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Rintze M. Zelle edited this page Oct 23, 2016
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This page provides background information on how Reference Extractor extracts item metadata from Word documents. Both Zotero and Mendeley (optionally) embed item metadata in Word documents within the citation fields as field codes. Within .docx files (which are basically just zipped files), these field codes can be found in the word/document.xml file. Each field code is wrapped in an <w:instrText/> element.
Below are some (HTML-unescaped) examples of how Zotero and Mendeley embed item metadata in these fields.
Examples generated with Zotero 4.0.29.10.
Full field:
<w:instrText xml:space="preserve"> ADDIN ZOTERO_ITEM CSL_CITATION {"citationID":"2lou5a94nk","properties":{"formattedCitation":"(Zelle, Shaw, & van Dijken, 2014)","plainCitation":"(Zelle, Shaw, & van Dijken, 2014)"},"citationItems":[{"id":255,"uris":["http://zotero.org/users/1031436/items/TVJVND6G"],"uri":["http://zotero.org/users/1031436/items/TVJVND6G"],"itemData":{"id":255,"type":"patent","title":"Method for acetate consumption during ethanolic fermentation of cellulosic feedstocks","abstract":"The present invention provides for novel metabolic pathways to detoxify biomass- derived acetate via metabolic conversion to ethanol, acetone, or isopropanol. More specifically, the invention provides for a recombinant microorganism comprising one or more native and/or heterologous enzymes that function in one or more first engineered metabolic pathways to achieve: (1) conversion of acetate to ethanol; (2) conversion of acetate to acetone; or (3) conversion of acetate to isopropanol; and one or more native and/or heterologous enzymes that function in one or more second engineered metabolic pathways to produce an electron donor used in the conversion of acetate to less inhibitory compounds; wherein the one or more native and/or heterologous enzymes is activated, upregulated, or downregulated., La présente invention concerne de nouvelles voies métaboliques pour détoxifier de l'acétate dérivé d'une biomasse par conversion métabolique en éthanol, acétone ou isopropanol. Plus spécifiquement, l'invention concerne un microorganisme recombiné comprenant une ou plusieurs enzymes natives et/ou hétérologues qui fonctionnent dans une ou plusieurs premières voies métaboliques modifiées pour permettre : (1) la conversion de l'acétate en éthanol; (2) la conversion de l'acétate en acétone; ou (3) la conversion de l'acétate en isopropanol; et une ou plusieurs enzymes natives et/ou hétérologues qui fonctionnent dans une ou plusieurs secondes voies métaboliques modifiées pour produire un donneur d'électrons utilisé dans la conversion de l'acétate en composés moins inhibiteurs, la ou les enzymes natives et/ou hétérologues étant activées, positivement régulées ou négativement régulées.","URL":"https://patentscope.wipo.int/search/en/WO2014074895","call-number":"PCT/US2013/069266","number":"WO2014074895","language":"English (EN)","author":[{"family":"Zelle","given":"Rintze Meindert"},{"family":"Shaw","given":"Arthur J."},{"family":"Dijken","given":"Johannes Pieter","non-dropping-particle":"van"}],"issued":{"date-parts":[["2014",5,16]]},"accessed":{"date-parts":[["2014",7,13]]}}}],"schema":"https://github.com/citation-style-language/schema/raw/master/csl-citation.json"} </w:instrText>
Reindented JSON:
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"citationID": "2lou5a94nk",
"properties": {
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"plainCitation": "(Zelle, Shaw, & van Dijken, 2014)"
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"type": "patent",
"title": "Method for acetate consumption during ethanolic fermentation of cellulosic feedstocks",
