Relevant bibliographies by topics / Amino acids Design

Academic literature on the topic 'Amino acids Design'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Amino acids Design"

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Standaert, Robert F., and Seung Bum Park. "Abc Amino Acids: Design, Synthesis, and Properties of New Photoelastic Amino Acids." Journal of Organic Chemistry 71, no. 21 (October 2006): 7952–66. http://dx.doi.org/10.1021/jo060763q.

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Bilgiçer, Basar, and Krishna Kumar. "Protein Design Using Unnatural Amino Acids." Journal of Chemical Education 80, no. 11 (November 2003): 1275. http://dx.doi.org/10.1021/ed080p1275.

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Swainston, Neil, Andrew Currin, Lucy Green, Rainer Breitling, Philip J. Day, and Douglas B. Kell. "CodonGenie: optimised ambiguous codon design tools." PeerJ Computer Science 3 (July 10, 2017): e120. http://dx.doi.org/10.7717/peerj-cs.120.

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CodonGenie, freely available from http://codon.synbiochem.co.uk, is a simple web application for designing ambiguous codons to support protein mutagenesis applications. Ambiguous codons are derived from specific heterogeneous nucleotide mixtures, which create sequence degeneracy when synthesised in a DNA library. In directed evolution studies, such codons are carefully selected to encode multiple amino acids. For example, the codon NTN, where the code N denotes a mixture of all four nucleotides, will encode a mixture of phenylalanine, leucine, isoleucine, methionine and valine. Given a user-defined target collection of amino acids matched to an intended host organism, CodonGenie designs and analyses all ambiguous codons that encode the required amino acids. The codons are ranked according to their efficiency in encoding the required amino acids while minimising the inclusion of additional amino acids and stop codons. Organism-specific codon usage is also considered.
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Aravinda, S., N. Shamala, Rituparna S. Roy, and P. Balaram. "Non-protein amino acids in peptide design." Journal of Chemical Sciences 115, no. 5-6 (October 2003): 373–400. http://dx.doi.org/10.1007/bf02708230.

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Yoder, Nicholas C., and Krishna Kumar. "Fluorinated amino acids in protein design and engineering." Chemical Society Reviews 31, no. 6 (September 13, 2002): 335–41. http://dx.doi.org/10.1039/b201097f.

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Lane, Jonathan W., and Randall L. Halcomb. "New design concepts for constraining glycosylated amino acids." Tetrahedron 57, no. 30 (July 2001): 6531–38. http://dx.doi.org/10.1016/s0040-4020(01)00545-2.

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Connor, Rebecca E., and David A. Tirrell. "Non‐Canonical Amino Acids in Protein Polymer Design." Polymer Reviews 47, no. 1 (April 2007): 9–28. http://dx.doi.org/10.1080/15583720601109552.

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IMPERIALI, B., R. S. ROY, G. K. WALKUP, and L. WANG. "ChemInform Abstract: Unnatural Amino Acids for the Design of Functional Proteins: Biomimetic Catalysis Using Coenzyme Amino Acids." ChemInform 28, no. 48 (August 2, 2010): no. http://dx.doi.org/10.1002/chin.199748331.

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Esgulian, Mathieu, Luc Camoin, Mathieu Cassien, Yves Toiron, Sylvia Pietri, and Sophie Thétiot-Laurent. "Design of New Probes for Oxidized Amino Acids Localization." Proceedings 22, no. 1 (August 8, 2019): 39. http://dx.doi.org/10.3390/proceedings2019022039.

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Koviach, Jennifer L., Mark D. Chappell, and Randall L. Halcomb. "Design and Synthesis of Conformationally Constrained Glycosylated Amino Acids." Journal of Organic Chemistry 66, no. 7 (April 2001): 2318–26. http://dx.doi.org/10.1021/jo001512z.

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Dissertations / Theses on the topic "Amino acids Design"

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Rubini, Marina. "Protein engineering and design with non canonical amino acids." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=974166073.

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McArthur, Duncan Robert. "Design and synthesis of novel sila-peptidomimetics." Thesis, University of Glasgow, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.250791.

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Bilgiçer, Zihni Basar. "Protein design using unnatural amino acids with fluorinated side chains /." Thesis, Connect to Dissertations & Theses @ Tufts University, 2005.

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Thesis (Ph.D.)--Tufts University, 2005.
Adviser: Krishna Kumar. Submitted to the Dept. of Chemistry. Includes bibliographical references. Access restricted to members of the Tufts University community. Also available via the World Wide Web;
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Petrillo, Betty. "Design and synthesis of artificial receptors for phosphorylated amino acids." Thesis, Cardiff University, 2006. http://orca.cf.ac.uk/54276/.

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The research detailed in this thesis describes the development of a high-throughput molecularly imprinted polymer (MIP) receptor that binds to phosphorylated serine residues. This new receptor would need to be biologically compatible (i.e. binds in aqueous media) and have a high degree of specificity and affinity for the phosphorylated residue compared to the non-phosphorylated amino acid. Importantly, the artificial receptor should not rely on neighbouring amino acid residues for its binding affinity or specificity. Different molecular imprinting approaches were investigated to imprint the template molecule, Boc-phospho-L-serine methyl ester. The most successful approach was found by using an amidine group in stoichiometric monomer-template interactions. To determine the binding affinity and specificity of the MIP, an equilibrium evaluation was used. Batch analyses for the template specie and a range of cross-reactants were performed in aqueous systems and the enantioselectivity was evaluated using the D-enantiomer of the template molecule. Furthermore, the selectivity of the MIP was investigated with a series of peptides containing phosphorylated serine. The results of these studies provide evidence of selective binding sites in the MIP for Boc-phospho-L-serine methyl ester. The thesis concludes by discussing some applications of the MIP in life sciences, e.g. as an alternative to antibody assays.
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Threlfall, Richard Neil. "Design and Synthesis of Foldamers Derived from Nucleoside B-Amino Acids." Thesis, University of Liverpool, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.507631.

