Proceedings of the Indiana Academy of Science
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David Manuel Nogueira Ribas Timization Using Indus
Universidade do Minho Escola de Ciências trial microbes David Manuel Nogueira Ribas timization using indus Structural-functional studies of carboxylic vel tools in production op s: no acid transporters: novel tools in production ter optimization using industrial microbes lic acid transpor xy tudies of carbo Structural-functional s a Ribas vid Manuel Nogueir Da 3 1 UMinho|20 October, 2013 Universidade do Minho Escola de Ciências David Manuel Nogueira Ribas Structural-functional studies of carboxylic acid transporters: novel tools in production optimization using industrial microbes Master Thesis Master in Molecular Genetics Work done under supervision of Professora Doutora Margarida Casal Professora Doutora Sandra Paiva October, 2013 DECLARAÇÃO Nome: David Manuel Nogueira Ribas Endereço eletrónico: [email protected] Número do bilhete de identidade: 13254792 Título da tese: Structural-functional studies of carboxylic acid transporters: novel tools in production optimization using industrial microbes Orientadores: Prof. Doutora Margarida Casal Prof. Doutora Sandra Paiva Ano de conclusão: 2013 Designação do mestrado: Genética Molecular DE ACORDO COM A LEGISLAÇÃO EM VIGOR, NÃO É PERMITIDA A REPRODUÇÃO DE QUALQUER PARTE DESTA TESE/TRABALHO Universidade do Minho:__/__/__ Assinatura:________________________________ iii ACKNOWLEDGMENTS/AGRADECIMENTOS À Professora Doutora Margarida Casal agradeço toda a confiança depositada em mim e a fantástica oportunidade de iniciar um projeto de investigação com um potencial enorme na minha área de formação, acrescendo o facto de ser gerido em parceria internacional com um instituto de investigação de conhecida reputação. Agradeço também a aposta na minha formação e no meu currículo e da qual me orgulho muito, assim como toda a ajuda e compreensão prestada ao longo de todo o mestrado. -
Improvement of D-Glucaric Acid Production in Escherichia Coli by Eric Chun-Jen Shiue
Improvement of D-Glucaric Acid Production in Escherichia coli by Eric Chun-Jen Shiue M.S. Chemical Engineering Practice Massachusetts Institute of Technology, 2011 B.S. Chemical Engineering University of California, Berkeley, 2008 Submitted to the Department of Chemical Engineering in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Engineering at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY February 2014 © 2014 Massachusetts Institute of Technology All rights reserved. Signature of Author . Eric Chun-Jen Shiue Department of Chemical Engineering December 17, 2013 Certifiedby .............................................................................................. Kristala L. Jones Prather Associate Professor of Chemical Engineering Thesis Supervisor Acceptedby ............................................................................................. Patrick S. Doyle Professor of Chemical Engineering Chairman, Committee for Graduate Students Improvement of D-Glucaric Acid Production in Escherichia coli by Eric Chun-Jen Shiue Submitted to the Department of Chemical Engineering on December 17, 2013 in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Chemical Engineering Abstract D-glucaric acid is a naturally occurring compound which has been explored for a plethora of potential uses, including biopolymer production, cancer and diabetes treatment, cholesterol reduction, and as a replacement for polyphosphates in detergents. This molecule was identified in 2004 as a “Top Value-Added Chemical from Biomass” by the U.S. Department of Energy (Werpy and Petersen, 2004), implying that production of D-glucaric acid could be economically feasible if biomass were used as a feedstock. A biosynthetic route to D-glucaric acid from D-glucose has been constructed in E. coli by our group (Moon et al., 2009b), and the goal of this thesis has been to improve the economic viability of this biological production route through improvements to pathway productivity and yield. -
Elimination of Galactaric Acid Catabolism by Using RNA Sequencing and CRISPR/Cas9 Joosu Kuivanen*†, Y.‑M
