Relevant bibliographies by topics / Amino acids – Analysis

Academic literature on the topic 'Amino acids – Analysis'

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Published: 4 June 2021
Last updated: 31 January 2023

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Journal articles on the topic "Amino acids – Analysis"

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Park, Kwang Sook, Sung-Youl Hong, Hyang Woo Lee, Sangduk Kim, and Woon Ki Paik. "HPLC analysis of methylated amino acids: Methylated amino acids on HPLC." Archives of Pharmacal Research 9, no. 1 (March 1986): 15–18. http://dx.doi.org/10.1007/bf02857700.

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Athmani, Hamza, and Nourreedine Benali-Cherif. "Structure and thermal analysis of amino acids." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C989. http://dx.doi.org/10.1107/s205327331409010x.

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The twenty amino acids are chemical compounds having two functional groups (carboxyl:-COOH, amine:-NH2) and an asymmetric carbon (except glycine). They are amphoteric and can exist as zwitterion. Because of the reactivity of amino acids (esterification, amidation, N-alkylisation, N-arylation, protonation), and their conformation (aliphatic, aromatic) chemical, properties (acid, base, and / or hydroxylated, solubility), and physical properties (absorbance, NLO), our laboratory contribute to the study (synthesis and X ray single crystal structures) of new organic-inorganic hybrid compounds which allows to the development of materials with novel properties [1-3]. Our work is also based on the relationship between the thermal decomposition of amino acids and their chemical structures, dozens compounds were selected and the results of the DTA, TG and DTG thermal decomposition was performed by several methods. Diffraction results are used for the identification of degradation mechanisms of the chemical structure, the stability of the compound studied and the anticipation of possible syntheses of hybrid compounds.
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Akhtar, Adil, and Tazid Ali. "Analysis of Unweighted Amino Acids Network." International Scholarly Research Notices 2014 (December 16, 2014): 1–6. http://dx.doi.org/10.1155/2014/350276.

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The analysis of amino acids network is very important to studying the various physicochemical properties of amino acids. In this paper we consider the amino acid network based on mutation of the codons. To analyze the relative importance of the amino acids we have discussed different measures of centrality. The measure of centrality is a powerful tool of graph theory for ranking the vertices and analysis of biological network. We have also investigated the correlation coefficients between various measures of centrality. Also we have discussed clustering coefficient as well as average clustering coefficient of the network. Finally we have discussed the degree of distribution as well as skewness.
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Campo, Vanessa L., Áurea D. L. Borges, and Ivone Carvalho. "HPLC analysis of glycosylated amino acids." Journal of the Brazilian Chemical Society 17, no. 4 (August 2006): 648–54. http://dx.doi.org/10.1590/s0103-50532006000400004.

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Sandberg, M., H. Hagberg, I. Jacobson, B. Karlsson, A. Lehmann, and A. Hamberger. "Analysis of amino acids: Neurochemical application." Life Sciences 41, no. 7 (August 1987): 829–32. http://dx.doi.org/10.1016/0024-3205(87)90173-1.

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Papadoyannis, Ioannis N., and Georgios A. Theodoridis. "ChemInform Abstract: Amino Acids: HPLC Analysis." ChemInform 41, no. 28 (June 17, 2010): no. http://dx.doi.org/10.1002/chin.201028272.

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Bora, Pranjal Kumar, Pankaj Hazarika, and Arun Kumar Baruah. "Distance based amino acids network analysis." Gene Reports 21 (December 2020): 100933. http://dx.doi.org/10.1016/j.genrep.2020.100933.

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Tsikas, Dimitrios, and Alexander A. Zoerner. "Analysis of eicosanoids, amino acids, organic acids, and microRNAs." Journal of Chromatography B 964 (August 2014): vii—viii. http://dx.doi.org/10.1016/j.jchromb.2014.06.001.

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Jacoby, George A., Marian A. Corcoran, Debra M. Mills, Caitlin M. Griffin, and David C. Hooper. "Mutational Analysis of Quinolone Resistance Protein QnrB1." Antimicrobial Agents and Chemotherapy 57, no. 11 (August 26, 2013): 5733–36. http://dx.doi.org/10.1128/aac.01533-13.

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ABSTRACTAlanine substitutions and selected deletions have been used to localize amino acids in QnrB essential for its protective activity. Essential amino acids are found at positions i and i−2in the pentapeptide repeat module and in the larger of two loops, where deletion of only a single amino acid compromises activity. Deletion of 10 amino acids at the N terminus is tolerated, but removal of 3 amino acids in the C-terminal dimerization unit destroys activity.
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Gu, Shuang-Xi, Hai-Feng Wang, Yuan-Yuan Zhu, and Fen-Er Chen. "Natural Occurrence, Biological Functions, and Analysis of D-Amino Acids." Pharmaceutical Fronts 02, no. 02 (June 2020): e79-e87. http://dx.doi.org/10.1055/s-0040-1713820.

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AbstractThis review covers the recent development on the natural occurrence, functional elucidations, and analysis of amino acids of the D (dextro) configuration. In the pharmaceutical field, amino acids are not only used directly as clinical drugs and nutriments, but also widely applied as starting materials, catalysts, or chiral ligands for the synthesis of active pharmaceutical ingredients. Earler belief hold that only L-amino acids exist in nature and D-amino acids were artificial products. However, increasing evidence indicates that D-amino acids are naturally occurring in living organisms including human beings, plants, and microorganisms, playing important roles in biological processes. While D-amino acids have similar physical and chemical characteristics with their respective L-enantiomers in an achiral measurement, the biological functions of D-amino acids are remarkably different from those of L-ones. With the rapid development of chiral analytical techniques for D-amino acids, studies on the existence, formation mechanisms, biological functions as well as relevant physiology and pathology of D-amino acids have achieved great progress; however, they are far from being sufficiently explored.
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Dissertations / Theses on the topic "Amino acids – Analysis"

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Wong, Wai Cheong. "Electroanalysis of amino acids and dithocarbamates." HKBU Institutional Repository, 1994. http://repository.hkbu.edu.hk/etd_ra/40.