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Turtle, Michelle Louise. "Design and synthesis of peptides derived from nucleoside β-amino acids." Thesis, University of Liverpool, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.569173.

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Naturally occurring macromolecules such as proteins and DNA adopt very specific conformations and three dimensional arrangements which allow them to perform their sophisticated functions in nature. Unnatural oligomerscan also adopt well defined conformations and these have been termed 'foldamers'. This project is concerned with the design and synthesis of β-peptide foldamers which are assembled from nucleoside derived β -amino acids. It was hoped that the combination of the inherent helix folding properties of peptides and the associated characteristics of nucleosides would allow us to create novel foldamers with specific recognition properties. The structure of the β -amino acids involves conversion of the 3'-hydroxyl group of the nucleoside sugar into an amino group (with retention of configuration) and oxidation of the 5'-hydroxymethylene group to a carboxylic acid. Beginning with the natural nucleosides thymidine and 2'-deoxyadenosine, syntheses of 4 different nucleoside β -amino acid monomers was accomplished. The syntheses were based around the use of 3'-azido-2'-deoxynucleosides as key synthetic intermediates and also required optimisation of protecting groups to prevent side reactions associated with cleavage of the glycosidic bond. In general, the preferred protecting group strategy involved the 3'-amino group being either protected with a fluorenylmethoxycarbonyl (Fmoc) group or being masked as an azide. The benzhydryl group also proved useful in the protection of the carboxylic acid function for couplings in solution. The synthesis of the β -peptides was investigated by both solid-phase peptide synthesis and standard couplings in solution. A range of peptide dimers, trimers and a tetramer were prepared, but the isolated yields of the final products were low due to difficulties with purification.
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Mavencamp, Terri Lynn. "Design, synthesis and biological evaluation of a family of excitatory amino acid transporter 3 (EAAT3) preferring inhibitors." [Missoula, Mont.] : The University of Montana, 2008. http://etd.lib.umt.edu/theses/available/etd-03212009-152926/unrestricted/Mavencamp_umt_0136D_10009.pdf.

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Eszes, Csilla Monika. "Re-design of proteins to alter enzymic activities." Thesis, University of Bristol, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.324246.

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Mata, David Garcia. "Understanding Protein Structure And Function Using Rational Design And Unnatural Amino Acids." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1338392020.

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Qiu, Wei. "Design and synthesis of conformationally and topographically constrained amino acids as peptidomimetics." Diss., The University of Arizona, 2001. http://hdl.handle.net/10150/280486.

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A major goal of peptide research has been to elucidate or understand the relationships between a peptide's three-dimensional structure and its biological activity. De Novo design of peptide mimetics requires assembling all components necessary for molecular recognition and transduction, which needs the proper choice of a template that can place the key side chain residues in 3D space. Two widely used methods are novel β-substituted amino acids and conformationally constrained secondary structure mimetics. In this thesis, we report our efforts to fulfill the aforementioned criteria in synthesizing β-isopropyl aromatic amino acids and constrained reverse turn dipeptide mimetics. Through asymmetric Michael addition reaction, highly topographically constrained β-isopropyl aromatic amino acids have been synthesized. In order to develop a general approach to synthesize these novel amino acids, we re-examined the reaction conditions for Evans' diastereoselective 1,4-addition, and found conditions which gave excellent diastereoselectivities and good chemical yields. A concise and straightforward five-step synthesis of [5.5]-bicyclic reverse turn dipeptide mimetic scaffolds with side chain functionality at the i+1 and i+2 positions has been developed. In the bicyclic structure, two dihedral angles (ψ₂ and φ₃) are greatly restricted. Further development of this synthesis will enable us to prepare various types of reverse turns with different backbone geometry and side chain topography. Enantiomerically pure (S)-trans-cinnamylglycine and (S)-α-trans-cinnamyl-α-alanine have been prepared via reaction of chiral Ni (II)-complexes of glycine and alanine respectively, with cinnamyl halides. Inexpensive and readily available reagents and solvents are used, including a recyclable chiral ligand. The simplicity of the experimental procedures and high stereochemical outcome make this method synthetically attractive for preparing the target amino acids on multi-gram scales. Further studies by incorporating these mimetics into potent peptide analogues will greatly help us to understand the bioactive conformation of the parent peptides.
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Books on the topic "Amino acids Design"

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1951-, Nielsen Peter E., ed. Pseudo-peptides in drug discovery. Weinheim: Wiley-VCH, 2004.

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Harren, Jhoti, and Leach Andrew R, eds. Structure-based drug discovery. Dordrecht: Springer, 2007.

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Povl, Krogsgaard-Larsen, and Hansen J. J. 1944-, eds. Excitatory amino acid receptors: Design of agonists and antagonists. New York: E. Horwood, 1992.

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Budisa, Nediljko. Engineering the Genetic Code: Expanding the Amino Acid Repertoire for the Design of Novel Proteins. Wiley-VCH Verlag GmbH, 2006.

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Budisa, Nediljko. Engineering the Genetic Code: Expanding the Amino Acid Repertoire for the Design of Novel Proteins. Wiley & Sons, Incorporated, John, 2006.

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Engineering the Genetic Code: Expanding the Amino Acid Repertoire for the Design of Novel Proteins. Wiley-VCH, 2006.

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James, Donald Andrew. Design of photoisomerizable amino acids and their incorporation into biological peptides and enzymes. 2004.

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Nielsen, Peter E. Pseudo-Peptides in Drug Discovery. Wiley & Sons, Incorporated, John, 2006.