Kuivanen et al. Microb Cell Fact (2016) 15:210 DOI 10.1186/s12934-016-0613-5 Microbial Cell Factories RESEARCH Open Access Engineering Aspergillus niger for galactaric acid production: elimination of galactaric acid catabolism by using RNA sequencing and CRISPR/Cas9 Joosu Kuivanen*†, Y.‑M. Jasmin Wang† and Peter Richard Abstract Background: meso-Galactaric acid is a dicarboxylic acid that can be produced by the oxidation of D-galacturonic acid, the main constituent of pectin. Mould strains can be engineered to perform this oxidation by expressing the bacterial enzyme uronate dehydrogenase. In addition, the endogenous pathway for D-galacturonic acid catabolism has to be inactivated. The filamentous fungus Aspergillus niger would be a suitable strain for galactaric acid produc‑ tion since it is efficient in pectin hydrolysis, however, it is catabolizing the resulting galactaric acid via an unknown catabolic pathway. Results: In this study, a transcriptomics approach was used to identify genes involved in galactaric acid catabolism. Several genes were deleted using CRISPR/Cas9 together with in vitro synthesized sgRNA. As a result, galactaric acid catabolism was disrupted. An engineered A. niger strain combining the disrupted galactaric and D-galacturonic acid catabolism with an expression of a heterologous uronate dehydrogenase produced galactaric acid from D-galactu‑ ronic acid. The resulting strain was also converting pectin-rich biomass to galactaric acid in a consolidated bioprocess. Conclusions: In the present study, we demonstrated the use of CRISPR/Cas9 mediated gene deletion technology in A. niger in an metabolic engineering application. As a result, a strain for the efficient production of galactaric acid from D-galacturonic acid was generated. -
Trichoderma Reesei Toni Paasikallio, Anne Huuskonen and Marilyn G
Paasikallio et al. Microb Cell Fact (2017) 16:119 DOI 10.1186/s12934-017-0736-3 Microbial Cell Factories RESEARCH Open Access Scaling up and scaling down the production of galactaric acid from pectin using Trichoderma reesei Toni Paasikallio, Anne Huuskonen and Marilyn G. Wiebe* Abstract Background: Bioconversion of D-galacturonic acid to galactaric (mucic) acid has previously been carried out in small scale (50–1000 mL) cultures, which produce tens of grams of galactaric acid. To obtain larger amounts of biologically produced galactaric acid, the process needed to be scaled up using a readily available technical substrate. Food grade pectin was selected as a readily available source of D-galacturonic acid for conversion to galactaric acid. Results: We demonstrated that the process using Trichoderma reesei QM6a Δgar1 udh can be scaled up from 1 L to 1 10 and 250 L, replacing pure D-galacturonic acid with commercially available pectin. T. reesei produced 18 g L− galac- 1 1 taric acid from food-grade pectin (yield 1.00 g [g D-galacturonate consumed]− ) when grown at 1 L scale, 21 g L− 1 1 galactaric acid (yield 1.11 g [g D-galacturonate consumed]− ) when grown at 10 L scale and 14 g L− galactaric acid 1 (yield 0.77 g [g D-galacturonate consumed]− ) when grown at 250 L scale. Initial production rates were similar to those observed in 500 mL cultures with pure D-galacturonate as substrate. Approximately 2.8 kg galactaric acid was precipitated from the 250 L culture, representing a recovery of 77% of the galactaric acid in the supernatant. -
Sigma Sugars and Carbohydrates
Sigma Sugars and Carbohydrates Library Listing – 614 spectra This library represents a material-specific subset of the larger Sigma Biochemical Condensed Phase Library relating to sugars and carbohydrates found in the Sigma Biochemicals and Reagents catalog. Spectra acquired by Sigma-Aldrich Co. which were examined and processed at Thermo Fisher Scientific. The spectra include compound name, molecular formula, CAS (Chemical Abstract Service) registry number, and Sigma catalog number. Sigma Sugars and Carbohydrates Index Compound Name Index Compound Name 255 (+/-)-Epi-inosose-2 475 2,3,4,6-Tetra-O-methyl-D-glucopyranose 468 1,2,3,4-Tetra-O-acetyl-6- 487 2,3,5-Tri-O-benzoyl-1-O-p-nitrobenzoyl diphenylphosphoryl-b-D-manopyranose D-ribofuranoside 471 1,2,3,4-Tetra-O-acetyl-b-D- 490 2,3,5-Tri-O-benzyl-1-O-p-nitrobenzoyl- glucopyranose D-arabinofuranoside 472 1,2,3,5-Tetra-O-acetyl-b-D-ribofuranose 488 2,3,5-Tri-O-benzyl-b-D-arabinofuranose 473 1,2,3,5-Tetra-O-benzoyl-a-D- 489 2,3,5-Tri-O-benzyl-b-L-arabinofuranose xylofuranose 107 2,3-Dehydro-2-deoxy-N- 258 1,2-O-Isopropylidene-3-O-benzyl-rac- acetylneuraminic acid glycerol 142 2,3-Diphospho-D-glyceric acid, 261 1,2-O-Isopropylidene-5-O-p-tosyl-a-D- penta(CHA) salt xylofuranose 143 2,3-Diphospho-D-glyceric acid, 259 1,2-O-Isopropylidene-D-glucofuranose pentasodium salt 262 1,2-O-Isopropylidene-D-xylofuranose 144 2,3-Diphospho-D-glyceric acid, tris salt 135 1,2:3,4-Di-O-isopropylidene-D- 260 2,3-O-Isopropylidene-b-D- galactopyranose ribofuranosylamine, tosylate salt 141 1,2:3,5-Di-O-isopropylidene-D- -
