@article{egertsdotter_zyl_mackay_peter_kirst_clark_whetten_sederoff_2004, title={Gene Expression during Formation of Earlywood and Latewood in Loblolly Pine: Expression Profiles of 350 Genes}, volume={6}, ISSN={1435-8603 1438-8677}, url={http://dx.doi.org/10.1055/s-2004-830383}, DOI={10.1055/s-2004-830383}, abstractNote={Abstract:  The natural variability of wood formation in trees affords opportunities to correlate transcript profiles with the resulting wood properties. We have used cDNA microarrays to study transcript abundance in developing secondary xylem of loblolly pine (Pinus taeda) over a growing season. The cDNAs were selected from a collection of 75 000 ESTs that have been sequenced and annotated (http:web.ahc.umn.edubiodatansfpine). Cell wall thickness and climatic data were related to earlywood and latewood formation at different time points during the growing season. Seventy‐one ESTs showed preferential expression in earlywood or latewood, including 23 genes with no significant similarity to genes in GenBank. Seven genes involved in lignin synthesis were preferentially expressed in latewood. The studies have provided initial insights into the variation of expression patterns of some of the genes related to the wood formation process.}, number={6}, journal={Plant Biology}, publisher={Wiley}, author={Egertsdotter, U. and Zyl, L. M. and MacKay, J. and Peter, G. and Kirst, M. and Clark, C. and Whetten, R. and Sederoff, R.}, year={2004}, month={Nov}, pages={654–663} }
 @inproceedings{yu_capanema_batista_josserand_johnson_nelson_mckeand_mackay_kadla_li_et al._2004, title={Tracking down the effects of a rare mutant gene in loblolly pine: a first report}, booktitle={2004 Paper Summit, Spring Technical and International Environmental Conference}, publisher={CD-ROM published by TAPPI,  Norcross, GA}, author={Yu, Q. and Capanema, E. and Batista, V. B. and Josserand, S. and Johnson, G. and Nelson, C. D. and McKeand, S. E. and MacKay, J. J. and Kadla, J. F. and Li, B. and et al.}, year={2004} }
 @article{ralph_lapierre_marita_kim_lu_hatfield_ralph_chapple_franke_hemm_et al._2001, title={Elucidation of new structures in lignins of CAD- and COMT-deficient plants by NMR}, volume={57}, ISSN={["0031-9422"]}, DOI={10.1016/S0031-9422(01)00109-1}, abstractNote={Studying lignin-biosynthetic-pathway mutants and transgenics provides insights into plant responses to perturbations of the lignification system, and enhances our understanding of normal lignification. When enzymes late in the pathway are downregulated, significant changes in the composition and structure of lignin may result. NMR spectroscopy provides powerful diagnostic tools for elucidating structures in the difficult lignin polymer, hinting at the chemical and biochemical changes that have occurred. COMT (caffeic acid O-methyl transferase) downregulation in poplar results in the incorporation of 5-hydroxyconiferyl alcohol into lignins via typical radical coupling reactions, but post-coupling quinone methide internal trapping reactions produce novel benzodioxane units in the lignin. CAD (cinnamyl alcohol dehydrogenase) downregulation results in the incorporation of the hydroxycinnamyl aldehyde monolignol precursors intimately into the polymer. Sinapyl aldehyde cross-couples 8-O-4 with both guaiacyl and syringyl units in the growing polymer, whereas coniferyl aldehyde cross-couples 8-O-4 only with syringyl units, reflecting simple chemical cross-coupling propensities. The incorporation of hydroxycinnamyl aldehyde and 5-hydroxyconiferyl alcohol monomers indicates that these monolignol intermediates are secreted to the cell wall for lignification. The recognition that novel units can incorporate into lignins portends significantly expanded opportunities for engineering the composition and consequent properties of lignin for improved utilization of valuable plant resources.}, number={6}, journal={PHYTOCHEMISTRY}, author={Ralph, J and Lapierre, C and Marita, JM and Kim, H and Lu, FC and Hatfield, RD and Ralph, S and Chapple, C and Franke, R and Hemm, MR and et al.}, year={2001}, month={Jul}, pages={993–1003} }