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Nielsen, Peter E. Pseudo-Peptides in Drug Discovery. Wiley & Sons, Limited, John, 2005.

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Trabocchi, Andrea, and Antonio Guarna. Peptidomimetics in Organic and Medicinal Chemistry: The Art of Transforming Peptides in Drugs. Wiley & Sons, Incorporated, John, 2014.

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Book chapters on the topic "Amino acids Design"

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Imperiali, B., R. Sinha Roy, G. K. Walkup, and L. Wang. "Unnatural Amino Acids for the Design of Functional Proteins: Biomimetic Catalysis Using Coenzyme-Amino Acids." In Molecular Design and Bioorganic Catalysis, 35–52. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-1679-1_3.

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Cudic, Mare, and Gayle D. Burstein. "Preparation of Glycosylated Amino Acids Suitable for Fmoc Solid-Phase Assembly." In Peptide-Based Drug Design, 187–208. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-419-3_11.

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Benedetti, Ettore, Rosa Iacovino, and Michele Saviano. "The Use of Uncoded α-Amino Acids Residues in Drug Design." In Structure-Based Drug Design, 103–12. Dordrecht: Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-015-9028-0_10.

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Hansen, William A., Jeremy H. Mills, and Sagar D. Khare. "Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids." In Methods in Molecular Biology, 173–85. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3569-7_10.

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Ballet, Steven, Karel Guillemyn, Olivier Van der Poorten, Ben Schurgers, Guido Verniest, and Dirk Tourwé. "Azepinone-Constrained Amino Acids in Peptide and Peptidomimetic Design." In Topics in Heterocyclic Chemistry, 177–209. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/7081_2015_161.

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Seel, Christian, Amalia Galán, and Javier Mendoza. "Molecular recognition of organic acids and anions — Receptor models for carboxylates, amino acids, and nucleotides." In Supramolecular Chemistry II — Host Design and Molecular Recognition, 101–32. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/3-540-58800-0_19.

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Saito, I., M. Takayama, H. Sugiyama, and T. Nakamura. "Design of Photoactivatable DNA-Cleaving Amino Acids with High Sequence Selectivity." In DNA and RNA Cleavers and Chemotherapy of Cancer and Viral Diseases, 163–76. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0251-0_12.

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Meng, He, Venkateshwarlu Kalsani, and Krishna Kumar. "Fluorinated Amino Acids and Reagents in Protein Design and Biomolecule Separation." In Current Fluoroorganic Chemistry, 487–99. Washington, DC: American Chemical Society, 2007. http://dx.doi.org/10.1021/bk-2007-0949.ch031.

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Lew, R. A., E. Boulos, K. M. Stewart, P. Perlmutter, M. F. Harte, S. Bond, S. B. Reeve, et al. "Use of β-Amino Acids in the Design of Substrate-Based Peptidase Inhibitors." In Peptides: The Wave of the Future, 553–54. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0464-0_257.

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Hicks, Rickey P., and Amanda L. Russell. "Application of Unnatural Amino Acids to the De Novo Design of Selective Antibiotic Peptides." In Methods in Molecular Biology, 135–67. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-331-8_9.

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Conference papers on the topic "Amino acids Design"

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Katti, Kalpana S., Dinesh R. Katti, and Avinash H. Ambre. "Unnatural Amino Acids Modified Clays for Design of Scaffolds for Bone Tissue Engineering." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13242.

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Here, we incorporate the results of our new “altered phase theory” (Sikdar et al. 2008a) into design of new polymer clay nanocomposites (PCNs) for bone biomaterials applications. Montmorillonite (MMT) clay was modified using unnatural amino acids as potentially new biocompatible modifiers. The longer carbon chain structures of the unnatural amino acids are expected to enhance non bonded interactions with clay as well as maintaining the usefulness of functional groups of natural amino acids. The specific choice of amino acids is based on both the antibacterial activity reported in literature and also our previous studies on role of chain length, functional groups etc of modifiers in influencing mechanical behavior in PCNs. Biocompatibility studies using cell culture experiments as well as mechanical behavior is evaluated for the PCNs. FTIR spectroscopy is used to compare changes to molecular structure. The increase in d001 spacing of modified clay compared to pure clay obtained from XRD experiments confirms successful intercalation of modifier. The osteoblast cells were found to grow and proliferate over the substrates. The major contribution of this work is the design of novel amino acid biopolymer-clay nanocomposites for biomaterials applications. Porous scaffold structures were also designed and fabricated.
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Arribat, Mathieu, Emmanuelle Rémond, Sébastien Richeter, Philippe Gerbier, Sébastien Clément, and Florine Cavelier. "Fluorogen-based amino acids with Aggregation-InducedEmission features for bioprobes design." In 35th European Peptide Symposium. Prompt Scientific Publishing, 2018. http://dx.doi.org/10.17952/35eps.2018.107.

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Honfroy, Aurélie, Grégory Chaume, Thierry Brigaud, Nathalie Lensen, Sophie Hernot, Steven Ballet, and Charlotte Martin. "Synthesis of Fluorinated Amino Acids for the Design of Injectable Hydrogels." In 36th European Peptide Symposium. The European Peptide Society, 2022. http://dx.doi.org/10.17952/36eps/36eps.2022.267.

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Pajpanova, Tamara. "Design, synthesis, analysis and pharmacological evaluation of neuropeptide mimetics containing unnatural amino acids." In XIth Conference Biologically Active Peptides. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2009. http://dx.doi.org/10.1135/css200911098.

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Liu, Danyi, and Edwin van der Heide. "Evaluating the Spatial Sonification of the Molecular Structures of Amino Acids Using Multiple Concurrently Sounding Sources." In ICAD 2021: The 26th International Conference on Auditory Display. icad.org: International Community for Auditory Display, 2021. http://dx.doi.org/10.21785/icad2021.013.