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Magnuson, David Stuart Keith. "Analysis of excitatory amino acid receptors in the rat spinal cord in vivo and in vitro." Thesis, University of British Columbia, 1988. http://hdl.handle.net/2429/29017.

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Several endogenous amino acids including L-glutamate and L-aspartate have potent excitatory effects in the central nervous system. They are thought to act as synaptic transmitters in many neural pathways including those in the spinal cord. Three distinct receptors have been described through which these excitatory amino acids exert their effects. These are referred to as quisqualate, kainate and N-methyl-D-aspartate (NMDA) receptors, after the exogenous excitants most specific for each. In addition, sub-types of the NMDA receptor have been proposed to account for differences observed in the actions of the endogenous excitant quinolinate (2,3-pyridine dicarboxylate) in various regions of the nervous system. The characterization of excitant amino acid receptors has been accomplished primarily using two or more potent antagonists which include D-(-)-2-amino-5-phosphonovalerate (APV), a specific NMDA antagonist, and kynurenate, a compound related to quinolinate which potently attenuates the actions of NMDA- and kainate-like excitants. Structure-activity studies of amino acid receptors were undertaken using standard extracellular recording and iontophoretic techniques in the dorsal horn of the spinal cord in vivo, and compared with the neocortex of the rat. In addition, a spinal cord slice preparation was developed wherein dorso-ventral longitudinal slices were prepared from the lumbar enlargement of weanling rats (50 - 125 g). The slices were maintained in an "interface" tissue bath of novel design. Extracellular recording of several hours duration and up to 8 hours after slice preparation were routinely possible. Conformationally restricted analogues of glutamate, aspartate and quinolinate were examined for agonist and antagonist actions in the rat spinal cord in vivo and in vitro. Compounds found to be excitants were compared directly with quisqualate, kainate, and NMDA for sensitivity to blockade by APV and kynurenate applied both iontophoretically and in the bathing medium; antagonist dose-response curves were constructed for the actions of APV and kynurenate against quisqualate, kainate, quinolinate and NMDA. The conformationally restricted compounds found to be antagonists were examined to determine their potency and specificity against excitations elicited by quisqualate, kainate, quinolinate and NMDA. Although quinolinate is known to be NMDA-like in the hippocampus and cortex, when compared to quisqualate, kainate and NMDA in the spinal cord in vitro, it proved to be unique. A fourth receptor (the "QUIN" receptor) is proposed to account for its actions in the spinal cord. Three of the isomers of 1-amino-1,3-cyclopentane dicarboxylate (ACPD), conformationally restricted analogues of glutamate, were potently blocked by APV and KYNA and were therefore classified as NMDA-like. The fourth, D-trans-ACPD. was indistinguishable from quinolinate in terms of both potency and sensitivity to antagonists. The (-) isomer of trans-1-amino-1,2-cyclopentane dicarboxylate proved to be an antagonist with greater potency against excitations elicited by quisqualate and kainate than those of NMDA. These findings are, in many ways, different from what has been observed in the hippocampal slice. Several pyridine derivatives were examined; 2,5- and 2,6-pyridine dicarboxylate were weak excitants behaving like quisqualate in the presence of APV and kynurenate. No other pyridines were excitatory; however 2,4-pyridine dicarboxylate was observed to be a weak, non-specific antagonist similar in action to acridinate (an antagonist closely related to kynurenate). None of the pyridine derivatives, save quinolinate, are excitatory in the hippocampus. Structural analysis of the active compounds tested, in consideration of previous studies, shows that three points of attachment (two carboxyl and one amino group) are necessary for activation of NMDA, quisqualate and quinolinate receptors in the spinal cord. The location of the distal or y-carboxyl group relative to the a ionic groups appears to be the primary factor determining the activity of a conforrnationally restricted compound. The absolute distance between the Y-carboxyl and α-carbon appears to play a secondary role in determining the action of a compound.
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Liyanapatirana, Chamindu. "Microfluidic analysis of free amino acids from different fish species." Master's thesis, Mississippi State : Mississippi State University, 2008. http://library.msstate.edu/etd/show.asp?etd=etd-02032008-193849.

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Orwar, Owe. "Laser-based ultra-trace analysis in liquid chromatography determination of neuroactive amino acids and peptides /." Göteborg : Dept. of Analytical and Marine Chemistry, University of Göteborg, 1994. http://catalog.hathitrust.org/api/volumes/oclc/39775021.html.

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Law, Gim Hoong Erica. "Mutational analysis of solvent-exposed amino acids in Photinus pyralis luciferase." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615816.

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Pirogova, Elena 1968. "Examination of physicochemical properties of amino acids within the resonant recognition model." Monash University, Dept. of Electrical and Computer Systems Engineering, 2001. http://arrow.monash.edu.au/hdl/1959.1/8424.

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Lao, Hongbai. "A study of the synthesis and properties of some long chain fatty acid esters containing azido, amino, amido and amino acid residues and the analysis of some seed oils used in Chinese medicine /." [Hong Kong : University of Hong Kong], 1989. http://sunzi.lib.hku.hk/hkuto/record.jsp?B12437141.

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Delaere, Ian. "The chemistry of Vivia sativa L. selection." Title page, contents and abstract only, 1996. http://web4.library.adelaide.edu.au/theses/09PH/09phd332.pdf.

