have, Gabrie A; Deutz, Nicolaas E

    2006-10-01

    A pathway from enteral L-glutamine as substrate for L-arginine synthesis is suggested by previous studies. L-Glutamine and L-glutamine dipeptides exhibit numerous beneficial effects in experimental and clinical studies. In trauma patients, enteral L-glutamine supply increased plasma L-arginine. The present study was designed to quantify the contribution of L-glutamine to the de novo L-citrulline and L-arginine synthesis in mice when L-glutamine is administered in a high dose of labeled L-glutamine or L-alanyl-L-glutamine by the enteral or parenteral route. For this purpose, male Swiss mice (n = 43) underwent a laparotomy, and catheters were inserted for sampling and infusion. A primed, constant, and continuous infusion of L-alanyl-L-[2-(15)N]glutamine (dipeptide groups) or L-[2-(15)N]glutamine (free L-glutamine groups), simultaneously with L-[ureido-(13)C,(2)H(2)]citrulline and L-[guanidino-(15)N(2),(2)H(2)]arginine, was given (steady-state model). Mice received the L-glutamine tracers intravenously (jugular vein) or enterally (duodenum). Enrichments of metabolites were measured by LC-MS. Arterial L-glutamine concentrations were the highest in the intravenous dipeptide group. L-Glutamine was converted to L-citrulline and L-arginine when L-[2-(15)N]glutamine and L-alanyl-L-[2-(15)N]glutamine were given by enteral or parenteral route. The contribution of L-glutamine to the de novo synthesis of L-citrulline and L-arginine was higher in the enteral groups when compared with the intravenous groups (P glutamine, provided as free molecule or dipeptide, to the de novo synthesis of L-arginine in mice.

  15. Metal Stabilization of Collagen and de Novo Designed Mimetic Peptides.

    Science.gov (United States)

    Parmar, Avanish S; Xu, Fei; Pike, Douglas H; Belure, Sandeep V; Hasan, Nida F; Drzewiecki, Kathryn E; Shreiber, David I; Nanda, Vikas

    2015-08-18

    We explore the design of metal binding sites to modulate triple-helix stability of collagen and collagen-mimetic peptides. Globular proteins commonly utilize metals to connect tertiary structural elements that are well separated in sequence, constraining structure and enhancing stability. It is more challenging to engineer structural metals into fibrous protein scaffolds, which lack the extensive tertiary contacts seen in globular proteins. In the collagen triple helix, the structural adjacency of the carboxy-termini of the three chains makes this region an attractive target for introducing metal binding sites. We engineered His3 sites based on structural modeling constraints into a series of designed homotrimeric and heterotrimeric peptides, assessing the capacity of metal binding to improve stability and in the case of heterotrimers, affect specificity of assembly. Notable enhancements in stability for both homo- and heteromeric systems were observed upon addition of zinc(II) and several other metal ions only when all three histidine ligands were present. Metal binding affinities were consistent with the expected Irving-Williams series for imidazole. Unlike other metals tested, copper(II) also bound to peptides lacking histidine ligands. Acetylation of the peptide N-termini prevented copper binding, indicating proline backbone amide metal-coordination at this site. Copper similarly stabilized animal extracted Type I collagen in a metal-specific fashion, highlighting the potential importance of metal homeostasis within the extracellular matrix.

  16. De novo design of a single-chain diphenylporphyrin metalloprotein.

    Science.gov (United States)

    Bender, Gretchen M; Lehmann, Andreas; Zou, Hongling; Cheng, Hong; Fry, H Christopher; Engel, Don; Therien, Michael J; Blasie, J Kent; Roder, Heinrich; Saven, Jeffrey G; DeGrado, William F

    2007-09-01

    We describe the computational design of a single-chain four-helix bundle that noncovalently self-assembles with fully synthetic non-natural porphyrin cofactors. With this strategy, both the electronic structure of the cofactor as well as its protein environment may be varied to explore and modulate the functional and photophysical properties of the assembly. Solution characterization (NMR, UV-vis) of the protein showed that it bound with high specificity to the desired cofactors, suggesting that a uniquely structured protein and well-defined site had indeed been created. This provides a genetically expressed single-chain protein scaffold that will allow highly facile, flexible, and asymmetric variations to enable selective incorporation of different cofactors, surface-immobilization, and introduction of spectroscopic probes.

  17. Olefin cross metathesis based de novo synthesis of a partially protected L-amicetose and a fully protected L-cinerulose derivative

    Directory of Open Access Journals (Sweden)

    Bernd Schmidt

    2014-05-01

    Full Text Available Cross metathesis of a lactate derived allylic alcohol and acrolein is the entry point to a de novo synthesis of 4-benzoate protected L-amicetose and a cinerulose derivative protected at C5 and C1.

  18. Olefin cross metathesis based de novo synthesis of a partially protected L-amicetose and a fully protected L-cinerulose derivative

    Science.gov (United States)

    Hauke, Sylvia

    2014-01-01

    Summary Cross metathesis of a lactate derived allylic alcohol and acrolein is the entry point to a de novo synthesis of 4-benzoate protected L-amicetose and a cinerulose derivative protected at C5 and C1. PMID:24991253

  19. De novo design, synthesis and spectroscopic characterization of chiral benzimidazole-derived amino acid Zn(II) complexes: Development of tryptophan-derived specific hydrolytic DNA artificial nuclease agent

    Science.gov (United States)

    Parveen, Shazia; Arjmand, Farukh

    2012-01-01

    Novel ternary dizinc(II) complexes 1- 3, derived from 1,2-bis(1H-benzimidazol-2-yl)ethane-1,2-diol and L-form of amino acids (viz., tryptophan, leucine and valine) were synthesized and characterized by spectroscopic (IR, 1H NMR, UV-vis, ESI-MS) and other analytical methods. To evaluate the biological preference of chiral drugs for inherently chiral target DNA, interaction of 1- 3 with calf thymus DNA in Tris-HCl buffer was studied by various biophysical techniques which reveal that all these complexes bind to CT DNA non-covalently via electrostatic interaction. The higher Kb value of L-tryptophan complex 1 suggested greater DNA binding propensity. Further, to evaluate the mode of action at the molecular level, interaction studies of complexes 1 and 2 with nucleotides (5'-GMP and 5'-TMP) were carried out by UV-vis titrations, 1H and 31P NMR which implicates the preferential selectivity of these complexes to N3 of thymine rather than N7 of guanine. Furthermore, complex 1 exhibits efficient DNA cleavage with supercoiled pBR322. The complex 1 cleaves DNA efficiently involving hydrolytic cleavage pathway. Such chiral synthetic hydrolytic nucleases with asymmetric centers are gaining considerable attention owing to their importance in biotechnology and drug design, in particular to cleave DNA with sequence selectivity different from that of the natural enzymes.

  20. De novo designed peptide-based amyloid fibrils.

    Science.gov (United States)

    López De La Paz, Manuela; Goldie, Kenneth; Zurdo, Jesús; Lacroix, Emmanuel; Dobson, Christopher M; Hoenger, Andreas; Serrano, Luis

    2002-12-10

    Identification of therapeutic strategies to prevent or cure diseases associated with amyloid fibril deposition in tissue (Alzheimer's disease, spongiform encephalopathies, etc.) requires a rational understanding of the driving forces involved in the formation of these organized assemblies rich in beta-sheet structure. To this end, we used a computer-designed algorithm to search for hexapeptide sequences with a high propensity to form homopolymeric beta-sheets. Sequences predicted to be highly favorable on this basis were found experimentally to self-associate efficiently into beta-sheets, whereas point mutations predicted to be unfavorable for this structure inhibited polymerization. However, the property to form polymeric beta-sheets is not a sufficient requirement for fibril formation because, under the conditions used here, preformed beta-sheets from these peptides with charged residues form well defined fibrils only if the total net charge of the molecule is +/-1. This finding illustrates the delicate balance of interactions involved in the formation of fibrils relative to more disordered aggregates. The present results, in conjunction with x-ray fiber diffraction, electron microscopy, and Fourier transform infrared measurements, have allowed us to propose a detailed structural model of the fibrils.

  1. Fatty Acid de Novo Synthesis in Adult Intrauterine Growth-Restricted Offspring, and Adult Male Response to a High Fat Diet.

    Science.gov (United States)

    Yee, Jennifer K; Han, Guang; Vega, Juan; Lee, Wai-Nang P; Ross, Michael G; Desai, Mina

    2016-12-01

    Intrauterine growth restriction (IUGR) with rapid catch-up growth leads to adult obesity and insulin resistance. We have previously shown that IUGR male rats demonstrated increased de novo fatty acid synthesis in the subcutaneous (SC) fat, but not the visceral fat, during the nursing period prior to the onset of obesity. Young IUGR females do not exhibit the same increase. We further hypothesized that in male IUGR offspring, de novo synthesis is a programmed intrinsic effect that persists to adulthood and does not suppress in response to a high fat diet. We measured fatty acid de novo synthesis in IUGR adult males (6 months) using deuterium-enriched drinking water as a stable isotope tracer, then further studied the response after consumption of an isocaloric high fat diet. Baseline de novo synthesis in adult females was also studied at age 9 months. Males demonstrated increased baseline de novo synthesis in both SC fat and visceral fat. Correspondingly, SC and visceral fat protein expression of lipogenic enzymes acetyl-coA carboxylase-α (ACCα) and fatty acid synthase were upregulated. After the isocaloric high fat diet, de novo synthesis was suppressed such that no differences remained between the two groups, although, IUGR SC fat demonstrated persistently increased lipogenic protein expression. In contrast, de novo synthesis among adult females is not impacted in IUGR. In conclusion, enhancement of male IUGR SC fat de novo synthesis appears to be an early consequence of metabolic programming, whereas enhancement in visceral fat appears to be a later consequence.

  2. De Novo Design of Metalloproteins and Metalloenzymes in a Three-Helix Bundle.

    Science.gov (United States)

    Plegaria, Jefferson S; Pecoraro, Vincent L

    2016-01-01

    For more than two decades, de novo protein design has proven to be an effective methodology for modeling native proteins. De novo design involves the construction of metal-binding sites within simple and/or unrelated α-helical peptide structures. The preparation of α3D, a single polypeptide that folds into a native-like three-helix bundle structure, has significantly expanded available de novo designed scaffolds. Devoid of a metal-binding site (MBS), we incorporated a 3Cys and 3His motif in α3D to construct a heavy metal and a transition metal center, respectively. These efforts produced excellent functional models for native metalloproteins/metalloregulatory proteins and metalloenzymes. Morever, these α3D derivatives serve as a foundation for constructing redox active sites with either the same (e.g., 4Cys) or mixed (e.g., 2HisCys) ligands, a feat that could be achieved in this preassembled framework. Here, we describe the process of constructing MBSs in α3D and our expression techniques.

  3. Adopting De Novo Programming Approach on IC Design Service Firms Resources Integration

    Directory of Open Access Journals (Sweden)

    James K. C. Chen

    2014-01-01

    Full Text Available The semiconductor industry has very important position in computer industry, ICT field, and new electronic technology developing. The IC design service is one of key factor of semiconductor industry development. There are more than 365 IC design service firms have been established around Hsinchu Science Park in Taiwan. Building an efficient planning model for IC design service firm resources integrating is very interest issue. This study aims to construct a planning model for IC design service firm implementation resources integration. This study uses the De Novo programming as an approach of criteria alternative to achieve optimal resource allocation on IC design firm. Results show the IC design service firm should conduct open innovation concept and utilizes design outsourcing obtains cost down and enhance IC design service business performance. This plan model of De Novo programming is not only for IC design service firm and also can apply to the other industrial implementation strategic alliance/integrating resource. This plan model is a universal model for the others industries field.

  4. Design, Sustainable Synthesis, and Programmed Reactions of Templated N-Heteroaryl-Fused Vinyl Sultams.

    Science.gov (United States)

    Laha, Joydev K; Sharma, Shubhra; Kirar, Seema; Banerjee, Uttam C

    2017-09-15

    A de novo design and synthesis of N-heteroaryl-fused vinyl sultams as templates for programming chemical reactions on vinyl sultam periphery or (hetero)aryl ring is described. The key features include rational designing and sustainable synthesis of the template, customized reactions of vinyl sultams at C═C bond or involving N-S bond cleavage, and reactions on the periphery of the heteroaryl ring for late-stage diversification. The simple, easy access to the template coupled with opportunities for the synthesis of diversely functionalized heterocyles from a single template constitutes a rare study in contemporary organic synthesis.

  5. Synthesis and Characterization of Metal-Organic Frameworks (MOFs) That Are Difficult to Access De Novo

    Science.gov (United States)

    Karagiaridi, Olga

    Metal-organic frameworks (MOFs) are a class of intriguing hybrid materials, comprised of metal-based nodes joined by organic linkers into a crystalline, porous, three-dimensional lattice. Their signature properties (well-defined surfaces, tailorability and ultra-high porosity) render them promising candidates for many applications, including, but not limited to, gas storage, gas separation, catalysis and sensing. One of the greatest challenges associated with MOF synthesis lies in the fact that obtaining a desired MOF structure that is tailored to perform a specific application is often not trivial. Traditional synthetic pathways termed "de novo synthesis" (typically one-pot reactions between the MOF structural building blocks under solvothermal conditions) often give rise to side products that do not possess the desired structure. To circumvent this problem, we have studied in depth two powerful MOF synthetic techniques -- solvent-assisted linker exchange (SALE) and transmetalation. These are heterogeneous reactions of parent MOF crystals with concentrated solutions of organic linkers and inorganic metal salts, respectively, that lead to the replacement of the linkers or metal nodes within the parent MOFs by the desired components, while the overall framework topology is preserved. The projects described in this dissertation have aimed to apply these techniques to transform simple (unfunctionalized) and easy to synthesize representative materials from various MOF systems to structurally and functionally interesting daughter products. Examples include synthesis of MOFs that are energetically "unfavorable", extension of MOF cages by longer linker incorporation, functionalization of MOF pores and endowment of MOFs with permanent and persistent porosity. Through these projects, we have been able to formulate a set of rules that can be applied to predict the successful outcome of SALE. Since the allure of MOFs lies in their applications, expanding the range of

  6. De novo design of peptide scaffolds as novel preorganized ligands for metal-ion coordination.

    Science.gov (United States)

    Gamble, Aimee J; Peacock, Anna F A

    2014-01-01

    This chapter describes how de novo designed peptides can be used as novel preorganized ligands for metal ion coordination. The focus is on the design of peptides which are programmed to spontaneously self-assemble into α-helical coiled coils in aqueous solution, and how metal ion binding sites can be engineered onto and into these structures. In addition to describing the various design principles, some key examples are covered illustrating the success of this approach, including a more detailed example in the case study.

  7. De novo synthesis and functional study of primitive polypeptides in the prebiotic protein world

    Science.gov (United States)

    Fujishima, Kosuke; Wang, Kendrick; Ferreira, Raphael; Rothschild, Lynn

    DNA, RNA and proteins within a lipid-bound membrane are the core components of life, but the order of their appearance during the origin and evolution of life is still under debate. The widely accepted “RNA World” hypothesis states that RNA likely emerged prior to proteins and DNA since RNA can serve both replicative and catalytic roles. While biochemists have reproduced the synthesis, polymerization, and replication of nucleotides/RNA under controlled prebiotic conditions, such complex organic molecules were not present in significant amounts on the prebiotic Earth. In contrast, amino acids are naturally abundant in various prebiotic contexts such as carbonaceous chondrites and Urey-Miller type experiments, and many studies have demonstrated plausible prebiotic conditions that could condense/polymerize amino acids to give rise to short peptides. These findings support the basis of a “Protein World” hypothesis for life, however little has been done to study the functions of such primitive peptides. Here, we present a novel synthetic biology-based approach to the de novo synthesis of over billions of primitive peptides/proteins derived from a limited set of naturally abundant proteinogenic amino acids. Of these peptides, ones with divalent metal-binding capability are of particular interest and will be screened and identified. Certain divalent metals are likely present in prebiotic environments and both coordinate well with amino acids and catalyze reactions, which are difficult to achieve in organic chemistry. Furthermore, since D-chiral and non-proteinogenic amino acids are also abundant in the universe and may provide insight into the pathway by which life developed, the methods to analyze primitive peptides consisting of these amino acids will be discussed. By understanding this natural pathway, we will be able to better understand how life developed here on Earth and the probability of life arising elsewhere.

  8. De novo synthesis of estrogen in pregnant uterus is critical for stromal decidualization and angiogenesis.

    Science.gov (United States)

    Das, Amrita; Mantena, Srinivasa Raju; Kannan, Athilakshmi; Evans, Dean B; Bagchi, Milan K; Bagchi, Indrani C

    2009-07-28

    Implantation is initiated when the embryo attaches to the uterine luminal epithelium during early pregnancy. Following this event, uterine stromal cells undergo steroid hormone-dependent transformation into morphologically and functionally distinct decidual cells in a unique process known as decidualization. An angiogenic network is also formed in the uterine stromal bed, critically supporting the early development of the embryo. The steroid-induced mechanisms that promote stromal differentiation and endothelial proliferation during decidualization are not fully understood. Although the role of ovarian progesterone as a key regulator of decidualization is well established, the requirement of ovarian estrogen (E) during this process remains unresolved. Here we show that the expression of P450 aromatase, a key enzyme that converts androgens to E, is markedly induced in mouse uterine stromal cells undergoing decidualization. The aromatase then acts in conjunction with other steroid biosynthetic enzymes present in the decidual tissue to support de novo synthesis of E. This locally produced E is able to support the advancement of the stromal differentiation program even in the absence ovarian E in an ovariectomized, progesterone-supplemented pregnant mouse model. Administration of letrozole, a specific aromatase inhibitor, to these mice blocked the stromal differentiation process. Gene expression profiling further revealed that the intrauterine E induces the expression of several stromal factors that promote neovascularization in the decidual tissue. Collectively, these studies identified the decidual uterus as a novel site of E biosynthesis and uncovered E-regulated maternal signaling pathways that critically control uterine differentiation and angiogenesis during early pregnancy.

  9. Trans-10, cis-12 conjugated linoleic acid decreases de novo lipid synthesis in human adipocytes

    DEFF Research Database (Denmark)

    Obsen, Thomas; Faergeman, Nils J; Chung, Soonkyu;

    2012-01-01

    Conjugated linoleic acid (CLA) reduces adiposity in vivo. However, mechanisms mediating these changes are unclear. Therefore, we treated cultures of human adipocytes with trans-10, cis-12 (10,12) CLA, cis-9, trans-11 (9,11) CLA or other trans fatty acids (FA), and measured indices of lipid......]-oleic or [(14)C]-linoleic acids. When using [(14)C]-acetic acid and [(14)C]-pyruvic acid as substrates, 30 μM 10,12 CLA, but not 9,11 CLA, decreased de novo synthesis of triglyceride, free FA, diacylglycerol, cholesterol esters, cardiolipin, phospholipids and ceramides within 3-24 h. Treatment with 30 μM 10......,12 CLA, but not 9,11 CLA, decreased total cellular lipids within 3 days and the ratio of monounsaturated FA (MUFA) to saturated FA, and increased C18:0 acyl-CoA levels within 24 h. Consistent with these data, stearoyl-CoA desaturase (SCD)-1 mRNA and protein levels were down-regulated by 10,12 CLA within...

  10. Design Analysis and Synthesis.

    Science.gov (United States)

    Redekop, David

    1984-01-01

    Encourages use of case studies to introduce "real-life" engineering assignments, suggesting that they should be given in a natural order as a series. Describes three such assignments being used at the University of the West Indies. Description, analysis, and design of an existing engineering system is included. (JM)

  11. The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations.

    Science.gov (United States)

    Wang, Moye; Hu, Jie; Zhang, Zhuqing

    2016-04-26

    As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5-10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.

  12. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets.

    Science.gov (United States)

    Allen, William J; Fochtman, Brian C; Balius, Trent E; Rizzo, Robert C

    2017-09-22

    De novo design can be used to explore vast areas of chemical space in computational lead discovery. As a complement to virtual screening, from-scratch construction of molecules is not limited to compounds in pre-existing vendor catalogs. Here, we present an iterative fragment growth method, integrated into the program DOCK, in which new molecules are built using rules for allowable connections based on known molecules. The method leverages DOCK's advanced scoring and pruning approaches and users can define very specific criteria in terms of properties or features to customize growth toward a particular region of chemical space. The code was validated using three increasingly difficult classes of calculations: (1) Rebuilding known X-ray ligands taken from 663 complexes using only their component parts (focused libraries), (2) construction of new ligands in 57 drug target sites using a library derived from ∼13M drug-like compounds (generic libraries), and (3) application to a challenging protein-protein interface on the viral drug target HIVgp41. The computational testing confirms that the de novo DOCK routines are robust and working as envisioned, and the compelling results highlight the potential utility for designing new molecules against a wide variety of important protein targets. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  13. De novo peptide design and experimental validation of histone methyltransferase inhibitors.

    Science.gov (United States)

    Smadbeck, James; Peterson, Meghan B; Zee, Barry M; Garapaty, Shivani; Mago, Aashna; Lee, Christina; Giannis, Athanassios; Trojer, Patrick; Garcia, Benjamin A; Floudas, Christodoulos A

    2014-01-01

    Histones are small proteins critical to the efficient packaging of DNA in the nucleus. DNA–protein complexes, known as nucleosomes, are formed when the DNA winds itself around the surface of the histones. The methylation of histone residues by enhancer of zeste homolog 2 (EZH2) maintains gene repression over successive cell generations. Overexpression of EZH2 can silence important tumor suppressor genes leading to increased invasiveness of many types of cancers. This makes the inhibition of EZH2 an important target in the development of cancer therapeutics. We employed a three-stage computational de novo peptide design method to design inhibitory peptides of EZH2. The method consists of a sequence selection stage and two validation stages for fold specificity and approximate binding affinity. The sequence selection stage consists of an integer linear optimization model that was solved to produce a rank-ordered list of amino acid sequences with increased stability in the bound peptide-EZH2 structure. These sequences were validated through the calculation of the fold specificity and approximate binding affinity of the designed peptides. Here we report the discovery of novel EZH2 inhibitory peptides using the de novo peptide design method. The computationally discovered peptides were experimentally validated in vitro using dose titrations and mechanism of action enzymatic assays. The peptide with the highest in vitro response, SQ037, was validated in nucleo using quantitative mass spectrometry-based proteomics. This peptide had an IC50 of 13.5 mM, demonstrated greater potency as an inhibitor when compared to the native and K27A mutant control peptides, and demonstrated competitive inhibition versus the peptide substrate. Additionally, this peptide demonstrated high specificity to the EZH2 target in comparison to other histone methyltransferases. The validated peptides are the first computationally designed peptides that directly inhibit EZH2. These inhibitors should

  14. De novo peptide design and experimental validation of histone methyltransferase inhibitors.

    Directory of Open Access Journals (Sweden)

    James Smadbeck

    Full Text Available Histones are small proteins critical to the efficient packaging of DNA in the nucleus. DNA–protein complexes, known as nucleosomes, are formed when the DNA winds itself around the surface of the histones. The methylation of histone residues by enhancer of zeste homolog 2 (EZH2 maintains gene repression over successive cell generations. Overexpression of EZH2 can silence important tumor suppressor genes leading to increased invasiveness of many types of cancers. This makes the inhibition of EZH2 an important target in the development of cancer therapeutics. We employed a three-stage computational de novo peptide design method to design inhibitory peptides of EZH2. The method consists of a sequence selection stage and two validation stages for fold specificity and approximate binding affinity. The sequence selection stage consists of an integer linear optimization model that was solved to produce a rank-ordered list of amino acid sequences with increased stability in the bound peptide-EZH2 structure. These sequences were validated through the calculation of the fold specificity and approximate binding affinity of the designed peptides. Here we report the discovery of novel EZH2 inhibitory peptides using the de novo peptide design method. The computationally discovered peptides were experimentally validated in vitro using dose titrations and mechanism of action enzymatic assays. The peptide with the highest in vitro response, SQ037, was validated in nucleo using quantitative mass spectrometry-based proteomics. This peptide had an IC50 of 13.5 mM, demonstrated greater potency as an inhibitor when compared to the native and K27A mutant control peptides, and demonstrated competitive inhibition versus the peptide substrate. Additionally, this peptide demonstrated high specificity to the EZH2 target in comparison to other histone methyltransferases. The validated peptides are the first computationally designed peptides that directly inhibit EZH2

  15. De novo peptide design and experimental validation of histone methyltransferase inhibitors.

    Directory of Open Access Journals (Sweden)

    James Smadbeck

    Full Text Available Histones are small proteins critical to the efficient packaging of DNA in the nucleus. DNA-protein complexes, known as nucleosomes, are formed when the DNA winds itself around the surface of the histones. The methylation of histone residues by enhancer of zeste homolog 2 (EZH2 maintains gene repression over successive cell generations. Overexpression of EZH2 can silence important tumor suppressor genes leading to increased invasiveness of many types of cancers. This makes the inhibition of EZH2 an important target in the development of cancer therapeutics. We employed a three-stage computational de novo peptide design method to design inhibitory peptides of EZH2. The method consists of a sequence selection stage and two validation stages for fold specificity and approximate binding affinity. The sequence selection stage consists of an integer linear optimization model that was solved to produce a rank-ordered list of amino acid sequences with increased stability in the bound peptide-EZH2 structure. These sequences were validated through the calculation of the fold specificity and approximate binding affinity of the designed peptides. Here we report the discovery of novel EZH2 inhibitory peptides using the de novo peptide design method. The computationally discovered peptides were experimentally validated in vitro using dose titrations and mechanism of action enzymatic assays. The peptide with the highest in vitro response, SQ037, was validated in nucleo using quantitative mass spectrometry-based proteomics. This peptide had an IC50 of 13.5 [Formula: see text]M, demonstrated greater potency as an inhibitor when compared to the native and K27A mutant control peptides, and demonstrated competitive inhibition versus the peptide substrate. Additionally, this peptide demonstrated high specificity to the EZH2 target in comparison to other histone methyltransferases. The validated peptides are the first computationally designed peptides that directly

  16. New frontiers in design synthesis

    Science.gov (United States)

    Goldin, D. S.; Venneri, S. L.; Noor, A. K.

    1999-01-01

    The Intelligent Synthesis Environment (ISE), which is one of the major strategic technologies under development at NASA centers and the University of Virginia, is described. One of the major objectives of ISE is to significantly enhance the rapid creation of innovative affordable products and missions. ISE uses a synergistic combination of leading-edge technologies, including high performance computing, high capacity communications and networking, human-centered computing, knowledge-based engineering, computational intelligence, virtual product development, and product information management. The environment will link scientists, design teams, manufacturers, suppliers, and consultants who participate in the mission synthesis as well as in the creation and operation of the aerospace system. It will radically advance the process by which complex science missions are synthesized, and high-tech engineering Systems are designed, manufactured and operated. The five major components critical to ISE are human-centered computing, infrastructure for distributed collaboration, rapid synthesis and simulation tools, life cycle integration and validation, and cultural change in both the engineering and science creative process. The five components and their subelements are described. Related U.S. government programs are outlined and the future impact of ISE on engineering research and education is discussed.

  17. An accurate binding interaction model in de novo computational protein design of interactions: if you build it, they will bind.

    Science.gov (United States)

    London, Nir; Ambroggio, Xavier

    2014-02-01

    Computational protein design efforts aim to create novel proteins and functions in an automated manner and, in the process, these efforts shed light on the factors shaping natural proteins. The focus of these efforts has progressed from the interior of proteins to their surface and the design of functions, such as binding or catalysis. Here we examine progress in the development of robust methods for the computational design of non-natural interactions between proteins and molecular targets such as other proteins or small molecules. This problem is referred to as the de novo computational design of interactions. Recent successful efforts in de novo enzyme design and the de novo design of protein-protein interactions open a path towards solving this problem. We examine the common themes in these efforts, and review recent studies aimed at understanding the nature of successes and failures in the de novo computational design of interactions. While several approaches culminated in success, the use of a well-defined structural model for a specific binding interaction in particular has emerged as a key strategy for a successful design, and is therefore reviewed with special consideration. Copyright © 2013 Elsevier Inc. All rights reserved.

  18. De Novo Synthesis and Degradation of Lx and V Cycle Pigments during Shade and Sun Acclimation in Avocado Leaves1

    Science.gov (United States)

    Förster, Britta; Osmond, C. Barry; Pogson, Barry J.

    2009-01-01

    The photoprotective role of the universal violaxanthin cycle that interconverts violaxanthin (V), antheraxanthin (A), and zeaxanthin (Z) is well established, but functions of the analogous conversions of lutein-5,6-epoxide (Lx) and lutein (L) in the selectively occurring Lx cycle are still unclear. We investigated carotenoid pools in Lx-rich leaves of avocado (Persea americana) during sun or shade acclimation at different developmental stages. During sun exposure of mature shade leaves, an unusual decrease in L preceded the deepoxidation of Lx to L and of V to A+Z. In addition to deepoxidation, de novo synthesis increased the L and A+Z pools. Epoxidation of L was exceptionally slow, requiring about 40 d in the shade to restore the Lx pool, and residual A+Z usually persisted overnight. In young shade leaves, the Lx cycle was reversed initially, with Lx accumulating in the sun and declining in the shade. De novo synthesis of xanthophylls did not affect α- and β-carotene pools on the first day, but during long-term acclimation α-carotene pools changed noticeably. Nonetheless, the total change in α- and β-branch carotenoid pools was equal. We discuss the implications for regulation of metabolic flux through the α- and β-branches of carotenoid biosynthesis and potential roles for L in photoprotection and Lx in energy transfer to photosystem II and explore physiological roles of both xanthophyll cycles as determinants of photosystem II efficiency. PMID:19060099

  19. The change in the chemical form of copper in fly ash in a suitable temperature region for de novo synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Takaoka, M.; Shiono, A.; Nishimura, K.; Takeda, N.; Oshita, K.; Matsumoto, T.; Harada, H. [Kyoto Univ. (Japan). Dept. of Urban and Environ. Eng.; Yamamoto, T. [Tokyo Inst. of Tech., Yokohama (Japan). Chemical Resources Lab.; Uruga, T. [JASRI, Hyogo (Japan); Tanaka, T. [Kyoto Univ. (Japan). Dept. of Molecular Eng.

    2004-09-15

    Copper chloride as an important catalyst generates many polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/DFs) and related compounds in heat experiments involving model fly ash. We investigated the chemical forms of copper in actual fly ash before heating experiments and discuss the relationship that we discovered between the copper species Cu(OH){sub 2}, CuO, and Cu(OH){sub 2}.CuCO{sub 3}.H{sub 2}O and the formation of chlorinated aromatics in actual fly ash using X-ray absorption near-edge spectroscopy (XANES). Other results using model fly ash differ from ours. The thermal stabilities of these compounds are not high, so these compounds might not exist in fly ash in the temperature region suitable for de novo synthesis. Therefore, we conducted in situ XANES experiments using actual fly ash and two models of fly ash to understand the behavior of copper in fly ash in the temperature region suitable for de novo synthesis.

  20. De novo design of protein kinase inhibitors by in silico identification of hinge region-binding fragments.

    Science.gov (United States)

    Urich, Robert; Wishart, Grant; Kiczun, Michael; Richters, André; Tidten-Luksch, Naomi; Rauh, Daniel; Sherborne, Brad; Wyatt, Paul G; Brenk, Ruth

    2013-05-17

    Protein kinases constitute an attractive family of enzyme targets with high relevance to cell and disease biology. Small molecule inhibitors are powerful tools to dissect and elucidate the function of kinases in chemical biology research and to serve as potential starting points for drug discovery. However, the discovery and development of novel inhibitors remains challenging. Here, we describe a structure-based de novo design approach that generates novel, hinge-binding fragments that are synthetically feasible and can be elaborated to small molecule libraries. Starting from commercially available compounds, core fragments were extracted, filtered for pharmacophoric properties compatible with hinge-region binding, and docked into a panel of protein kinases. Fragments with a high consensus score were subsequently short-listed for synthesis. Application of this strategy led to a number of core fragments with no previously reported activity against kinases. Small libraries around the core fragments were synthesized, and representative compounds were tested against a large panel of protein kinases and subjected to co-crystallization experiments. Each of the tested compounds was active against at least one kinase, but not all kinases in the panel were inhibited. A number of compounds showed high ligand efficiencies for therapeutically relevant kinases; among them were MAPKAP-K3, SRPK1, SGK1, TAK1, and GCK for which only few inhibitors are reported in the literature.

  1. Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

    Science.gov (United States)

    Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F

    2017-01-01

    Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

  2. The De Novo Synthesis of Horsepox Virus: Implications for Biosecurity and Recommendations for Preventing the Reemergence of Smallpox.

    Science.gov (United States)

    Koblentz, Gregory D

    2017-08-24

    In March 2017, the American biotech company Tonix announced that a Canadian scientist had synthesized horsepox virus as part of a project to develop a safer vaccine against smallpox. The first de novo synthesis of an orthopoxvirus, a closely related group of viruses that includes horsepox and the variola virus that causes smallpox, crosses an important Rubicon in the field of biosecurity. The synthesis of horsepox virus takes the world one step closer to the reemergence of smallpox as a threat to global health security. That threat has been held at bay for the past 40 years by the extreme difficulty of obtaining variola virus and the availability of effective medical countermeasures. The techniques demonstrated by the synthesis of horsepox have the potential to erase both of these barriers. The primary risk posed by this research is that it will open the door to the routine and widespread synthesis of other orthopoxviruses, such as vaccinia, for use in research, public health, and medicine. The normalization and globalization of orthopoxvirus synthesis for these beneficial applications will create a cadre of laboratories and scientists that will also have the capability and expertise to create infectious variola virus from synthetic DNA. Unless the safeguards against the synthesis of variola virus are strengthened, the capability to reintroduce smallpox into the human population will be globally distributed and either loosely or completely unregulated, providing the foundation for a disgruntled or radicalized scientist, sophisticated terrorist group, unscrupulous company, or rogue state to recreate one of humanity's most feared microbial enemies. The reemergence of smallpox-because of a laboratory accident or an intentional release-would be a global health disaster. International organizations, national governments, the DNA synthesis industry, and the synthetic biology community all have a role to play in devising new approaches to preventing the reemergence of

  3. De novo design of caseinolytic protein proteases inhibitors based on pharmacophore and 2D molecular fingerprints.

    Science.gov (United States)

    Wu, Guanzhong; Zhang, Zhen; Chen, Hong; Lin, Kejiang

    2015-06-01

    Caseinolytic protein proteases (ClpP) are large oligomeric protein complexes that contribute to cell homeostasis as well as virulence regulation in bacteria. Inhibitors of ClpP can significantly attenuate the capability to produce virulence factors of the bacteria. In this work, we developed a workflow to expand the chemical space of potential ClpP inhibitors based on a set of β-lactones. In our workflow, an artificial pharmacophore model was generated based on HipHop and HYPOGEN method. A de novo compound library based on molecular fingerprints was constructed and virtually screened by the pharmacophore model. The results were further investigated by molecular docking study. The workflow successfully achieved potential ClpP inhibitors. It could be applied to design more novel potential ClpP inhibitors and provide theoretical basis for the further optimization of the hit compounds.

  4. De novo design of potential RecA inhibitors using multi objective optimization.

    Science.gov (United States)

    Sengupta, Soumi; Bandyopadhyay, Sanghamitra

    2012-01-01

    De novo ligand design involves optimization of several ligand properties such as binding affinity, ligand volume, drug likeness, etc. Therefore, optimization of these properties independently and simultaneously seems appropriate. In this paper, the ligand design problem is modeled in a multiobjective using Archived MultiObjective Simulated Annealing (AMOSA) as the underlying search algorithm. The multiple objectives considered are the energy components similarity to a known inhibitor and a novel drug likeliness measure based on Lipinski's rule of five. RecA protein of Mycobacterium tuberculosis, causative agent of tuberculosis, is taken as the target for the drug design. To gauge the goodness of the results, they are compared to the outputs of LigBuilder, NEWLEAD, and Variable genetic algorithm (VGA). The same problem has also been modeled using a well-established genetic algorithm-based multiobjective optimization technique, Nondominated Sorting Genetic Algorithm-II (NSGA-II), to find the efficacy of AMOSA through comparative analysis. Results demonstrate that while some small molecules designed by the proposed approach are remarkably similar to the known inhibitors of RecA, some new ones are discovered that may be potential candidates for novel lead molecules against tuberculosis.

  5. Experimental evidence for de novo synthesis of PBDD/PBDF and PXDD/PXDF as well as dioxins in the thermal processes of ash samples

    Energy Technology Data Exchange (ETDEWEB)

    Kawamoto, K.; Ishikawa, N. [National Inst. for Environmental Studies, Tsukuba (Japan)

    2005-07-01

    Fly ash in gasification-melting plants and conventional incineration plants can form dioxins through a process known as de novo synthesis. This paper investigated the de novo synthesis of dioxins formed as a result of fly ash catalysis activities. Thermal experiments using fly ash were performed using a flow-through reactor to investigate the formation of brominated and chlorinated-brominated dibenzodioxins (PBDD/F) and dibenzofurans (PXDD/F). Ash samples were collected at conventional stoker incineration and gasification-melting plants. Samples included ash from a bag filter (Ash A); ash from a fluidized gasification and melting furnace plant (Ash C); boiler ash (Ash B); and ash containing tetrabromobisphenol (Ash D). Samples were subjected to a thermal treatment at 300 degrees C. Results showed that dioxin levels were very high for Ash A, which suggested that temperature had a significant influence on de novo synthesis. Dioxin concentrations for Ash C had a relatively low carbon content. Considerable concentrations of PXDD/PXDF were determined for Ash A. High PBDD, PBDF, PXDD and PXDF were observed for Ash D and Ash B. The total amount of dioxins in Ash A were relatively slow to change before and after the thermal treatment of the sample. The homologue distribution patterns of PCDD and PCDF in Ash A showed significant alterations after treatment. It was concluded that de novo dioxin synthesis occurred during the experimental procedure. Results suggested that carbon content plays an important role in the production of dioxins. 3 refs., 2 tabs., 4 figs.

  6. Type synthesis to design variable camber mechanisms

    Directory of Open Access Journals (Sweden)

    Gang Li

    2016-08-01

    Full Text Available This article proposes multiple hinges’ type spectrum that provides an effective description of the multiple hinges of planar kinematic chains. The relationships between characteristic invariants are established and applied into type synthesis methods. A type synthesis method for planar kinematic chains, which is called the characteristic spectrum analysis type synthesis method, is proposed. A systematic design method for variable camber mechanisms is proposed. Using the results of the type synthesis and the systematic design method, three design schemes are proposed and the mathematic models are set up. Some simulation analysis has been done. All these analyses can verify the deformation performance of the proposed mechanism.

  7. De novo design of protein-protein interactions through modification of inter-molecular helix-helix interface residues.

    Science.gov (United States)

    Yagi, Sota; Akanuma, Satoshi; Yamagishi, Manami; Uchida, Tatsuya; Yamagishi, Akihiko

    2016-05-01

    For de novo design of protein-protein interactions (PPIs), information on the shape and chemical complementarity of their interfaces is generally required. Recent advances in computational PPI design have allowed for de novo design of protein complexes, and several successful examples have been reported. In addition, a simple and easy-to-use approach has also been reported that arranges leucines on a solvent-accessible region of an α-helix and places charged residues around the leucine patch to induce interactions between the two helical peptides. For this study, we adopted this approach to de novo design a new PPI between the helical bundle proteins sulerythrin and LARFH. A non-polar patch was created on an α-helix of LARFH around which arginine residues were introduced to retain its solubility. The strongest interaction found was for the LARFH variant cysLARFH-IV-3L3R and the sulerythrin mutant 6L6D (KD=0.16 μM). This artificial protein complex is maintained by hydrophobic and ionic interactions formed by the inter-molecular helical bundle structure. Therefore, by the simple and easy-to-use approach to create de novo interfaces on the α-helices, we successfully generated an artificial PPI. We also created a second LARFH variant with the non-polar patch surrounded by positively charged residues at each end. Upon mixing this LARFH variant with 6L6D, mesh-like fibrous nanostructures were observed by atomic force microscopy. Our method may, therefore, also be applicable to the de novo design of protein nanostructures. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Thymidylate synthesis and utilization via the de novo pathway in normal and megaloblastic human bone marrow cells

    Energy Technology Data Exchange (ETDEWEB)

    Matthews, J.H.; Armitage, J.; Wickramasinghe, S.N. (Department of Haematology, St. Mary' s Hospital Medical School, London (UK))

    1989-01-01

    We have measured the thymidylate synthetase activity of intact bone marrow cells using a {sup 3}H{sub 2}O release assay. The mean thymidylate synthetase activity of vitamin B{sub 12}- or folate-deficient megaloblastic marrow cells was reduced only in severely anaemic patients. There was a correlation between thymidylate synthetase activity and RBC in patients with megaloblastic haemopoiesis. The mean rate of incorporation into DNA of 6-{sup 3}H deoxyuridine was similar in megaloblastic and normoblastic marrows. The rate of thymidylate synthesis exceeded its incorporation into DNA in all marrows, and the mean ratio between synthesis and incorporation was similar in normoblastic and megaloblastic patients, being independent of both thymidylate synthetase activity and RBC. Thus de novo thymine nucleotides were not utilized more efficiently in megaloblastic marrow cells. These data suggest that impaired thymidylate synthesis may not be the central defect in megaloblastic haemopoiesis, and that there is only a single pool of thymidine triphosphate in human bone marrow cells. (author).

  9. Myristic acid potentiates palmitic acid-induced lipotoxicity and steatohepatitis associated with lipodystrophy by sustaning de novo ceramide synthesis.

    Science.gov (United States)

    Martínez, Laura; Torres, Sandra; Baulies, Anna; Alarcón-Vila, Cristina; Elena, Montserrat; Fabriàs, Gemma; Casas, Josefina; Caballeria, Joan; Fernandez-Checa, Jose C; García-Ruiz, Carmen

    2015-12-08

    Palmitic acid (PA) induces hepatocyte apoptosis and fuels de novo ceramide synthesis in the endoplasmic reticulum (ER). Myristic acid (MA), a free fatty acid highly abundant in copra/palmist oils, is a predictor of nonalcoholic steatohepatitis (NASH) and stimulates ceramide synthesis. Here we investigated the synergism between MA and PA in ceramide synthesis, ER stress, lipotoxicity and NASH. Unlike PA, MA is not lipotoxic but potentiated PA-mediated lipoapoptosis, ER stress, caspase-3 activation and cytochrome c release in primary mouse hepatocytes (PMH). Moreover, MA kinetically sustained PA-induced total ceramide content by stimulating dehydroceramide desaturase and switched the ceramide profile from decreased to increased ceramide 14:0/ceramide16:0, without changing medium and long-chain ceramide species. PMH were more sensitive to equimolar ceramide14:0/ceramide16:0 exposure, which mimics the outcome of PA plus MA treatment on ceramide homeostasis, than to either ceramide alone. Treatment with myriocin to inhibit ceramide synthesis and tauroursodeoxycholic acid to prevent ER stress ameliorated PA plus MA induced apoptosis, similar to the protection afforded by the antioxidant BHA, the pan-caspase inhibitor z-VAD-Fmk and JNK inhibition. Moreover, ruthenium red protected PMH against PA and MA-induced cell death. Recapitulating in vitro findings, mice fed a diet enriched in PA plus MA exhibited lipodystrophy, hepatosplenomegaly, increased liver ceramide content and cholesterol levels, ER stress, liver damage, inflammation and fibrosis compared to mice fed diets enriched in PA or MA alone. The deleterious effects of PA plus MA-enriched diet were largely prevented by in vivo myriocin treatment. These findings indicate a causal link between ceramide synthesis and ER stress in lipotoxicity, and imply that the consumption of diets enriched in MA and PA can cause NASH associated with lipodystrophy.

  10. Dependency on de novo protein synthesis and proteomic changes during metamorphosis of the marine bryozoan Bugula neritina

    KAUST Repository

    Wong, Yue Him

    2010-05-24

    Background: Metamorphosis in the bryozoan Bugula neritina (Linne) includes an initial phase of rapid morphological rearrangement followed by a gradual phase of morphogenesis. We hypothesized that the first phase may be independent of de novo synthesis of proteins and, instead, involves post-translational modifications of existing proteins, providing a simple mechanism to quickly initiate metamorphosis. To test our hypothesis, we challenged B. neritina larvae with transcription and translation inhibitors. Furthermore, we employed 2D gel electrophoresis to characterize changes in the phosphoproteome and proteome during early metamorphosis. Differentially expressed proteins were identified by liquid chromatography tandem mass spectrometry and their gene expression patterns were profiled using semi-quantitative real time PCR.Results: When larvae were incubated with transcription and translation inhibitors, metamorphosis initiated through the first phase but did not complete. We found a significant down-regulation of 60 protein spots and the percentage of phosphoprotein spots decreased from 15% in the larval stage to12% during early metamorphosis. Two proteins--the mitochondrial processing peptidase beta subunit and severin--were abundantly expressed and phosphorylated in the larval stage, but down-regulated during metamorphosis. MPPbeta and severin were also down-regulated on the gene expression level.Conclusions: The initial morphogenetic changes that led to attachment of B. neritina did not depend on de novo protein synthesis, but the subsequent gradual morphogenesis did. This is the first time that the mitochondrial processing peptidase beta subunit or severin have been shown to be down-regulated on both gene and protein expression levels during the metamorphosis of B. neritina. Future studies employing immunohistochemistry to reveal the expression locality of these two proteins during metamorphosis should provide further evidence of the involvement of these two

  11. Enzymic capacities of purine de Novo and salvage pathways for nucleotide synthesis in normal and neoplastic tissues.

    Science.gov (United States)

    Natsumeda, Y; Prajda, N; Donohue, J P; Glover, J L; Weber, G

    1984-06-01

    The enzymic capacities of the de novo and the salvage pathways for purine nucleotide synthesis were compared in rat in normal, differentiating, and regenerating liver, and in three hepatomas of widely different growth rates. The activities of the key de novo and salvage enzymes were also determined in mouse lung and Lewis lung carcinoma, in human kidney and liver, and in renal cell carcinoma and hepatocellular carcinomas. A precise and reproducible assay was worked out for measuring the activities of adenine phosphoribosyltransferase (EC 2.4.2.7) and hypoxanthine-guanine phosphoribosyltransferase (HGPRT; EC 2.4.2.8) in crude liver and hepatoma systems. Kinetic studies on the salvage enzymes were carried out in the crude 100,000 X g supernatant fluid from normal liver and rapidly growing hepatoma 3924A. In both tissue extracts, Michaelis-Menten kinetics was observed for adenine phosphoribosyltransferase and HGPRT. The reciprocal plots for 5-phosphoribosyl-1-pyrophosphate (PRPP) of liver and hepatoma enzymes gave apparent KmS of 2 microM for adenine phosphoribosyltransferase and 4 microM for HGPRT, showing two orders of magnitude higher affinities for PRPP than that of the rate-limiting enzyme of de novo purine synthesis, amidophosphoribosyltransferase (EC 2.4.2.14) (Km = 400 to 900 microM). The apparent Km values for adenine of liver and hepatoma adenine phosphoribosyltransferase were 0.6 to 0.9 microM, respectively. For both liver and hepatoma HGPRT, the reciprocal plots for hypoxanthine and guanine yielded the same Km of 3 microM. The specific activities of purine phosphoribosyltransferases were markedly higher than that of amidophosphoribosyltransferase in rat thymus, spleen, testis, bone marrow, colon, liver, kidney cortex, lung, heart, brain, and skeletal muscle, but were lower in the small intestine. In hepatomas and regenerating and differentiating liver, the activities of the salvage enzymes were 2.1- to 32-fold higher than that of

  12. De Novo Design of Skin-Penetrating Peptides for Enhanced Transdermal Delivery of Peptide Drugs.

    Science.gov (United States)

    Menegatti, Stefano; Zakrewsky, Michael; Kumar, Sunny; De Oliveira, Joshua Sanchez; Muraski, John A; Mitragotri, Samir

    2016-03-09

    Skin-penetrating peptides (SPPs) are attracting increasing attention as a non-invasive strategy for transdermal delivery of therapeutics. The identification of SPP sequences, however, currently performed by experimental screening of peptide libraries, is very laborious. Recent studies have shown that, to be effective enhancers, SPPs must possess affinity for both skin keratin and the drug of interest. We therefore developed a computational process for generating and screening virtual libraries of disulfide-cyclic peptides against keratin and cyclosporine A (CsA) to identify SPPs capable of enhancing transdermal CsA delivery. The selected sequences were experimentally tested and found to bind both CsA and keratin, as determined by mass spectrometry and affinity chromatography, and enhance transdermal permeation of CsA. Four heptameric sequences that emerged as leading candidates (ACSATLQHSCG, ACSLTVNWNCG, ACTSTGRNACG, and ACSASTNHNCG) were tested and yielded CsA permeation on par with previously identified SPP SPACE (TM) . An octameric peptide (ACNAHQARSTCG) yielded significantly higher delivery of CsA compared to heptameric SPPs. The safety profile of the selected sequences was also validated by incubation with skin keratinocytes. This method thus represents an effective procedure for the de novo design of skin-penetrating peptides for the delivery of desired therapeutic or cosmetic agents.

  13. De novo cholesterol synthesis at the crossroads of adaptive response to extracellular stress through SREBP.

    Science.gov (United States)

    Robichon, Céline; Dugail, Isabelle

    2007-02-01

    Cell sterol supply is subjected to tight negative feedback regulation through the SREBP pathway. Upon cholesterol depletion, SREBP transcription factors become activated by cleavage of a membrane bound precursor form, which stimulates the expression of the genes encoding proteins of the cholesterol synthesis pathway. In this paper, we discuss two situations of extracellular stress (hypoxia and heat shock) in which the cholesterol synthesis pathway and SREBPs are directly impacted to generate an adaptive response to cell damage. On one hand, the lack of oxygen in fission yeast Saccharomyces pombe induces a drop in cholesterol synthesis which in turn activates SREBP-mediated transcription. The presence of genes involved in the anaerobic growth program among SREBP target genes in fission yeast, indicates that SREBP behaves as an oxygen sensor, required for adaptive growth in low oxygen. On the other hand, upon heat shock in mammalian cells, SREBP-responsive heat shock proteins have been characterized, which were able to upregulate sterol synthesis by targeting the activity of HMG-CoA reductase, the rate limiting enzyme in this pathway. Although not yet proven, high rates of sterol synthesis can be viewed as an adaptive response to correct structural membrane damage and bilayer fluidification induced by thermal stress. Together these situations illustrate how the highly regulated SREBP pathway for the control of sterol synthesis can be used to achieve cell adaptive responses to extracellular stresses.

  14. Cycloheximide prevents the de novo polypeptide synthesis required to recover from acetylene inhibition in Nitrosopumilus maritimus.

    Science.gov (United States)

    Vajrala, Neeraja; Bottomley, Peter J; Stahl, David A; Arp, Daniel J; Sayavedra-Soto, Luis A

    2014-06-01

    Developing methods to differentiate the relative contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to ammonia (NH3) oxidation has been challenging due to the lack of compounds that selectively inhibit AOA. In this study, we investigated the effects of specific bacteria- and eukaryote-selective protein synthesis inhibitors on the recovery of acetylene (C2H2)-inactivated NH3 oxidation in the marine AOA Nitrosopumilus maritimus and compared the results with recovery of the AOB Nitrosomonas europaea. C2 H2 irreversibly inhibited N. maritimus NH3 oxidation in a similar manner to what was observed previously with N. europaea. However, cycloheximide (CHX), a widely used eukaryotic protein synthesis inhibitor, but not bacteria-specific protein synthesis inhibitors (kanamycin and gentamycin), inhibited the recovery of NH3-oxidizing activity in N. maritimus. CHX prevented the incorporation of (14)CO2 -labeling into cellular proteins, providing further evidence that CHX acts as a protein synthesis inhibitor in N. maritimus. If the effect of CHX on protein synthesis can be confirmed among other isolates of AOA, the combination of C2H2 inactivation followed by recovery of NH3 oxidation either in the presence of bacteria-selective protein synthesis inhibitors or CHX might be used to estimate the relative contributions of AOB and AOA to NH3 oxidation in natural environments.

  15. A design language for synthesis and systematization

    DEFF Research Database (Denmark)

    Andreasen, Mogens Myrup; Mortensen, Niels Henrik

    1998-01-01

    This paper establishes a proposal for a basic theory of technical systems and a design language for synthesis and modelling. Based upon this language is made an explanation and comparison of current design related areas like product modelling, feature based design, object parameters, and configur......This paper establishes a proposal for a basic theory of technical systems and a design language for synthesis and modelling. Based upon this language is made an explanation and comparison of current design related areas like product modelling, feature based design, object parameters...

  16. Integrative analysis of circadian transcriptome and metabolic network reveals the role of de novo purine synthesis in circadian control of cell cycle.

    Science.gov (United States)

    Li, Ying; Li, Guang; Görling, Benjamin; Luy, Burkhard; Du, Jiulin; Yan, Jun

    2015-02-01

    Metabolism is the major output of the circadian clock in many organisms. We developed a computational method to integrate both circadian gene expression and metabolic network. Applying this method to zebrafish circadian transcriptome, we have identified large clusters of metabolic genes containing mostly genes in purine and pyrimidine metabolism in the metabolic network showing similar circadian phases. Our metabolomics analysis found that the level of inosine 5'-monophosphate (IMP), an intermediate metabolite in de novo purine synthesis, showed significant circadian oscillation in larval zebrafish. We focused on IMP dehydrogenase (impdh), a rate-limiting enzyme in de novo purine synthesis, with three circadian oscillating gene homologs: impdh1a, impdh1b and impdh2. Functional analysis revealed that impdh2 contributes to the daily rhythm of S phase in the cell cycle while impdh1a contributes to ocular development and pigment synthesis. The three zebrafish homologs of impdh are likely regulated by different circadian transcription factors. We propose that the circadian regulation of de novo purine synthesis that supplies crucial building blocks for DNA replication is an important mechanism conferring circadian rhythmicity on the cell cycle. Our method is widely applicable to study the impact of circadian transcriptome on metabolism in complex organisms.

  17. Anti-plasmodial action of de novo-designed, cationic, lysine-branched, amphipathic, helical peptides

    Directory of Open Access Journals (Sweden)

    Kaushik Naveen K

    2012-08-01

    Full Text Available Abstract Background A lack of vaccine and rampant drug resistance demands new anti-malarials. Methods In vitro blood stage anti-plasmodial properties of several de novo-designed, chemically synthesized, cationic, amphipathic, helical, antibiotic peptides were examined against Plasmodium falciparum using SYBR Green assay. Mechanistic details of anti-plasmodial action were examined by optical/fluorescence microscopy and FACS analysis. Results Unlike the monomeric decapeptides {(Ac-GXRKXHKXWA-NH2 (X = F,ΔF (Fm, ΔFm IC50 >100 μM}, the lysine-branched,dimeric versions showed far greater potency {IC50 (μM Fd 1.5 , ΔFd 1.39}. The more helical and proteolytically stable ΔFd was studied for mechanistic details. ΔFq, a K-K2 dendrimer of ΔFm and (ΔFm2 a linear dimer of ΔFm showed IC50 (μM of 0.25 and 2.4 respectively. The healthy/infected red cell selectivity indices were >35 (ΔFd, >20 (ΔFm2 and 10 (ΔFq. FITC-ΔFd showed rapid and selective accumulation in parasitized red cells. Overlaying DAPI and FITC florescence suggested that ΔFd binds DNA. Trophozoites and schizonts incubated with ΔFd (2.5 μM egressed anomalously and Band-3 immunostaining revealed them not to be associated with RBC membrane. Prematurely egressed merozoites from peptide-treated cultures were found to be invasion incompetent. Conclusion Good selectivity (>35, good resistance index (1.1 and low cytotoxicity indicate the promise of ΔFd against malaria.

  18. Zinc oxide nanoparticles delay human neutrophil apoptosis by a de novo protein synthesis-dependent and reactive oxygen species-independent mechanism

    OpenAIRE

    Goncalves, David M.; Girard, D

    2014-01-01

    International audience; Highlights ZnO nanoparticles are antiapoptotic for human neutrophils. ZnO nanoparticles do not increase ROS production in human neutrophils. ZnO nanoparticles induce de novo protein synthesis in human neutrophils. Abstract Inflammation is one of the major toxic effects reported in the literature following nanoparticle (NP) exposure. Knowing the importance of neutrophils to orchestrate inflammation, it is surprising that the direct role of NPs on neutrophil biology is p...

  19. Synthesis and characterization of new ionic liquids; Sintese e caracterizacao de novos liquidos ionicos

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, L.M.C. de; Mattedi, S.; Boaventura, J.S., E-mail: luanaufrn@hotmail.co [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil). Escola Politecnica. Programa de Pos-Graduacao em Engenharia Quimica; Iglesias, M. [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil). Escola Politecnica. Programa de Pos-Graduacao em Engenharia Quimica; Universidad de Santiago de Compostela (Spain). Escuela Tecnica Superior de Ingenieria. Dept. de Ingenieria Quimica

    2010-07-01

    In recent years, ionic liquids have been highlighted for its potential in various industrial applications. Among them, the salts of Broensted has a promising profile for the low toxicity, low cost and simple synthesis. This paper presents the synthesis and characterization of new salts of Bronsted with branched (lactate) or large chain anions (oleate) for future use as additives promoters of proton conductivity in fuel cells of ethanol. Experimental data were measured for density, sound velocity and conductivity of pure ionic liquids and mixtures. The density decreases linearly with increasing temperature, and sound velocity shows a similar trend, but not linear. The conductivity increases according to the Arrhenius model with activation energy less than 10 J/mol. Tests NMR, FTIR and TGA confirm ionic structure and thermal stability up to 165 deg C. (author)

  20. Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis.

    Science.gov (United States)

    Rabinovich, Shiran; Adler, Lital; Yizhak, Keren; Sarver, Alona; Silberman, Alon; Agron, Shani; Stettner, Noa; Sun, Qin; Brandis, Alexander; Helbling, Daniel; Korman, Stanley; Itzkovitz, Shalev; Dimmock, David; Ulitsky, Igor; Nagamani, Sandesh C S; Ruppin, Eytan; Erez, Ayelet

    2015-11-19

    Cancer cells hijack and remodel existing metabolic pathways for their benefit. Argininosuccinate synthase (ASS1) is a urea cycle enzyme that is essential in the conversion of nitrogen from ammonia and aspartate to urea. A decrease in nitrogen flux through ASS1 in the liver causes the urea cycle disorder citrullinaemia. In contrast to the well-studied consequences of loss of ASS1 activity on ureagenesis, the purpose of its somatic silencing in multiple cancers is largely unknown. Here we show that decreased activity of ASS1 in cancers supports proliferation by facilitating pyrimidine synthesis via CAD (carbamoyl-phosphate synthase 2, aspartate transcarbamylase, and dihydroorotase complex) activation. Our studies were initiated by delineating the consequences of loss of ASS1 activity in humans with two types of citrullinaemia. We find that in citrullinaemia type I (CTLN I), which is caused by deficiency of ASS1, there is increased pyrimidine synthesis and proliferation compared with citrullinaemia type II (CTLN II), in which there is decreased substrate availability for ASS1 caused by deficiency of the aspartate transporter citrin. Building on these results, we demonstrate that ASS1 deficiency in cancer increases cytosolic aspartate levels, which increases CAD activation by upregulating its substrate availability and by increasing its phosphorylation by S6K1 through the mammalian target of rapamycin (mTOR) pathway. Decreasing CAD activity by blocking citrin, the mTOR signalling, or pyrimidine synthesis decreases proliferation and thus may serve as a therapeutic strategy in multiple cancers where ASS1 is downregulated. Our results demonstrate that ASS1 downregulation is a novel mechanism supporting cancerous proliferation, and they provide a metabolic link between the urea cycle enzymes and pyrimidine synthesis.

  1. De novo synthesis of natural products via the asymmetric hydration of polyenes.

    Science.gov (United States)

    Wang, Yanping; Xing, Yalan; Zhang, Qi; O'Doherty, George A

    2011-08-14

    For the last ten years our group has been working toward the development of an asymmetric hydration approach to polyketide natural products based on the regioselective hydration of di- and tri-enoates. Key to the success of this approach is the recognition that both high regiocontrol and asymmetric induction could be obtained by the use of a Sharpless asymmetric dihydroxylation reaction. Herein we describe the development of the method and its application to natural product total synthesis.

  2. Detection of heme oxygenase activity in a library of four-helix bundle proteins: towards the de novo synthesis of functional heme proteins.

    Science.gov (United States)

    Monien, Bernhard H; Drepper, Friedel; Sommerhalter, Monika; Lubitz, Wolfgang; Haehnel, Wolfgang

    2007-08-17

    Design and chemical synthesis of de novo heme proteins with enzymatic activity on cellulose membranes is described. 352 antiparallel four-helix bundle proteins with a single histidine for heme ligation were assembled from three different sets of short amphipathic helices on membrane-bound peptide templates. The templates were coupled by linkers to cellulose membranes of microplate format, which could be cleaved for control of intermediate and final products. The incorporation of heme and the heme oxygenase activity of the 352 proteins were monitored by measuring UV-visible spectra directly on the cellulose. The kinetics of the heme oxygenase reaction was studied by monitoring the decrease of the Soret band and the transient absorbance of verdoheme being an intermediate product in the formation of biliverdin. Four of the proteins covering a broad range of the enzymatic rate constants were selected and synthesized in solution for further characterization. Detailed studies by redox potentiometry, analytical ultracentrifugation, and electron paramagnetic resonance spectroscopy yielded information about the aggregation state of the proteins, the spin state and the putative coordination environment of the iron. The amount of five-coordinated high-spin iron and a positive reduction potential were found to promote the oxygenase activity of the proteins.

