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A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell-specific lignin reduction.

Liang Y, Eudes A, Yogiswara S, Jing B, Benites VT, Yamanaka R, Cheng-Yue C, Baidoo EE, Mortimer JC, Scheller HV, Loqué D.

Biotechnol Biofuels. 2019 May 23;12:130. doi: 10.1186/s13068-019-1467-y. eCollection 2019.


Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification.

Li G, Jones KC, Eudes A, Pidatala VR, Sun J, Xu F, Zhang C, Wei T, Jain R, Birdseye D, Canlas PE, Baidoo EEK, Duong PQ, Sharma MK, Singh S, Ruan D, Keasling JD, Mortimer JC, Loqué D, Bartley LE, Scheller HV, Ronald PC.

BMC Biotechnol. 2018 Sep 4;18(1):54. doi: 10.1186/s12896-018-0464-8.


Increased drought tolerance in plants engineered for low lignin and low xylan content.

Yan J, Aznar A, Chalvin C, Birdseye DS, Baidoo EEK, Eudes A, Shih PM, Loqué D, Zhang A, Scheller HV.

Biotechnol Biofuels. 2018 Jul 18;11:195. doi: 10.1186/s13068-018-1196-7. eCollection 2018.


Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly.

Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, Cho H, Karaoz U, Loqué D, Bowen BP, Firestone MK, Northen TR, Brodie EL.

Nat Microbiol. 2018 Apr;3(4):470-480. doi: 10.1038/s41564-018-0129-3. Epub 2018 Mar 19.


A transgene design for enhancing oil content in Arabidopsis and Camelina seeds.

Zhu Y, Xie L, Chen GQ, Lee MY, Loque D, Scheller HV.

Biotechnol Biofuels. 2018 Feb 21;11:46. doi: 10.1186/s13068-018-1049-4. eCollection 2018.


Production of muconic acid in plants.

Eudes A, Berthomieu R, Hao Z, Zhao N, Benites VT, Baidoo EEK, Loqué D.

Metab Eng. 2018 Mar;46:13-19. doi: 10.1016/j.ymben.2018.02.002. Epub 2018 Feb 21.


Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass.

Aznar A, Chalvin C, Shih PM, Maimann M, Ebert B, Birdseye DS, Loqué D, Scheller HV.

Biotechnol Biofuels. 2018 Jan 9;11:2. doi: 10.1186/s13068-017-1007-6. eCollection 2018.


Lignin Valorization: Two Hybrid Biochemical Routes for the Conversion of Polymeric Lignin into Value-added Chemicals.

Wu W, Dutta T, Varman AM, Eudes A, Manalansan B, Loqué D, Singh S.

Sci Rep. 2017 Aug 21;7(1):8420. doi: 10.1038/s41598-017-07895-1.


SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum.

Eudes A, Dutta T, Deng K, Jacquet N, Sinha A, Benites VT, Baidoo EEK, Richel A, Sattler SE, Northen TR, Singh S, Simmons BA, Loqué D.

PLoS One. 2017 Jun 8;12(6):e0178160. doi: 10.1371/journal.pone.0178160. eCollection 2017.


Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants.

Liang Y, Richardson S, Yan J, Benites VT, Cheng-Yue C, Tran T, Mortimer J, Mukhopadhyay A, Keasling JD, Scheller HV, Loqué D.

ACS Synth Biol. 2017 May 19;6(5):806-816. doi: 10.1021/acssynbio.6b00295. Epub 2017 Feb 8.


Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast.

Eudes A, Mouille M, Robinson DS, Benites VT, Wang G, Roux L, Tsai YL, Baidoo EE, Chiu TY, Heazlewood JL, Scheller HV, Mukhopadhyay A, Keasling JD, Deutsch S, Loqué D.

Microb Cell Fact. 2016 Nov 21;15(1):198.


A robust gene-stacking method utilizing yeast assembly for plant synthetic biology.

Shih PM, Vuu K, Mansoori N, Ayad L, Louie KB, Bowen BP, Northen TR, Loqué D.

Nat Commun. 2016 Oct 26;7:13215. doi: 10.1038/ncomms13215.


Expression of S-adenosylmethionine Hydrolase in Tissues Synthesizing Secondary Cell Walls Alters Specific Methylated Cell Wall Fractions and Improves Biomass Digestibility.

Eudes A, Zhao N, Sathitsuksanoh N, Baidoo EE, Lao J, Wang G, Yogiswara S, Lee TS, Singh S, Mortimer JC, Keasling JD, Simmons BA, Loqué D.