 @article{dimmel_mackay_althen_parks_sederoff_2001, title={Pulping and bleaching of CAD-deficient wood}, volume={21}, ISSN={["1532-2319"]}, DOI={10.1081/WCT-100102651}, abstractNote={Mutant loblolly pine trees that are deficient in the enzyme cinnamyl alcohol dehydrogenase (CAD) have been obtained through directed breeding. The lignin in the wood of CAD-deficient trees has a different pool of precursors, resulting in high levels of pulping-resistant C-5 linkages. Wood from a 12-year-old CAD-deficient tree has been pulped under soda and kraft conditions in microdigestors. In comparison to a normal 12-year-old loblolly pine, the CAD-deficient wood was much more easily delignified. In addition, the pulp from CAD-deficient wood was as easy to bleach as a control pulp. The high reactivity of CAD-deficient wood may be related to the lignin size and phenolic content. The molecular weight of an isolated milled wood lignin from CAD-deficient pine was ∼35% less than that from a normal pine tree.}, number={1}, journal={JOURNAL OF WOOD CHEMISTRY AND TECHNOLOGY}, author={Dimmel, DR and MacKay, JJ and Althen, EM and Parks, C and Sederoff, RR}, year={2001}, pages={1–17} }
 @article{lapierre_pollet_mackay_sederoff_2000, title={Lignin structure in a mutant pine deficient in cinnamyl alcohol dehydrogenase}, volume={48}, ISSN={["0021-8561"]}, DOI={10.1021/jf991398p}, abstractNote={Cinnamyl alcohol dehydrogenase (CAD) activity is deficient in loblolly pine (Pinus taeda L.) harboring a mutated allele of the cad gene (cad-n1). We compared lignin structure of CAD-deficient and wild-type pines, both types segregating within full-sib families obtained by controlled crosses. The type and frequency of lignin building units and distribution of interunit bonds were determined from the GC-MS analysis of thioacidolysis monomers and dimers. While the lignin content was only slightly reduced, the lignin structure was dramatically modified by the mutation in both mature and juvenile trees. Lignins from CAD-deficient pine displayed unusually high levels of coniferaldehyde and dihydroconiferyl alcohol. In addition, biphenyl and biphenyl ether bonds were in large excess in these abnormal lignins. These results suggest that the CAD-deficient pines efficiently compensate for the shortage in normal lignin precursors by utilizing nontraditional wall phenolics to construct unusual lignins particularly enriched in resistant interunit bonds.}, number={6}, journal={JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY}, author={Lapierre, C and Pollet, B and MacKay, JJ and Sederoff, RR}, year={2000}, month={Jun}, pages={2326–2331} }
 @article{wu_remington_mackay_mckeand_dm o'malley_1999, title={Average effect of a mutation in lignin biosynthesis in loblolly pine}, volume={99}, ISSN={["0040-5752"]}, DOI={10.1007/s001220051287}, abstractNote={Cinnamyl alcohol dehydrogenase (CAD, E.C. 1.1.1.195) is a monolignol biosynthetic enzyme that catalyzes the final step of lignin subunit biosynthesis in higher plants. Recently, a mutant allele of the cad gene, cad-n1, encoding for the CAD enzyme, was discovered in loblolly pine. By reducing the expression of the cad gene, this mutant has a decreased lignin content and major changes in the lignin composition in wood. In this study, we found that the substitution of a wild-type allele by cad-n1 was associated with a significant effect on 2nd-year shoot elongation in a half-sib family of loblolly pine (designated family 7-1037). The average effect of cad-n1 appeared to increase with tree growth and was greater for stem radial growth than height growth. An increase of 14.1% in de-barked volume in year 4 was associated with cad-n1. Co-segregation analysis indicated that the cad locus itself might represent a gene that governs stem growth in pine. The significance of the mutation cad-n1 for tree growth and wood processing is discussed.}, number={3-4}, journal={THEORETICAL AND APPLIED GENETICS}, author={Wu, RL and Remington, DL and MacKay, JJ and McKeand, SE and DM O'Malley}, year={1999}, month={Aug}, pages={705–710} }