An Access-Dictionary of Internationalist High Tech Latinate English
An Access-Dictionary of Internationalist High Tech Latinate English Excerpted from Word Power, Public Speaking Confidence, and Dictionary-Based Learning, Copyright © 2007 by Robert Oliphant, columnist, Education News Author of The Latin-Old English Glossary in British Museum MS 3376 (Mouton, 1966) and A Piano for Mrs. Cimino (Prentice Hall, 1980) INTRODUCTION Strictly speaking, this is simply a list of technical terms: 30,680 of them presented in an alphabetical sequence of 52 professional subject fields ranging from Aeronautics to Zoology. Practically considered, though, every item on the list can be quickly accessed in the Random House Webster’s Unabridged Dictionary (RHU), updated second edition of 2007, or in its CD – ROM WordGenius® version. So what’s here is actually an in-depth learning tool for mastering the basic vocabularies of what today can fairly be called American-Pronunciation Internationalist High Tech Latinate English. Dictionary authority. This list, by virtue of its dictionary link, has far more authority than a conventional professional-subject glossary, even the one offered online by the University of Maryland Medical Center. American dictionaries, after all, have always assigned their technical terms to professional experts in specific fields, identified those experts in print, and in effect held them responsible for the accuracy and comprehensiveness of each entry. Even more important, the entries themselves offer learners a complete sketch of each target word (headword). Memorization. For professionals, memorization is a basic career requirement. Any physician will tell you how much of it is called for in medical school and how hard it is, thanks to thousands of strange, exotic shapes like <myocardium> that have to be taken apart in the mind and reassembled like pieces of an unpronounceable jigsaw puzzle. -
Experiment 20 Identification of Some Carbohydrates
Experiment 20 Identification of Some Carbohydrates Carbohydrates are the direct product of the photosynthetic combination of carbon dioxide and water. By weight, they are the most common organic compounds on earth. Since most have the empirical formula CnH2nOn = Cn(H2O)n it was initially believed that they were hydrates of carbon. Hence the name. In actuality they are polyhydroxylaldehydes and ketones and exist as cyclic hemi- and full acetals. The cyclic forms may be five-membered rings (furanose) or six-membered rings (pyranose). They are classified as mono-, di-, and polysaccharides. The term sugar applies to mono-, di-, and oligosaccharides, which are all soluble in water and thereby distinguished from polysaccharides, which are not soluble in water. The most commonly encountered carbohydrates are starch, glycogen, inulin, cellulose, sucrose, fructose, arabinose, mannose, glucose, maltose, galactose, and lactose. The method of analysis used in this experiment is one of elimination. The assumption is made that the compound is a single carbohydrate and tests are applied sequentially until a positive result is obtained. The carbohydrate giving the positive test is thus identified. The sugars that we will identify are shown below. Figure 20.1 Monosaccharides Aldohexoses O H C O H CH OH 2 O H C OH C HO OH HO C H HO HO C H OH H C OH HOCH OH HO C H 2 O H C OH D-glucose H C OH HO OH HO H C OH CH2OH D-mannose CH2OH O H C OH H C OH CH2OH CH2OH ketohexose O O C OH HO C H HO HOCH2 O OH HO C H HO C H HO D-galactose H C OH HO H C OH CH2OH CH OH -
ACIDS of MANY USES from CORN 783 Investigation of the Practical Applica- Acids