  3. Biochemical characterization of GDP-L-fucose de novo synthesis pathway in fungus Mortierella alpina

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Yan [TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin 300457 (China); Perepelov, Andrei V. [N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991 Moscow (Russian Federation); Wang, Haiyan [TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin 300457 (China); Zhang, Hao [State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 (China); Knirel, Yuriy A. [N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991 Moscow (Russian Federation); Wang, Lei [TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin 300457 (China); Chen, Wei, E-mail: weichen@jiangnan.edu.cn [State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 (China)

    2010-01-22

    Mortierella alpina is a filamentous fungus commonly found in soil, which is able to produce large amount of polyunsaturated fatty acids. L-Fucose is an important sugar found in a diverse range of organisms, playing a variety of biological roles. In this study, we characterized the de novo biosynthetic pathway of GDP-L-fucose (the nucleotide-activated form of L-fucose) in M. alpina. Genes encoding GDP-D-mannose 4,6-dehydratase (GMD) and GDP-keto-6-deoxymannose 3,5-epimerase/4-reductase (GMER) were expressed heterologously in Escherichia coli. The recombinant enzymes were produced as His-tagged fusion proteins. Conversion of GDP-mannose to GDP-4-keto-6-deoxy mannose by GMD and GDP-4-keto-6-deoxy mannose to GDP-L-fucose by GMER were analyzed by capillary electrophoresis, electro-spray ionization-mass spectrometry, and nuclear magnetic resonance spectroscopy. The k{sub m} values of GMD for GDP-mannose and GMER for GDP-4-keto-6-deoxy mannose were determined to be 0.77 mM and 1.047 mM, respectively. Both NADH and NADPH may be used by GMER as the coenzyme. The optimum temperature and pH were determined to be 37 {sup o}C and pH 9.0 (GMD) or pH 7.0 (GMER). Divalent cations are not required for GMD and GMER activity, and the activities of both enzymes may be enhanced by DTT. To our knowledge this is the first report on the characterization of GDP-L-fucose biosynthetic pathway in fungi.

  4. Biochemical characterization of GDP-L-fucose de novo synthesis pathway in fungus Mortierella alpina.

    Science.gov (United States)

    Ren, Yan; Perepelov, Andrei V; Wang, Haiyan; Zhang, Hao; Knirel, Yuriy A; Wang, Lei; Chen, Wei

    2010-01-22

    Mortierella alpina is a filamentous fungus commonly found in soil, which is able to produce large amount of polyunsaturated fatty acids. L-fucose is an important sugar found in a diverse range of organisms, playing a variety of biological roles. In this study, we characterized the de novo biosynthetic pathway of GDP-L-fucose (the nucleotide-activated form of L-fucose) in M. alpina. Genes encoding GDP-D-mannose 4,6-dehydratase (GMD) and GDP-keto-6-deoxymannose 3,5-epimerase/4-reductase (GMER) were expressed heterologously in Escherichia coli. The recombinant enzymes were produced as His-tagged fusion proteins. Conversion of GDP-mannose to GDP-4-keto-6-deoxy mannose by GMD and GDP-4-keto-6-deoxy mannose to GDP-L-fucose by GMER were analyzed by capillary electrophoresis, electro-spray ionization-mass spectrometry, and nuclear magnetic resonance spectroscopy. The k(m) values of GMD for GDP-mannose and GMER for GDP-4-keto-6-deoxy mannose were determined to be 0.77 mM and 1.047 mM, respectively. Both NADH and NADPH may be used by GMER as the coenzyme. The optimum temperature and pH were determined to be 37 degrees C and pH 9.0 (GMD) or pH 7.0 (GMER). Divalent cations are not required for GMD and GMER activity, and the activities of both enzymes may be enhanced by DTT. To our knowledge this is the first report on the characterization of GDP-L-fucose biosynthetic pathway in fungi. Copyright 2009 Elsevier Inc. All rights reserved.

  5. Modular optimization of heterologous pathways for de novo synthesis of (2S-naringenin in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Junjun Wu

    Full Text Available Due to increasing concerns about food safety and environmental issues, bio-based production of flavonoids from safe, inexpensive, and renewable substrates is increasingly attracting attention. Here, the complete biosynthetic pathway, consisting of 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (DAHPS, chorismate mutase/prephenate dehydrogenase (CM/PDH, tyrosine ammonia lyase (TAL, 4-coumarate:CoA ligase (4CL, chalcone synthase (CHS, chalcone isomerase (CHI, malonate synthetase, and malonate carrier protein, was constructed using pre-made modules to overproduce (2S-naringenin from D-glucose. Modular pathway engineering strategies were applied to the production of the flavonoid precursor (2S-naringenin from L-tyrosine to investigate the metabolic space for efficient conversion. Modular expression was combinatorially tuned by modifying plasmid gene copy numbers and promoter strengths to identify an optimally balanced pathway. Furthermore, a new modular pathway from D-glucose to L-tyrosine was assembled and re-optimized with the identified optimal modules to enable de novo synthesis of (2S-naringenin. Once this metabolic balance was achieved, the optimum strain was capable of producing 100.64 mg/L (2S-naringenin directly from D-glucose, which is the highest production titer from D-glucose in Escherichia coli. The fermentation system described here paves the way for the development of an economical process for microbial production of flavonoids.

  6. Induction of fatty liver by Coleus forskohlii extract through enhancement of de novo triglyceride synthesis in mice

    Directory of Open Access Journals (Sweden)

    Keizo Umegaki

    2014-01-01

    Full Text Available Coleus forskohlii extract (CFE, an herbal ingredient, is used for weight-loss products. CFE's alleged efficacy is attributed to forskolin. However, CFE has been shown to induce fatty liver in mice, with components other than forskolin playing a part in this effect. The present study addressed the underlying mechanism of CFE-induced fatty liver by analyzing changes in CFE-treated mice of lipid concentrations and of the levels of mRNAs encoding enzymes and transcription factors known to be related to fatty liver. Mice were fed a diet containing 0, 0.3 and 1% CFE for 2 weeks. CFE at 1% clearly induced fatty liver, as demonstrated by histological examination and confirmed by increases in triglyceride concentrations in liver. However, treated mice did not exhibit elevation in plasma levels of non-esterified fatty acids. Comprehensive analysis of liver mRNA levels revealed accumulation of multiple transcripts, including mRNAs encoding enzymes acetyl-CoA carboxylase and long-chain elongase; transcription factor peroxisome proliferator-activated receptor gamma (PPARγ; and lipid-droplet-associated fat-specific protein 27 (Fsp27. These findings suggest that the de novo synthesis and accumulation of triglyceride in the liver, through the enhanced expression of specific lipogenic mRNAs, is a major underlying mechanism of fatty liver induction by CFE.

  7. MiR-155 induction by microbes/microbial ligands requires NF-kB-dependent de novo protein synthesis

    Directory of Open Access Journals (Sweden)

    Susheela eTridandapani

    2012-06-01

    Full Text Available MiR-155 regulates numerous aspects of innate and adaptive immune function. This miR is induced in response to toll-like receptor ligands, cytokines, and microbial infection. We have previously shown that miR-155 is induced in monocytes/macrophages infected with Francisella tularensis and suppresses expression of the inositol phosphatase SHIP to enhance activation of the PI3K/Akt pathway, which in turn promotes favorable responses for the host. Here we examined how miR-155 expression is regulated during infection. First, our data demonstrate that miR-155 can be induced through soluble factors of bacterial origin and not the host. Second, miR-155 induction is not a direct effect of infection and it requires NF-κB signaling to up-regulate fos/jun transcription factors. Finally, we demonstrate that the requirement for NF-κB-dependent de novo protein synthesis is globally shared by microbial ligands and live bacteria. This study provides new insight into the complex regulation of miR-155 during microbial infection.

  8. Induction of fatty liver by Coleus forskohlii extract through enhancement of de novo triglyceride synthesis in mice.

    Science.gov (United States)

    Umegaki, Keizo; Yamazaki, Yuko; Yokotani, Kaori; Chiba, Tsuyoshi; Sato, Yoko; Shimura, Fumio

    2014-01-01

    Coleus forskohlii extract (CFE), an herbal ingredient, is used for weight-loss products. CFE's alleged efficacy is attributed to forskolin. However, CFE has been shown to induce fatty liver in mice, with components other than forskolin playing a part in this effect. The present study addressed the underlying mechanism of CFE-induced fatty liver by analyzing changes in CFE-treated mice of lipid concentrations and of the levels of mRNAs encoding enzymes and transcription factors known to be related to fatty liver. Mice were fed a diet containing 0, 0.3 and 1% CFE for 2 weeks. CFE at 1% clearly induced fatty liver, as demonstrated by histological examination and confirmed by increases in triglyceride concentrations in liver. However, treated mice did not exhibit elevation in plasma levels of non-esterified fatty acids. Comprehensive analysis of liver mRNA levels revealed accumulation of multiple transcripts, including mRNAs encoding enzymes acetyl-CoA carboxylase and long-chain elongase; transcription factor peroxisome proliferator-activated receptor gamma (PPARγ); and lipid-droplet-associated fat-specific protein 27 (Fsp27). These findings suggest that the de novo synthesis and accumulation of triglyceride in the liver, through the enhanced expression of specific lipogenic mRNAs, is a major underlying mechanism of fatty liver induction by CFE.

  9. Strategies of chemical anti-predator defences in leaf beetles: is sequestration of plant toxins less costly than de novo synthesis?

    Science.gov (United States)

    Zvereva, Elena L; Zverev, Vitali; Kruglova, Oksana Y; Kozlov, Mikhail V

    2017-01-01

    The evolution of defensive traits is driven both by benefits gained from protection against enemies and by costs of defence production. We tested the hypothesis that specialisation of herbivores on toxic host plants, accompanied by the ability to acquire plant defensive compounds for herbivore defence, is favoured by the lower costs of sequestration compared to de novo synthesis of defensive compounds. We measured physiological costs of chemical defence as a reduction in larval performance in response to repeated removal of secretions (simulating predator attack) and compared these costs between five species synthesising defences de novo and three species sequestering salicylic glucosides (SGs) from their host plants. Experiments simulating low predator pressure revealed no physiological costs in terms of survival, weight and duration of development in any of study species. However, simulation of high predation caused reduction in relative growth rate in Chrysomela lapponica larvae producing autogenous defences more frequently, than in larvae sequestering SGs. Still meta-analysis of combined data showed no overall difference in costs of autogenous and sequestered defences. However, larvae synthesising their defences de novo demonstrated secretion-conserving behaviour, produced smaller amounts of secretions, replenished them at considerably lower rates and employed other types of defences (regurgitation, evasion) more frequently when compared to sequestering larvae. These latter results provide indirect evidence for biosynthetic constraints for amounts of defensive secretions produced de novo, resulting in low defence effectiveness. Lifting these constraints by sequestration may have driven some leaf beetle lineages toward sequestration of plant allelochemicals as the main defensive strategy.

  10. De novo designed proteins from a library of artificial sequences function in Escherichia coli and enable cell growth.

    Directory of Open Access Journals (Sweden)

    Michael A Fisher

    Full Text Available A central challenge of synthetic biology is to enable the growth of living systems using parts that are not derived from nature, but designed and synthesized in the laboratory. As an initial step toward achieving this goal, we probed the ability of a collection of >10(6 de novo designed proteins to provide biological functions necessary to sustain cell growth. Our collection of proteins was drawn from a combinatorial library of 102-residue sequences, designed by binary patterning of polar and nonpolar residues to fold into stable 4-helix bundles. We probed the capacity of proteins from this library to function in vivo by testing their abilities to rescue 27 different knockout strains of Escherichia coli, each deleted for a conditionally essential gene. Four different strains--ΔserB, ΔgltA, ΔilvA, and Δfes--were rescued by specific sequences from our library. Further experiments demonstrated that a strain simultaneously deleted for all four genes was rescued by co-expression of four novel sequences. Thus, cells deleted for ∼0.1% of the E. coli genome (and ∼1% of the genes required for growth under nutrient-poor conditions can be sustained by sequences designed de novo.

  11. Zinc oxide nanoparticles delay human neutrophil apoptosis by a de novo protein synthesis-dependent and reactive oxygen species-independent mechanism.

    Science.gov (United States)

    Goncalves, David M; Girard, D

    2014-08-01

    Inflammation is one of the major toxic effects reported in the literature following nanoparticle (NP) exposure. Knowing the importance of neutrophils to orchestrate inflammation, it is surprising that the direct role of NPs on neutrophil biology is poorly documented. Here, we investigated if ZnO NPs can alter neutrophil biology. We found that ZnO NPs increased the cell size, induced cell shape changes, activated phosphorylation events, enhanced cell spreading onto glass, but did not induce the generation of reactive oxygen species (ROS). Treatment of neutrophils with ZnO NPs markedly and significantly inhibited apoptosis and increased de novo protein synthesis, as demonstrated by gel electrophoresis of metabolically [(35)S]-labeled cells. Utilization of the protein synthesis inhibitor, cycloheximide, reversed such antiapoptotic effect. We conclude that ZnO NPs are activators of several human neutrophil functions and that they inhibit apoptosis by a de novo protein synthesis-dependent and ROS-independent mechanism. This is the first example that a NP acts on the neo-synthesis of polypeptides.

  12. Design synthesis and shape generation

    DEFF Research Database (Denmark)

    McKay, Alison; Chase, Scott Curland; Garner, Steven

    2009-01-01

    If we are to capitalise on the potential that a design approach might bring to innovation in business and society, we need to build a better understanding of the evolving skill-sets that designers will need and the contexts within which design might operate. This demands more discourse between th...

  13. Synthesis - Based Software Architecture Design

    NARCIS (Netherlands)

    Tekinerdogan, Bedir; Aksit, Mehmet; Akşit, Mehmet

    2001-01-01

    During the last decade several architecture design approaches have been introduced. These approaches however have to cope with several obstacles and software architecture design remains a difficult problem. To cope with these obstacles this chapter introduces a novel architecture design approach. Th

  14. Melatonin Improves the Photosynthetic Apparatus in Pea Leaves Stressed by Paraquat via Chlorophyll Breakdown Regulation and Its Accelerated de novo Synthesis

    Directory of Open Access Journals (Sweden)

    Katarzyna Szafrańska

    2017-05-01

    Full Text Available The positive effect of melatonin on the function of the photosynthetic apparatus is known, but little is known about the specific mechanisms of melatonin's action in plants. The influence of melatonin on chlorophyll metabolism of 24-day-old Pisum sativum L. seedlings during paraquat (PQ-induced oxidative stress was investigated in this study. Seeds were hydro-primed with water (H, 50 and 200 μM melatonin/water solutions (H-MEL50, H-MEL200, while non-primed seeds were used as controls (C. Increases in chlorophyllase activity (key enzyme in chlorophyll degradation and 5-aminolevulinic acid contents (the first compound in the porphyrin synthesis pathway were observed in H-MEL50 and H-MEL200 leaf disks. This suggests that melatonin may accelerate damaged chlorophyll breakdown and its de novo synthesis during the first hours of PQ treatment. Elevated level of pheophytin in control leaf disks following 24 h of PQ incubation probably was associated with an enhanced rate of chlorophyll degradation through formation of pheophytin as a chlorophyll derivative. This validates the hypothesis that chlorophyllide, considered for many years, as a first intermediate of chlorophyll breakdown is not. This is indicated by the almost unchanged chlorophyll to chlorophyllide ratio after 24 h of PQ treatment. However, prolonged effects of PQ-induced stress (48 h revealed extensive discolouration of control and water-treated leaf disks, while melatonin treatment alleviated PQ-induced photobleaching. Also the ratio of chlorophyll to chlorophyllide and porphyrin contents were significantly higher in plants treated with melatonin, which may indicate that this indoleamine both retards chlorophyll breakdown and stimulates its de novo synthesis during extended stress. We concluded that melatonin added into the seeds enhances the ability of pea seedlings to accelerate chlorophyll breakdown and its de novo synthesis before stress appeared and for several hours after, while

  15. Intratumoral de novo steroid synthesis activates androgen receptor in castration-resistant prostate cancer and is upregulated by treatment with CYP17A1 inhibitors.

    Science.gov (United States)

    Cai, Changmeng; Chen, Sen; Ng, Patrick; Bubley, Glenn J; Nelson, Peter S; Mostaghel, Elahe A; Marck, Brett; Matsumoto, Alvin M; Simon, Nicholas I; Wang, Hongyun; Chen, Shaoyong; Balk, Steven P

    2011-10-15

    Relapse of castration-resistant prostate cancer (CRPC) that occurs after androgen deprivation therapy of primary prostate cancer can be mediated by reactivation of the androgen receptor (AR). One important mechanism mediating this AR reactivation is intratumoral conversion of the weak adrenal androgens DHEA and androstenedione into the AR ligands testosterone and dihydrotestosterone. DHEA and androstenedione are synthesized by the adrenals through the sequential actions of the cytochrome P450 enzymes CYP11A1 and CYP17A1, so that CYP17A1 inhibitors such as abiraterone are effective therapies for CRPC. However, the significance of intratumoral CYP17A1 and de novo androgen synthesis from cholesterol in CRPC, and the mechanisms contributing to CYP17A1 inhibitor resistance/relapse, remain to be determined. We report that AR activity in castration-resistant VCaP tumor xenografts can be restored through CYP17A1-dependent de novo androgen synthesis, and that abiraterone treatment of these xenografts imposes selective pressure for increased intratumoral expression of CYP17A1, thereby generating a mechanism for development of resistance to CYP17A1 inhibitors. Supporting the clinical relevance of this mechanism, we found that intratumoral expression of CYP17A1 was markedly increased in tumor biopsies from CRPC patients after CYP17A1 inhibitor therapy. We further show that CRPC cells expressing a progesterone responsive T877A mutant AR are not CYP17A1 dependent, but that AR activity in these cells is still steroid dependent and mediated by upstream CYP11A1-dependent intraturmoral pregnenolone/progesterone synthesis. Together, our results indicate that CRPCs resistant to CYP17A1 inhibition may remain steroid dependent and therefore responsive to therapies that can further suppress de novo intratumoral steroid synthesis.

  16. Using texture synthesis in fractal pattern design

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Traditional fractal pattern design has some disadvantages such as inability to effectively reflect the characteristics of real scenery and texture. We propose a novel pattern design technique combining fractal geometry and image texture synthesis to solve these problems. We have improved Wei and Levoy (2000)'s texture synthesis algorithm by first using two-dimensional autocorrelation function to analyze the structure and distribution of textures, and then determining the size of L neighborhood.Several special fractal sets were adopted and HSL (Hue, Saturation, and Light) color space was chosen. The fractal structure was used to manipulate the texture synthesis in HSL color space where the pattern's color can be adjusted conveniently. Experiments showed that patterns with different styles and different color characteristics can be more efficiently generated using the new technique.

  17. Collagen study and regulation of the de novo synthesis by IGF-I in hemocytes from the gastropod mollusc, Haliotis tuberculata.

    Science.gov (United States)

    Serpentini, A; Ghayor, C; Poncet, J M; Hebert, V; Galéra, P; Pujol, J P; Boucaud-Camou, E; Lebel, J M

    2000-09-01

    To evidence a collagen synthesis and identify which type(s) of collagen is present in hemocytes from the mollusc Haliotis tuberculata, we have performed three separate approaches, namely, de novo synthesis by cultured cells, immunological approaches, and northern blot analysis. We demonstrated first that after 40-hr labeling, the de novo synthesis of collagen in the cell layer of cultured hemocytes represents 9.48 +/- 1.25% with respect to the total [(3)H]proline-labeled protein synthesis. In addition, IGF-I elicited a significant stimulation of collagen synthesis in cultured hemocytes in a dose-dependent manner from 10(-10) to 10(-8) M. The maximal stimulation (10(-9) M) induced an increase of 286 +/- 56% with respect to 100% control. By immunocytochemistry and immunoblotting, we showed that hemocytes present immunoreactive molecules to antibodies directed against the type I fibrillar collagen. In addition, using as a probe Hf 677 corresponding to a human pro alpha1(I) collagen cDNA and which encompasses the (Gly-X-Y) repeated sequence found in all Metazoa, four collagen transcripts of approximately 6.4, 5, 2.2, and 2 kb in length have been detected. These data suggest the presence of fibrillar type I collagen in hemocytes and are compatible with the concept that these cells are involved in the extracellular matrix deposition, a cardinal function in tissue repair as well as in developmental processes. Our model may appear as an excellent system to study the role of growth factors on the regulation of collagen synthesis by molluscan hemocytes. J. Exp. Zool. 287:275-284, 2000.

  18. A unified model for de novo design of elastin-like polypeptides with tunable inverse transition temperatures.

    Science.gov (United States)

    McDaniel, Jonathan R; Radford, D Christopher; Chilkoti, Ashutosh

    2013-08-12

    Elastin-like polypeptides (ELPs) are stimulus-responsive peptide polymers that exhibit inverse temperature phase transition behavior, causing an ELP to aggregate above its inverse transition temperature (T(t)). Although this property has been exploited in a variety of biotechnological applications, de novo design of ELPs that display a specific T(t) is not trivial because the T(t) of an ELP is a complex function of several variables, including its sequence, chain length, polypeptide concentration, and the type and concentration of cosolutes in solution. This paper provides a quantitative model that predicts the T(t) of a family of ELPs (Val-Pro-Gly-Xaa-Gly, where Xaa = Ala and/or Val) from their composition, chain length, and concentration in phosphate buffered saline. This model will enable de novo prediction of the amino acid sequence and chain length of ELPs that will display a predetermined T(t) in physiological buffer within a specified concentration regime, thereby greatly facilitating the design of new ELPs for applications in medicine and biotechnology.

  19. Cooperative catalysis designing efficient catalysts for synthesis

    CERN Document Server

    Peters, René

    2015-01-01

    Written by experts in the field, this is a much-needed overview of the rapidly emerging field of cooperative catalysis. The authors focus on the design and development of novel high-performance catalysts for applications in organic synthesis (particularly asymmetric synthesis), covering a broad range of topics, from the latest progress in Lewis acid / Br?nsted base catalysis to e.g. metal-assisted organocatalysis, cooperative metal/enzyme catalysis, and cooperative catalysis in polymerization reactions and on solid surfaces. The chapters are classified according to the type of cooperating acti

  20. NOVO DESIGN PARA A REDE FEDERAL DE EDUCAÇÃO TECNOLÓGICA

    Directory of Open Access Journals (Sweden)

    Francisco das Chagas Mariz Fernandes

    2009-03-01

    Full Text Available RESUMO A partir do ano de 2003, o Governo Lula iniciou ações voltadas à democratização da oferta da educação técnica no país, através de um plano estruturante de expansão da Rede Federal de Educação Profissional e Tecnológica. A primeira fase do plano compreendeu a construção de 64 novas Unidades de Ensino para somar às 140 que já existiam. Ao mesmo tempo, o Ministério da Educação logo deu início à segunda fase do projeto, para a implantação de mais 150 novas Escolas, devendo totalizar, até 2010, a meta de 354 instituições. Nesse contexto, surge a proposta de constituição de 38 Institutos Federais de Educação, Ciência e Tecnologia para integrar, a partir do exercício de 2009, essas Unidades de Ensino, bem como constituir a Rede Federal de Educação Profissional, Científica e Tecnológica. Cada Instituto Federal é estruturado com uma Reitoria e vários Campi, com gestão interdependente entre ambos. Territorialmente, à Reitoria competirá a função estratégica de definição de políticas, supervisão e controle. Para tanto, necessita de uma estrutura administrativa que congregue, além do gabinete, pró-reitorias e diretorias de atuação sistêmica, cabendo a esses órgãos a função de trabalhar matricialmente vinculados às unidades afins dos Campi. Cada Campus, por sua vez, responsável pela execução dos objetivos finalísticos institucionais, necessita de uma estruturação híbrida, através da associação da departamentalização funcional e a matricial – para viabilizar o diálogo e interação dos departamentos da área acadêmica com as unidades operacionais dos demais departamentos das áreas de administração, de apoio ao ensino, de extensão e de pesquisa. Na realidade, o arranjo situacional dos Institutos Federais é novo e caracteriza-se como próprio de uma estrutura em rede, para integrar sistemicamente diversas organizações de ensino através de um núcleo central – no

  1. Apoprotein Structure and Metal Binding Characterization of a de Novo Designed Peptide, α3DIV, that Sequesters Toxic Heavy Metals.

    Science.gov (United States)

    Plegaria, Jefferson S; Dzul, Stephen P; Zuiderweg, Erik R P; Stemmler, Timothy L; Pecoraro, Vincent L

    2015-05-12

    De novo protein design is a biologically relevant approach that provides a novel process in elucidating protein folding and modeling the metal centers of metalloproteins in a completely unrelated or simplified fold. An integral step in de novo protein design is the establishment of a well-folded scaffold with one conformation, which is a fundamental characteristic of many native proteins. Here, we report the NMR solution structure of apo α3DIV at pH 7.0, a de novo designed three-helix bundle peptide containing a triscysteine motif (Cys18, Cys28, and Cys67) that binds toxic heavy metals. The structure comprises 1067 NOE restraints derived from multinuclear multidimensional NOESY, as well as 138 dihedral angles (ψ, φ, and χ1). The backbone and heavy atoms of the 20 lowest energy structures have a root mean square deviation from the mean structure of 0.79 (0.16) Å and 1.31 (0.15) Å, respectively. When compared to the parent structure α3D, the substitution of Leu residues to Cys enhanced the α-helical content of α3DIV while maintaining the same overall topology and fold. In addition, solution studies on the metalated species illustrated metal-induced stability. An increase in the melting temperatures was observed for Hg(II), Pb(II), or Cd(II) bound α3DIV by 18-24 °C compared to its apo counterpart. Further, the extended X-ray absorption fine structure analysis on Hg(II)-α3DIV produced an average Hg(II)-S bond length at 2.36 Å, indicating a trigonal T-shaped coordination environment. Overall, the structure of apo α3DIV reveals an asymmetric distorted triscysteine metal binding site, which offers a model for native metalloregulatory proteins with thiol-rich ligands that function in regulating toxic heavy metals, such as ArsR, CadC, MerR, and PbrR.

  2. Design and synthesis of disubstituted (4-piperidinyl)-piperazine derivatives as potent acetyl-CoA carboxylase inhibitors.

    Science.gov (United States)

    Chonan, Tomomichi; Tanaka, Hiroaki; Yamamoto, Daisuke; Yashiro, Miyoko; Oi, Takahiro; Wakasugi, Daisuke; Ohoka-Sugita, Ayumi; Io, Fusayo; Koretsune, Hiroko; Hiratate, Akira

    2010-07-01

    Acetyl-CoA carboxylases (ACCs), the rate limiting enzymes in de novo lipid synthesis, play important roles in modulating energy metabolism. The inhibition of ACC has demonstrated promising therapeutic potential for treating obesity and type 2 diabetes mellitus in transgenic mice and preclinical animal models. We describe herein the structure-based design and synthesis of a novel series of disubstituted (4-piperidinyl)-piperazine derivatives as ACC inhibitors. Our structure-based approach led to the discovery of the indole derivatives 13i and 13j, which exhibited potent in vitro ACC inhibitory activity.

  3. De novo pyrimidine nucleotide synthesis mainly occurs outside of plastids, but a previously undiscovered nucleobase importer provides substrates for the essential salvage pathway in Arabidopsis.

    Science.gov (United States)

    Witz, Sandra; Jung, Benjamin; Fürst, Sarah; Möhlmann, Torsten

    2012-04-01

    Nucleotide de novo synthesis is highly conserved among organisms and represents an essential biochemical pathway. In plants, the two initial enzymatic reactions of de novo pyrimidine synthesis occur in the plastids. By use of green fluorescent protein fusions, clear support is provided for a localization of the remaining reactions in the cytosol and mitochondria. This implies that carbamoyl aspartate, an intermediate of this pathway, must be exported and precursors of pyrimidine salvage (i.e., nucleobases or nucleosides) are imported into plastids. A corresponding uracil transport activity could be measured in intact plastids isolated from cauliflower (Brassica oleracea) buds. PLUTO (for plastidic nucleobase transporter) was identified as a member of the Nucleobase:Cation-Symporter1 protein family from Arabidopsis thaliana, capable of transporting purine and pyrimidine nucleobases. A PLUTO green fluorescent protein fusion was shown to reside in the plastid envelope after expression in Arabidopsis protoplasts. Heterologous expression of PLUTO in an Escherichia coli mutant lacking the bacterial uracil permease uraA allowed a detailed biochemical characterization. PLUTO transports uracil, adenine, and guanine with apparent affinities of 16.4, 0.4, and 6.3 μM, respectively. Transport was markedly inhibited by low concentrations of a proton uncoupler, indicating that PLUTO functions as a proton-substrate symporter. Thus, a protein for the absolutely required import of pyrimidine nucleobases into plastids was identified.

  4. S-deficiency responsive accumulation of amino acids is mainly due to hydrolysis of the previously synthesized proteins - not to de novo synthesis in Brassica napus.

    Science.gov (United States)

    Lee, Bok-Rye; Muneer, Sowbiya; Kim, Kil-Yong; Avice, Jean-Christophe; Ourry, Alain; Kim, Tae-Hwan

    2013-03-01

    To characterize the mechanisms of amino acid accumulation under sulphur (S)-deficiency and its physiological significance in Brassica napus, stable isotopes (15) N and (34) S were employed. The plants were exposed for 9 days to S-deficient conditions (0.05 mM vs 1.5 mM sulphate). After 9 days of S-deficiency, leaf-osmotic potential and total chlorophyll content significantly decreased. S uptake decreased by 94%, whereas N uptake and biomass were not significantly changed. Using (15) N and (34) S labelling, de novo synthesis of amino acids and proteins derived from newly absorbed NO(3) (-) and SO(4) (2) (-) and the content of N and S in the previously synthesized amino acids and proteins were quantified. At the whole plant level, S-deficiency increased the pool of amino acids but resulted in strong decrease of incorporation of newly absorbed NO(3) (-) and SO(4) (2) (-) into amino acids by 22.2 and 76.6%, respectively, compared to the controls. Total amount of N and S incorporated into proteins also decreased by 28.8 and 62.1%, respectively. The levels of (14) N- and (32) S-proteins (previously synthesized proteins) strongly decreased, mainly in mature leaves. The data thus indicate that amino acid accumulation under short-term S-deficiency results from the degradation of previously synthesized proteins rather than from de novo synthesis. Copyright © Physiologia Plantarum 2012.

  5. De novo design of signal sequences to localize cargo to the 1,2-propanediol utilization microcompartment.

    Science.gov (United States)

    Jakobson, Christopher M; Slininger Lee, Marilyn F; Tullman-Ercek, Danielle

    2017-05-01

    Organizing heterologous biosyntheses inside bacterial cells can alleviate common problems owing to toxicity, poor kinetic performance, and cofactor imbalances. A subcellular organelle known as a bacterial microcompartment, such as the 1,2-propanediol utilization microcompartment of Salmonella, is a promising chassis for this strategy. Here we demonstrate de novo design of the N-terminal signal sequences used to direct cargo to these microcompartment organelles. We expand the native repertoire of signal sequences using rational and library-based approaches and show that a canonical leucine-zipper motif can function as a signal sequence for microcompartment localization. Our strategy can be applied to generate new signal sequences localizing arbitrary cargo proteins to the 1,2-propanediol utilization microcompartments. © 2017 The Protein Society.

  6. Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.

    Science.gov (United States)

    Wang, Ling; Althoff, Eric A; Bolduc, Jill; Jiang, Lin; Moody, James; Lassila, Jonathan K; Giger, Lars; Hilvert, Donald; Stoddard, Barry; Baker, David

    2012-01-20

    We report the cocrystal structures of a computationally designed and experimentally optimized retro-aldol enzyme with covalently bound substrate analogs. The structure with a covalently bound mechanism-based inhibitor is similar to, but not identical with, the design model, with an RMSD of 1.4 Å over active-site residues and equivalent substrate atoms. As in the design model, the binding pocket orients the substrate through hydrophobic interactions with the naphthyl moiety such that the oxygen atoms analogous to the carbinolamine and β-hydroxyl oxygens are positioned near a network of bound waters. However, there are differences between the design model and the structure: the orientation of the naphthyl group and the conformation of the catalytic lysine are slightly different; the bound water network appears to be more extensive; and the bound substrate analog exhibits more conformational heterogeneity than typical native enzyme-inhibitor complexes. Alanine scanning of the active-site residues shows that both the catalytic lysine and the residues around the binding pocket for the substrate naphthyl group make critical contributions to catalysis. Mutating the set of water-coordinating residues also significantly reduces catalytic activity. The crystal structure of the enzyme with a smaller substrate analog that lacks naphthyl ring shows the catalytic lysine to be more flexible than in the naphthyl-substrate complex; increased preorganization of the active site would likely improve catalysis. The covalently bound complex structures and mutagenesis data highlight the strengths and weaknesses of the de novo enzyme design strategy.

  7. Data-driven computer aided synthesis design.

    Science.gov (United States)

    Ravitz, Orr

    2013-09-01

    Enabled by an increasing body of electronically available experimental data and by advances in computer hardware and software, new technologies are emerging that are designed to support the creativity of chemists during synthesis planning. Leading this development are innovative synthetic route prediction tools that are designed to suggest new reactions and paths to target molecules as an idea-generating engine. Other tools are using known reactions in a combinatorial fashion to suggest new routes that are cost-optimized or satisfy some other global criteria. We review the latest developments and the main tools in this domain.

  8. Title A de novo synthesis citrate transporter VuMATE confers aluminum resistance in rice bean (vigna umbellata)

    Science.gov (United States)

    Al-activated organic acid anion efflux from roots is an important Al resistance mechanism in plants. We have conducted the homologous cloning and isolation of VuMATE (Vigna umbellata multidrug and toxic compound extrusion), a gene encoding a de novo citrate transporter from rice bean. Al treatment u...

  9. Design of nanomaterial synthesis by aerosol processes.

    Science.gov (United States)

    Buesser, Beat; Pratsinis, Sotiris E

    2012-01-01

    Aerosol synthesis of materials is a vibrant field of particle technology and chemical reaction engineering. Examples include the manufacture of carbon blacks, fumed SiO(2), pigmentary TiO(2), ZnO vulcanizing catalysts, filamentary Ni, and optical fibers, materials that impact transportation, construction, pharmaceuticals, energy, and communications. Parallel to this, development of novel, scalable aerosol processes has enabled synthesis of new functional nanomaterials (e.g., catalysts, biomaterials, electroceramics) and devices (e.g., gas sensors). This review provides an access point for engineers to the multiscale design of aerosol reactors for the synthesis of nanomaterials using continuum, mesoscale, molecular dynamics, and quantum mechanics models spanning 10 and 15 orders of magnitude in length and time, respectively. Key design features are the rapid chemistry; the high particle concentrations but low volume fractions; the attainment of a self-preserving particle size distribution by coagulation; the ratio of the characteristic times of coagulation and sintering, which controls the extent of particle aggregation; and the narrowing of the aggregate primary particle size distribution by sintering.

  10. Design of Nanomaterial Synthesis by Aerosol Processes

    Science.gov (United States)

    Buesser, Beat; Pratsinis, Sotiris E.

    2013-01-01

    Aerosol synthesis of materials is a vibrant field of particle technology and chemical reaction engineering. Examples include the manufacture of carbon blacks, fumed SiO2, pigmentary TiO2, ZnO vulcanizing catalysts, filamentary Ni, and optical fibers, materials that impact transportation, construction, pharmaceuticals, energy, and communications. Parallel to this, development of novel, scalable aerosol processes has enabled synthesis of new functional nanomaterials (e.g., catalysts, biomaterials, electroceramics) and devices (e.g., gas sensors). This review provides an access point for engineers to the multiscale design of aerosol reactors for the synthesis of nanomaterials using continuum, mesoscale, molecular dynamics, and quantum mechanics models spanning 10 and 15 orders of magnitude in length and time, respectively. Key design features are the rapid chemistry; the high particle concentrations but low volume fractions; the attainment of a self-preserving particle size distribution by coagulation; the ratio of the characteristic times of coagulation and sintering, which controls the extent of particle aggregation; and the narrowing of the aggregate primary particle size distribution by sintering. PMID:22468598

  11. Introduction to Space Systems Design and Synthesis

    CERN Document Server

    Aguirre, Miguel A

    2013-01-01

    The definition of all space systems starts with the establishment of its fundamental parameters: requirements to be fulfilled, overall system and satellite design, analysis and design of the critical elements, developmental approach, cost, and schedule. There are only a few texts covering early design of space systems and none of them has been specifically dedicated to it. Furthermore all existing space engineering books concentrate on analysis. None of them deal with space system synthesis – with the interrelations between all the elements of the space system. Introduction to Space Systems concentrates on understanding the interaction between all the forces, both technical and non-technical, which influence the definition of a space system. This book refers to the entire system: space and ground segments, mission objectives as well as to cost, risk, and mission success probabilities. Introduction to Space Systems is divided into two parts. The first part analyzes the process of space system design in an ab...

  12. Synthesis and Design of Processing Networks

    DEFF Research Database (Denmark)

    Quaglia, Alberto; Sarup, Bent; Sin, Gürkan

    2012-01-01

    In this contribution, we propose an integrated business and engineering framework for synthesis and design of processing networks under uncertainty. In our framework, an adapted formulation of the transhipment problem is integrated with a superstructure, leading to a Stochastic Mixed Integer Non...... Linear Program (sMINLP), which is solved to determine simultaneously the optimal strategic and tactical decisions with respect to the processing network, the material flows, raw material and product portfolio. The framework allows time-effective and robust formulation, solution and analysis of largescale...... synthesis problems in presence of uncertainty parameters, contributing to broaden the range of application of stochastic programming and optimization to real industrial problems. The framework is applied to an industrial case study based on soybean processing, to identify the optimal processing network...

  13. Synthesis and Design of Processing Networks

    DEFF Research Database (Denmark)

    Quaglia, Alberto; Sarup, Bent; Sin, Gürkan

    2012-01-01

    In this contribution, we propose an integrated business and engineering framework for synthesis and design of processing networks under uncertainty. In our framework, an adapted formulation of the transhipment problem is integrated with a superstructure, leading to a Stochastic Mixed Integer Non...... Linear Program (sMINLP), which is solved to determine simultaneously the optimal strategic and tactical decisions with respect to the processing network, the material flows, raw material and product portfolio. The framework allows time-effective and robust formulation, solution and analysis of largescale...... synthesis problems in presence of uncertainty parameters, contributing to broaden the range of application of stochastic programming and optimization to real industrial problems. The framework is applied to an industrial case study based on soybean processing, to identify the optimal processing network...

  14. OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes.

    Directory of Open Access Journals (Sweden)

    Tong Li

    Full Text Available Antibody-based therapeutics provides novel and efficacious treatments for a number of diseases. Traditional experimental approaches for designing therapeutic antibodies rely on raising antibodies against a target antigen in an immunized animal or directed evolution of antibodies with low affinity for the desired antigen. However, these methods remain time consuming, cannot target a specific epitope and do not lead to broad design principles informing other studies. Computational design methods can overcome some of these limitations by using biophysics models to rationally select antibody parts that maximize affinity for a target antigen epitope. This has been addressed to some extend by OptCDR for the design of complementary determining regions. Here, we extend this earlier contribution by addressing the de novo design of a model of the entire antibody variable region against a given antigen epitope while safeguarding for immunogenicity (Optimal Method for Antibody Variable region Engineering, OptMAVEn. OptMAVEn simulates in silico the in vivo steps of antibody generation and evolution, and is capable of capturing the critical structural features responsible for affinity maturation of antibodies. In addition, a humanization procedure was developed and incorporated into OptMAVEn to minimize the potential immunogenicity of the designed antibody models. As case studies, OptMAVEn was applied to design models of neutralizing antibodies targeting influenza hemagglutinin and HIV gp120. For both HA and gp120, novel computational antibody models with numerous interactions with their target epitopes were generated. The observed rates of mutations and types of amino acid changes during in silico affinity maturation are consistent with what has been observed during in vivo affinity maturation. The results demonstrate that OptMAVEn can efficiently generate diverse computational antibody models with both optimized binding affinity to antigens and reduced

  15. Transferable coarse-grained potential for $\\textit{de novo}$ protein folding and design

    CERN Document Server

    Coluzza, Ivan

    2014-01-01

    Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and folding is introduced. With computer simulations it is shown that, for a large set of real protein structures, the model produces designed sequences with similar physical properties to the corresponding natural occurring sequences. The designed sequences are not yet fully realistic and require further experimental testing. For an independent set of proteins, notoriously difficult to fold, the correct folding of both the designed and the natural sequences is also demonstrated. The folding properties are characterized by free energy calculations. which not only are consistent among natural and designed proteins, but we also show a remarkable precision when the folded structures are compared to the experimentally determined ones. Ultimately, this novel coarse-grained protein model ...

  16. Design and Synthesis of Caspase Inhibitors

    Institute of Scientific and Technical Information of China (English)

    BAI; Xu

    2001-01-01

    Apoptosis (programmed cell death) is an evolutionarily conserved process of cell suicide. It requires specialized machinery which involving a family of proteases named caspases. Manipulation of apoptosis through inhibiting or activating caspases has been of great therapeutic interests in the pharmaceutical industry.  Using substrate based approach, a systematic investigation of conformationally constrained peptidomimetic inhibitors has led to the discovery of highly selective ones against selected members of the caspase family. It also resulted novel dipeptide inhibitors as useful tools and possible therapeutic agents against diseases caused by excessive apoptotic cell death. This presentation will focus on the design, synthesis and application of novel caspase inhibitors.  ……

  17. Multifunctional Nanomaterials: Design, Synthesis and Application Properties

    Directory of Open Access Journals (Sweden)

    Marisa Martinelli

    2017-02-01

    Full Text Available The immense scope of variation in dendritic molecules (hyper-branching, nano-sized, hydrophobicity/hydrophilicity, rigidity/flexibility balance, etc. and their versatile functionalization, with the possibility of multivalent binding, permit the design of highly improved, novel materials. Dendritic-based materials are therefore viable alternatives to conventional polymers. The overall aim of this work is to show the advantages of dendronization processes by presenting the synthesis and characterization of three different dendronized systems: (I microbeads of functionalized chitosan; (II nanostructuration of polypropylene surfaces; and (III smart dendritic nanogels. The particular properties yielded by these systems could only be achieved thanks to the dendronization process.

  18. Design and Synthesis of Caspase Inhibitors

    Institute of Scientific and Technical Information of China (English)

    BAI Xu

    2001-01-01

    @@ Apoptosis (programmed cell death) is an evolutionarily conserved process of cell suicide. It requires specialized machinery which involving a family of proteases named caspases. Manipulation of apoptosis through inhibiting or activating caspases has been of great therapeutic interests in the pharmaceutical industry. Using substrate based approach, a systematic investigation of conformationally constrained peptidomimetic inhibitors has led to the discovery of highly selective ones against selected members of the caspase family. It also resulted novel dipeptide inhibitors as useful tools and possible therapeutic agents against diseases caused by excessive apoptotic cell death. This presentation will focus on the design, synthesis and application of novel caspase inhibitors.

  19. De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity

    Science.gov (United States)

    Boyken, Scott E.; Chen, Zibo; Groves, Benjamin; Langan, Robert A.; Oberdorfer, Gustav; Ford, Alex; Gilmore, Jason; Xu, Chunfu; DiMaio, Frank; Pereira, Jose Henrique; Sankaran, Banumathi; Seelig, Georg; Zwart, Peter H.; Baker, David

    2017-01-01

    In nature, structural specificity in DNA and proteins is encoded quite differently: in DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen bond networks with atomic accuracy is a milestone for protein design and enables the programming of protein interaction specificity for a broad range of synthetic biology applications. PMID:27151862

  20. Formation of PCDF, PCDD, PCB, and PCN in de novo synthesis from PAH: mechanistic aspects and correlation to fluidized bed incinerators.

    Science.gov (United States)

    Weber, R; Lino, F; Imagawa, T; Takeuchi, M; Sakurai, T; Sadakata, M

    2001-09-01

    The difference of polychlorinated dibenzofurans (PCDF) isomer patterns between stoker type incinerators and some fluidized bed incinerators (FBI) is a key to understand the formation mechanisms in both types of incinerators. The total yield and the isomer patterns of PCDF, polychlorinated biphenyls (PCB), polychlorinated naphthalenes (PCN), and polychlorinated benzenes (PCBz) formed via de novo synthesis from polycyclic aromatic hydrocarbons (PAH) indicate that chlorinated aromatics in the FBI are formed as a result of PAH breakdown. The detailed analysis of the isomer patterns of PCDF, PCB and PCN gives a first insight into the transformation mechanism of the PAHs and the sequence of degradation, chlorination and oxygen insertion. The major chlorination takes part at the position of the C-C cleavage during degradation of the PAHs. Further chlorination of the hydrogen position of the former PAH takes part preferably in ortho-position to this chlorination or is directed by incorporated oxygen. A perylene structure in soot is proposed as basis for the observed PCDF pattern in the FBI. Polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated phenols (PxCP) were formed in lower concentrations from the de novo experiments indicating an additional formation pathway for these compounds in the FBI.

  1. The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70.

    Science.gov (United States)

    Bhowmick, Asmit; Sharma, Sudhir C; Honma, Hallie; Head-Gordon, Teresa

    2016-07-28

    Side chain entropy and mutual entropy information between residue pairs have been calculated for two de novo designed Kemp eliminase enzymes, KE07 and KE70, and for their most improved versions at the end of laboratory directed evolution (LDE). We find that entropy, not just enthalpy, helped to destabilize the preference for the reactant state complex of the designed enzyme as well as favoring stabilization of the transition state complex for the best LDE enzymes. Furthermore, residues with the highest side chain couplings as measured by mutual information, when experimentally mutated, were found to diminish or annihilate catalytic activity, some of which were far from the active site. In summary, our findings demonstrate how side chain fluctuations and their coupling can be an important design feature for de novo enzymes, and furthermore could be utilized in the computational steps in lieu of or in addition to the LDE steps in future enzyme design projects.

  2. An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis.

    Science.gov (United States)

    Mitra, Pralay; Shultis, David; Brender, Jeffrey R; Czajka, Jeff; Marsh, David; Gray, Felicia; Cierpicki, Tomasz; Zhang, Yang

    2013-10-01

    Computational protein design is a reverse procedure of protein folding and structure prediction, where constructing structures from evolutionarily related proteins has been demonstrated to be the most reliable method for protein 3-dimensional structure prediction. Following this spirit, we developed a novel method to design new protein sequences based on evolutionarily related protein families. For a given target structure, a set of proteins having similar fold are identified from the PDB library by structural alignments. A structural profile is then constructed from the protein templates and used to guide the conformational search of amino acid sequence space, where physicochemical packing is accommodated by single-sequence based solvation, torsion angle, and secondary structure predictions. The method was tested on a computational folding experiment based on a large set of 87 protein structures covering different fold classes, which showed that the evolution-based design significantly enhances the foldability and biological functionality of the designed sequences compared to the traditional physics-based force field methods. Without using homologous proteins, the designed sequences can be folded with an average root-mean-square-deviation of 2.1 Å to the target. As a case study, the method is extended to redesign all 243 structurally resolved proteins in the pathogenic bacteria Mycobacterium tuberculosis, which is the second leading cause of death from infectious disease. On a smaller scale, five sequences were randomly selected from the design pool and subjected to experimental validation. The results showed that all the designed proteins are soluble with distinct secondary structure and three have well ordered tertiary structure, as demonstrated by circular dichroism and NMR spectroscopy. Together, these results demonstrate a new avenue in computational protein design that uses knowledge of evolutionary conservation from protein structural families to engineer

  3. Structural principles for computational and de novo design of 4Fe-4S metalloproteins.

    Science.gov (United States)

    Nanda, Vikas; Senn, Stefan; Pike, Douglas H; Rodriguez-Granillo, Agustina; Hansen, Will A; Khare, Sagar D; Noy, Dror

    2016-05-01

    Iron-sulfur centers in metalloproteins can access multiple oxidation states over a broad range of potentials, allowing them to participate in a variety of electron transfer reactions and serving as catalysts for high-energy redox processes. The nitrogenase FeMoCO cluster converts di-nitrogen to ammonia in an eight-electron transfer step. The 2(Fe4S4) containing bacterial ferredoxin is an evolutionarily ancient metalloprotein fold and is thought to be a primordial progenitor of extant oxidoreductases. Controlling chemical transformations mediated by iron-sulfur centers such as nitrogen fixation, hydrogen production as well as electron transfer reactions involved in photosynthesis are of tremendous importance for sustainable chemistry and energy production initiatives. As such, there is significant interest in the design of iron-sulfur proteins as minimal models to gain fundamental understanding of complex natural systems and as lead-molecules for industrial and energy applications. Herein, we discuss salient structural characteristics of natural iron-sulfur proteins and how they guide principles for design. Model structures of past designs are analyzed in the context of these principles and potential directions for enhanced designs are presented, and new areas of iron-sulfur protein design are proposed. This article is part of a Special issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, protein networks, edited by Ronald L. Koder and J.L Ross Anderson.

  4. De novo-designed metallopeptides with type 2 copper centers: modulation of reduction potentials and nitrite reductase activities.

    Science.gov (United States)

    Yu, Fangting; Penner-Hahn, James E; Pecoraro, Vincent L

    2013-12-04

    Enzymatic reactions involving redox processes are highly sensitive to the local electrostatic environment. Despite considerable effort, the complex interactions among different influential factors in native proteins impede progress toward complete understanding of the structure-function relationship. Of particular interest is the type 2 copper center Cu(His)3, which may act as an electron transfer center in peptidylglycine α-hydroxylating monooxygenase (PHM) or a catalytic center in copper nitrite reductase (CuNiR). A de novo design strategy is used to probe the effect of modifying charged amino acid residues around, but not directly bound to, a Cu(His)3 center embedded in three-stranded coiled coils (TRI-H)3 [TRI-H = Ac-G WKALEEK LKALEEK LKALEEK HKALEEK G-NH2]. Specifically, the peptide TRI-EH (=TRI-HK22E) alters an important lysine to glutamate just above the copper binding center. With a series of TRI-EH peptides mutated below the metal center, we use a variety of spectroscopies (EPR, UV-vis, XAS) to show a direct impact on the protonation equilibria, copper binding affinities, reduction potentials, and nitrite reductase activities of these copper-peptide complexes. The potentials at a specific pH vary by 100 mV, and the nitrite reductase activities range over a factor of 4 in rates. We also observe that the affinities, potentials, and catalytic activities are strongly influenced by the pH conditions (pH 5.8-7.4). In general, Cu(II) affinities for the peptides are diminished at low pH values. The interplay among these factors can lead to a 200 mV shift in reduction potential across these peptides, which is determined by the pH-dependent affinities of copper in both oxidation states. This study illustrates the strength of de novo protein design in elucidating the influence of ionizable residues on a particular redox system, an important step toward understanding the factors that govern the properties of this metalloenzyme with a goal of eventually improving the

  5. A novel human scFv fragment against TNF-alpha from de novo design method.

    Science.gov (United States)

    Chang, Hong; Qin, Weisong; Li, Yan; Zhang, Jiyan; Lin, Zhou; Lv, Ming; Sun, Yingxun; Feng, Jiannan; Shen, Beifen

    2007-07-01

    Anti-TNF antibody has been an effective therapeutic strategy for the diseases related to aberrant production of TNF-alpha, such as rheumatoid arthritis (RA) and Crohn's disease. The limitations of large molecule inhibitors in the therapy of these diseases prompted the search for other potent novel TNF-alpha antagonists. Antagonistic peptides, derived directly or designed rationally from complementarity-determining regions (CDRs) of neutralizing antibodies against TNF-alpha, have been demonstrated for their ability of inhibiting TNF-alpha. However, their activity is very low. In this study, to increase the affinity and bioactivity, human antibody variable region was used as scaffold to display antagonistic peptides, which were designed on the interaction between TNF-alpha and its neutralizing monoclonal antibody (mAb Z12). Based on the previously designed domain antibody (framework V(H)5), framework V(kappa)1 was used as light chain scaffold. On the basis of computer-guided molecular design method, a novel human scFv fragment (named as TSA1) was designed. Theoretical analysis showed that TSA1 could bind to TNF-alpha with more hydrogen bonds and lower binding free energy than the designed domain antibody. The biological experiments demonstrated that TSA1 could directly bind with TNF-alpha, competitively inhibit the binding of mAb Z12 to TNF-alpha and block the binding of TNF-alpha to TNFR I and TNFR II. TSA1 could also inhibit TNF-induced cytotoxicity on L929 cells and TNF-mediated NF-kappaB activation on HEK-293T cells. The bioactivity of TSA1 was significantly increased over the domain antibody. This study indicated that the framework of antibody variable region could serve as an ideal scaffold for displaying the peptides and provides a novel strategy to design TNF-alpha inhibitors with the ability to block the deleterious biological effects of TNF-alpha.

  6. Structural principles for computational and de novo design of 4Fe-4S metalloproteins

    Science.gov (United States)

    Nanda, Vikas; Senn, Stefan; Pike, Douglas H.; Rodriguez-Granillo, Agustina; Hansen, Will; Khare, Sagar D.; Noy, Dror

    2017-01-01

    Iron-sulfur centers in metalloproteins can access multiple oxidation states over a broad range of potentials, allowing them to participate in a variety of electron transfer reactions and serving as catalysts for high-energy redox processes. The nitrogenase FeMoCO cluster converts di-nitrogen to ammonia in an eight-electron transfer step. The 2(Fe4S4) containing bacterial ferredoxin is an evolutionarily ancient metalloprotein fold and is thought to be a primordial progenitor of extant oxidoreductases. Controlling chemical transformations mediated by iron-sulfur centers such as nitrogen fixation, hydrogen production as well as electron transfer reactions involved in photosynthesis are of tremendous importance for sustainable chemistry and energy production initiatives. As such, there is significant interest in the design of iron-sulfur proteins as minimal models to gain fundamental understanding of complex natural systems and as lead-molecules for industrial and energy applications. Herein, we discuss salient structural characteristics of natural iron-sulfur proteins and how they guide principles for design. Model structures of past designs are analyzed in the context of these principles and potential directions for enhanced designs are presented, and new areas of iron-sulfur protein design are proposed. PMID:26449207

  7. Experimental colitis in rats induces de novo synthesis of cytokines at distant intestinal sites: role of capsaicin-sensitive primary afferent fibers.

    Science.gov (United States)

    Mourad, Fadi H; Hamdi, Tamim; Barada, Kassem A; Saadé, Nayef E

    2016-06-01

    Increased levels of pro- and anti-inflammatory cytokines were observed in various segments of histologically-intact small intestine in animal models of acute and chronic colitis. Whether these cytokines are produced locally or spread from the inflamed colon is not known. In addition, the role of gut innervation in this upregulation is not fully understood. To examine whether cytokines are produced de novo in the small intestine in two rat models of colitis; and to investigate the role of capsaicin-sensitive primary afferents in the synthesis of these inflammatory cytokines. Colitis was induced by rectal instillation of iodoacetamide (IA) or trinitrobenzene sulphonic acid (TNBS) in adult Sprague-Dawley rats. Using reverse transcriptase (RT) and real-time PCR, TNF-α, and IL-10 mRNA expression was measured in mucosal scrapings of the duodenum, jejunum, ileum and colon at different time intervals after induction of colitis. Capsaicin-sensitive primary afferents (CSPA) were ablated using subcutaneous injections of capsaicin at time 0, 8 and 32 h, and the experiment was repeated at specific time intervals to detect any effect on cytokines expression. TNF-α mRNA expression increased by 3-40 times in the different intestinal segments (pcolitis. CSPA ablation completely inhibited this upregulation in the small intestine, but not in the colon. Similar results were obtained in TNBS-induced colitis at 24 h. Intestinal IL-10 mRNA expression significantly decreased at 12 h and then increased by 6-43 times (pcolitis induction, respectively (both pcolitis induction. Inflammatory cytokines are produced de novo in distant intestinal segments in colitis. CSPA fibers play a key role in the upregulation of this synthesis.

  8. De Novo Assembly of Highly Substituted Morpholines and Piperazines

    Science.gov (United States)

    2017-01-01

    The morpholine and piperazine with their remarkable physical and biochemical properties are popular heterocycles in organic and medicinal chemistry used in rational property design. However, in the majority of cases these rings are added to an existing molecule in a building block approach thus limiting their substitution pattern and diversity. Here we introduce a versatile de novo synthesis of the morpholine and piperazine rings using multicomponent reaction chemistry. The large scale amenable building blocks can be further substituted at up to four positions, making this a very versatile scaffold synthesis strategy. Our methods thus fulfill the increasing demand for novel building block design and nontraditional scaffolds which previously were not accessible PMID:28102692

  9. Predictive modelling-based design and experiments for synthesis and spinning of bioinspired silk fibres

    Science.gov (United States)

    Lin, Shangchao; Ryu, Seunghwa; Tokareva, Olena; Gronau, Greta; Jacobsen, Matthew M.; Huang, Wenwen; Rizzo, Daniel J.; Li, David; Staii, Cristian; Pugno, Nicola M.; Wong, Joyce Y.; Kaplan, David L.; Buehler, Markus J.

    2015-05-01

    Scalable computational modelling tools are required to guide the rational design of complex hierarchical materials with predictable functions. Here, we utilize mesoscopic modelling, integrated with genetic block copolymer synthesis and bioinspired spinning process, to demonstrate de novo materials design that incorporates chemistry, processing and material characterization. We find that intermediate hydrophobic/hydrophilic block ratios observed in natural spider silks and longer chain lengths lead to outstanding silk fibre formation. This design by nature is based on the optimal combination of protein solubility, self-assembled aggregate size and polymer network topology. The original homogeneous network structure becomes heterogeneous after spinning, enhancing the anisotropic network connectivity along the shear flow direction. Extending beyond the classical polymer theory, with insights from the percolation network model, we illustrate the direct proportionality between network conductance and fibre Young's modulus. This integrated approach provides a general path towards de novo functional network materials with enhanced mechanical properties and beyond (optical, electrical or thermal) as we have experimentally verified.

  10. Predictive modelling-based design and experiments for synthesis and spinning of bioinspired silk fibres.

    Science.gov (United States)

    Lin, Shangchao; Ryu, Seunghwa; Tokareva, Olena; Gronau, Greta; Jacobsen, Matthew M; Huang, Wenwen; Rizzo, Daniel J; Li, David; Staii, Cristian; Pugno, Nicola M; Wong, Joyce Y; Kaplan, David L; Buehler, Markus J

    2015-05-28

    Scalable computational modelling tools are required to guide the rational design of complex hierarchical materials with predictable functions. Here, we utilize mesoscopic modelling, integrated with genetic block copolymer synthesis and bioinspired spinning process, to demonstrate de novo materials design that incorporates chemistry, processing and material characterization. We find that intermediate hydrophobic/hydrophilic block ratios observed in natural spider silks and longer chain lengths lead to outstanding silk fibre formation. This design by nature is based on the optimal combination of protein solubility, self-assembled aggregate size and polymer network topology. The original homogeneous network structure becomes heterogeneous after spinning, enhancing the anisotropic network connectivity along the shear flow direction. Extending beyond the classical polymer theory, with insights from the percolation network model, we illustrate the direct proportionality between network conductance and fibre Young's modulus. This integrated approach provides a general path towards de novo functional network materials with enhanced mechanical properties and beyond (optical, electrical or thermal) as we have experimentally verified.

  11. Designer cells for stereocomplementary de novo enzymatic cascade reactions based on laboratory evolution.

    Science.gov (United States)

    Agudo, Rubén; Reetz, Manfred T

    2013-12-04

    Designer cells for a synthetic cascade reaction harnessing selective redox reactions were devised, featuring two successive regioselective P450-catalyzed CH-activating oxidations of 1-cyclohexene carboxylic acid methyl ester followed by stereoselective olefin-reduction catalysed by (R)- or (S)-selective mutants of an enoate reductase.

  12. Installing hydrolytic activity into a completely de novo protein framework

    Science.gov (United States)

    Burton, Antony J.; Thomson, Andrew R.; Dawson, William M.; Brady, R. Leo; Woolfson, Derek N.

    2016-09-01

    The design of enzyme-like catalysts tests our understanding of sequence-to-structure/function relationships in proteins. Here we install hydrolytic activity predictably into a completely de novo and thermostable α-helical barrel, which comprises seven helices arranged around an accessible channel. We show that the lumen of the barrel accepts 21 mutations to functional polar residues. The resulting variant, which has cysteine-histidine-glutamic acid triads on each helix, hydrolyses p-nitrophenyl acetate with catalytic efficiencies that match the most-efficient redesigned hydrolases based on natural protein scaffolds. This is the first report of a functional catalytic triad engineered into a de novo protein framework. The flexibility of our system also allows the facile incorporation of unnatural side chains to improve activity and probe the catalytic mechanism. Such a predictable and robust construction of truly de novo biocatalysts holds promise for applications in chemical and biochemical synthesis.

  13. An Efficient Synthesis of de novo Imidates via Aza-Claisen Rearrangements of N-Allyl Ynamides.

    Science.gov (United States)

    Dekorver, Kyle A; North, Troy D; Hsung, Richard P

    2010-10-01

    A novel thermal 3-aza-Claisen rearrangement of N-allyl ynamides for the synthesis of α-allyl imidates is described. Also, a sequential aza-Claisen, Pd-catalyzed Overman rearrangement is described for the synthesis of azapine-2-ones.

  14. Structure-based de novo design, molecular docking and molecular dynamics of primaquine analogues acting as quinone reductase II inhibitors.