Front Bioeng Biotechnol. 2016 Jul 19;4:58. doi: 10.3389/fbioe.2016.00058. eCollection 2016.


Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops.

Shih PM, Liang Y, Loqué D.

Plant J. 2016 Jul;87(1):103-17. doi: 10.1111/tpj.13176. Epub 2016 Jun 20. Review.


Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin.

Eudes A, Pereira JH, Yogiswara S, Wang G, Teixeira Benites V, Baidoo EE, Lee TS, Adams PD, Keasling JD, Loqué D.

Plant Cell Physiol. 2016 Mar;57(3):568-79. doi: 10.1093/pcp/pcw016. Epub 2016 Feb 8.


Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS.

Deng K, Guenther JM, Gao J, Bowen BP, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR.

Front Bioeng Biotechnol. 2015 Oct 13;3:153. doi: 10.3389/fbioe.2015.00153. eCollection 2015.


Precursor-Directed Combinatorial Biosynthesis of Cinnamoyl, Dihydrocinnamoyl, and Benzoyl Anthranilates in Saccharomyces cerevisiae.

Eudes A, Teixeira Benites V, Wang G, Baidoo EE, Lee TS, Keasling JD, Loqué D.

PLoS One. 2015 Oct 2;10(10):e0138972. doi: 10.1371/journal.pone.0138972. eCollection 2015.


Biochemical characterization of Arabidopsis APYRASE family reveals their roles in regulating endomembrane NDP/NMP homoeostasis.

Chiu TY, Lao J, Manalansan B, Loqué D, Roux SJ, Heazlewood JL.

Biochem J. 2015 Nov 15;472(1):43-54. doi: 10.1042/BJ20150235. Epub 2015 Sep 3.


Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

Patron NJ, Orzaez D, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farré G, Rogers C, Smith A, Hibberd J, Webb AA, Locke J, Schornack S, Ajioka J, Baulcombe DC, Zipfel C, Kamoun S, Jones JD, Kuhn H, Robatzek S, Van Esse HP, Sanders D, Oldroyd G, Martin C, Field R, O'Connor S, Fox S, Wulff B, Miller B, Breakspear A, Radhakrishnan G, Delaux PM, Loqué D, Granell A, Tissier A, Shih P, Brutnell TP, Quick WP, Rischer H, Fraser PD, Aharoni A, Raines C, South PF, Ané JM, Hamberger BR, Langdale J, Stougaard J, Bouwmeester H, Udvardi M, Murray JA, Ntoukakis V, Schäfer P, Denby K, Edwards KJ, Osbourn A, Haseloff J.

New Phytol. 2015 Oct;208(1):13-9. doi: 10.1111/nph.13532. Epub 2015 Jul 14. Erratum in: New Phytol. 2016 Jan;209(2):885.


Restricting lignin and enhancing sugar deposition in secondary cell walls enhances monomeric sugar release after low temperature ionic liquid pretreatment.

Scullin C, Cruz AG, Chuang YD, Simmons BA, Loque D, Singh S.

Biotechnol Biofuels. 2015 Jul 4;8:95. doi: 10.1186/s13068-015-0275-2. eCollection 2015.


Tight regulation of plant immune responses by combining promoter and suicide exon elements.

Gonzalez TL, Liang Y, Nguyen BN, Staskawicz BJ, Loqué D, Hammond MC.

Nucleic Acids Res. 2015 Aug 18;43(14):7152-61. doi: 10.1093/nar/gkv655. Epub 2015 Jul 2.


Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte.

Schicklberger M, Shapiro N, Loqué D, Woyke T, Chakraborty R.

Genome Announc. 2015 Jun 11;3(3). pii: e00607-15. doi: 10.1128/genomeA.00607-15.


Engineering of plant cell walls for enhanced biofuel production.

Loqué D, Scheller HV, Pauly M.

Curr Opin Plant Biol. 2015 Jun;25:151-61. doi: 10.1016/j.pbi.2015.05.018. Epub 2015 Jun 3. Review.


Correction: Fluorescent sensors reporting the activity of ammonium transceptors in live cells.

De Michele R, Ast C, Loqué D, Ho CH, Andrade SL, Lanquar V, Grossmann G, Gehne S, Kumke MU, Frommer WB.

Elife. 2015 Feb 18;4. doi: 10.7554/eLife.06986. No abstract available.


Engineering temporal accumulation of a low recalcitrance polysaccharide leads to increased C6 sugar content in plant cell walls.

Vega-Sánchez ME, Loqué D, Lao J, Catena M, Verhertbruggen Y, Herter T, Yang F, Harholt J, Ebert B, Baidoo EE, Keasling JD, Scheller HV, Heazlewood JL, Ronald PC.