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Bibliography: leaves 151-166. This thesis describes the development of two novel and complementary analytical approaches for assaying cyanoalanine non-protein amino acids. These assays are used to determine the distribution of these compounds both within and between plants and to identify accessions of common vetch which contain low levels of the cyanoalanine non-protein amino acids in germplasm collections. These analytical tools are used to correlate toxicity observed in animal feeding experiments with the cyanoalanine content. This thesis covers also the first report of the use of diffuse reflectance using dispersive infrared spectrometry for the "in situ" quantification of specific organic components from plant tissue as well as the first use of micellar electrokinetic chromatography for the quantitative analysis of 9-fluorenylmethyl chloroformate (FMOC) derivatised and non-derivatised components of extracts from plant material.
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Lee, Johnny Chien-Yi Biotechnology &amp Biomolecular Sciences Faculty of Science UNSW. "Transcriptional and metabolic responses of yeast Saccharomyces cerevisiae to the addition of L-serine." Publisher:University of New South Wales. Biotechnology & Biomolecular Sciences, 2008. http://handle.unsw.edu.au/1959.4/41012.

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Sudden changes in nutrient resources are common in the natural environment. Cells are able to adapt and propagate under changing environmental conditions by making adjustments in their cellular processes. These cellular adaptations involve genome-wide transcriptional reprogramming that results in the induction or repression of metabolic pathways. Specific enzymes are then synthesised and activated to maximise the use of the newly available nutrient sources. L-serine is one of the twenty proteinogenic amino acids, and can be synthesised in yeast by the glycolytic and gluconeogenic pathways when growing on fermentable or non-fermentable carbon sources or taken up from the environment when available. L-serine is metabolically linked to glycine and is a predominant donor of one-carbon units in one-carbon metabolism. L-serine is also a source of pyruvate and ammonia and contributes to other cellular processes including the biosynthesis of cysteine and phospholipids. Previous work has shown that yeast cells exhibit transcriptional induction of the one-carbon pathway and the genes involved in the synthesis of purine and methionine after the addition of 10 mM glycine. Here it is shown that addition of 10 mM L-serine did not, however, elicit the same transcriptional response. This is primarily due to differences in the uptake of glycine and L-serine in yeast. High concentrations of extracellular L-serine were required for yeast to show an increase in intracellular L-serine concentration of the magnitude required to trigger a noticeable cellular response. Despite L-serine and glycine being interconvertable via the SHMT isozymes and being a one-carbon donor, the genome-wide transcriptional response exhibited by cells in response to L-serine addition was markedly different to that seen for glycine. The predominant response to an increase in intracellular L-serine was the induction of the general amino acid control system and the CHA1 gene encoding the serine (threonine) dehydratase. Unlike glycine, addition of L-serine triggered only minor induction of the one-carbon pathway. A large portion of intracellular L-serine was converted to pyruvate and ammonia in the mitochondrion as the result of induction of CHA1. The high intracellular concentration of L-serine stimulated the cell to increase the production of oxaloacetate and to increase the biosynthesis of L-aspartate. Transient increases in the intracellular L-glutamate and L-glutamine were also observed after the addition of L-serine. The work presented in this study shows that large increase in the intracellular concentration of amino acid is required to trigger a significant transcriptional response. Yeast cells exhibit different transcriptional and metabolic responses to the addition of L-serine and glycine even though these two amino acids are closely metabolically linked. Addition of L-serine provokes the GAAC response, expression of the CHA1 gene and stimulates the biosynthesis of L-aspartate in yeast whereas addition of glycine induces the one-carbon pathway which leads to the biosynthesis of the purine nucleotides.
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Dale, Ryan K. "Temperature and the biological response a multivariate statistical analysis of the variation in genomic organization, oligopeptide frequencies, and environmental temperature /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 235 p, 2009. http://proquest.umi.com/pqdweb?did=1654488371&sid=7&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Books on the topic "Amino acids – Analysis"

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Kazutomo, Imahori, Sakiyama Fumio, and International Conference on Methods in Protein Sequence Analysis (9th : 1992 : Otsu, Japan), eds. Methods in protein sequence analysis. New York: Plenum Press, 1993.

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Z, Atassi M., and Appella Ettore, eds. Methods in protein structure analysis. New York: Plenum Press, 1995.

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Amino acid analysis: Methods and protocols. New York, N.Y: Humana Press, 2012.

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M, Griffin Annette, and Griffin Hugh G, eds. Computer analysis of sequence data. Totowa, N.J: Humana Press, 1994.

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Konno, Ryuichi. D-amino acids: Practical methods and protocols. Hauppauge, N.Y: Nova Science, 2009.

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Ryuichi, Konno, ed. D-amino acids: Practical methods and protocols. Hauppauge, N.Y: Nova Science, 2009.

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Ophir, Frieder, and Martino Robert L, eds. High performance computational methods for biological sequence analysis. Boston: Kluwer Academic Publishers, 1996.

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Oliver, R. W. A. On the analysis of PTH-amino acids by HPLC. (Macclesfield): HPLC, 1986.

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Kagakkai, Nihon Bunseki. Aminosan, seitai amin bunseki. Tōkyō: Maruzen Shuppan, 2012.

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Ibolya, Molnár-Perl, ed. Quantitation of amino acids and amines by chromatography: Methods and protocols. Amsterdam: Elsevier, 2005.

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Book chapters on the topic "Amino acids – Analysis"

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Brückner, Hans, Robert Wittner, and Herbert Godel. "Amino acid analysis by derivatization with o-phthaldialdehyde and chiral thiols." In Amino Acids, 143–51. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-011-2262-7_17.

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Rodriguez-Sierra, Jorge F., Stephanie R. Burns, Robert A. Earl, Bobbie L. Schneider, and Barbara J. Morley. "Infant rats exposure to aspartate and glutamate: Neuroendocrinopathies and structural analysis of brain damage." In Amino Acids, 529–37. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-011-2262-7_62.