    Science.gov (United States)

    Murce, Erika; Cuya-Guizado, Teobaldo Ricardo; Padilla-Chavarria, Helmut Isaac; França, Tanos Celmar Costa; Pimentel, Andre Silva

    2015-11-01

    Primaquine is a traditional antimalarial drug with low parasitic resistance and generally good acceptance at higher doses, which has been used for over 60 years in malaria treatment. However, several limitations related to its hematotoxicity have been reported. It is believed that this toxicity comes from the hydroxylation of the C-5 and C-6 positions of its 8-aminoquinoline ring before binding to the molecular target: the quinone reductase II (NQO2) human protein. In this study we propose primaquine derivatives, with substitution at position C-6 of the 8-aminoquinoline ring, planned to have better binding to NQO2, compared to primaquine, but with a reduced toxicity related to the C-5 position being possible to be oxidized. On this sense the proposed analogues were suggested in order to reduce or inhibit hydroxylation and further oxidation to hemotoxic metabolites. Five C-6 substituted primaquine analogues were selected by de novo design and further submitted to docking and molecular dynamics simulations. Our results suggest that all analogues bind better to NQO2 than primaquine and may become better antimalarials. However, the analogues 3 and 4 are predicted to have a better activity/toxicity balance.

  15. Molecular design and downstream processing of turoctocog alfa (NovoEight), a B-domain truncated factor VIII molecule.

    Science.gov (United States)

    Ahmadian, Haleh; Hansen, Ernst B; Faber, Johan H; Sejergaard, Lars; Karlsson, Johan; Bolt, Gert; Hansen, Jens J; Thim, Lars

    2016-07-01

    Turoctocog alfa (NovoEight) is a third-generation recombinant factor VIII (rFVIII) with a truncated B-domain that is manufactured in Chinese hamster ovary cells. No human or animal-derived materials are used in the process. The aim of this study is to describe the molecular design and purification process for turoctocog alfa. A five-step purification process is applied to turoctocog alfa: protein capture on mixed-mode resin; immunoaffinity chromatography using a unique, recombinantly produced anti-FVIII mAb; anion exchange chromatography; nanofiltration and size exclusion chromatography. This process enabled reduction of impurities such as host cell proteins (HCPs) and high molecular weight proteins (HMWPs) to a very low level. The immunoaffinity step is very important for the removal of FVIII-related degradation products. Manufacturing scale data shown in this article confirmed the robustness of the purification process and a reliable and consistent reduction of the impurities. The contribution of each step to the final product purity is described and shown for three manufacturing batches. Turoctocog alfa, a third-generation B-domain truncated rFVIII product is manufactured in Chinese hamster ovary cells without the use of animal or human-derived proteins. The five-step purification process results in a homogenous, highly purified rFVIII product.

  16. Structural optimization and de novo design of dengue virus entry inhibitory peptides.

    Directory of Open Access Journals (Sweden)

    Joshua M Costin

    Full Text Available Viral fusogenic envelope proteins are important targets for the development of inhibitors of viral entry. We report an approach for the computational design of peptide inhibitors of the dengue 2 virus (DENV-2 envelope (E protein using high-resolution structural data from a pre-entry dimeric form of the protein. By using predictive strategies together with computational optimization of binding "pseudoenergies", we were able to design multiple peptide sequences that showed low micromolar viral entry inhibitory activity. The two most active peptides, DN57opt and 1OAN1, were designed to displace regions in the domain II hinge, and the first domain I/domain II beta sheet connection, respectively, and show fifty percent inhibitory concentrations of 8 and 7 microM respectively in a focus forming unit assay. The antiviral peptides were shown to interfere with virus:cell binding, interact directly with the E proteins and also cause changes to the viral surface using biolayer interferometry and cryo-electron microscopy, respectively. These peptides may be useful for characterization of intermediate states in the membrane fusion process, investigation of DENV receptor molecules, and as lead compounds for drug discovery.

  17. Rational design of inducible CRISPR guide RNAs for de novo assembly of transcriptional programs

    Science.gov (United States)

    Ferry, Quentin R. V.; Lyutova, Radostina; Fulga, Tudor A.

    2017-01-01

    CRISPR-based transcription regulators (CRISPR-TRs) have transformed the current synthetic biology landscape by allowing specific activation or repression of any target gene. Here we report a modular and versatile framework enabling rapid implementation of inducible CRISPR-TRs in mammalian cells. This strategy relies on the design of a spacer-blocking hairpin (SBH) structure at the 5′ end of the single guide RNA (sgRNA), which abrogates the function of CRISPR-transcriptional activators. By replacing the SBH loop with ligand-controlled RNA-cleaving units, we demonstrate conditional activation of quiescent sgRNAs programmed to respond to genetically encoded or externally delivered triggers. We use this system to couple multiple synthetic and endogenous target genes with specific inducers, and assemble gene regulatory modules demonstrating parallel and orthogonal transcriptional programs. We anticipate that this ‘plug and play' approach will be a valuable addition to the synthetic biology toolkit, facilitating the understanding of natural gene circuits and the design of cell-based therapeutic strategies. PMID:28256578

  18. De Novo Synthesis of Benzenoid Compounds by the Yeast Hanseniaspora vineae Increases the Flavor Diversity of Wines.

    Science.gov (United States)

    Martin, Valentina; Giorello, Facundo; Fariña, Laura; Minteguiaga, Manuel; Salzman, Valentina; Boido, Eduardo; Aguilar, Pablo S; Gaggero, Carina; Dellacassa, Eduardo; Mas, Albert; Carrau, Francisco

    2016-06-08

    Benzyl alcohol and other benzenoid-derived metabolites of particular importance in plants confer floral and fruity flavors to wines. Among the volatile aroma components in Vitis vinifera grape varieties, benzyl alcohol is present in its free and glycosylated forms. These compounds are considered to originate from grapes only and not from fermentative processes. We have found increased levels of benzyl alcohol in red Tannat wine compared to that in grape juice, suggesting de novo formation of this metabolite during vinification. In this work, we show that benzyl alcohol, benzaldehyde, p-hydroxybenzaldehyde, and p-hydroxybenzyl alcohol are synthesized de novo in the absence of grape-derived precursors by Hanseniaspora vineae. Levels of benzyl alcohol produced by 11 different H. vineae strains were 20-200 times higher than those measured in fermentations with Saccharomyces cerevisiae strains. These results show that H. vineae contributes to flavor diversity by increasing grape variety aroma concentration in a chemically defined medium. Feeding experiments with phenylalanine, tryptophan, tyrosine, p-aminobenzoic acid, and ammonium in an artificial medium were tested to evaluate the effect of these compounds either as precursors or as potential pathway regulators for the formation of benzenoid-derived aromas. Genomic analysis shows that the phenylalanine ammonia-lyase (PAL) and tyrosine ammonia lyase (TAL) pathways, used by plants to generate benzyl alcohols from aromatic amino acids, are absent in the H. vineae genome. Consequently, alternative pathways derived from chorismate with mandelate as an intermediate are discussed.

  19. Electrochemical and spectroscopic investigations of immobilized de novo designed heme proteins on metal electrodes

    DEFF Research Database (Denmark)

    Albrecht, Tim; Li, WW; Ulstrup, Jens;

    2005-01-01

    On the basis of rational design principles, template-assisted four-helix-bundle proteins that include two histidines for coordinative binding of a heme were synthesized. Spectroscopic and thermodynamic characterization of the proteins in solution reveals the expected bis-histidine coordinated heme...... methods. For all proteins, immobilization causes a decrease in protein stability and a loosening of the helix packing, as reflected by a partial dissociation of a histidine ligand in the ferrous state and very low redox potentials. For the covalently attached MOP-C, the overall interfacial redox process...... involves the coupling of electron transfer and heme ligand dissociation, which was analyzed by time-resolved SERR spectroscopy. Electron transfer was found to be significantly slower for the mono-histidine-coordinated than for the bis-histidine-coordinated heme. For the latter, the formal heterogeneous...

  20. De novo designed coiled-coil proteins with variable conformations as components of molecular electronic devices.

    Science.gov (United States)

    Shlizerman, Clara; Atanassov, Alexander; Berkovich, Inbal; Ashkenasy, Gonen; Ashkenasy, Nurit

    2010-04-14

    Conformational changes of proteins are widely used in nature for controlling cellular functions, including ligand binding, oligomerization, and catalysis. Despite the fact that different proteins and artificial peptides have been utilized as electron-transfer mediators in electronic devices, the unique propensity of proteins to switch between different conformations has not been used as a mechanism to control device properties and performance. Toward this aim, we have designed and prepared new dimeric coiled-coil proteins that adopt different conformations due to parallel or antiparallel relative orientations of their monomers. We show here that controlling the conformation of these proteins attached as monolayers to gold, which dictates the direction and magnitude of the molecular dipole relative to the surface, results in quantitative modulation of the gold work function. Furthermore, charge transport through the proteins as molecular bridges is controlled by the different protein conformations, producing either rectifying or ohmic-like behavior.

  1. iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan.

    Science.gov (United States)

    Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

    2011-06-01

    The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

  2. Synthesis and design of optimal biorefinery

    DEFF Research Database (Denmark)

    Cheali, Peam

    of a large numberof alternatives at their optimality. The result is the identification of the optimal rawmaterial, the product (single vs multi) portfolio and the corresponding process technology selection for a given market scenario. The economic risk of investment due to market uncertainties is further...... products from bio-based feedstock. Since there are several bio-basedfeedstock sources, this has motivated development of different conversion concepts producing various desired products. This results in a number of challenges for the synthesis and design of the optimal biorefinery concept at the early...... process feasibility analysis is of a multidisciplinary nature, often limited and uncertain; (iii) Complexity challenge: this problem is complex requiring multi-criteria evaluation (technical, economic,sustainability). This PhD project aims to develop a decision support tool for identifying optimal...

  3. Analog Electronic Filters Theory, Design and Synthesis

    CERN Document Server

    Dimopoulos, Hercules G

    2012-01-01

    Filters are essential subsystems in a huge variety of electronic systems. Filter applications are innumerable; they are used for noise reduction, demodulation, signal detection, multiplexing, sampling, sound and speech processing, transmission line equalization and image processing, to name just a few. In practice, no electronic system can exist without filters. They can be found in everything from power supplies to mobile phones and hard disk drives and from loudspeakers and MP3 players to home cinema systems and broadband Internet connections. This textbook introduces basic concepts and methods and the associated mathematical and computational tools employed in electronic filter theory, synthesis and design.  This book can be used as an integral part of undergraduate courses on analog electronic filters. Includes numerous, solved examples, applied examples and exercises for each chapter. Includes detailed coverage of active and passive filters in an independent but correlated manner. Emphasizes real filter...

  4. The selective target of capsaicin on FASN expression and de novo fatty acid synthesis mediated through ROS generation triggers apoptosis in HepG2 cells.

    Directory of Open Access Journals (Sweden)

    Hathaichanok Impheng

    Full Text Available The inhibition of the mammalian de novo synthesis of long-chain saturated fatty acids (LCFAs by blocking the fatty acid synthase (FASN enzyme activity in tumor cells that overexpress FASN can promote apoptosis, without apparent cytotoxic to non-tumor cells. The present study aimed to focus on the potent inhibitory effect of capsaicin on the fatty acid synthesis pathway inducing apoptosis of capsaicin in HepG2 cells. The use of capsaicin as a source for a new FASN inhibitor will provide new insight into its possible application as a selective anti-cancer therapy. The present findings showed that capsaicin promoted apoptosis as well as cell cycle arrest in the G0/G1 phase. The onset of apoptosis was correlated with a dissipation of mitochondrial membrane potential (ΔΨm. Apoptotic induction by capsaicin was mediated by inhibition of FASN protein expression which was accompanied by decreasing its activity on the de novo fatty acid synthesis. The expression of FASN was higher in HepG2 cells than in normal hepatocytes that were resistant to undergoing apoptosis following capsaicin administration. Moreover, the inhibitory effect of capsaicin on FASN expression and activity was found to be mediated by an increase of intracellular reactive oxygen species (ROS generation. Treatment of HepG2 cells with capsaicin failed to alter ACC and ACLY protein expression, suggesting ACC and ACLY might not be the specific targets of capsaicin to induce apoptosis. An accumulation of malonyl-CoA level following FASN inhibition represented a major cause of mitochondrial-dependent apoptotic induction instead of deprivation of fatty acid per se. Here, we also obtained similar results with C75 that exhibited apoptosis induction by reducing the levels of fatty acid without any change in the abundance of FASN expression along with increasing ROS production. Collectively, our results provide novel evidence that capsaicin exhibits a potent anti-cancer property by targeting

  5. The Selective Target of Capsaicin on FASN Expression and De Novo Fatty Acid Synthesis Mediated through ROS Generation Triggers Apoptosis in HepG2 Cells

    Science.gov (United States)

    Impheng, Hathaichanok; Pongcharoen, Sutatip; Richert, Lysiane; Pekthong, Dumrongsak; Srisawang, Piyarat

    2014-01-01

    The inhibition of the mammalian de novo synthesis of long-chain saturated fatty acids (LCFAs) by blocking the fatty acid synthase (FASN) enzyme activity in tumor cells that overexpress FASN can promote apoptosis, without apparent cytotoxic to non-tumor cells. The present study aimed to focus on the potent inhibitory effect of capsaicin on the fatty acid synthesis pathway inducing apoptosis of capsaicin in HepG2 cells. The use of capsaicin as a source for a new FASN inhibitor will provide new insight into its possible application as a selective anti-cancer therapy. The present findings showed that capsaicin promoted apoptosis as well as cell cycle arrest in the G0/G1 phase. The onset of apoptosis was correlated with a dissipation of mitochondrial membrane potential (ΔΨm). Apoptotic induction by capsaicin was mediated by inhibition of FASN protein expression which was accompanied by decreasing its activity on the de novo fatty acid synthesis. The expression of FASN was higher in HepG2 cells than in normal hepatocytes that were resistant to undergoing apoptosis following capsaicin administration. Moreover, the inhibitory effect of capsaicin on FASN expression and activity was found to be mediated by an increase of intracellular reactive oxygen species (ROS) generation. Treatment of HepG2 cells with capsaicin failed to alter ACC and ACLY protein expression, suggesting ACC and ACLY might not be the specific targets of capsaicin to induce apoptosis. An accumulation of malonyl-CoA level following FASN inhibition represented a major cause of mitochondrial-dependent apoptotic induction instead of deprivation of fatty acid per se. Here, we also obtained similar results with C75 that exhibited apoptosis induction by reducing the levels of fatty acid without any change in the abundance of FASN expression along with increasing ROS production. Collectively, our results provide novel evidence that capsaicin exhibits a potent anti-cancer property by targeting FASN protein in Hep

  6. D-Cysteine Ligands Control Metal Geometries within de Novo Designed Three-Stranded Coiled Coils.

    Science.gov (United States)

    Pecoraro, Vincent Louis; Ruckthong, Leela; Peacock, Anna F A; Pascoe, Cherilyn E; Hemmingsen, Lars; Stuckey, Jeanne A

    2017-04-06

    While metal ion binding to naturally occurring L-amino acid proteins is well documented, understanding the impact of the opposite chirality (D) amino acids on the structure and stereochemistry of metals is in its infancy. We examine the effect of a D-configuration cysteine within a designed L-amino acid three-stranded coiled coil in order to enforce a precise coordination number on a metal center. The D-chirality does not alter the native fold, but the side-chain reorientation modifies the sterics of the metal binding pocket. L-Cys side-chains within the coiled-coil have previously been shown to rotate substantially from their preferred positions in the apo structure to create a binding site for a tetra-coordinate metal ion. However, here we show by x-ray crystallography that D-Cys side chains are preorganized with suitable geometry to bind such a ligand. This is confirmed by comparison of the Zn(II)Cl(CSL16DC)₃²¯ to the published Zn(II)(H₂O)(GRAND-CSL12AL16LC)₃¯.¹ Spectroscopic analysis indicates that the Cd(II) geometry observed using L-Cys ligands (a mixture of 3- and 4- coordinate Cd(II)) is altered to a single 4-coordinate specie when D-Cys is present. This work opens a new avenue for the control of metal site environment in man-made proteins, by simply altering the binding ligand with its mirror imaged D-configuration. Thus, use of D amino acids in a metal's coordination sphere promises to be a powerful tool for controlling the properties of future metalloproteins.

  7. Enzymic Mechanism of Starch Breakdown in Germinating Rice Seeds: 9. DE NOVO SYNTHESIS OF beta-AMYLASE.

    Science.gov (United States)

    Okamoto, K; Akazawa, T

    1980-01-01

    Germinating rice seeds were fed with [(35)S]methionine and the incorporation of (35)S into beta-amylase demonstrated by quantitative immunoprecipitation using rabbit anti-beta-amylase immunoglobulin G fraction. Separation of the antigen-antibody complex by Na-dodecylsulfate gel electrophoresis and subsequent radioautography clearly showed the radioactive labeling of the beta-amylase molecule. The specific radioactivity of beta-amylase derived from scutellum by immunoprecipitation was significantly greater than that of the endosperm. The results strongly indicate that at the onset of germination of rice seeds beta-amylase is synthesized de novo in the scutellum and that in later stages there occurs activation of an inactive, latent form of the enzyme associated with starch granules in the endosperm. In later stages of germination this activated form of the enzyme becomes dominant.

  8. Increased de novo riboflavin synthesis and hydrolysis of FMN are involved in riboflavin secretion from Hyoscyamus albus hairy roots under iron deficiency.

    Science.gov (United States)

    Higa, Ataru; Khandakar, Jebunnahar; Mori, Yuko; Kitamura, Yoshie

    2012-09-01

    Riboflavin secretion by Hyoscyamus albus hairy roots under Fe deficiency was examined to determine where riboflavin is produced and whether production occurs via an enhancement of riboflavin biosynthesis or a stimulation of flavin mononucleotide (FMN) hydrolysis. Confocal fluorescent microscopy showed that riboflavin was mainly localized in the epidermis and cortex of the root tip and, at the cellular level, in the apoplast. The expressions of three genes involved in the de novo biosynthesis of riboflavin (GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase; 6,7-dimethyl-8-ribityllumazine synthase; riboflavin synthase) were compared between Fe-starved and Fe-replete roots over a time-course of 7 days, using RT-PCR. All three genes were found to be highly expressed over the period 1-7 days in the roots cultured under Fe deficiency. Since riboflavin secretion began to be detected only from 3 days, there was a lag phase observed between the increased transcript accumulations and riboflavin secretion. To determine whether FMN hydrolysis might contribute to the riboflavin secretion in Fe-deficient root cultures, FMN hydrolase activity was determined and was found to be substantially increased after 3 days, when riboflavin secretion became detectable. These results suggested that not only de novo riboflavin synthesis but also the hydrolysis of FMN contributes to riboflavin secretion under conditions of Fe deficiency. Respiration activity was assayed during the time-course, and was also found to be enhanced after 3 days under Fe deficiency, suggesting a possible link with riboflavin secretion. On the other hand, several respiratory inhibitors were found not to affect riboflavin synthase transcript accumulation.

  9. De novo molecular design

    CERN Document Server

    Schneider, Gisbert

    2013-01-01

    Systematically examining current methods and strategies, this ready reference covers a wide range of molecular structures, from organic-chemical drugs to peptides, Proteins and nucleic acids, in line with emerging new drug classes derived from biomacromolecules. A leader in the field and one of the pioneers of this young discipline has assembled here the most prominent experts from across the world to provide first-hand knowledge. While most of their methods and examples come from the area of pharmaceutical discovery and development, the approaches are equally applicable for chemical probes an

  10. Method for innovative synthesis-design of chemical process flowsheets

    OpenAIRE

    Kumar Tula, Anjan; Gani, Rafiqul

    2015-01-01

    Chemical process synthesis-design involve the identification of the processing route to reach a desired product from a specified set of raw materials, design of the operations involved in the processing route, the calculations of utility requirements, the calculations of waste and emission to the surrounding and many more. Different methods (knowledge-based [1], mathematical programming [2], hybrid, etc.) have been proposed and are also currently employed to solve these synthesis-design probl...

  11. Glycogenesis and de novo lipid synthesis from dietary starch in juvenile gilthead sea bream (Sparus aurata) quantified with stable isotopes

    DEFF Research Database (Denmark)

    Ekmann, Kim Schøn; Dalsgaard, Anne Johanne Tang; Holm, Jørgen;

    2013-01-01

    the metabolic fate of dietary starch, 0·7% wheat starch was replaced with isotope-labelled starch (.98% 13C). Fish were fed the experimental diets for three consecutive 10 d periods, and isotope ratio MS was applied to quantify 13C enrichment of liver and whole-body glycogen and lipid pools over the three...... feeding periods. Glycogenesis originating from dietary starch accounted for up to 68·8 and 38·8% of the liver and whole-body glycogen pools, respectively, while up to 16·7% of the liver lipid could be attributed to dietary starch. Between 5 and 8% of dietary starch carbon was recovered in whole-body lipid......, and estimated deposition rates of de novo synthesised lipid originating from starch ranged from 18·7 to 123·7 mg/kg biomass per d. Dietary treatments did not significantly affect growth, feed performance or body composition of the fish, while the hepatosomatic index and glycogen content of whole fish and livers...

  12. Role of lipid raft components and actin cytoskeleton in fibronectin-binding, surface expression, and de novo synthesis of integrin subunits in PGE2- or 8-Br-cAMP-stimulated mastocytoma P-815 cells.

    Science.gov (United States)

    Okada, Yasuyo; Nishikawa, Jyun-ichi; Semma, Masanori; Ichikawa, Atsushi

    2014-04-01

    Integrins are heterodimeric adhesion receptors essential for adhesion of non-adherent cells to extracellular ligands such as extracellular matrix components. The affinity of integrins for ligands is regulated through a process termed integrin activation and de novo synthesis. Integrin activation is regulated by lipid raft components and the actin structure. However, there is little information on the relationship between integrin activation and its de novo synthesis. Cancerous mouse mast cells, mastocytoma P-815 cells (P-815 cells) are known to bind to fibronectin through de novo synthesis of integrin subtypes by prostaglandin (PG) E2 stimulation. The purpose of this study was to clarify the relationship between lipid raft components and the actin cytoskeleton, and PGE2-induced P-815 cells adhesion to fibronectin and the increase in surface expression and mRNA and protein levels of αvβ3 and αIIbβ3 integrins. Cholesterol inhibitor 6-O-α-maltosyl-β cyclodextrin, glycosylphosphatidylinositol-anchored proteins inhibitor phosphatidylinositol-specific phospholipase C and actin inhibitor cytochalasin D inhibited PGE2-induced cell adhesion to fibronectin, but did not regulate the surface expression and mRNA and protein levels of αv and αIIb, and β3 integrin subunits. In addition, inhibitor of integrin modulate protein CD47 had no effect on PGE2- and 8-Br-cAMP-induced cell adhesion. These results suggest that lipid raft components and the actin cytoskeleton are directly involved in increasing of adhesion activity of integrin αIIb, αv and β3 subunits to fibronectin but not in stimulating of de novo synthesis of them in PGE2-stimulated P-815 cells. The modulation of lipid rafts and the actin structure is essential for P-815 cells adhesion to fibronectin.

  13. Design and synthesis of multifunctional phospholipids

    NARCIS (Netherlands)

    Drakopoulou, E; Tsivgoulis, GM; Mukhopadhyay, A; Brisson, A

    2000-01-01

    The synthesis of a bifunctionalized phosholipid capable of binding streptavidin or poly-histidine-tagged proteins is reported for the first time. The head group containing both a biotin and an NTA chelator is synthesized via a new approach using solid phase synthesis. (C) 2000 Elsevier Science Ltd.

  14. The role of de novo protein synthesis and SIRT1 in ER stress-induced Atf4 and Chop mRNA expression in mammalian cells.

    Science.gov (United States)

    Chan, Stanley M H; Zhao, Xuechan; Elfowiris, Abdulsalam; Ratnam, Cherubina; Herbert, Terence P

    2017-07-01

    Endoplasmic reticulum (ER) stress and the activation of the unfolded protein response (UPR) have been implicated in the pathogenesis of many common human diseases. Integral to the UPR and an important determinant in cell fate is the expression of the pro-apoptotic transcription factor C/EBP homologous protein (CHOP). This is promoted by activating transcription factor 4 (ATF4) whose expression is rapidly up-regulated in response to ER stress through an eIF2α phosphorylation-dependent increase in protein synthesis. Our data demonstrates that this ER stress-induced increase in ATF4 and CHOP expression is initiated by an increase in Atf4 and Chop mRNA, which is also dependent upon eIF2α phosphorylation. Despite being dependent on eIF2α phosphorylation, we provide evidence that these increases in Atf4 and Chop mRNA expression may occur independently of de novo protein synthesis. Moreover, we show that ER stress-induced Chop mRNA expression is exacerbated by Sirtuin-1 (SIRT1) inhibition indicating that changes in the energy status of the cell may play an important role in its regulation. This work highlights and extends previous findings, and provides important new insights into the mechanism of ER stress-induced expression of Atf4 and Chop mRNA that clearly warrants further investigation. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  15. RNA synthesis by the brome mosaic virus RNA-dependent RNA polymerase in human cells reveals requirements for de novo initiation and protein-protein interaction.

    Science.gov (United States)

    Subba-Reddy, Chennareddy V; Tragesser, Brady; Xu, Zhili; Stein, Barry; Ranjith-Kumar, C T; Kao, C Cheng

    2012-04-01

    Brome mosaic virus (BMV) is a model positive-strand RNA virus whose replication has been studied in a number of surrogate hosts. In transiently transfected human cells, the BMV polymerase 2a activated signaling by the innate immune receptor RIG-I, which recognizes de novo-initiated non-self-RNAs. Active-site mutations in 2a abolished RIG-I activation, and coexpression of the BMV 1a protein stimulated 2a activity. Mutations previously shown to abolish 1a and 2a interaction prevented the 1a-dependent enhancement of 2a activity. New insights into 1a-2a interaction include the findings that helicase active site of 1a is required to enhance 2a polymerase activity and that negatively charged amino acid residues between positions 110 and 120 of 2a contribute to interaction with the 1a helicase-like domain but not to the intrinsic polymerase activity. Confocal fluorescence microscopy revealed that the BMV 1a and 2a colocalized to perinuclear region in human cells. However, no perinuclear spherule-like structures were detected in human cells by immunoelectron microscopy. Sequencing of the RNAs coimmunoprecipitated with RIG-I revealed that the 2a-synthesized short RNAs are derived from the message used to translate 2a. That is, 2a exhibits a strong cis preference for BMV RNA2. Strikingly, the 2a RNA products had initiation sequences (5'-GUAAA-3') identical to those from the 5' sequence of the BMV genomic RNA2 and RNA3. These results show that the BMV 2a polymerase does not require other BMV proteins to initiate RNA synthesis but that the 1a helicase domain, and likely helicase activity, can affect RNA synthesis by 2a.

  16. De novo synthesis, constitutive expression of Aspergillus sulphureus beta-xylanase gene in Pichia pastoris and partial enzymic characterization.

    Science.gov (United States)

    Cao, Yunhe; Qiao, Jiayun; Li, Yihang; Lu, Wenqing

    2007-09-01

    The endo-beta-1, 4-xylanase gene xynA from Aspergillus sulphureus, encoded a lack-of-signal peptide protein of 184 amino acids, was de novo synthesized by splicing overlap extension polymerase chain reaction according to Pichia pastoris protein's codon bias. The synthetic DNA, composed of 572 nucleotides, was ligated into the downstream sequence of an alpha-mating factor in a constitutive expression vector pGAPzalphaA and electrotransformed into the P. pastoris X-33 strain. The transformed yeast screened by Zeocin was able to constitutively secrete the xylanase in yeast-peptone-dextrose liquid medium. The heterogenous DNA was stabilized in the strain by 20-times passage culture. The recombinant enzyme was expressed with a yield of 120 units/mL under the flask culture at 28 degrees C for 3 days. The enzyme showed optimal activity at 50 degrees C and pH 2.4-3.4. Residual activity of the raw recombinant xylanase was not less than 70% when fermentation broth was directly heated at 80 degrees C for 30 min. However, the dialyzed xylanase supernatant completely lost the catalytic activity after being heated at 60 degrees C for 30 min. The recombinant xylanase showed no obvious activity alteration by being pretreated with Na(2)HPO(4)-citric acid buffer of pH 2.4 for 2 h. The xylanase also showed resistance to certain metal ions (Na(+), Mg(2+), Ca(2+), K(+), Ba(2+), Zn(2+), Fe(2+), and Mn(2+)) and EDTA. These biochemical characteristics suggest that the recombinant xylanase has a prospective application in feed industry as an additive.

  17. The cobY gene of the archaeon Halobacterium sp. strain NRC-1 is required for de novo cobamide synthesis.

    Science.gov (United States)

    Woodson, J D; Peck, R F; Krebs, M P; Escalante-Semerena, J C

    2003-01-01

    Genetic and nutritional analyses of mutants of the extremely halophilic archaeon Halobacterium sp. strain NRC-1 showed that open reading frame (ORF) Vng1581C encodes a protein with nucleoside triphosphate:adenosylcobinamide-phosphate nucleotidyltransferase enzyme activity. This activity was previously associated with the cobY gene of the methanogenic archaeon Methanobacterium thermoautotrophicum strain DeltaH, but no evidence was obtained to demonstrate the direct involvement of this protein in cobamide biosynthesis in archaea. Computer analysis of the Halobacterium sp. strain NRC-1 ORF Vng1581C gene and the cobY gene of M. thermoautotrophicum strain DeltaH showed the primary amino acid sequence of the proteins encoded by these two genes to be 35% identical and 48% similar. A strain of Halobacterium sp. strain NRC-1 carrying a null allele of the cobY gene was auxotrophic for cobinamide-GDP, a known intermediate of the late steps of cobamide biosynthesis. The auxotrophic requirement for cobinamide-GDP was corrected when a wild-type allele of cobY was introduced into the mutant strain, demonstrating that the lack of cobY function was solely responsible for the observed block in cobamide biosynthesis in this archaeon. The data also show that Halobacterium sp. strain NRC-1 possesses a high-affinity transport system for corrinoids and that this archaeon can synthesize cobamides de novo under aerobic growth conditions. To the best of our knowledge this is the first genetic and nutritional analysis of cobalamin biosynthetic mutants in archaea.

  18. Adipose Weight Gain during Chronic Insulin Treatment of Mice Results from Changes in Lipid Storage without Affecting De Novo Synthesis of Palmitate

    Science.gov (United States)

    Frikke-Schmidt, Henriette; Pedersen, Thomas Åskov; Fledelius, Christian; Olsen, Grith Skytte; Hellerstein, Marc

    2013-01-01

    Insulin treatment is associated with increased adipose mass in both humans and mice. However, the underlying dynamic basis of insulin induced lipid accumulation in adipose tissue remains elusive. To assess this, young female C57BL6/J mice were fed a low fat diet for 3 weeks, treated subsequently with 7 days of constant subcutaneous insulin infusion by osmotic minipumps and compared to mice with only buffer infused. To track changes in lipid deposition during insulin treatment, metabolic labeling was conducted with heavy water for the final 4 days. Blood glucose was significantly lowered within one hour after implantation of insulin loaded mini pumps and remained lower throughout the study. Insulin treated animals gained significantly more weight during treatment and the mean weight of the subcutaneous adipose depots was significantly higher with the highest dose of insulin. Surprisingly, de novo palmitate synthesis within the subcutaneous and the gonadal depots was not affected significantly by insulin treatment. In contrast insulin treatment caused accumulation of triglycerides in both depots due to either deposition of newly synthesised triglycerides (subcutaneous depot) or inhibition of lipolysis (gonadal depot). PMID:24069458

  19. Role of Hydroxytyrosol-dependent Regulation of HO-1 Expression in Promoting Wound Healing of Vascular Endothelial Cells via Nrf2 De Novo Synthesis and Stabilization.

    Science.gov (United States)

    Zrelli, Houda; Kusunoki, Miki; Miyazaki, Hitoshi

    2015-07-01

    Hydroxytyrosol (HT), an olive plant (Olea europaea L.) polyphenol, has proven atheroprotective effects. We previously demonstrated that heme oxygenase-1 (HO-1) is involved in the HT dependent prevention of dysfunction induced by oxidative stress in vascular endothelial cells (VECs). Here, we further investigated the signaling pathway of HT-dependent HO-1 expression in VECs. HT dose- and time-dependently increased HO-1 mRNA and protein levels through the PI3K/Akt and ERK1/2 pathways. Cycloheximide and actinomycin D inhibited both increases, suggesting that HT-triggered HO-1 induction is transcriptionally regulated and that de novo protein synthesis is necessary for this HT effect. HT stimulated nuclear accumulation of nuclear factor E2-related factor 2 (Nrf2). This Nrf2 accumulation was blocked by actinomycin D and cycloheximide whereas HT in combination with the 26S proteasome inhibitor MG132 enhanced the accumulation. HT also extended the half-life of Nrf2 proteins by decelerating its turnover. Moreover, HO-1 inhibitor, ZnppIX and CO scavenger, hemoglobin impaired HT-dependent wound healing while CORM-2, a CO generator, accelerated wound closure. Together, these data demonstrate that HT upregulates HO-1 expression by stimulating the nuclear accumulation and stabilization of Nrf2, leading to the wound repair of VECs crucial in the prevention of atherosclerosis.

  20. Heterotrophic bicarbonate assimilation is the main process of de novo organic carbon synthesis in hadal zone of the Hellenic Trench, the deepest part of Mediterranean Sea.

    Science.gov (United States)

    Yakimov, Michail M; La Cono, Violetta; Smedile, Francesco; Crisafi, Francesca; Arcadi, Erika; Leonardi, Marcella; Decembrini, Franco; Catalfamo, Maurizio; Bargiela, Rafael; Ferrer, Manuel; Golyshin, Peter N; Giuliano, Laura

    2014-12-01

    Ammonium-oxidizing chemoautotrophic members of Thaumarchaea are proposed to be the key players in the assimilation of bicarbonate in the dark (ABD). However, this process may also involve heterotrophic metabolic pathways, such as fixation of carbon dioxide (CO2) via various anaplerotic reactions. We collected samples from the depth of 4900 m at the Matapan-Vavilov Deep (MVD) station (Hellenic Trench, Eastern Mediterranean) and used the multiphasic approach to study the ABD mediators in this deep-sea ecosystem. At this depth, our analysis indicated the occurrence of actively CO2-fixing heterotrophic microbial assemblages dominated by Gammaproteobacteria with virtually no Thaumarchaea present. [14C]-bicarbonate incorporation experiments combined with shotgun [14C]-proteomic analysis identified a series of proteins of gammaproteobacterial origin. More than quarter of them were closely related with Alteromonas macleodii ‘deep ecotype’ AltDE, the predominant organism in the microbial community of MVD. The present study demonstrated that in the aphotic/hadal zone of the Mediterranean Sea, the assimilation of bicarbonate is associated with both chemolithoauto- and heterotrophic ABD. In some deep-sea areas, the latter may predominantly contribute to the de novo synthesis of organic carbon which points at the important and yet underestimated role heterotrophic bacterial populations can play the in global carbon cycle/sink in the ocean interior.

  1. Contribution of de novo synthesis of Gαs-proteins to 1-methyladenine production in starfish ovarian follicle cells stimulated by relaxin-like gonad-stimulating substance.

    Science.gov (United States)

    Mita, Masatoshi; Haraguchi, Shogo; Uzawa, Haruka; Tsutsui, Kazuyoshi

    2013-11-01

    In starfish, the peptide hormone gonad-stimulating substance (GSS) secreted from nervous tissue stimulates oocyte maturation to induce 1-methyladenine (1-MeAde) production by ovarian follicle cells. The hormonal action of GSS on follicle cells involves its receptor, G-proteins and adenylyl cyclase. However, GSS failed to induce 1-MeAde and cAMP production in follicle cells of ovaries during oogenesis. At the maturation stage, follicle cells acquired the potential to respond to GSS by producing 1-MeAde and cAMP. Adenylyl cyclase activity in follicle cells of fully grown stage ovaries was also stimulated by GSS in the presence of GTP. These activations depended on the size of oocytes in ovaries. The α subunit of Gs-proteins was not detected immunologically in follicle cells of oogenesis stage ovaries, although Gαi and Gαq were detectable. Using specific primers for Gαs and Gαi, expression levels of Gαs in follicle cells were found to increase significantly as the size of oocytes in ovaries increased, whereas the mRNA levels of Gαi were almost constant regardless of oocyte size. These findings strongly suggest the potential of follicle cells to respond to GSS by producing 1-MeAde and cAMP is brought by de novo synthesis of Gαs-proteins.

  2. Synthesis Optimization for Finite State Machine Design in FPGAs

    Directory of Open Access Journals (Sweden)

    R.UMA

    2012-12-01

    Full Text Available Synthesis optimization plays a vital role in modern FPGAs in order to achieve high performance, in terms of resource utilization and reducing time consuming test process. Cell-based design techniques, such as standard-cells and FPGAs, together with versatile hardware synthesis are rudiments for a high productivity in ASIC design. As the capacity of FPGAs increases, synthesis tools and efficient synthesis methods for targeted device become more significant to efficiently exploit the resources and logic capacity.The synthesis tool provides the selection of different constraint to optimize the circuit. This paper present s the design and synthesis optimization constraints in FPGA for Finite state machine. The primary goal ofthis sequential logic design is to optimize the speed and area by choosing the proper options available inthe synthesis tool. More over the work focuses the design of FSM with more processes operates at a faster rate and the number of slices utilized in an FPGA is also reduced when compare to single process. Themodule functionality are described using Verilog HDL and performance issues like slice utilized,simulation time, percentage of logic utilization, level of logic are analyzed at 90 nm process technology using SPARTAN6 XC6SLX150 XILINX ISE12.1 tool.

  3. Quantum circuit physical design methodology with emphasis on physical synthesis

    Science.gov (United States)

    Mohammadzadeh, Naser; Saheb Zamani, Morteza; Sedighi, Mehdi

    2013-11-01

    In our previous works, we have introduced the concept of "physical synthesis" as a method to consider the mutual effects of quantum circuit synthesis and physical design. While physical synthesis can involve various techniques to improve the characteristics of the resulting quantum circuit, we have proposed two techniques (namely gate exchanging and auxiliary qubit selection) to demonstrate the effectiveness of the physical synthesis. However, the previous contributions focused mainly on the physical synthesis concept, and the techniques were proposed only as a proof of concept. In this paper, we propose a methodological framework for physical synthesis that involves all previously proposed techniques along with a newly introduced one (called auxiliary qubit insertion). We will show that the entire flow can be seen as one monolithic methodology. The proposed methodology is analyzed using a large set of benchmarks. Experimental results show that the proposed methodology decreases the average latency of quantum circuits by about 36.81 % for the attempted benchmarks.

  4. AN AUTOMATED ANALYSIS-SYNTHESIS PACKAGE FOR DESIGN ...

    African Journals Online (AJOL)

    automation in the process of design optimization is achieved ... In this paper, the stiffuess method of analysis will be adapted. ..... The synthesis algorithm calls other user-supplied routines to ... mistakes that creep into manual formulation of.

  5. Computerized Design Synthesis (CDS), A database-driven multidisciplinary design tool

    Science.gov (United States)

    Anderson, D. M.; Bolukbasi, A. O.

    1989-01-01

    The Computerized Design Synthesis (CDS) system under development at McDonnell Douglas Helicopter Company (MDHC) is targeted to make revolutionary improvements in both response time and resource efficiency in the conceptual and preliminary design of rotorcraft systems. It makes the accumulated design database and supporting technology analysis results readily available to designers and analysts of technology, systems, and production, and makes powerful design synthesis software available in a user friendly format.

  6. A Generic Synthesis Algorithm for Well-Defined Parametric Design

    NARCIS (Netherlands)

    Schotborgh, W.O.; Kokkeler, F.G.M.; Tragter, H.; Bomhoff, M.J.; Houten, van F.J.A.M.

    2008-01-01

    This paper aims to improve the way synthesis tools can be built by formalizing: 1) the design artefact, 2) related knowledge and 3) an algorithm to generate solutions. This paper focuses on well-defined parametric engineering design, ranging from machine elements to industrial products. A design art

  7. Structure and models of artifactual routine design for computational synthesis

    NARCIS (Netherlands)

    Jauregui Becker, Juan Manuel; Tragter, Hendrik; van Houten, Frederikus J.A.M.

    2009-01-01

    Computational synthesis (CS) researches the automatic generation of solutions to design problems. The aim is to shorten design times and present the user with multiple design solutions. However, initializing a new CS process has not received much attention in literature. With this motivation, this p

  8. Acyl-chain remodeling of dioctanoyl-phosphatidylcholine in Saccharomyces cerevisiae mutant defective in de novo and salvage phosphatidylcholine synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Kishino, Hideyuki; Eguchi, Hiroki; Takagi, Keiko; Horiuchi, Hiroyuki; Fukuda, Ryouichi; Ohta, Akinori, E-mail: aaohta@isc.chubu.ac.jp

    2014-03-07

    Highlights: • Dioctanoyl-PC (diC8PC) supported growth of a yeast mutant defective in PC synthesis. • diC8PC was converted to PC species containing longer acyl residues in the mutant. • Both acyl residues of diC8PC were replaced by longer fatty acids in vitro. • This system will contribute to the elucidation of the acyl chain remodeling of PC. - Abstract: A yeast strain, in which endogenous phosphatidylcholine (PC) synthesis is controllable, was constructed by the replacement of the promoter of PCT1, encoding CTP:phosphocholine cytidylyltransferase, with GAL1 promoter in a double deletion mutant of PEM1 and PEM2, encoding phosphatidylethanolamine methyltransferase and phospholipid methyltransferase, respectively. This mutant did not grow in the glucose-containing medium, but the addition of dioctanoyl-phosphatidylcholine (diC8PC) supported its growth. Analyses of the metabolism of {sup 13}C-labeled diC8PC ((methyl-{sup 13}C){sub 3}-diC8PC) in this strain using electrospray ionization tandem mass spectrometry revealed that it was converted to PC species containing acyl residues of 16 or 18 carbons at both sn-1 and sn-2 positions. In addition, both acyl residues of (methyl-{sup 13}C){sub 3}-diC8PC were replaced with 16:1 acyl chains in the in vitro reaction using the yeast cell extract in the presence of palmitoleoyl-CoA. These results indicate that PC containing short acyl residues was remodeled to those with acyl chains of physiological length in yeast.

  9. Differential requirements of hippocampal de novo protein and mRNA synthesis in two long-term spatial memory tests: Spontaneous place recognition and delay-interposed radial maze performance in rats.

    Science.gov (United States)

    Ozawa, Takaaki; Yamada, Kazuo; Ichitani, Yukio

    2017-01-01

    Hippocampal de novo mRNA and protein synthesis has been suggested to be critical for long-term spatial memory. However, its requirement in each memory process (i.e. encoding, consolidation and retrieval) and the differences in the roles of de novo mRNA and protein synthesis in different situations where spatial memory is tested have not been thoroughly investigated. To address these questions, we examined the effects of hippocampal administration of the protein synthesis inhibitors, anisomycin (ANI) and emetine (EME), as well as that of an mRNA synthesis inhibitor, 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB), on rat performance in two long-term spatial memory tests. In a spontaneous place recognition test with a 6 h delay, ANI, administered either before or immediately after the sample phase, but not before the test phase, eliminated the exploratory preference for the object in a novel place. This amnesic effect was replicated by both EME and DRB. In a 6 h delay-interposed radial maze task, however, administering ANI before the first-half and before the second-half, but not immediately or 2 h after the first-half, impaired performance in the second-half. This disruptive effect of ANI was successfully replicated by EME. However, DRB administered before the first-half performance did not impair the second-half performance, while it did impair it if injected before the second-half. None of these drugs caused amnesic effects during the short (5 min)/non-delayed conditions in either tests. These results suggest that 1) hippocampal protein synthesis is required for the consolidation of spatial memory, while mRNA synthesis is not necessarily required, and 2) hippocampal mRNA and protein synthesis requirement for spatial memory retrieval depends on the types of memory tested, probably because their demands are different.

  10. Differential requirements of hippocampal de novo protein and mRNA synthesis in two long-term spatial memory tests: Spontaneous place recognition and delay-interposed radial maze performance in rats

    Science.gov (United States)

    Ozawa, Takaaki; Yamada, Kazuo; Ichitani, Yukio

    2017-01-01

    Hippocampal de novo mRNA and protein synthesis has been suggested to be critical for long-term spatial memory. However, its requirement in each memory process (i.e. encoding, consolidation and retrieval) and the differences in the roles of de novo mRNA and protein synthesis in different situations where spatial memory is tested have not been thoroughly investigated. To address these questions, we examined the effects of hippocampal administration of the protein synthesis inhibitors, anisomycin (ANI) and emetine (EME), as well as that of an mRNA synthesis inhibitor, 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB), on rat performance in two long-term spatial memory tests. In a spontaneous place recognition test with a 6 h delay, ANI, administered either before or immediately after the sample phase, but not before the test phase, eliminated the exploratory preference for the object in a novel place. This amnesic effect was replicated by both EME and DRB. In a 6 h delay-interposed radial maze task, however, administering ANI before the first-half and before the second-half, but not immediately or 2 h after the first-half, impaired performance in the second-half. This disruptive effect of ANI was successfully replicated by EME. However, DRB administered before the first-half performance did not impair the second-half performance, while it did impair it if injected before the second-half. None of these drugs caused amnesic effects during the short (5 min)/non-delayed conditions in either tests. These results suggest that 1) hippocampal protein synthesis is required for the consolidation of spatial memory, while mRNA synthesis is not necessarily required, and 2) hippocampal mRNA and protein synthesis requirement for spatial memory retrieval depends on the types of memory tested, probably because their demands are different. PMID:28178292

  11. A de novo NADPH generation pathway for improving lysine production of Corynebacterium glutamicum by rational design of the coenzyme specificity of glyceraldehyde 3-phosphate dehydrogenase.

    Science.gov (United States)

    Bommareddy, Rajesh Reddy; Chen, Zhen; Rappert, Sugima; Zeng, An-Ping

    2014-09-01

    Engineering the cofactor availability is a common strategy of metabolic engineering to improve the production of many industrially important compounds. In this work, a de novo NADPH generation pathway is proposed by altering the coenzyme specificity of a native NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPDH) to NADP, which consequently has the potential to produce additional NADPH in the glycolytic pathway. Specifically, the coenzyme specificity of GAPDH of Corynebacterium glutamicum is systematically manipulated by rational protein design and the effect of the manipulation for cellular metabolism and lysine production is evaluated. By a combinatorial modification of four key residues within the coenzyme binding sites, different GAPDH mutants with varied coenzyme specificity were constructed. While increasing the catalytic efficiency of GAPDH towards NADP enhanced lysine production in all of the tested mutants, the most significant improvement of lysine production (~60%) was achieved with the mutant showing similar preference towards both NAD and NADP. Metabolic flux analysis with (13)C isotope studies confirmed that there was no significant change of flux towards the pentose phosphate pathway and the increased lysine yield was mainly attributed to the NADPH generated by the mutated GAPDH. The present study highlights the importance of protein engineering as a key strategy in de novo pathway design and overproduction of desired products.

  12. Fast, cheap and out of control--Insights into thermodynamic and informatic constraints on natural protein sequences from de novo protein design.

    Science.gov (United States)

    Brisendine, Joseph M; Koder, Ronald L

    2016-05-01

    The accumulated results of thirty years of rational and computational de novo protein design have taught us important lessons about the stability, information content, and evolution of natural proteins. First, de novo protein design has complicated the assertion that biological function is equivalent to biological structure - demonstrating the capacity to abstract active sites from natural contexts and paste them into non-native topologies without loss of function. The structure-function relationship has thus been revealed to be either a generality or strictly true only in a local sense. Second, the simplification to "maquette" topologies carried out by rational protein design also has demonstrated that even sophisticated functions such as conformational switching, cooperative ligand binding, and light-activated electron transfer can be achieved with low-information design approaches. This is because for simple topologies the functional footprint in sequence space is enormous and easily exceeds the number of structures which could have possibly existed in the history of life on Earth. Finally, the pervasiveness of extraordinary stability in designed proteins challenges accepted models for the "marginal stability" of natural proteins, suggesting that there must be a selection pressure against highly stable proteins. This can be explained using recent theories which relate non-equilibrium thermodynamics and self-replication. This article is part of a Special Issue entitled Biodesign for Bioenergetics--The design and engineering of electronc transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Interfacing heat exchanger network synthesis and detailed heat exchanger design

    Energy Technology Data Exchange (ETDEWEB)

    Polley, G.T.; Panjeh Shahi, M.H. (Manchester Univ. (United Kingdom). Inst. of Science and Technology)

    1991-11-01

    Current heat exchanger network synthesis targeting and design procedures involve the use of assumed stream heat transfer coefficients. However, during detailed heat exchanger design, allowable pressure drops are often the most critical factors. The result can be big differences between the exchanger sizes and costs anticipated by the network designer and those realised by the exchanger designer. This in turn prejudices any optimisation attempted at the network design stage. In this paper it is shown how allowable pressure drop can be used as a basis of network design and consistency between expectation and realisation achieved. (author).

  14. Comparative proteomics of oxidative stress response of Lactobacillus acidophilus NCFM reveals effects on DNA repair and cysteine de novo synthesis

    DEFF Research Database (Denmark)

    Calderini, Elia; Celebioglu, Hasan Ufuk; Villarroel, Julia

    2017-01-01

    acidophilus NCFM to H2O2, simulating an oxidative environment. Bacterial growth was monitored by BioScreen and batch cultures were harvested at exponential phase for protein profiling of stress responses by 2D gel-based comparative proteomics. Proteins identified in 19 of 21 spots changing in abundance due...... to H2O2 were typically related to carbohydrate and energy metabolism, cysteine biosynthesis, and stress. In particular, increased cysteine synthase activity may accumulate a cysteine pool relevant for protein stability, enzyme catalysis and the disulfide-reducing pathway. The stress response further...... by refolding. The proteome analysis provides novel insight into resistance mechanisms in lactic acid bacteria against reactive oxygen species and constitutes a valuable starting point for improving industrial processes, food design or strain engineering preserving microorganism viability....

  15. Corpus Design for Malay Corpus-based Speech Synthesis System

    Directory of Open Access Journals (Sweden)

    Tian-Swee Tan

    2009-01-01

    Full Text Available Problem statement: Speech corpus is one of the major components in corpus-based synthesis. The quality and coverage in speech corpus will affect the quality of synthesis speech sound. Approach: This study proposes a corpus design for Malay corpus-based speech synthesis system. This includes the study of design criteria in corpus-based speech synthesis, Malay corpus based database design and the concatenation engine in Malay corpus-based synthesis system. A set of 10 millions digital text corpuses for Malay language has been collected from Malay internet news. This text corpus had been analyzed using word frequency count to find out all high frequency words to be used for designing the sentences for speech corpus. Results: Altogether 381 sentences for speech corpus had been designed using 70% of high frequency words from 10 million text corpus. It consists of 16826 phoneme units and the total storage size is 37.6Mb. All the phone units are phonetically transcribed to preserve the phonetic context of its origin that will be used for phonetic context unit. This speech corpus had been labeled at phoneme level and used for variable length continuous phoneme based concatenation. Speech corpus is one of the major components in corpus-based synthesis. The quality and coverage in speech corpus will affect the quality of synthesized speech sound. Conclusion/Recommendation: This study has proposed a platform for designing speech corpus especially for Malay Text to Speech which can be further enhanced to support more coverage and higher naturalness of synthetic speech.

  16. General aviation design synthesis utilizing interactive computer graphics

    Science.gov (United States)

    Galloway, T. L.; Smith, M. R.

    1976-01-01

    Interactive computer graphics is a fast growing area of computer application, due to such factors as substantial cost reductions in hardware, general availability of software, and expanded data communication networks. In addition to allowing faster and more meaningful input/output, computer graphics permits the use of data in graphic form to carry out parametric studies for configuration selection and for assessing the impact of advanced technologies on general aviation designs. The incorporation of interactive computer graphics into a NASA developed general aviation synthesis program is described, and the potential uses of the synthesis program in preliminary design are demonstrated.

  17. Analysis, synthesis and design of chemical processes

    Energy Technology Data Exchange (ETDEWEB)

    Turton, R. [West Virginia Univ., Morgantown, WV (United States); Bailie, R.C.; Whiting, W.B.

    1998-12-31

    The book illustrates key concepts through a running example from the real world: the manufacture of benzene; covers design, economic considerations, troubleshooting and health/environmental safety; and includes exclusive software for estimating chemical manufacturing equipment capital costs. This book will help chemical engineers optimize the efficiency of production processes, by providing both a philosophical framework and detailed information about chemical process design. Design is the focal point of the chemical engineering practice. This book helps engineers and senior-level students hone their design skills through process design rather than simply plant design. It introduces all the basics of process simulation. Learn how to size equipment, optimize flowsheets, evaluate the economics of projects, and plan the operation of processes. Learn how to use Process Flow Diagrams; choose the operating conditions for a process; and evaluate the performance of existing processes and equipment. Finally, understand how chemical process design impacts health, safety, the environment and the community.

  18. Property Based Process and Product Synthesis and Design

    DEFF Research Database (Denmark)

    Eden, Mario Richard

    2003-01-01

    This thesis describes the development of a general framework for solving process and product design problems. Targeting the desired performance of the system in a systematic manner relieves the iterative nature of conventional design techniques. Furthermore, conventional component based methods...... roles a property model plays at different stages of the solution to a design problem, it is discovered that by decoupling the constitutive equations, that make up the property model, from the balance and constraint equations of the process or product model, a significant reduction in problem complexity...... in terms of the constitutive (synthesis/design) variables instead of the process variables, thus providing the synthesis/design targets. The second reverse problem (reverse property prediction) solves the constitutive equations to identify unit operations, operating conditions and/or products by matching...

  19. Robust decentralized controller design for UPFC using μ-synthesis

    Science.gov (United States)

    Taher, Seyed Abbas; Akbari, Shahabeddin; Abdolalipour, Ali; Hematti, Reza

    2010-08-01

    In this paper a new method based on structured singular value ( μ-synthesis) is proposed for the robust decentralized unified power flow controller (UPFC) design. To achieve decentralization, using the Schauder fixed point theorem the synthesis and analysis of multi-input multi-output (MIMO) control system is transformed into a set of equivalent multi-input single-output (MISO) control system. To cope with power system uncertainties μ-synthesis technique is being used for designing of UPFC controllers. The proposed μ-based controller has a decentralized scheme which has the advantage of reduction in the controller complexity and suitability for practical implementation. The effectiveness of the proposed control strategy on damping low frequency oscillations is evaluated under different operating conditions and compared with the conventional controller to demonstrate its robust performance through nonlinear simulation and some performance indices.

  20. Teaching Process Design through Integrated Process Synthesis

    Science.gov (United States)

    Metzger, Matthew J.; Glasser, Benjamin J.; Patel, Bilal; Hildebrandt, Diane; Glasser, David

    2012-01-01

    The design course is an integral part of chemical engineering education. A novel approach to the design course was recently introduced at the University of the Witwatersrand, Johannesburg, South Africa. The course aimed to introduce students to systematic tools and techniques for setting and evaluating performance targets for processes, as well as…

  1. PLD based design with VHDL RTL design, synthesis and implementation

    CERN Document Server

    Taraate, Vaibbhav

    2017-01-01

    This book covers basic fundamentals of logic design and advanced RTL design concepts using VHDL. The book is organized to describe both simple and complex RTL design scenarios using VHDL. It gives practical information on the issues in ASIC prototyping using FPGAs, design challenges and how to overcome practical issues and concerns. It describes how to write an efficient RTL code using VHDL and how to improve the design performance. The design guidelines by using VHDL are also explained with the practical examples in this book. The book also covers the ALTERA and XILINX FPGA architecture and the design flow for the PLDs. The contents of this book will be useful to students, researchers, and professionals working in hardware design and optimization. The book can also be used as a text for graduate and professional development courses.

  2. Flow Chemistry for Designing Sustainable Chemical Synthesis (journal article)

    Science.gov (United States)

    An efficiently designed continuous flow chemical process can lead to significant advantages in developing a sustainable chemical synthesis or process. These advantages are the direct result of being able to impart a higher degree of control on several key reactor and reaction par...

  3. Molecular design, synthesis and evaluation of chemical biology tools

    NARCIS (Netherlands)

    Hoogenboom, Jorin

    2017-01-01

    Chapter 1 provides a perspective of synthetic organic chemistry as a discipline involved in the design, synthesis and evaluation of complex molecules. The reader is introduced with a brief history of synthetic organic chemistry, all the while dealing with different aspects of synthe

  4. Design and synthesis of paramagnetic probes for structural biology

    NARCIS (Netherlands)

    Liu, Wei-Min

    2013-01-01

    The majority of the work presented in this thesis involves the design and synthesis of paramagnetic NMR probes, including lanthanoids caged probes and spin labels. An overview of the development of different types of lanthanoids caged probes is given. Among all of the reported lanthanoid probes, the

  5. Rudder-Roll Damping Controller Design using Mu Synthesis

    DEFF Research Database (Denmark)

    Yang, C.; Blanke, M.

    1998-01-01

    The effectiveness of rudder roll damping control is very sensitive to uncertainty in ship dynamic parameters. In this paper, an H-infinity controller is designed using mu synthesis and an uncertainty model for roll and yaw that was identified earlier from experiments at sea. The properties...

  6. Methods for Solving Highly Symmetric De Novo Designed Metalloproteins: Crystallographic Examination of a Novel Three-Stranded Coiled-Coil Structure Containing d-Amino Acids.

    Science.gov (United States)

    Ruckthong, L; Stuckey, J A; Pecoraro, V L

    2016-01-01

    The core objective of de novo metalloprotein design is to define metal-protein relationships that control the structure and function of metal centers by using simplified proteins. An essential requirement to achieve this goal is to obtain high resolution structural data using either NMR or crystallographic studies in order to evaluate successful design. X-ray crystal structures have proven that a four heptad repeat scaffold contained in the three-stranded coiled coil (3SCC), called CoilSer (CS), provides an excellent motif for modeling a three Cys binding environment capable of chelating metals into geometries that resemble heavy metal sites in metalloregulatory systems. However, new generations of more complicated designs that feature, for example, a d-amino acid or multiple metal ligand sites in the helical sequence require a more stable construct. In doing so, an extra heptad was introduced into the original CS sequence, yielding a GRAND-CoilSer (GRAND-CS) to retain the 3SCC folding. An apo-(GRAND-CSL12DLL16C)3 crystal structure, designed for Cd(II)S3 complexation, proved to be a well-folded parallel 3SCC. Because this structure is novel, protocols for crystallization, structural determination, and refinements of the apo-(GRAND-CSL12DLL16C)3 are described. This report should be generally useful for future crystallographic studies of related coiled-coil designs.

  7. Design, synthesis and study of coordination complexes for quantum computing

    OpenAIRE

    Aguilà Avilés, David

    2013-01-01

    This thesis presents different strategies for the design of molecular complexes with the requirements to be used as two-qubit quantum gates. The approaches followed towards the preparation of potential qubit systems have been carried out focusing on the synthesis of ligands with β-diketone coordination units, which are very versatile for the design of metallocluster assemblies. One of the main advantages of using this kind of ligands is that they can be easily prepared through simple Claisen ...

  8. Computer-aided synthesis and design of plant utility systems

    Energy Technology Data Exchange (ETDEWEB)

    Petroulas, T.; Reklaitis, G.V.

    1984-01-01

    A design synthesis procedure is developed for preliminary design of utility systems. Given known steam sources (waste heat and auxiliary boilers) and sinks (heating, process injection, and driver horsepower needs), the algorithm determines the optimal header pressure levels, the distribution of steam turbines in the network, and the steam flows between all devices so as to maximize the real work recovered from the sources. Any number of pressure levels can be accommodated at only modest increase in computational effort.

  9. Synthesis design of artificial magnetic metamaterials using a genetic algorithm.

    Science.gov (United States)

    Chen, P Y; Chen, C H; Wang, H; Tsai, J H; Ni, W X

    2008-08-18

    In this article, we present a genetic algorithm (GA) as one branch of artificial intelligence (AI) for the optimization-design of the artificial magnetic metamaterial whose structure is automatically generated by computer through the filling element methodology. A representative design example, metamaterials with permeability of negative unity, is investigated and the optimized structures found by the GA are presented. It is also demonstrated that our approach is effective for the synthesis of functional magnetic and electric metamaterials with optimal structures. This GA-based optimization-design technique shows great versatility and applicability in the design of functional metamaterials.

  10. Sustainable DME synthesis-design with CO2 utilization

    DEFF Research Database (Denmark)

    Prasertsri, Weeranut; Frauzem, Rebecca; Suriyapraphadilok, Uthaiporn

    valuable chemical that can be produced via thermochemical CO2 conversion reactions. The aim of this study is to identify the most promising processing route for sustainable production of DME in terms of CO2 emission, economic indicators and sustainable indicators. The three processing routes are generated......: (A) dry reforming step, methanol synthesis step, and methanoldehydration step; (B) CO2 hydrogenation step followed by methanol dehydration step;and (C) dry reforming step followed by direct DME synthesis step. Starting with a base-case design, the process flow sheets for the three routes are studied...

  11. Sustainable DME synthesis-design with CO2 utilization

    DEFF Research Database (Denmark)

    Prasertsri, Weeranut; Frauzem, Rebecca; Suriyapraphadilok, Uthaiporn

    2016-01-01

    valuable chemical that can be produced via thermochemical CO2 conversion reactions. The aim of this study is to identify the most promising processing route for sustainable production of DME in terms of CO2 emission, economic indicators and sustainable indicators. The three processing routes are generated......: (A) dry reforming step, methanol synthesis step, and methanol dehydration step; (B) CO2 hydrogenation step followed by methanol dehydration step; and (C) dry reforming step followed by direct DME synthesis step. Starting with a base-case design, the process flow sheets for the three routes...

  12. Design and Synthesis of Biaryl DNA-Encoded Libraries.

    Science.gov (United States)

    Ding, Yun; Franklin, G Joseph; DeLorey, Jennifer L; Centrella, Paolo A; Mataruse, Sibongile; Clark, Matthew A; Skinner, Steven R; Belyanskaya, Svetlana

    2016-10-10

    DNA-encoded library technology (ELT) is a powerful tool for the discovery of new small-molecule ligands to various protein targets. Here we report the design and synthesis of biaryl DNA-encoded libraries based on the scaffold of 5-formyl 3-iodobenzoic acid. Three reactions on DNA template, acylation, Suzuki-Miyaura coupling and reductive amination, were applied in the library synthesis. The three cycle library of 3.5 million diversity has delivered potent hits for phosphoinositide 3-kinase α (PI3Kα).