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We have designed an interactive form of sonification in which the listener navigates through the molecular structures of amino acids over the network of carbon atoms. We use pitch and density as the two main features for the sound design of the four common chemical elements (H, C, N, O). We use multiple concurrently sounding sources to spatially sonify the atoms around a certain carbon atom of the amino acids. The main goal of this paper is to evaluate this sonification approach. We cover the design, execution and evaluation of two separate cycles of experiments that aim to evaluate our sonification approach and get insight in factors that may influence the individual performance of the concurrently sounding source identification and localization.
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de la Calle, Inmaculada, Isela Lavilla, Francisco Javier Pena, Vanesa Romero, and Carlos Bendicho. "SYSTEMATIC DESIGN OF ACID-BASE TITRATIONS FOR UNDERGRADUATE STUDENTS: APPLICATION TO THE RESOLUTION OF A MIXTURE OF TWO AMINO ACIDS." In 12th International Conference on Education and New Learning Technologies. IATED, 2020. http://dx.doi.org/10.21125/edulearn.2020.0955.

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Khurana, Tarun K., Moran Bercovici, and Juan G. Santiago. "Indirect Fluorescence Detection of Non Fluorescent Analytes Using Isotachophoretic Mobility Markers." In ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2008. http://dx.doi.org/10.1115/icnmm2008-62027.

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We have developed a method to detect non-fluorescent analytes on standard microfluidic chip platforms equipped with fluorescence detection. We leverage isotachophoresis (ITP) to electrophoretically segregate both analytes and fluorescent species termed mobility markers into distinct zones. The fluorescent marker zones bound analyte zones, so that gaps in the fluorescent signal indicate the presence and concentration of analytes. We here demonstrate separation and indirect detection of amino acids, serine and phenylalanine and organic acids, acetic acid and phenylpropionic acid (∼10 μM) using this technique. We also present an indirect detection of the environmental toxin phenol [1][2] (∼10 μM) using two mobility markers. We show preliminary numerical simulation results that provide useful guidelines in design and optimization of our indirect detection assay.
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Liu, Danyi, and Edwin van der Heide. "Interactive Auditory Navigation in the Molecular Structures of Amino Acids: A Case Study Using Multiple Concurrent Sound Sources Representing Nearby Atoms." In ICAD 2019: The 25th International Conference on Auditory Display. Newcastle upon Tyne, United Kingdom: Department of Computer and Information Sciences, Northumbria University, 2019. http://dx.doi.org/10.21785/icad2019.049.

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We are interested in sonifying the molecular structures of amino acids. This paper describes the context and the first design choices for our approach. So far, we believe an amino acid molecule is too complex to be perceived at once. Therefore, we have designed an interactive form of sonification in which the listener navigates through the molecule over the network of carbon atoms. We describe our different approaches and discuss the topic of immediacy: the time it takes to recognize the structure surrounding the listener’s position while navigating. Furthermore, we touch upon the question how many atoms we can sonify simultaneously and the role auditory masking plays in this context. To overcome auditory masking, we propose to use irregular but easy to recognize sounds. We conclude with an interest in a three-dimensional navigation environment using general molecular structures for further research and development.
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Wu, Hsin-Jui, Yiwei Yan, Y. C. Lee, and Michael Stowell. "Design, Fabrication of High-Throughput Microarray Microfluidic Device for Membrane Protein Polyhedra Formation." In ASME 2011 International Mechanical Engineering Congress and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/imece2011-62792.

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In this paper, we designed and fabricated High-throughput Microfluidic device for membrane protein polyhedral. Protein is the most important functional element in our human body and also it could be applied to the key application areas of drug bonding and drug delivery. However protein stucture is difficult to be analyzed due to the complex and variable geometry of protein stucture which can be randomly formed by 20 amino acids and also plused 3D folding of stucture possibly. Based on this, we could imagine it would be a huge variable number of protein stucture, let’s say billion possibilities. Therefore if we can successful discover protein stucture, then we can expect that will improve drug delivery of medical technology forward to a big step.
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Tomar, Aishwarya, and AK Shankhwar. "Design and Performance Investigation of Symmetrical Dual Gate Doping-less TFET for Biomolecule Recognition." In International Conference on Women Researchers in Electronics and Computing. AIJR Publisher, 2021. http://dx.doi.org/10.21467/proceedings.114.72.

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This manuscript presents a dielectric modulated doping-less dual metal Gate Tunnel Field Effect Transistor (DL-DMG-TFET) sensor. In which a nano-cavity is presented above the tunnelling point to recognize the bio-molecule like amino acids (AAs), protein, and so on the proposed P+ and N+ sections are invented relying on the electrode's work-function on silicon body. The impacts of metal work regulation, cavity length and thickness variety are investigated for improving band-to-band tunnelling probability at the source-channel intersection. The proposed structure shows perceptible affectability results for neutral and charged biomolecules. The sensitivity of the higher dielectric constant bio-molecules are higher as compared to bio-molecule having lower dielectric constant; the drain current sensitivity of the Gelatin (k=12) is assessed as which is 13% and 35% higher than the affectability of Keratin (k=10) and Bacteriophage T7 (k=5) separately at the nano-cavity length of 30 nm.
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Reports on the topic "Amino acids Design"

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Oldstone, Michael B. Diagnosis of AIDS Using Designed Amino Acid Peptides Representing Immunodominant Epitopes of HIV. Fort Belvoir, VA: Defense Technical Information Center, July 1990. http://dx.doi.org/10.21236/ada232068.

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Oldstone, Michael B. Diagnosis of Aids Using Designed Amino Acid Peptides Representing Immunodominant Epitopes of HIV. Fort Belvoir, VA: Defense Technical Information Center, April 1989. http://dx.doi.org/10.21236/ada222413.