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Marshall, Elizabeth F., F. Hassanyeh, S. Wright-Honari, and C. H. Ashton. "A brief preliminary analysis of the biochemical data from patients who have attempted suicide." In Amino Acids, 757–61. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-011-2262-7_91.

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Teichberg, V. I., and O. Goldberg. "Analysis of Excitatory Amino Acid Receptor Function with 22Na+ Fluxes in Brain Slices." In Excitatory Amino Acids, 337–54. London: Palgrave Macmillan UK, 1986. http://dx.doi.org/10.1007/978-1-349-08479-1_22.

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Ough, C. S. "Acids and Amino Acids in Grapes and Wines." In Wine Analysis, 92–146. Berlin, Heidelberg: Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-83340-3_5.

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Fujii, Noriko, Takumi Takata, Norihiko Fujii, Kenzo Aki, and Hiroaki Sakaue. "d-Amino Acid Residues in Proteins Related to Aging and Age-Related Diseases and a New Analysis of the Isomers in Proteins." In D-Amino Acids, 241–54. Tokyo: Springer Japan, 2016. http://dx.doi.org/10.1007/978-4-431-56077-7_15.

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Gale, Ernest F. "Determination of Amino Acids by Use of Bacterial Amino Acid Decarboxylases." In Methods of Biochemical Analysis, 285–306. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/9780470110201.ch8.

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Fox, Alvin, Kimio Ueda, and Stephen L. Morgan. "Analysis of Bacterial Amino Acids." In Analytical Microbiology Methods, 89–99. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4899-3564-9_6.

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Aristoy, M. Concepción, and Fidel Toldrá. "Amino Acids in Dairy Foods." In Handbook of Dairy Foods Analysis, 9–31. 2nd ed. Second edition. | Boca Raton : CRC Press, 2021.: CRC Press, 2021. http://dx.doi.org/10.1201/9780429342967-3.

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Zhang, Hao, Yunhe Liu, and Pingya Li. "Analysis of Amino Acids in Ginseng." In Ginseng Nutritional Components and Functional Factors, 1–27. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-4688-4_1.

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Conference papers on the topic "Amino acids – Analysis"

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Brändström, A., and M. Rånby. "t-PA PROTEIN DETERMINATION: IMPROVED ACCURACY THROUGH COMPOSITION CONSIOUS AMINO ACID ANALYSIS (CCAAA)." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644408.

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Protein determination by composition consious amino acid analysis (CCAAA) is generally applicable to polypeptides with known amino acid composition.Traditionally, in protein determination by AAA the mass of protein substance in a preparation is quantitated by simple summation of the mass of all amino acid residues found, although some amino acids e.g. Trp, Ser, Thr, Cys are unsatisfactorily determined. In this study we have explored the, possibility of improving protein determination by AAA in cases where the amino acid composition of the preparation is precisely known from sequence data. In CCAAA protein determination the molar amounts of amino acids that are known to be quantitatively recovered are divided by the number of residues known to be present in the polypeptide. The mean of these values is identified as the molar quantity of polypeptide in the sample. In addition, the standard deviation of the mean serves as identification and homogeneity control. In this study the accuracy of the method was checked gravimetrically.CCAAA was applied on t-PA prepared from cultured Bowes melanoma cells by immunopurification on PAMl-Sepharose 6BFF and subsequent gelfiltration in 1 mol/L NH4HCO3 on Sephacryl SA-200. About 2 pg of lyophilized protein was hydrolysed in 6 mol/L HC1 under vacuum for 24 hours at 110°C and amino acid analysed. Amino acids selected for calculation of the molar quantity were (number of residues within parentheses) Asp+Asn(50), Glu+Gln(52), Pro(29), Ala(32.5), Val(25), Leu(39), His(16), Lys(21) and Arg(35.5). To obtain the gravimetric quantity the molar quantity was multiplied with the theoretical molecular weight as calculated from the sequence and with the carbohydrate content taken into account.For t-PA the standard deviation of the mean molar quantity typically was less than 5%. The result from CCAAA was about 10% higher than that obtained from conventional AAA. The result from CCAAA was within 10% of that found gravimetrically. The absorbtivity of t-PA was estimated to 1.75 (g/L)-1cm-1.In summary, composition consious amino acid analysis (CCAAA) is recommended as reference method for protein determination of well defined protein preparations where the amino acid composition is known.
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Zhang, Ying, Changjiang Ding, and Jun Lu. "Recognition of protein phosphorylation site based on amino acids sequence features." In NUMERICAL ANALYSIS AND APPLIED MATHEMATICS ICNAAM 2012: International Conference of Numerical Analysis and Applied Mathematics. AIP, 2012. http://dx.doi.org/10.1063/1.4756458.

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Bouaynaya, Nidhal, and Dan Schonfeld. "Biological Evolution: Distribution and Convergence Analysis of Amino Acids." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.260191.

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Bouaynaya, Nidhal, and Dan Schonfeld. "Biological Evolution: Distribution and Convergence Analysis of Amino Acids." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.4397837.

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MOURA, V. B., R. SCATENA, W. H. PRIETO, and M. A. CREMASCO. "SHANNON ENTROPY ANALYSIS FROM AROMATIC AMINO ACIDS CHROMATOGRAPHIC PULSES." In XXII Congresso Brasileiro de Engenharia Química. São Paulo: Editora Blucher, 2018. http://dx.doi.org/10.5151/cobeq2018-co.130.

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Casey, Abigail, Nyia Chusan, Carleah Dorsey, and Gregory E. Triplett. "Raman spectroscopy analysis of conformation changes in amino acids." In Biomedical Applications of Light Scattering XI, edited by Adam Wax and Vadim Backman. SPIE, 2021. http://dx.doi.org/10.1117/12.2575998.

