About
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Introduction
My research interests cover a broad range of topics in forestry, plant biology, and biochemistry. Current research in my group follows three general themes:
- Development of genomic resources for the study of gymnosperms, particularly conifers
- Understanding forest health problems, including pest and disease resistance as well as abiotic stress, at the level of molecular mechanisms
- Studies of xylem development as it pertains to the character of 'woodiness' across plant species
Current institution
Additional affiliations
October 2008 - July 2014
July 2001 - June 2006
May 1996 - June 2001
Education
September 1980 - November 1986
September 1976 - June 1980
Publications
Publications (129)
![FIGURE 2 Percent absorption of [ 14 C]2,4-D on cotton seedlings of...](publication/364234576/figure/fig2/AS:11431281088531129@1665156091536/Percent-absorption-of-14-C2-4-D-on-cotton-seedlings-of-TM-1-CS-B15sh-31-4_Q320.jpg)
![Translocation of [ 14 C]2,4-D in the cotton accessions after 24 h of...](publication/364234576/figure/tbl1/AS:11431281088531130@1665156091836/Translocation-of-14-C2-4-D-in-the-cotton-accessions-after-24-h-of-treatment-a_Q320.jpg)
Upland cotton is sensitive to 2,4-dichlorophenoxyacetic acid (2,4-D), and spray drift from adjacent crops can cause yield loss. The identification of potentially 2,4-D-tolerant cotton chromosome substitution (CS) lines with well-characterized tolerance mechanisms could provide a significant step into the development and genetic improvement of uplan...
The cotton chromosome substitution line, CS-B15sh, exhibits 41% lower injury from 2,4-D when applied at the field recommended rate of 1.12 kg ae ha⁻¹ (1×) than does Texas Marker-1 (TM-1). CS-B15sh was developed in the genetic background of Gossypium hirsutum L. cv TM-1 and has chromosome introgression on the short arm of chromosome 15 from Gossypiu...
Upland cotton is sensitive to 2,4-dichlorophenoxyacetic acid (2,4-D), and the identification of potentially 2,4-D tolerant cotton chromosome substitution (CS) lines and understanding tolerance mechanisms provide a significant step into the development and genetic improvement of upland cotton to reduce yield loss caused by 2,4-D herbicide effects in...
Sirex noctilio F. (Hymenoptera: Siricidae) is a major exotic pest of pines (Pinus spp.) in the Southern Hemisphere and has become established in northeastern North America. We investigated the suitability of bolts of six economically and ecologically important U.S. pine species grown in the southeastern United States, including eastern white (P. st...
Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive,...
Significance:
The woodwasp Sirex noctilio is an invasive species in many parts of the world, including Australia and North America, where it is considered within the top 10 most serious forest insects. Where they have been introduced, the female woodwasps attack living pine trees, causing significant economic losses. Central to this destruction is...
Background
During their lifetime, conifer trees are exposed to numerous herbivorous insects. To protect themselves against pests, trees have developed a broad repertoire of protective mechanisms. Many of the plant’s defence reactions are activated upon an insect attack, and the underlying regulatory mechanisms are not entirely understood yet, in pa...
During oviposition, female Sirex noctilio (F.) (Siricidae) woodwasps inject their conifer hosts with a venom gland secretion. The secretion induces a variety of host physiological changes that facilitate subsequent lethal infection by a symbiotic fungus. A heat-stable factor that can migrate from the site of oviposition in the trunk through the xyl...
The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination.
We develop a novel strategy to sequence the genome of loblolly pine that combines unique asp...
It is during embryogenesis that the plant body plan is established and the meristems responsible for all post-embryonic growth are specified. The molecular mechanisms governing conifer embryogenesis are still largely unknown. Their elucidation may contribute valuable information to clarify if the distinct features of embryo development in angiosper...
Background
Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for tim...
Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation...
Conifers comprise an ancient and widespread plant lineage of enormous commercial and ecological value. However, compared to model woody angiosperms, such as Populus and Eucalyptus, our understanding of conifers remains quite limited at a genomic level. Large genome sizes (10,000–40,000 Mbp) and large amounts of repetitive DNA have limited efforts t...
Sirex noctilio F., a Eurasian horntail woodwasp recently introduced into North America, oviposits in pines and other conifers and in the process spreads a phytopathogenic fungus that serves as a food source for its larvae. During oviposition the woodwasp also deposits mucus produced in its acid (venom) gland that alters pine defense responses and f...
Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation...
Phenylalanine ammonia lyase (PAL) is a key enzyme of the phenylpropanoid pathway that catalyzes the deamination of phenylalanine to trans-cinnamic acid, a precursor for the lignin and flavonoid biosynthetic pathways. To date, PAL genes have been less extensively studied in gymnosperms than in angiosperms. Our interest in PAL genes stems from their...
Nucleotide sequences used for analysis. The given file contains sequences downloaded from the public database for angiosperms and few of the gymnosperms. It also contains assembled consensus sequences for gymnosperms. These sequences were used for getting amino acid as well as codons for evolutionary analysis. Primers specific to PtPAL were designe...