Plant Biotechnol J. 2015 Sep;13(7):903-14. doi: 10.1111/pbi.12326. Epub 2015 Jan 14.


Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency.

Eudes A, Sathitsuksanoh N, Baidoo EE, George A, Liang Y, Yang F, Singh S, Keasling JD, Simmons BA, Loqué D.

Plant Biotechnol J. 2015 Dec;13(9):1241-50. doi: 10.1111/pbi.12310. Epub 2015 Jan 13.


A gene stacking approach leads to engineered plants with highly increased galactan levels in Arabidopsis.

Gondolf VM, Stoppel R, Ebert B, Rautengarten C, Liwanag AJ, Loqué D, Scheller HV.

BMC Plant Biol. 2014 Dec 10;14:344. doi: 10.1186/s12870-014-0344-x.


The plant glycosyltransferase clone collection for functional genomics.

Lao J, Oikawa A, Bromley JR, McInerney P, Suttangkakul A, Smith-Moritz AM, Plahar H, Chiu TY, González Fernández-Niño SM, Ebert B, Yang F, Christiansen KM, Hansen SF, Stonebloom S, Adams PD, Ronald PC, Hillson NJ, Hadi MZ, Vega-Sánchez ME, Loqué D, Scheller HV, Heazlewood JL.

Plant J. 2014 Aug;79(3):517-29. doi: 10.1111/tpj.12577. Epub 2014 Jul 9. Erratum in: Plant J. 2014 Dec;80(5):936.


Histochemical staining of Arabidopsis thaliana secondary cell wall elements.

Pradhan Mitra P, Loqué D.

J Vis Exp. 2014 May 13;(87). doi: 10.3791/51381.


Lignin bioengineering.

Eudes A, Liang Y, Mitra P, Loqué D.

Curr Opin Biotechnol. 2014 Apr;26:189-98. doi: 10.1016/j.copbio.2014.01.002. Epub 2014 Feb 28. Review.


Visualization of plant cell wall lignification using fluorescence-tagged monolignols.

Tobimatsu Y, Wagner A, Donaldson L, Mitra P, Niculaes C, Dima O, Kim JI, Anderson N, Loque D, Boerjan W, Chapple C, Ralph J.

Plant J. 2013 Nov;76(3):357-66. doi: 10.1111/tpj.12299. Epub 2013 Aug 23.


Fluorescent sensors reporting the activity of ammonium transceptors in live cells.

De Michele R, Ast C, Loqué D, Ho CH, Andrade S, Lanquar V, Grossmann G, Gehne S, Kumke MU, Frommer WB.

Elife. 2013 Jul 2;2:e00800. doi: 10.7554/eLife.00800. Erratum in: Elife. 2015;4. doi: 10.7554/eLife.06986.


Production of hydroxycinnamoyl anthranilates from glucose in Escherichia coli.

Eudes A, Juminaga D, Baidoo EE, Collins FW, Keasling JD, Loqué D.

Microb Cell Fact. 2013 Jun 28;12:62. doi: 10.1186/1475-2859-12-62. Erratum in: Microb Cell Fact. 2014;13:8.


Allosteric regulation of transport activity by heterotrimerization of Arabidopsis ammonium transporter complexes in vivo.

Yuan L, Gu R, Xuan Y, Smith-Valle E, Loqué D, Frommer WB, von Wirén N.

Plant Cell. 2013 Mar;25(3):974-84. doi: 10.1105/tpc.112.108027. Epub 2013 Mar 5.


Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants.

Petersen PD, Lau J, Ebert B, Yang F, Verhertbruggen Y, Kim JS, Varanasi P, Suttangkakul A, Auer M, Loqué D, Scheller HV.

Biotechnol Biofuels. 2012 Nov 26;5(1):84. doi: 10.1186/1754-6834-5-84.


Engineering secondary cell wall deposition in plants.

Yang F, Mitra P, Zhang L, Prak L, Verhertbruggen Y, Kim JS, Sun L, Zheng K, Tang K, Auer M, Scheller HV, Loqué D.

Plant Biotechnol J. 2013 Apr;11(3):325-35. doi: 10.1111/pbi.12016. Epub 2012 Nov 12.


AtAPY1 and AtAPY2 function as Golgi-localized nucleoside diphosphatases in Arabidopsis thaliana.

Chiu TY, Christiansen K, Moreno I, Lao J, Loqué D, Orellana A, Heazlewood JL, Clark G, Roux SJ.