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Yang, Yang, Liping Chang, Yumeng Lu, and Luyuan Yang. "Analysis of amino acids in foodstuff by Nuclear Magnetic Resonance." In 2010 3rd International Conference on Biomedical Engineering and Informatics (BMEI). IEEE, 2010. http://dx.doi.org/10.1109/bmei.2010.5640080.

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Li, Mingrui, and Meng Su. "Phylogenetic Analysis of aaRS Reveals the Kinship of Amino Acids." In ICCBB '21: 2021 5th International Conference on Computational Biology and Bioinformatics. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3512452.3512459.

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Casey, Abigail, Caroline A. Campbell, and Gregory E. Triplett. "Optical absorbance study of three phosphorylatable amino acids using confocal Raman Spectroscopy." In Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XVII, edited by Daniel L. Farkas, James F. Leary, and Attila Tarnok. SPIE, 2019. http://dx.doi.org/10.1117/12.2509843.

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Siderius, Michael, and Filip Jagodzinski. "Identifying amino acids sensitive to mutations using high-throughput rigidity analysis." In 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2016. http://dx.doi.org/10.1109/bibm.2016.7822779.

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Reports on the topic "Amino acids – Analysis"

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Veldkamp, T., J. W. van Riel, R. A. Dekker, S. Khalaji, V. Khaksar, H. Hashemipour, M. M. van Krimpen, and M. C. Blok. Estimating requirement values for standardised ileal digestible amino acids in broilers by a meta-analysis approach. Wageningen: Wageningen UR Livestock Research, 2016. http://dx.doi.org/10.18174/388691.

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McGuire, Mark A., Amichai Arieli, Israel Bruckental, and Dale E. Bauman. Increasing Mammary Protein Synthesis through Endocrine and Nutritional Signals. United States Department of Agriculture, January 2001. http://dx.doi.org/10.32747/2001.7574338.bard.

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Objectives To determine endocrine factors that regulate the partitioning of amino acids by the mammary gland. To evaluate dietary flow and supply of energy and amino acids and their effects on milk protein synthesis and endocrine status. To use primary cultures of cow mammary epithelial cells to examine the role of specific factors on the rates and pattern of milk protein synthesis. Milk protein is an increasingly valuable component of milk but little is known regarding the specific hormonal and nutritional factors controlling milk protein synthesis. The research conducted for this project has determined that milk protein synthesis has the potential to be enhanced much greater than previously believed. Increases of over 25% in milk protein percent and yield were detected in studies utilizing abomasal infusion of casein and a hyperinsulinemic-euglycemic clamp. Thus, it appears that insulin, either directly or indirectly, can elicit a substantial increase in milk protein synthesis if additional amino acids are supplied. For additional amino acids, casein provided the best response even though substantial decreases in branched chain amino acids occur when the insulin clamp is utilized. Branched chain amino acids alone are incapable of supporting the enhanced milk protein output. The mammary gland can vary both blood flow and extraction efficiency of amino acids to support protein synthesis. A mammary culture system was used to demonstrate specific endocrine effects on milk protein synthesis. Insulin-like growth factor-I when substituted for insulin was able to enhance casein and a-lactalbumin mRNA. This suggests that insulin is a indirect regulator of milk protein synthesis working through the IGF system to control mammary production of casein and a-lactalbumin. Principal component analysis determined that carbohydrate had the greatest effect on milk protein yield with protein supply only having minor effects. Work in cattle determined that the site of digestion of starch did not affect milk composition alone but the degradability of starch and protein in the rumen can interact to alter milk yield. Cows fed diets with a high degree of rumen undegradability failed to specifically enhance milk protein but produced greater milk yield with similar composition. The mammary gland has an amazing ability to produce protein of great value. Research conducted here has demonstrated the unprecedented potential of the metabolic machinery in the mammary gland. Insulin, probably signaling the mammary gland through the IGF system is a key regulator that must be combined with adequate nutrition in order for maximum response.
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Whitham, Steven A., Amit Gal-On, and Tzahi Arazi. Functional analysis of virus and host components that mediate potyvirus-induced diseases. United States Department of Agriculture, March 2008. http://dx.doi.org/10.32747/2008.7591732.bard.