  13. Design and synthesis of reactive separation systems

    Energy Technology Data Exchange (ETDEWEB)

    Doherty, M.F.

    1992-01-01

    During the last decade there has been a rapid upturn in interest in reactive distillation. The chemical process industry recognizes the favorable economics of carrying out reaction simultaneously with distillation for certain classes of reacting systems, and many new processes have been built based on this technology. Interest is also increasing by academics and software vendors. Systematic design methods for reactive distillation systems have only recently begun to emerge. In this report we survey the available design techniques and point out the contributions made by our group at the University of Massachusetts.

  14. De novo asymmetric synthesis and biological analysis of the daumone pheromones in Caenorhabditis elegans and in the soybean cyst nematode Heterodera glycines

    Science.gov (United States)

    The de novo asymmetric total syntheses of daumone 1, daumone 2 and analogs are described. The key steps of our approach are the diastereoselective palladium catalyzed glycosylation reaction, the Noyori reduction of a acetylfuran and a propargyl ketone, which introduce the absolute stereochemistry of...

  15. Dimensional Synthesis Design of Novel Parallel Machine Tool

    Institute of Scientific and Technical Information of China (English)

    汪劲松; 唐晓强; 段广洪; 尹文生

    2002-01-01

    This paper presents dimensional synthesis design theory for a novel planar 3-DOF (degrees of freedom) parallel machine tool. Closed-form solutions are developed for both the inverse and direct kinematics. The formulation of the dexterity and the definitions of the theoretical workspace and the valid workspace are used to analyze the effects of the design parameters on the dexterity and workspace. The analysis results are used to propose an approach to satisfy the platform motion requirement while realizing orientation capability, dexterity and valid workspace. A design example is given to illustrate the effectiveness of this approach.

  16. A computational framework for the design of optimal protein synthesis.

    Science.gov (United States)

    Racle, Julien; Overney, Jan; Hatzimanikatis, Vassily

    2012-08-01

    Despite the establishment of design principles to optimize codon choice for heterologous expression vector design, the relationship between codon sequence and final protein yield remains poorly understood. In this work, we present a computational framework for the identification of a set of mutant codon sequences for optimized heterologous protein production, which uses a codon-sequence mechanistic model of protein synthesis. Through a sensitivity analysis on the optimal steady state configuration of protein synthesis we are able to identify the set of codons, that are the most rate limiting with respect to steady state protein synthesis rate, and we replace them with synonymous codons recognized by charged tRNAs more efficient for translation, so that the resulting codon-elongation rate is higher. Repeating this procedure, we iteratively optimize the codon sequence for higher protein synthesis rate taking into account multiple constraints of various types. We determine a small set of optimized synonymous codon sequences that are very close to each other in sequence space, but they have an impact on properties such as ribosomal utilization or secondary structure. This limited number of sequences can then be offered for further experimental study. Overall, the proposed method is very valuable in understanding the effects of the different properties of mRNA sequences on the final protein yield in heterologous protein production and it can find applications in synthetic biology and biotechnology.

  17. Conjugated microporous polymers: design, synthesis and application.

    Science.gov (United States)

    Xu, Yanhong; Jin, Shangbin; Xu, Hong; Nagai, Atsushi; Jiang, Donglin

    2013-10-21

    Conjugated microporous polymers (CMPs) are a class of organic porous polymers that combine π-conjugated skeletons with permanent nanopores, in sharp contrast to other porous materials that are not π-conjugated and with conventional conjugated polymers that are nonporous. As an emerging material platform, CMPs offer a high flexibility for the molecular design of conjugated skeletons and nanopores. Various chemical reactions, building blocks and synthetic methods have been developed and a broad variety of CMPs with different structures and specific properties have been synthesized, driving the rapid growth of the field. CMPs are unique in that they allow the complementary utilization of π-conjugated skeletons and nanopores for functional exploration; they have shown great potential for challenging energy and environmental issues, as exemplified by their excellent performance in gas adsorption, heterogeneous catalysis, light emitting, light harvesting and electrical energy storage. This review describes the molecular design principles of CMPs, advancements in synthetic and structural studies and the frontiers of functional exploration and potential applications.

  18. Robust parameter design for automatically controlled systems and nanostructure synthesis

    Science.gov (United States)

    Dasgupta, Tirthankar

    2007-12-01

    This research focuses on developing comprehensive frameworks for developing robust parameter design methodology for dynamic systems with automatic control and for synthesis of nanostructures. In many automatically controlled dynamic processes, the optimal feedback control law depends on the parameter design solution and vice versa and therefore an integrated approach is necessary. A parameter design methodology in the presence of feedback control is developed for processes of long duration under the assumption that experimental noise factors are uncorrelated over time. Systems that follow a pure-gain dynamic model are considered and the best proportional-integral and minimum mean squared error control strategies are developed by using robust parameter design. The proposed method is illustrated using a simulated example and a case study in a urea packing plant. This idea is also extended to cases with on-line noise factors. The possibility of integrating feedforward control with a minimum mean squared error feedback control scheme is explored. To meet the needs of large scale synthesis of nanostructures, it is critical to systematically find experimental conditions under which the desired nanostructures are synthesized reproducibly, at large quantity and with controlled morphology. The first part of the research in this area focuses on modeling and optimization of existing experimental data. Through a rigorous statistical analysis of experimental data, models linking the probabilities of obtaining specific morphologies to the process variables are developed. A new iterative algorithm for fitting a Multinomial GLM is proposed and used. The optimum process conditions, which maximize the above probabilities and make the synthesis process less sensitive to variations of process variables around set values, are derived from the fitted models using Monte-Carlo simulations. The second part of the research deals with development of an experimental design methodology, tailor

  19. Design and Synthesis of a Dual Linker for Solid Phase Synthesis of Oleanolic Acid Derivatives

    Directory of Open Access Journals (Sweden)

    Shaorong Wang

    2011-06-01

    Full Text Available A hydrophilic amino-terminated poly(ethylene glycol-type dual linker for solid phase synthesis of oleanolic acid derivatives using trityl chloride resin was designed and synthesized for the first time. Model reactions in both liquid and solid phase were performed to show the feasibility of its selective cleavage at two different sites. The biological assay results indicated that the long and flexible alkyl ether functionality in the linker is less likely to be critical for the binding event. Following the successful solid-phase synthesis of model compounds, the potential of this dual linker in reaction monitoring and target identification is deemed worthy of further study.

  20. Metabolic design for cyanobacterial chemical synthesis.

    Science.gov (United States)

    Oliver, John W K; Atsumi, Shota

    2014-06-01

    Photosynthetic chemical production in cyanobacteria is a promising technology for renewable energy, CO2 mitigation, and fossil fuel replacement. Metabolic engineering has enabled a direct biosynthetic process from CO2 fixation to chemical feedstocks and biofuels, without requiring costly production, storage, and breakdown of cellulose or sugars. However, direct production technology is challenged by a need to achieve high-carbon partitioning to products in order to be competitive. This review discusses principles for the design of biosynthetic pathways in cyanobacteria and describes recent advances in relevant genetic tools. This field is at a critical juncture in assessing the strength and feasibility of carbon partitioning. To address this, we have included the stoichiometry of reducing equivalents and carbon conservation for heterologous pathways, and a method for calculating product yields against a theoretical maximum.

  1. Design, synthesis, and characterization of biomimetic oligomers

    DEFF Research Database (Denmark)

    Laursen, Jonas Striegler

    . Using NMR spectroscopy, X-ray crystallographic analysis, and density functional theory (DFT) calculations, we found evidence for the presence of thioamide–aromatic interactions through Csp2-H···Samide hydrogen bonding. Based on these studies we designed a ß-peptoid oligomer from residues prone to fit......Peptides and proteins made from the 20 canonical amino acids are responsible for many processes necessary for organisms to function. Beside their composition, proteins obtain their activity and unique selectivity through an ability to display functionalities accurately in the three......, for their ability to mimic the structural elements seen in proteins. Two prominent peptidomimetics are ß-peptides and a-peptoids (N-alkylglycines), which have been shown to fold into helical and sheet-like arrangements. To expand the chemical space available for mimicking protein structure their features have been...

  2. Graphitic nanocapsules: design, synthesis and bioanalytical applications.

    Science.gov (United States)

    Ding, Ding; Xu, Yiting; Zou, Yuxiu; Chen, Long; Chen, Zhuo; Tan, Weihong

    2017-08-03

    Graphitic nanocapsules are emerging nanomaterials which are gaining popularity along with the development of carbon nanomaterials. Their unique physical and chemical properties, as well as good biocompatibility, make them desirable agents for biomedical and bioanalytical applications. Through rational design, integrating graphitic nanocapsules with other materials provides them with additional properties which make them versatile nanoplatforms for bioanalysis. In this feature article, we present the use and performance of graphitic nanocapsules in a variety of bioanalytical applications. Based on their chemical properties, the specific merits and limitations of magnetic, hollow, and noble metal encapsulated graphitic nanocapsules are discussed. Detection, multi-modal imaging, and therapeutic applications are included. Future directions and potential solutions for further biomedical applications are also suggested.

  3. Computer-assisted design of organic synthesis

    Science.gov (United States)

    Kaminaka, H.

    1986-01-01

    The computer programs to design synthetic pathways of organic compounds have been utilized throughout the world since the first system was reported by Corey in 1969, and the LHASA was reported in1972 to become the predominant system. Many programs have been reported mainly in the United States and Europe, and groups of corporations, especially chemical companies, have been trying to improve programs and increase the efficiency of research. In Japan, unfortunately, no concrete movement in this area has been seen. Of course, it goes without saying that these kinds of programs are effective for efficient research, but the remarkable aspect is that these can present unexpected data to the researchers to stimulate them to develop new ideas.

  4. Design and synthesis of a photoswitchable guanidine catalyst

    Directory of Open Access Journals (Sweden)

    Philipp Viehmann

    2012-10-01

    Full Text Available A novel design as well as a straight-forward synthesis for a photoswitchable guanidine catalyst is reported. Intense studies of the photochromic properties demonstrated the reversible switchability of its photosensitive azobenzene moiety. Its activity in the ring-opening polymerization (ROP of rac-lactide was investigated as well. The obtained results are discussed, and an additional guanidine was synthesized and utilized in the ROP of rac-lactide in order to explain the findings.

  5. Design and synthesis of pathway genes for polyketide biosynthesis.

    Science.gov (United States)

    Peirú, Salvador; Gramajo, Hugo; Menzella, Hugo G

    2009-01-01

    In this chapter we describe novel methods for the design and assembly of synthetic pathways for the synthesis of polyketides and tailoring sugars. First, a generic design for type I polyketide synthase genes is presented that allows their facile assembly for the expression of chimeric enzymes in an engineered Escherichia coli host. The sequences of the synthetic genes are based on naturally occurring polyketide synthase genes but they are redesigned by custom-made software to optimize codon usage to maximize expression in E. coli and to provide a standard set of restriction sites to allow combinatorial assembly into unnatural enzymes. The methodology has been validated by building a large number of bimodular mini-PKSs that make easily assayed triketide products. Learning from the successful bimodules, a conceptual advance was made by assembling genes encoding functional trimodular enzymes, capable of making tetraketide products. Second, methods for the rapid assembly and exchange of sugar pathway genes into functional operons are described. The approach was validated by the assembly of the 15 genes for the synthesis of mycarose and desosamine in two operons, which yielded erythromycin C when coexpressed with the corresponding PKS genes. These methods are important enabling steps toward the goals of making designer drugs by polyketide synthase and sugar pathway engineering and, in the shorter term, producing by fermentation advanced intermediates for the synthesis of compounds that otherwise require large numbers of chemical steps.

  6. System Synthesis in Preliminary Aircraft Design Using Statistical Methods

    Science.gov (United States)

    DeLaurentis, Daniel; Mavris, Dimitri N.; Schrage, Daniel P.

    1996-01-01

    This paper documents an approach to conceptual and early preliminary aircraft design in which system synthesis is achieved using statistical methods, specifically Design of Experiments (DOE) and Response Surface Methodology (RSM). These methods are employed in order to more efficiently search the design space for optimum configurations. In particular, a methodology incorporating three uses of these techniques is presented. First, response surface equations are formed which represent aerodynamic analyses, in the form of regression polynomials, which are more sophisticated than generally available in early design stages. Next, a regression equation for an Overall Evaluation Criterion is constructed for the purpose of constrained optimization at the system level. This optimization, though achieved in an innovative way, is still traditional in that it is a point design solution. The methodology put forward here remedies this by introducing uncertainty into the problem, resulting in solutions which are probabilistic in nature. DOE/RSM is used for the third time in this setting. The process is demonstrated through a detailed aero-propulsion optimization of a High Speed Civil Transport. Fundamental goals of the methodology, then, are to introduce higher fidelity disciplinary analyses to the conceptual aircraft synthesis and provide a roadmap for transitioning from point solutions to probabilistic designs (and eventually robust ones).

  7. High Surface Area Ceria Nanoparticles via Hydrothermal Synthesis Experiment Design

    Directory of Open Access Journals (Sweden)

    Stanislav Kurajica

    2016-01-01

    Full Text Available Hydrothermal synthesis of CeO2 was optimized on two reactant concentrations and synthesis temperature and duration, in order to achieve material having the greatest specific surface area (SSA. Taguchi method of experimental design was employed in evaluation of the relative importance of synthesis parameters. CeO2 nanoparticles were characterized using X-ray diffraction, nitrogen adsorption-desorption isotherms, and scanning electron microscopy. Optimum conditions for obtaining particles with greater SSA were calculated according to Taguchi’s model “the-higher-the-better.” Synthesis temperature was found to be the only parameter significant for enabling nanoparticles with greater SSA. Mesoporous nanocrystalline ceria with SSA as great as 226 m2 g−1 was achieved, which is unprecedented for the hydrothermally synthesized ceria. The reason for this achievement was found in temperature dependence of the diffusion coefficient which, when low, favors nucleation yielding with fine particles, while when high it favors crystal growth and formation of one-dimensional structures. The occurrence of 1D-structure in sample exhibiting the smallest SSA was confirmed. Very fine crystallites with crystallite size as low as 5.9 nm have been obtained being roughly inverse proportional to SSA. Selected samples were tested as catalyst for soot oxidation. Catalyst morphology turned out to be decisive factor for catalytic activity.

  8. Computer-Aided Sustainable Process Synthesis-Design and Analysis

    DEFF Research Database (Denmark)

    Kumar Tula, Anjan

    Process synthesis involves the investigation of chemical reactions needed to produce the desired product, selection of the separation techniques needed for downstream processing, as well as taking decisions on sequencing the involved separation operations. For an effective, efficient and flexible...... purity etc. In this way, the entire list of feasible chemical process flowsheets are quickly generated, screened and selected for further analysis. In the next stage, the design of the most promising process flowsheet candidates is performed through a reverse simulation approach, where the design...

  9. Synergistic Integration of Experimental and Simulation Approaches for the de Novo Design of Silk-Based Materials.

    Science.gov (United States)

    Huang, Wenwen; Ebrahimi, Davoud; Dinjaski, Nina; Tarakanova, Anna; Buehler, Markus J; Wong, Joyce Y; Kaplan, David L

    2017-04-18

    Tailored biomaterials with tunable functional properties are crucial for a variety of task-specific applications ranging from healthcare to sustainable, novel bio-nanodevices. To generate polymeric materials with predictive functional outcomes, exploiting designs from nature while morphing them toward non-natural systems offers an important strategy. Silks are Nature's building blocks and are produced by arthropods for a variety of uses that are essential for their survival. Due to the genetic control of encoded protein sequence, mechanical properties, biocompatibility, and biodegradability, silk proteins have been selected as prototype models to emulate for the tunable designs of biomaterial systems. The bottom up strategy of material design opens important opportunities to create predictive functional outcomes, following the exquisite polymeric templates inspired by silks. Recombinant DNA technology provides a systematic approach to recapitulate, vary, and evaluate the core structure peptide motifs in silks and then biosynthesize silk-based polymers by design. Post-biosynthesis processing allows for another dimension of material design by controlled or assisted assembly. Multiscale modeling, from the theoretical prospective, provides strategies to explore interactions at different length scales, leading to selective material properties. Synergy among experimental and modeling approaches can provide new and more rapid insights into the most appropriate structure-function relationships to pursue while also furthering our understanding in terms of the range of silk-based systems that can be generated. This approach utilizes nature as a blueprint for initial polymer designs with useful functions (e.g., silk fibers) but also employs modeling-guided experiments to expand the initial polymer designs into new domains of functional materials that do not exist in nature. The overall path to these new functional outcomes is greatly accelerated via the integration of

  10. Method for innovative synthesis-design of chemical process flowsheets

    DEFF Research Database (Denmark)

    Kumar Tula, Anjan; Gani, Rafiqul

    of chemical processes, where, chemical process flowsheets could be synthesized in the same way as atoms or groups of atoms are synthesized to form molecules in computer aided molecular design (CAMD) techniques [4]. That, from a library of building blocks (functional process-groups) and a set of rules to join......, the implementation of the computer-aided process-group based flowsheet synthesis-design framework is presented together with an extended library of flowsheet property models to predict the environmental impact, safety factors, product recovery and purity, which are employed to screen the generated alternatives. Also...... flowsheet (the well-known Hydrodealkylation of toluene process) and another for a biochemical process flowsheet (production of ethanol from lignocellulose). In both cases, not only the reported designs are found and matched, but also new innovative designs are found, which is possible because...

  11. Integration of thermodynamic insights and MINLP optimisation for the synthesis, design and analysis of process flowsheets

    DEFF Research Database (Denmark)

    Hostrup, Martin; Gani, Rafiqul; Kravanja, Zdravko

    1999-01-01

    This paper presents an integrated approach to the solution of process synthesis, design and analysis problems. Integration is achieved by combining two different techniques, synthesis based on thermodynamic insights and structural optimization together with a simulation engine and a properties...

  12. Computational analysis of novel drugs designed for use as acetylcholinesterase inhibitors and histamine H3 receptor antagonists for Alzheimer's disease by docking, scoring and de novo evolution.

    Science.gov (United States)

    Chen, Po-Yuan; Tsai, Ching-Tsan; Ou, Che-Yen; Hsu, Wei-Tse; Jhuo, Mien-De; Wu, Chieh-Hsi; Shih, Tzu-Ching; Cheng, Tzu-Hurng; Chung, Jing-Gung

    2012-04-01

    Alzheimer's disease (AD) was first described by Alois Alzheimer in 1907. AD is the most prevalent dementia- related disease, affecting over 20 million individuals worldwide. Currently, however, only a handful of drugs are available and they are at best only able to offer some relief of symptoms. Acetylcholinesterase (AChE) inhibitors, antioxidants, metal chelators, monoamine oxidase inhibitors, anti-inflammatory drugs and NMDA inhibitors are usually used to attempt to cure this disease. AChE inhibitors are the most effective therapy for AD at present. Researchers have found that histamine H3 receptor antagonists decrease re-uptake of acetylcholine and the nervous transmitter substance acetylcholine increases. In this study, we designed compounds by using docking, de novo evolution and adsorption, distribution, metabolism, excretion and toxicity (ADMET) analysis to AChE inhibitors as well as histamine H3 receptor antagonists to forward drug research and investigate the potent compounds which can pass through the blood-brain barrier. The novel drugs may be useful for the treatment of AD, based on the results of this theoretical calculation study. We will subsequently examine them in future experiments.

  13. Inducible Expression of the De-Novo Designed Antimicrobial Peptide SP1-1 in Tomato Confers Resistance to Xanthomonas campestris pv. vesicatoria

    Science.gov (United States)

    Herrera Diaz, Areli; Kovacs, Izabella; Lindermayr, Christian

    2016-01-01

    Antimicrobial peptides (AMPs) are small peptides with less than 50 amino acids and are part of the innate immune response in almost all organisms, including bacteria, vertebrates, invertebrates and plants. AMPs are active against a broad-spectrum of pathogens. The inducible expression of AMPs in plants is a promising approach to combat plant pathogens with minimal negative side effects, such as phytotoxicity or infertility. In this study, inducible expression of the de-novo designed AMP SP1-1 in Micro Tom tomato protected tomato fruits against bacterial spot disease caused by Xanthomonas campestris pv. vesicatoria. The peptide SP1-1 was targeted to the apoplast which is the primary infection site for plant pathogens, by fusing SP1-1 peptide to the signal peptide RsAFP1 of radish (Raphanus sativus). The pathogen inducibility of the expression was enabled by using an optimized inducible 4XW2/4XS promoter. As a result, the tomato fruits of independently generated SP1-1 transgenic lines were significantly more resistant to X. campestris pv. vesicatoria than WT tomato fruits. In transgenic lines, bacterial infection was reduced up to 65% in comparison to the infection of WT plants. Our study demonstrates that the combination of the 4XW2/4XS cis-element from parsley with the synthetic antimicrobial peptide SP1-1 is a good alternative to protect tomato fruits against infections with X. campestris pv. vesicatoria. PMID:27706237

  14. Membrane interaction and secondary structure of de novo designed arginine-and tryptophan peptides with dual function

    KAUST Repository

    Rydberg, Hanna A.

    2012-10-01

    Cell-penetrating peptides and antimicrobial peptides are two classes of positively charged membrane active peptides with several properties in common. The challenge is to combine knowledge about the membrane interaction mechanisms and structural properties of the two classes to design peptides with membrane-specific actions, useful either as transporters of cargo or as antibacterial substances. Membrane active peptides are commonly rich in arginine and tryptophan. We have previously designed a series of arg/trp peptides and investigated how the position and number of tryptophans affect cellular uptake. Here we explore the antimicrobial properties and the interaction with lipid model membranes of these peptides, using minimal inhibitory concentrations assay (MIC), circular dichroism (CD) and linear dichroism (LD). The results show that the arg/trp peptides inhibit the growth of the two gram positive strains Staphylococcus aureus and Staphylococcus pyogenes, with some individual variations depending on the position of the tryptophans. No inhibition of the gram negative strains Proteus mirabilis or Pseudomonas aeruginosa was noticed. CD indicated that when bound to lipid vesicles one of the peptides forms an α-helical like structure, whereas the other five exhibited rather random coiled structures. LD indicated that all six peptides were somehow aligned parallel with the membrane surface. Our results do not reveal any obvious connection between membrane interaction and antimicrobial effect for the studied peptides. By contrast cell-penetrating properties can be coupled to both the secondary structure and the degree of order of the peptides. © 2012 Elsevier Inc.

  15. Function of heterologous Mycobacterium tuberculosis InhA, a type 2 fatty acid synthase enzyme involved in extending C20 fatty acids to C60-to-C90 mycolic acids, during de novo lipoic acid synthesis in Saccharomyces cerevisiae.

    Science.gov (United States)

    Gurvitz, Aner; Hiltunen, J Kalervo; Kastaniotis, Alexander J

    2008-08-01

    We describe the physiological function of heterologously expressed Mycobacterium tuberculosis InhA during de novo lipoic acid synthesis in yeast (Saccharomyces cerevisiae) mitochondria. InhA, representing 2-trans-enoyl-acyl carrier protein reductase and the target for the front-line antituberculous drug isoniazid, is involved in the activity of dissociative type 2 fatty acid synthase (FASII) that extends associative type 1 fatty acid synthase (FASI)-derived C(20) fatty acids to form C(60)-to-C(90) mycolic acids. Mycolic acids are major constituents of the protective layer around the pathogen that contribute to virulence and resistance to certain antimicrobials. Unlike FASI, FASII is thought to be incapable of de novo biosynthesis of fatty acids. Here, the genes for InhA (Rv1484) and four similar proteins (Rv0927c, Rv3485c, Rv3530c, and Rv3559c) were expressed in S. cerevisiae etr1Delta cells lacking mitochondrial 2-trans-enoyl-thioester reductase activity. The phenotype of the yeast mutants includes the inability to produce sufficient levels of lipoic acid, form mitochondrial cytochromes, respire, or grow on nonfermentable carbon sources. Yeast etr1Delta cells expressing mitochondrial InhA were able to respire, grow on glycerol, and produce lipoic acid. Commensurate with a role in mitochondrial de novo fatty acid biosynthesis, InhA could accept in vivo much shorter acyl-thioesters (C(4) to C(8)) than was previously thought (>C(12)). Moreover, InhA functioned in the absence of AcpM or protein-protein interactions with its native FASII partners KasA, KasB, FabD, and FabH. None of the four proteins similar to InhA complemented the yeast mutant phenotype. We discuss the implications of our findings with reference to lipoic acid synthesis in M. tuberculosis and the potential use of yeast FASII mutants for investigating the physiological function of drug-targeted pathogen enzymes involved in fatty acid biosynthesis.

  16. The de novo synthesis of numerous proteins is decreased during vitamin D3 deficiency and is gradually restored by 1, 25-dihydroxyvitamin D3 repletion in the islets of langerhans of rats.

    Science.gov (United States)

    Bourlon, P M; Faure-Dussert, A; Billaudel, B

    1999-07-01

    Since both the release and de novo biosynthesis of insulin are severely decreased by vitamin D3 deficiency and improved by 1, 25-dihydroxyvitamin D3 (1,25(OH)2D3) repletion following a 6-h delay in the rat, the present experiments investigated the effects of vitamin D3 deficiency on the biosynthesis of heavier molecular weight proteins using electrophoretic separation. Gel protein staining by Coomassie blue showed very different profiles for islets protein production from 4-week vitamin D3-deficient rats compared with normal islets. The pattern was characterised by a decrease in high molecular weight proteins, concomitantly accompanied by an increase in low molecular weight proteins. This tendency was partially reversed in vivo by 1,25(OH)2D3 repletion treatment for 7 days and was evident after only 16 h of treatment. In parallel with these in vivo observations, which represent a static index of islets protein production, a kinetic study was performed in vitro by a double-labelling method allowing us to measure the de novo synthesis of proteins in islets during a strong 16.7 mM glucose stimulation. Comparison of 3H and 14C labelled samples was achieved via coelectrophoresis to avoid experimental artefacts. The study of the ratio of d.p.m. 3H/d.p.m. 14C for each molecular weight protein in islets stimulated by 16.7 mM glucose (versus basal 4.2 mM glucose) showed an increase in the height of certain peaks: 150, 130 and 8.5 kDa. Under the same conditions, islets from 4-week vitamin D3-deficient rats (versus normal islets) presented a large deficit of numerous newly synthesised proteins and particularly those implicated in the response to glucose stimulation. In vitro repletion of 1,25(OH)2D3 tended to reverse, at least in part, the deleterious effect of vitamin D3 deficiency on the de novo protein synthesis of islets but these effects were gradual. Indeed, there was no detectable effect at 2 h incubation, but 1,25(OH)2D3 increased the 60 to 65 kDa, 55 kDa, and 9 to 8

  17. Advances in molecular design and synthesis of regioregular polythiophenes.

    Science.gov (United States)

    Osaka, Itaru; McCullough, Richard D

    2008-09-01

    Regioregular poly(3-alkylthiophene)s (rrP3ATs) are an important class of pi-conjugated polymers that can be used in plastic electronic devices such as solar cells and field-effect transistors. rrP3ATs can be ordered in three dimensions: conformational ordering along the backbone, pi-stacking of flat polymer chains, and lamellar stacking between chains. All of these features lead to the excellent electrical properties of these materials. Creative molecular design and advanced synthesis are critical in controlling the properties of the materials as well as their device performance. This Account reports the advances in molecular design of new functional polythiophenes as well as the associated polymerization methods. Many functionalized regioregular polythiophenes have been designed and synthesized and show fascinating properties such as high conductivity, mobility, chemosensitivity, liquid crystallinity, or chirality. The methods for the synthesis of rrP3ATs are also applicable to other functional side chains. Di- and triblock copolymers consisting of rrP3AT and polyacrylate or polystyrene have also been successfully synthesized, which can facilitate the assembly of the polythiophene segments. The synthesis of rrP3ATs has evolved into a simple and economical system in which the synthesis can be carried out quickly at room temperature and is thus suitable for large-scale manufacturing. Intensive study has revealed that the regioregular polymerization of 3-alkylthiophenes proceeds by a chain-growth mechanism and can be made into a living system. This feature enables precise control of the molecular weight and facile end-group functionalization of the polymer chains, leading to tailor-made regioregular polythiophenes for specific applications. In addition, researchers have recently designed and synthesized regiosymmetric polythiophenesthese are regioregular but not coupled in a head-to-tail fashionby various methods. These reports indicate that these regiosymmetric

  18. Intelligent Agents for Design and Synthesis Environments: My Summary

    Science.gov (United States)

    Norvig, Peter

    1999-01-01

    This presentation gives a summary of intelligent agents for design synthesis environments. We'll start with the conclusions, and work backwards to justify them. First, an important assumption is that agents (whatever they are) are good for software engineering. This is especially true for software that operates in an uncertain, changing environment. The "real world" of physical artifacts is like that: uncertain in what we can measure, changing in that things are always breaking down, and we must interact with non-software entities. The second point is that software engineering techniques can contribute to good design. There may have been a time when we wanted to build simple artifacts containing little or no software. But modern aircraft and spacecraft are complex, and rely on a great deal of software. So better software engineering leads to better designed artifacts, especially when we are designing a series of related artifacts and can amortize the costs of software development. The third point is that agents are especially useful for design tasks, above and beyond their general usefulness for software engineering, and the usefulness of software engineering to design.

  19. Self-repairable polymeric networks: Synthesis and network design

    Science.gov (United States)

    Ghosh, Biswajit

    This dissertation describes the design, synthesis and development of a new class of polymeric networks that exhibit self-repairing properties under UV exposure. It consists of two parts: (a) modification and synthesis of oxetane (OXE), and oxolane (OXO) substituted chitosan (CHI) macromonomer, and (b) design, and synthesis of self-repairing polyurethane (PUR) networks consisting of modified chitosan. Unmodified CHI consisting of acetamide (-NHCOCH3), primary hydroxyl (-OH), and amine (-NH2) functional groups were reacted with OXE or OXO compounds under basic conditions in order to substitute the 1° --OH groups, and at the same time, convert -NHCOCH 3 functionalities into -NH2 groups, while maintaining their un-reacted form to generate OXE/OXO-substituted CHI macromonomer. These substituted CHI macromonomers were incorporated within the PUR backbone by reacting with trifunctional isocyanate in the presence of polyethylene glycol (PEG) and dibutyl tin dilaurate catalyst (DBTDL). Utilizing spectroscopic analysis combined with optical microscopy, these studies showed that the kinetics of self-repair depends on the stoichiometry of the individual entities as well as the time required for self-repairing to occur decrease with increasing OXE quantity within the network. Internal reflection infrared imaging (IRIRI) of OXE/OXO-CHI-PUR networks as well as Raman and Fourier transform IR (FT-IR) studies of OXE/OXO-CHI macromonomers revealed that cationic OXE/OXO ring opening, free radical polyurea (PUA)-to-PUR conversion, along with chair-to-boat conformational changes of CHI backbone are responsible for repairing the damaged network. The network remodeling process, investigated by utilizing micro-thermal analyzer (muTA), revealed that mechanical damage generates small fragments or oligomers within the scratch, therefore glass transition temperature (Tg) decreases, and under UV exposure cross-linking reactions propagate from the bottom of the scratch to the top resulting in

  20. Finite-Element Model-Based Design Synthesis of Axial Flux PMBLDC Motors

    DEFF Research Database (Denmark)

    Fasil, Muhammed; Mijatovic, Nenad; Jensen, Bogi Bech

    2016-01-01

    This paper discusses design synthesis of a permanent magnet brushless DC (PMBLDC) machine using a finite element (FE) model. This work differentiates itself from the past studies by following a synthesis approach, in which many designs that satisfy performance criteria are considered instead...... of a unique solution. The designer can later select a design, based on comparing parameters of the designs, which are critical to the application that the motor will be used. The presented approach makes it easier to define constraints for a design synthesis problem. A detailed description of the setting up...... is demonstrated by designing a segmented axial torus PMBLDC motor for an electric two-wheeler....

  1. Design and synthesis of DNA four-helix bundles

    Energy Technology Data Exchange (ETDEWEB)

    Rangnekar, Abhijit; Gothelf, Kurt V [Department of Chemistry, Centre for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C (Denmark); LaBean, Thomas H, E-mail: kvg@chem.au.dk, E-mail: thl@cs.duke.edu [Department of Chemistry, Duke University, Durham, NC 27708 (United States)

    2011-06-10

    The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

  2. Synthesis and Design of Integrated Process and Water Networks

    DEFF Research Database (Denmark)

    2015-01-01

    possible options with respect to the topology of the process and water networks, leading to Mixed Integer Non Linear Programming (MINLP) problem. A solution strategy to solve the multi-network problem accounts explicitly the interactions between the networks by selecting suitable technologies in order......This work presents the development of a systematic framework for a simultaneous synthesis and design of process and water networks using the superstructure-based optimization approach. In this framework, a new superstructure combining both networks is developed by attempting to consider all...... to transform raw materials into products and produce clean water to be reused in the process at the early stage of design. Since the connection between the process network and the wastewater treatment network is not a straight forward connection, a new converter interval is introduced in order to convert...

  3. Site-specific thermodynamic stability and unfolding of a de novo designed protein structural motif mapped by 13C isotopically edited IR spectroscopy.

    Science.gov (United States)

    Kubelka, Ginka S; Kubelka, Jan

    2014-04-23

    The mechanism of protein folding remains poorly understood, in part due to limited experimental information available about partially folded states. Isotopically edited infrared (IR) spectroscopy has emerged as a promising method for studying protein structural changes with site-specific resolution, but its full potential to systematically probe folding at multiple protein sites has not yet been realized. We have used (13)C isotopically edited IR spectroscopy to investigate the site-specific thermal unfolding at seven different locations in the de novo designed helix-turn-helix protein αtα. As one of the few stable helix-turn-helix motifs, αtα is an excellent model for studying the roles of secondary and tertiary interactions in folding. Circular dichroism (CD) experiments on the full αtα motif and its two peptide fragments show that interhelical tertiary contacts are critical for stabilization of the secondary structure. The site-specific thermal unfolding probed by (13)C isotopically edited IR is likewise consistent with primarily tertiary stabilization of the local structure. The least thermally stable part of the αtα motif is near the turn where the interhelical contacts are rather loose, while the motif's center with best established core packing has the highest stability. Similar correlation between the local thermal stability and tertiary contacts was found previously for a naturally occurring helix-turn-helix motif. These results underline the importance of native-like tertiary stabilizing interactions in folding, in agreement with recent state-of-the art folding simulations as well as simplified, native-centric models.

  4. Molecular mechanism of pancreatic tumor metastasis inhibition by Gd@C82(OH)22 and its implication for de novo design of nanomedicine

    Energy Technology Data Exchange (ETDEWEB)

    Kang, S. -g.; Zhou, G.; Yang, P.; Liu, Y.; Sun, B.; Huynh, T.; Meng, H.; Zhao, L.; Xing, G.; Chen, C.; Zhao, Y.; Zhou, R.

    2012-09-18

    Pancreatic adenocarcinoma is the most lethal of the solid tumors and the fourth-leading cause of cancer-related death in North America. Matrix metalloproteinases (MMPs) have long been targeted as a potential anticancer therapy because of their seminal role in angiogenesis and extracellular matrix (ECM) degradation of tumor survival and invasion. However, the inhibition specificity to MMPs and the molecular-level understanding of the inhibition mechanism remain largely unresolved. Here, we found that endohedral metallofullerenol Gd@C82(OH)22 can successfully inhibit the neoplastic activity with experiments at animal, tissue, and cellular levels. Gd@C82(OH)22 effectively blocks tumor growth in human pancreatic cancer xenografts in a nude mouse model. Enzyme activity assays also show Gd@C82(OH)22 not only suppresses the expression of MMPs but also significantly reduces their activities. We then applied large-scale molecular-dynamics simulations to illustrate the molecular mechanism by studying the Gd@C82(OH)22–MMP-9 interactions in atomic detail. Our data demonstrated that Gd@C82(OH)22 inhibits MMP-9 mainly via an exocite interaction, whereas the well-known zinc catalytic site only plays a minimal role. Steered by nonspecific electrostatic, hydrophobic, and specific hydrogen-bonding interactions, Gd@C82(OH)22 exhibits specific binding modes near the ligand-specificity loop S1', thereby inhibiting MMP-9 activity. Both the suppression of MMP expression and specific binding mode make Gd@C82(OH)22 a potentially more effective nanomedicine for pancreatic cancer than traditional medicines, which usually target the proteolytic sites directly but fail in selective inhibition. Finally, our findings provide insights for de novo design of nanomedicines for fatal diseases such as pancreatic cancer.

  5. Oleanolic Acid Diminishes Liquid Fructose-Induced Fatty Liver in Rats: Role of Modulation of Hepatic Sterol Regulatory Element-Binding Protein-1c-Mediated Expression of Genes Responsible for De Novo Fatty Acid Synthesis

    Directory of Open Access Journals (Sweden)

    Changjin Liu

    2013-01-01

    Full Text Available Oleanolic acid (OA, contained in more than 1620 plants and as an aglycone precursor for naturally occurred and synthesized triterpenoid saponins, is used in China for liver disorders in humans. However, the underlying liver-protecting mechanisms remain largely unknown. Here, we found that treatment of rats with OA (25 mg/kg/day, gavage, once daily over 10 weeks diminished liquid fructose-induced excess hepatic triglyceride accumulation without effect on total energy intake. Attenuation of the increased vacuolization and Oil Red O staining area was evident on histological examination of liver in OA-treated rats. Hepatic gene expression profile demonstrated that OA suppressed fructose-stimulated overexpression of sterol regulatory element-binding protein-(SREBP- 1/1c mRNA and nuclear protein. In accord, overexpression of SREBP-1c-responsive genes responsible for fatty acid synthesis was also downregulated. In contrast, overexpressed nuclear protein of carbohydrate response element-binding protein and its target genes liver pyruvate kinase and microsomal triglyceride transfer protein were not altered. Additionally, OA did not affect expression of peroxisome proliferator-activated receptor-gamma- and -alpha and their target genes. It is concluded that modulation of hepatic SREBP-1c-mediated expression of the genes responsible for de novo fatty acid synthesis plays a pivotal role in OA-elicited diminishment of fructose-induced fatty liver in rats.

  6. Rational design, synthesis, and pharmacological evaluation of 2-azanorbornane-3-exo,5-endo-dicarboxylic acid

    DEFF Research Database (Denmark)

    Bunch, Lennart; Liljefors, Tommy; Greenwood, Jeremy R

    2003-01-01

    The design and synthesis of conformationally restricted analogues of alpha-amino acids is an often used strategy in medicinal chemistry research. Here we present the rational design, synthesis, and pharmacological evaluation of 2-azanorbornane-3-exo,5-endo-dicarboxylic acid (1), a novel conformat......The design and synthesis of conformationally restricted analogues of alpha-amino acids is an often used strategy in medicinal chemistry research. Here we present the rational design, synthesis, and pharmacological evaluation of 2-azanorbornane-3-exo,5-endo-dicarboxylic acid (1), a novel...

  7. Progesterone-receptor antagonists and statins decrease de novo cholesterol synthesis and increase apoptosis in rat and human periovulatory granulosa cells in vitro.

    Science.gov (United States)

    Rung, Emilia; Friberg, P Anders; Shao, Ruijin; Larsson, D G Joakim; Nielsen, Eva Ch; Svensson, Per-Arne; Carlsson, Björn; Carlsson, Lena M S; Billig, Håkan

    2005-03-01

    Progesterone-receptor (PR) stimulation promotes survival in rat and human periovulatory granulosa cells. To investigate the mechanisms involved, periovulatory rat granulosa cells were incubated in vitro with or without the PR-antagonist Org 31710. Org 31710 caused the expected increase in apoptosis, and expression profiling using cDNA microarray analysis revealed regulation of several groups of genes with functional and/or metabolic connections. This regulation included decreased expression of genes involved in follicular rupture, increased stress responses, decreased angiogenesis, and decreased cholesterol synthesis. A decreased cholesterol synthesis was verified in experiments with both rat and human periovulatory granulosa cells treated with the PR-antagonists Org 31710 or RU 486 by measuring incorporation of [14C]acetate into cholesterol, cholesterol ester, and progesterone. Correspondingly, specific inhibition of cholesterol synthesis in periovulatory rat granulosa cells using 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors (lovastatin, mevastatin, or simvastatin) increased apoptosis, measured as DNA fragmentation and caspase-3/7 activity. The increase in apoptosis caused by simvastatin was reversed by addition of the cholesterol synthesis-intermediary mevalonic acid. These results show that PR antagonists reduce cholesterol synthesis in periovulatory granulosa cells and that cholesterol synthesis is important for granulosa cell survival.

  8. Rational design and synthesis of excavated trioctahedral Au nanocrystals

    Science.gov (United States)

    Chen, Qiaoli; Jia, Yanyan; Shen, Wei; Xie, Shuifen; Yang, Yanan; Cao, Zhenming; Xie, Zhaoxiong; Zheng, Lansun

    2015-06-01

    Excavated polyhedral nanostructures, possessing the features of high surface area and well-defined surface structure with a specific crystal facet and avoidance of aggregation, could be one of the best choices for the purpose of reducing consumption and improving performance of noble metals in many application fields. However, the formation of the excavated structures is thermodynamically unfavourable and its rational synthesis is far beyond our knowledge. In this work, taking overgrowth of Pd onto trioctahedral Au nanocrystals as a model, we present a deep insight study for synthesizing an excavated structure relying on the protection role of surfactants under suitable crystal growth kinetics. Based on the abovementioned understanding, we designed a simple and effective strategy to synthesize Au nanocrystals with excavated trioctahedral structure in one step. Due to the novel feature of the excavated structure and exposed high energy {110} facets, excavated trioctahedral Au NCs exhibited optical extinction at the near-infrared region and showed high catalytic activity towards the reduction of p-nitrophenol. Moreover, the synthetic strategy can be extended to the synthesis of excavated Au-Pd alloys.Excavated polyhedral nanostructures, possessing the features of high surface area and well-defined surface structure with a specific crystal facet and avoidance of aggregation, could be one of the best choices for the purpose of reducing consumption and improving performance of noble metals in many application fields. However, the formation of the excavated structures is thermodynamically unfavourable and its rational synthesis is far beyond our knowledge. In this work, taking overgrowth of Pd onto trioctahedral Au nanocrystals as a model, we present a deep insight study for synthesizing an excavated structure relying on the protection role of surfactants under suitable crystal growth kinetics. Based on the abovementioned understanding, we designed a simple and effective

  9. Design and manufacturing interface modelling for manufacturing processes selection and knowledge synthesis in design

    OpenAIRE

    SKANDER, Achraf; Roucoules, Lionel; KLEIN MEYER, Jean-Sébastien

    2008-01-01

    This research is part of the regional French project IFP2R : " Manufacturing constraints integration in rapid prototyped part design " with IFTS (Higher Technical Formation Institute of Charleville Mézières- France).; The research results presented in this paper are related to the specification of a method and models that tackle the problem of manufacturing processes selection and the integration, as soon as possible, of their constraints in the product modelling (i.e. information synthesis)....

  10. Synthesis, design and operation optimization of a marine energy system

    Energy Technology Data Exchange (ETDEWEB)

    Dimopoulos, George G.; Kougioufas, Aristotelis V.; Frangopoulos, Christos A. [National Technical University of Athens, School of Naval Architecture and Marine Engineering, Heroon Polytechniou 9, 157 73 Zografou (Greece)

    2008-02-15

    Recent developments in the global fuel markets imposed the need of increased fuel economy and cost effectiveness of sea-going vessels. Optimization of the ship's total energy system, as a whole, is now a demand of the marine industry sector in order to address the significant increase of installation and operational costs. This study is focused on the synthesis, design and operation optimization of a marine energy system. A realistic example of a cruise liner energy system has been selected. Basic technology options have been identified and a generic energy system model has been constructed. Various configuration options, types of technologies and existence of components have been incorporated in the generic system. In addition, time varying operational requirements for this cruise liner ship have been considered, resulting in a time dependent operation optimization problem. The complete optimization problem has been solved using a novel algorithm, inspired by evolutionary and social behavior metaphors. A parametric analysis with respect to the fuel price demonstrated changes in the optimum synthesis of the system. (author)

  11. Design of new carbonaceous catalysts and photocatalysts for organic synthesis

    Science.gov (United States)

    Rajpara, Vikul B.

    Pristine and modified carbonaceous materials are introduced as convenient catalysts for oxidation, photooxidation and alkylation of aromatic hydrocarbons. Oxidation reactions have been carried out by air and effect of cyclohexene and light has also been investigated. Availability of the reagents, light source (ambient light), minimum chemical waste, low toxicity and reusability of the catalysts make developed processes green alternatives of traditional methods for the synthesis of industrially important organic compounds. Catalytic performance and selectivity of carbonaceous materials have been linked to their morphology (graphite, carbon black, multi-walled, single-walled carbon nanotubes, fullerene C60) and modification oxidation, conjugation with nanoparticles). The reported study is the first step toward targeted design of new carbonaceous catalysts for organic synthesis. Graphite is known for its electric conductivity and quantum dots are known for transfer of energy to attached molecules and their conjugation may provide a unique hybrid material for photocatalysis of organic reactions. Quantum dots with known number of functional group hold an especially great promise in the field of catalysis. However, controlling the number of functionalities on the surface of quantum dots is very challenging. We demonstrated monofuncationalization of gold nanoparticles using trityl (solid) support. Similar approach was used for the monofunctionalization of quantum dots and our preliminary data showed that quantum dots can be attached and detached from the solid support under mild conditions.

  12. Pb(II) and Hg(II) binding to $\\textit{de novo}$ designed proteins studied by $^{204m}$Pb- and $^{199m}$Hg-Perturbed Angular Correlation of $\\gamma$-rays (PAC) spectroscopy : Clues to heavy metal toxicity

    CERN Multimedia

    2002-01-01

    $\\textit{De novo}$ design of proteins combined with PAC spectroscopy offers a unique and powerful approach to the study of fundamental chemistry of heavy metal-protein interactions, and thus of the mechanisms underlying heavy metal toxicity. In this project we focus on Pb(II) and Hg(II) binding to designed three stranded coiled coil proteins with one or two binding sites, mimicking a variety of naturally occurring thiolate-rich metal ion binding sites in proteins. The $^{204m}$Pb- and $^{199m}$Hg-PAC experiments will complement data already recorded with EXAFS, NMR, UV-Vis and CD spectroscopies.

  13. Towards a framework for modular service design synthesis

    DEFF Research Database (Denmark)

    Løkkegaard, Martin; Mortensen, Niels Henrik; McAloone, Tim C.

    2016-01-01

    , and there is scope for an explicit definition of elements related to the development of modular service platforms and architectures. A study of the existing literature, combined with a comprehensive case study in a global engineering consultancy, has created the basis for development and evaluation of the conceptual......This paper seeks to improve the understanding of how service-based companies can benefit from developing and delivering service offerings from a standardised core of service modules, which are organised through a service architecture. Research within the field is relatively sparse...... model for modular service design synthesis presented in this paper. The case study is based on internal documentation and a high level of interview data. Inductive research methods have been used for the analysis. The presented conceptual model defines three suggested dimensions (Market Segmentation...

  14. Optimization of MCM-48 synthesis using factorial design

    Energy Technology Data Exchange (ETDEWEB)

    Nascimento, A.R. do; Medeiros, R.L.B. de A.; Melo, M. A. de F.; Melo, D.M. de A. [Universitdade Federal do Rio Grande do Norte (UFRN), Natal (Brazil); Souza, M.J.B. de, E-mail: ale3ufs@yahoo.com.br [Universidade Federal de Sergipe (UFS), Sao Cristovao (Brazil)

    2016-10-15

    MCM-48 mesoporous materials were hydrothermally synthesized according to the 2{sup 2} factorial design by varying the crystallization time and temperature of the synthesis gel, and characterized by means of X-ray diffraction analysis and adsorption of N{sub 2} . In the crystallization temperature and time conditions used, specific areas between 924 to 1102 m{sup 2}.g{sup -1}, pore volumes between 0.015 to 0.087 cm{sup 3}.g{sup -1} and pore diameters between 3.2 to 4.0 nm were obtained. It was observed that for the syntheses performed at high temperature, the crystallization time should be reduced so that the material structure is formed. (author)

  15. The Immucillins: Design, Synthesis and Application of Transition- State Analogues.

    Science.gov (United States)

    Evans, Gary B; Schramm, Vern L; Tyler, Peter C

    2015-01-01

    Transition-state analysis based on kinetic isotope effects and computational chemistry provides electrostatic potential maps to serve as blueprints for the design and chemical synthesis of transition-state analogues. The utility of these molecules is exemplified by potential clinical applications toward leukemia, autoimmune disorders, gout, solid tumors, bacterial quorum sensing and bacterial antibiotics. In some cases, transition-state analogues have chemical features that have allowed them to be repurposed for new indications, including potential antiviral use. Three compounds from this family have entered clinical trials. The transition-state analogues bind to their target proteins with high affinity and specificity. The physical and structural properties of binding teach valuable and often surprising lessons about the nature of tight-binding inhibitors.

  16. Synthesis and Design of a Sustainable CO2 Utilization Network

    DEFF Research Database (Denmark)

    Frauzem, Rebecca; Gani, Rafiqul

    In response to increasing regulations and concern about the impact of greenhouse gases on the environment, carbon dioxide (CO2) emissions are targeted for reduction. One method is the conversion of CO2 to useful compounds via chemical reactions. However, conversion is still in its infancy...... a superstructure-based approach a network of utilization alternatives is created linking CO2 and other raw materials with various products using processing blocks. This will then be optimized and verified for sustainability. Detailed design has also been performed for a case study on the methanol synthesis...... processing block. CO2 conversion processes show promise as an additional method for the sustainable reduction of CO2 emissions....

  17. Working mechanism of immunoglobulin A1 (IgA1) protease: cleavage of IgA1 antibody to Neisseria meningitidis PorA requires de novo synthesis of IgA1 Protease

    DEFF Research Database (Denmark)

    Vidarsson, G; Overbeeke, N; Stemerding, AM

    2005-01-01

    Neisseria meningitidis secretes a protease that specifically cleaves the hinge region of immunoglobulin A1 (IgA1), releasing the effector (Fc) domain of IgA1 from the antigen binding (Fab) determinants. Theoretically, the remaining Fab fragments can block pathogen receptors or toxins and still....... No cleavage of IgA1 was found on an isogenic H44/76 strain lacking IgA1 protease. Furthermore, our data indicate that PorA-bound IgA1 is masked by the serogroup B polysaccharide capsule, rendering the IgA1 less accessible to degradation by secreted IgA1 protease present in the bacterial surroundings....... Experiments with protein synthesis inhibitors showed that de novo production of IgA1 protease was responsible for cleavage of PorA-bound IgA1 on encapsulated bacteria. Finally, our data suggest that cleavage of IgA1 by IgA1 protease releases a significant proportion of Fab fragments from the bacterium...

  18. Stimulation of de novo synthesis of L-phenylalanine ammonia-lyase in relation to phytoalexin accumulation in Colletotrichum lindemuthianum elicitor-treated cell suspension cultures of french bean (Phaseolus vulgaris).

    Science.gov (United States)

    Dixon, R A; Lamb, C J

    1979-09-03

    (1) The regulation of the accumulation of the isoflavonoid-derived phytoalexin phaseollin in cell suspension cultures of Dwarf French Bean (Phaseolus vulgaris/ has been investigated. (2) An elicitor preparation from cell walls of Colletotrichum lindemuthianum, the causal agent of anthracnose disease of French bean, caused a marked accumulation of phaseollin in the cultures. The elicitor induced phaseollin accumulation to a level of 60% that obtained with the artificial elicitor autoclaved ribonuclease A and was maximally active at a concentration (weight basis) of at least 50 times lower than required for maximal response to ribonuclease. (3) Elicitor preparations from cell walls of Phytophthora megasperma var. sojae, a fungal pathogen of soybean, and Botrytis cinerea, the common grey mould, were much less effective than the C. lindemuthianum wall-released elicitor. (4) There was a marked but transient increase in the extractable activity of phenylalanine ammonia-lyase, the enzyme catalysing the first reaction in the biosynthesis of phaseollin from L-phenylalanine, in response to the elicitor from C. lindemuthianum. (5) Comparative density labelling with 2H from 2H2O indicated that the elicitor stimulates de novo synthesis of phenylalanine ammonie findings provide the basis of a scheme for elicitor induction of phytoalexin accumulation.

  19. De novo purine biosynthesis by two pathways in Burkitt lymphoma cells and in human spleen.

    Science.gov (United States)

    Reem, G H

    1972-05-01

    This study was designed to answer the question whether human lymphocytes and spleen cells were capable of de novo purine biosynthesis. Experiments were carried out in cell-free extracts prepared from human spleen, and from a cell line established from Burkitt lymphoma. Burkitt lymphoma cells and human spleen cells could synthesize the first and second intermediates of the purine biosynthetic pathway. Cell-free extracts of all cell lines studied contained the enzyme systems which catalyze the synthesis of phosphoribosyl-1-amine, the first intermediate unique to the purine biosynthetic pathway and of phosphoribosyl glycinamide, the second intermediate of this pathway. Phosphoribosyl-1-amine could be synthesized in cell-free extracts from alpha-5-phosphoribosyl-1-pyrophosphate (PRPP) and glutamine, from PRPP and ammonia, and by an alternative pathway, directly from ribose-5-phosphate and ammonia. These findings suggest that extrahepatic tissues may be an important source for the de novo synthesis of purine ribonucleotide in man. They also indicate that ammonia may play an important role in purine biosynthesis. The alternative pathway for the synthesis of phosphoribosyl-1-amine from ribose-5-phosphate and ammonia was found to be subject to inhibition by the end products of the purine synthetic pathway, particularly by adenylic acid and to a lesser degree by guanylic acid. The alternative pathway for phosphoribosyl-1-amine synthesis from ribose-5-phosphate and ammonia may contribute significantly towards the regulation of the rate of de novo purine biosynthesis in the normal state, in metabolic disorders in which purines are excessively produced and in myeloproliferative diseases.

  20. Modular Engineering Concept at Novo Nordisk Engineering

    DEFF Research Database (Denmark)

    Moelgaard, Gert; Miller, Thomas Dedenroth

    1997-01-01

    This report describes the concept of a new engineering method at Novo Nordisk Engineering: Modular Engineering (ME). Three tools are designed to support project phases with different levels of detailing and abstraction. ME supports a standard, cross-functional breakdown of projects that facilitates...

  1. Modular Engineering Concept at Novo Nordisk Engineering

    DEFF Research Database (Denmark)

    Moelgaard, Gert; Miller, Thomas Dedenroth

    1997-01-01

    This report describes the concept of a new engineering method at Novo Nordisk Engineering: Modular Engineering (ME). Three tools are designed to support project phases with different levels of detailing and abstraction. ME supports a standard, cross-functional breakdown of projects that facilitates...

  2. Degradation and de novo synthesis of D1 protein and psbA transcript in reinhardtii during UV-B inactivation of photosynthesis

    Indian Academy of Sciences (India)

    Ratnesh Haturvedi; Adhey Hyam

    2000-03-01

    UV-B induces intensity and time dependent inhibition of photosynthetic O evolution and PS II electron transport Chlamydomonas reinhardtii chloroplast membranes are rapidly and essential for the repair of damaged PS II as chloramphenicol accelerated UV-B inactivation of photosynthesis and psb for the D1 protein. Cells showing 72% inhibition of PS II protein. This shows that synthesis of D1 protein is not the only component involved in the recovery process. Our events, which in turn may limit the repair of damaged PS II.

  3. Cobalt-based Magnetic Nanoparticles: Design, Synthesis and Characterization

    Science.gov (United States)

    Zamanpour, Mehdi

    magnet is also reported. To synthesize MnAlC-FeCo, mechanical alloying and dry mixing of MnAlC and FeCo nanoparticles are accomplished followed by annealing in a furnace. Morphological and magnetic properties of the nanoparticles are obtained by scanning electron microscopy (SEM), x-ray diffractometry (XRD), vibrating sample magnetometry (VSM) and physical property measuring system (PPMS) magnetometry, respectively. Overall, the achieved results in this work enable synthesis of high moment FeCo and high coercivity CoxC with desired structure and magnetic properties obtained through polyol method. In particular, this Dissertation provides the technique to fabricate cobalt carbide nanoparticles without using rare earth elements as a catalyst or as heterogeneous seed nuclei at any stage: pre-processing, synthesis and post-processing. Although the experimental results of this work suggest successful fabrication of desired materials, there are many unanswered questions and unresolved challenges regarding reaction mechanism and optimizing the magnetic properties of these materials. Therefore, some recommendations are provided at the end of this Dissertation for further studies and future work. It should be noted that, implementing first principal calculations on these particles will provide better explanations and enable prediction of structure and magnetic properties of the nanoparticles and facilitate designing more complex heterostructures.

  4. Design, synthesis, characterization and study of novel conjugated polymers

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Wu [Iowa State Univ., Ames, IA (United States)

    1997-06-24

    After introducing the subject of conjugated polymers, the thesis has three sections each containing a literature survey, results and discussion, conclusions, and experimental methods on the following: synthesis, characterization of electroluminescent polymers containing conjugated aryl, olefinic, thiophene and acetylenic units and their studies for use in light-emitting diodes; synthesis, characterization and study of conjugated polymers containing silole unit in the main chain; and synthesis, characterization and study of silicon-bridged and butadiene-linked polythiophenes.

  5. Synthesis and characterization of new methacrylate based hydrogels Síntese e caracterização de novos hidrogéis à base de metacrilato

    Directory of Open Access Journals (Sweden)

    Paula Ferreira

    2006-09-01

    Full Text Available Hydrogels have been used for several applications, including production of contact lenses, sanitary products and materials for wound dressing. The aim of this work was the development of new methacrylate based hydrogels. These materials present the advantage of being easily produced with different compositions and consequently different permeability and diffusion patterns. Therefore it becomes possible to synthesize hydrogels that can be used to immobilize a variety of compounds, such as drugs, proteins or even cells. During this work new polymers based on methacrylate monomers were prepared. Their characterization was accomplished by several techniques, e.g. Fourier Transform Infrared Spectroscopy (FTIR, swelling measurement, Differential Scanning Calorimetry (DSC and evaluation of mechanical properties. Their subacute subcutaneous toxicity was also evaluated by using Wistar rats.Hidrogéis têm sido utilizados para diversas aplicações, incluindo produção de lentes de contato, produtos sanitários e materiais para encerramento de ferimentos. O objetivo deste trabalho consistiu no desenvolvimento de novos hidrogéis a base de metacrilato. Estes materiais apresentam a vantagem de serem facilmente produzidos com diferentes composições e conseqüentemente com distintas permeabilidades e padrões de difusão. Por este motivo, torna-se possível sintetizar hidrogéis que possam ser usados para imobilizar uma grande variedade de compostos, tais como fármacos, proteínas ou mesmo células e tecidos. Neste trabalho foram preparados diferentes polímeros baseados em monômeros de metacrilato. A sua caracterização foi realizada através de diferentes técnicas, como Espectroscopia no Infravermelho com Transformada de Fourier (FTIR, avaliação da capacidade de intumescimento, Calorimetria Diferencial de Varredura (DSC e avaliação das propriedades mecânicas. A sua toxicidade subaguda subcutânea foi também determinada utilizando ratos Wistar.

  6. Design and synthesis of biotin analogues reversibly binding with streptavidin.

    Science.gov (United States)

    Yamamoto, Tomohiro; Aoki, Kiyoshi; Sugiyama, Akira; Doi, Hirofumi; Kodama, Tatsuhiko; Shimizu, Yohei; Kanai, Motomu

    2015-04-01

    Two new biotin analogues, biotin carbonate 5 and biotin carbamate 6, have been synthesized. These molecules were designed to reversibly bind with streptavidin by replacing the hydrogen-bond donor NH group(s) of biotin's cyclic urea moiety with oxygen. Biotin carbonate 5 was synthesized from L-arabinose (7), which furnishes the desired stereochemistry at the 3,4-cis-dihydroxy groups, in 11% overall yield (over 10 steps). Synthesis of biotin carbamate 6 was accomplished from L-cysteine-derived chiral aldehyde 33 in 11% overall yield (over 7 steps). Surface plasmon resonance analysis of water-soluble biotin carbonate analogue 46 and biotin carbamate analogue 47 revealed that KD values of these compounds for binding to streptavidin were 6.7×10(-6)  M and 1.7×10(-10)  M, respectively. These values were remarkably greater than that of biotin (KD =10(-15)  M), and thus indicate the importance of the nitrogen atoms for the strong binding between biotin and streptavidin.

  7. Um novo procedimento de síntese da zeólita A empregando argilas naturais A new procedure for a zeolite synthesis from natural clays

    Directory of Open Access Journals (Sweden)

    Reus T. Rigo

    2009-01-01

    Full Text Available This work proposes the synthesis of zeolite A by IZA standard proceedures starting from a natural clay. The clay was used in its natural form and after calcination at 900ºC. The resulting materials were characterized by X-ray diffraction (XRD, scanning electron microscopy (SEM and porosity analysis by nitrogen adsorption. Results showed low surface area for Na-A zeolite in sodium form, but a higher one in CaA based on the nitrogen accessibility. The presence of cubic crystals for the A phase was observed in the SEM micrographies. The new procedure starting from natural clay favors the formation of sodalite while that using the calcinated clay gives A.

  8. Enabling Lean Design Through Computer Aided Synthesis: The Injection Moulding Cooling Case

    NARCIS (Netherlands)

    Jauregui Becker, Juan M.; Wits, Wessel W.