 @article{mackay_presnell_jameel_taneda_d o'malley_sederoff_1999, title={Modified lignin and delignification with a CAD-deficient loblolly pine}, volume={53}, ISSN={["0018-3830"]}, DOI={10.1515/HF.1999.067}, abstractNote={Summary}, number={4}, journal={HOLZFORSCHUNG}, author={MacKay, J and Presnell, T and Jameel, H and Taneda, H and D O'Malley and Sederoff, R}, year={1999}, pages={403–410} }
 @misc{sederoff_mackay_ralph_hatfield_1999, title={Unexpected variation in lignin}, volume={2}, ISSN={["1879-0356"]}, DOI={10.1016/S1369-5266(99)80029-6}, abstractNote={Recent studies on mutant and transgenic plants indicate that lignification may be far more flexible than previously realized. Pines with a mutation affecting the biosynthesis of the major lignin precursor, coniferyl alcohol, show a high level of an unusual subunit, dihydroconiferyl alcohol. These results argue in favor of an increased potential for genetic modification of lignin and indicate that our knowledge of the biosynthesis of lignin is far from complete.}, number={2}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Sederoff, RR and MacKay, JJ and Ralph, J and Hatfield, RD}, year={1999}, month={Apr}, pages={145–152} }
 @article{stoop_williamson_conkling_mackay_pharr_1998, title={Characterization of NAD-dependent mannitol dehydrogenase from celery as affected by ions, chelators, reducing agents and metabolites}, volume={131}, ISSN={["0168-9452"]}, DOI={10.1016/S0168-9452(97)00243-4}, abstractNote={NAD-dependent mannitol dehydrogenase (MTD) from celery (Apium graveolens L. var. dulce (Mill.) Pers.) provides the initial step by which mannitol is committed to central metabolism and plays a critical role in regulating mannitol concentration in the plant. The pH optimum for mannitol oxidation occurs at pH 9.5 whereas the optimum for mannose reduction occurs at pH 6.5. Michaelis–Menten kinetics were exhibited for mannitol and NAD with Km values of 64 and 0.14 mM, respectively at pH 9.5. The Km for mannose and NADH were 745 mM and 1.27 μM, respectively at pH 6.5. The high Km for mannose is consistent with a reaction in situ favoring mannitol oxidation rather than mannose reduction. The observed down-regulation of MTD in salt stressed celery is not due to a direct inhibition by NaCl or macronutrients. Inhibition by the chelator 1,10-phenanthroline suggests that zinc is required for MTD activity. Reducing agents DTT, DTE and β-mercaptoethanol inactivated MTD reversibly. At pH 7.0, ADP and to a lesser extend AMP and ATP were competitive inhibitors, with respect to NAD, having apparent Ki’s of 0.24, 0.64 and 1.10 mM, respectively.}, number={1}, journal={PLANT SCIENCE}, author={Stoop, JMH and Williamson, JD and Conkling, MA and MacKay, JJ and Pharr, DM}, year={1998}, month={Jan}, pages={43–51} }
 @misc{mackay_o'malley_whetten_sederoff_1998, title={Method of altering lignin in trees}, volume={5,824,842}, number={1998 Oct. 20}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={MacKay, J. and O'Malley, D. and Whetten, R. and Sederoff, R.}, year={1998} }
 @misc{whetten_mackay_sederoff_1998, title={Recent advances in understanding lignin biosynthesis}, volume={49}, ISSN={["1040-2519"]}, DOI={10.1146/annurev.arplant.49.1.585}, abstractNote={▪ Abstract  After a long period of little change, the basic concepts of lignin biosynthesis have been challenged by new results from genetic modification of lignin content and composition. New techniques for making directed genetic changes in plants, as well as improvements in the analytical techniques used to determine lignin content and composition in plant cell walls, have been used in experimental tests of the accepted lignin biosynthetic pathway. The lignins obtained from genetically modified plants have shown unexpected properties, and these findings have extended the known range of variation in lignin content and composition. These results argue that the accepted lignin biosynthetic pathway is either incomplete or incorrect, or both; and also suggest that plants may have a high level of metabolic plasticity in the formation of lignins. If this is so, the properties of novel lignins could be of significant scientific and practical interest.}, number={1998}, journal={ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY}, author={Whetten, RW and MacKay, JJ and Sederoff, RR}, year={1998}, pages={585–609} }