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Altstein, Miriam, and Ronald Nachman. Rationally designed insect neuropeptide agonists and antagonists: application for the characterization of the pyrokinin/Pban mechanisms of action in insects. United States Department of Agriculture, October 2006. http://dx.doi.org/10.32747/2006.7587235.bard.

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The general objective of this BARD project focused on rationally designed insect neuropeptide (NP) agonists and antagonists, their application for the characterization of the mechanisms of action of the pyrokinin/PBAN (PK-PBAN) family and the development of biostable, bioavailable versions that can provide the basis for development of novel, environmentally-friendly pest insect control agents. The specific objectives of the study, as originally proposed, were to: (i) Test stimulatory potencies of rationally designed backbone cyclic (BBC) peptides on pheromonotropic, melanotropic, myotropic and pupariation activities; (ii) Test the inhibitory potencies of the BBC compounds on the above activities evoked either by synthetic peptides (PBAN, LPK, myotropin and pheromonotropin) or by the natural endogenous mechanism; (iii) Determine the bioavailability of the most potent BBC compounds that will be found in (ii); (iv) Design, synthesize and examine novel PK/PBAN analogs with enhanced bioavailability and receptor binding; (v) Design and synthesize ‘magic bullet’ analogs and examine their ability to selectively kill cells expressing the PK/PBAN receptor. To achieve these goals the agonistic and antagonistic activities/properties of rationally designed linear and BBC neuropeptide (NP) were thoroughly studied and the information obtained was further used for the design and synthesis of improved compounds toward the design of an insecticide prototype. The study revealed important information on the structure activity relationship (SAR) of agonistic/antagonistic peptides, including definitive identification of the orientation of the Pro residue as trans for agonist activity in 4 PK/PBANbioassays (pheromonotropic, pupariation, melanotropic, & hindgut contractile) and a PK-related CAP₂b bioassay (diuretic); indications that led to the identification of a novel scaffold to develop biostbiostable, bioavailable peptidomimetic PK/PBANagonists/antagonists. The work led to the development of an arsenal of PK/PBAN antagonists with a variety of selectivity profiles; whether between different PKbioassays, or within the same bioassay between different natural elicitors. Examples include selective and non-selective BBC and novel amphiphilic PK pheromonotropic and melanotropic antagonists some of which are capable of penetrating the moth cuticle in efficacious quantities. One of the latter analog group demonstrated unprecedented versatility in its ability to antagonize a broad spectrum of pheromonotropic elicitors. A novel, transPro mimetic motif was proposed & used to develop a strong, selective PK agonist of the melanotropic bioassay in moths. The first antagonist (pure) of PK-related CAP₂b diuresis in flies was developed using a cisPro mimetic motif; an indication that while a transPro orientation is associated with receptor agonism, a cisPro orientation is linked with an antagonist interaction. A novel, biostablePK analog, incorporating β-amino acids at key peptidase-susceptible sites, exhibited in vivo pheromonotropic activity that by far exceeded that of PBAN when applied topically. Direct analysis of neural tissue by state-of-the-art MALDI-TOF/TOF mass spectrometry was used to identify specific PK/PK-related peptides native to eight arthropod pest species [house (M. domestica), stable (S. calcitrans), horn (H. irritans) & flesh (N. bullata) flies; Southern cattle fever tick (B. microplus), European tick (I. ricinus), yellow fever mosquito (A. aegypti), & Southern Green Stink Bug (N. viridula)]; including the unprecedented identification of mass-identical Leu/Ile residues and the first identification of NPs from a tick or the CNS of Hemiptera. Evidence was obtained for the selection of Neb-PK-2 as the primary pupariation factor of the flesh fly (N. bullata) among native PK/PK-related candidates. The peptidomic techniques were also used to map the location of PK/PK-related NP in the nervous system of the model fly D. melanogaster. Knowledge of specific PK sequences can aid in the future design of species specific (or non-specific) NP agonists/antagonists. In addition, the study led to the first cloning of a PK/PBAN receptor from insect larvae (S. littoralis), providing the basis for SAR analysis for the future design of 2ⁿᵈgeneration selective and/or nonselective agonists/antagonists. Development of a microplate ligand binding assay using the PK/PBAN pheromone gland receptor was also carried out. The assay will enable screening, including high throughput, of various libraries (chemical, molecular & natural product) for the discovery of receptor specific agonists/antagonists. In summary, the body of work achieves several key milestones and brings us significantly closer to the development of novel, environmentally friendly pest insect management agents based on insect PK/PBANNPs capable of disrupting critical NP-regulated functions.
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4

Zlotkin, Eliahu, Shizuo G. Kamita, Nor Chejanovsky, and S. Maeda. Targeting of an Expressed Insect Selective Neurotoxin by its Recombinant Baculovirus: Pharmacokinetic and Pharmacodynamic Aspects. United States Department of Agriculture, July 1995. http://dx.doi.org/10.32747/1995.7571354.bard.