    2015-01-01

    This paper explores the application of Computer Aided Synthesis (CAS) to support the implementation of Set-Based Concurrent Engineering (SBCE) and Just In Time Decision Making (JIT-DM), which are considered as two of the cornerstones of the Lean Design method. Computer Aided Synthesis refers to a ne

  9. Integration of thermodynamic insights and MINLP optimisation for the synthesis, design and analysis of process flowsheets

    DEFF Research Database (Denmark)

    Hostrup, Martin; Gani, Rafiqul; Kravanja, Zdravko;

    1999-01-01

    This paper presents an integrated approach to the solution of process synthesis, design and analysis problems. Integration is achieved by combining two different techniques, synthesis based on thermodynamic insights and structural optimization together with a simulation engine and a properties...... prediction package. Results from three case studies, highlighting different features of the integrated approach, are presented....

  10. Low Power Design with High-Level Power Estimation and Power-Aware Synthesis

    CERN Document Server

    Ahuja, Sumit; Shukla, Sandeep Kumar

    2012-01-01

    Low-power ASIC/FPGA based designs are important due to the need for extended battery life, reduced form factor, and lower packaging and cooling costs for electronic devices. These products require fast turnaround time because of the increasing demand for handheld electronic devices such as cell-phones, PDAs and high performance machines for data centers. To achieve short time to market, design flows must facilitate a much shortened time-to-product requirement. High-level modeling, architectural exploration and direct synthesis of design from high level description enable this design process. This book presents novel research techniques, algorithms,methodologies and experimental results for high level power estimation and power aware high-level synthesis. Readers will learn to apply such techniques to enable design flows resulting in shorter time to market and successful low power ASIC/FPGA design. Integrates power estimation and reduction for high level synthesis, with low-power, high-level design; Shows spec...

  11. A Behavioral Synthesis Frontend to the Haste/TiDE Design Flow

    DEFF Research Database (Denmark)

    Nielsen, Sune Fallgaard; Sparsø, Jens; Jensen, Jonas Braband;

    2009-01-01

    This paper presents a complete design tool which performs automatic behavioral synthesis of asynchronous circuits (resource sharing, scheduling and binding). The tool targets a traditional control-datapath-style template architecture. Within the limitations set by this template architecture...

  12. Automated design synthesis of robotic/human workcells for improved manufacturing system design in hazardous environments

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Joshua M. [Los Alamos National Laboratory

    2012-06-12

    Manufacturing tasks that are deemed too hazardous for workers require the use of automation, robotics, and/or other remote handling tools. The associated hazards may be radiological or nonradiological, and based on the characteristics of the environment and processing, a design may necessitate robotic labor, human labor, or both. There are also other factors such as cost, ergonomics, maintenance, and efficiency that also effect task allocation and other design choices. Handling the tradeoffs of these factors can be complex, and lack of experience can be an issue when trying to determine if and what feasible automation/robotics options exist. To address this problem, we utilize common engineering design approaches adapted more for manufacturing system design in hazardous environments. We limit our scope to the conceptual and embodiment design stages, specifically a computational algorithm for concept generation and early design evaluation. In regard to concept generation, we first develop the functional model or function structure for the process, using the common 'verb-noun' format for describing function. A common language or functional basis for manufacturing was developed and utilized to formalize function descriptions and guide rules for function decomposition. Potential components for embodiment are also grouped in terms of this functional language and are stored in a database. The properties of each component are given as quantitative and qualitative criteria. Operators are also rated for task-relevant criteria which are used to address task compatibility. Through the gathering of process requirements/constraints, construction of the component database, and development of the manufacturing basis and rule set, design knowledge is stored and available for computer use. Thus, once the higher level process functions are defined, the computer can automate the synthesis of new design concepts through alternating steps of embodiment and function structure

  13. Design and Synthesis of Microscale Opto-Magnetic Trapping Handles

    Science.gov (United States)

    Lawson, Joseph L.

    Opto-Magnetic Trapping (OMT) is a novel micromanipulation technology capable of translating particles with nanometer precision and producing forces on the order of pico-Newtons. OMT combines the benefits of optical trapping (OT) to manipulate handle particles in translational directions and magnetic trapping (MT) to provide rotational control. This combined manipulation technology shows promise for applications ranging from novel single molecule force spectroscopy to advanced manufacturing of smart micro or nano structures. Successful OMT requires handles containing material properties amenable to both OT and MT individually. Since these material properties are traditionally exclusive, novel anisotropic handles must be synthesized to accommodate both micromanipulation technologies. This body of research advances the state of the art in micromanipulation technology by addressing the fundamental material incompatibility issues associated with OMT. Novel micro-scale "patchy" handle particles were fabricated using a glancing angle deposition (GLAD) process. Due to their composite design combining dielectric and ferromagnetic materials, these particles successfully demonstrated OMT manipulation. These particles, along with the developed GLAD fabrication process, improve upon the current state of the art by enabling the robust synthesis of a wider range of particle sizes. Furthermore, the magnetic moments of these particles can be more accurately controlled over a wider range including producing magnetic moments grater than is capable with current techniques. A thorough numerical simulation was also conducted to identify the variation of OT performance of these patchy particles with respect to standard dielectric-only OT handles. While variations in trapping location do exist, they were found to be within an acceptable range for OMT applications and are still capable of manipulation with nanometer precision.

  14. Design, Synthesis, and Characterization of High Performance Polymer Electrolytes for Printed Electronics and Energy Storage

    Science.gov (United States)

    2016-03-31

    linked in a second annealing step, thereby providing greatly enhanced toughness. The ABA triblock was a poly(styrene-b- ethylene oxide -b-styrene...AFRL-AFOSR-VA-TR-2016-0168 Design, Synthesis , and Characterization of High Performance Polymer Electrolytes for Printed Electronics and Energy...Sep 2015 4. TITLE AND SUBTITLE Design, Synthesis , and Characterization of High Performance Polymer Electrolytes for Printed Electronics and Energy

  15. Sensitivity to Flg22 Is Modulated by Ligand-Induced Degradation and de Novo Synthesis of the Endogenous Flagellin-Receptor FLAGELLIN-SENSING2[W][OPEN

    Science.gov (United States)

    Smith, John M.; Salamango, Daniel J.; Leslie, Michelle E.; Collins, Carina A.; Heese, Antje

    2014-01-01

    FLAGELLIN-SENSING2 (FLS2) is the plant cell surface receptor that perceives bacterial flagellin or flg22 peptide, initiates flg22-signaling responses, and contributes to bacterial growth restriction. Flg22 elicitation also leads to ligand-induced endocytosis and degradation of FLS2 within 1 h. Why plant cells remove this receptor precisely at the time during which its function is required remains mainly unknown. Here, we assessed in planta flg22-signaling competency in the context of ligand-induced degradation of endogenous FLS2 and chemical interference known to impede flg22-dependent internalization of FLS2 into endocytic vesicles. Within 1 h after an initial flg22 treatment, Arabidopsis (Arabidopsis thaliana) leaf tissue was unable to reelicit flg22 signaling in a ligand-, time-, and dose-dependent manner. These results indicate that flg22-induced degradation of endogenous FLS2 may serve to desensitize cells to the same stimulus (homologous desensitization), likely to prevent continuous signal output upon repetitive flg22 stimulation. In addition to impeding ligand-induced FLS2 degradation, pretreatment with the vesicular trafficking inhibitors Wortmannin or Tyrphostin A23 impaired flg22-elicited reactive oxygen species production that was partially independent of BRASSINOSTEROID INSENSITIVE1-ASSOCIATED KINASE1. Interestingly, these inhibitors did not affect flg22-induced mitogen-activated protein kinase phosphorylation, indicating the ability to utilize vesicular trafficking inhibitors to target different flg22-signaling responses. For Tyrphostin A23, reduced flg22-induced reactive oxygen species could be separated from the defect in FLS2 degradation. At later times (>2 h) after the initial flg22 elicitation, recovery of FLS2 protein levels positively correlated with resensitization to flg22, indicating that flg22-induced new synthesis of FLS2 may prepare cells for a new round of monitoring the environment for flg22. PMID:24220680

  16. Structure and models of artifactual routine design problems for computational synthesis

    NARCIS (Netherlands)

    Jauregui Becker, J.M.; Tragter, H.; Houten, van F.J.A.M.

    2009-01-01

    Computational synthesis (CS) researches the automatic generation of solutions to design problems. The aim is to shorten design times and present the user with multiple design solutions. However, initializing a new CS process has not received much attention in literature. With this motivation, this p

  17. Uncertainty analysis in raw material and utility cost of biorefinery synthesis and design

    DEFF Research Database (Denmark)

    Cheali, Peam; Quaglia, Alberto; Gernaey, Krist;

    2014-01-01

    This study presents the impact of uncertain data on the solution obtained by using a superstructure-based optimization approach in synthesis and design of biorefinery processing networks. In the early stages of biorefinery design, many of the data required for the formulation of the design proble...

  18. Macromolecule-Assisted de novo Protein Folding

    Science.gov (United States)

    Choi, Seong Il; Son, Ahyun; Lim, Keo-Heun; Jeong, Hotcherl; Seong, Baik L.

    2012-01-01

    In the processes of protein synthesis and folding, newly synthesized polypeptides are tightly connected to the macromolecules, such as ribosomes, lipid bilayers, or cotranslationally folded domains in multidomain proteins, representing a hallmark of de novo protein folding environments in vivo. Such linkage effects on the aggregation of endogenous polypeptides have been largely neglected, although all these macromolecules have been known to effectively and robustly solubilize their linked heterologous proteins in fusion or display technology. Thus, their roles in the aggregation of linked endogenous polypeptides need to be elucidated and incorporated into the mechanisms of de novo protein folding in vivo. In the classic hydrophobic interaction-based stabilizing mechanism underlying the molecular chaperone-assisted protein folding, it has been assumed that the macromolecules connected through a simple linkage without hydrophobic interactions and conformational changes would make no effect on the aggregation of their linked polypeptide chains. However, an increasing line of evidence indicates that the intrinsic properties of soluble macromolecules, especially their surface charges and excluded volume, could be important and universal factors for stabilizing their linked polypeptides against aggregation. Taken together, these macromolecules could act as folding helpers by keeping their linked nascent chains in a folding-competent state. The folding assistance provided by these macromolecules in the linkage context would give new insights into de novo protein folding inside the cell. PMID:22949867

  19. Procafd: Computer Aided Tool for Synthesis-Design & Analysis of Chemical Process Flowsheets

    DEFF Research Database (Denmark)

    Kumar Tula, Anjan; Eden, Mario R.; Gani, Rafiqul

    2015-01-01

    In practice, chemical process synthesis-design involves identification of the processing route to reach a desired product from a specified set of raw materials, design of the operations involved in the processing route, the calculations of utility requirements, the calculations of waste...... are synthesized to form molecules in computer-aided molecular design (CAMD) techniques [4]. The main idea here was to apply the principle of group-contribution approach from chemical property estimation to the synthesis and design of chemical process flowsheets. That is, use process-groups representing different...... of mathematical programming techniques, (c) hybrid approach which combine two or more approaches. D’Anterroches [3] proposed a group contribution based hybrid approach to solve the synthesis-design problem where, chemical process flowsheets could be synthesized in the same way as atoms or groups of atoms...

  20. Design and synthesis of mixed oxides nanoparticles for biofuel applications

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Senniang [Iowa State Univ., Ames, IA (United States)

    2010-05-15

    The work in this dissertation presents the synthesis of two mixed metal oxides for biofuel applications and NMR characterization of silica materials. In the chapter 2, high catalytic efficiency of calcium silicate is synthesized for transesterfication of soybean oil to biodisels. Chapter 3 describes the synthesis of a new Rh based catalyst on mesoporous manganese oxides. The new catalyst is found to have higher activity and selectivity towards ethanol. Chapter 4 demonstrates the applications of solid-state Si NMR in the silica materials.

  1. Group Contribution Based Process Flowsheet Synthesis, Design and Modelling

    DEFF Research Database (Denmark)

    Gani, Rafiqul; d'Anterroches, Loïc

    2004-01-01

    This paper presents a process-group-contribution Method to model. simulate and synthesize a flowsheet. The process-group based representation of a flowsheet together with a process "property" model are presented. The process-group based synthesis method is developed on the basis of the computer...

  2. Design and Synthesis of New Breast Cancer Chemotherapeutic Agents

    Science.gov (United States)

    1999-08-01

    of Ingenol," Synlett 1995 , 533-535. 47. H. Li, S. Narasimhulu, L. Havran, J. Winkler, T. Poulos, "Crystal Structure of Cytochrome P-450 Complexed...Müller T: Synlett 1997 1010-1012; b) Furstner A; Langemann K: Synthesis 1997 792-803. [15] Taylor R; Haley H: Tetrahedron Lett. 1997 55:2061-2064 and

  3. Direct Visualization of De novo Lipogenesis in Single Living Cells

    Science.gov (United States)

    Li, Junjie; Cheng, Ji-Xin

    2014-10-01

    Increased de novo lipogenesis is being increasingly recognized as a hallmark of cancer. Despite recent advances in fluorescence microscopy, autoradiography and mass spectrometry, direct observation of de novo lipogenesis in living systems remains to be challenging. Here, by coupling stimulated Raman scattering (SRS) microscopy with isotope labeled glucose, we were able to trace the dynamic metabolism of glucose in single living cells with high spatial-temporal resolution. As the first direct visualization, we observed that glucose was largely utilized for lipid synthesis in pancreatic cancer cells, which occurs at a much lower rate in immortalized normal pancreatic epithelial cells. By inhibition of glycolysis and fatty acid synthase (FAS), the key enzyme for fatty acid synthesis, we confirmed the deuterium labeled lipids in cancer cells were from de novo lipid synthesis. Interestingly, we also found that prostate cancer cells exhibit relatively lower level of de novo lipogenesis, but higher fatty acid uptake compared to pancreatic cancer cells. Together, our results demonstrate a valuable tool to study dynamic lipid metabolism in cancer and other disorders.

  4. Control law design to meet constraints using SYNPAC-synthesis package for active controls

    Science.gov (United States)

    Adams, W. M., Jr.; Tiffany, S. H.

    1982-01-01

    Major features of SYNPAC (Synthesis Package for Active Controls) are described. SYNPAC employs constrained optimization techniques which allow explicit inclusion of design criteria (constraints) in the control law design process. Interrelationships are indicated between this constrained optimization approach, classical and linear quadratic Gaussian design techniques. Results are presented that were obtained by applying SYNPAC to the design of a combined stability augmentation/gust load alleviation control law for the DAST ARW-2.

  5. De novo design of chiral organotin cancer drug candidates: validation of enantiopreferential binding to molecular target DNA and 5'-GMP by UV-visible, fluorescence, (1)H and (31)P NMR.

    Science.gov (United States)

    Arjmand, Farukh; Sharma, Girish Chandra; Sayeed, Fatima; Muddassir, Mohd; Tabassum, Sartaj

    2011-12-02

    N,N-bis[(R-/S-)-1-benzyl-2-ethoxyethane] tin (IV) complexes were synthesized by applying de novo design strategy by the condensation reaction of (R-/S-)2-amino-2-phenylethanol and dibromoethane in presence of dimethyltin dichloride and thoroughly characterized by elemental analysis, conductivity measurements, IR, ESI-MS, (1)H, (13)C and (119)Sn, multinuclear NMR spectroscopy and XRD study. Enantioselective and specific binding profile of R-enantiomer 1 in comparison to S-enantiomer 2 with ultimate molecular target CT-DNA was validated by UV-visible, fluorescence, circular dichroism, (1)H and (31)P NMR techniques. This was further corroborated well by interaction of 1 and 2 with 5'-GMP. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Brain-specific modulation of kynurenic acid synthesis in the rat

    DEFF Research Database (Denmark)

    Gramsbergen, J B; Hodgkins, P S; Rassoulpour, A;

    1997-01-01

    This study was designed to investigate modulatory mechanisms that control the synthesis of the neuroprotective endogenous excitatory amino acid receptor antagonist kynurenate. De novo kynurenate formation was examined in vitro using tissue slices from rat brain, liver, and kidney. In slices from ...

  7. Integration of thermodynamic insights and MINLP optimization for synthesis, design and analysis of process flowsheets

    DEFF Research Database (Denmark)

    Gani, Rafiqul; Hostrup, Martin; Kravanja, Z.

    2001-01-01

    This paper presents an integrated approach to the solution of process synthesis, design and analysis problems. Integration is achieved by combining two different process synthesis techniques, one based on thermodynamic insights and the other based on structural optimisation, together...... with a simulation engine and a properties prediction package. Process flowsheets with or without reaction blocks are considered in this paper. Results from three illustrative case studies, highlighting different features of the integrated approach, are presented. (C) 2001 Elsevier Science Ltd. All rights reserved....

  8. Design and synthesis of ruthenium indenylidene-based catalysts for olefin metathesis

    OpenAIRE

    Urbina-Blanco, César A

    2013-01-01

    As part of a European wide effort to develop metathesis catalysts for use in fine chemical and pharmaceutical compound synthesis, this study focuses on the design and synthesis of ruthenium based catalysts for olefin metathesis. The aim, of this work was simple: to develop new, more active, more stable, easy to synthesise and commercially viable Ruthenium based catalysts, as well trying to rationalize the effect of structural changes on reactivity. Two different approaches w...

  9. Design, Synthesis, and Some Aspects of the Biological Activity of Mitochondria-Targeted Antioxidants.

    Science.gov (United States)

    Korshunova, G A; Shishkina, A V; Skulachev, M V

    2017-07-01

    This review summarizes for the first time data on the design and synthesis of biologically active compounds of a new generation - mitochondria-targeted antioxidants, which are natural (or synthetic) p-benzoquinones conjugated via a lipophilic linker with (triphenyl)phosphonium or ammonium cations with delocalized charge. It also describes the synthesis of mitochondria-targeted antioxidants - uncouplers of oxidative phosphorylation - based on fluorescent dyes.

  10. Design and rationale of the HITTS randomized controlled trial: Effect of High-intensity Interval Training in de novo Heart Transplant Recipients in Scandinavia.

    Science.gov (United States)

    Nytrøen, Kari; Yardley, Marianne; Rolid, Katrine; Bjørkelund, Elisabeth; Karason, Kristjan; Wigh, Julia Philip; Dall, Christian Have; Arora, Satish; Aakhus, Svend; Lunde, Ketil; Solberg, Ole Geir; Gustafsson, Finn; Prescott, Eva Irene Bossano; Gullestad, Lars

    2016-02-01

    There is no consensus on how, when, and at what intensity exercise should be performed and organized after heart transplantation (HTx). Most rehabilitation programs are conducted in HTx centers, which might be impractical and costly. We have recently shown that high-intensity interval training (HIT) is safe, well tolerated, and efficacious in maintenance HTx recipients, but there are no studies among de novo patients, and whether HIT is feasible and superior to moderate training in HTx recipients is unclear. A total of 120 clinically stable HTx recipients older than 18 years will be recruited from 3 Scandinavian HTx centers. Participants are randomized to HIT or moderate training, shortly after surgery. All exercises are supervised in the patients' local communities. Testing at baseline and follow-up includes the following: VO2peak (primary end point), muscle strength, body composition, quality of life, myocardial performance, endothelial function, biomarkers, and progression of cardiac allograft vasculopathy. A subgroup (n = 90) will also be tested at 3-year follow-up to assess long-term effects of exercise. So far, the HIT intervention is well tolerated, without any serious adverse events. We aim to test whether decentralized HIT is feasible, safe, and superior to moderate training, and whether it will lead to significant improvement in exercise capacity and less long-term complications.

  11. Design and synthesis of multipurpose batch plant using a robust scheduling platform

    CSIR Research Space (South Africa)

    Seid, ER

    2013-10-01

    Full Text Available of operating conditions. They are also suitable for producing different products within the same facility. In spite of this advantage, the design, synthesis, and scheduling of multipurpose batch plants can be a challenging task. This paper addresses design...

  12. A generic methodology for processing route synthesis and design based on superstructure optimization

    DEFF Research Database (Denmark)

    Bertran, Maria-Ona; Frauzem, Rebecca; Sanchez-Arcilla, Ana Sofia

    2017-01-01

    In this paper, a systematic framework for novel and sustainable synthesis-design of processing routes is presented along with the associated computer-aided methods and tools. In Stage 1, superstructure optimization is used to determine the optimal processing route(s). In Stage 2, the design issue...

  13. Perspective: Toward "synthesis by design": Exploring atomic correlations during inorganic materials synthesis

    Science.gov (United States)

    Soderholm, L.; Mitchell, J. F.

    2016-05-01

    Synthesis of inorganic extended solids is a critical starting point from which real-world functional materials and their consequent technologies originate. However, unlike the rich mechanistic foundation of organic synthesis, with its underlying rules of assembly (e.g., functional groups and their reactivities), the synthesis of inorganic materials lacks an underpinning of such robust organizing principles. In the latter case, any such rules must account for the diversity of chemical species and bonding motifs inherent to inorganic materials and the potential impact of mass transport on kinetics, among other considerations. Without such assembly rules, there is less understanding, less predictive power, and ultimately less control of properties. Despite such hurdles, developing a mechanistic understanding for synthesis of inorganic extended solids would dramatically impact the range of new material discoveries and resulting new functionalities, warranting a broad call to explore what is possible. Here we discuss our recent approaches toward a mechanistic framework for the synthesis of bulk inorganic extended solids, in which either embryonic atomic correlations or fully developed phases in solutions or melts can be identified and tracked during product selection and crystallization. The approach hinges on the application of high-energy x-rays, with their penetrating power and large Q-range, to explore reaction pathways in situ. We illustrate this process using two examples: directed assembly of Zr clusters in aqueous solution and total phase awareness during crystallization from K-Cu-S melts. These examples provide a glimpse of what we see as a larger vision, in which large scale simulations, data-driven science, and in situ studies of atomic correlations combine to accelerate materials discovery and synthesis, based on the assembly of well-defined, prenucleated atomic correlations.

  14. Sustainable DME synthesis-design with CO2utilization

    DEFF Research Database (Denmark)

    Prasertsri, Weeranut; Frauzem, Rebecca; Suriyapraphadilok, Uthaiporn;

    2016-01-01

    ) dry reforming step, methanol synthesis step, and methanoldehydration step; (B) CO2 hydrogenation step followed by methanol dehydration step;and (C) dry reforming step followed by direct DME synthesis step. Starting with a basecasedesign, the process flow sheets for the three routes are studied......Minimizing CO2 emission, while achieving economic feasibility in CO2 utilization for producing valuable chemicals is a challenging problem, as reported in recent studies.Due to its high Cetane number, clean-burning, and non-toxic, DME is a promising fuelalternative, and therefore, potentially...... valuable chemical that can be produced viathermochemical CO2 conversion reactions. The aim of this study is to identify the mostpromising processing route for sustainable production of DME in terms of CO2 emission, economic indicators and sustainable indicators. The three processing routesare generated: (A...

  15. Design and synthesis of fused tetrahydroisoquinoline-iminoimidazolines.

    Science.gov (United States)

    Moas-Héloire, Valeria; Renault, Nicolas; Batalha, Vania; Arias, Angela Rincon; Marchivie, Mathieu; Yous, Said; Deguine, Noémie; Buée, Luc; Chavatte, Philippe; Blum, David; Lopes, Luisa; Melnyk, Patricia; Agouridas, Laurence

    2015-12-01

    In the aim of identifying new privileged structures, we describe the 5-steps synthesis of cyclic guanidine compounds "tetrahydroisoquinoline-iminoimidazolines" derived from tetrahydroisoquinoline-hydantoin core. In order to evaluate this new minimal structure and the impact of replacing a carbonyle by a guanidine moiety, their affinity towards adenosine receptor A2A was evaluated and compared to those of tetrahydroisoquinoline-hydantoin compounds.

  16. Design and Synthesis of Novel Peptide Nucleic Acid Monomers

    Institute of Scientific and Technical Information of China (English)

    白金泉; 李英; 刘克良

    2001-01-01

    All of the four nucleobases in DNA have replaced the 4-hydroxy group of N-[2-(tert-butoxycarbonylaminomethyl)-trams-4-hydroxy]tetrahydropyrrole acetic acid methyl ester with cis-stereochemistry. An efficient route for the synthesis of N-[2-(tert-butoxycarbonylaminomethyl)-trans-4-hydroxy]-tetrahydropyrrole acetic acid methyl ester has been developed.Starting with this intermediate, the protected monmers were synthesized by the Mitsunobu reaction or via its tosylate.

  17. Application of CAPEC Lipid Property Databases in the Synthesis and Design of Biorefinery Networks

    DEFF Research Database (Denmark)

    Bertran, Maria-Ona; Cunico, Larissa; Gani, Rafiqul

    processes are not. Lipids are present in biorefinery processes: they represent feedstock (vegetable oil, waste cooking oil, microalgal oil), intermediate products (fatty acids, glycerol) and final products in biorefineries, thus the prediction of their properties is of relevance for the synthesis and design......]. The wide variety and complex nature of components in biorefineries poses a challenge with respect to the synthesis and design of these types of processes. Whereas physical and thermodynamic property data or models for petroleum-based processes are widely available, most data and models for biobased...... of biorefinery networks. The objective of this work is to show the application of databases of physical and thermodynamic properties of lipid components to the synthesis and design of biorefinery networks....

  18. Knowledge-based synthesis of custom VLSI physical design tools: First steps

    Science.gov (United States)

    Setliff, Dorothy E.; Rutenbar, Rob A.

    A description is given of how program synthesis techniques can be applied to the synthesis of technology-sensitive VLSI physical design tools. Physical design refers to the process of reducing a structural description of a piece of hardware down to the geometric layout of an integrated circuit. Successful physical design tools must cope with shifting technology and application environments. The goal is to automatically generate a tool's implementation to match the application. The authors describe a synthesis architecture that combines knowledge of the application domain and knowledge of generic programming mechanics. The approach uses a very high-level language to describe algorithms, domain and programming knowledge to select appropriate algorithms and data structures, and code generation to arrive at final executable code. Results are presented detailing the performance and implementation of ELF, a prototype generator for wire-routing applications. Comparisons between a hand-crafted router and an automatically synthesized router are presented.

  19. Design Features Of Microfluidic Reactor For [18F]FDG Radiopharmaceutical Synthesis

    Science.gov (United States)

    Oh, J. H.; Lee, B. N.; Nam, K. R.; Attla, G. A.; Lee, K. C.; Cjai, J. S.

    2011-06-01

    Microfluidic reactor exhibits advantages for radiopharmaceutical synthesis. Microfluidic chips can reduce the time for radiosynthesis using tiny quantities of chemical compounds. It also has a good heat transfer, performance and provides an integrated system including synthesis, separation, and purification. These advantages make FDG production. So we have designed a microreactor chip which included the whole chemical processing; water evaporation, solvent exchange, radiofluorination and so on. It was designed by using a commercial 3D CAD modeling program CATIA V5, heat transfer performance was analyzed by ANSYS, and CFX was used for analyzing fluid performance. This paper described the design of FDG synthesis system on a microchip, the relevant locations of its parts, both heat and fluid performance efficiency analysis.

  20. Systematic methods for synthesis and design of sustainable chemical and biochemical processes

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    , biomass, coal, natural gas, rock, etc., that are usually extracted), to a bigger set of basic chemical products (such as, ethylene, benzene sulfuric acid, ammonia, etc., that are produced in large quantities), to an even bigger set of intermediates (such as, methanol, urea, succinic acid, ethylene glycol...... from the renewable resources, the sustainability of the product and therefore the process can be improved. Also, the number of alternatives that exist provide opportunities and challenges to find the best synthesis routes, for example, for process intensification or a multi-product processing complex...... like a biorefinery. The process synthesis design problem can be formulated as one where first a synthesis-design target (a process with desired qualities) is defined and then design alternatives (process flowsheets for different raw material-product connection) that match the target are identified...

  1. Digital logic design using verilog coding and RTL synthesis

    CERN Document Server

    Taraate, Vaibbhav

    2016-01-01

    This book is designed to serve as a hands-on professional reference with additional utility as a textbook for upper undergraduate and some graduate courses in digital logic design. This book is organized in such a way that that it can describe a number of RTL design scenarios, from simple to complex. The book constructs the logic design story from the fundamentals of logic design to advanced RTL design concepts. Keeping in view the importance of miniaturization today, the book gives practical information on the issues with ASIC RTL design and how to overcome these concerns. It clearly explains how to write an efficient RTL code and how to improve design performance. The book also describes advanced RTL design concepts such as low-power design, multiple clock-domain design, and SOC-based design. The practical orientation of the book makes it ideal for training programs for practicing design engineers and for short-term vocational programs. The contents of the book will also make it a useful read for students a...

  2. Thesis Antithesis And Synthesis Ekslibris Art And Interior Design

    OpenAIRE

    Tomak, Sena; Tomak, Ali

    2016-01-01

    From time to time different fields of art and design can exhibit various similarities and partnerships. This can be seen in the holistic approach or the solution methods for the design problems and human relations during the creation and the evaluation of the concepts about design. This study aimed to develop a thesis related to the correlations and similarities between exlibris and the interior design. Despite various factors and variables in different application areas, this thesis was de...

  3. Design, Synthesis and Biological Evaluation of Quorum Sensing Modulators

    DEFF Research Database (Denmark)

    Hansen, Mette Reimert

    is applied in the coupling of functionalized building blocks. Diversification by functional group pairing was envisioned to provide a diverse range of cyclized products. Triphosgene mediated carbonylative stiching of the 1,2-hydrazido alcohol from the Petasis 3-CR afforded a mixture of oxazolidinone...... and oxadiazolone products. Optimization afforded a method for the selective synthesis of either oxazolidinones or oxadiazolones and a small compound library was synthesized. Ring-closing metathesis of Abstract iv appropriately situated alkene moieties incorporated in the Petasis 3-CR products yielded five...

  4. The influence of heat exchanger design on the synthesis of heat exchanger networks

    Directory of Open Access Journals (Sweden)

    Liporace F.S.

    2000-01-01

    Full Text Available Heat exchanger network (HEN synthesis has been traditionally performed without accounting for a more detailed unit design, which is important since the final HEN may require unfeasible units. Recently, publications on this matter have appeared, as well as softwares that simultaneously perform synthesis and units design. However, these publications do not clearly show the influence of the new added features on the final HEN. Hence, this work aims at showing that units' design can strongly affect the final HEN. Improvements on heat transfer area and total annual cost estimations, which influence the HEN structural evolution, are the main responsible for that. It is also shown the influence of some design bounds settings, which can indicate an unfeasible unit design and, therefore, the need for a new match search or the maintenance of a loop. An example reported in the literature is used to illustrate the discussion.

  5. Design of Digital Synthesis Filters for Hybrid Filter Bank A/D Converters Using Semidefinite Programming

    Directory of Open Access Journals (Sweden)

    Wei Wang

    2014-05-01

    Full Text Available Hybrid filter bank (HFB analog-to-digital systems permit wideband, high frequency conversion. This paper presents mixed norm optimal design of digital synthesis filters of a HFB. The mixed norm is a convex combination of the 2-norm and the Chebyshev norm with a weighting parameter. Robust HFB design method based on worst-case ellipsoidal uncertainty in analog filters errors is also proposed. Both the problems can be solved using semidefinite programming. The proposed mixed norm method allows designers to select the best suitable filters among a family of synthesis filters for specific applications, and the robust design method is more insensitive to analog filters errors than the nominal minimax design

  6. Design of Modern Reactors for Synthesis of Thermally Expanded Graphite

    Science.gov (United States)

    Strativnov, Eugene V.

    2015-05-01

    One of the most progressive trends in the development of modern science and technology is the creation of energy-efficient technologies for the synthesis of nanomaterials. Nanolayered graphite (thermally exfoliated graphite) is one of the key important nanomaterials of carbon origin. Due to its unique properties (chemical and thermal stability, ability to form without a binder, elasticity, etc.), it can be used as an effective absorber of organic substances and a material for seal manufacturing for such important industries as gas transportation and automobile. Thermally expanded graphite is a promising material for the hydrogen and nuclear energy industries. The development of thermally expanded graphite production is resisted by high specific energy consumption during its manufacturing and by some technological difficulties. Therefore, the creation of energy-efficient technology for its production is very promising.

  7. Design of Modern Reactors for Synthesis of Thermally Expanded Graphite.

    Science.gov (United States)

    Strativnov, Eugene V

    2015-12-01

    One of the most progressive trends in the development of modern science and technology is the creation of energy-efficient technologies for the synthesis of nanomaterials. Nanolayered graphite (thermally exfoliated graphite) is one of the key important nanomaterials of carbon origin. Due to its unique properties (chemical and thermal stability, ability to form without a binder, elasticity, etc.), it can be used as an effective absorber of organic substances and a material for seal manufacturing for such important industries as gas transportation and automobile. Thermally expanded graphite is a promising material for the hydrogen and nuclear energy industries. The development of thermally expanded graphite production is resisted by high specific energy consumption during its manufacturing and by some technological difficulties. Therefore, the creation of energy-efficient technology for its production is very promising.

  8. A prototype computerized synthesis methodology for generic space access vehicle (SAV) conceptual design

    Science.gov (United States)

    Huang, Xiao

    2006-04-01

    Today's and especially tomorrow's competitive launch vehicle design environment requires the development of a dedicated generic Space Access Vehicle (SAV) design methodology. A total of 115 industrial, research, and academic aircraft, helicopter, missile, and launch vehicle design synthesis methodologies have been evaluated. As the survey indicates, each synthesis methodology tends to focus on a specific flight vehicle configuration, thus precluding the key capability to systematically compare flight vehicle design alternatives. The aim of the research investigation is to provide decision-making bodies and the practicing engineer a design process and tool box for robust modeling and simulation of flight vehicles where the ultimate performance characteristics may hinge on numerical subtleties. This will enable the designer of a SAV for the first time to consistently compare different classes of SAV configurations on an impartial basis. This dissertation presents the development steps required towards a generic (configuration independent) hands-on flight vehicle conceptual design synthesis methodology. This process is developed such that it can be applied to any flight vehicle class if desired. In the present context, the methodology has been put into operation for the conceptual design of a tourist Space Access Vehicle. The case study illustrates elements of the design methodology & algorithm for the class of Horizontal Takeoff and Horizontal Landing (HTHL) SAVs. The HTHL SAV design application clearly outlines how the conceptual design process can be centrally organized, executed and documented with focus on design transparency, physical understanding and the capability to reproduce results. This approach offers the project lead and creative design team a management process and tool which iteratively refines the individual design logic chosen, leading to mature design methods and algorithms. As illustrated, the HTHL SAV hands-on design methodology offers growth

  9. Design and synthesis of copper-cobalt catalysts for the selective conversion of synthesis gas to ethanol and higher alcohols.

    Science.gov (United States)

    Prieto, Gonzalo; Beijer, Steven; Smith, Miranda L; He, Ming; Au, Yuen; Wang, Zi; Bruce, David A; de Jong, Krijn P; Spivey, James J; de Jongh, Petra E

    2014-06-16

    Combining quantum-mechanical simulations and synthesis tools allows the design of highly efficient CuCo/MoO(x) catalysts for the selective conversion of synthesis gas (CO+H2) into ethanol and higher alcohols, which are of eminent interest for the production of platform chemicals from non-petroleum feedstocks. Density functional theory calculations coupled to microkinetic models identify mixed Cu-Co alloy sites, at Co-enriched surfaces, as ideal for the selective production of long-chain alcohols. Accordingly, a versatile synthesis route is developed based on metal nanoparticle exsolution from a molybdate precursor compound whose crystalline structure isomorphically accommodates Cu(2+) and Co(2+) cations in a wide range of compositions. As revealed by energy-dispersive X-ray nanospectroscopy and temperature-resolved X-ray diffraction, superior mixing of Cu and Co species promotes formation of CuCo alloy nanocrystals after activation, leading to two orders of magnitude higher yield to high alcohols than a benchmark CuCoCr catalyst. Substantiating simulations, the yield to high alcohols is maximized in parallel to the CuCo alloy contribution, for Co-rich surface compositions, for which Cu phase segregation is prevented.

  10. Design and Synthesis of Distillation Systems using a Driving Force Based Approach

    DEFF Research Database (Denmark)

    Bek-Pedersen, Erik; Gani, Rafiqul

    2004-01-01

    A new integrated framework for synthesis, design and operation of distillation-based separation schemes is presented here. This framework is based on the driving force approach, which provides a measure of the differences in chemical/physical properties between two co-existing phases in a separat...

  11. Design and evaluation of a gesture driven wavefield synthesis auditory game

    DEFF Research Database (Denmark)

    Grani, Francesco; Paisa, Razvan; Banas, Jan Stian

    2016-01-01

    An auditory game has been developed as a part of research in Wavefield Synthesis. In order to design and implement this game, a number of technologies have been incorporated in the development process. By pairing motion capture with a WiiMote new dimension of movement input was achieved. We present...... an evaluation study where the game was assessed....

  12. Computer-aided Framework for Synthesis, Design and Retrofit of Wastewater Treatment Plants

    DEFF Research Database (Denmark)

    Bozkurt, Hande

    plant (WWTP) design is a formidable challenge. One of the key steps involved is the process synthesis - defined as the selection of treatment processes as a combination of unit operations and processes to create the process flow diagram.As a consequence of the emerging technological developments...

  13. Design, synthesis and biological activity of novel peptidyl benzyl ketone FVIIa inhibitors

    DEFF Research Database (Denmark)

    Storgaard, Morten; Henriksen, Signe Teuber; Zaragoza, Florencio

    2011-01-01

    Herein is described the synthesis of a novel class of peptidyl FVIIa inhibitors having a C-terminal benzyl ketone group. This class is designed to be potentially suitable as stabilization agents of liquid formulations of rFVIIa, which is a serine protease used for the treatment of hemophilia...

  14. Design and Synthesis of Chiral Molecular Tweezers Based on Deoxycholic Acid

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A series of new chiral molecular tweezers have been designed and synthesized by using deoxycholic acid as spacer and aromatic amines as arms.Instead of using toxic phosgene,the triphosgene was employed in synthesis of the molecular tweezers receptors.These chiral molecular tweezers showed good enantioselectivity for D-amino acid methyl esters.

  15. Phenomena-based Process Synthesis and Design to achieve Process Intensification

    DEFF Research Database (Denmark)

    Lutze, Philip; Gani, Rafiqul; Woodley, John

    2011-01-01

    In order to improve processes incorporating process intensification and to allow them to go beyond pre-defined unit operations, the process has to be viewed at a lower level of aggregation, namely the phenomena scale. In this contribution, an approach for aggregating processes through phenomena...... level. This phenomena-based synthesis/design methodology is tested through a case study....

  16. Design, synthesis, and biological evaluation of potent discodermolide fluorescent and photoaffinity molecular probes.

    Science.gov (United States)

    Smith, Amos B; Rucker, Paul V; Brouard, Ignacio; Freeze, B Scott; Xia, Shujun; Horwitz, Susan Band

    2005-11-10

    [structure: see text] The design, synthesis, and biological evaluation of a series of (+)-discodermolide molecular probes possessing photoaffinity and fluorescent appendages has been achieved. Stereoselective olefin cross-metathesis comprised a key tactic for construction of two of the molecular probes. Three photoaffinity probes were radiolabeled with tritium.

  17. Design, synthesis and biological evaluation of Erythrina alkaloid analogues as neuronal nicotinic acetylcholine receptor antagonists

    DEFF Research Database (Denmark)

    Crestey, François; Jensen, Anders A.; Borch, Morten

    2013-01-01

    The synthesis of a new series of Erythrina alkaloid analogues and their pharmacological characterization at various nicotine acetylcholine receptor (nAChR) subtypes are described. The compounds were designed to be simplified analogues of aromatic erythrinanes with the aim of obtaining subtype...

  18. An Integrated Business and Engineering Framework for Synthesis and Design of Processing Networks

    DEFF Research Database (Denmark)

    Quaglia, Alberto

    The problem of synthesis and design of processing networks corresponds to the generation, evaluation and selection among alternatives with respect to raw materials, process technologies and configurations and product portfolio compositions. This results in a complex and multi-disciplinary problem...

  19. Interdisciplinary Learning for Chemical Engineering Students from Organic Chemistry Synthesis Lab to Reactor Design to Separation

    Science.gov (United States)

    Armstrong, Matt; Comitz, Richard L.; Biaglow, Andrew; Lachance, Russ; Sloop, Joseph

    2008-01-01

    A novel approach to the Chemical Engineering curriculum sequence of courses at West Point enabled our students to experience a much more realistic design process, which more closely replicated a real world scenario. Students conduct the synthesis in the organic chemistry lab, then conduct computer modeling of the reaction with ChemCad and…

  20. Interdisciplinary Learning for Chemical Engineering Students from Organic Chemistry Synthesis Lab to Reactor Design to Separation

    Science.gov (United States)

    Armstrong, Matt; Comitz, Richard L.; Biaglow, Andrew; Lachance, Russ; Sloop, Joseph

    2008-01-01

    A novel approach to the Chemical Engineering curriculum sequence of courses at West Point enabled our students to experience a much more realistic design process, which more closely replicated a real world scenario. Students conduct the synthesis in the organic chemistry lab, then conduct computer modeling of the reaction with ChemCad and…

  1. Design, Synthesis, and Inhibitory Activity of Potent, Photoswitchable Mast Cell Activation Inhibitors

    NARCIS (Netherlands)

    Velema, Willem A.; van der Toorn, Marco; Szymanski, Wiktor; Feringa, Ben L.

    2013-01-01

    Allergic reactions affect millions of people worldwide. The need for new and effective antiallergic agents is evident, and insight into the underlying mechanisms that lead to allergic events is necessary. Herein, we report the design, synthesis, and activity of photoswitchable mast cell activation

  2. Design, synthesis of novel antifungal triazole derivatives with high activities against Aspergillus fumigatus

    Institute of Scientific and Technical Information of China (English)

    Qiu Qin He; Chao Mei Liu; Ke Li; Yong Bing Cao

    2007-01-01

    Based on the active site of Aspergillusfumigatus lanosterol 14α-demethylase (AF-CYP51), novel triazole compounds were designed. Their chemical synthesis and the antifungal activities were reported. The results showed that all the target compounds exhibited excellent activities with broad spectrum; in which compounds 4, 12 and 15 showed comparable activities against A.fumigatus to the control drug itraconazole.

  3. Phenomena-based Process Synthesis and Design to achieve Process Intensification

    DEFF Research Database (Denmark)

    Lutze, Philip; Babi, Deenesh Kavi; Woodley, John

    2012-01-01

    at the lowest level of aggregation: phenomena. Therefore, in this paper, a phenomena-based synthesis/design methodology is presented. Using this methodology, a systematic identification of necessary and desirable (integrated) phenomena as well as generation and screening of phenomena-based flowsheet options...

  4. A General framework for the Synthesis and Operational Design of Batch Processes

    DEFF Research Database (Denmark)

    The objective of this paper is to present a general problem formulation and a general methodlogy for the synthesis of batch operations and the operational design of individual batch processes, such as mixing, reaction and separation. The general methodology described supplies the batch routes...

  5. Design, Synthesis, and Inhibitory Activity of Potent, Photoswitchable Mast Cell Activation Inhibitors

    NARCIS (Netherlands)

    Velema, Willem A.; van der Toorn, Marco; Szymanski, Wiktor; Feringa, Ben L.

    2013-01-01

    Allergic reactions affect millions of people worldwide. The need for new and effective antiallergic agents is evident, and insight into the underlying mechanisms that lead to allergic events is necessary. Herein, we report the design, synthesis, and activity of photoswitchable mast cell activation i

  6. Capturing the essence of organic synthesis: from bioactive natural products to designed molecules in today's medicine.

    Science.gov (United States)

    Ghosh, Arun K

    2010-12-03

    In this Perspective, I outline my group's research involving the chemical syntheses of medicinally important natural products, exploration of their bioactivity, and the development of new asymmetric carbon-carbon bond-forming reactions. This paper also highlights our approach to molecular design and synthesis of conceptually novel inhibitors against target proteins involved in the pathogenesis of human diseases, including AIDS and Alzheimer's disease.

  7. Design, synthesis, and characterization of nucleosomes containing site-specific DNA damage.

    Science.gov (United States)

    Taylor, John-Stephen

    2015-12-01

    How DNA damaged is formed, recognized, and repaired in chromatin is an area of intense study. To better understand the structure activity relationships of damaged chromatin, mono and dinucleosomes containing site-specific damage have been prepared and studied. This review will focus on the design, synthesis, and characterization of model systems of damaged chromatin for structural, physical, and enzymatic studies.

  8. Design and Synthesis of Polypyrazolyl Compounds as a New Type of Versatile Building Blocks

    Institute of Scientific and Technical Information of China (English)

    LI,Sheng-Hui; HUANG,Hai-Ping; YU,Shu-Yan; LI,Xian-Ping

    2006-01-01

    The design and synthesis of novel polypyrazolyl aromatic bridging ligands 1,3,5-tris(3,5-dimethyl-1H-pyrazol-4-yl)benzene and 2,4,6-tris(4-(3,5-dimethyl-1H-pyrazol-4-yl)phenyl)-1,3,5-triazine from simple starting materials mesitylene and p-tolunitrile were reported.

  9. Synthesis and Design of Biorefinery Processing Networks with Uncertainty and Sustainability analysis

    DEFF Research Database (Denmark)

    Cheali, Peam; Gernaey, Krist; Sin, Gürkan

    -criteria assessment including technical, economics and sustainability. The expanded database and superstructure with uncertainty and sustainability analysis form a powerful process synthesis toolbox to be used in design of future biorefineries with multi-criteria evaluation (technical and economic feasibility...... for processing renewable feedstocks, with the aim of bridging the gap for fuel, chemical and material production. This project is focusing on biorefinery network design, in particular for early stage design and development studies. Optimal biorefinery design is a challenging problem. It is a multi...... to support the evaluation of processes and the generation of sustainable alternatives for identifying the optimal processing routes. One particular challenge here is to include proactively sustainability analysis as part of the synthesis of biorefinery networks. Another challenge is the handling of several...

  10. Adaptive subsystem aided design synthesis units REA on minicomputers

    Directory of Open Access Journals (Sweden)

    Yu. F. Zin'kovskii

    1986-04-01

    Full Text Available Questions of construction sub-aided design CAD integrated electronics units based on the principles of adaptation and self-tuning software and mathematical software for solving a specific problem.

  11. Design and Synthesis of Matrix Metalloprotease Photoaffinity Trimodular Probes

    Institute of Scientific and Technical Information of China (English)

    QIU,Wenwei; XU,Jie; LI,Xin; ZHONG,Li; LI,Jingya; LI,Jia; NAN,Fajun

    2009-01-01

    To explore the molecular mechanism of the matrix metalloproteinases (MMPs) in tumor processes,two photoaffinity trimodular probes were designed and synthesized based on the structure activity relationship and the following photoaffinity labelling experiments afforded positive results.

  12. Design, synthesis and computational validation of novel benzimidazole/indole-based PPARα and PPARγ partial agonists

    Indian Academy of Sciences (India)

    Raman K Verma; Prithwish Ghosh; Vijay Kumar; Lalit K Wadhwa

    2013-11-01

    The design and synthesis of benzimidazolyl and indolyl linked -alkoxy phenylpropanoic acid derivatives and the -keto ester analogues in an effort to develop novel peroxisome proliferator activated receptors ligands expected to exhibit PPAR and PPAR partial agonism in the management of hyperglycemia and hyperlipidemia for the treatment of type 2 diabetes is reported. Computational validation of the designed molecules through activity prediction and docking studies showed expected results.

  13. Design, synthesis, and biological evaluation of CXCR4 ligands.

    Science.gov (United States)

    Mona, Christine E; Besserer-Offroy, Élie; Cabana, Jérôme; Leduc, Richard; Lavigne, Pierre; Heveker, Nikolaus; Marsault, Éric; Escher, Emanuel

    2016-11-02

    A combination of the CXCR4 inverse agonist T140 with N-terminal CXCL12 oligopeptides has produced the first nanomolar synthetic CXCR4 agonists. In these agonists, the inverse agonistic portion provides affinity whereas the N-terminal CXCL12 sequence induces receptor activation. Several CXCR4 crystal structures exist with either CVX15, an inverse agonist closely related to T140 and IT1t, a small molecule; we therefore attempted to produce another CXCL12 oligopeptide combination with IT1t. For this purpose, a primary amino group was introduced by total synthesis into one of the methyl groups of IT1t, serving as an anchoring point for the oligopeptide graft. The introduction of the oligopeptides on this analog however yielded antagonists, one compound displaying high affinity. On the other hand, the amino-substituted analogue itself proved to be an inverse agonist with a binding affinity of 2.6 nM compared to 11.5 nM for IT1t. This IT1t-like analog is hitherto one of the most potent non-peptidic CXCR4 inverse agonists reported.

  14. Design, synthesis and antibacterial activity of new phthalazinedione derivatives

    Directory of Open Access Journals (Sweden)

    ABD EL-GALIL M. KHALIL

    2011-03-01

    Full Text Available Dibenzobarallene (1 was utilized as the key intermediate for the synthesis of some new 2-substituted 1,4-dioxo-3,4,4a,5,10,10a-hexahydro-1H-5,10-[1’,2’]-benzenobenzo[g]phthalazine: 2, 5a–d, 8a–c and 10. Condensation of 2 with benzaldehyde or anisaldehyde gave the corresponding acrylonitrile derivatives 3a and b, respectively. Thiophene derivatives 4a and b were obtained via the Gewald reaction of 2 with cyclohexanone or cyclopentanone, respectively. Treatment of 5d with acetyl chloride or p-toluenesulfonyl chloride afforded the corresponding esters 6 and 7, respectively. Cyclization of 8a–c with formalin afforded the corresponding triazine derivatives 9a–c. Ring opening of 10 with sodium hydroxide gave the corresponding triazole derivative 11, which when alkylated with pentyl bromide afforded the pentylthio derivative 12. Representative compounds of the synthesized products were established and evaluated as antibacterial agents.

  15. Design and Synthesis of Triangulated DNA Origami Trusses.

    Science.gov (United States)

    Matthies, Michael; Agarwal, Nayan P; Schmidt, Thorsten L

    2016-03-01

    DNA nanotechnology offers unique control over matter on the nanoscale. Here, we extend the DNA origami method to cover a range of wireframe truss structures composed of equilateral triangles, which use less material per volume than standard multiple-helix bundles. From a flat truss design, we folded tetrahedral, octahedral, or irregular dodecahedral trusses by exchanging few connector strands. Other than standard origami designs, the trusses can be folded in low-salt buffers that make them compatible with cell culture buffers. The structures also have defined cavities that may in the future be used to precisely position functional elements such as metallic nanoparticles or enzymes. Our graph routing program and a simple design pipeline will enable other laboratories to make use of this valuable and potent new construction principle for DNA-based nanoengineering.

  16. Design of Reversible Sequential Circuit Using Reversible Logic Synthesis

    Directory of Open Access Journals (Sweden)

    Md. Belayet Ali

    2011-12-01

    Full Text Available Reversible logic is one of the most vital issue at present time and it has different areas for its application,those are low power CMOS, quantum computing, nanotechnology, cryptography, optical computing, DNA computing, digital signal processing (DSP, quantum dot cellular auto meta, communication, computer graphics. It is not possible to realize quantum computing without implementation of reversible logic. The main purposes of designing reversible logic are to decrease quantum cost, depth of the circuits and the number of garbage outputs. In this paper, we have proposed a new reversible gate. And we have designed RS flip flop and D flip flop by using our proposed gate and Peres gate. The proposed designs are better than the existing proposed ones in terms of number of reversible gates and garbage outputs. So, this realization is more efficient and less costly than other realizations.

  17. Design of Reversible Sequential Circuit Using Reversible Logic Synthesis

    Directory of Open Access Journals (Sweden)

    Md. Mosharof Hossin

    2012-01-01

    Full Text Available Reversible logic is one of the most vital issue at present time and it has different areas for its application, those are low power CMOS, quantum computing, nanotechnology, cryptography, optical computing, DNA computing, digital signal processing (DSP, quantum dot cellular automata, communication, computer graphics. It is not possible to realize quantum computing without implementation of reversible logic. The main purposes of designing reversible logic are to decrease quantum cost, depth of the circuits and the number of garbage outputs. In this paper, we have proposed a new reversible gate. And we have designedRS flip flop and D flip flop by using our proposed gate and Peres gate. The proposed designs are better than the existing proposed ones in terms of number of reversible gates and garbage outputs. So, this realization is more efficient and less costly than other realizations.

  18. Pfizer Global Virtual Library (PGVL): a chemistry design tool powered by experimentally validated parallel synthesis information.

    Science.gov (United States)

    Hu, Qiyue; Peng, Zhengwei; Sutton, Scott C; Na, Jim; Kostrowicki, Jaroslav; Yang, Bo; Thacher, Thomas; Kong, Xianjun; Mattaparti, Sarathy; Zhou, Joe Zhongxiang; Gonzalez, Javier; Ramirez-Weinhouse, Michele; Kuki, Atsuo

    2012-11-12

    An unprecedented amount of parallel synthesis information was accumulated within Pfizer over the past 12 years. This information was captured by an informatics tool known as PGVL (Pfizer Global Virtual Library). PGVL was used for many aspects of drug discovery including automated reactant mining and reaction product formation to build a synthetically feasible virtual compound collection. In this report, PGVL is discussed in detail. The chemistry information within PGVL has been used to extract synthesis and design information using an intuitive desktop Graphic User Interface, PGVL Hub. Several real-case examples of PGVL are also presented.

  19. Design, diversity-oriented synthesis and structure activity relationship studies of quinolinyl heterocycles as antimycobacterial agents.

    Science.gov (United States)

    Rachakonda, Venkatesham; Alla, Manjula; Kotipalli, Sudha Sravanti; Ummani, Ramesh

    2013-01-01

    The current study reports design and diversity oriented synthesis of novel bis heterocycles with a common 2-methyl, C-4 unsubstituted quinoline moiety as the central key heterocycle. Employing reagent based skeletal diversity approach; a facile synthesis of bis heterocycles with different heterocyclic rings at C-3 position of the quinoline moiety has been accomplished. A broad range of heterocyclic frameworks thus obtained were evaluated for their antimycobacterial activity. The active scaffolds were further explored by a parallel library generation in order to establish SAR. Further, low cytotoxicity against A549 cell line enhances the potential of the synthesized molecules as promising antimycobacterial agents.

  20. Design and synthesis of new biprivileged molecular scaffolds: indolo-fused benzodiazepinyl/quinoxalinyl benzimidazoles.

    Science.gov (United States)

    Barve, Indrajeet J; Chen, Chan-Yu; Salunke, Deepak B; Chung, Wen-Sheng; Sun, Chung-Ming

    2012-06-01

    The present article describes the design and synthesis of new biprivileged molecular scaffolds with diverse structural features. Commercially available, simple heterocyclic building blocks such as 4-fluoro-3-nitrobenzoic acid, 2-chloro-3-nitrobenzoic acid, and indoline were utilized for the synthesis of the novel heterocycles. Pictet-Spengler-type condensation was used as a key step to construct tetracyclic indolo-benzodiazepines and indolo-quinoxalines linked with substituted benzimidazoles. Analysis of single crystals of representative compounds showed that these molecular skeletons have the potential to present various substituents with distinct three-dimensional orientations.

  1. Design and synthesis of an array of selective androgen receptor modulators.

    Science.gov (United States)

    Trump, Ryan P; Blanc, Jean-Baptiste E; Stewart, Eugene L; Brown, Peter J; Caivano, Matilde; Gray, David W; Hoekstra, William J; Willson, Timothy M; Han, Bajin; Turnbull, Philip

    2007-01-01

    We describe the design, using shape comparison and fast docking computer algorithms, and rapid parallel synthesis of a 1300 member array based on GSK7721, a 4-aminobenzonitrile androgen receptor (AR) antagonist identified by focused screening of the GSK compound collection. The array yielded 352 submicromolar and 17 subnanomolar AR agonists as measured by a cell-based reporter gene functional assay. The rapid synthesis of a large number of active compounds provided valuable information in the optimization of AR modulators, which may be useful in treating androgen deficiency in aging males.

  2. Systematic process synthesis and design methods for cost effective waste minimization

    Energy Technology Data Exchange (ETDEWEB)

    Biegler, L.T.; Grossman, I.E.; Westerberg, A.W. [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    1995-12-31

    We present progress on our work to develop synthesis methods to aid in the design of cost effective approaches to waste minimization. Work continues to combine the approaches of Douglas and coworkers and of Grossmann and coworkers on a hierarchical approach where bounding information allows it to fit within a mixed integer programming approach. We continue work on the synthesis of reactors and of flexible separation processes. In the first instance, we strive for methods we can use to reduce the production of potential pollutants, while in the second we look for ways to recover and recycle solvents.

  3. Convergent and sequential synthesis designs: implications for conducting and reporting systematic reviews of qualitative and quantitative evidence.

    Science.gov (United States)

    Hong, Quan Nha; Pluye, Pierre; Bujold, Mathieu; Wassef, Maggy

    2017-03-23

    Systematic reviews of qualitative and quantitative evidence can provide a rich understanding of complex phenomena. This type of review is increasingly popular, has been used to provide a landscape of existing knowledge, and addresses the types of questions not usually covered in reviews relying solely on either quantitative or qualitative evidence. Although several typologies of synthesis designs have been developed, none have been tested on a large sample of reviews. The aim of this review of reviews was to identify and develop a typology of synthesis designs and methods that have been used and to propose strategies for synthesizing qualitative and quantitative evidence. A review of systematic reviews combining qualitative and quantitative evidence was performed. Six databases were searched from inception to December 2014. Reviews were included if they were systematic reviews combining qualitative and quantitative evidence. The included reviews were analyzed according to three concepts of synthesis processes: (a) synthesis methods, (b) sequence of data synthesis, and (c) integration of data and synthesis results. A total of 459 reviews were included. The analysis of this literature highlighted a lack of transparency in reporting how evidence was synthesized and a lack of consistency in the terminology used. Two main types of synthesis designs were identified: convergent and sequential synthesis designs. Within the convergent synthesis design, three subtypes were found: (a) data-based convergent synthesis design, where qualitative and quantitative evidence is analyzed together using the same synthesis method, (b) results-based convergent synthesis design, where qualitative and quantitative evidence is analyzed separately using different synthesis methods and results of both syntheses are integrated during a final synthesis, and (c) parallel-results convergent synthesis design consisting of independent syntheses of qualitative and quantitative evidence and an

  4. Design and synthesis of reactive separation systems. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Doherty, M.F.

    1992-12-31

    During the last decade there has been a rapid upturn in interest in reactive distillation. The chemical process industry recognizes the favorable economics of carrying out reaction simultaneously with distillation for certain classes of reacting systems, and many new processes have been built based on this technology. Interest is also increasing by academics and software vendors. Systematic design methods for reactive distillation systems have only recently begun to emerge. In this report we survey the available design techniques and point out the contributions made by our group at the University of Massachusetts.

  5. Rational design and synthesis of semi-conducting polymers.

    Energy Technology Data Exchange (ETDEWEB)

    Wong, Bryan Matthew; Reeder, Craig; Cordaro, Joseph Gabriel

    2010-12-01

    A rational approach was used to design polymeric materials for thin-film electronics applications, whereby theoretical modeling was used to determine synthetic targets. Time-dependent density functional theory calculations were used as a tool to predict the electrical properties of conjugated polymer systems. From these results, polymers with desirable energy levels and band-gaps were designed and synthesized. Measurements of optoelectronic properties were performed on the synthesized polymers and the results were compared to those of the theoretical model. From this work, the efficacy of the model was evaluated and new target polymers were identified.

  6. Design,Synthesis and Antifungal Activity of Novel Triazole Derivatives

    Institute of Scientific and Technical Information of China (English)

    Chun Quan SHENG; Wan Nian ZHANG; Hai Tao JI; Yun Long SONG; Min ZHANG; You Jun ZHOU; Jia Guo LU; Jü ZHU

    2004-01-01

    Twenty-one 1-(1H-1,2,4-triazolyl)-2-(2,4-diflurophenyl)-3-(4-substituted-1- piperazinyl)-2-propanol derivatives were designed and synthesized,on the basis of the active site of lanosterol 14(-demethylase.In vitro antifungal activities showed that some of the target compounds had higher antifungal activity and broader antifungal spectrum than fluconazole.

  7. Design, synthesis and evaluation of multivalent glycodendrimers as multivalent ligands

    NARCIS (Netherlands)

    Branderhorst, H.M.

    2008-01-01

    Carbohydrates are more and more of interest in drug design as they are important mediators in a whole range of biological processes. Because of the low affinity of carbohydrates for their receptors, multivalent ligand presentation was introduced. Multivalent compounds were shown to improve the affin

  8. Benchmark Design and Installation: A synthesis of Existing Information.

    Science.gov (United States)

    1987-07-01

    included. Slater and Slater (1979) and Floyd (1978) point out that benchmark designs and installation procedures have remained virtually unchanged for...structures Table 85 Splks, nails Tables 2,63 T9. 0 1 - In trees, posts, poles Fig. 39 0 - In roads, pavements Fig. 39, Table 33 0 libro than 10 ft dee

  9. Design and Synthesis of Muramyl Dipeptide Cyclic Analogue

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A new conformationally restricted cyclic analogue of muramyl dipeptide was designed and manually synthesized by our "Meshed-Bag Gathered-Bunch" method with a combination of Fmoc, allyl and N-1-(4,4-dimethyl-2,6-dioxocyclo-hexylidene)ethyl chemical protection strategy.

  10. Design of a process template for amine synthesis

    DEFF Research Database (Denmark)

    Singh, Ravendra; Godfrey, Andy; Gregertsen, Björn;

    A conceptual nitro reduction process template that should be generic such that it can handle a series of substrates with sim ilar molecular functionality has been designed. The reduction process is based on a continuo us plug-flow slurry reactor. The process template aims at speeding up the process...