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The mechanisms underlying the development of symptoms in response to virus infection remain to be discovered in plants. Insight into symptoms induced by potyviruses comes from evidence implicating the potyviral HC-Pro protein in symptom development. In particular, recent studies link the development of symptoms in infected plants to HC-Pro's ability to interfere with small RNA metabolism and function in plant hosts. Moreover, mutation of the highly conserved FRNK amino acid motif to FINK in the HC-Pro of Zucchini yellow mosaic virus (ZYMV) converts a severe strain into an asymptomatic strain, but does not affect virus accumulation in cucurbit hosts. The ability of this FINK mutation to uncouple symptoms from virus accumulation creates a unique opportunity to study symptom etiology, which is usually confounded by simultaneous attenuation of both symptoms and virus accumulation. Our goal was to determine how mutations in the conserved FRNK motif affect host responses to potyvirus infection in cucurbits and Arabidopsis thaliana. Our first objective was to define those amino acids in the FRNK motif that are required for symptoms by mutating the FRNK motif in ZYMV and Turnip mosaic virus (TuMV). Symptom expression and accumulation of resulting mutant viruses in cucurbits and Arabidopsis was determined. Our second objective was to identify plant genes associated with virus disease symptoms by profiling gene expression in cucurbits and Arabidopsis in response to mutant and wild type ZYMV and TuMV, respectively. Genes from the two host species that are differentially expressed led us to focus on a subset of genes that are expected to be involved in symptom expression. Our third objective was to determine the functions of small RNA species in response to mutant and wild type HC-Pro protein expression by monitoring the accumulation of small RNAs and their targets in Arabidopsis and cucurbit plants infected with wild type and mutant TuMV and ZYMV, respectively. We have found that the maintenance of the charge of the amino acids in the FRNK motif of HC-Pro is required for symptom expression. Reduced charge (FRNA, FRNL) lessen virus symptoms, and maintain the suppression of RNA silencing. The FRNK motif is involved in binding of small RNA species including microRNAs (miRNA) and short interfering RNAs (siRNA). This binding activity mediated by the FRNK motif has a role in protecting the viral genome from degradation by the host RNA silencing system. However, it also provides a mechanism by which the FRNK motif participates in inducing the symptoms of viral infection. Small RNA species, such as miRNA and siRNA, can regulate the functions of plant genes that affect plant growth and development. Thus, this binding activity suggests a mechanism by which ZYMVHC-Pro can interfere with plant development resulting in disease symptoms. Because the host genes regulated by small RNAs are known, we have identified candidate host genes that are expected to play a role in symptoms when their regulation is disrupted during viral infections. As a result of this work, we have a better understanding of the FRNK amino acid motif of HC-Pro and its contribution to the functions of HC-Pro, and we have identified plant genes that potentially contribute to symptoms of virus infected plants when their expression becomes misregulated during potyviral infections. The results set the stage to establish the roles of specific host genes in viral pathogenicity. The potential benefits include the development of novel strategies for controlling diseases caused by viruses, methods to ensure stable expression of transgenes in genetically improved crops, and improved potyvirus vectors for expression of proteins or peptides in plants.
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Sengupta-Gopalan, Champa, Shmuel Galili, and Rachel Amir. Improving Methionine Content in Transgenic Forage Legumes. United States Department of Agriculture, February 2001. http://dx.doi.org/10.32747/2001.7580671.bard.

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Leguminous forage crops are high in proteins but deficient in S- amino acids. It has been shown that both wool quality and milk production can be limited by the post-ruminal supply of sulfur-containing amino acids. Efforts to use conventional plant breeding and cell selection techniques to increase the S-amino acid content of alfalfa have met with little success. With the objective to increase the S-amino acid content of forage legumes, the goal of this project was to co- express the methionine rich zein genes from corn along with a gene for a key enzyme in methionine biosynthesis, aspartate kinase(AK). The zeins are seed storage proteins from corn and are groupec into four distinct classes based on their amino acid sequence homologies. The b-zein (15kd) and the 6zein (10kD and 18kD) have proportionately high levels of methionine (10%, 22% and 28%, respectively). Initial studies from our lab had shown that while the 15kD zein accumulated to high levels in vegetative tissues of transgenic tobacco the l0kD zein did not. However, co-expression of the 10kD zein with the 15kD zein genes in tobacco showed stabilization of the 10kD zein and the co-localization of the 10kD and 15kD zein proteins in unique ER derived protein bodies. AK is the key enzyme for producing carbon skeletons for all amino acids of the aspartate family including methionine. It is, however, regulated by end-product feedback inhibition. The specific objectives of this proposal were: i. to co-express the 15kD zein with the 10/18kD zein genes in alfalfa in order to enhance the level of accumulation of the 10/18kD zein; ii. to increase methionine pools by expressing a feedback insensitive AK gene in transformants co-expressing the 15kD and 10/18kD zein genes. The Israeli partners were successful in expressing the AK gene in alfalfa which resulted in an increase in free and bound threonine but not in methionine (Galili et al., 2000). Since our target was to increase methionine pools, we changed our second objective to replace the AK gene with the gene for cystathionine gamma synthase (CGS) in the co-expression studies. The first methionine specific reaction is catalyzed by CGS. An additional objective was to develop a transformation system for Berseem clover, and to introduce the appropriate gene constructs into it with the goal of improving their methionine content. Genes for the 15kD zein along with the genes for either the 10kD or 18kD zein have been introduced into the same alfalfa plant both by sexual crosses and by re-transformation. Analysis of these zein co-expressors have shown that both the IOkD and 18kD zein levels go up 5 to 10 fold when co-expressed with the 15kD zein (Bagga et al., MS in preparation). Incubation of the leaves of transgenic alfalfa co-expressing the 15kD and 10kD zein genes, in the rumen of cows have shown that the zein proteins are stable in the rumen. To increase the level of zein accumulation in transgenic alfalfa different promoters have been used to drive the zein genes in alfalfa and we have concluded that the CaMV 35S promoter is superior to the other strong leaf -specific promoters. By feeding callus tissue of alfalfa plants co-expressing the 15kD and 10kD zein genes with methionine and its precursors, we have shown that the zein levels could be significantly enhanced by increasing the methionine pools. We have now introduced the CGS gene (from Arabidopsis; kindly provided to us by Dr. Leustek), into the 15kD zein transformants and experiments are in progress to check if the expression of the CGS gene indeed increases the level of zein accumulation in alfalfa. We were not successful in developing a transformation protocol for Berseem clover.
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Jander, Georg, Gad Galili, and Yair Shachar-Hill. Genetic, Genomic and Biochemical Analysis of Arabidopsis Threonine Aldolase and Associated Molecular and Metabolic Networks. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7696546.bard.