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Objectives: 1) Clarification of the mode of potentiation of an expressed insect selective neurotoxin (AaIT) by its recombinant baculovirus. 2) In vitro formation and/or modification of neuroactive polypeptides for the design of new improved recombinant baculoviruses. Results: 1) A combined utilization of bioassays, LM-cytochemistry, the highly resolutive EM immunogold and electrical recording from the CNS of baculovirus and AaIT - expressing – recombinant baculovirus infected larvae it has been shown that the recombinant virus potentiates the effect of the toxin. Potentiation is achieved through its continuous expression in the infected tracheal epithelia thus providing a: a) Local supply of freshly produced toxin in the vicinity of its traget sites; b) Translocation of the expressed toxin to the insect CNS. The latter exposes the recombinant toxin to new, critical, target sites which are inaccessible through the natural route of scorpion envenomation. 2) Subjecting a recombinant AaIT toxin to a newly designed system of random mutagenesis results in large numbers of new AaIT genes with amino acid substitutions. The new or modified toxin genes were inserted into a linear BmNPV expressed in silkworm cell culture and assayed on blowfly and silkworm larvae. Thus a system for mass formation and screening of neuroactive agents was developed. Contribution to agriculture: 1) Demonstration of the insecticidal mechanism, capacity and utility of the combination of neuroactive polypeptides and recombinant pathogens. 2) Development of a simple in vitro system for the formation and selection of new neuroactive polypeptides.
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5

Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593390.bard.

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The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mutant receptors, cell lines and pheromone glands (at tissue and organism levels) against selected, designed compounds to confirm if compounds are agonists or antagonists. (2) The elucidation ofthemolecular regulationmechanisms of PBAN-R by:(a) age-dependence of gene expression; (b) the effect of hormones and; (c) PBAN-R characterization in male hair-pencil complexes. Background to the topic Insects have several closely related G protein-coupled receptors (GPCRs) belonging to the pyrokinin/PBAN family, one with the ligand pheromone biosynthesis activating neuropeptide or pyrokinin-2 and another with diapause hormone or pyrokinin-1 as a ligand. We were unable to identify the diapause hormone receptor from Helicoverpa zea despite considerable effort. A third, related receptor is activated by a product of the capa gene, periviscerokinins. The pyrokinin/PBAN family of GPCRs and their ligands has been identified in various insects, such as Drosophila, several moth species, mosquitoes, Triboliumcastaneum, Apis mellifera, Nasoniavitripennis, and Acyrthosiphon pisum. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates pheromone production in moths plus other functions indicating the pleiotropic nature of these ligands. Based on the alignment of annotated genomic sequences, the primary and secondary structures of the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors found in vertebrates. Major conclusions, solutions, achievements Evolutionary trace analysisof receptor extracellular domains exhibited several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding. Through site-directed point mutations, the 3rd extracellular domain of PBAN-R was shown to be critical for ligand selection. We identified three receptors that belong to the PBAN family of GPCRs and a partial sequence for the periviscerokinin receptor from the European corn borer, Ostrinianubilalis. Functional expression studies confirmed that only the C-variant of the PBAN-R is active. We identified a non-peptide agonist that will activate the PBAN-receptor from H. zea. We determined that there is transcriptional control of the PBAN-R in two moth species during the development of the pupa to adult, and we demonstrated that this transcriptional regulation is independent of juvenile hormone biosynthesis. This transcriptional control also occurs in male hair-pencil gland complexes of both moth species indicating a regulatory role for PBAN in males. Ultimate confirmation for PBAN's function in the male tissue was revealed through knockdown of the PBAN-R using RNAi-mediated gene-silencing. Implications, both scientific and agricultural The identification of a non-peptide agonist can be exploited in the future for the design of additional compounds that will activate the receptor and to elucidate the binding properties of this receptor. The increase in expression levels of the PBAN-R transcript was delineated to occur at a critical period of 5 hours post-eclosion and its regulation can now be studied. The mysterious role of PBAN in the males was elucidated by using a combination of physiological, biochemical and molecular genetics techniques.
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Gurevitz, Michael, Michael Adams, and Eliahu Zlotkin. Insect Specific Alpha Neurotoxins from Scorpion Venoms: Mode of Action and Structure-Function Relationships. United States Department of Agriculture, June 1996. http://dx.doi.org/10.32747/1996.7613029.bard.

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This study was motivated by the need to develop new means and approaches to the design of future, environmentally-safe, insecticides. Utilization of anti-insect selective toxins from scorpion venoms and clarification of the molecular basis for their specificity, are a major focus in this project and may have an applicative value. Our study concentrated on the highly insecticidal toxin, LqhaIT, and was devoted to: (I) Characterization of the neuropharmacological and electrophysiological features of this toxin. (II) Establishment of a genetic system for studying structure/activity relationships of the toxin. (III) Analysis of the insecticidal efficacy of an entomopathogenic baculovirus engineered and expressing LqhaIT. The results obtained in this project suggest that: 1) The receptor binding site of LqhaIT on insect sodium channels differs most likely from its analogous receptor site 3 on vertebrate sodium channels. 2) The effects of LqhaIT are presynaptic. Hyperexcitation at the neuromuscular results from dramatic slowing of sodium channel inactivation and enhanced peak sodium currents causes by LqhaIT. 3) The putative toxic surface of LqhaIT involves aromatic and charged amino acid residues located around the C-terminal region and five-residue-turn of the toxin (unpublished). 4) The anti-insect/anti-mammalian toxicity ratio can be altered by site-directed mutagenesis (publication 8). This effect was partly shown at the level of sodium channel function. 5) The insecticidal efficacy of AcNPV baculovirus increased to a great extent when infection was accompanied by expression of LqhaIT (publication 5).
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7

Gershoni, Jonathan M., David E. Swayne, Tal Pupko, Shimon Perk, Alexander Panshin, Avishai Lublin, and Natalia Golander. Discovery and reconstitution of cross-reactive vaccine targets for H5 and H9 avian influenza. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7699854.bard.