  11. Design and Synthesis of Muramyl Dipeptide Cyclic Analogue

    Institute of Scientific and Technical Information of China (English)

    SuoDeZHANG; GangLIU; 等

    2002-01-01

    A new conformationalloy restricted cyclic analogue of muramyl dipeptide was designed and manually synthesized by our “Meshed-Bag Gathered-Bunch” method with a combination of Fmoc,ally and N-1-(4,4-dimethyl-2,6-dioxocyclo-hexylidene) ethyl chemical protection strategy.

  12. Design, synthesis and antibacterial activity of a novel hybrid ...

    African Journals Online (AJOL)

    ajl user 1

    2012-01-26

    Jan 26, 2012 ... Antimicrobial peptides produced by many tissues and cell types of invertebrates, insects and humans as part of ... Key words: Antimicrobial peptides, design, LfcinB, melittin, antibacterial activity. ... from the Heilongjiang Type Culture Collection (Harbin, China). .... antibacterial experiments were carried out.

  13. Fungal mediated silver nanoparticle synthesis using robust experimental design and its application in cotton fabric

    Science.gov (United States)

    Velhal, Sulbha Girish; Kulkarni, S. D.; Latpate, R. V.

    2016-09-01

    Among the different methods employed for the synthesis of nanoparticles, the biological method is most favorable and quite well established. In microorganisms, use of fungi in the biosynthesis of silver nanoparticles has a greater advantage over other microbial mediators. In this study, intracellular synthesis of silver nanoparticles from Aspergillus terrerus (Thom) MTCC632 was carried out. We observed that synthesis of silver nanoparticles depended on factors such as temperature, amount of biomass and concentration of silver ions in the reaction mixture. Hence, optimization of biosynthesis using these parameters was carried out using statistical tool `robust experimental design'. Size and morphology of synthesized nanoparticles were determined using X-ray diffraction technique, field emission scanning electron microscopy, energy dispersion spectroscopy, and transmission electron microscopy. Nano-embedded cotton fabric was further prepared and studied for its antibacterial properties.

  14. Frequency invariant beamforming via optimal array pattern synthesis and FIR filters design

    Institute of Scientific and Technical Information of China (English)

    YAN Shefeng; MA Yuanliang

    2005-01-01

    An approach to designing time domain broadband frequency invariant beamformer via optimal array pattern synthesis and optimal FIR filters design is proposed. First, the working frequency band is decomposed into a number of narrow band frequency bins. The array weights at each frequency bin are designed via optimal array pattern synthesis methods to insure that the synthesized pattern approximates the desired one within the mainlobe area.Then, a bank of FIR filters corresponding to the input channels are designed to provide the frequency responses that approximate the array weights in the working frequency band for each sensor. Finally, each sensor feeds a FIR filter and the filter outputs are summed to produce the beam output time series. Both array pattern synthesis and FIR filters design problems are formulated as the second-order cone programming (SOCP), which can be easily solved using well-developed interior-point methods. Results of computer simulations and lake-experiment for a twelve-element semicircular array demonstrate satisfactory performance of the proposed approach.

  15. The synthesis, design and applications of lanthanide cored complexes

    Science.gov (United States)

    Phelan, Gregory David

    Novel luminescent materials based on lanthanide cored complexes have been designed and synthesized. The complexes consist of a beta-diketone ligand chelated to a lanthanide metal such as europium or gadolinium. A series of beta-diketone ligands were designed and synthesized. The ligands consist of a polycyclic aromatic sensitizer, phenanthrene, and a second functional group. The second groups consisted of another unit of phenanthrene, a dendritic structure, or a fluorinated alkyl chain. The europium complexes have been incorporated into organic light emitting devices that have a major emission at 615 nm and a maximum brightness of 300 cd/m2. The gadolinium complexes were used to dope into the resulting organic light emitting devices to help improve the efficiency of the device. The use of the gadolinium complexes results in a 25 fold increase in efficiency.

  16. Exploring qualitative research synthesis: the role of patients' perspectives in health policy design and decision making.

    Science.gov (United States)

    Hansen, Helle Ploug; Draborg, Eva; Kristensen, Finn Børlum

    2011-01-01

    Health systems are placing more and more emphasis on the design and delivery of services that are focused on the patient, and there is a growing interest in patient involvement in health policy research and health technology assessment (HTA). Furthermore, there is a growing research interest in eliciting patients' views, not only on 'what works' for patients but also on the need for intervention and on factors influencing the implementation of particular health technologies, their appropriateness and acceptability. This article focuses on qualitative research synthesis in eliciting patients' perspectives. Its aim is to bring research closer to policy development and decision making, to facilitate better use of research findings for health and welfare, to generate a body of evidence, and to ensure that effective and appropriate information is used in health policy decision design. A variety of synthesizing approaches in qualitative research are explored, such as meta-synthesis, meta-summary, meta-ethnography, and meta-study, focusing especially on methodology. Meta-synthesis and meta-ethnography are probably the most frequently cited approaches in qualitative research synthesis and have perhaps the most developed methodology. The implications of these various synthesizing approaches in relation to health policy and HTA are discussed, and we suggest that meta-synthesis and meta-summary are particularly useful approaches. They have an explicit focus on 'evidence synthesis', fairly clear methodologies, and they are designed to not only present interpretations of the findings but also integrate research findings. Qualitative research synthesis enables researchers to synthesize findings from multiple qualitative studies on patients' perspectives instead of establishing new, expensive, and perhaps redundant studies that might intrude on the lives of patients. Qualitative research synthesis is highly recommended by decision makers and in health policy research and HTA. In

  17. Design, synthesis and antifungal activity of novel triazole derivatives

    Institute of Scientific and Technical Information of China (English)

    Qing lie Zhao; Yan Song; Hong Gang Hu; Shi Chong Yu; Qiu Ye Wu

    2007-01-01

    Twenty-three 1 -(1H-1,2,4-triazole-1-yl)-2-(2,4-difluorophenyl)-3-(N-cycloproyl-N-substituted-amino)-2-propanols were designed and synthesized on the basis of the active site of lanosterol 14α-demethylase.In vitro antifungal activities showed that some of the title compounds had higher antifungal activity and broader antifungal spectrum than fluconazole.

  18. Human Systems Integration Synthesis Model for Ship Design

    Science.gov (United States)

    2012-09-01

    design of experiments addresses the researcher’s stated hypotheses, while considering the following three principles : 1) one cannot prove hypotheses...DISPLACEMENT A ship’s displacement is a function of its mass and weight. A simplistic description of displacement is Archimedes ’ Law. The law states, “that...maintenance requirements. Watson (1998, p. 74) noted the following concerning cost and power requirements: A first principles approach to the determination

  19. Rational design of the gram-scale synthesis of nearly monodisperse semiconductor nanocrystals

    Directory of Open Access Journals (Sweden)

    Renard Olivier

    2011-01-01

    Full Text Available Abstract We address two aspects of general interest for the chemical synthesis of colloidal semiconductor nanocrystals: (1 the rational design of the synthesis protocol aiming at the optimization of the reaction parameters in a minimum number of experiments; (2 the transfer of the procedure to the gram scale, while maintaining a low size distribution and maximizing the reaction yield. Concerning the first point, the design-of-experiment (DOE method has been applied to the synthesis of colloidal CdSe nanocrystals. We demonstrate that 16 experiments, analyzed by means of a Taguchi L16 table, are sufficient to optimize the reaction parameters for controlling the mean size of the nanocrystals in a large range while keeping the size distribution narrow (5-10%. The DOE method strongly reduces the number of experiments necessary for the optimization as compared to trial-and-error approaches. Furthermore, the Taguchi table analysis reveals the degree of influence of each reaction parameter investigated (e.g., the nature and concentration of reagents, the solvent, the reaction temperature and indicates the interactions between them. On the basis of these results, the synthesis has been scaled up by a factor of 20. Using a 2-L batch reactor combined with a high-throughput peristaltic pump, different-sized samples of CdSe nanocrystals with yields of 2-3 g per synthesis have been produced without sacrificing the narrow size distribution. In a similar setup, the gram-scale synthesis of CdSe/CdS/ZnS core/shell/shell nanocrystals exhibiting a fluorescence quantum yield of 81% and excellent resistance of the photoluminescence in presence of a fluorescent quencher (aromatic thiol has been achieved. PACS: 81.20.Ka, 81.07.Bc, 78.67.Bf

  20. Rational design of the gram-scale synthesis of nearly monodisperse semiconductor nanocrystals

    Science.gov (United States)

    Protière, Myriam; Nerambourg, Nicolas; Renard, Olivier; Reiss, Peter

    2011-07-01

    We address two aspects of general interest for the chemical synthesis of colloidal semiconductor nanocrystals: (1) the rational design of the synthesis protocol aiming at the optimization of the reaction parameters in a minimum number of experiments; (2) the transfer of the procedure to the gram scale, while maintaining a low size distribution and maximizing the reaction yield. Concerning the first point, the design-of-experiment (DOE) method has been applied to the synthesis of colloidal CdSe nanocrystals. We demonstrate that 16 experiments, analyzed by means of a Taguchi L16 table, are sufficient to optimize the reaction parameters for controlling the mean size of the nanocrystals in a large range while keeping the size distribution narrow (5-10%). The DOE method strongly reduces the number of experiments necessary for the optimization as compared to trial-and-error approaches. Furthermore, the Taguchi table analysis reveals the degree of influence of each reaction parameter investigated (e.g., the nature and concentration of reagents, the solvent, the reaction temperature) and indicates the interactions between them. On the basis of these results, the synthesis has been scaled up by a factor of 20. Using a 2-L batch reactor combined with a high-throughput peristaltic pump, different-sized samples of CdSe nanocrystals with yields of 2-3 g per synthesis have been produced without sacrificing the narrow size distribution. In a similar setup, the gram-scale synthesis of CdSe/CdS/ZnS core/shell/shell nanocrystals exhibiting a fluorescence quantum yield of 81% and excellent resistance of the photoluminescence in presence of a fluorescent quencher (aromatic thiol) has been achieved. PACS: 81.20.Ka, 81.07.Bc, 78.67.Bf

  1. Design and Synthesis of Novel Discotic Liquid Crystals

    Science.gov (United States)

    Kayal, Himadri Sekhar

    Columnar mesophases of discotic liquid crystals (DLCs) have attracted much attention as organic semiconductors and have been tested as active materials in light-emitting diodes, photovoltaic solar cells, and field-effect transistors. However, devices based on DLCs have shown lower performance than devices based on polymeric and small molecule glass semiconductors, despite their superior charge conducting and advantages self-organizing properties. Most DLCs also require relatively complex processing conditions for the preparation of electronic devices, which is another significant disadvantage. Consequently, new types of DLCs are sought-after to overcome these limitations and described in this thesis are new types of discotic materials and their synthesis. Chapters 2 and 3 describe star-shaped discotic molecules for donor-acceptor columnar structures and as novel flexible core discotic molecules. Presented are the first examples of star-shaped heptamers of donor and acceptor discotic molecules which have six hexaalkoxy triphenylene ligands and a hexaazatriphenylene hexacarboxylate core or a hexaazatriphenylene hexaamide core. The hexaazatriphenylene cores were chosen because of their electron deficient character while the hexaalkoxy triphenylenes are known to be electron rich. Envisioned is the formation of super-columns in which the heptamers stack on top of each other and generate a material with electron acceptor and electron donor channels separated by aliphatic chains. This is an important difference to previously reported donor-acceptor star-shaped structures that were connected via conjugated linkers and do not form separate columnar stacks. Star-shaped DLCs based on small aromatic groups linked together by short flexible spacers may represent a novel type of discotic core structure that does not require peripheral flexible chains. Softening of the core by the spacer group is expected to sufficiently lower melting points and not interfere with the columnar

  2. The Synthesis Approach to Analysing Educational Design Dataset: Application of Three Scaffolds to a Learning by Design Task for Postgraduate Education Students

    Science.gov (United States)

    Thompson, Kate; Carvalho, Lucila; Aditomo, Anindito; Dimitriadis, Yannis; Dyke, Gregory; Evans, Michael A.; Khosronejad, Maryam; Martinez-Maldonado, Roberto; Reimann, Peter; Wardak, Dewa

    2015-01-01

    The aims of the Synthesis and Scaffolding Project were to understand: the role of specific scaffolds in relation to the activity of learners, and the activity of learners during a collaborative design task from multiple perspectives, through the collection and analysis of multiple streams of data and the adoption of a synthesis approach to the…

  3. Simulation and Design Optimization of Ammonia SynthesisConverter

    Institute of Scientific and Technical Information of China (English)

    叶启亮; 应卫勇; 房鼎业

    2001-01-01

    One-dimensional pseudo-homogeneous model of an axial flow converter and one-dimensional heteroge-neous model of a horizontal converter have been presented, which describe the distribution of gaseous composition,temperature and pressure along the height in the two converters, respectively. Design optimization methods of the two converters have been proposed, by which the minimum catalyst volume can be obtained to satisfy the productive capacity of 1000 tons per day, when the operating pressure is 15.0, 10.0 and 7.5 MPa, respectively.

  4. Design synthesis and biological evaluation of 3-substituted triazole derivatives

    Institute of Scientific and Technical Information of China (English)

    Bao Gang Wang; Shi Chong Yu; Xiao Yun Chai; Yong Zheng Yan; Hong Gang Hu; Qiu Ye Wu

    2011-01-01

    Based on the active site of lanosterol 14α-demethylase of azole antifungal agents, sixteen l-(lH-l,2,4-triazole-l-yl)- 2-(2,4-difluorophenyl)-3-(N-n-butyl-N-l-substitutedbenzyl-4-methylene-lH-l,2,3-triazole)-2-propanols have been designed, synthesized and evaluated as antifungal agents. Results of preliminary antifungal tests against eight human pathogenic fungi in vitro showed that some of the compounds exhibited excellent activities with broad spectrum.

  5. Design and synthesis of a noncentrosymmetric Dipyrromethene Dye

    Energy Technology Data Exchange (ETDEWEB)

    Meinhardt, M.B.; Cahill, P.A. [Sandia National Labs., Albuquerque, NM (United States); Kowalczyk, T.C.; Singer, K.D. [Case Western Reserve Univ., Cleveland, OH (United States). Dept. of Physics

    1994-12-31

    Semiempirical methods were applied to the design of a new second order nonlinear optical (NLO) dye through noncentrosymmetric modifications to the symmetric dipyrromethene boron difluoride chromophore. Computational evaluations of candidate structures suggested that a synthetically accessible methoxyindole modification would have second order NLO properties. This new dye consists of 4 fused rings, is soluble in polar organic solvents and has a large molar extinction coefficient (86 {times} 103). Its measured hyperpolarizability, {beta}, is -44 {times} 10{sup {minus}30} esu at 1367 nm. The methoxyindole therefore induces moderate asymmetry to the chromophore.

  6. Novo desenvolvimentismo e liberalismo enraizado

    OpenAIRE

    Gonçalves,Reinaldo

    2012-01-01

    O objetivo geral deste artigo é discutir a evolução da formulação político‑ideológica de desenvolvimento econômico conhecida como novo desenvolvimentismo. O objetivo específico é demonstrar a hipótese de que o novo desenvolvimentismo é mais uma versão do liberalismo enraizado, que exprime o compromisso entre as diretrizes estratégicas do liberalismo e a intervenção estatal orientada para a estabilização macroeconômica.

  7. De Novo Design of Boron-Based Host Materials for Highly Efficient Blue and White Phosphorescent OLEDs with Low Efficiency Roll-Off.

    Science.gov (United States)

    Xue, Miao-Miao; Huang, Chen-Chao; Yuan, Yi; Cui, Lin-Song; Li, Yong-Xi; Wang, Bo; Jiang, Zuo-Quan; Fung, Man-Keung; Liao, Liang-Sheng

    2016-08-10

    Borane is an excellent electron-accepting species, and its derivatives have been widely used in a variety of fields. However, the use of borane derivatives as host materials in OLEDs has rarely reported because the device performance is generally not satisfactory. In this work, two novel spiro-bipolar hosts with incorporated borane were designed and synthesized. The strategies used in preparing these materials were to increase the spatial separation of the highest occupied molecular orbitals (HOMOs) and lowest unoccupied molecular orbitals (LUMOs) in the molecules, tune the connecting positions of functional groups, and incorporate specific functional groups with desirable thermal stability. Based on these designs, phosphorescent OLEDs with borane derivatives as hosts and with outstanding device performances were obtained. In particular, devices based on SAF-3-DMB/FIrpic exhibited an external quantum efficiency (EQE) of >25%. More encouragingly, the device was found to have quite a low efficiency roll-off, giving an efficiency of >20% even at a high brightness of 10000 cd/m(2). Furthermore, the EQE of the three-color-based (R + G + B) white OLED employing SAF-3-DMB as a host was also as high as 22.9% with CIE coordinates of (x, y) = (0.40, 0.48). At a brightness of 5000 cd/m(2), there was only a 3% decrease in EQE from its maximum value, implying a very low efficiency roll-off.

  8. Design, Synthesis, and Bioevaluation of Novel Strobilurin Derivatives

    Institute of Scientific and Technical Information of China (English)

    朱晓磊; 王福; 李慧; 杨文超; 陈琼; 杨光富

    2012-01-01

    Strobilurins are one of the most important natural products with fungicidal activities and well known for their novel action mode, broad fungicidal spectrum, lower toxicity against mammalian cells, and environmentally benign characteristics. Design and syntheses of strobilurin analogues therefore have attracted great attention in the field of agrochemistry. Previously, we successfully developed a new molecular design method of pharmacophore-linked fragment virtual screening (PFVS) and discovered a lead compound (E)-methyl-2-(2-(((3-(imino-(phenyl)- methyl)phenyl)thio)methyl)phenyl)-3-methoxyacrylate (1). To discover new strobilurin analogues with higher fun- gicidal activity, the structural modification of compound 1 was carried out guided by bioisosterism. A series of benzophenone derivatives 2a--2j were synthesized, among which compound 2j with a Ki value of 1.89 nmol/L was identified as the most promising inhibitor of porcine cytocbrome bcl complex, 157-fold improved binding affinity compared to the commercially available bCl inhibitor Azoxystrobin (AZ). In addition, most of the new compounds displayed excellent fungicidal activity against Sphaerothecafuliginea at the concentration of 200μmol/L. The pre- sent work indicates that strobilurin analogues containing benzophenone side chains may be the ideal leads for future fungicide discovery.

  9. Monoterpene emissions from boreal tree species: Determination of de novo and pool emissions

    Science.gov (United States)

    Ghirardo, Andrea; Koch, Kristine; Taipale, Risto; Zimmer, Ina; Schnitzler, Joerg-Peter; Rinne, Janne

    2010-05-01

    Boreal forests emit a large amount of monoterpenes into the atmosphere. Traditionally these emissions are assumed to originate as evaporation from large storage pools. Thus their diurnal cycle would depend mostly on temperature. However, there is indication that a significant part of the monoterpene emission would originate directly from de novo synthesis. By applying 13CO2 fumigation and analyzing the isotope fractions with proton transfer reaction mass spectrometry (PTR-MS) and classical GC-MS we studied the origin of monoterpene emissions from some major Eurasian boreal and alpine tree species. We determined the fractions originating from de novo biosynthesis and from large internal monoterpene storages for three coniferous tree species with specialized monoterpene storage structures and one dicotyledon species without such structures. The emission from dicotyledon species Betula pendula originated solely from the de novo synthesis. The origin of the emissions from coniferous species was mixed with varying fraction originating from de novo synthesis (Pinus sylvestris 58 %, Picea abies 33.5 %, Larix decidua 9.8 %) and the rest from large internal monoterpene storage pools. We have also measured the ecosystem scale monoterpene emission fluxes from a boreal Pinus sylvestris forest by disjunct eddy covariance technique. Application of the observed fraction of emission originating from de novo synthesis and large storage pools in a hybrid emission algorithm resulted in a better description of ecosystem scale monoterpene emissions, as compared to the measured fluxes.

  10. Metal Organic Frameworks: Explorations and Design Strategies for MOF Synthesis

    KAUST Repository

    AbdulHalim, Rasha

    2016-11-27

    Metal-Organic Frameworks (MOFs) represent an emerging new class of functional crystalline solid-state materials. In the early discovery of this now rapidly growing class of materials significant challenges were often encountered. However, MOFs today, with its vast structural modularity, reflected by the huge library of the available chemical building blocks, and exceptional controlled porosity, stand as the most promising candidate to address many of the overbearing societal challenges pertaining to energy and environmental sustainability. A variety of design strategies have been enumerated in the literature which rely on the use of predesigned building blocks paving the way towards potentially more predictable structures. The two major design strategies presented in this work are the molecular building block (MBB) and supermolecular building block (SBB) -based approaches for the rationale assembly of functional MOF materials with the desired structural features. In this context, we targeted two highly connected MOF platforms, namely rht-MOF and shp-MOF. These two MOF platforms are classified based on their topology, defined as the underlying connectivity of their respective net, as edge transitive binodal nets; shp being (4,12)-connected net and rht being (3,24)-connected net. These highly connected nets were deliberately targeted due to the limited number of possible nets for connecting their associated basic building units. Two highly porous materials were designed and successfully constructed; namely Y-shp-MOF-5 and rht-MOF-10. The Y-shp-MOF-5 features a phenomenal water stability with an exquisite behavior when exposed to water, positioning this microporous material as the best adsorbent for moisture control applications. The shp-MOF platform proved to be modular to ligand functionalization and thus imparting significant behavioral changes when hydrophilic and hydrophobic functionalized ligands were introduced on the resultant MOF. On the other hand, rht

  11. Design, Synthesis, Assembly, and Engineering of Peptoid Nanosheets.

    Science.gov (United States)

    Robertson, Ellen J; Battigelli, Alessia; Proulx, Caroline; Mannige, Ranjan V; Haxton, Thomas K; Yun, Lisa; Whitelam, Stephen; Zuckermann, Ronald N

    2016-03-15

    Two-dimensional (2D) atomically defined organic nanomaterials are an important material class with broad applications. However, few general synthetic methods exist to produce such materials in high yields and to precisely functionalize them. One strategy to form ordered 2D organic nanomaterials is through the supramolecular assembly of sequence-defined synthetic polymers. Peptoids, one such class of polymer, are designable bioinspired heteropolymers whose main-chain length and monomer sequence can be precisely controlled. We have recently discovered that individual peptoid polymers with a simple sequence of alternating hydrophobic and ionic monomers can self-assemble into highly ordered, free-floating nanosheets. A detailed understanding of their molecular structure and supramolecular assembly dynamics provides a robust platform for the discovery of new classes of nanosheets with tunable properties and novel applications. In this Account, we discuss the discovery, characterization, assembly, molecular modeling, and functionalization of peptoid nanosheets. The fundamental properties of peptoid nanosheets, their mechanism of formation, and their application as robust scaffolds for molecular recognition and as templates for the growth of inorganic minerals have been probed by an arsenal of experimental characterization techniques (e.g., scanning probe, electron, and optical microscopy, X-ray diffraction, surface-selective vibrational spectroscopy, and surface tensiometry) and computational techniques (coarse-grained and atomistic modeling). Peptoid nanosheets are supramolecular assemblies of 16-42-mer chains that form molecular bilayers. They span tens of microns in lateral dimensions and freely float in water. Their component chains are highly ordered, with chains nearly fully extended and packed parallel to one another as a result of hydrophobic and electrostatic interactions. Nanosheets form via a novel interface-catalyzed monolayer collapse mechanism. Peptoid

  12. Achieving More Sustainable Designs through a Process Synthesis-Intensification Framework

    DEFF Research Database (Denmark)

    Babi, Deenesh Kavi; Woodley, John; Gani, Rafiqul

    2014-01-01

    More sustainable process designs refer to design alternatives that correspond to lowervalues of a set of targeted performance criteria. In this paper, a multi-level frameworkfor process synthesis-intensification that leads to more sustainable process designs ispresented. At the highest level...... of aggregation, process flowsheets are synthesized interms of a sequence of unit operations that correspond to acceptable values for a set oftargeted performance criteria. This defines the upper-bound of the performance criteriaand the design is called the base-case design. At the next lower level, tasks...... representingunit operations are identified and analysedin terms of means-ends to find moreflowsheet alternatives that improve the base-case design and correspond to lower valuesof the set of targeted performance criteria. Atthe lowest level, phenomena employed toperform the specific tasks areidentified...

  13. Design, Synthesis and Bioactivity of Novel Glycosylthiadiazole Derivatives

    Directory of Open Access Journals (Sweden)

    Guanghui Zong

    2014-06-01

    Full Text Available A series of novel glycosylthiadiazole derivatives, namely 2-phenylamino-5-glycosyl-1,3,4-thiadiazoles, were designed and synthesized by condensation between sugar aldehydes A/B and substituted thiosemicarbazide C followed by oxidative cyclization by treating with manganese dioxide. The original fungicidal activities results showed that some title compounds exhibited excellent fungicidal activities against Sclerotinia sclerotiorum (Lib. de Bary and Pyricularia oryzae Cav, especially compounds F-5 and G-8 which displayed better fungicidal activities than the commercial fungicide chlorothalonil. At the same time, the preliminary studies based on the Elson-Morgan method indicated that many compounds exhibited some inhibitory activity toward glucosamine-6-phosphate synthase (GlmS. The structure-activity relationships (SAR are discussed in terms of the effects of the substituents on both the benzene and the sugar ring.

  14. Design, Synthesis and Inclusion Properties of Butterfly-shaped Hosts

    Institute of Scientific and Technical Information of China (English)

    郭文生; 徐赫男; 郭放; 佟健

    2005-01-01

    Two kinds of """"buuerfly-shaped"""" host compounds, 2,5-bis(triphenylmethyl)hydroquinone (1) and 2,5-bis(diphenylmethyl)hydroquinone (2) were designed and synthesized. 1 and 2 can form inclusion complexes with various small organic molecules. These inclusion complexes were determined by 1H NMR spectroscopy, and the results were as follows: 1·DMF (1:2), 1·DMSO (1:2), lopyridine (1:2), locyclopentanone (2:3); 2oDMF (12), 2·THF (1:1), 2·benzaidehyde (1:2), 2·2,5-hexanedione (1:1), 2·N-methyl-2-pyrrolidone (1:3). The complex structure of 2 with benzaldehyde was determined by single crystal X-my diffraction analysis and the crystalstructure is stabilized by intermolecular hydrogen bonds.

  15. Design, Synthesis and Insecticidal Activity of Novel Phenylurea Derivatives

    Directory of Open Access Journals (Sweden)

    Jialong Sun

    2015-03-01

    Full Text Available A series of novel phenylurea derivatives were designed and synthesized according to the method of active groups linkage and the principle of aromatic groups bioisosterism in this study. The structures of the novel phenylurea derivatives were confirmed based on ESI-MS, IR and 1H-NMR spectral data. All of the compounds were evaluated for the insecticidal activity against the third instars larvae of Spodoptera exigua Hiibner, Plutella xyllostella Linnaeus, Helicoverpa armigera Hubner and Pieris rapae Linne respectively, at the concentration of 10 mg/L. The results showed that all of the derivatives displayed strong insecticidal activity. Most of the compounds presented higher insecticidal activity against S. exigua than the reference compounds tebufenozide, chlorbenzuron and metaflumizone. Among the synthesized compounds, 3b, 3d, 3f, 4b and 4g displayed broad spectrum insecticidal activity.

  16. Design, synthesis and insecticidal activity of novel phenylurea derivatives.

    Science.gov (United States)

    Sun, Jialong; Zhou, Yuanming

    2015-03-19

    A series of novel phenylurea derivatives were designed and synthesized according to the method of active groups linkage and the principle of aromatic groups bioisosterism in this study. The structures of the novel phenylurea derivatives were confirmed based on ESI-MS, IR and 1H-NMR spectral data. All of the compounds were evaluated for the insecticidal activity against the third instars larvae of Spodoptera exigua Hiibner, Plutella xyllostella Linnaeus, Helicoverpa armigera Hubner and Pieris rapae Linne respectively, at the concentration of 10 mg/L. The results showed that all of the derivatives displayed strong insecticidal activity. Most of the compounds presented higher insecticidal activity against S. exigua than the reference compounds tebufenozide, chlorbenzuron and metaflumizone. Among the synthesized compounds, 3b, 3d, 3f, 4b and 4g displayed broad spectrum insecticidal activity.

  17. 76 FR 61103 - Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification...

    Science.gov (United States)

    2011-10-03

    ... Food, Drug, and Cosmetic Act (FD&C Act), also known as the de novo classification process. FDA is... HUMAN SERVICES Food and Drug Administration Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification Process (Evaluation of Automatic Class III Designation);...

  18. A prospective evaluation of the safety and efficacy of the TAXUS Element paclitaxel-eluting coronary stent system for the treatment of de novo coronary artery lesions: Design and statistical methods of the PERSEUS clinical program

    Directory of Open Access Journals (Sweden)

    Wehrenberg Scott

    2010-01-01

    Full Text Available Abstract Background Paclitaxel-eluting stents decrease angiographic and clinical restenosis following percutaneous coronary intervention compared to bare metal stents. TAXUS Element is a third-generation paclitaxel-eluting stent which incorporates a novel, thinner-strut, platinum-enriched metal alloy platform. The stent is intended to have enhanced radiopacity and improved deliverability compared to other paclitaxel-eluting stents. The safety and efficacy of the TAXUS Element stent are being evaluated in the pivotal PERSEUS clinical trials. Methods/Design The PERSEUS trials include two parallel studies of the TAXUS Element stent in single, de novo coronary atherosclerotic lesions. The PERSEUS Workhorse study is a prospective, randomized (3:1, single-blind, non-inferiority trial in subjects with lesion length ≤28 mm and vessel diameter ≥2.75 mm to ≤4.0 mm which compares TAXUS Element to the TAXUS Express2 paclitaxel-eluting stent system. The Workhorse study employs a novel Bayesian statistical approach that uses prior information to limit the number of study subjects exposed to the investigational device and thus provide a safer and more efficient analysis of the TAXUS Element stent. PERSEUS Small Vessel is a prospective, single-arm, superiority trial in subjects with lesion length ≤20 mm and vessel diameter ≥2.25 mm to Discussion The TAXUS PERSEUS clinical trial program uses a novel statistical approach to evaluate whether design and metal alloy iterations in the TAXUS Element stent platform provide comparable safety and improved procedural performance compared to the previous generation Express stent. PERSEUS trial enrollment is complete and primary endpoint data are expected in 2010. PERSEUS Workhorse and Small Vessel are registered at http://www.clinicaltrials.gov, identification numbers NCT00484315 and NCT00489541.

  19. Using Taguchi robust design method to develop an optimized synthesis procedure of nanocrystalline cancrinite

    Science.gov (United States)

    Azizi, Seyed Naser; Asemi, Neda; Samadi-Maybodi, Abdolrouf

    2012-09-01

    In this study, perlite was used as a low-cost source of Si and Al to synthesis of nanocrystalline cancrinite zeolite. The synthesis of cancrinite zeolite from perlite by using the alkaline hydrothermal treatment under saturated steam pressure was investigated. A statistical Taguchi design of experiments was employed to evaluate the effects of the process variables such as type of aging, aging time and hydrothermal crystallization time on the crystallnity of synthesized zeolite. The optimum conditions for maximum crystallinity of nanocrystalline cancrinite were obtained as microwave-assisted aging, 60 min aging time and 6 h hydrothermal crystallization time from statistical analysis of the experimental results using Taguchi design. The synthetic samples were characterization by XRD, FT-IR and FE-SEM techniques. The results showed that the microwave-assisted aging can shorten the crystallization time and reduced the crystal size to form nanocrystalline cancrinite zeolite.

  20. An integrated knowledge-based framework for synthesis and design of enterprise-wide processing networks

    DEFF Research Database (Denmark)

    Sin, Gürkan

    , the synthesis and design of processing networks is a complex and multidisciplinary problem, which involves many strategic and tactical decisions at business (considering financial criteria, market competition, supply chain network, etc) and engineering levels (considering synthesis, design and optimization......Today chemical processing industries manufacture a wide range of products and provide services that touch billions of people’s lives across the globe in many different ways. Making this requires an effective management of innovation in product and process development. On the other hand...... is presented. A systematic approach is used to manage the complexity and solving simultaneously both the business and the engineering dimension of the problem. This allows generation and comparison of a large number of alternatives at their optimal point. The result is the identification of the optimal raw...

  1. Design and Synthesis of Functional Silsesquioxane-Based Hybrids by Hydrolytic Condensation of Bulky Triethoxysilanes

    Directory of Open Access Journals (Sweden)

    Hideharu Mori

    2012-01-01

    Full Text Available This paper presents a short overview of recent advances in the design and synthesis of organic-inorganic hybrids using silsesquioxane-based nanoparticles having nanometer size, relatively narrow size distribution, high functionalities, and various characteristic features, mainly focusing on our recent researches related to the subject. A highlight of this paper is the water-soluble silsesquioxane-based nanoparticles, including hydroxyl-functionalized and cationic silsesquioxanes, which were synthesized via the one-step condensation of the bulky triethoxysilane precursors. The design and synthesis of R-SiO1.5/SiO2 and R-SiO1.5/TiO2 hybrids by hydrolytic cocondensation of a triethoxysilane precursor and metal alkoxides are briefly introduced. This paper also deals with recent results in stimuli-responsive hybrids based on the water-soluble silsesquioxane nanoparticles and fluorinated and amphiphilic silsesquioxane hybrids.

  2. Magnetic iron oxide nanoparticles: Recent trends in design and synthesis of magnetoresponsive nanosystems.

    Science.gov (United States)

    Tombácz, Etelka; Turcu, Rodica; Socoliuc, Vlad; Vékás, Ladislau

    2015-12-18

    Recent developments in nanotechnology and application of magnetic nanoparticles, in particular in magnetic iron oxide nanosystems, offer exciting possibilities for nanomedicine. Facile and precise synthesis procedures, high magnetic response, tunable morphologies and multiple bio-functionalities of single- and multi-core magnetic particles designed for nanomedicine applications are thoroughly appraised. This review focuses on the structural and magnetic characterization of the cores, the synthesis of single- and multicore iron oxide NPs, especially the design of the latter, as well as their protection, stabilization and functionalization by desired coating in order to protect against the corrosion of core, to prevent non-specific protein adsorption and particle aggregation in biological media, and to provide binding sites for targeting and therapeutic agents. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. NovoPen Echo® insulin delivery device

    Directory of Open Access Journals (Sweden)

    Hyllested-Winge J

    2016-01-01

    Full Text Available Jacob Hyllested-Winge,1 Thomas Sparre,2 Line Kynemund Pedersen2 1Novo Nordisk Pharma Ltd, Tokyo, Japan; 2Novo Nordisk A/S, Søborg, Denmark Abstract: The introduction of insulin pen devices has provided easier, well-tolerated, and more convenient treatment regimens for patients with diabetes mellitus. When compared with vial and syringe regimens, insulin pens offer a greater clinical efficacy, improved quality of life, and increased dosing accuracy, particularly at low doses. The portable and discreet nature of pen devices reduces the burden on the patient, facilitates adherence, and subsequently contributes to the improvement in glycemic control. NovoPen Echo® is one of the latest members of the NovoPen® family that has been specifically designed for the pediatric population and is the first to combine half-unit increment (=0.5 U of insulin dosing with a simple memory function. The half-unit increment dosing amendments and accurate injection of 0.5 U of insulin are particularly beneficial for children (and insulin-sensitive adults/elders, who often require small insulin doses. The memory function can be used to record the time and amount of the last dose, reducing the fear of double dosing or missing a dose. The memory function also provides parents with extra confidence and security that their child is taking insulin at the correct doses and times. NovoPen Echo is a lightweight, durable insulin delivery pen; it is available in two different colors, which may help to distinguish between different types of insulin, providing more confidence for both users and caregivers. Studies have demonstrated a high level of patient satisfaction, with 80% of users preferring NovoPen Echo to other pediatric insulin pens. Keywords: NovoPen Echo®, memory function, half-unit increment dosing, adherence, children, adolescents 

  4. De novo design of a D2-symmetrical protein that reproduces the diheme four-helix bundle in cytochrome bc1.

    Science.gov (United States)

    Ghirlanda, Giovanna; Osyczka, Artur; Liu, Weixia; Antolovich, Michael; Smith, Kevin M; Dutton, P Leslie; Wand, A Joshua; DeGrado, William F

    2004-07-07

    An idealized, water-soluble D(2)-symmetric diheme protein is constructed based on a mathematical parametrization of the backbone coordinates of the transmembrane diheme four-helix bundle in cytochrome bc(1). Each heme is coordinated by two His residues from diagonally apposed helices. In the model, the imidazole rings of the His ligands are held in a somewhat unusual perpendicular orientation as found in cytochrome bc(1), which is maintained by a second-shell hydrogen bond to a Thr side chain on a neighboring helix. The resulting peptide is unfolded in the apo state but assembles cooperatively upon binding to heme into a well-folded tetramer. Each tetramer binds two hemes with high affinity at low micromolar concentrations. The equilibrium reduction midpoint potential varies between -76 mV and -124 mV vs SHE in the reducing and oxidizing direction, respectively. The EPR spectrum of the ferric complex indicates the presence of a low-spin species, with a g(max) value of 3.35 comparable to those obtained for hemes b of cytochrome bc(1) (3.79 and 3.44). This provides strong support for the designed perpendicular orientation of the imidazole ligands. Moreover, NMR spectra show that the protein exists in solution in a unique conformation and is amenable to structural studies. This protein may provide a useful scaffold for determining how second-shell ligands affect the redox potential of the heme cofactor.

  5. New design of logistics for export of ethanol: a long-term vision; Novo desenho logistico para exportacao de etanol: uma visao de longo prazo

    Energy Technology Data Exchange (ETDEWEB)

    Scandiffio, Mirna Ivonne Gaya [Universidade Estadual de Campinas (NIPE/UNICAMP), SP (Brazil). Nucleo Interdisciplinar de Planejamento Energetico], e-mail: mirna@fem.unicamp.br; Leal, Manoel Regis Lima Verde [Centro de Energias Alternativas e Meio Ambiente - CENEA, Fortaleza, CE (Brazil)], e-mail: regislv@energiabr.org.br

    2008-07-01

    Production of ethanol from sugarcane, in Brazil, has presented continued expansion. Estimates of harvest from season 2007-2008 show a production of near 27 million m3 of ethanol, 20% over the previous season. Internal market responded, in 2005, for close to eighty five percent of national supply and the remaining 3.5 million m3 were sent abroad. A prospective study from NIPE-UNICAMP projects an increase in exports to reach 105 million m3 by 2025. All that projected growth, whether for internal consumption or exports, is not reflected in the very small amounts of investment in infrastructure in the last decades, pointing out the fragility and distortion of the transportation matrix of the country. Above sixty percent of national cargo is made by roads. Transportation of ethanol using pipelines represented, in the Eighties, close to 13% and hydro ways were responsible for 22% of its flow. Nowadays, ethanol dedicated pipelines respond only for 2%. Ethanol transportation by pipes seems to be the more competitive way of transporting when considering cost, time and delivery credibility, plus its positive environmental impact due to the substitution of diesel use. The experience of 30 years, since the launch of the National Program of Alcohol PROALCOOL, gives the country a solid knowledge, not only regarding the agricultural area and ethanol production, but also in logistics transporting by pipelines. The objective of this article is to analyze a new logistic design for transporting ethanol supported by a long term view, up to 2025. (author)

  6. Synthesis of berberine loaded polymeric nanoparticles by central composite design

    Science.gov (United States)

    Mehra, Meenakshi; Sheorain, Jyoti; Kumari, Santosh

    2016-04-01

    Berberine is an isoquinoline alkaloid which is extracted from bark and roots of Berberis vulgaris plant. It has been used in ayurvedic medicine as it possess antimicrobial, antidiabetic, anticancer, antioxidant properties etc. But poor solubility of berberine leads to poor stability and bioavailability in medical formulations decreasing its efficacy. Hence nanoformulations of berberine can help in removing the limiting factors of alkaloid enhancing its utilization in pharmaceutical industry. Sodium alginate polymer was used to encapsulate berberine within nanoparticles by emulsion solvent evaporation method using tween 80 as a surfactant. Two factors and three level in central composite design was used to study the formulation. The optimized formulation (1% v/v of Tween 80 and 0.01% w/v of sodium alginate) of polymeric nanoparticles was taken for further evaluations. The size of synthesized nanoparticles was found to be 71.18 nm by particle size analysis (PSA). The berberine loaded polymeric nanoparticles showed better antibacterial activity compared to aqueous solution of berberine by well diffusion assay.

  7. Design, synthesis, and functional testing of recombinant cell penetrating peptides

    Science.gov (United States)

    Widyaningtyas, S. T.; Soebandrio, A.; Ibrahim, F.; Bela, B.

    2017-08-01

    Cell penetrating peptides (CPP) are one of the most attractive DNA delivery systems currently in development. In this research, in silico CPP development was performed based on a literature study to look for peptides that induce endosome escape, have the ability to bind DNA, and pass through cell membranes and/or nuclear membranes with a final goal of creating a new CPP to be used as a DNA delivery system. We report herein the successful isolation of three candidate CPP molecules, which have all been successfully expressed and purified by NiNTA. One of the determinants of CPP success as a DNA carrier is the ability of the CPP to bind and protect DNA from the effects of nucleases. The DNA binding test results show that all three CPPs can bind to DNA and protect it from the effects of serum nucleases. These three CPP candidates designed in silico and synthesized in the prokaryote system are eligible candidates for further testing of their ability to deliver DNA in vitro and in vivo.

  8. [Design, synthesis and activities of novel benzothiazole derivatives containing arylpiperazine].

    Science.gov (United States)

    Liu, Wen-Hu; Chang, Jin-Xia; Liu, Yi; Luo, Jie-Wei; Zhang, Jian-Wu

    2013-08-01

    Twenty-four novel benzothiazole derivatives containing arylpiperazine were designed and synthesized by bioisosterism principle. Anti-proliferative effect of these synthesized compounds against four cancer cell and two normal cell lines were evaluated in vitro by the standard MTT assay. Pharmacological test showed that most of the compounds exhibited potent antitumor activity. Some of the compounds (II2, II3, II6, II7) showed strong anti-proliferation activities against HepG2 and HeLa229 cell lines with the IC 50 values of 1.6-4.5 micromol x L(-1) and 2.5-5.3 micromol x L(-1), respectively, and compounds having cyan in p-substituted benzene ring (I4, I8, I12, II4, II8 and II12) were found to have better antitumor activities against AsPC-1 cell lines with the IC50 values of 5.2-11.3 micromol x L(-1). The structure-activity relationship of benzothiazole derivatives containing arylpiperazine was also discussed preliminarily.

  9. Design, Synthesis and Fungicidal Activities of Some Novel Pyrazole Derivatives

    Directory of Open Access Journals (Sweden)

    Xue-Ru Liu

    2014-09-01

    Full Text Available In order to discover new compounds with good fungicidal activities, 32 pyrazole derivatives were designed and synthesized. The structures of the target compounds were confirmed by 1H-NMR, 13C-NMR, and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS, and their fungicidal activities against Botrytis cinerea, Rhizoctonia solani Kuhn, Valsa mali Miyabe et Yamada, Thanatephorus cucumeris (Frank Donk, Fusarium oxysporum (S-chl f.sp. cucumerinum Owen, and Fusarium graminearum Schw were tested. The bioassay results indicated that most of the derivatives exhibited considerable antifungal activities, especially compound 26 containing a p-trifluoromethyl- phenyl moiety showed the highest activity, with EC50 values of 2.432, 2.182, 1.787, 1.638, 6.986, and 6.043 μg/mL against B. cinerea, R. solani, V. mali, T. cucumeris, F. oxysporum, and F. graminearum, respectively. Moreover, the activities of compounds such as compounds 27–32 were enhanced by introducing isothiocyanate and carboxamide moieties to the 5-position of the pyrazole ring.

  10. Design, synthesis and insecticidal evaluation of aryloxy dihalopropene derivatives.

    Science.gov (United States)

    Yang, Ji-Chun; Li, Miao; Wu, Qiao; Liu, Chang-Ling; Chang, Xiu-Hui

    2016-02-01

    Plutella xylostella (P. xylostella) is a highly migratory, cosmopolitan species and one of the most important pest of cruciferous crops worldwide. Pyridalyl as a novel class of insecticides has good efficacy against P. xylostella. On the basis of the commercial insecticide pyridalyl, a series of new aryloxy dihalopropene derivatives were designed and synthesized by using Intermediate Derivatization Methods. Their chemical structures were confirmed by (1)H NMR, high-resolution mass spectrum (HRMS), and single-crystal X-ray diffraction analysis. The insecticidal activities of the new compounds against P. xylostella were evaluated. The results of bioassays indicated that most of the compounds showed moderate to high activities at the tested concentration, especially compounds 10e and 10g displayed more than 75% insecticidal activity against P. xylostella at 6.25mg/L, while pyridalyl showed 50% insecticidal activity at the same concentration. The field trials result of the insecticidal activities showed that compound 10e as a 10% emulsifiable concentrate (EC) was effective in the control of P. xylostella at 75-150g a.i./ha, and the mortality of P. xylostella for treatment with compound 10e at 75g a.i./ha was equivalent to pyridalyl at 105g a.i./ha.

  11. A systematic synthesis and design methodology to achieve process intensification in (bio) chemical processes

    OpenAIRE

    Lutze, Philip; Woodley, John; Gani, Rafiqul

    2011-01-01

    Process intensification (PI) has the potential to improve existing processes or create new process options which are needed in order to produce products using more sustainable methods. Potentially, PI creates an enormous number of process options. For identification where and how the process should be intensified for biggest improvement, process synthesis and design tools are applied which results in the development of a systematic methodology incorporating PI. In order to manage the complexi...

  12. Design, total synthesis, and evaluation of C13-C14 cyclopropane analogues of (+)-discodermolide.

    Science.gov (United States)

    Smith, Amos B; Xian, Ming; Liu, Fenghua

    2005-10-13

    [structure: see text] The design, total synthesis, and biological evaluation of two C13-C14-cyclopropyl analogues [(+)-1 and (+)-2] of (+)-discodermolide have been achieved. Key features of the syntheses include highly stereoselective, hydroxyl-directed cyclopropanations of vinyl iodides and higher order cuprate-mediated cross-coupling reactions between cyclopropyl iodides and alkyl iodides. Biological evaluation revealed that neither orientation of the cyclopropyl methylene completely substitutes for the C14 methyl found in (+)-discodermolide (3).

  13. Design, synthesis, and biological evaluation of novel histone deacetylase 1 inhibitors through click chemistry.

    Science.gov (United States)

    Sun, Qiao; Yao, Yiwu; Liu, Chunping; Li, Hua; Yao, Hequan; Xue, Xiaowen; Liu, Jinsong; Tu, Zhengchao; Jiang, Sheng

    2013-06-01

    We report the design, synthesis, and biological evaluation of a new series of HDAC1 inhibitors using click chemistry. Compound 17 bearing a phenyl ring at meta-position was identified to show much better selectivity for HDAC1 over HDAC7 than SAHA. The compond 17 also showed better in vitro anticancer activities against several cancer cell lines than that of SAHA. This work could serve as a foundation for further exploration of selective HDAC inhibitors using the compound 17 molecular scaffold.

  14. Molecular Design, Synthesis, and Evaluation of SNIPER(ER) That Induces Proteasomal Degradation of ERα.

    Science.gov (United States)

    Okuhira, Keiichiro; Demizu, Yosuke; Hattori, Takayuki; Ohoka, Nobumichi; Shibata, Norihito; Kurihara, Masaaki; Naito, Mikihiko

    2016-01-01

    Manipulation of protein stability using small molecules has a great potential for both basic research and clinical therapy. Based on our protein knockdown technology, we recently developed a novel small molecule SNIPER(ER) that targets the estrogen receptor alpha (ERα) for degradation via the ubiquitin-proteasome system. This chapter describes the design and synthesis of SNIPER(ER) compounds, and methods for the evaluation of their activity in cellular system.

  15. Peptide crosslinked micelles: a new strategy for the design and synthesis of peptide vaccines

    OpenAIRE

    Hao, Jihua; Kwissa, Marcin; Pulendran, Bali; Murthy, Niren

    2006-01-01

    This report presents a new and simple methodology for the synthesis of multicomponent peptide vaccines, named the peptide crosslinked micelles (PCMs). The PCMs are core shell micelles designed to deliver peptide antigens and immunostimulatory DNA to antigen-presenting cells (APCs). They are composed of immunostimulatory DNA, peptide antigen, and a thiopyridal derived poly(ethylene glycol)-polylysine block copolymer. The peptide antigen acts as a crosslinker in the PCM strategy, which allows t...

  16. Design, synthesis and in vitro evaluation of novel anti-cancer compounds

    OpenAIRE

    McCormack, Emmet Martin

    2003-01-01

    The purpose of this thesis was the design, synthesis and in vitro appraisal of a novel class of ITP/APN dual inhibitory compounds. Additionally, a class of novel biaryls, which were synthesised within the research group, were assayed to evaluate their ability to inhibit tubulin polymerisation (ITP). The introductory chapter commences with brief overview of the history of cancer and role of natural products in conventional chemotherapeutic regimes and adjuvant immunotherapies. Subsequently, th...

  17. Design, synthesis and photochemical properties of the first examples of iminosugar clusters based on fluorescent cores

    Directory of Open Access Journals (Sweden)

    Mathieu L. Lepage

    2015-05-01

    Full Text Available The synthesis and photophysical properties of the first examples of iminosugar clusters based on a BODIPY or a pyrene core are reported. The tri- and tetravalent systems designed as molecular probes and synthesized by way of Cu(I-catalysed azide–alkyne cycloadditions are fluorescent analogues of potent pharmacological chaperones/correctors recently reported in the field of Gaucher disease and cystic fibrosis, two rare genetic diseases caused by protein misfolding.

  18. Design, synthesis, and evaluation of potent bryostatin analogs that modulate PKC translocation selectivity.

    Science.gov (United States)

    Wender, Paul A; Baryza, Jeremy L; Brenner, Stacey E; DeChristopher, Brian A; Loy, Brian A; Schrier, Adam J; Verma, Vishal A

    2011-04-26

    Modern methods for the identification of therapeutic leads include chemical or virtual screening of compound libraries. Nature's library represents a vast and diverse source of leads, often exhibiting exquisite biological activities. However, the advancement of natural product leads into the clinic is often impeded by their scarcity, complexity, and nonoptimal properties or efficacy as well as the challenges associated with their synthesis or modification. Function-oriented synthesis represents a strategy to address these issues through the design of simpler and therefore synthetically more accessible analogs that incorporate the activity-determining features of the natural product leads. This study illustrates the application of this strategy to the design and synthesis of functional analogs of the bryostatin marine natural products. It is specifically directed at exploring the activity-determining role of bryostatin A-ring functionality on PKC affinity and selectivity. The resultant functional analogs, which were prepared by a flexible, modular synthetic strategy, exhibit excellent affinity to PKC and differential isoform selectivity. These and related studies provide the basic information needed for the design of simplified and thus synthetically more accessible functional analogs that target PKC isoforms, major targets of therapeutic interest.

  19. Synthesis of a metal binding protein designed on the alpha/beta scaffold of charybdotoxin.

    Science.gov (United States)

    Pierret, B; Virelizier, H; Vita, C

    1995-12-01

    The alpha/beta scaffold of the scorpion toxin charybdotoxin has been used for the engineering of a metal binding site. Nine substitutions, including three histidines as metal ligands, have been introduced into the original toxin sequence. The newly designed sequence, 37 amino acids long, has been assembled by solid-phase synthesis and HBTU (2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate) coupling of Fmoc-protected amino acids. Formation of the three disulfide bonds occurred efficiently and rapidly in the presence of glutathione, and this post-synthesis modification has facilitated the purification task enormously. The process of synthesis and purification was performed in less than a week with an overall 10.2% yield. Circular dichroism analysis showed that the newly designed protein is folded in a alpha/beta structure, similarly to the parent toxin. Electronic absorption spectroscopy, circular dichroism and gel filtration experiments have been used to show that Cu2+ and Zn2+ ions bind with high affinity to the newly engineered protein. These results demonstrate that the alpha/beta fold, common to all scorpion toxins, is a very versatile basic structure, tolerant for substitutions and able to present new sequences in a predetermined conformation. The chemical approach is shown to be effective, rapid and practical for the production of novel designed small proteins.

  20. Controller design for wind turbine load reduction via multiobjective parameter synthesis

    Science.gov (United States)

    Hoffmann, A. F.; Weiβ, F. A.

    2016-09-01

    During the design process for a wind turbine load reduction controller many different, sometimes conflicting requirements must be fulfilled simultaneously. If the requirements can be expressed as mathematical criteria, such a design problem can be solved by a criterion-vector and multi-objective design optimization. The software environment MOPS (Multi-Objective Parameter Synthesis) supports the engineer for such a design optimization. In this paper MOPS is applied to design a multi-objective load reduction controller for the well-known DTU 10 MW reference wind turbine. A significant reduction in the fatigue criteria especially the blade damage can be reached by the use of an additional Individual Pitch Controller (IPC) and an additional tower damper. This reduction is reached as a trade-off with an increase of actuator load.

  1. Design, synthesis, and evaluation of mitomycin-tethered phosphorothioate oligodeoxynucleotides.

    Science.gov (United States)

    Huh, N; Rege, A A; Yoo, B; Kogan, T P; Kohn, H

    1996-01-01

    separate from 22. In the second procedure, phosphorothioate oligodexynucleotides that contained a hexylamino spacer at the 5'termini were coupled to 10-des(carbamoyloxy)-10-isothiocyanatoporfiromycin (9). Compound 9 was prepared in four steps from 11. Mesylation (methanesulfonyl chloride/pyridine) of 11 gave the C(10) mesylate 13, which was then treated with NaN3 (dimethylformamide, 90 degrees C) to give 10-des(carbamoyloxy)-10-azidoporfiromycin (14). Catalytic reduction (PtO2, H2) of 14 in pyridine afforded C(10) amine 15. Treatment of 15 with di-2-pyridyl thionocarbonate provided the desired 10-des(carbamoyloxy)-10-isothiocyanatoporfiromycin (9). Compound 9 readily coupled with 17 and base in both methylene chloride and aqueous buffered solutions to give 25. Use of the 5'hexylaminophosphorothioate oligodeoxynucleotides 32-35 in place of 17 gave the conjugated adducts 28-31, respectively, in a 12% to near-quantitative yield. The products were purified by semipreparative HPLC. Antisense agents 28-31 were designed to target a 30-base-long region from the coding region of the human FGFR1 gene. One adduct, 29, reduced the number of FGFR1 receptors in human aortic smooth cells for bFGF on the cell surface, which suggested down-regulation of FGFR1 gene expression. Further, 29 inhibited cultured human aortic smooth muscle cell proliferation and was less cytotoxic than porfiromycin (2). The biological assay data suggest that the phosphorothioate oligodexynucleotide porfiromycin conjugates may be more target selective and less toxic than either mitomycin or porfiromycin and thus be promising therapeutic agents.

  2. Airline Maintenance Manpower Optimization from the De Novo Perspective

    Science.gov (United States)

    Liou, James J. H.; Tzeng, Gwo-Hshiung

    Human resource management (HRM) is an important issue for today’s competitive airline marketing. In this paper, we discuss a multi-objective model designed from the De Novo perspective to help airlines optimize their maintenance manpower portfolio. The effectiveness of the model and solution algorithm is demonstrated in an empirical study of the optimization of the human resources needed for airline line maintenance. Both De Novo and traditional multiple objective programming (MOP) methods are analyzed. A comparison of the results with those of traditional MOP indicates that the proposed model and solution algorithm does provide better performance and an improved human resource portfolio.

  3. Design and Synthesis of a Novel Ganglioside Ligand for Influenza A Viruses

    Directory of Open Access Journals (Sweden)

    Tomohiro Nohara

    2012-08-01

    Full Text Available A novel ganglioside bearing Neua2-3Gal and Neua2-6Gal structures as distal sequences was designed as a ligand for influenza A viruses. The efficient synthesis of the designed ganglioside was accomplished by employing the cassette coupling approach as a key reaction, which was executed between the non-reducing end of the oligosaccharide and the cyclic glucosylceramide moiety. Examination of its binding activity to influenza A viruses revealed that the new ligand is recognized by Neua2-3 and 2-6 type viruses.

  4. A general framework for the synthesis and operational design of batch processes

    DEFF Research Database (Denmark)

    Papaeconomou, Eirini; Gani, Rafiqul; Jørgensen, Sten Bay

    2002-01-01

    , for the operational design of batch reactors. A case study involving the feasible operation of a batch reactor with multiple desirable and undesirable reactions and operational constraints is presented. Application results including verification of the generated operational sequences (alternatives) through dynamic......The objective of this paper is to present a general problem formulation and a general methodology for the synthesis of batch operations and the operational design of individual batch processes, such as mixing, reaction and separation. The general methodology described supplies the batch routes...

  5. Design and Synthesis of Pyrazole-3-one Derivatives as Hypoglycaemic Agents

    Directory of Open Access Journals (Sweden)

    Prasanna A. Datar

    2015-01-01

    Full Text Available Pyrazole-3-one compounds were designed on the basis of docking studies of previously reported antidiabetic pyrazole compounds. The amino acid residues found during docking studies were used as guidelines for the modification of aromatic substitutions on pyrazole-3-one structure. Depending on the docking score, the designed compounds were selectively prioritized for synthesis. The synthesized compounds were subjected to in vivo hypoglycemic activity using alloxan induced diabetic rats and metformin as a standard. Compound 4 having sulphonamide derivative was found to be the most potent compound among the series.

  6. Novel meta-surface design synthesis via nature-inspired optimization algorithms

    Science.gov (United States)

    Bayraktar, Zikri

    Heuristic numerical optimization algorithms have been gaining interest over the years as the computational power of the digital computers increases at an unprecedented level every year. While mature techniques such as the Genetic Algorithm increase their application areas, researchers also try to come up with new algorithms by simply observing the highly tuned processes provided by the nature. In this dissertation, the well-known Genetic Algorithm (GA) will be utilized to tackle various novel electromagnetic optimization problems, along with parallel implementation of the Clonal Selection Algorithm (CLONALG) and newly introduced the Wind Driven Optimization (WDO) technique. The utility of the CLONALG parallelization and the efficiency of the WDO will be illustrated by applying them to multi-dimensional and multi-modal electromagnetics problems such as antenna design and metamaterial surface synthesis. One of the metamaterial application areas is the design synthesis of 90 degrees rotationally symmetric ultra-small unit cell artificial magnetic conducting (AMC) surfaces. AMCs are composite metallo-dielectric structures designed to behave as perfect magnetic conductors (PMC) over a certain frequency range, those exhibit a reflection coefficient magnitude of unity with an phase angle of zero degrees at the center of the band. The proposed designs consist of ultra small sized frequency selective surface (FSS) unit cells that are tightly packed and highly intertwined, yet achieve remarkable AMC band performance and field of view when compared to current state-of-the-art AMCs. In addition, planar double-sided AMC (DSAMC) structures are introduced and optimized as AMC ground planes for low profile antennas in composite platforms and separator slabs for vertical antenna applications. The proposed designs do not possess complete metallic ground planes, which makes them ideal for composite and multi-antenna systems. The versatility of the DSAMC slabs is also illustrated

  7. Pesquisa de novos elementos Pesquisa de novos elementos

    Directory of Open Access Journals (Sweden)

    Gil Mário de Macedo Grassi

    1978-11-01

    Full Text Available The present study deals with the discovery of new elements synthesized by man. The introduction discusses in general the theories about nuclear transmutation, which is the method employed in these syntheses. The study shows the importance of the Periodical Table since it is through this table that one can reach a prevision of new elements and its, properties. The discoveries of the transuranic elements, together wich the data of their first preparations are also tabulated The stability of these elements is also discussed, and future speculations are showedNeste trabalho estuda-se, teoricamente, a descoberta de novos elementos sintetizados pelo homem Na introdução apresentamos um apanhado geral sobre as teorias a respeito da transmutação nuclear, que é o método utilizado nestas sínteses. Em seguida, mostramos a importância da Tabela Periódica, pois é através dela que se chega à previsão dos novos elementos e de suas propriedades. As descobertas dos transurânicos, Já realizadas com êxito, juntamente com os dados de suas primeiras preparações são tabelados. A estabilidade destes novos elementos também é discutida, e apresentadas futuras especulações.

  8. A Method for Sustainable Carbon Dioxide Utilization Process Synthesis and Design

    DEFF Research Database (Denmark)

    Frauzem, Rebecca; Fjellerup, Kasper; Roh, Kosan

    for the process synthesis, design and more sustainable design. Using a superstructure-based approach a network of utilization alternatives is created linking CO2 and other raw materials with various products using processing blocks. This will then be optimized and verified for sustainability. Detailed design has...... also been performed for various case studies. These case studies include multiple pathways for the production of methanol and the production of dimethyl carbonate (DMC). From detailed design and analysis, CO2 conversion processes show promise as an additional method for the sustainable reduction of CO2...... compounds via chemical reactions. However, conversion is still in its infancy and requires work for implementation at an industrial level. One aspect of this is the development of a methodology for the formulation and optimization of sustainable conversion processes. This methodology follows three stages...

  9. Particle swarm optimisation driven low cost single event transient fault secured design during architectural synthesis

    Directory of Open Access Journals (Sweden)

    Anirban Sengupta

    2017-04-01

    Full Text Available Owing to aggressive shrinking in nanometre scale as well as faster devices, particle strike manifesting itself into transient fault spanning multiple cycle and multiple units will be the centre-focus of application specific datapath generated through high-level synthesis (HLS/architectural synthesis. Addressing each problem above separately leads to large area/delay overhead; thus tackling both problems concurrently, leads to huge incurred overhead. To tackle this complex problem, this paper proposes a novel low cost particle swarm optimisation driven dual modular redundant (DMR based HLS methodology for generation of a transient fault secured design secured against its temporal and spatial effects. The authors' approach provides a low cost optimised fault secured solution through a particle swarm optimisation exploration framework based on user area-delay constraints. Results indicated that proposed approach obtains an area overhead reduction of 34.08% and latency overhead reduction of 5.8% compared with a recent approach.