"abstract": "The present invention provides for novel metabolic pathways to detoxify biomass- derived acetate via metabolic conversion to ethanol, acetone, or isopropanol. More specifically, the invention provides for a recombinant microorganism comprising one or more native and/or heterologous enzymes that function in one or more first engineered metabolic pathways to achieve: (1) conversion of acetate to ethanol; (2) conversion of acetate to acetone; or (3) conversion of acetate to isopropanol; and one or more native and/or heterologous enzymes that function in one or more second engineered metabolic pathways to produce an electron donor used in the conversion of acetate to less inhibitory compounds; wherein the one or more native and/or heterologous enzymes is activated, upregulated, or downregulated., La présente invention concerne de nouvelles voies métaboliques pour détoxifier de l'acétate dérivé d'une biomasse par conversion métabolique en éthanol, acétone ou isopropanol. Plus spécifiquement, l'invention concerne un microorganisme recombiné comprenant une ou plusieurs enzymes natives et/ou hétérologues qui fonctionnent dans une ou plusieurs premières voies métaboliques modifiées pour permettre : (1) la conversion de l'acétate en éthanol; (2) la conversion de l'acétate en acétone; ou (3) la conversion de l'acétate en isopropanol; et une ou plusieurs enzymes natives et/ou hétérologues qui fonctionnent dans une ou plusieurs secondes voies métaboliques modifiées pour produire un donneur d'électrons utilisé dans la conversion de l'acétate en composés moins inhibiteurs, la ou les enzymes natives et/ou hétérologues étant activées, positivement régulées ou négativement régulées.",
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<w:instrText xml:space="preserve"> ADDIN ZOTERO_ITEM CSL_CITATION {"citationID":"2e69rb87ph","properties":{"formattedCitation":"(Abbott, Zelle, Pronk, & Van Maris, 2009; Henningsen et al., 2015)","plainCitation":"(Abbott, Zelle, Pronk, & Van Maris, 2009; Henningsen et al., 2015)"},"citationItems":[{"id":223,"uris":["http://zotero.org/users/1031436/items/RWDHMJ3F"],"uri":["http://zotero.org/users/1031436/items/RWDHMJ3F"],"itemData":{"id":223,"type":"article-journal","title":"Metabolic engineering of Saccharomyces cerevisiae for production of carboxylic acids: current status and challenges","container-title":"FEMS Yeast Research","page":"1123–1136","volume":"9","issue":"8","source":"Wiley Online Library","abstract":"To meet the demands of future generations for chemicals and energy and to reduce the environmental footprint of the chemical industry, alternatives for petrochemistry are required. Microbial conversion of renewable feedstocks has a huge potential for cleaner, sustainable industrial production of fuels and chemicals. Microbial production of organic acids is a promising approach for production of chemical building blocks that can replace their petrochemically derived equivalents. Although Saccharomyces cerevisiae does not naturally produce organic acids in large quantities, its robustness, pH tolerance, simple nutrient requirements and long history as an industrial workhorse make it an excellent candidate biocatalyst for such processes. Genetic engineering, along with evolution and selection, has been successfully used to divert carbon from ethanol, the natural endproduct of S. cerevisiae, to pyruvate. Further engineering, which included expression of heterologous enzymes and transporters, yielded strains capable of producing lactate and malate from pyruvate. Besides these metabolic engineering strategies, this review discusses the impact of transport and energetics as well as the tolerance towards these organic acids. In addition to recent progress in engineering S. cerevisiae for organic acid production, the key limitations and challenges are discussed in the context of sustainable industrial production of organic acids from renewable feedstocks.","URL":"http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2009.00537.x/abstract","DOI":"10.1111/j.1567-1364.2009.00537.x","ISSN":"1567-1364","shortTitle":"Metabolic engineering of Saccharomyces cerevisiae for production of carboxylic acids","language":"en","author":[{"family":"Abbott","given":"Derek A."},{"family":"Zelle","given":"Rintze M."},{"family":"Pronk","given":"Jack T."},{"family":"Van Maris","given":"Antonius J.A."