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Research objectives: Identification of highly conserved B-cell epitopes common to either H5 or H9 subtypes of AI Reconstruction of conserved epitopes from (1) as recombinantimmunogens, and testing their suitability to be used as universal vaccine components by measuring their binding to Influenza vaccinated sera of birds Vaccination of chickens with reconstituted epitopes and evaluation of successful vaccination, clinical protection and viral replication Development of a platform to investigate the dynamics of immune response towards infection or an epitope based vaccine Estimate our ability to focus the immune response towards an epitope-based vaccine using the tool we have developed in (D) Summary: This study is a multi-disciplinary study of four-way collaboration; The SERPL, USDA, Kimron-Israel, and two groups at TAU with the purpose of evaluating the production and implementation of epitope based vaccines against avian influenza (AI). Systematic analysis of the influenza viral spike led to the production of a highly conserved epitope situated at the hinge of the HA antigen designated “cluster 300” (c300). This epitope consists of a total of 31 residues and was initially expressed as a fusion protein of the Protein 8 major protein of the bacteriophagefd. Two versions of the c300 were produced to correspond to the H5 and H9 antigens respectively as well as scrambled versions that were identical with regard to amino acid composition yet with varied linear sequence (these served as negative controls). The recombinantimmunogens were produced first as phage fusions and then subsequently as fusions with maltose binding protein (MBP) or glutathioneS-transferase (GST). The latter were used to immunize and boost chickens at SERPL and Kimron. Furthermore, vaccinated and control chickens were challenged with concordant influenza strains at Kimron and SEPRL. Polyclonal sera were obtained for further analyses at TAU and computational bioinformatics analyses in collaboration with Prof. Pupko. Moreover, the degree of protection afforded by the vaccination was determined. Unfortunately, no protection could be demonstrated. In parallel to the main theme of the study, the TAU team (Gershoni and Pupko) designed and developed a novel methodology for the systematic analysis of the antibody composition of polyclonal sera (Deep Panning) which is essential for the analyses of the humoral response towards vaccination and challenge. Deep Panning is currently being used to monitor the polyclonal sera derived from the vaccination studies conducted at the SEPRL and Kimron.
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8

Hedrick, Ronald, and Herve Bercovier. Characterization and Control of KHV, A New Herpes Viral Pathogen of Koi and Common Carp. United States Department of Agriculture, January 2004. http://dx.doi.org/10.32747/2004.7695871.bard.

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In this project we proposed to characterize the virus genome and the structural virion polypeptides to allow development of improved diagnostic approaches and potential vaccination strategies. These goals have been mostly achieved and the corresponding data were published in three papers (see below) and three more manuscripts are in preparation. The virion polypeptides of KHV strains isolated from USA (KHV-U) and Israel (KHV-I) were found to be identical. Purified viral DNA analyzed with a total of 5 restriction enzymes demonstrated no fragment length polymorphism between KHV-I and KHV-U but both KHV isolates differed significantly from the cyprinid herpesvirus (CHV) and the ictalurid herpesvirus (channel catfish virus or CCV). Using newly obtained viral DNA sequences two different PCR assays were developed that need to be now further tested in the field. We determined by pulse field analysis that the size of KHV genome is around 280 kbp (1-1. Bercovier, unpublished results). Sequencing of the viral genome of KHV has reached the stage where 180 kbp are sequenced (twice and both strands). Four hypothetical genes were detected when DNA sequences were translated into amino acid sequences. The finding of a gene of real importance, the thymidine kinase (TK) led us to extend the study of this specific gene. Four other genes related to DNA synthesis were found. PCR assays based on defined sequences were developed. The PCR assay based on TK gene sequence has shown improved sensitivity in the detection of KHV DNA compared to regular PCR assays. </P> <P><SPAN>With the ability to induce experimental infections in koi with KHV under controlled laboratory conditions we have studied the progress and distribution of virus in host tissues, the development of immunity and the establishment of latent infections. Also, we have investigated the important role of water temperature on severity of infections and mortality of koi following infections with KHV. These initial studies need to be followed by an increased focus on long-term fate of the virus in survivors. This is essential in light of the current &quot;controlled exposure program&quot; used by farmers to produce KHV &quot;naturally resistant fish&quot; that may result in virus or DNA carriers. </SPAN></P> <P><SPAN>The information gained from the research of this project was designed to allow implementation of control measures to prevent the spread of the virus both by improved diagnostic approaches and preventive measures. We have accomplished most of these goals but further studies are needed to establish even more reliable methods of prevention with increased emphases on improved diagnosis and a better understanding of the ecology of KHV. </SPAN>
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9

Shpigel, Muki, Allen Place, William Koven, Oded (Odi) Zmora, Sheenan Harpaz, and Mordechai Harel. Development of Sodium Alginate Encapsulation of Diatom Concentrates as a Nutrient Delivery System to Enhance Growth and Survival of Post-Larvae Abalone. United States Department of Agriculture, September 2001. http://dx.doi.org/10.32747/2001.7586480.bard.