  10. Rational design, synthesis, purification, and activation of metal-organic framework materials.

    Science.gov (United States)

    Farha, Omar K; Hupp, Joseph T

    2010-08-17

    The emergence of metal-organic frameworks (MOFs) as functional ultrahigh surface area materials is one of the most exciting recent developments in solid-state chemistry. Now constituting thousands of distinct examples, MOFs are an intriguing class of hybrid materials that exist as infinite crystalline lattices with inorganic vertices and molecular-scale organic connectors. Useful properties such as large internal surface areas, ultralow densities, and the availability of uniformly structured cavities and portals of molecular dimensions characterize functional MOFs. Researchers have effectively exploited these unusual properties in applications such as hydrogen and methane storage, chemical separations, and selective chemical catalysis. In principle, one of the most attractive features of MOFs is the simplicity of their synthesis. Typically they are obtained via one-pot solvothermal preparations. However, with the simplicity come challenges. In particular, MOF materials, especially more complex ones, can be difficult to obtain in pure form and with the optimal degree of catenation, the interpenetration or interweaving of identical independent networks. Once these two issues are satisfied, the removal of the guest molecules (solvent from synthesis) without damaging the structural integrity of the material is often an additional challenge. In this Account, we review recent advances in the synthetic design, purification, and activation of metal-organic framework materials. We describe the rational design of a series of organic struts to limit framework catenation and thereby produce large pores. In addition, we demonstrate the rapid separation of desired MOFs from crystalline and amorphous contaminants cogenerated during synthesis based on their different densities. Finally, we discuss the mild and efficient activation of initially solvent-filled pores with supercritical carbon dioxide, yielding usable channels and high internal surface areas. We expect that the

  11. Total synthesis of crocacins A, C and D: new antibiotics isolated from Chondromyces crocatus and Chondromyces pediculatus; Sinteses totais das crocacinas A, C e D: novos antibioticos isolados de Chondromyces crocatus e Chondromyces pediculatus

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Luciana G. de; Dias, Luiz C.; Rosso, Giovanni B. [Universidade Estadual de Campinas (UNICAMP), Campinas, SP (Brazil). Inst. de Quimica]. E-mail: luciana@iqm.unicamp.br

    2008-07-01

    This review describes the endeavors that led to the total synthesis of a novel class of antibiotic compounds: the crocacins A-D. Other aspects such as isolation, structural elucidation as well as the biological activities are also presented. (author)

  12. Expediting analog design retargeting by design knowledge re-use and circuit synthesis: a practical example on a Delta-Sigma modulator

    Science.gov (United States)

    Webb, Matthew; Tang, Hua

    2016-08-01

    In the past decade or two, due to constant and rapid technology changes, analog design re-use or design retargeting to newer technologies has been brought to the table in order to expedite the design process and improve time-to-market. If properly conducted, analog design retargeting could significantly cut down design cycle compared to designs starting from the scratch. In this article, we present an empirical and general method for efficient analog design retargeting by design knowledge re-use and circuit synthesis (CS). The method first identifies circuit blocks that compose the source system and extracts the performance parameter specifications of each circuit block. Then, for each circuit block, it scales the values of design variables (DV) from the source design to derive an initial design in the target technology. Depending on the performance of this initial target design, a design space is defined for synthesis. Subsequently, each circuit block is automatically synthesised using state-of-art analog synthesis tools based on a combination of global and local optimisation techniques to achieve comparable performance specifications to those extracted from the source system. Finally, the overall system is composed of those synthesised circuit blocks in the target technology. We illustrate the method using a practical example of a complex Delta-Sigma modulator (DSM) circuit.

  13. Maximum Entropy/Optimal Projection (MEOP) control design synthesis: Optimal quantification of the major design tradeoffs

    Science.gov (United States)

    Hyland, D. C.; Bernstein, D. S.

    1987-01-01

    The underlying philosophy and motivation of the optimal projection/maximum entropy (OP/ME) stochastic modeling and reduced control design methodology for high order systems with parameter uncertainties are discussed. The OP/ME design equations for reduced-order dynamic compensation including the effect of parameter uncertainties are reviewed. The application of the methodology to several Large Space Structures (LSS) problems of representative complexity is illustrated.

  14. Toward Developing Made-to-Order Metal-Organic Frameworks: Design, Synthesis and Applications

    KAUST Repository

    Ashri, Lubna Y.

    2016-05-26

    Synthesis of materials with certain properties for targeted applications is an ongoing challenge in materials science. One of the most interesting classes of solid-state materials that have been recently introduced with the potential to address this is metal-organic frameworks (MOFs). MOFs chemistry offers a higher degree of control over materials to be synthesized utilizing various new design strategies, such as the molecular building blocks (MBBs) and the supermolecular building layers (SBLs) approaches. Depending on using predetermined building blocks, these strategies permit the synthesis of MOFs with targeted topologies and enable fine tuning of their properties. This study examines a number of aspects of the design and synthesis of MOFs while exploring their possible utilization in two diverse fields related to energy and pharmaceutical applications. Concerning MOFs design and synthesis, the work presented here explores the rational design of various MOFs with predicted topologies and tunable cavities constructed by pillaring pre-targeted 2-periodic SBLs using the ligand-to-axial and six-connected axial-to-axial pillaring strategies. The effect of expanding the confined spaces in prepared MOFs or modifying their functionalities, while preserving the underlying network topology, was investigated. Additionally, The MBBs approach was employed to discover new modular polynuclear rare earth (RE)-MBBs in the presence of different angular polytopic ligands containing carboxylate and nitrogen moieties with the aid of a modulator. The goal was to assess the diverse possible coordination modes and construct highly-connected nets for utility in the design of new MOFs and enhance the predictability of structural outcomes. The effect of adjusting ligands’ length-to-width ratio on the prepared MOFs was also evaluated. As a result, the reaction conditions amenable for reliable formation of the unprecedented octadecanuclear, octanuclear and double tetranuclear RE-MBBs were

  15. The significance of different diacylgycerol synthesis pathways on plant oil composition and bioengineering

    Directory of Open Access Journals (Sweden)

    Philip David Bates

    2012-07-01

    Full Text Available The unique properties of vegetable oils from different plants utilized for food, industrial feedstocks, and fuel is dependent on the fatty acid (FA composition of triacylglycerol (TAG. Plants can use two main pathways to produce diacylglycerol (DAG, the immediate precursor molecule to TAG synthesis: 1 De novo DAG synthesis, and 2 conversion of the membrane lipid phosphatidylcholine (PC to DAG. The FA esterified to PC are also the substrate for FA modification (e.g. desaturation, hydroxylation, etc., such that the FA composition of PC-derived DAG can be substantially different than that of de novo DAG. Since DAG provides two of the three FA in TAG, the relative flux of TAG synthesis from de novo DAG or PC-derived DAG can greatly affect the final oil FA composition. Here we review how the fluxes through these two alternate pathways of DAG/TAG synthesis are determined and present evidence that suggests which pathway is utilized in different plants. Additionally, we present examples of how the endogenous DAG synthesis pathway in a transgenic host plant can produce bottlenecks for engineering of plant oil FA composition, and discuss alternative strategies to overcome these bottlenecks to produce crop plants with designer vegetable oil compositions.

  16. A robust variable sampling time BLDC motor control design based upon μ-synthesis.

    Science.gov (United States)

    Hung, Chung-Wen; Yen, Jia-Yush

    2013-01-01

    The variable sampling rate system is encountered in many applications. When the speed information is derived from the position marks along the trajectory, one would have a speed dependent sampling rate system. The conventional fixed or multisampling rate system theory may not work in these cases because the system dynamics include the uncertainties which resulted from the variable sampling rate. This paper derived a convenient expression for the speed dependent sampling rate system. The varying sampling rate effect is then translated into multiplicative uncertainties to the system. The design then uses the popular μ-synthesis process to achieve a robust performance controller design. The implementation on a BLDC motor demonstrates the effectiveness of the design approach.

  17. A Robust Variable Sampling Time BLDC Motor Control Design Based upon μ-Synthesis

    Directory of Open Access Journals (Sweden)

    Chung-Wen Hung

    2013-01-01

    Full Text Available The variable sampling rate system is encountered in many applications. When the speed information is derived from the position marks along the trajectory, one would have a speed dependent sampling rate system. The conventional fixed or multisampling rate system theory may not work in these cases because the system dynamics include the uncertainties which resulted from the variable sampling rate. This paper derived a convenient expression for the speed dependent sampling rate system. The varying sampling rate effect is then translated into multiplicative uncertainties to the system. The design then uses the popular μ-synthesis process to achieve a robust performance controller design. The implementation on a BLDC motor demonstrates the effectiveness of the design approach.

  18. Systemic design methodologies for electrical energy systems analysis, synthesis and management

    CERN Document Server

    Roboam, Xavier

    2012-01-01

    This book proposes systemic design methodologies applied to electrical energy systems, in particular analysis and system management, modeling and sizing tools. It includes 8 chapters: after an introduction to the systemic approach (history, basics & fundamental issues, index terms) for designing energy systems, this book presents two different graphical formalisms especially dedicated to multidisciplinary devices modeling, synthesis and analysis: Bond Graph and COG/EMR. Other systemic analysis approaches for quality and stability of systems, as well as for safety and robustness analysis tools are also proposed. One chapter is dedicated to energy management and another is focused on Monte Carlo algorithms for electrical systems and networks sizing. The aim of this book is to summarize design methodologies based in particular on a systemic viewpoint, by considering the system as a whole. These methods and tools are proposed by the most important French research laboratories, which have many scientific partn...

  19. Alcohol Dehydrogenase 5 Is a Source of Formate for De Novo Purine Biosynthesis in HepG2 Cells.

    Science.gov (United States)

    Bae, Sajin; Chon, James; Field, Martha S; Stover, Patrick J

    2017-04-01

    Background: Formate provides one-carbon units for de novo purine and thymidylate (dTMP) synthesis and is produced via both folate-dependent and folate-independent pathways. Folate-independent pathways are mediated by cytosolic alcohol dehydrogenase 5 (ADH5) and mitochondrial aldehyde dehydrogenase 2 (ALDH2), which generate formate by oxidizing formaldehyde. Formate is a potential biomarker of B-vitamin-dependent one-carbon metabolism.Objective: This study investigated the contributions of ADH5 and ALDH2 to formate production and folate-dependent de novo purine and dTMP synthesis in HepG2 cells.Methods:ADH5 knockout and ALDH2 knockdown HepG2 cells were cultured in folate-deficient [0 nM (6S) 5-formyltetrahydrofolate] or folate-sufficient [25 nM (6S) 5-formyltetrahydrofolate] medium. Purine biosynthesis was quantified as the ratio of [(14)C]-formate to [(3)H]-hypoxanthine incorporated into genomic DNA, which indicates the contribution of the de novo purine synthesis pathway relative to salvage synthesis. dTMP synthesis was quantified as the ratio of [(14)C]-deoxyuridine to [(3)H]-thymidine incorporation into genomic DNA, which indicates the capacity of de novo dTMP synthesis relative to salvage synthesis.Results: The [(14)C]-formate-to-[(3)H]-hypoxanthine ratio was greater in ADH5 knockout than in wild-type HepG2 cells, under conditions of both folate deficiency (+30%; P HepG2 cells, indicating decreased use of exogenous formate, or increased endogenous formate synthesis, for de novo purine biosynthesis.Conclusions: In HepG2 cells, ADH5 is a source of formate for de novo purine biosynthesis, especially during folate deficiency when folate-dependent formate production is limited. Formate is also shown to be limiting in the growth of HepG2 cells. © 2017 American Society for Nutrition.

  20. Software-based high-level synthesis design of FPGA beamformers for synthetic aperture imaging.

    Science.gov (United States)

    Amaro, Joao; Yiu, Billy Y S; Falcao, Gabriel; Gomes, Marco A C; Yu, Alfred C H

    2015-05-01

    Field-programmable gate arrays (FPGAs) can potentially be configured as beamforming platforms for ultrasound imaging, but a long design time and skilled expertise in hardware programming are typically required. In this article, we present a novel approach to the efficient design of FPGA beamformers for synthetic aperture (SA) imaging via the use of software-based high-level synthesis techniques. Software kernels (coded in OpenCL) were first developed to stage-wise handle SA beamforming operations, and their corresponding FPGA logic circuitry was emulated through a high-level synthesis framework. After design space analysis, the fine-tuned OpenCL kernels were compiled into register transfer level descriptions to configure an FPGA as a beamformer module. The processing performance of this beamformer was assessed through a series of offline emulation experiments that sought to derive beamformed images from SA channel-domain raw data (40-MHz sampling rate, 12 bit resolution). With 128 channels, our FPGA-based SA beamformer can achieve 41 frames per second (fps) processing throughput (3.44 × 10(8) pixels per second for frame size of 256 × 256 pixels) at 31.5 W power consumption (1.30 fps/W power efficiency). It utilized 86.9% of the FPGA fabric and operated at a 196.5 MHz clock frequency (after optimization). Based on these findings, we anticipate that FPGA and high-level synthesis can together foster rapid prototyping of real-time ultrasound processor modules at low power consumption budgets.

  1. Design, Specification, and Synthesis of Aircraft Electric Power Systems Control Logic

    Science.gov (United States)

    Xu, Huan

    Cyber-physical systems integrate computation, networking, and physical processes. Substantial research challenges exist in the design and verification of such large-scale, distributed sensing, actuation, and control systems. Rapidly improving technology and recent advances in control theory, networked systems, and computer science give us the opportunity to drastically improve our approach to integrated flow of information and cooperative behavior. Current systems rely on text-based specifications and manual design. Using new technology advances, we can create easier, more efficient, and cheaper ways of developing these control systems. This thesis will focus on design considerations for system topologies, ways to formally and automatically specify requirements, and methods to synthesize reactive control protocols, all within the context of an aircraft electric power system as a representative application area. This thesis consists of three complementary parts: synthesis, specification, and design. The first section focuses on the synthesis of central and distributed reactive controllers for an aircraft elec- tric power system. This approach incorporates methodologies from computer science and control. The resulting controllers are correct by construction with respect to system requirements, which are formulated using the specification language of linear temporal logic (LTL). The second section addresses how to formally specify requirements and introduces a domain-specific language for electric power systems. A software tool automatically converts high-level requirements into LTL and synthesizes a controller. The final sections focus on design space exploration. A design methodology is proposed that uses mixed-integer linear programming to obtain candidate topologies, which are then used to synthesize controllers. The discrete-time control logic is then verified in real-time by two methods: hardware and simulation. Finally, the problem of partial observability and

  2. Automatic Synthesis of UML Designs from Requirements in an Iterative Process

    Science.gov (United States)

    Schumann, Johann; Whittle, Jon; Clancy, Daniel (Technical Monitor)

    2001-01-01

    The Unified Modeling Language (UML) is gaining wide popularity for the design of object-oriented systems. UML combines various object-oriented graphical design notations under one common framework. A major factor for the broad acceptance of UML is that it can be conveniently used in a highly iterative, Use Case (or scenario-based) process (although the process is not a part of UML). Here, the (pre-) requirements for the software are specified rather informally as Use Cases and a set of scenarios. A scenario can be seen as an individual trace of a software artifact. Besides first sketches of a class diagram to illustrate the static system breakdown, scenarios are a favorite way of communication with the customer, because scenarios describe concrete interactions between entities and are thus easy to understand. Scenarios with a high level of detail are often expressed as sequence diagrams. Later in the design and implementation stage (elaboration and implementation phases), a design of the system's behavior is often developed as a set of statecharts. From there (and the full-fledged class diagram), actual code development is started. Current commercial UML tools support this phase by providing code generators for class diagrams and statecharts. In practice, it can be observed that the transition from requirements to design to code is a highly iterative process. In this talk, a set of algorithms is presented which perform reasonable synthesis and transformations between different UML notations (sequence diagrams, Object Constraint Language (OCL) constraints, statecharts). More specifically, we will discuss the following transformations: Statechart synthesis, introduction of hierarchy, consistency of modifications, and "design-debugging".

  3. Exploration of dual supply voltage logic synthesis in state-of-the-art ASIC design flows

    Directory of Open Access Journals (Sweden)

    T. Mahnke

    2003-01-01

    Full Text Available Dual supply voltage scaling (DSVS for logiclevel power optimization at the has increasingly attracted attention over the last few years. However, mainly due to the fact that the most widely used design tools do not support this new technique, it has still not become an integral part of real-world design flows. In this paper, a novel logic synthesis methodology that enables DSVS while relying entirely on standard tools is presented. The key to this methodology is a suitably modeled dual supply voltage (DSV standard cell library. A basic evaluation of the methodology has been carried out on a number of MCNC benchmark circuits. In all these experiments, the results of state-of-the-art powerdriven single supply voltage (SSV logic synthesis have been used as references in order to determine the true additional benefit of DSVS. Compared with the results of SSV power optimization, additional power reductions of 10% on average have been achieved. The results prove the feasibility of the new approach and reveal its greater efficiency in comparison with a well-known dedicated DSVS algorithm. Finally, the methodology has been applied to an embedded microcontroller core in order to further explore the potentials and limitations of DSVS in an existing industrial design environment.

  4. Optimal hardware/software co-synthesis for core-based SoC designs

    Institute of Scientific and Technical Information of China (English)

    Zhan Jinyu; Xiong Guangze

    2006-01-01

    A hardware/software co-synthesis method is presented for SoC designs consisting of both hardware IP cores and software components on a graph-theoretic formulation. Given a SoC integrated with a set of functions and a set of performance factors, a core for each function is selected from a set of alternative IP cores and software components, and optimal partitions is found in a way to evenly balance the performance factors and to ultimately reduce the overall cost, size, power consumption and runtime of the core-based SoC. The algorithm formulates IP cores and components into the corresponding mathematical models, presents a graph-theoretic model for finding the optimal partitions of SoC design and transforms SoC hardware/software co-synthesis problem into finding optimal paths in a weighted, directed graph. Overcoming the three main deficiencies of the traditional methods, this method can work automatically, evaluate more performance factors at the same time and meet the particularity of SoC designs.At last, the approach is illustrated that is practical and effective through partitioning a practical system.

  5. Synthesis/design optimization of SOFC-PEM hybrid system under uncertainty

    Institute of Scientific and Technical Information of China (English)

    Lingjun Tan; Chen Yang; Nana Zhou

    2015-01-01

    Solid oxide fuel cell–proton exchange membrane (SOFC–PEM) hybrid system is being foreseen as a valuable alternative for power generation. As this hybrid system is a conceptual design, many uncertainties involving input values should be considered at the early stage of process optimization. We present in this paper a general-ized framework of multi-objective optimization under uncertainty for the synthesis/design optimization of the SOFC–PEM hybrid system. The framework is based on geometric, economic and electrochemical models and focuses on evaluating the effect of uncertainty in operating parameters on three conflicting objectives:electricity efficiency, SOFC current density and capital cost of system. The multi-objective optimization provides solutions in the form of a Pareto surface, with a range of possible synthesis/design solutions and a logical procedure for searching the global optimum solution for decision maker. Comparing the stochastic and deterministic Pareto surfaces of different objectives, we conclude that the objectives are considerably influenced by uncertainties because the two trade-off surfaces are different.

  6. Understanding Mechanism and Designing Strategies for Sustainable Synthesis of Zeolites: A Personal Story.

    Science.gov (United States)

    Wang, Yeqing; Xiao, Feng-Shou

    2016-06-01

    Zeolites with intricate micropores have been widely studied for a long time as an important class of porous materials in different areas of industrial processes such as gas adsorption and separation, ion exchange, and shape-selective catalysis. However, their industrial syntheses are not sustainable, and normally require the presence of expensive organic templates and a large amount of solvents such as water. The presence of organic templates not only increases zeolite cost but also produces harmful gases during the removal of these templates by calcination, while the use of solvents significantly increases the amount of polluted water. This Personal Account briefly summarizes recent sustainable routes for the synthesis of zeolites in our group according to our understanding of the synthetic mechanism, and mainly focuses on the organotemplate-free synthesis of zeolites in the presence of zeolite seeds, the design of environmentally friendly templates, and solvent-free synthesis of zeolites. © 2016 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Design for robustness using the μ-synthesis applied to launcher attitude and vibration control

    Science.gov (United States)

    Morita, Yasuhiro; Goto, Shinichi

    2008-01-01

    The M-V launch vehicle of Japan Aerospace Exploration Agency (JAXA) has successfully injected Japan's fifth X-ray space telescope "SUZAKU" into its low earth orbit in this past July. The attitude and vibration control algorithm of the M-V rocket used to be highlighted by its H∞ robust stability since its first flight conducted in 1997. Beyond this, its robustness character has been further enhanced using the μ-synthesis approach to get better robust characteristics not only in stability but in tracking performance under uncertainty of the system dynamics. The performance has been validated by the latest back-to-back successful flights of the vehicle: in May 2003 to directly inject Japan's first asteroid sample return spaceship "HAYABUSA" into the planned inter-planetary trajectory and in this past July to launch the telescope. The μ-synthesis has been applied for the first time ever for Japan's launcher control beyond the reliable H∞ design. The plant dynamics has an extremely high-order and unstable characteristics, thus the standard μ-synthesis format cannot be directly applied. The paper gives a unique methodology to apply the theory to such a real high-order complicated system.

  8. Design and synthesis of organic-inorganic hybrid capsules for biotechnological applications.

    Science.gov (United States)

    Shi, Jiafu; Jiang, Yanjun; Wang, Xiaoli; Wu, Hong; Yang, Dong; Pan, Fusheng; Su, Yanlei; Jiang, Zhongyi

    2014-08-07

    Organic-inorganic hybrid capsules, which typically possess a hollow lumen and a hybrid wall, have emerged as a novel and promising class of hybrid materials and have attracted enormous attention. In comparison to polymeric capsules or inorganic capsules, the hybrid capsules combine the intrinsic physical/chemical properties of the organic and inorganic moieties, acquire more degrees of freedom to manipulate multiple interactions, create hierarchical structures and integrate multiple functionalities. Thus, the hybrid capsules exhibit superior mechanical strength (vs. polymeric capsules) and diverse functionalities (vs. inorganic capsules), which may give new opportunities to produce high-performance materials. Much effort has been devoted to exploring innovative and effective methods for the synthesis of hybrid capsules that exhibit desirable performance in target applications. This tutorial review firstly presents a brief description of the capsular structure and hybrid materials in nature, then classifies the hybrid capsules into molecule-hybrid capsules and nano-hybrid capsules based upon the size of the organic and inorganic moieties in the capsule wall, followed by a detailed discussion of the design and synthesis of the hybrid capsules. For each kind of hybrid capsule, the state-of-the-art synthesis methods are described in detail and a critical comment is embedded. The applications of these hybrid capsules in biotechnological areas (biocatalysis, drug delivery, etc.) have also been summarized. Hopefully, this review will offer a perspective and guidelines for the future research and development of hybrid capsules.

  9. Design, Synthesis and in Vivo Evaluation of Novel Glycosylated Sulfonylureas as Antihyperglycemic Agents.

    Science.gov (United States)

    Suaifan, Ghadeer A R Y; Shehadeh, Mayadah B; Darwish, Rula M; Al-Ijel, Hebah; Abbate, Vincenzo

    2015-11-06

    Sulphonylurea compounds have versatile activities such as antidiabetic, diuretic, herbicide, oncolytic, antimalarial, antifungal and anticancer. The present study describes the design, synthesis and in vivo testing of novel glycosylated aryl sulfonylurea compounds as antihyperglycaemic agents in streptozocine-induced diabetic mice. The rational for the introduction of the glucosamine moiety is to enhance selective drug uptake by pancreatic β-cells in order to decrease the cardiotoxic side effect commonly associated with sulfonylurea agents. 2-Deoxy-2-(4-chlorophenylsulfonylurea)-D-glucopyranose was found to be the most potent antihyperglycaemic agents among the synthesized compounds in diabetic mice. This investigation indicates the importance of this novel class as potential antihyperglycaemic agents.

  10. Molecular design, synthesis and biological activities of amidines as new ketol-acid reductoisomerase inhibitors

    Institute of Scientific and Technical Information of China (English)

    Bao Lei Wang; Yong Hong Li; Jian Guo Wang; Yi Ma; Zheng Ming Li

    2008-01-01

    Diamidine (A) was identified in our in vitro bio-assay as a possible inhibitor of ketol-acid reductoisomerase (KARI) from the ACD database search based on the known three-dimensional crystal structure of KARI. An investigation on interaction of A on KARI active sites, led to the design and synthesis of 15 novel monoamidines. Some of those showed better biological activity than A on rice KARI (in vitro) and in greenhouse herbicidal tests (in vivo). The structure-biological activity relationship was investigated, which provides valuable information to further study of potential KARI inhibitors.

  11. Design, synthesis and initial biological evaluation of a novel pladienolide analog scaffold.

    Science.gov (United States)

    Gundluru, Mahesh Kumar; Pourpak, Alan; Cui, Xiaoli; Morris, Stephan W; Webb, Thomas R

    2011-01-01

    A novel and simplified synthetic scaffold based on pladienolide was designed using a consensus pharmacophore hypothesis. An initial target was synthesized and evaluated to examine the role of the 3-hydroxy group and the methyl groups present at positions 10, 16, 20, 22 in 1, on biological activity. We report the first totally synthetic analog of this macrolide that shows biological activity. Our novel synthetic strategy enables the rapid synthesis of other new analogs of pladienolide in order to develop selective anticancer lead compounds.

  12. Process Synthesis, Design and Analysis using Process-Group Contribution Method

    DEFF Research Database (Denmark)

    Kumar Tula, Anjan; Eden, Mario Richard; Gani, Rafiqul

    Process synthesis implies the investigation of chemical reactions needed to produce the desired product, selection of the separation tec hniques needed for downstream processing, as well as making decisions on sequencing the involved reaction and separation operations. This work highlights...... the development of computer aided methodology for fast , reliable and consistent generation of process flowsheets and rank them based on various flowsheet performance indices. This Computer Aided Flowsheet Design methodology is a hybrid approach[1] that combines the physical insights of the knowledge based...

  13. Zeolite-like metal–organic frameworks (ZMOFs): design, synthesis, and properties

    KAUST Repository

    Eddaoudi, Mohamed

    2014-10-24

    This review highlights various design and synthesis approaches toward the construction of ZMOFs, which are metal–organic frameworks (MOFs) with topologies and, in some cases, features akin to traditional inorganic zeolites. The interest in this unique subset of MOFs is correlated with their exceptional characteristics arising from the periodic pore systems and distinctive cage-like cavities, in conjunction with modular intra- and/or extra-framework components, which ultimately allow for tailoring of the pore size, pore shape, and/or properties towards specific applications.

  14. Design and synthesis of new polyaromatic scaffolds for nano-scale applications

    OpenAIRE

    de Mendoza Bonmatí, Paula

    2010-01-01

    Design and Synthesis of New Polyaromatic Scaffolds for Nano-Scale ApplicationsResumen: En la última década, el diseño y la síntesis de nuevos sistemas poliaromáticos han resultado de gran interés gracias a sus propiedades únicas y sus aplicaciones potenciales para la obtención de dispositivos electrónicos, y como precursores de fullerenos. Hemos estudiado el mecanismo que procede a través de la activación del enlace C-H en la reacción intramolecular de arilación directa catalizada por paladio...

  15. Design, Synthesis, Antinociceptive and Anti-Inflammatory Activities of Novel Piroxicam Analogues

    Directory of Open Access Journals (Sweden)

    Eliezer J. Barreiro

    2012-11-01

    Full Text Available In this paper we report the design, synthesis, antinociceptive and anti-inflammatory activities of a series of benzothiazine N-acylhydrazones 14a–h, planned by structural modification of piroxicam (1, a non steroidal anti-inflammatory drug. Among the synthesized analogues, compounds 14f (LASSBio-1637 and 14g (LASSBio-1639 were identified as novel antinociceptive and anti-inflammatory prototypes, active by oral administration, acting by a mechanism of action that seems to be different from that of piroxicam, since they were inactive as an inhibitor of cyclooxygenase (COX-1 and COX-2 at concentrations of 10 mM.

  16. Design, synthesis, antinociceptive and anti-inflammatory activities of novel piroxicam analogues.

    Science.gov (United States)

    de Miranda, Amanda Silva; Bispo Júnior, Walfrido; da Silva, Yolanda Karla Cupertino; Alexandre-Moreira, Magna Suzana; Castro, Rosane de Paula; Sabino, José Ricardo; Lião, Luciano Morais; Lima, Lídia Moreira; Barreiro, Eliezer J

    2012-11-28

    In this paper we report the design, synthesis, antinociceptive and anti-inflammatory activities of a series of benzothiazine N-acylhydrazones 14a–h, planned by structural modification of piroxicam (1), a non steroidal anti-inflammatory drug. Among the synthesized analogues, compounds 14f (LASSBio-1637) and 14g (LASSBio-1639) were identified as novel antinociceptive and anti-inflammatory prototypes, active by oral administration, acting by a mechanism of action that seems to be different from that of piroxicam, since they were inactive as an inhibitor of cyclooxygenase (COX-1 and COX-2) at concentrations of 10 mM.

  17. Design,Synthesis,and Hypnotic Activity of Pyrazolo[1,5-a]pyrimidine Derivatives

    Institute of Scientific and Technical Information of China (English)

    Song Qing WANG; Lin FANG; Xiu Jie LIU; Kang ZHAO

    2004-01-01

    On the basis of the Zaleplon structure, novel pyrazolo[1,5-a]pyrimidines were designed and prepared for studies on their hypnotic activity.This paper reported the synthesis of twelve new 5-methyl-7-substituted-pyrazolo[1,5-a]pyrimidine-3-carbonitrile derivatives by using simple starting materials such as propane dinitrile and triethyl orthoformate.The structures of the derived target compounds were confirmed by their IR and 1H-NMR spectroscopic data.The preliminary pharmacological evaluations indicated that some compounds showed hypnotic activity, while derivative 1c was the most potent one.

  18. Rational Design, Synthesis and Evaluation of Coumarin Derivatives as Protein-protein Interaction Inhibitors.

    Science.gov (United States)

    De Luca, Laura; Agharbaoui, Fatima E; Gitto, Rosaria; Buemi, Maria Rosa; Christ, Frauke; Debyser, Zeger; Ferro, Stefania

    2016-09-01

    Herein we describe the design and synthesis of a new series of coumarin derivatives searching for novel HIV-1 integrase (IN) allosteric inhibitors. All new obtained compounds were tested in order to evaluate their ability to inhibit the interaction between the HIV-1 IN enzyme and the nuclear protein lens epithelium growth factor LEDGF/p75. A combined approach of docking and molecular dynamic simulations has been applied to clarify the activity of the new compounds. Specifically, the binding free energies by using the method of molecular mechanics-generalized Born surface area (MM-GBSA) was calculated, whereas hydrogen bond occupancies were monitored throughout simulations methods.

  19. Síntese e caracterização de um novo complexo de platina (IV a partir de seu análogo de platina (II utilizando iodo molecular como agente oxidante: uma rota sintética interessante para obtenção de novos complexos de platina Synthesis and characterization of a novel platinum (IV complex from its platinum (II analogue using molecular iodine as an oxidizing agent: an interesting synthetic route for the preparation of new platinum complexes

    Directory of Open Access Journals (Sweden)

    Wendell Guerra

    2007-02-01

    Full Text Available In an attempt to reduce toxicity and widen the spectrum of activity of cisplatin and its analogues, much attention has been focused on designing new platinum complexes. This work reports the synthesis and characterization of novel compounds of the platinum (II and platinum (IV containing 2-furoic hydrazide acid and iodide as ligands. Although the prepared compounds do not present the classical structure of biologically active platinum analogues, they could be potentially active or useful as precursors to prepare antitumor platinum complexes. The reported compounds were characterized by ¹H NMR, 13C NMR, 195Pt NMR, IR and elemental analyses.

  20. 'What-if' design: a synthesis method in the design process

    NARCIS (Netherlands)

    Lutters, Diederick; Vaneker, Thomas H.J.; van Houten, Frederikus J.A.M.

    2004-01-01

    In integrating functions, information and control in the design and engineering cycle, the information content acts as a facilitator, whereas the processes involved actually effectuate the results of the development cycle. As combining processes in an effective and efficient manner becomes increasin

  1. Synthesis of minimal-size ZnO nanoparticles through sol-gel method: Taguchi design optimisation

    OpenAIRE

    2015-01-01

    Zinc oxide (ZnO) has excellent potential to be used in water and wastewater treatment, either as a photocatalyst or in membrane incorporation. In this work, the synthesis of smaller ZnO NPs through a sol-gel approach was enhanced by applying Taguchi design. Recent work on the synthesis of ZnO NPs was optimised to ensure relatively smaller sized particles were obtained. Several parameters of the synthesis process, such as molar ratio of starting materials, molar concentration and calcination t...

  2. Synthesis of nucleotide–amino acid conjugates designed for photo-CIDNP experiments by a phosphotriester approach

    Directory of Open Access Journals (Sweden)

    Tatyana V. Abramova

    2013-12-01

    Full Text Available Conjugates of 2’-deoxyguanosine, L-tryptophan and benzophenone designed to study pathways of fast radical reactions by the photo Chemically Induced Dynamic Nuclear Polarization (photo-CIDNP method were obtained by the phosphotriester block liquid phase synthesis. The phosphotriester approach to the oligonucleotide synthesis was shown to be a versatile and economic strategy for preparing the required amount of high quality samples of nucleotide–amino acid conjugates.

  3. Exploration of Visible-Light Photocatalysis in Heterocycle Synthesis and Functionalization: Reaction Design and Beyond.

    Science.gov (United States)

    Chen, Jia-Rong; Hu, Xiao-Qiang; Lu, Liang-Qiu; Xiao, Wen-Jing

    2016-09-20

    Visible-light photocatalysis has recently received increasing attention from chemists because of its wide application in organic synthesis and its significance for sustainable chemistry. This catalytic strategy enables the generation of various reactive species, frequently without stoichiometric activation reagents under mild reaction conditions. Manipulation of these reactive intermediates can result in numerous synthetically useful bond formations in a controllable manner. In this Account, we describe our recent advances in the rational design and strategic application of photocatalysis in the synthesis of various synthetically and biologically important heterocycles. Our main research efforts toward this goal can be classified into four categories: formal cycloaddition and cyclization reactions, radical-mediated olefin functionalization/cyclization cascades, photocatalytic generation and cyclization of N-centered radicals, and photocatalytic functionalization of heterocycles by visible-light-induced dual catalysis. Inspired by the wide application of tertiary amines as reductive additives in photoredox catalysis, we exploited a series of readily accessible or rationally designed tertiary amines with reactive sites in a range of photocatalytic formal cycloaddition and cyclization reactions, providing efficient access to diverse nitrogen heterocycles. Employing various photogenerated radical species, we further developed a series of radical-mediated olefin functionalization/cyclization cascade reactions to successfully assemble various five- and six-membered heterocycles. We have also achieved for the first time the direct catalytic conversion of recalcitrant N-H bonds into neutral N-centered radicals through a visible-light-photocatalytic oxidative deprotonation electron transfer. Using this generic strategy, we have devised several types of radical cyclizations of unsaturated hydrazones, leading to the construction of diversely functionalized pyrazoline and

  4. De novo trisomy 16p

    Energy Technology Data Exchange (ETDEWEB)

    Juan, J.L.C.; Cigudosa, J.C.; Gomez, A.O. [Univ. of La Laguna, Tenerife, Canary Islands (Spain)] [and others

    1997-01-20

    We report on a patient with psychomotor retardation and a pattern of malformations comprising single umbilical artery, craniofacial anomalies, severe truncal hypotonia, and lower-limb hyporreflexia. G-banding cytogenetics demonstrated a 16p+ chromosome. Parental chromosomes were normal. The use of fluorescent in situ hybridization (FISH) showed that this extra material derived from chromosome 16. High-resolution G-banding demonstrated a duplicated segment on the 16p arm, confirming our suspicion of a de novo tandem duplication; hence, the cytogenetic diagnosis was given as 46,XY,dir dup(16)(p11.2{r_arrow}p12). 9 refs., 3 figs.

  5. De novo peptide sequencing by deep learning.

    Science.gov (United States)

    Tran, Ngoc Hieu; Zhang, Xianglilan; Xin, Lei; Shan, Baozhen; Li, Ming

    2017-07-18

    De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing. We evaluated the method on a wide variety of species and found that DeepNovo considerably outperformed state of the art methods, achieving 7.7-22.9% higher accuracy at the amino acid level and 38.1-64.0% higher accuracy at the peptide level. We further used DeepNovo to automatically reconstruct the complete sequences of antibody light and heavy chains of mouse, achieving 97.5-100% coverage and 97.2-99.5% accuracy, without assisting databases. Moreover, DeepNovo is retrainable to adapt to any sources of data and provides a complete end-to-end training and prediction solution to the de novo sequencing problem. Not only does our study extend the deep learning revolution to a new field, but it also shows an innovative approach in solving optimization problems by using deep learning and dynamic programming.

  6. Design and Synthesis of Novel Block Copolymers for Efficient Opto-Electronic Applications

    Science.gov (United States)

    Sun, Sam-Shajing; Fan, Zhen; Wang, Yiqing; Taft, Charles; Haliburton, James; Maaref, Shahin

    2002-01-01

    It has been predicted that nano-phase separated block copolymer systems containing electron rich donor blocks and electron deficient acceptor blocks may facilitate the charge carrier separation and migration in organic photovoltaic devices due to improved morphology in comparison to polymer blend system. This paper presents preliminary data describing the design and synthesis of a novel Donor-Bridge-Acceptor (D-B-A) block copolymer system for potential high efficient organic optoelectronic applications. Specifically, the donor block contains an electron donating alkyloxy derivatized polyphenylenevinylene (PPV), the acceptor block contains an electron withdrawing alkyl-sulfone derivatized polyphenylenevinylene (PPV), and the bridge block contains an electronically neutral non-conjugated aliphatic hydrocarbon chain. The key synthetic strategy includes the synthesis of each individual block first, then couple the blocks together. While the donor block stabilizes and facilitates the transport of the holes, the acceptor block stabilizes and facilitates the transport of the electrons, the bridge block is designed to hinder the probability of electron-hole recombination. Thus, improved charge separation and stability are expected with this system. In addition, charge migration toward electrodes may also be facilitated due to the potential nano-phase separated and highly ordered block copolymer ultra-structure.

  7. Systematic network synthesis and design: Problem formulation, superstructure generation, data management and solution

    DEFF Research Database (Denmark)

    Quaglia, Alberto; Gargalo, Carina L.; Chairakwongsa, Siwanat;

    2015-01-01

    The developments obtained in recent years in the field of mathematical programming considerably reduced the computational time and resources needed to solve large and complex Mixed Integer Non Linear Programming (MINLP) problems. Nevertheless, the application of these methods in industrial practice...... when large problems are considered. In an earlier work, we proposed a computer-aided framework for synthesis and design of process networks. In this contribution, we expand the framework by including methods and tools developed to structure, automate and simplify the mathematical formulation...... is still limited by the complexity associated with the mathematical formulation of some problems. In particular, the tasks of design space definition and representation as superstructure, as well as the data collection, validation and handling may become too complex and cumbersome to execute, especially...

  8. Design and synthesis of zinc-selective chelators for extracellular applications.

    Science.gov (United States)

    Kawabata, Eri; Kikuchi, Kazuya; Urano, Yasuteru; Kojima, Hirotatsu; Odani, Akira; Nagano, Tetsuo

    2005-01-26

    Zinc (Zn2+) is found in every cell in human bodies. A few millimolar of free Zn2+ exists in the vesicles of presynaptic neurons in the mammalian brain and is released by synaptic activity or depolarization, modulating the function of certain ion channels and receptors. Although various chemical tools for measuring Zn2+ in biological samples, such as fluorescent probes for Zn2+, have been developed, Zn2+-selective chelators have room to be improved. Research on Zn2+ signals in the brain has traditionally employed several chelators, which have several shortcomings for biological applications. Here we report the design, synthesis, and properties of new membrane-impermeable chelators selective for Zn2+ and describe biological applications in hippocampal slices. As a result, our newly designed chelator revealed the first biological implication that presynaptic Zn2+ can be released in the CA1 region. This confirms the utility of these new chelatotrs as extracellular Zn2+ chelators for biological applications.

  9. Corrosion Protection Properties of PPy-ND Composite Coating: Sonoelectrochemical Synthesis and Design of Experiment

    Science.gov (United States)

    Ashassi-Sorkhabi, H.; Bagheri, R.; Rezaei-Moghadam, B.

    2016-02-01

    In this research, the nanocomposite coatings comprising the polypyrrole-nanodiamond, PPy-ND, on St-12 steel electrodes were electro-synthesized using in situ polymerization process under ultrasonic irradiation. The corrosion protection performance and morphology characterization of prepared coatings were investigated by electrochemical methods and scanning electron microscopy, SEM, respectively. Also, the experimental design was employed to determine the best values considering the effective parameters such as the concentration of nanoparticles, the applied current density and synthesis time to achieve the most protective films. A response surface methodology, RSM, involving a central composite design, CCD, was applied to the modeling and optimization of the PPy-ND nanocomposite deposition. Pareto graphic analysis of the parameters indicated that the applied current density and some of the interactions were effective on the response. The electrochemical results proved that the embedment of diamond nanoparticle, DNP, improves the corrosion resistance of PPy coatings significantly. Therefore, desirable correlation exists between predicted data and experimental results.

  10. Mixed transition-metal oxides: design, synthesis, and energy-related applications.

    Science.gov (United States)

    Yuan, Changzhou; Wu, Hao Bin; Xie, Yi; Lou, Xiong Wen David

    2014-02-03

    A promising family of mixed transition-metal oxides (MTMOs) (designated as Ax B3-x O4 ; A, B=Co, Ni, Zn, Mn, Fe, etc.) with stoichiometric or even non-stoichiometric compositions, typically in a spinel structure, has recently attracted increasing research interest worldwide. Benefiting from their remarkable electrochemical properties, these MTMOs will play significant roles for low-cost and environmentally friendly energy storage/conversion technologies. In this Review, we summarize recent research advances in the rational design and efficient synthesis of MTMOs with controlled shapes, sizes, compositions, and micro-/nanostructures, along with their applications as electrode materials for lithium-ion batteries and electrochemical capacitors, and efficient electrocatalysts for the oxygen reduction reaction in metal-air batteries and fuel cells. Some future trends and prospects to further develop advanced MTMOs for next-generation electrochemical energy storage/conversion systems are also presented.

  11. Design, synthesis and biological evaluation of novel aminothiazoles as antiviral compounds acting against human rhinovirus.

    Science.gov (United States)

    Décor, Anne; Grand-Maître, Chantal; Hucke, Oliver; O'Meara, Jeff; Kuhn, Cyrille; Constantineau-Forget, Léa; Brochu, Christian; Malenfant, Eric; Bertrand-Laperle, Mégan; Bordeleau, Josée; Ghiro, Elise; Pesant, Marc; Fazal, Gulrez; Gorys, Vida; Little, Michael; Boucher, Colette; Bordeleau, Sylvain; Turcotte, Pascal; Guo, Tim; Garneau, Michel; Spickler, Catherine; Gauthier, Annick

    2013-07-01

    We describe here the design, synthesis and biological evaluation of antiviral compounds acting against human rhinovirus (HRV). A series of aminothiazoles demonstrated pan-activity against the HRV genotypes screened and productive structure-activity relationships. A comprehensive investigational library was designed and performed allowing the identification of potent compounds with lower molecular weight and improved ADME profile. 31d-1, 31d-2, 31f showed good exposures in CD-1 mice. The mechanism of action was discovered to be a host target: the lipid kinase phosphatidylinositol 4-kinase III beta (PI4KIIIß). The identification of the pan-HRV active compound 31f combined with a structurally distinct literature compound T-00127-HEV1 allowed the assessment of target related tolerability of inhibiting this kinase for a short period of time in order to prevent HRV replication.

  12. Design and Synthesis of an MOF Thermometer with High Sensitivity in the Physiological Temperature Range.

    Science.gov (United States)

    Zhao, Dian; Rao, Xingtang; Yu, Jiancan; Cui, Yuanjing; Yang, Yu; Qian, Guodong

    2015-12-07

    An important result of research on mixed-lanthanide metal-organic frameworks (M'LnMOFs) is the realization of highly sensitive ratiometric luminescent thermometers. Here, we report the design and synthesis of the new M'LnMOF Tb0.80Eu0.20BPDA with high relative sensitivity in the physiological temperature regime (298-318 K). The emission intensity and luminescence lifetime were investigated and compared to those of existing materials. It was found that the temperature-dependent luminescence properties of Tb0.80Eu0.20BPDA are strongly associated with the distribution of the energy levels of the ligand. Such a property can be useful in the design of highly sensitive M'LnMOF thermometers.

  13. Bioactive Glass Nanoparticles: From Synthesis to Materials Design for Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Charlotte Vichery

    2016-04-01

    Full Text Available Thanks to their high biocompatibility and bioactivity, bioactive glasses are very promising materials for soft and hard tissue repair and engineering. Because bioactivity and specific surface area intrinsically linked, the last decade has seen a focus on the development of highly porous and/or nano-sized materials. This review emphasizes the synthesis of bioactive glass nanoparticles and materials design strategies. The first part comprehensively covers mainly soft chemistry processes, which aim to obtain dispersible and monodispersed nanoparticles. The second part discusses the use of bioactive glass nanoparticles for medical applications, highlighting the design of materials. Mesoporous nanoparticles for drug delivery, injectable systems and scaffolds consisting of bioactive glass nanoparticles dispersed in a polymer, implant coatings and particle dispersions will be presented.

  14. MRUniNovo: an efficient tool for de novo peptide sequencing utilizing the hadoop distributed computing framework.

    Science.gov (United States)

    Li, Chuang; Chen, Tao; He, Qiang; Zhu, Yunping; Li, Kenli

    2016-12-19

    Tandem mass spectrometry-based de novo peptide sequencing is a complex and time-consuming process. The current algorithms for de novo peptide sequencing cannot rapidly and thoroughly process large mass spectrometry datasets. In this paper, we propose MRUniNovo, a novel tool for parallel de novo peptide sequencing. MRUniNovo parallelizes UniNovo based on the Hadoop compute platform. Our experimental results demonstrate that MRUniNovo significantly reduces the computation time of de novo peptide sequencing without sacrificing the correctness and accuracy of the results, and thus can process very large datasets that UniNovo cannot.

  15. Acetate Dose-Dependently Stimulates Milk Fat Synthesis in Lactating Dairy Cows.

    Science.gov (United States)

    Urrutia, Natalie L; Harvatine, Kevin J

    2017-05-01

    Background: Acetate is a short-chain fatty acid (FA) that is especially important to cows because it is the major substrate for de novo FA synthesis. However, the effect of acetate supply on mammary lipid synthesis is not clear.Objective: The objective of this experiment was to determine the effect of increasing acetate supply on milk fat synthesis in lactating dairy cows.Methods: Six multiparous lactating Holstein cows were randomly assigned to treatments in a replicated design to investigate the effect of acetate supply on milk fat synthesis. Treatments were 0 (control), 5, 10, and 15 mol acetate/d continuously infused into the rumen for 4 d. Rumen short-chain FAs, plasma hormones and metabolites, milk fat concentration, and milk FA profile were analyzed on day 4 of each treatment. Polynomial contrasts were used to test the linear and quadratic effects of increasing acetate supply.Results: Acetate increased milk fat yield quadratically (P synthesis pathways. Apparent transfer of acetate to milk fat was 33.4%, 36.2%, and 20.6% for 5, 10, and 15 mol/d, respectively. Acetate infusion linearly increased the relative concentration of rumen acetate (P synthesis, suggesting that nutritional strategies that increase ruminal acetate absorption would be expected to increase milk fat by increasing de novo FA synthesis. © 2017 American Society for Nutrition.

  16. Síntese e caracterização de novos complexos de platina (II com ligantes derivados do furano e nitrofurano Synthesis and characterization of new platinum (II complexes containing furan and nitrofuran derived ligands

    Directory of Open Access Journals (Sweden)

    Wendell Guerra

    2005-10-01

    Full Text Available Platinum (II complexes, for example, cisplatin and carboplatin, have been used as chemotherapeutic agents for the treatment of various types of cancer. Several other complexes of this metallic ion are also under clinical evaluation. This work describes the synthesis of five new platinum (II complexes having furan and 5-nitrofuran derivatives and chloride as ligands. The compounds were characterized by NMR, IR and elemental analysis.

  17. Design, Synthesis and Characterization of Functional Metal-Organic Framework Materials

    KAUST Repository

    Alamer, Badriah

    2015-06-01

    Over the past few decades, vast majority of industrial and academic research throughout the world has witnessed the emergence of materials that can serve as ideal candidates for potential utility in desired applications, and these materials are known as Metal Organic Framework (MOFs). This exceptional new family of porous materials is fabricated by linkage of metal ions or clusters and organic linkers via strong bonds. MOFs have been awarded with remarkable interest and widely studied due to their inherent structural methodology (e.g. use of various metals, expanded library of organic building blocks with different geometry and functionality particularly frameworks designed from carboxylate organic linkers) and unquestionably unique structural and chemical features for many practical applications. (i.e. gas storage/separation, catalysis, drug delivery etc). Simply, metal organic frameworks epitomize the beauty of porous chemical structures. From a design perspective, the introduction of the Molecular Building Block (MBB) approach is actively being pursued pathway by researchers toward the construction of MOFs by employing inorganic building blocks and organic linkers and taking advantage of not only their multiple coordination modes and geometries but also the way in which they are reticulated to generate final framework. In this thesis, research studies will be directed toward (i) the investigation of the relationship between experimental parameters and synthesis of well-known fcu –MOF, (ii) rational design and synthesis of new rare earth (RE) based MOFs, (ii) isoreticular materials based on particular MBB ([M3O(RCO2)6]), M= p-and d-block metals, and (iv) zeolite- like metal organic framework assembled from single-metal ion based MBB ([MN2(CO2)4]) via 2-, 3-,and 4-connected organic linkers. Consequently, the porosity, chemical and thermal stability, and gas sorption properties will be evaluated and detailed.

  18. Disubstituted 1-aryl-4-aminopiperidine library synthesis using computational drug design and high-throughput batch and flow technologies.

    Science.gov (United States)

    Bryan, Marian C; Hein, Christopher D; Gao, Hua; Xia, Xiaoyang; Eastwood, Heather; Bruenner, Bernd A; Louie, Steven W; Doherty, Elizabeth M

    2013-09-09

    A platform that incorporates computational library design, parallel solution-phase synthesis, continuous flow hydrogenation, and automated high throughput purification and reformatting technologies was applied to the production of a 120-member library of 1-aryl-4-aminopiperidine analogues for drug discovery screening. The application described herein demonstrates the advantages of computational library design coupled with a flexible, modular approach to library synthesis. The enabling technologies described can be readily adopted by the traditional medicinal chemist without extensive training and lengthy process development times.

  19. Synthesis of nanocrystalline Y2O3 in a specially designed atmospheric pressure radio frequency thermal plasma reactor

    Science.gov (United States)

    Dhamale, G. D.; Mathe, V. L.; Bhoraskar, S. V.; Sahasrabudhe, S. N.; Ghorui, S.

    2015-10-01

    Synthesis of yttrium oxide nanoparticles in a specially designed radio frequency thermal plasma reactor is reported. Good crystallinity, narrow size distribution, low defect state concentration, high purity, good production rate, single-step synthesis, and simultaneous formation of nanocrystalline monoclinic and cubic phases are some of the interesting features observed. Synthesized particles are characterized through X-ray diffraction, transmission electron microscopy, scanning electron microscopy, Fourier transform infrared spectroscopy, thermo-luminescence (TL), and Brunauer-Emmett-Teller surface area analysis. Polymorphism of the nanocrystalline yttria is addressed in detail. Synthesis mechanism is explored through in-situ emission spectroscopy. Post-synthesis environmental effects and possible methods to eliminate the undesired phases are probed. Defect states are investigated through the study of TL spectra.

  20. Origin of monoterpene emissions from boreal tree species: Determination of de novo and pool emissions by 13CO2 labeling

    Science.gov (United States)

    Rinne, J.; Ghirardo, A.; Koch, K.; Taipale, R.; Zimmer, I.; Schnitzler, J.

    2009-12-01

    Boreal forests emit a large amount of monoterpenes into the atmosphere. Traditionally these emissions are assumed to originate as evaporation from large storage pools. Thus their diurnal cycle would depend mostly on temperature. However, there is indication that a significant part of the monoterpene emission would originate directly from de novo synthesis. By applying 13CO2 fumigation and analyzing the isotope fractions with proton transfer reaction mass spectrometry (PTR-MS) and classical GC-MS we studied the origin of monoterpene emissions from some major Eurasian boreal and alpine tree species. We determined the fractions originating from de novo biosynthesis and from large internal monoterpene storages for three coniferous tree species with specialized monoterpene storage structures and one dicotyledon species without such structures. The emission from dicotyledon species Betula pendula originated solely from the de novo synthesis. The origin of the emissions from coniferous species was mixed with varying fraction originating from de novo synthesis (Pinus sylvestris 58%, Picea abies 33.5%, Larix decidua 9.8%) and the rest from large internal monoterpene storage pools. Application of the observed fractions of emission originating from de novo synthesis and large storage pools in a hybrid emission algorithm resulted in a better description of ecosystem scale monoterpene emissions from a boreal Scots pine forest stand.

  1. Understanding the drivers for the development of design rules for the synthesis of cylindrical flexures

    Directory of Open Access Journals (Sweden)

    M. J. Telleria

    2012-04-01

    Full Text Available Cylindrical flexures (CFs, defined as flexures with only one finite radius of curvature loaded normal to the plane of curvature, present an interesting research direction in compliant mechanisms. CFs are constructed out of a cylindrical stock which leads to geometry, manufacturability, and compatibility advantages. Synthesis rules must be developed to design these new systems effectively. Current knowledge in flexure design pertains to straight-beam flexures or curved flexures loaded along the plane of curvature. CFs present a challenge because their mechanics differ from those of straight beams, and although their modelling has been researched thoroughly it has yet to be distilled into element and system creation rules. This paper uses models and finite element analysis to demonstrate that current design rules for straight-beam flexures are insufficient and inadequate for the design of CF systems. The presented discussion will show that CFs differ both at the element and systems levels, and therefore future research will focus on developing the three components of the building block approach: (i reworking of element mechanics models to reveal the parameters which cause the kinematics of the curved beam to differ from those of the straight beam, (ii development of a visual stiffness representation, and (iii formation of system creation rules.

  2. Design, synthesis and characterization of novel nonlinear optical chromophores for electro-optical applications

    Science.gov (United States)

    Liu, Feng

    This dissertation involves the design, synthesis and characterization of second order nonlinear optical chromophores for electro-optic applications. The design concept, that poling efficiency and macroscopic nonlinearities can be improved by modifying a chromophore's shape, has been explored. Chapter 1 gives an introduction into theoretical background of nonlinear optics and electro-optic phenomenon in organic molecules and poled polymers. Chapter 2 involves the design and synthesis of GLD-2 and GLD-3 chromophores, both with bulky substituents on the ring-fused bridge. The optical studies and HRS measurement show that the two alkyl groups on the bridge blueshift the lambdamax in chloroform by 20 nm and decrease the beta values. DSC and TGA thermal analysis show Td of GLD-2 and GLD-3 over 240°C. The maximum achievable r33 of GLD-2/PMMA is 61 pm/V, compared to the 92.4 pm/V of GLD-1/PMMA. But GLD-2/APC shows r33 of 45.2pm/V, higher than GLD-1/APC due to the improved compatibility with APC. The optical loss of 13 wt% GLD-2/PMMA at 1.55mum is 1.4 dB compared to the 2.3 dB of 17 wt% GLD-1/PMMA. Optical loss studies prove that adding two bulky substituents on bridge help attenuate electrostatic interactions. GLD-3 show deteriorated solubility in common used organic solvents, probably due to the combination of two TBDMS and two lengthy alkyl groups. Chapter 3 presents synthesis of thiophene-based chromophores with variously positioned TBDMS groups. The optical studies of these chromophores show one TBDMSO substitution on the thiophene bridge yields little influence on the lambda max in chloroform. FTCDS chromophore with two TBDMS groups, one on donor and one on thiophene bridge, shows to be the best structure with regards the thermal stability and achievable maximum EO coefficient value, 65.9 pm/V, at only 24 wt% loading density at 1.3 mum. Chapter 4 deals with three novel bridges for NLO chromophores. Synthetic methodologies of the diketone precursor of rigidified

  3. Integrated design and synthesis of smart material systems: an overview of the ARPA SPICES program

    Science.gov (United States)

    Jacobs, Jack H.

    1995-05-01

    The Synthesis and Processing of Intelligent Cost Effective Structures (SPICES) program is comprised of a consortium of industrial, academic and government labs to develop cost effective material processing and synthesis technologies to enable new products using active vibration suppression and control devices to be brought to market. Each team member possesses a specialty in the area of smart structures which has been focused towards the development of several actively controlled smart material systems. Since smart structures involve the integration of multiple engineering disciplines, it is the objective of the consortium to establish cost effective design processes between this multiorganizational team for future incorporation of this new technology into each members respective product lines. To accomplish this task, the disciplines of materials, manufacturing, analytical modeling, actuation, sensing, signal processing, and control had to be synthesized into a unified approach between all ten consortium members. The process developed for intelligent structural systems can truly be classified as multiorganization/multidiciplined Integrated Product Development. This process is described in detail as it applies to the SPICES development articles and smart material fabrication in general.

  4. Design and synthesis of polymer-functionalized NIR fluorescent dyes--magnetic nanoparticles for bioimaging.

    Science.gov (United States)

    Yen, Swee Kuan; Jańczewski, Dominik; Lakshmi, Jeeva Lavanya; Dolmanan, Surani Bin; Tripathy, Sudhiranjan; Ho, Vincent H B; Vijayaragavan, Vimalan; Hariharan, Anushya; Padmanabhan, Parasuraman; Bhakoo, Kishore K; Sudhaharan, Thankiah; Ahmed, Sohail; Zhang, Yong; Tamil Selvan, Subramanian

    2013-08-27

    The fluorescent probes having complete spectral separation between absorption and emission spectra (large Stokes shift) are highly useful for solar concentrators and bioimaging. In bioimaging application, NIR fluorescent dyes have a greater advantage in tissue penetration depth compared to visible-emitting organic dyes or inorganic quantum dots. Here we report the design, synthesis, and characterization of an amphiphilic polymer, poly(isobutylene-alt-maleic anhyride)-functionalized near-infrared (NIR) IR-820 dye and its conjugates with iron oxide (Fe3O4) magnetic nanoparticles (MNPs) for optical and magnetic resonance (MR) imaging. Our results demonstrate that the Stokes shift of unmodified dye can be tuned (from ~106 to 208 nm) by the functionalization of the dye with polymer and MNPs. The fabrication of bimodal probes involves (i) the synthesis of NIR fluorescent dye (IR-820 cyanine) functionalized with ethylenediamine linker in high yield, >90%, (ii) polymer conjugation to the functionalized NIR fluorescent dye, and (iii) grafting the polymer-conjugated dyes on iron oxide MNPs. The resulting uniform, small-sized (ca. 6 nm) NIR fluorescent dye-magnetic hybrid nanoparticles (NPs) exhibit a wider emissive range (800-1000 nm) and minimal cytotoxicity. Our preliminary studies demonstrate the potential utility of these NPs in bioimaging by means of direct labeling of cancerous HeLa cells via NIR fluorescence microscopy and good negative contrast enhancement in T2-weighted MR imaging of a murine model.

  5. Finite element synthesis of structural or acoustic receptances in view of practical design applications

    Science.gov (United States)

    Lagache, Jean-Marie; Assaf, Samir; Schulte, Christian

    2008-02-01

    The present study addresses the modal synthesis of dynamic responses or receptances, which can be considered as a major issue in vibratory or acoustic design. A new method termed "method of orthocomplement" offers to increase the accuracy of modal superposition. Two apparently independent domains are considered: first, the numerical control of round-off errors in finite-dimensional models; second, the regularization of modal boundary discontinuities in infinite-dimensional formulations. Concerning the finite-dimensional systems, using the proposed method in conjunction with pseudo-inversion theorems, proves that "inertia relief corrections" remedy modal truncation problems in singular floating systems, just as static corrections do for simply supported systems. The proof is based on hitherto unpublished expressions of inertial contributions in terms of orthogonal projectors. It is worth noting that such expressions present by themselves some technical interest. Modal formulae being delivered in closed form, a thorough analysis of errors becomes possible. Special "spectrograms" are introduced to appraise the convergence of ordinary or modified modal sums. When applied to infinite-dimensional modal boundary discontinuities, the method of orthocomplement eliminates the Gibbs oscillations that affect the ordinary spectral sums, and produces the same corrected formulae as it did for finite-dimensional examples. Effective solutions for the computation of vibratory or acoustic boundary receptances, are developed in that way. The paper once again illustrates how orthogonal projectors can contribute to the determination of static corrections. Future applications to coupling problems, model reduction and modal synthesis are briefly presented at the end of the text.

  6. Design and Synthesis of Bis-thioureas Ligands for Pd-Catalyzed Heck Reaction

    Institute of Scientific and Technical Information of China (English)

    CHEN Wei; CHEN Ying-Chun; WU Yong

    2004-01-01

    The palladium-catalyzed arylation of olefins (the Heck reaction) is one of the most versatile tools for C-C bond formation in organic synthesis. Phosphine ligands are generally used to stabilize the reactive palladium intermediates, the air-sensitivity of phosphine ligands, however,places significant limits on their synthetic applications. Recently, Yang1 and we2 have reported Heck and Suzuki reactions of highly active arenediazonium salts and halides catalyzed by air-stable monothiourea-Pd complexes.In this presentation, we disclose our results on the design and synthesis of novel bis-thiourea ligands. We report that the bis-thiourea-Pd(0) complexes are highly air-, moisture- and thermally stable catalysts for Heck reactions of aryl halides. We tested the catalytic activity of their complexes with Pd (0) in the Heck reaction between iodobenzene and n-butyl acrylate. Our work shows that in NMP at 180℃, quantitative yield was achieved within 0.5h when 0.001mol% Pd was used (TOF up to 200,000). Furthermore, solvent-free condition can be applied in our catalytic system and very high TON (up to 1,000,000) is obtained within 12h.Further investigations aimed at clarification of the reaction scope are currently in progress.