}],"issued":{"date-parts":[["2009"]]},"accessed":{"date-parts":[["2012",7,13]]}}},{"id":1249,"uris":["http://zotero.org/users/1031436/items/AWBCXKXR"],"uri":["http://zotero.org/users/1031436/items/AWBCXKXR"],"itemData":{"id":1249,"type":"article-journal","title":"Increasing anaerobic acetate consumption and ethanol yield in Saccharomyces cerevisiae with NADPH-specific alcohol dehydrogenase","container-title":"Applied and Environmental Microbiology","source":"PubMed","abstract":"Saccharomyces cerevisiae has recently been engineered to use acetate, a primary inhibitor in lignocellulosic hydrolysates, as co-substrate during anaerobic ethanolic fermentation. However, the original metabolic pathway devised to convert acetate to ethanol uses NADH-specific acetylating acetaldehyde dehydrogenase and alcohol dehydrogenase, and quickly becomes constrained by limited NADH availability, even when glycerol formation is abolished.We present alcohol dehydrogenase as a novel target for anaerobic redox engineering of S. cerevisiae. Introduction of an NADPH-specific alcohol dehydrogenase not only reduces the NADH demand of the acetate-to-ethanol pathway, but also allows the cell to effectively exchange NADPH for NADH during sugar fermentation. Unlike NADH, NADPH can be freely generated under anaerobic conditions, via the oxidative pentose phosphate pathway.We show that an industrial bioethanol strain engineered with the original pathway (expressing acetylating acetaldehyde dehydrogenase from Bifidobacterium adolescentis and with deletions of glycerol-3-phosphate dehydrogenases GPD1 and GPD2) consumed 1.9 g l(-1) acetate during fermentation of 114 g l(-1) glucose. Combined with a decrease in glycerol production from 4.0 to 0.1 g l(-1), this increased the ethanol yield by 4% over the wild type. We provide evidence that acetate consumption in this strain is indeed limited by NADH availability. By introducing an NADPH-ADH from Entamoeba histolytica and overexpressing ACS2 and ZWF1, we increased acetate consumption to 5.3 g l(-1) and raised the ethanol yield to 7% above the wild-type level.","DOI":"10.1128/AEM.01689-15","ISSN":"1098-5336","note":"PMID: 26386051","journalAbbreviation":"Appl. Environ. 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Reindented JSON:
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"properties": {
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"URL": "http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2009.00537.x/abstract",
"DOI": "10.1111/j.1567-1364.2009.00537.x",
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"type": "article-journal",
"title": "Increasing anaerobic acetate consumption and ethanol yield in Saccharomyces cerevisiae with NADPH-specific alcohol dehydrogenase",
"container-title": "Applied and Environmental Microbiology",
"source": "PubMed",
"abstract": "Saccharomyces cerevisiae has recently been engineered to use acetate, a primary inhibitor in lignocellulosic hydrolysates, as co-substrate during anaerobic ethanolic fermentation. However, the original metabolic pathway devised to convert acetate to ethanol uses NADH-specific acetylating acetaldehyde dehydrogenase and alcohol dehydrogenase, and quickly becomes constrained by limited NADH availability, even when glycerol formation is abolished.We present alcohol dehydrogenase as a novel target for anaerobic redox engineering of S. cerevisiae. Introduction of an NADPH-specific alcohol dehydrogenase not only reduces the NADH demand of the acetate-to-ethanol pathway, but also allows the cell to effectively exchange NADPH for NADH during sugar fermentation. Unlike NADH, NADPH can be freely generated under anaerobic conditions, via the oxidative pentose phosphate pathway.We show that an industrial bioethanol strain engineered with the original pathway (expressing acetylating acetaldehyde dehydrogenase from Bifidobacterium adolescentis and with deletions of glycerol-3-phosphate dehydrogenases GPD1 and GPD2) consumed 1.9 g l(-1) acetate during fermentation of 114 g l(-1) glucose. Combined with a decrease in glycerol production from 4.0 to 0.1 g l(-1), this increased the ethanol yield by 4% over the wild type. We provide evidence that acetate consumption in this strain is indeed limited by NADH availability. By introducing an NADPH-ADH from Entamoeba histolytica and overexpressing ACS2 and ZWF1, we increased acetate consumption to 5.3 g l(-1) and raised the ethanol yield to 7% above the wild-type level.",
"DOI": "10.1128/AEM.01689-15",
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"given": "Trisha F."