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The major bottlenecks in rearing the highly priced gastropod abalone (Haliotis spp.) are the slow growth rate and the high mortality during the first 8 to 12 weeks following metamorphosis and settling. The most likely reason flor these problems is related to nutritional deficiencies in the diatom diet on which the post larvae (PL) feed almost exclusively in captivity. Higher survival and improved growth rate will reduce the considerable expense of hatchery-nursery resisdence time and thereflore the production costs. BARD supported our research for one year only and the support was given to us in order to prove that "(1) Abalone PL feed on encapsulated diatoms, and (2) heterotrophic diatoms can be mass produced." In the course of this year we have developed a novel nutrient delivery system specifically designed to enhance growth and survival of post-larval abalone. This approach is based on the sodium-alginate encapsulation of heterotrophically grown diatoms or diatom extracts, including appetite-stimulating factors. Diatom species that attract the PL and promote the highest growth and survival have been identified. These were also tested by incorporating them (either intact cells or as cell extracts) into a sodium-alginate matrix while comparing the growth to that achieved when using diatoms (singel sp. or as a mixture). A number of potential chemoattractants to act as appetite-stimulating factors for abalone PL have been tested. Preliminary results show that the incorporation of the amino acid methionine at a level of 10-3M to the sodim alginate matrix leads to a marked enhancement of growth. The results ol these studies provided basic knowledge on the growth of abalone and showed that it is possible to obtain, on a regular basis, survival rates exceeding 10% for this stage. Prior to this study the survival rates ranged between 2-4%, less than half of the values achieved today. Several diatom species originated from the National Center for Mariculture (Nitzchia laevis, Navicula lenzi, Amphora T3, and Navicula tennerima) and Cylindrotheca fusiformis (2083, 2084, 2085, 2086 and 2087 UTEX strains, Austin TX) were tested for heterotrophic growth. Axenic colonies were initially obtained and following intensive selection cycles and mutagenesis treatments, Amphora T3, Navicula tennerima and Cylindrotheca fusiformis (2083 UTEX strain) were capable of growing under heterotrophic conditions and to sustain highly enriched mediums. A highly efficient selection procedure as well as cost effective matrix of media components were developed and optimized. Glucose was identified as the best carbon source for all diatom strains. Doubling times ranging from 20-40 h were observed, and stable heterotroph cultures at a densities range of 103-104 were achieved. Although current growth rates are not yet sufficient for full economical fermentation, we estimate that further selections and mutagenesis treatments cycles should result in much faster growing colonies suitable for a fermentor scale-up. As rightfully pointed out by one of the reviewers, "There would be no point in assessing the optimum levels of dietary inclusions into micro-capsules, if the post-larvae cannot be induced to consume those capsules in the first place." We believe that the results of the first year of research provide a foundationfor the continuation of this research following the objectives put forth in the original proposal. Future work should concentrate on the optimization of incorporation of intact cells and cell extracts of the developed heterotrophic strains in the alginate matrix, as well as improving this delivery system by including liposomes and chemoattractants to ensure food consumption and enhanced growth.
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10

Phillips, Donald A., Yitzhak Spiegel, and Howard Ferris. Optimizing nematode management by defining natural chemical bases of behavior. United States Department of Agriculture, November 2006. http://dx.doi.org/10.32747/2006.7587234.bard.

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This project was based on the hypothesis that nematodes interacting with plants as either parasites or beneficial saprophytes are attracted to their host by natural products. This concept was supported by numerous observations that parasitic nematodes are attracted to root exudates. Our overall goal was to identify nematode sensory compounds from root exudates and to use that information for reducing nematicide applications. We applied skills of the investigators to achieve three specific objectives: 1) Identify nematode behavioral cues (e.g., attractants or repellents) in root exudates; 2) Identify new natural nematicidal compounds; and 3) Combine a natural attractant and a nematicide into a nematode trap. Because saprophytic nematodes benefit plants by mineralizing organic matter, we sought compounds attractive primarily to parasitic nematodes. The project was constructed on several complementary foundations. First, data from Dr. Spiegel’s lab showed that under aseptic conditions Ditylenchus dipsaci, a parasite on onion, is attracted to certain fractions of onion root exudates. Second, PI Phillips had a sizeable collection of natural plant products he had identified from previous work on Rhizobium-legume interactions, which could be tested “off the shelf”. Third, Dr. Ferris had access to aseptic and natural populations of various saprophytic and parasitic nematodes. The project focused on five nematode species: D.dipsaci, Heterodera avenae, and Tylenchulussemipenetransat ARO, and Meloidogyne javanicand Caenorhabditis elegans at UCD. Ten pure plant compounds, mostly flavonoids, were tested on the various nematode species using six different assay systems. Results obtained with assorted test systems and by various scientists in the same test systems were essentially irreproducible. Many convincing, Many convincing, i.e. statistically significant, results in one system or with one investigator could not be repeated with other assays or different people. A recent report from others found that these compounds, plus another 30, were inactive as attractants in three additional parasitic nematode species (Wuyts et al. Nematology 8:89- 101, 2006). Assays designed to test the hypothesis that several compounds together are required to attract nematodes have thus far failed to find a reproducibly active combination. In contrast to results using pure plant compounds, complex unfractionated exudates from aseptic onion root reproducibly attracted D. dipsaci in both the ARO and UCD labs. Onion root exudate collection, separation into HPLC fractions, assays using D. dipsaci and MS-MS experiments proceeded collaboratively between ARO and UCD without any definitive identification of an active compound. The final active fraction contained two major molecules and traces of several other compounds. In the end, analytical studies were limited by the amount of onion root exudate and the complexity of the purification process. These tests showed that aseptic plant roots release attractant molecules, but whether nematodes influence that release, as insects trigger release of attractants from plants, is unknown. Related experiments showed that the saprophyte C. elegans stimulates its prey, Pseudomonas bacteria, to increase production of 2, 4-diacetylphloroglucinol (DAPG) a compound that promotes amino acid exudation by plant roots. It is thus possible that saprophytic nematodes are attracted primarily to their bacterial or fungal prey and secondarily to effects of those microorganisms on root exudation. These observations offer promising avenues for understanding root-zone interactions, but no direct routes to controlling nematodes in agriculture were evident. Extracts from two plant sources, Chrysanthemum coronarium and Sequoia sempervirens, showed nematicidal activity at ARO and UCD, respectively. Attempts to purify an active compound from S. sempervirens failed, but preliminary results from C. coronarium are judged to form a potential basis for further work at ARO. These results highlight the problems of studying complex movement patterns in sentient organisms like nematodes and the issues associated with natural product isolation from complex mixtures. Those two difficulties combined with complications now associated with obtaining US visas, slowed and ultimately limited progress on this project. As a result, US investigators expended only 65% of the $207,400 originally planned for this project. The Israeli side of the project advanced more directly toward its scientific goals and lists its expenditures in the customary financial report.
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