 @article{ralph_mackay_hatfield_omalley_whetten_sederoff_1997, title={Abnormal lignin in a loblolly pine mutant}, volume={277}, ISSN={["1095-9203"]}, DOI={10.1126/science.277.5323.235}, abstractNote={
            Novel lignin is formed in a mutant loblolly pine (
            Pinus taeda
            L.) severely depleted in cinnamyl alcohol dehydrogenase (E.C. 1.1.1.195), which converts coniferaldehyde to coniferyl alcohol, the primary lignin precursor in pines. Dihydroconiferyl alcohol, a monomer not normally associated with the lignin biosynthetic pathway, is the major component of the mutant's lignin, accounting for ∼30 percent (versus ∼3 percent in normal pine) of the units. The level of aldehydes, including new 2-methoxybenzaldehydes, is also increased. The mutant pines grew normally indicating that, even within a species, extensive variations in lignin composition need not disrupt the essential functions of lignin.
          }, number={5323}, journal={SCIENCE}, author={Ralph, J and MacKay, JJ and Hatfield, RD and OMalley, DM and Whetten, RW and Sederoff, RR}, year={1997}, month={Jul}, pages={235–239} }
 @article{mackay_omalley_presnell_booker_campbell_whetten_sederoff_1997, title={Inheritance, gene expression, and lignin characterization in a mutant pine deficient in cinnamyl alcohol dehydrogenase}, volume={94}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.94.15.8255}, abstractNote={
            We have discovered a mutant loblolly pine (
            Pinus taeda
            L.) in which expression of the gene encoding cinnamyl alcohol dehydrogenase (CAD; EC
            1.1.1.195
            ) is severely reduced. The products of CAD, cinnamyl alcohols, are the precursors of lignin, a major cell wall polymer of plant vascular tissues. Lignin composition in this mutant shows dramatic modifications, including increased incorporation of the substrate of CAD (coniferaldehyde), indicating that CAD may modulate lignin composition in pine. The recessive
            cad-n1
            allele, which causes this phenotype, was discovered in a tree heterozygous for this mutant allele. It is inherited as a simple Mendelian locus that maps to the same genomic region as the
            cad
            locus. In mutant plants, CAD activity and abundance of
            cad
            RNA transcript are low, and free CAD substrate accumulates to a high level. The wood of the mutant is brown, whereas the wood in wild types is nearly white. The wood phenotype resembles that of brown midrib (
            bm
            ) mutants and some transgenic plants in which xylem is red-brown due to a reduction in CAD activity. However, unlike transgenics with reduced CAD, the pine mutant has decreased lignin content. Wood in which the composition of lignin varies beyond previous expectations still provides vascular function and mechanical support.
          }, number={15}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={MacKay, JJ and OMalley, DM and Presnell, T and Booker, FL and Campbell, MM and Whetten, RW and Sederoff, RR}, year={1997}, month={Jul}, pages={8255–8260} }
 @article{mackay_liu_whetten_sederoff_o'malley_1995, title={Genetic analysis of cinnamyl alcohol dehydrogenase in loblolly pine: Single gene inheritance, molecular characterization and evolution}, volume={247}, number={5}, journal={Molecular and General Genetics}, author={MacKay, J. J. and Liu, W. W. and Whetten, R. and Sederoff, R. R. and O'Malley, D. M.}, year={1995}, pages={537} }