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}, {
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"given": "Allan C."
}, {
"family": "Zelle",
"given": "Rintze M."
}],
"issued": {
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["2015", 9, 18]
]
},
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}
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<w:instrText xml:space="preserve"> ADDIN ZOTERO_BIBL {"uncited":[["http://zotero.org/users/1031436/items/HU4NC489"],["http://zotero.org/users/1031436/items/WZFNPG9D"]],"custom":[]} CSL_BIBLIOGRAPHY </w:instrText>
It seems that, even with the "Store references in Document" option checked, Zotero 4.0.29.10 does not store item metadata within .docx Word documents for so-called 'uncited' items that are added directly to the bibliography via Zotero's "Edit Bibliography" button.
Examples generated with Mendeley Desktop v1.16.3.
Full field:
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Reindented JSON:
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<w:instrText xml:space="preserve">ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1128/AEM.02591-07", "abstract" : "Malic acid is a potential biomass-derivable \u201cbuilding block\u201d for chemical synthesis. Since wild-type Saccharomyces cerevisiae strains produce only low levels of malate, metabolic engineering is required to achieve efficient malate production with this yeast. A promising pathway for malate production from glucose proceeds via carboxylation of pyruvate, followed by reduction of oxaloacetate to malate. This redox- and ATP-neutral, CO2-fixing pathway has a theoretical maximum yield of 2 mol malate (mol glucose)\u22121. A previously engineered glucose-tolerant, C2-independent pyruvate decarboxylase-negative S. cerevisiae strain was used as the platform to evaluate the impact of individual and combined introduction of three genetic modifications: (i) overexpression of the native pyruvate carboxylase encoded by PYC2, (ii) high-level expression of an allele of the MDH3 gene, of which the encoded malate dehydrogenase was retargeted to the cytosol by deletion of the C-terminal peroxisomal targeting sequence, and (iii) functional expression of the Schizosaccharomyces pombe malate transporter gene SpMAE1. While single or double modifications improved malate production, the highest malate yields and titers were obtained with the simultaneous introduction of all three modifications. In glucose-grown batch cultures, the resulting engineered strain produced malate at titers of up to 59 g liter\u22121 at a malate yield of 0.42 mol (mol glucose)\u22121. Metabolic flux analysis showed that metabolite labeling patterns observed upon nuclear magnetic resonance analyses of cultures grown on 13C-labeled glucose were consistent with the envisaged nonoxidative, fermentative pathway for malate production. The engineered strains still produced substantial amounts of pyruvate, indicating that the pathway efficiency can be further improved.", "author" : [ { "dropping-particle" : "", "family" : "Zelle", "given" : "Rintze M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hulster", "given" : "Erik", "non-dropping-particle" : "de", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Winden", "given" : "Wouter A.", "non-dropping-particle" : "van", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Waard", "given" : "Pieter", "non-dropping-particle" : "de", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Dijkema", "given" : "Cor", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Winkler", "given" : "Aaron A.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Geertman", "given" : "Jan-Maarten A.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Dijken", "given" : "Johannes P.", "non-dropping-particle" : "van", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pronk", "given" : "Jack T.