Acids of Many Uses gents, and medicines. More attention is being given, consequently, to the de- velopment of practical methods for ob- taining them from dextrose. From Corn Processes for the fermentation of dextrose to citric, gluconic, 2-keto- C L. Mehltretter giuconic, 5-ketogluconic, a-kctoglu- taric, and itaconic, and similar acids have been developed in the laboratories of the Department of Agriculture. Some, particularly those for citric and Most of the commercial sugar acids gluconic acids, have achieved commer- come from dextrose, the sugar derived cial importance. The large-scale pro- from corn. They are cheap and mild duction of itaconic acid appears and, chemically, maids-of-all-work. promising. Lactic acid, a widely used Their uses range from the simple proc- food acid, is being produced in large ess of cleaning milk cans and bottles volumes by the corn-products indus- to the complex production of vitamins. tries by fermentation of cornstarch Veterinarians and farmers know hyclrolyzates. best the calcium salt of gluconic acid, The acids I have mentioned have which they use for the treatment of also been made by nonfermentative milk fever in cows and which doctors methods, but of the purely chemical sometimes recommend for bee stings. processes only those for obtaining glu- The housewife is most familiar with conic and itaconic acids merit con- cream of tartar, an ingredient of the sideration from a practical standpoint. baking powder she uses for her pies and Some years ago workers at the National cakes. Citric acid, the acid that gives Bureau of Standards devised a proce- the tang to citrus fruit?, she also uses dure for the electrolytic oxidation of for flavoring lemon pies. -
Food Waste Conversion to Galactaric Acid
Food waste conversion to Galactaric acid KT Consortium Maria do Carmo Cabral Sacadura, John Woodley, Rafiqul Gani Annual Meeting KT Consortium, Department of Chemical and Biochemical Engineering, Technical University of Denmark June 2017 Introduction Galactaric acid (GA), also known as mucic acid, is a symmetrical six carbon diacid. GA is used as a chelator and in skin care products and has the potential application in polymer synthesis as a platform chemical. Its market is limited to the pharmaceutical and cosmetic industry. Currently, GA is commercially produced by oxidation of galactose with nitric acid or from D-galacturonic acid (D-galUA) by electrolytic oxidation. An alternative source of D-galUA is pectin, an abundant component in non- woody plant biomass such as in fruit peels. Citrus Processing Waste (CPW) is mainly generated from the industry of juice production which generates 10 million tonnes of wet CPW. Thus, it represents an available and inexpensive source for production of GA. The present project suggests an alternative route for production of GA through extraction of pectin from dry citrus peel, and its hydrolysis releasing D-galUA which is later oxidized to GA. An innovative, sustainable and environment-friendly solution is sought and analyzed through an economical and environmental assessment based on calculations done with simple derived models. The aim is to produce 2000 tonnes per year of GA. Figure 1. Chemical structure of Galactaric acid. For the extraction of pectin from dry citrus peel (TK1), citric acid and water are used as solvents (TK2) and the operation runs for 60 min at the solution’s boiling point (around 100 Process flowsheet ºC) and pH 2.3. -
Supplementary Material
Supplementary Material Table S1. Drought impacts on higher plant metabolism. Site and Metabolic Species Metabolic Pathways Bibliographic Treatment/Gr Metabolic Pathways and/or Nº (Organs Statistical Methods Bioinformatic Tools and/or Metabolites Data adient Platform Metabolites Studied) Up-regulated Conditions Down-regulated Foito et al. (2009) Lolium Water Glucose, raffinose, Plant Multivariate analyses in AMDISTM, 1 perenne manipulation GC-MS fructose, trehalose, Fatty acids Biotechnology Genstat version 9.2.0.153 XCALIBURTM (leaves) in greenhouse maltose Journal Cramer et al. Vitis Water Malate, chloride, Succinate, (2007) Functional ANOVAs of all 2 vinifera manipulation GC-MS proline, phosphate, fumarate, Integrative determined metabolites (leaves) in greenhouse glucose aspartate, sucrose Genomics PERMANOVA (PERMANOVA+ for Water supply 1D and 2D PRIMER v.6). ANOVAs, polyphenolic Erica TopSpin 1.3 (Bruker Rivas-Ubach et manipulation 1H NMR post hoc tests, PCAs, compounds, quinic 3 multiflora Biospin), AMIX al. (2012) PNAS in field spectroscop Kolmogorov–Smirnov acid, tartaric acid, (leaves) (Bruker Biospin) conditions y tests, and