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Since the amino acids threonine and isoleucine can be limiting in mammalian diet and there is interest in increasing their abundance in certain crop plants. To meet this need, a BARD proposal was written with two main research objectives: (i) investigate new avenues for manipulating threonine and isoleucine content in plants and (ii) study the role of threonine aldolase in plant metabolism. Research conducted to meet these goals included analysis of the sub-cellular localization of threonine aldolase in the plant, analysis of metabolic flux in developing embryos, over- and under-expression of Arabidopsis threonine aldolases, and transcriptional and metabolic analysis of perturbations resulting from altered threonine aldolase expression. Additionally, the broader metabolic effects of increasing lysine biosynthesis were investigated. An interesting observation that came up in the course of the project is that threonine aldolase activity affects methionine gamma-lyase in Arabidopsis. Further research showed that threonine deaminase and methionine gamma-lyase both contribute to isoleucine biosynthesis in plants. Therefore, isoleucine content can be altered by manipulating the expression of either or both of these enzymes. Additionally, both enzymes contribute to the up to 100-fold increase in isoleucine that is observed in drought-stressed Arabidopsis. Toward the end of the project it was discovered that through different projects, both groups had been able to independently up-regulate phenylalanine accumulation by different mechanisms. The Galili lab transformed Arabidopsis with a feedbackinsensitive bacterial enzyme and the Jander lab found a feedback insensitive mutation in Arabidopsis arogenate dehydratase. Exchange of the respective plant lines has allowed a comparative analysis of the different methods for increasing phenylalanine content and the creation of double mutants. The research that was conducted as part of this BARD project has led to new insights into plant amino acid metabolism. Additionally, new approaches that were found to increase the accumulation of threonine, isoleucine, and phenylalanine in plants have potential practical applications. Increased threonine and isoleucine levels can increase the nutritional value of crop plants. Elevated isoleucine accumulation may increase the osmotic stress tolerance of plants. Up-regulation of phenylalanine biosynthesis can be used to increase the production of downstream higher-value plant metabolites of biofuel feed stocks.
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Myers, G., B. Foley, B. Korber, J. W. Mellors, K. T. Jeang, and S. Wain-Hobson. Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences. Office of Scientific and Technical Information (OSTI), April 1997. http://dx.doi.org/10.2172/463607.

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Dudareva, Natalia, Alexander Vainstein, Eran Pichersky, and David Weiss. Integrating biochemical and genomic approaches to elucidate C6-C2 volatile production: improvement of floral scent and fruit aroma. United States Department of Agriculture, September 2007. http://dx.doi.org/10.32747/2007.7696514.bard.

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The specific objectives of approved proposal include to: 1. Elucidate the C6-C2 biochemical pathways leading to the biosynthesis of phenylacetaldehyde, phenylethyl alcohol and phenylethyl acetate in floral tissues of ornamentally important plants, pefunia and roses. 2. Isolate and characterrze genes responsible for the production of these C6-C2 compounds and those involved in the regulation of the pathway using genomic and transcriptomic tools. 3. Determine whether altering the expression of key genes of this pathway can result in changing the aroma characteristics of flowers. Aldehydes are intermediates in a variety of biochemical pathways including those involved in the metabolism of carbohydrates, vitamins, steroids, amino acids, benzylisoquinoline alkaloids, hormones, and lipids. In plants they are also synthesized in response to environmental stresses such as salinity, cold, and heat shock or as flavors and aromas in fruits and flowers. Phenylacetaldehyde along with 2-phenylethanol and its acetate ester, are important scent compounds in numerous flowers, including petunias and roses. However, little is known about the biosynthesis of these volatile compounds in plants. We have shown that the formation PHA and 2-phenylethanol from Phe does not occur via trans-cinnamic acid and instead competes with the key enzyme of phenypropanoid metabolism Pheammonia-lyase (PAL) for Phe utilization. Using functional genomic approach and comparative gene expression profiling, we have isolated and characterized a novel enzyme from petunia and rose flowers that catalyzes the formation of the Ca-Czcompound phenylacetaldehyde (PHA) from L-phenylalanine (Phe) by the removal of both the carboxyl and amino groups. This enzyme, designated as phenylacetaldehyde synthases (PAAS), is a bifunctional enzyme that catalyzes the unprecedented efficient coupling of phenylalanine decarboxylation to oxidation, generating phenylacetaldehyde, CO2, ammonia, and hydrogen peroxide in stoichiometric amounts. Down-regulation of PAAS expression via RNA interference-based (RNAi) technology in petunia resulted in no PHA emission when compared with controls. These plants also produced no 2-phenylethanol, supporting our conclusion that PHA is a precursor of 2-phenylethanol. To understand the regulation of scent formation in plants we have also generated transgenic petunia and tobacco plants expressing the rose alcohol acetyltransferase (RhAAT) gene under the control of a CaMV-35S promoter. Although the preferred substrate of RhAAT in vitro is geraniol, in transgenic petunia flowers, it used phenylethyl alcohol and benzyl alcohol to produce the corresponding acetate esters, not generated by control flowers. These results strongly point to the dependence of volatile production on substrate availability. Analysis of the diurnal regulation of scent production in rose flowers revealed that although the daily emission of most scent compounds is synchronized, various independently evolved mechanisms control the production, accumulation and release of different volatiles. This research resulted in a fundamental discovery of biochemical pathway, enzymes and genes involved in biosynthesis of C6-C2s compounds, and provided the knowledge for future engineering plants for improved scent quality.
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Barefoot, Susan F., Bonita A. Glatz, Nathan Gollop, and Thomas A. Hughes. Bacteriocin Markers for Propionibacteria Gene Transfer Systems. United States Department of Agriculture, June 2000. http://dx.doi.org/10.32747/2000.7573993.bard.