Sirex noctilio uses an unusual, two-component approach to kill pine trees and provide a source of nutrition for its developing larvae. A
substantial amount of research was undertaken in the 1960s and 1970s to examine the mechanisms by which these two components
– a mucus produced in the woodwasp acid – (venom) gland, and a pathogenic fungus, Amylos...
We assessed the colonization and oviposition preferences of an exotic woodwasp species, Sirex noctilio Fabricius, in 2010 on six southeastern pine species. Specifically, we focused on loblolly, shortleaf, slash, longleaf, eastern white, and Virginia pine with Scots pine as a control species. We conducted host choice and no-choice experiments on S....
Phenylalanine ammonia lyase (PAL) is a key enzyme of the phenylpropanoid pathway. PAL genes are less extensively studied in gymnosperms than angiosperms. Our interest in the PAL genes in Pinus taeda stems from their potential role in pine defense mechanisms. Despite the number of characterized gymnosperm PAL genes, the functional diversity of these...
RNA transcripts are the first discrete products on the path linking genomes to function and phenotype. Thus, characterization of the transcriptome, which is the sum total of all transcripts produced from the genome, establishes the cast of players working on the cellular stage to create a biological outcome. The enormity of conifer genomes has so f...
Rapid advancement of the ‘omic’ sciences has resulted from the recent development of new technologies driven in large part by investment from the human biomedical arena. Thus, in considering what might lie ahead for conifer genomics, current and near-future genomic research in human biomedicine provides a good yardstick. This chapter relates curren...
Global transcriptional analysis of loblolly pine (Pinus taeda L.) is challenging due to limited molecular tools. PtGen2, a 26,496 feature cDNA microarray, was fabricated and used to assess drought-induced gene expression in loblolly pine propagule roots. Statistical analysis of differential expression and weighted gene correlation network analysis...
Microarray reference sample composition. This file shows the composition of the microarray reference sample used in all hybridizations. And includes information regarding the tissue, maternal genotype, treatment, tissue origin, and mass of total RNA used to make the reference standard. NA = not applicable, WW = well-watered, DS = drought stressed,...
This Excel file contains the complete PtGen2 master file including annotations and print tip information (3A), the list of duplicate spotted validation cDNAs and buffer blanks that were excluded from statistical analysis (3B), and 251 probes removed from statistical analysis since they mapped to contigs already represented by other cDNAs. 3A (PtGen...
R-script code for WGCNA. This file contains the modified R-script code used to perform WGCNA for generation of the loblolly pine root transcriptome gene network.
Quantitative PCR analysis of highly differentially expressed genes and moderately expressed transcription factors. This file contains the results of qPCR analysis performed on 16 genes that were used to compare fold expression levels with those determined using PtGen2. RT-qPCR values were corrected to Actin 1 gene for each sample. For each treatmen...
Primer pair sets used in the RT-qPCR analysis. This file contains the sequences of primer pairs used in qPCR analysis. Gene ID = unique probe address (metarow, metacolumn, row, column), UniScript = Fungen assembly contig ID.
R-correlation analysis of 384 replicated probes. This file contains the results of an R-correlation analysis of BRB filtered log2 ratios for a set of 384 replicate probes on PtGen2.
Sample ID = CCLONE genotype identifier followed by treatment, WW = well-watered, DS = drought-stressed, DR = drought plus 48 hr recovery. Six paired hybridizations were...
Expression Results for differentially expressed genes (DEGs) identified after interrogation of PtGen2. This Excel file contains three separate sheets that list the normalized log2 mean ratios for differentially expressed genes exhibiting at least a 1.5-fold difference obtained after pair wise comparisons for each of the three water availability tre...
Gene correlation analysis and module membership data generated using WGCNA. This file contains the WGCNA module memberships for the 2445 differentially expressed genes identified in the drought stressed versus well-watered analysis as well as log2 mean ratios and BlastX annotation information. Each module color represents a grouping of genes whose...
Promoters from an ACC oxidase gene (PtACO1) and its nearly identical paralog (NIP) (PtACO2) of loblolly pine (Pinus taeda L.) were recovered from genomic DNA using PCR amplification. Transgenic Arabidopsis plants harboring genetic constructs from which beta-glucuronidase (GUS) expression was driven by the full-length (pACO1:GUS, pACO2:GUS) or trunc...
1-Aminocyclopropane-1-carboxylate (ACC) oxidase catalyzes the final reaction of the ethylene biosynthetic pathway, converting the unusual cyclic amino acid, ACC, into ethylene. Past studies have shown a possible link between ethylene and compression wood formation in conifers, but the relationship has received no more than modest study at the gene...
Tissues isolated from conifer species, particularly those belonging to the Pinaceae family, such as loblolly pine (Pinus taeda L.), contain high concentrations of phenolic compounds and polysaccharides that interfere with RNA purification. Isolation of high-quality RNA from these species requires rigorous tissue collection procedures in the field a...