  7. Zr-based metal-organic frameworks: design, synthesis, structure, and applications.

    Science.gov (United States)

    Bai, Yan; Dou, Yibo; Xie, Lin-Hua; Rutledge, William; Li, Jian-Rong; Zhou, Hong-Cai

    2016-04-21

    Among the large family of metal-organic frameworks (MOFs), Zr-based MOFs, which exhibit rich structure types, outstanding stability, intriguing properties and functions, are foreseen as one of the most promising MOF materials for practical applications. Although this specific type of MOF is still in its early stage of development, significant progress has been made in recent years. Herein, advances in Zr-MOFs since 2008 are summarized and reviewed from three aspects: design and synthesis, structure, and applications. Four synthesis strategies implemented in building and/or modifying Zr-MOFs as well as their scale-up preparation under green and industrially feasible conditions are illustrated first. Zr-MOFs with various structural types are then classified and discussed in terms of different Zr-based secondary building units and organic ligands. Finally, applications of Zr-MOFs in catalysis, molecule adsorption and separation, drug delivery, and fluorescence sensing, and as porous carriers are highlighted. Such a review based on a specific type of MOF is expected to provide guidance for the in-depth investigation of MOFs towards practical applications.

  8. Molecular Design of Bioinspired Nanostructures for Biomedical Applications: Synthesis, Self-Assembly and Functional Properties

    Science.gov (United States)

    Xu, Hesheng Victor; Zheng, Xin Ting; Mok, Beverly Yin Leng; Ibrahim, Salwa Ali; Yu, Yong; Tan, Yen Nee

    2016-08-01

    Biomolecules are the nanoscale building blocks of cells, which play multifaceted roles in the critical biological processes such as biomineralization in a living organism. In these processes, the biological molecules such as protein and nucleic acids use their exclusive biorecognition properties enabled from their unique chemical composition, shape and function to initiate a cascade of cellular events. The exceptional features of these biomolecules, coupled with the recent advancement in nanotechnology, have led to the emergence of a new research field that focuses on the molecular design of bioinspired nanostructures that inherit the extraordinary function of natural biomaterials. These “bioinspired” nanostructures could be formulated by biomimetic approaches through either self-assembling of biomolecules or acting as a biomolecular template/precursor to direct the synthesis of nanocomposite. In either situation, the resulting nanomaterials exhibit phenomenal biocompatibility, superb aqueous solubility and excellent colloidal stability, branding them exceptionally desirable for both in vitro and in vivo biomedical applications. In this review, we will present the recent developments in the preparation of “bioinspired” nanostructures through biomimetic self-assembly and biotemplating synthesis, as well as highlight their functional properties and potential applications in biomedical diagnostics and therapeutic delivery. Lastly, we will conclude this topic with some personal perspective on the challenges and future outlooks of the “bioinspired” nanostructures for nanomedicine.

  9. Design, Synthesis, and Mechanistic Evaluation of Iron-Based Catalysis for Synthesis Gas Conversion to Fuels and Chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Enrique Iglesia

    2004-09-30

    This project explores the extension of previously discovered Fe-based catalysts with unprecedented Fischer-Tropsch synthesis rate, selectivity, and ability to convert hydrogen-poor synthesis gas streams typical of those produced from coal and biomass sources. Contract negotiations were completed on December 9, 2004. During the first reporting period, we certified a microreactor, installed required analytical equipment, and reproduced synthetic protocols and catalytic performance previously reported. During this second reporting period, we have prepared and tested several Fe-based compositions for Fischer-Tropsch synthesis and tested the effects of product recycle under both subcritical and supercritical conditions. These studies established modest improvements in rates and selectivities with light hydrocarbon recycle without any observed deleterious effects, opening up the opportunities for using of recycle strategies to control temperature profiles in fixed-bed Fe-based Fischer-Tropsch synthesis reactors without any detectable kinetic detriment. In a parallel study, we examined similar effects of recycle for cobalt-based catalysts; marked selectivity improvements were observed as a result of the removal of significant transport restrictions on these catalysts. Finally, we have re-examined some previously unanalyzed data dealing with the mechanism of the Fischer-Tropsch synthesis, specifically kinetic isotope effects on the rate and selectivity of chain growth reactions on Fe-based catalysts.

  10. De novo glomerular diseases after renal transplantation.

    Science.gov (United States)

    Ponticelli, Claudio; Moroni, Gabriella; Glassock, Richard J

    2014-08-07

    Glomerular diseases developing in the kidney allograft are more often recurrences of the original disease affecting the native kidneys. However, in an undefined number of cases de novo, glomerular diseases unrelated to the original disease in the native kidneys can develop in the transplanted kidney. The clinical presentation and histologic features of de novo diseases are often similar to those features observed in patients with primary or secondary GN in the native kidneys. However, in transplanted kidneys, the glomerular, vascular, and tubulointerstitial changes are often intertwined with structural abnormalities already present at the time of transplant or caused by antibody- or cell-mediated allograft rejection, immunosuppressive drugs, or superimposed infection (most often of a viral nature). The pathophysiology of de novo glomerular diseases is quite variable. In rare cases of de novo minimal change disease, circulating factors increasing the glomerular permeability likely participate. Maladaptive hemodynamic changes and tissue fibrosis caused by calcineurin inhibitors or other factors may be involved in the pathogenesis of de novo FSGS. The exposure of cryptic podocyte antigens may favor the development of de novo membranous nephropathy. Many cases of de novo membranoproliferative GN are related to hepatitis C virus infection. Patients with Alport syndrome lacking antigenic epitopes in their glomerular basement membrane may develop antibodies against these glomerular basement membrane antigens expressed in the transplanted kidney. Infection may cause acute GN to have a heterogeneous clinical presentation and outcome. De novo pauci-immune GN in renal transplant is rare. Preexisting or acquired intolerance to glucose may, in the long term, cause diabetic nephropathy. The prognosis of de novo diseases depends on the type of GN, the severity of lesions caused by the alloimmune response, or the efficacy of immunosuppressive therapy. In most cases, the management

  11. A Public Trial De Novo

    DEFF Research Database (Denmark)

    Vedel, Jane Bjørn; Gad, Christopher

    2011-01-01

    This article addresses the concept of “industrial interests” and examines its role in a topical controversy about a large research grant from a private foundation, the Novo Nordisk Foundation, to the University of Copenhagen. The authors suggest that the debate took the form of a “public trial......” where the grant and close(r) intermingling between industry and public research was prosecuted and defended. First, the authors address how the grant was framed in the media. Second, they redescribe the case by introducing new “evidence” that, because of this framing, did not reach “the court.......” The article ends with a discussion of some implications of the analysis, including that policy making, academic research, and public debates might benefit from more detailed accounts of interests and stakes....

  12. Design, synthesis and crystallization of a novel glucagon analog as a therapeutic agent

    Energy Technology Data Exchange (ETDEWEB)

    Li, Pengyun; Rogers, Tanya; Smiley, David; DiMarchi, Richard D.; Zhang, Faming, E-mail: fzhang@indiana.edu [Department of Chemistry and Biochemistry Program, Indiana University, Bloomington, Indiana 47405 (United States)

    2007-07-01

    The synthesis and crystallization of glucagon-Cex are reported. Glucagon and glucagon-like peptide 1 (GLP-1) are drugs or drug candidates for the treatment of metabolic diseases such as diabetes and obesity. The native hormones have pharmacological deficiencies such as short half-life and poor solubility. A novel glucagon receptor agonist named glucagon-Cex has been designed, synthesized and crystallized. This peptide was highly soluble under physiological conditions and crystallized readily. The crystal diffracted X-rays to 2.2 Å resolution and the diffraction was consistent with space group P23, with unit-cell parameters a = b = c = 48.20 Å, α = β = γ = 90.0°. The crystals were suitable for a full structural determination to reveal the conformational differences between glucagon-Cex and the native hormone.

  13. Design, synthesis, and antifungal activities of novel triazole derivatives containing the benzyl group

    Directory of Open Access Journals (Sweden)

    Xu K

    2015-03-01

    Full Text Available Kehan Xu,1,* Lei Huang,1,* Zheng Xu,2 Yanwei Wang,1,3 Guojing Bai,1 Qiuye Wu,1 Xiaoyan Wang,1 Shichong Yu,1 Yuanying Jiang1 1School of Pharmacy, Second Military Medical University, Shanghai, 2Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 3Number 422 Hospital of PLA, Zhanjiang, People’s Republic of China *These authors contributed equally to this work Abstract: In previous studies undertaken by our group, a series of 1-(1H-1,2,4-triazole-1-yl-2-(2,4-difluorophenyl-3-substituted-2-propanols (1a–r, which were analogs of fluconazole, was designed and synthesized by click chemistry. In the study reported here, the in vitro antifungal activities of all the target compounds were evaluated against eight human pathogenic fungi. Compounds 1a, 1q, and 1r showed the more antifungal activity than the others. Keywords: triazole, synthesis, antifungal activity, CYP51

  14. Design and Synthesis of a Novel Peptidomimetic Inhibitor of Caspase-3

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Caspases, a family of cysteine proteases, comprise of highly homologous enzymes that play an important role in apoptotic cell death. Caspase-3 shows key functions in apoptosis, mediating apoptotic cascade from the intrinsic and extrinsic activation pathways. Therefore, caspase-3 is an attractive target for therapeutic intervention. For instance,inhibitors of caspase-3 have been described as promising cardioprotectants, neuroprotectants and antiarthritic agents.A novel peptidomimetic inhibitor of caspase-3, has been designed, which still has the properties of a reversible inhibitor, while the P1 site at the C-terminal remains, and only L-amino acid has been replaced by D-amino acid. Also presented here is the synthesis of the inhibitor and its inhibitory activity against caspase-3, which was tested by the fluorescent activity assay.

  15. Design, automated synthesis and immunological evaluation of NOD2-ligand–antigen conjugates

    Directory of Open Access Journals (Sweden)

    Marian M. J. H. P. Willems

    2014-06-01

    Full Text Available The covalent attachment of an innate immune system stimulating agent to an antigen can provide active vaccine modalities capable of eliciting a potent immune response against the incorporated antigen. Here we describe the design, automated synthesis and immunological evaluation of a set of four muramyl dipeptide–peptide antigen conjugates. Muramyl dipeptide (MDP represents a well-known ligand for the intracellular NOD2 receptor and our study shows that covalently linking an MDP-moiety to an antigenic peptide can lead to a construct that is capable of stimulating the NOD2 receptor if the ligand is attached at the anomeric center of the muramic acid. The constructs can be processed by dendritic cells (DCs and the conjugation does not adversely affect the presentation of the incorporated SIINFEKL epitope on MHC-I molecules. However, stimulation of the NOD2 receptor in DCs was not sufficient to provide a strong immunostimulatory signal.

  16. A systematic synthesis and design methodology to achieve process intensification in (bio) chemical processes

    DEFF Research Database (Denmark)

    Lutze, Philip; Roman Martinez, Alicia; Woodley, John

    2012-01-01

    Process intensification (PI) has the potential to improve existing processes or create new process options, which are needed in order to produce products using more sustainable methods. In principle, an enormous number of process options can be generated but where and how the process should...... be intensified for the biggest improvement is difficult to identify. In this paper the development of a systematic computer aided model-based synthesis and design methodology incorporating PI is presented. In order to manage the complexities involved, the methodology employs a decomposition-based solution...... approach. Starting from an analysis of existing processes, the methodology generates a set of process options and reduces their number through several screening steps until from the remaining options, the optimal is found. The application of the methodology is highlighted through a case study involving...

  17. A systematic framework for enterprise-wide optimization: Synthesis and design of processing network under uncertainty

    DEFF Research Database (Denmark)

    Quaglia, Alberto; Sarup, Bent; Sin, Gürkan

    2013-01-01

    technologies andproduct portfolio) which is feasible and have optimal performances over the entire uncertainty domain.Through the integration of different methods, tools, algorithms and databases, the framework guidesthe user in dealing with the mathematical complexity of the problems, allowing efficient......In this paper, a systematic framework for synthesis and design of processing networks under uncertaintyis presented. Through the framework, an enterprise-wide optimization problem is formulated and solvedunder uncertain conditions, to identify the network (composed of raw materials, process...... formulationand solution of large and complex enterprise-wide optimization problem. Tools for the analysis of theuncertainty, of its consequences on the decision-making process and for the identification of strategiesto mitigate its impact on network performances are integrated in the framework. A decomposition...

  18. A systematic synthesis and design methodology to achieve process intensification in (bio) chemical processes

    DEFF Research Database (Denmark)

    Lutze, Philip; Woodley, John; Gani, Rafiqul

    be intensified for biggest improvement, process synthesis and design tools are applied which results in the development of a systematic methodology incorporating PI. In order to manage the complexity of PI process options in which a feasible and optimal process solution may exist, the solution procedure......Process intensification (PI) has the potential to improve existing processes or create new process options which are needed in order to produce products using more sustainable methods. Potentially, PI creates an enormous number of process options. For identification where and how the process should...... of this methodology is based on the decomposition approach. Starting from an analysis of existing processes, this methodology generates a set of feasible process options and reduces their number through several screening steps until from the remaining feasible options, the optimal is found. In this presentation...

  19. Statistical analysis of sonochemical synthesis of SAPO-34 nanocrystals using Taguchi experimental design

    Energy Technology Data Exchange (ETDEWEB)

    Askari, Sima [Faculty of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), P.O. Box 15875-4413, Hafez Ave., Tehran (Iran, Islamic Republic of); Halladj, Rouein, E-mail: halladj@aut.ac.ir [Faculty of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), P.O. Box 15875-4413, Hafez Ave., Tehran (Iran, Islamic Republic of); Nazari, Mahdi [Faculty of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), P.O. Box 15875-4413, Hafez Ave., Tehran (Iran, Islamic Republic of)

    2013-05-15

    Highlights: ► Sonochemical synthesis of SAPO-34 nanocrystals. ► Using Taguchi experimental design (L9) for optimizing the experimental procedure. ► The significant effects of all the ultrasonic parameters on the response. - Abstract: SAPO-34 nanocrystals with high crystallinity were synthesized by means of sonochemical method. An L9 orthogonal array of the Taguchi method was implemented to investigate the effects of sonication conditions on the preparation of SAPO-34 with respect to crystallinity of the final product phase. The experimental data establish the favorable phase crystallinity which is improved by increasing the ultrasonic power and the sonication temperature. In the case of ultrasonic irradiation time, however, an initial increases in crystallinity from 5 min to 15 min is followed by a decrease in crystallinity for longer sonication time.

  20. Design, Synthesis and Biological Evaluation of Novel Etoposide Analogues as Cytotoxic Agents

    Institute of Scientific and Technical Information of China (English)

    LIU Ying-Qian; YANG Hua; TIAN Xuan

    2006-01-01

    Five novel compounds composed of etoposide and 5-fluorouracil derivatives joined by an ester linkage were prepared and evaluated for their antitumor potential. Most of these analogues have exhibited promising in vitro cytotoxic activity against cell cultures of murine leukaemia P-388 and human lung carcinoma A-549. The results presented herein challenged the long-standing structure-activity relationships, which proposed that a free 4'-hydroxyl group is essential structural requirement for etoposide-like activity. And in addition, the 4'-position was suggested to tolerate chemical modifications such as esterification. The preliminary testing results also indicated that the design and synthesis of these compounds were beneficial for therapeutic values of etoposide.

  1. Design and synthesis of protein kinase C epsilon selective diacylglycerol lactones (DAG-lactones).

    Science.gov (United States)

    Ann, Jihyae; Yoon, Suyoung; Baek, Jisoo; Kim, Da Hye; Lewin, Nancy E; Hill, Colin S; Blumberg, Peter M; Lee, Jeewoo

    2015-01-27

    DAG-lactones afford a synthetically accessible, high affinity platform for probing structure activity relationships at the C1 regulatory domain of protein kinase C (PKC). Given the central role of PKC isoforms in cellular signaling, along with their differential biological activities, a critical objective is the design of isoform selective ligands. Here, we report the synthesis of a series of DAG-lactones varying in their side chains, with a particular focus on linoleic acid derivatives. We evaluated their selectivity for PKC epsilon versus PKC alpha both under standard lipid conditions (100% phosphatidylserine, PS) as well as in the presence of a nuclear membrane mimetic lipid mixture (NML). We find that selectivity for PKC epsilon versus PKC alpha tended to be enhanced in the presence of the nuclear membrane mimetic lipid mixture and, for our lead compound, report a selectivity of 32-fold.

  2. Design, synthesis and applications of core-shell, hollow core, and nanorattle multifunctional nanostructures.

    Science.gov (United States)

    El-Toni, Ahmed Mohamed; Habila, Mohamed A; Labis, Joselito Puzon; ALOthman, Zeid A; Alhoshan, Mansour; Elzatahry, Ahmed A; Zhang, Fan

    2016-02-01

    With the evolution of nanoscience and nanotechnology, studies have been focused on manipulating nanoparticle properties through the control of their size, composition, and morphology. As nanomaterial research has progressed, the foremost focus has gradually shifted from synthesis, morphology control, and characterization of properties to the investigation of function and the utility of integrating these materials and chemical sciences with the physical, biological, and medical fields, which therefore necessitates the development of novel materials that are capable of performing multiple tasks and functions. The construction of multifunctional nanomaterials that integrate two or more functions into a single geometry has been achieved through the surface-coating technique, which created a new class of substances designated as core-shell nanoparticles. Core-shell materials have growing and expanding applications due to the multifunctionality that is achieved through the formation of multiple shells as well as the manipulation of core/shell materials. Moreover, core removal from core-shell-based structures offers excellent opportunities to construct multifunctional hollow core architectures that possess huge storage capacities, low densities, and tunable optical properties. Furthermore, the fabrication of nanomaterials that have the combined properties of a core-shell structure with that of a hollow one has resulted in the creation of a new and important class of substances, known as the rattle core-shell nanoparticles, or nanorattles. The design strategies of these new multifunctional nanostructures (core-shell, hollow core, and nanorattle) are discussed in the first part of this review. In the second part, different synthesis and fabrication approaches for multifunctional core-shell, hollow core-shell and rattle core-shell architectures are highlighted. Finally, in the last part of the article, the versatile and diverse applications of these nanoarchitectures in

  3. Synthesis, solubility, plasma stability, and pharmacological evaluation of novel sulfonylhydrazones designed as anti-diabetic agents

    Directory of Open Access Journals (Sweden)

    Zapata-Sudo G

    2016-09-01

    Full Text Available Gisele Zapata-Sudo,1,2 Isabelle Karine da Costa Nunes,2 Josenildo Segundo Chaves Araujo,1,2 Jaqueline Soares da Silva,2 Margarete Manhães Trachez,2,3 Tiago Fernandes da Silva,1 Filipe P da Costa,2 Roberto Takashi Sudo,1,2 Eliezer J Barreiro,1,2 Lídia Moreira Lima1,2 1National Institute of Science and Technology on Drugs and Medicines, Federal University of Rio de Janeiro, Laboratory of Evaluation and Synthesis of Bioactive Compounds, Center of Health Sciences, Rio de Janeiro, Brazil; 2Program of Research in Drug Development, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; 3Department of Anesthesiology, Fluminense Federal University, Rio de Janeiro, Brazil Abstract: Neuropathy is a serious complication of diabetes that has a significant socioeconomic impact, since it frequently demands high levels of health care consumption and compromises labor productivity. Recently, LASSBio-1471 (3 was demonstrated to improve oral glucose tolerance, reduce blood glucose levels, and display an anti-neuropathy effect in a murine streptozotocin-induced diabetes model. In the present work, we describe the design, synthesis, solubility, plasma stability, and pharmacological evaluation of novel sulfonylhydrazone derivatives (referred to herein as compounds 4–9, which were designed by molecular modification based on the structure of the prototype LASSBio-1471 (3. Among the compounds tested, better plasma stability was observed with 4, 5, and 9 in comparison to compounds 6, 7, and 8. LASSBio-1773 (7, promoted not only hypoglycemic activity but also the reduction of thermal hyperalgesia and mechanical allodynia in a murine model of streptozotocin-induced diabetic neuropathic pain. Keywords: diabetes, sulfonylhydrazone, hypoglycemic activity, druglikeness, plasma stability, metabolite

  4. Design, synthesis and applications of core-shell, hollow core, and nanorattle multifunctional nanostructures

    Science.gov (United States)

    El-Toni, Ahmed Mohamed; Habila, Mohamed A.; Labis, Joselito Puzon; Alothman, Zeid A.; Alhoshan, Mansour; Elzatahry, Ahmed A.; Zhang, Fan

    2016-01-01

    With the evolution of nanoscience and nanotechnology, studies have been focused on manipulating nanoparticle properties through the control of their size, composition, and morphology. As nanomaterial research has progressed, the foremost focus has gradually shifted from synthesis, morphology control, and characterization of properties to the investigation of function and the utility of integrating these materials and chemical sciences with the physical, biological, and medical fields, which therefore necessitates the development of novel materials that are capable of performing multiple tasks and functions. The construction of multifunctional nanomaterials that integrate two or more functions into a single geometry has been achieved through the surface-coating technique, which created a new class of substances designated as core-shell nanoparticles. Core-shell materials have growing and expanding applications due to the multifunctionality that is achieved through the formation of multiple shells as well as the manipulation of core/shell materials. Moreover, core removal from core-shell-based structures offers excellent opportunities to construct multifunctional hollow core architectures that possess huge storage capacities, low densities, and tunable optical properties. Furthermore, the fabrication of nanomaterials that have the combined properties of a core-shell structure with that of a hollow one has resulted in the creation of a new and important class of substances, known as the rattle core-shell nanoparticles, or nanorattles. The design strategies of these new multifunctional nanostructures (core-shell, hollow core, and nanorattle) are discussed in the first part of this review. In the second part, different synthesis and fabrication approaches for multifunctional core-shell, hollow core-shell and rattle core-shell architectures are highlighted. Finally, in the last part of the article, the versatile and diverse applications of these nanoarchitectures in

  5. synthesis of new schiff bases as materials for the design of ...

    African Journals Online (AJOL)

    Kasmi-Mir S, ElKebich M, Dembahri Z, Haouzi A and Kirsch G

    1 mai 2016 ... SYNTHESIS OF NEW SCHIFF BASES AS MATERIALS FOR THE ... We describe the synthesis of new organic Schiff bases chromophores 5 containing a ...... solar cells controlled by nanocrystalline-TiO2 electrode thickness.

  6. DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy.

    Science.gov (United States)

    Halligan, Brian D; Ruotti, Victor; Twigger, Simon N; Greene, Andrew S

    2005-07-01

    One of the core activities of high-throughput proteomics is the identification of peptides from mass spectra. Some peptides can be identified using spectral matching programs like Sequest or Mascot, but many spectra do not produce high quality database matches. De novo peptide sequencing is an approach to determine partial peptide sequences for some of the unidentified spectra. A drawback of de novo peptide sequencing is that it produces a series of ordered and disordered sequence tags and mass tags rather than a complete, non-degenerate peptide amino acid sequence. This incomplete data is difficult to use in conventional search programs such as BLAST or FASTA. DeNovoID is a program that has been specifically designed to use degenerate amino acid sequence and mass data derived from MS experiments to search a peptide database. Since the algorithm employed depends on the amino acid composition of the peptide and not its sequence, DeNovoID does not have to consider all possible sequences, but rather a smaller number of compositions consistent with a spectrum. DeNovoID also uses a geometric indexing scheme that reduces the number of calculations required to determine the best peptide match in the database. DeNovoID is available at http://proteomics.mcw.edu/denovoid.

  7. Synthesis and cell-free cloning of DNA libraries using programmable microfluidics.

    Science.gov (United States)

    Ben Yehezkel, Tuval; Rival, Arnaud; Raz, Ofir; Cohen, Rafael; Marx, Zipora; Camara, Miguel; Dubern, Jean-Frédéric; Koch, Birgit; Heeb, Stephan; Krasnogor, Natalio; Delattre, Cyril; Shapiro, Ehud

    2016-02-29

    Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and applied them to de novo synthesis, combinatorial assembly and cell-free cloning of genes, respectively. Proof-of-concept for these methods was demonstrated by programming an autonomous microfluidic system to construct and clone libraries of yeast ribosome binding sites and bacterial Azurine, which were then retrieved in individual droplets and validated. The ability to rapidly and robustly generate designer DNA molecules in an autonomous manner should have wide application in biological research and development.

  8. Design, Synthesis of Novel Platinum(II) Glycoconjugates, and Evaluation of Their Antitumor Effects.

    Science.gov (United States)

    Han, Jianbin; Gao, Xiangqian; Liu, Ran; Yang, Jinna; Zhang, Menghua; Mi, Yi; Shi, Ying; Gao, Qingzhi

    2016-06-01

    A new series of sugar-conjugated (trans-R, R-cyclohexane-1, 2-diamine)-2-halo-malonato-platinum(II) complexes were designed and synthesized to target tumor-specific glucose transporters (GLUTs). The water solubility of the sugar-conjugated platinum (II) complexes was greatly improved by average of 570-fold, 33-fold, and 94-fold, respectively, compared to cisplatin (1.0 mg/mL), carboplatin (17.1 mg/mL), and the newest generation of clinical drug oxaliplatin (6.0 mg/mL). Despite the high water solubility, the platinum(II) glycoconjugates exhibited a notable increase in cytotoxicity by a margin of 1.5- to 6.0-fold in six different human cancer cell lines with respect to oxaliplatin. The potential GLUT1 transportability of the complexes was investigated through a molecular docking study and was confirmed with GLUT1 inhibitor-mediated cytotoxicity dependency evaluation. The results showed that the sugar-conjugated platinum(II) complexes can be recognized by the glucose recognition binding site of GLUT1 and their cell killing effect depends highly on the GLUT1 inhibitor, quercetin. The research presenting a prospective concept for targeted therapy anticancer drug design, and with the analysis of the synthesis, water solubility, antitumor activity, and the transportability of the platinum(II) glycoconjugates, this study provides fundamental data supporting the inherent potential of these designed conjugates as lead compounds for GLUT-mediated tumor targeting.

  9. Determining the Parameters of Importance of a Graphene Synthesis Process Using Design-of-Experiments Method

    Directory of Open Access Journals (Sweden)

    Udit Narula

    2016-07-01

    Full Text Available A systematic method to identify key factors that control the synthesis of Physical Vapor Deposition (PVD-based graphene on copper is necessary for engineering graphene growth. The statistical design-of-experiments method is employed and demonstrated in this work in order to fulfill the necessity. Full-factorial design-of-experiments are performed to examine the significance of the main effects and the extent of the interactions of the controlling factors, which are responsible for the number of layers and the quality of the grown graphene. We found that a thinner amorphous carbon layer and a higher annealing temperature are suitable for the growth of mono-layer/few-layer graphene with low defects, while the effect of annealing time has a trade-off and needs to be optimized further. On the other hand, the same treatment, but with larger annealing times will result in multi-layer graphene and low defects. The results obtained from the analysis of the design-of-experiments are verified experimentally with Raman characterization.

  10. Design and Stereoselective Preparation of a New Class of Chiral Olefin Metathesis Catalysts and Application to Enantioselective Synthesis of Quebrachamine: Catalyst Development Inspired by Natural Product Synthesis

    Science.gov (United States)

    Sattely, Elizabeth S.; Meek, Simon J.; Malcolmson, Steven J.; Schrock, Richard R.; Hoveyda, Amir H.

    2010-01-01

    A total synthesis of the Aspidosperma alkaloid quebrachamine in racemic form is first described. A key catalytic ring-closing metathesis of an achiral triene is used to establish the all-carbon quaternary stereogenic center and the tetracyclic structure of the natural product; the catalytic transformation proceeds with reasonable efficiency through the use of existing achiral Ru or Mo catalysts. Ru- or Mo-based chiral olefin metathesis catalysts have proven to be inefficient and entirely nonselective in cases where the desired product is observed. In the present study, the synthesis route thus serves as a platform for the discovery of new olefin metathesis catalysts that allow for efficient completion of an enantioselective synthesis of quebrachamine. Accordingly, on the basis of mechanistic principles, stereogenic-at-Mo complexes bearing only monodentate ligands have been designed. The new catalysts provide significantly higher levels of activity than observed with the previously reported Ru- or Mo-based complexes. Enantiomerically enriched chiral alkylidenes are generated through diastereoselective reactions involving achiral Mo-based bispyrrolides and enantiomerically pure silyl-protected binaphthols. Such chiral catalysts initiate the key enantioselective ring-closing metathesis step in the total synthesis of quebrachamine efficiently (1 mol % loading, 22 °C, 1 h, >98% conversion, 84% yield) and with high selectivity (98:2 er, 96% ee). PMID:19113867

  11. Low Band Gap Polymers for Roll-to-Roll Coated Organic Photovoltaics – Design, Synthesis and Characterization

    DEFF Research Database (Denmark)

    Bundgaard, Eva; Hagemann, Ole; Jørgensen, Mikkel

    2011-01-01

    In this paper we present the design and synthesis of 25 new low band gap polymers. The polymers were characterized by UV-vis spectroscopy which showed optical band gaps of 2.0–0.9 eV. The polymers which were soluble enough were applied in organic photovoltaics, both small area devices with a spin...

  12. Benign by design: catalyst-free in-water, on-water green chemical methodologies in organic synthesis

    Science.gov (United States)

    The development of organic synthesis under sustainable conditions is a primary goal of practicing green chemists who want to prevent pollution and design safer pathways. Although, it is challenging to avoid the use of catalysts, or solvents in all the organic reactions but progre...

  13. Design and modular parallel synthesis of a MCR derived α-helix mimetic protein-protein interaction inhibitor scaffold

    NARCIS (Netherlands)

    Antuch, Walfrido; Menon, Sanjay; Chen, Quin-Zene; Lu, Yingchun; Sakamuri, Sukumar; Beck, Barbara; Schauer-Vukašinović, Vesna; Agarwal, Seema; Hess, Sibylle; Dömling, Alexander

    2006-01-01

    A terphenyl α-helix mimetic scaffold recognized to be capable of disrupting protein-protein interactions was structurally morphed into an easily amenable and versatile multicomponent reaction (MCR) backbone. The design, modular in-parallel library synthesis, initial cell based biological data, and p

  14. Workshop Synthesis: Stated Preference Surveys and Experimental Design, an Audit of the Journey so far and Future Research Perspectives

    DEFF Research Database (Denmark)

    Cherchi, Elisabetta; Hensher, David A.

    2015-01-01

    This paper is a synthesis of the discussions and ideas that were generated during the workshop on “Stated preference surveys and experimental design” at the 2014 Travel Survey Methods Conference in Leura (Australia). The workshop addressed the challenges related to the design and implementation...

  15. Design, synthesis and evaluation of seleno-dihydropyrimidinones as potential multi-targeted therapeutics for Alzheimer's disease.

    Science.gov (United States)

    Canto, Rômulo F S; Barbosa, Flavio A R; Nascimento, Vanessa; de Oliveira, Aldo S; Brighente, Inês M C; Braga, Antonio Luiz

    2014-06-07

    In this paper we report the design, synthesis and evaluation of a series of seleno-dihydropyrimidinones as potential multi-targeted therapeutics for Alzheimer's disease. The compounds show excellent results as acetylcholinesterase inhibitors, being as active as the standard drug. All these compounds also show very good antioxidant activity through different mechanisms of action.

  16. Benign by design: catalyst-free in-water, on-water green chemical methodologies in organic synthesis

    Science.gov (United States)

    The development of organic synthesis under sustainable conditions is a primary goal of practicing green chemists who want to prevent pollution and design safer pathways. Although, it is challenging to avoid the use of catalysts, or solvents in all the organic reactions but progre...

  17. Plasmodium falciparum is dependent on de novo myo-inositol biosynthesis for assembly of GPI glycolipids and infectivity.

    Science.gov (United States)

    Macrae, James I; Lopaticki, Sash; Maier, Alexander G; Rupasinghe, Thusitha; Nahid, Amsha; Cowman, Alan F; McConville, Malcolm J

    2014-02-01

    Intra-erythrocytic stages of the malaria parasite, Plasmodium falciparum, are thought to be dependent on de novo synthesis of phosphatidylinositol, as red blood cells (RBC) lack the capacity to synthesize this phospholipid. The myo-inositol headgroup of PI can either be synthesized de novo or scavenged from the RBC. An untargeted metabolite profiling of P. falciparum infected RBC showed that trophozoite and schizont stages accumulate high levels of myo-inositol-3-phosphate, indicating increased de novo biosynthesis of myo-inositol from glucose 6-phosphate. Metabolic labelling studies with (13) C-U-glucose in the presence and absence of exogenous inositol confirmed that de novo myo-inositol synthesis occurs in parallel with myo-inositol salvage pathways. Unexpectedly, while both endogenous and scavenged myo-inositol was used to synthesize bulk PI, only de novo-synthesized myo-inositol was incorporated into GPI glycolipids. Moreover, gene disruption studies suggested that the INO1 gene, encoding myo-inositol 3-phosphate synthase, is essential in asexual parasite stages. Together these findings suggest that P. falciparum asexual stages are critically dependent on de novo myo-inositol biosynthesis for assembly of a sub-pool of PI species and GPI biosynthesis. These findings highlight unexpected complexity in phospholipid biosynthesis in P. falciparum and a lack of redundancy in some nutrient salvage versus endogenous biosynthesis pathways.

  18. Building Next-Generation Technologies for Low-Cost Gene Synthesis and High-Accuracy Genome Engineering

    OpenAIRE

    2014-01-01

    The technologies that enable writing and editing of DNA form the foundation of modern molecular biology and biotechnology. However, a number of methodological barriers have limited the widespread adoption of both high-throughput de novo gene synthesis and large-scale genome alteration. Increasingly, work in the fields of synthetic biology, protein design, and gene therapy has been hindered by shortcomings in current DNA writing and editing technologies. The goal of this dissertation has be...

  19. Hierarchical Modeling and Robust Synthesis for the Preliminary Design of Large Scale Complex Systems

    Science.gov (United States)

    Koch, Patrick N.

    1997-01-01

    Large-scale complex systems are characterized by multiple interacting subsystems and the analysis of multiple disciplines. The design and development of such systems inevitably requires the resolution of multiple conflicting objectives. The size of complex systems, however, prohibits the development of comprehensive system models, and thus these systems must be partitioned into their constituent parts. Because simultaneous solution of individual subsystem models is often not manageable iteration is inevitable and often excessive. In this dissertation these issues are addressed through the development of a method for hierarchical robust preliminary design exploration to facilitate concurrent system and subsystem design exploration, for the concurrent generation of robust system and subsystem specifications for the preliminary design of multi-level, multi-objective, large-scale complex systems. This method is developed through the integration and expansion of current design techniques: Hierarchical partitioning and modeling techniques for partitioning large-scale complex systems into more tractable parts, and allowing integration of subproblems for system synthesis; Statistical experimentation and approximation techniques for increasing both the efficiency and the comprehensiveness of preliminary design exploration; and Noise modeling techniques for implementing robust preliminary design when approximate models are employed. Hierarchical partitioning and modeling techniques including intermediate responses, linking variables, and compatibility constraints are incorporated within a hierarchical compromise decision support problem formulation for synthesizing subproblem solutions for a partitioned system. Experimentation and approximation techniques are employed for concurrent investigations and modeling of partitioned subproblems. A modified composite experiment is introduced for fitting better predictive models across the ranges of the factors, and an approach for

  20. IVA: accurate de novo assembly of RNA virus genomes.

    Science.gov (United States)

    Hunt, Martin; Gall, Astrid; Ong, Swee Hoe; Brener, Jacqui; Ferns, Bridget; Goulder, Philip; Nastouli, Eleni; Keane, Jacqueline A; Kellam, Paul; Otto, Thomas D

    2015-07-15

    An accurate genome assembly from short read sequencing data is critical for downstream analysis, for example allowing investigation of variants within a sequenced population. However, assembling sequencing data from virus samples, especially RNA viruses, into a genome sequence is challenging due to the combination of viral population diversity and extremely uneven read depth caused by amplification bias in the inevitable reverse transcription and polymerase chain reaction amplification process of current methods. We developed a new de novo assembler called IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected people and demonstrated that IVA outperforms all other virus de novo assemblers. The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva © The Author 2015. Published by Oxford University Press.

  1. Sizing up surfactant synthesis.

    Science.gov (United States)

    Han, SeungHye; Mallampalli, Rama K

    2014-08-01

    Phosphatidylcholine is generated through de novo synthesis and remodeling involving a lysophospholipid. In this issue of Cell Metabolism, research from the Shimizu lab (Harayama et al., 2014) demonstrates the highly selective enzymatic behavior of lysophospholipid acyltransferases. The authors present an enzymatic model for phosphatidylcholine molecular species diversification that impacts surfactant formation.

  2. Metal-Organic Frameworks: Building Block Design Strategies for the Synthesis of MOFs.

    KAUST Repository

    Luebke, Ryan

    2014-09-01

    A significant and ongoing challenge in materials chemistry and furthermore solid state chemistry is to design materials with the desired properties and characteristics. The field of Metal-Organic Frameworks (MOFs) offers several strategies to address this challenge and has proven fruitful at allowing some degree of control over the resultant materials synthesized. Several methodologies for synthesis of MOFs have been developed which rely on use of predetermined building blocks. The work presented herein is focused on the utilization of two of these design principles, namely the use of molecular building blocks (MBBs) and supermolecular building blocks (SBBs) to target MOF materials having desired connectivities (topologies). These design strategies also permit the introduction of specific chemical moieties, allowing for modification of the MOFs properties. This research is predominantly focused on two platforms (rht-MOFs and ftw-MOFs) which topologically speaking are edge transitive binodal nets; ftw being a (4,12)-connected net and rht being a (3,24)-connected net. These highly connected nets (at least one node having connectivity greater than eight) have been purposefully targeted to increase the predictability of structural outcome. A general trend in topology is that there is an inverse relationship between the connectivity of the node(s) and the number of topological outcomes. Therefore the key to this research (and to effective use of the SBB and MBB approaches) is identification of conditions which allow for reliable formation of the targeted MBBs and SBBs. In the case of the research presented herein: a 12-connected Group IV or Rare Earth based hexanuclear MBB and a 24-connected transition metal based SBB were successfully targeted and synthesized. These two synthetic platforms will be presented and used as examples of how these design methods have been (and can be further) utilized to modify existing materials or develop new materials for gas storage and

  3. Design, synthesis and anti-HIV activity of novel quinoxaline derivatives.

    Science.gov (United States)

    Patel, Saloni B; Patel, Bhumika D; Pannecouque, Christophe; Bhatt, Hardik G

    2016-07-19

    In order to design novel anti-HIV agents, pharmacophore modelling, virtual screening, 3D-QSAR and molecular docking studies were performed. Pharmacophore model was generated using 17 structurally diverse molecules using DISCOtech followed by refinement with GASP module of Sybyl X. The best model containing four features; two donor sites, one acceptor atom and one hydrophobic region; was used as a query for virtual screening in NCI database and 6 compounds with Qfit value ≥98 were retrieved. The quinoxaline ring which is the bio-isostere of pteridine ring, retrieved as a hit in virtual screening, was selected as a core moiety. 3D-QSAR was carried on thirty five 5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxamide derivatives. Contour map analysis of best CoMFA and CoMSIA model suggested incorporation of hydrophobic, bulky and electronegative groups to increase potency of the designed compounds. 50 quinoxaline derivatives with different substitutions were designed on basis of both ligand based drug design approaches and were mapped on the best pharmacophore model. From this, best 32 quinoxaline derivatives were docked onto the active site of integrase enzyme and in-silico ADMET properties were also predicted. From this data, synthesis of top 7 quinoxaline derivatives was carried out and were characterized using Mass, (1)H-NMR and (13)C-NMR spectroscopy. Purity of compounds were checked using HPLC. These derivatives were evaluated for anti-HIV activity on III-B strain of HIV-1 and cytotoxicity studies were performed on VERO cell line. Two quinoxaline derivatives (7d and 7e) showed good results, which can be further explored to develop novel anti-HIV agents.

  4. Design and synthesis of flexible switching 1 × 2 antenna array on Kapton substrate

    Science.gov (United States)

    Georges Rabobason, Yvon; Rigas, Grigorios; Swaisaenyakorn, Srijittar; Mirkhaydarov, Bobur; Ravelo, Blaise; Shkunov, Maxim; Young, Paul; Benjelloun, Nabil

    2016-06-01

    Flexible front- and back-end RF/analogue system antennas were recently emerged. However, little flexible antenna system design is available so far, in planar hybrid technology with surface mounted components. This paper describes the design feasibility of flexible switching 1 × 2 antenna array system. It acts as a switching antenna implemented in hexapole configuration. The system is comprised of a key element RF switch terminated by two identical patch antennas associated to half-wave elementary transmission lines (TLs). A detailed theory illustrating the global S-parameter model determination in function of the given RF-switch return and insertion losses is established. In difference to the conventional microwave circuit theory, the proposed equivalent S-parameter model is originally built with the non-standard optimized antenna load. Thus, the synthesis method of the terminal antenna input impedance and the output access line characteristic impedance is formulated in function of the specified return and optimal transmission losses. The design method and theoretical approach feasibility is verified with the demonstrator of flexible switching 1 × 2 antenna array printed on Kapton substrate. The circuit prototype is implemented in hybrid planar technology integrating patch antenna operating at about 6 GHz and a packaged GaAs RF switch associated to the RF/DC signal decoupling accessory mounted surface components. Simulations of the designed circuit transmission and isolation losses from 5.5 GHz to 7 GHz were carried out by using the commercial RF switch S-parameter touchstone model provided by the manufacturer. The simulated and measured return losses are compared and discussed. Then, the measured radiation patterns confirm the proposed switched antenna concept feasibility.

  5. Computer-guided design, synthesis, and protein kinase C affinity of a new salicylate-based class of bryostatin analogs.

    Science.gov (United States)

    Wender, Paul A; Nakagawa, Yu; Near, Katherine E; Staveness, Daryl

    2014-10-03

    Bryostatin 1 is in clinical trials for the treatment of cancer and Alzheimer's disease and is a candidate for a first-in-class approach to HIV/AIDS eradication. It is neither readily available nor optimally suited for clinical use. Using a function oriented synthesis strategy, a new class of bryostatin-inspired analogs was designed with a simplified salicylate-derived subunit, enabling step-economical synthesis (23 total steps) of agents exhibiting bryostatin-like affinity to protein kinase C (PKC).

  6. Design and synthesis of labeled analogs of PhTX-56, a potent and selective AMPA receptor antagonist

    DEFF Research Database (Denmark)

    Andersen, Trine F; Vogensen, Stine B; Jensen, Lars S

    2005-01-01

    antagonist of Ca2+-permeable AMPA receptors. PhTX-56 and its labeled derivatives are promising tools for structure-function studies of the ion channel of the AMPA receptor. We now describe the design and synthesis of 3H-, 13C-, and 15N-labeled derivatives of PhTX-56 for molecular level studies of AMPA....... These analogs can provide detailed information on the ligand-receptor interaction. In conclusion, synthesis of labeled derivatives of PhTX-56 provides important tools for future studies of the pore-forming region of AMPA receptors....

  7. Design and synthesis of monofunctionalized, water-soluble conjugated polymers for biosensing and imaging applications.

    Science.gov (United States)

    Traina, Christopher A; Bakus, Ronald C; Bazan, Guillermo C

    2011-08-17

    Water-soluble conjugated polymers with controlled molecular weight characteristics, absence of ionic groups, high emission quantum yields, and end groups capable of selective reactions of wide scope are desirable for improving their performance in various applications and, in particular, fluorescent biosensor schemes. The synthesis of such a structure is described herein. 2-Bromo-7-iodofluorene with octakis(ethylene glycol) monomethyl ether chains at the 9,9'-positions, i.e., compound 4, was prepared as the reactive premonomer. A high-yielding synthesis of the organometallic initiator (dppe)Ni(Ph)Br (dppe = 1,2-bis(diphenylphosphino)ethane) was designed and implemented, and the resulting product was characterized by single-crystal X-ray diffraction techniques. Polymerization of 4 by (dppe)Ni(Ph)Br can be carried out in less than 30 s, affording excellent control over the average molecular weight and polydispersity of the product. Quenching of the polymerization with [2-(trimethylsilyl)ethynyl]magnesium bromide yields silylacetylene-terminated water-soluble poly(fluorene) with a photoluminescence quantum efficiency of 80%. Desilylation, followed by copper-catalyzed azide-alkyne cycloaddition reaction, yields a straightforward route to introduce a wide range of specific end group functionalities. Biotin was used as an example. The resulting biotinylated conjugated polymer binds to streptavidin and acts as a light-harvesting chromophore to optically amplify the emission of Alexa Fluor-488 chromophores bound onto the streptavidin. Furthermore, the biotin end group makes it possible to bind the polymer onto streptavidin-functionalized cross-linked agarose beads and thereby incorporate a large number of optically active segments.

  8. Design, synthesis and structure of new potential electrochemically active boronic acid-based glucose sensors

    DEFF Research Database (Denmark)

    Norrild, Jens Chr.; Søtofte, Inger

    2002-01-01

    In the course of our investigations on new boronic acid based carbohydrate sensors three new boronic acids 3, 7 and 11 containing a ferrocene moiety were synthesised. Their design includes an intramolecular B-N bonding motif in order to facilitate binding at physiological pH. We report the synthe......In the course of our investigations on new boronic acid based carbohydrate sensors three new boronic acids 3, 7 and 11 containing a ferrocene moiety were synthesised. Their design includes an intramolecular B-N bonding motif in order to facilitate binding at physiological pH. We report...... the synthesis of the compounds and our investigations on glucose complexation as studied by C-13 NMR spectroscopy. The crystal structure of 2,4,6-tris[2-(N-ferrocenylmethyl-N-methylaminomethyl) phenyl] boroxin (13) (boroxin of boronic acid 3) (boroxin = cyclotriboroxane) was obtained and compared...... with structures obtained of 2,4,6-tris[2-(N,N-dimethylaminomethyl)phenyl]boroxin (14) and 2,2-dimethyl-1,3-diyl[2-(N,N-dimethylaminomethyl)phenyl]boronate (15). The structure of 13 shows the existence of intramolecular B-N bonds in the solid phase....

  9. An allpass filter design method with application to piano string synthesis

    Science.gov (United States)

    Abel, Jonathan S.; Smith, Julius O.; Bensa, Julien

    2005-04-01

    A nonparametric allpass filter design method for matching a desired group delay as a function of frequency is presented. The technique is useful in physical modeling synthesis of musical instruments exhibiting dispersive wave propagation in which different frequency bands travel at different speeds. While current group delay filter design methods suffer from numerical difficulties except at low filter orders, the technique presented here is numerically robust, producing an allpass filter in cascaded biquad form, and with the filter poles following a smooth loop within the unit circle. The technique was inspired by the observation that a pole-zero pair arranged in allpass form has 2π total group delay when integrated around the unit circle, regardless of the pole location. To match a given group delay characteristic, the method divides the frequency axis into sections containing 2π total group delay, and assigns a pole-zero allpass pair to each. In this way, the method incorporates an order selection technique, and by adding a pure delay to the desired group delay, allows the trading of increased filter order for improved fit to the frequency-dependent group delay. Results are presented for modeling the group delay of a stiff piano string under several computational constraints.

  10. Rational design and synthesis of freestanding photoelectric nanodevices as highly efficient photocatalysts.

    Science.gov (United States)

    Qu, Yongquan; Liao, Lei; Cheng, Rui; Wang, Yue; Lin, Yung-Chen; Huang, Yu; Duan, Xiangfeng

    2010-05-12

    Photocatalysts are of significant interest in solar energy harvesting and conversion into chemical energy. However, the photocatalysts available to date are limited by either poor efficiency in the visible light range or insufficient photoelectrochemical stability. Here we report the rational design of a new generation of freestanding photoelectric nanodevices as highly efficient and stable photocatalysts by integrating a nanoscale photodiode with two redox catalysts in a single nanowire heterostructure. We show that a platinum-silicon-silver nanowire heterostructure can be synthesized to integrate a nanoscale metal-semiconductor Schottky diode encased in a protective insulating shell with two exposed metal catalysts. We further demonstrated that the Schottky diodes exhibited a pronounced photovoltaic effect with nearly unity internal quantum efficiency and that the integrated nanowire heterostructures could be used as highly efficient photocatalysts for a wide range of thermodynamically downhill and uphill reactions including the photocatalytic degradation of organic dyes and the reduction of metal ions and carbon dioxide using visible light. Our studies for the first time demonstrated the integration of multiple distinct functional components into a single nanostructure to form a standalone active nanosystem and for the first time successfully realized a photoelectric nanodevice that is both highly efficient and highly stable throughout the entire solar spectrum. It thus opens a rational avenue to the design and synthesis of a new generation of photoelectric nanosystems with unprecedented efficiency and stability and will have a broad impact in areas including environmental remediation, artificial photosynthesis and solar fuel production.

  11. De novo Families: Lesbian Motherhood.

    Science.gov (United States)

    Hayman, Brenda; Wilkes, Lesley

    2017-01-01

    The aim of this recent Australian study was to explore the experiences of lesbian women choosing motherhood. Participants included 30 self-identifying lesbian mothers. Data were collected via interviews, data collection sheets, and online journaling. The interview and journaling data were analyzed using constant comparative analysis and subsequently illuminated three main themes: becoming mothers, constructing motherhood, and legitimizing our family. These papers described the journey to motherhood and specifically explored the various methods of conception and other decisions that participants made when planning their family, the challenge of heteronormativity in health care, and legitimizing the role of the non-birth mother in de novo families. This article aims to present the participants' experiences of motherhood that was a constant topic found woven throughout all three of the identified themes. Participants identified that they had a unique opportunity to create their own mothering roles in the absence of significant "lesbian mother" role models and that they were able to adjust and to adapt their roles depending on fluctuating circumstances.

  12. De novo Transcriptome Analysis in Perennial Ryegrass

    DEFF Research Database (Denmark)

    Farrell, Jacqueline Danielle; Byrne, Stephen; Asp, Torben

    selection will be the availability of a reference genome, and efforts are underway within our group to deliver this. An important step in de novo assembly will be defining the gene set, and the availability of transcriptome sequencing data will greatly aid gene prediction and validation, and the development...... of functional markers for improved ryegrass breeding. Therefore, the goal of this study is to analyze a de novo assembly of the perennial ryegrass transcriptome from the same inbred genotype being used for de novo genome assembly. Furthermore, we also conducted de novo transcriptome assembly with other......Perennial ryegrass (Lolium perenne L.) is an important grass species for both forage and amenity purposes for temperate regions worldwide. It is envisaged that breeding efforts may be enhanced with the assistance of new breeding technologies such as genomic selection. A major step towards genomic...

  13. A design of experiments investigation of the effects of synthesis conditions on the quality of CVD graphene

    Science.gov (United States)

    Shanmugam, Ramakrishnan; Rangarajan, Murali; Devanathan, Sriram; Sathe, Vasant G.; Senthilkumar, R.; Kothurkar, Nikhil K.

    2016-12-01

    Control over quality of graphene and the number of layers is vital for various applications. This is the first methodical report which quantitatively relates the process conditions in the chemical vapor deposition (CVD) of graphene with crystallinity and number of graphene layers, using a design of experiments approach. This report investigates the effects of three vital synthesis parameters namely (i) carbon source (benzene, naphthalene and anthracene) (ii) synthesis temperature and (iii) mass flow rate of the carbon source, on the crystallinity and the number of layers of graphene, as inferred through micro-Raman analysis. These results give a preliminary indication of how the quality of graphene synthesized through CVD could be controlled. These results throw light on further experiments, simulations, and analysis needed to precisely determine how to control the synthesis of graphene.

  14. Design, synthesis and decoration of molecular scaffolds for exploitation in the production of alkaloid-like libraries.

    Science.gov (United States)

    Craven, Philip; Aimon, Anthony; Dow, Mark; Fleury-Bregeot, Nicolas; Guilleux, Rachel; Morgentin, Remy; Roche, Didier; Kalliokoski, Tuomo; Foster, Richard; Marsden, Stephen P; Nelson, Adam

    2015-06-01

    The design, synthesis and decoration of six small molecule libraries is described. Each library was inspired by structures embedded in the framework of specific alkaloid natural products. The development of optimised syntheses of the required molecular scaffolds is described, in which reactions including Pd-catalysed aminoarylation and diplolar cycloadditions have been exploited as key steps. The synthesis of selected exemplar screening compounds is also described. In five cases, libraries were subsequently nominated for production on the basis of the scope and limitations of the validation work, as well as predicted molecular properties. In total, the research has led to the successful synthesis of >2500 novel alkaloid-like compounds for addition to the screening collection (the Joint European Compound Library, JECL) of the European Lead Factory.

  15. De novo centriole formation in human cells is error-prone and does not require SAS-6 self-assembly.

    Science.gov (United States)

    Wang, Won-Jing; Acehan, Devrim; Kao, Chien-Han; Jane, Wann-Neng; Uryu, Kunihiro; Tsou, Meng-Fu Bryan

    2015-11-26

    Vertebrate centrioles normally propagate through duplication, but in the absence of preexisting centrioles, de novo synthesis can occur. Consistently, centriole formation is thought to strictly rely on self-assembly, involving self-oligomerization of the centriolar protein SAS-6. Here, through reconstitution of de novo synthesis in human cells, we surprisingly found that normal looking centrioles capable of duplication and ciliation can arise in the absence of SAS-6 self-oligomerization. Moreover, whereas canonically duplicated centrioles always form correctly, de novo centrioles are prone to structural errors, even in the presence of SAS-6 self-oligomerization. These results indicate that centriole biogenesis does not strictly depend on SAS-6 self-assembly, and may require preexisting centrioles to ensure structural accuracy, fundamentally deviating from the current paradigm.

  16. Solution-based synthesis and design of late transition metal chalcogenide materials for oxygen reduction reaction (ORR).

    Science.gov (United States)

    Gao, Min-Rui; Jiang, Jun; Yu, Shu-Hong

    2012-01-09

    Late transition metal chalcogenide (LTMC) nanomaterials have been introduced as a promising Pt-free oxygen reduction reaction (ORR) electrocatalysts because of their low cost, good ORR activity, high methanol tolerance, and facile synthesis. Herein, an overview on the design and synthesis of LTMC nanomaterials by solution-based strategies is presented along with their ORR performances. Current solution-based synthetic approaches towards LTMC nanomaterials include a hydrothermal/solvothermal approach, single-source precursor approach, hot-injection approach, template-directed soft synthesis, and Kirkendall-effect-induced soft synthesis. Although the ORR activity and stability of LTMC nanomaterials are still far from what is needed for practical fuel-cell applications, much enhanced electrocatalytic performance can be expected. Recent advances have emphasized that decorating the surface of the LTMC nanostructures with other functional nanoparticles can lead to much better ORR catalytic activity. It is believed that new synthesis approaches to LTMCs, modification techniques of LTMCs, and LTMCs with desirable morphology, size, composition, and structures are expected to be developed in the future to satisfy the requirements of commercial fuel cells.

  17. Biophysical characterization of a de novo elastin

    Science.gov (United States)

    Greenland, Kelly Nicole

    Natural human elastin is found in tissue such as the lungs, arteries, and skin. This protein is formed at birth with no mechanism present to repair or supplement the initial quantity formed. As a result, the functionality and durability of elastin's elasticity is critically important. To date, the mechanics of this ability to stretch and recoil is not fully understood. This study utilizes de novo protein design to create a small library of simplistic versions of elastin-like proteins, demonstrate the elastin-like proteins, maintain elastin's functionality, and inquire into its structure using solution nuclear magnetic resonance (NMR). Elastin is formed from cross-linked tropoelastin. Therefore, the first generation of designed proteins consisted of one protein that utilized homogony of interspecies tropoelastin by using three common domains, two hydrophobic and one cross-linking domains. Basic modifications were made to open the hydrophobic region and also to make the protein easier to purify and characterize. The designed protein maintained its functionality, self-aggregating as the temperature increased. Uniquely, the protein remained self-aggregated as the temperature returned below the critical transition temperature. Self-aggregation was additionally induced by increasing salt concentrations and by modifying the pH. The protein appeared to have little secondary structure when studied with solution NMR. These results fueled a second generation of designed elastin-like proteins. This generation contained variations designed to study the cross-linking domain, one specific hydrophobic domain, and the effect of the length of the elastin-like protein. The cross-linking domain in one variation has been significantly modified while the flanking hydrophobic domains have remained unchanged. This characterization of this protein will answer questions regarding the specificity of the homologous nature of the cross-linking domain of tropoelastin across species. A second

  18. Design, Synthesis, and Mechanistic Evaluation of Iron-Based Catalysis for Synthesis Gas Conversion to Fuels and Chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Enrique Iglesia; Akio Ishikawa; Manual Ojeda; Nan Yao

    2007-09-30

    A detailed study of the catalyst composition, preparation and activation protocol of Fe-based catalysts for the Fischer-Tropsch Synthesis (FTS) have been carried out in this project. We have studied the effects of different promoters on the catalytic performance of Fe-based catalysts. Specifically, we have focused on how their sequence of addition dramatically influences the performance of these materials in the Fischer-Tropsch synthesis. The resulting procedures have been optimized to improve further upon the already unprecedented rates and C{sub 5+} selectivities of the Fe-based catalysts that we have developed as part of this project. Selectivity to C{sub 5+} hydrocarbon was close to 90 % (CO{sub 2}-free basis) and CO conversion rate was about 6.7 mol h{sup -1} g-at Fe{sup -1} at 2.14 MPa, 508 K and with substoichiometric synthesis gas; these rates were larger than any reported previously for Fe-based FTS catalysts at these conditions. We also tested the stability of Fe-based catalysts during FTS reaction (10 days); as a result, the high hydrocarbon formation rates were maintained during 10 days, though the gradual deactivation was observed. Our investigation has also focused on the evaluation of Fe-based catalysts with hydrogen-poor synthesis gas streams (H{sub 2}/CO=1). We have observed that the Fe-based catalysts prepared in this project display also a high hydrocarbon synthesis rate with substoichiometric synthesis gas (H{sub 2}/CO=1) stream, which is a less desirable reactant mixture than stoichiometric synthesis gas (H{sub 2}/CO=2). We have improved the catalyst preparation protocols and achieved the highest FTS reaction rates and selectivities so far reported at the low temperatures required for selectivity and stability. Also, we have characterized the catalyst structural change and active phases formed, and their catalytic behavior during the activation process to evaluate their influences on FTS reaction. The efforts of this project led to (i

  19. Donepezil-like multifunctional agents: Design, synthesis, molecular modeling and biological evaluation.

    Science.gov (United States)

    Wu, Ming-Yu; Esteban, Gerard; Brogi, Simone; Shionoya, Masahi; Wang, Li; Campiani, Giuseppe; Unzeta, Mercedes; Inokuchi, Tsutomu; Butini, Stefania; Marco-Contelles, Jose

    2016-10-01

    Currently available drugs against Alzheimer's disease (AD) are only able to ameliorate the disease symptoms resulting in a moderate improvement in memory and cognitive function without any efficacy in preventing and inhibiting the progression of the pathology. In an effort to obtain disease-modifying anti-Alzheimer's drugs (DMAADs) following the multifactorial nature of AD, we have recently developed multifunctional compounds. We herein describe the design, synthesis, molecular modeling and biological evaluation of a new series of donepezil-related compounds possessing metal chelating properties, and being capable of targeting different enzymatic systems related to AD (cholinesterases, ChEs, and monoamine oxidase A, MAO-A). Among this set of analogues compound 5f showed excellent ChEs inhibition potency and a selective MAO-A inhibition (vs MAO-B) coupled to strong complexing properties for zinc and copper ions, both known to be involved in the progression of AD. Moreover, 5f exhibited moderate antioxidant properties as found by in vitro assessment. This compound represents a novel donepezil-hydroxyquinoline hybrid with DMAAD profile paving the way to the development of a novel class of drugs potentially able to treat AD.

  20. Design and synthesis of calcium responsive magnetic resonance imaging agent: Its relaxation and luminescence studies.

    Science.gov (United States)

    Tanwar, Jyoti; Datta, Anupama; Chauhan, Kanchan; Kumaran, S Senthil; Tiwari, Anjani K; Kadiyala, K Ganesh; Pal, Sunil; Thirumal, M; Mishra, Anil K

    2014-07-23

    Calcium concentration modulation both inside and outside cell is of considerable interest for nervous system function in normal and pathological conditions. MRI has potential for very high spatial resolution at molecular/cellular level. Design, synthesis and evaluation of Gd-DO3A-AME-NPHE, a calcium responsive MRI contrast agent is presented. The probe is comprised of a Gd(3+)-DO3A core coupled to iminoacetate coordinating groups for calcium induced relaxivity switching. In the absence of Ca(2+) ions, inner sphere water binding to the Gd-DO3A-AME-NPHE is restricted with longitudinal relaxivity, r1 = 4.37 mM(-1) s(-1) at 4.7 T. However, addition of Ca(2+) triggers a marked enhancement in r1 = 6.99 mM(-1) s(-1) at 4.7 T (60% increase). The construct is highly selective for Ca(2+) over competitive metal ions at extracellular concentration. The r1 is modulated by changes in the hydration number (0.2 to 1.05), which was confirmed by luminescence emission lifetimes of the analogous Eu(3+) complex. T1 phantom images establish the capability of complex of visualizing changes in [Ca(2+)] by MRI.