Plant Cell Physiol. 2012 Nov;53(11):1913-25. doi: 10.1093/pcp/pcs131. Epub 2012 Oct 3.


Ammonium and urea transporter inventory of the selaginella and physcomitrella genomes.

De Michele R, Loqué D, Lalonde S, Frommer WB.

Front Plant Sci. 2012 Apr 9;3:62. doi: 10.3389/fpls.2012.00062. eCollection 2012.


Amino Acid transporter inventory of the selaginella genome.

Wipf D, Loqué D, Lalonde S, Frommer WB.

Front Plant Sci. 2012 Apr 9;3:36. doi: 10.3389/fpls.2012.00036. eCollection 2012.


Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification.

Eudes A, George A, Mukerjee P, Kim JS, Pollet B, Benke PI, Yang F, Mitra P, Sun L, Cetinkol OP, Chabout S, Mouille G, Soubigou-Taconnat L, Balzergue S, Singh S, Holmes BM, Mukhopadhyay A, Keasling JD, Simmons BA, Lapierre C, Ralph J, Loqué D.

Plant Biotechnol J. 2012 Jun;10(5):609-20. doi: 10.1111/j.1467-7652.2012.00692.x. Epub 2012 Mar 28.


Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis.

Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Smith-Moritz AM, Morrison S, McInerney P, Hadi MZ, Auer M, Mukhopadhyay A, Petzold CJ, Scheller HV, Loqué D, Heazlewood JL.

Plant Physiol. 2012 May;159(1):12-26. doi: 10.1104/pp.111.193151. Epub 2012 Mar 19.


Rapid determination of syringyl: guaiacyl ratios using FT-Raman spectroscopy.

Sun L, Varanasi P, Yang F, Loqué D, Simmons BA, Singh S.

Biotechnol Bioeng. 2012 Mar;109(3):647-56. doi: 10.1002/bit.24348. Epub 2011 Nov 6.


The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.

Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV.

Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810. Epub 2011 May 5.


N-terminal cysteines affect oligomer stability of the allosterically regulated ammonium transporter LeAMT1;1.

Graff L, Obrdlik P, Yuan L, Loqué D, Frommer WB, von Wirén N.

J Exp Bot. 2011 Feb;62(4):1361-73. doi: 10.1093/jxb/erq379. Epub 2010 Dec 2.


Production of tranilast [N-(3',4'-dimethoxycinnamoyl)-anthranilic acid] and its analogs in yeast Saccharomyces cerevisiae.

Eudes A, Baidoo EE, Yang F, Burd H, Hadi MZ, Collins FW, Keasling JD, Loqué D.

Appl Microbiol Biotechnol. 2011 Feb;89(4):989-1000. doi: 10.1007/s00253-010-2939-y. Epub 2010 Oct 24.


Advances in modifying lignin for enhanced biofuel production.

Simmons BA, Loqué D, Ralph J.

Curr Opin Plant Biol. 2010 Jun;13(3):313-20. doi: 10.1016/j.pbi.2010.03.001. Epub 2010 Mar 30. Review.


A membrane protein/signaling protein interaction network for Arabidopsis version AMPv2.

Lalonde S, Sero A, Pratelli R, Pilot G, Chen J, Sardi MI, Parsa SA, Kim DY, Acharya BR, Stein EV, Hu HC, Villiers F, Takeda K, Yang Y, Han YS, Schwacke R, Chiang W, Kato N, Loqué D, Assmann SM, Kwak JM, Schroeder JI, Rhee SY, Frommer WB.

Front Physiol. 2010 Sep 22;1:24. doi: 10.3389/fphys.2010.00024. eCollection 2010.


Feedback inhibition of ammonium uptake by a phospho-dependent allosteric mechanism in Arabidopsis.

Lanquar V, Loqué D, Hörmann F, Yuan L, Bohner A, Engelsberger WR, Lalonde S, Schulze WX, von Wirén N, Frommer WB.

Plant Cell. 2009 Nov;21(11):3610-22. doi: 10.1105/tpc.109.068593. Epub 2009 Nov 30.


Pore mutations in ammonium transporter AMT1 with increased electrogenic ammonium transport activity.

Loqué D, Mora SI, Andrade SL, Pantoja O, Frommer WB.

J Biol Chem. 2009 Sep 11;284(37):24988-95. doi: 10.1074/jbc.M109.020842. Epub 2009 Jul 6.


Next-generation biomass feedstocks for biofuel production.

Simmons BA, Loque D, Blanch HW.

Genome Biol. 2008;9(12):242. doi: 10.1186/gb-2008-9-12-242. Epub 2008 Dec 29.

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