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Maris", "given" : "Antonius J. A.", "non-dropping-particle" : "van", "parse-names" : false, "suffix" : "" } ], "container-title" : "Applied and Environmental Microbiology", "id" : "ITEM-1", "issue" : "9", "issued" : { "date-parts" : [ [ "2008" ] ] }, "page" : "2766-2777", "title" : "Malic Acid Production by Saccharomyces cerevisiae: Engineering of Pyruvate Carboxylation, Oxaloacetate Reduction, and Malate Export", "type" : "article-journal", "volume" : "74" }, "uris" : [ "http://www.mendeley.com/documents/?uuid=23d11864-e841-3d60-8a56-32eefa603948" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1128/AEM.01077-10", "abstract" : "Pyruvate carboxylase is the sole anaplerotic enzyme in glucose-grown cultures of wild-type Saccharomyces cerevisiae. Pyruvate carboxylase-negative (Pyc \u060a) S. cerevisiae strains cannot grow on glucose unless media are supplemented with C 4 compounds, such as aspartic acid. In several succinate-producing prokaryotes, phos-phoenolpyruvate carboxykinase (PEPCK) fulfills this anaplerotic role. However, the S. cerevisiae PEPCK encoded by PCK1 is repressed by glucose and is considered to have a purely decarboxylating and gluconeogenic function. This study investigates whether and under which conditions PEPCK can replace the anaplerotic function of pyruvate carboxylase in S. cerevisiae. Pyc \u060a S. cerevisiae strains constitutively overexpressing the PEPCK either from S. cerevisiae or from Actinobacillus succinogenes did not grow on glucose as the sole carbon source. However, evolutionary engineering yielded mutants able to grow on glucose as the sole carbon source at a maximum specific growth rate of ca. 0.14 h \u060a1 , one-half that of the (pyruvate carboxylase-positive) reference strain grown under the same conditions. Growth was dependent on high carbon dioxide concentrations, indicating that the reaction catalyzed by PEPCK operates near thermodynamic equilibrium. Analysis and reverse engineering of two independently evolved strains showed that single point mutations in pyruvate kinase, which competes with PEPCK for phosphoenolpyruvate, were sufficient to enable the use of PEPCK as the sole anaplerotic enzyme. The PEPCK reaction produces one ATP per carboxylation event, whereas the original route through pyruvate kinase and pyruvate carboxylase is ATP neutral. This increased ATP yield may prove crucial for engineering of efficient and low-cost anaerobic production of C 4 dicarboxylic acids in S. cerevisiae. Interest in biotechnological production of the four-carbon dicarboxylic acids fumarate, succinate, and malate from sugars has strongly increased in recent years (19), as these sugar-derived acids are seen as potential replacements for oil-derived chemical intermediates such as maleic anhydride (41). Meta-bolic engineering of Escherichia coli has resulted in strains capable of producing 73 g liter \u03ea1 succinate at pH 7.0 with a yield that, at 1.61 mol per mol glucose (21), is at 94% of the theoretical maximum. The crucial role of carboxylation reac-tions in this biotechnological process is illustrated by a carbon yield of 1.07 C mol succinate per C mol of glucose\u2026", "author" : [ { "dropping-particle" : "", "family" : "Zelle", "given" : "Rintze M", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Trueheart", "given" : "Josh", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Harrison", "given" : "Jacob C", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pronk", "given" : "Jack T", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Maris", "given" : "Antonius J A", "non-dropping-particle" : "van", "parse-names" : false, "suffix" : "" } ], "container-title" : "Applied and Environmental Microbiology", "id" : "ITEM-2", "issue" : "16", "issued" : { "date-parts" : [ [ "2010" ] ] }, "page" : "5383-5389", "title" : "Phosphoenolpyruvate Carboxykinase as the Sole Anaplerotic Enzyme in Saccharomyces cerevisiae", "type" : "article-journal", "volume" : "76" }, "uris" : [ "http://www.mendeley.com/documents/?uuid=1916c171-8e1e-3ad9-b16b-f99beef40f81" ] } ], "mendeley" : { "formattedCitation" : "<sup>2,3</sup>", "plainTextFormattedCitation" : "2,3", "previouslyFormattedCitation" : "<sup>2,3</sup>" }, "properties" : { "noteIndex" : 0 }, "schema" : "https://github.com/citation-style-language/schema/raw/master/csl-citation.json" }</w:instrText>
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