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The antibotulinal baceriocins, propionicin PLG-1 and jenseniin G., were the first to be identified, purified and characterized for the dairy propionibaceria and are produced by Propionibacterium thoenii P127 and P. thoenii/jensenii P126, respectively. Objectives of this project were to (a) produce polyclonal antibodies for detection, comparison and monitoring of propionicin PLG-1; (b) identify, clone and characterize the propionicin PLG-1 (plg-1) and jenseniin G (jnG) genes; and (3) develop gene transfer systems for dairy propionibacteria using them as models. Polyclonal antibodies for detection, comparison and monitoring of propionicin PLG-1 were produced in rabbits. Anti-PLG-1 antiserum had high titers (256,000 to 512,000), neutralized PLG-1 activity, and detected purified PLG-1 at 0.10 mg/ml (indirect ELISA) and 0.033 mg/ml (competitive indirect ELISA). Thirty-nine of 158 strains (most P. thoenii or P. jensenii) yielded cross-reacting material; four strains of P. thoenii, including two previously unidentified bacteriocin producers, showed biological activity. Eight propionicin-negative P127 mutants produced neither ELISA response nor biological activity. Western blot analyses of supernates detected a PLG-1 band at 9.1 kDa and two additional protein bands with apparent molecular weights of 16.2 and 27.5 kDa. PLG-1 polyclonal antibodies were used for detection of jenseniin G. PLG-1 antibodies neutralized jenseniin G activity and detected a jenseniin G-sized, 3.5 kDa peptide. Preliminary immunoprecipitation of crude preparations with PLG-1 antibodies yielded three proteins including an active 3-4 kDa band. Propionicin PLG-1 antibodies were used to screen a P. jensenii/thoenii P126 genomic expression library. Complete sequencing of a cloned insert identified by PLG-1 antibodies revealed a putative response regulator, transport protein, transmembrane protein and an open reading frame (ORF) potentially encoding jenseniin G. PCR cloning of the putative plg-1 gene yielded a 1,100 bp fragment with a 355 bp ORF encoding 118 amino acids; the deduced N-terminus was similar to the known PLG-1 N-terminus. The 118 amino acid sequence deduced from the putative plg-1 gene was larger than PLG-1 possibly due to post-translational processing. The product of the putative plg-1 gene had a calculated molecular weight of 12.8 kDa, a pI of 11.7, 14 negatively charged residues (Asp+Glu) and 24 positively charged residues (Arg+Lys). The putative plg-1 gene was expressed as an inducible fusion protein with a six-histidine residue tag. Metal affinity chromatography of the fused protein yielded a homogeneous product. The fused purified protein sequence matched the deduced putative plg-1 gene sequence. The data preliminarily suggest that both the plg-1 and jnG genes have been identified and cloned. Demonstrating that antibodies can be produced for propionicin PLG-1 and that those antibodies can be used to detect, monitor and compare activity throughout growth and purification was an important step towards monitoring PLG-1 concentrations in food systems. The unexpected but fortunate cross-reactivity of PLG-1 antibodies with jenseniin G led to selective recovery of jenseniin G by immunoprecipitation. Further refinement of this separation technique could lead to powerful affinity methods for rapid, specific separation of the two bacteriocins and thus facilitate their availability for industrial or pharmaceutical uses. Preliminary identification of genes encoding the two dairy propionibacteria bacteriocins must be confirmed; further analysis will provide means for understanding how they work, for increasing their production and for manipulating the peptides to increase their target species. Further development of these systems would contribute to basic knowledge about dairy propionibacteria and has potential for improving other industrially significant characteristics.
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Myers, G., B. Korber, S. Wain-Hobson, R. F. Smith, and G. N. Pavlakis. Human Retroviruses and AIDS. A compilation and analysis of nucleic acid and amino acid sequences: I--II; III--V. Office of Scientific and Technical Information (OSTI), December 1993. http://dx.doi.org/10.2172/10116407.

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10

Schuster, Gadi, and David Stern. Integrated Studies of Chloroplast Ribonucleases. United States Department of Agriculture, September 2011. http://dx.doi.org/10.32747/2011.7697125.bard.

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Gene regulation at the RNA level encompasses multiple mechanisms in prokaryotes and eukaryotes, including splicing, editing, endo- and exonucleolytic cleavage, and various phenomena related to small or interfering RNAs. Ribonucleases are key players in nearly all of these post-transcriptional mechanisms, as the catalytic agents. This proposal continued BARD-funded research into ribonuclease activities in the chloroplast, where RNase mutation or deficiency can cause metabolic defects and is often associated with plant chlorosis, embryo or seedling lethality, and/or failure to tolerate nutrient stress. The first objective of this proposal was to examined a series of point mutations in the PNPase enzyme of Arabidopsis both in vivo and in vitro. This goal is related to structure-function analysis of an enzyme whose importance in many cellular processes in prokaryotes and eukaryotes has only begun to be uncovered. PNPase substrates are mostly generated by endonucleolytic cleavages for which the catalytic enzymes remain poorly described. The second objective of the proposal was to examine two candidate enzymes, RNase E and RNase J. RNase E is well-described in bacteria but its function in plants was still unknown. We hypothesized it catalyzes endonucleolytic cleavages in both RNA maturation and decay. RNase J was recently discovered in bacteria but like RNase E, its function in plants had yet to be explored. The results of this work are described in the scientific manuscripts attached to this report. We have completed the first objective of characterizing in detail TILLING mutants of PNPase Arabidopsis plants and in parallel introducing the same amino acids changes in the protein and characterize the properties of the modified proteins in vitro. This study defined the roles for both RNase PH core domains in polyadenylation, RNA 3’-end maturation and intron degradation. The results are described in the collaborative scientific manuscript (Germain et al 2011). The second part of the project aimed at the characterization of the two endoribonucleases, RNase E and RNase J, also in this case, in vivo and in vitro. Our results described the limited role of RNase E as compared to the pronounced one of RNase J in the elimination of antisense transcripts in the chloroplast (Schein et al 2008; Sharwood et al 2011). In addition, we characterized polyadenylation in the chloroplast of the green alga Chlamydomonas reinhardtii, and in Arabidopsis (Zimmer et al 2009). Our long term collaboration enabling in vivo and in vitro analysis, capturing the expertise of the two collaborating laboratories, has resulted in a biologically significant correlation of biochemical and in planta results for conserved and indispensable ribonucleases. These new insights into chloroplast gene regulation will ultimately support plant improvement for agriculture.
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