discriminant and choline analyses with Statistica v8.0 (Statsoft) --glucose, sucrose, LC-MS PERMANOVA adenine, Water supply Rivas-Ubach et Quercus 1D and 2D (PERMANOVA+ for polyphenols, -Arginine, manipulation 4 al. (2014) New ilex 1H NMR PRIMER v.6). PCA and MZMINE 2.10 phenolic acids, alanine, in field Phytologist (leaves) spectroscop PLS-DA with mixOmics quinic acid, catechin, pyridoxine conditions y package of R chlorogenic, epicachetin Gargallo-Garriga Holcus -Phenilalanine, SA, -Tartate, Water supply The PCAs were et al. (2014) lanatus LC-MS thymine, adenine, pyruvate, 5 manipulation performed with TopSpin 3.1 software Scientific Reports and uracil, catequin, Jasmonic acid, in semi- mixOmics package of R. -
FAUSTINO JOVITA MALAGUTI Sugar, Substitution Theory, and Amides
Revista CENIC. Ciencias Químicas ISSN: 1015-8553 ISSN: 2221-2442 [email protected] Centro Nacional de Investigaciones Científicas Cuba FAUSTINO JOVITA MALAGUTI Sugar, substitution theory, and amides Wisniak, Jaime FAUSTINO JOVITA MALAGUTI Sugar, substitution theory, and amides Revista CENIC. Ciencias Químicas, vol. 50, no. 1, 2019 Centro Nacional de Investigaciones Científicas, Cuba Available in: https://www.redalyc.org/articulo.oa?id=181662291006 PDF generated from XML JATS4R by Redalyc Project academic non-profit, developed under the open access initiative Jaime Wisniak. FAUSTINO JOVITA MALAGUTI Sugar, substitution theory, and amides Reseñas FAUSTINO JOVITA MALAGUTI Sugar, substitution theory, and amides FAUSTINO JOVITA MALAGUTI Azúcar, teoría de sustitución y amidas. Jaime Wisniak * Redalyc: https://www.redalyc.org/articulo.oa? Ben-Gurion University of the Negev, Israel id=181662291006 [email protected] Received: 31 July 2019 Accepted: 20 September 2019 Abstract: Faustino Jovita Malaguti (1802-1878), an Italian-French pharmacist, proved that diluted, even very diluted acids, at temperatures below 95 .C, acted in an identical manner upon sugar and that the final result was a mixture of ulmic and formic acid or only ulmic acid, depending if the reaction was conducted in the presence or absence of atmospheric air. Malaguti studied the preparation of mucic and paramucic acid and their derivatives, ethyl citrate and the formula of citric acid, crystalline camphoric acid by the prolonged action of nitric acid on camphor, the preparation and properties of several derivatives of camphoric acid, studied the chlorination of a large number of ethers to prove that the assumption of the substitution theory that one atom of hydrogen could be replaced by one atom of chlorine. -
Proceedings of the Indiana Academy of Science
Saccharic Acid Preparation by the Nitric Acid Oxidation of Glucose* Albert A. Dietz and J. W. Mench with Ed. F. Degering, Purdue University, and H. H. Schopmeyer, American Maize-Products Co. Saccharic acid has long been known as a product of the oxidation of glucose, but its preparation has never become industrially important. At present it is priced far too high. It is believed that it could be manufactured and sold in competition with tartaric acid. Derivatives of these two acids have common properties. Tartaric acid is manufactured almost solely from wine lees (1), but because of recent shortages, interest has been aroused in its synthesis from other sources (2). Several patents exist for its direct manufacture by the nitric acid oxidation of starch, or indirectly from 5-ketogluconic acid (6). In a search for other derivatives that could be prepared by the oxidation of glucose, interest centered on saccharic acid. It is commonly prepared by the method of Fischer as modified by Kiliani (3), but the method has been insufficiently studied for application to large scale production. In this work a study was made of the methods of improving the yields and simplifying the procedure. One of the best known of the nitric acid oxidations of carbohydrates is that of galactosides to yield mucic acid. A study has been reported also of the oxidation of xylose (5), as a possible outlet for the utilization of waste pentosans. The most extensive study of the oxidation of glucose has been that of Kiliani (4). Although the methods used in the preparation of saccharic acid are much the same as those used for the manufacture of mucic acid, they are complicated by the fact that the former is soluble in the oxidation mixture.