PtGen2 is a 26,496 feature cDNA microarray containing amplified loblolly pine ESTs. The array is produced in our laboratory for use by researchers studying gene expression in pine and other conifer species. PtGen2 was developed as a result of our gene discovery efforts in loblolly pine, and is comprised of sequences identified primarily from root t...
Loblolly pine (Pinus taeda L.), the most widely planted tree species in the United States, is an important source of wood and wood fibers for a multitude of consumer products. Wood fibers are primarily composed of secondary cell walls, and cellulose, hemicelluloses and lignin are major components of wood. Fiber morphology and cell wall composition...
1-Aminocyclopropane-1-carboxylate (ACC) synthase catalyzes what is typically the rate-limiting step in the biosynthesis of ethylene, a gaseous plant growth regulator that plays numerous roles in the growth and development of higher plants. Although ACC synthase genes have been characterized from a wide variety of angiosperm plant species, no ACC sy...
Expressed sequence tags (ESTs) remain a dominant approach for characterizing the protein-encoding portions of various genomes.
Due to inherent deficiencies, they also present serious challenges for data quality control. Before GenBank submission, EST
sequences are typically screened and trimmed of vector and adapter/linker sequences, as well as pol...
With the advent of low-cost, high-throughput sequencing, the amount of public domain Expressed Sequence Tag (EST) sequence data available for both model and non-model organism is growing exponentially. While these data are widely used for characterizing various genomes, they also present a serious challenge for data quality control and validation d...
The forest products industry has traditionally viewed trees as merely a raw, and more or less immutable, natural resource.
However, unlike such inanimate resources as metallic ores, trees have the potential to be modified genetically, essentially
transmuting lead into gold. Increasingly, modern alchemists are applying the tools of biotechnology in...
Drought stress is the principal cause of seedling mortality in pine forests of the southeastern United States and in many other forested regions around the globe. As part of a larger effort to discover loblolly pine genes, this study subjected rooted cuttings of three unrelated pine genotypes to three watering regimens. Expressed sequence tags (EST...
Genomic techniques and technologies are revolutionizing the biological sciences, and the impact that this new approach to biology will have on forestry will be nothing short of profound. A hallmark of the genomic sciences is rapid release of large datasets to the public via the Internet with the expectation that important and useful information wil...
Arabidopsis thaliana root transcriptome responses to the munition, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), were assessed using serial analysis of gene expression (SAGE). Sequencing of SAGE libraries from control and RDX-exposed root tissues revealed induction of genes known to respond to a variety of general stresses. Among the highly induce...
Arabidopsis thaliana root transcriptome responses to the munition, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), were assessed using serial analysis of gene expression (SAGE). Sequencing of SAGE libraries from control and RDX-exposed root tissues revealed induction of genes known to respond to a variety of general stresses. Among the highly induce...
Completed genome sequences have made it clear that multicopper oxidases related to laccase are widely distributed as multigene families in higher plants. Laccase-like multicopper oxidase (LMCO) sequences culled from GenBank and the Arabidopsis thaliana genome, as well as those from several newly cloned genes, were used to construct a gene phylogeny...
Introduction
Potential Applications
Challenges
Historical Outline
Chemistry
Biology
Lignin Mutants
Brown Midrib Monocots
Loblolly Pine
Arabidopsis
Lignin Transgenics
The Shikimate Pathway and Phenylalanine Ammonia Lyase
Cinnamate 4‐Hydroxylase and 4‐Coumarate‐3‐Hydroxylase
4‐Coumarate:CoA Ligase
O ‐Methyltransferases
Cinnamoyl‐CoA Re...
Sequence-based transcriptional profiling reveals unexpected transcriptome complexity in Arabidopsis thaliana and an enhanced gene catalog to facilitate genome annotation.
On or before Jul 29, 2011 this sequence version replaced gi:50363317, gi:50363318, gi:50363316.
On or before Jul 29, 2011 this sequence version replaced gi:50363321, gi:50363322, gi:50363323, gi:50363320.
On or before Jul 29, 2011 this sequence version replaced gi:51557333, gi:51557334, gi:51557332.
On or before Jul 29, 2011 this sequence version replaced gi:50363357, gi:50363358, gi:50363359, gi:50363356.
On or before Jul 29, 2011 this sequence version replaced gi:50363312, gi:50363313, gi:50363314, gi:50363311.
On or before Jul 29, 2011 this sequence version replaced gi:50363342, gi:50363343, gi:50363344, gi:50363341.
On or before Jul 29, 2011 this sequence version replaced gi:50363331, gi:50363332, gi:50363333, gi:50363330.
On or before Jul 29, 2011 this sequence version replaced gi:50363347, gi:50363348, gi:50363349, gi:50363346.
On or before Jul 29, 2011 this sequence version replaced gi:50363352, gi:50363353, gi:50363354, gi:50363351.
On or before Jul 29, 2011 this sequence version replaced gi:50363362, gi:50363363, gi:50363364, gi:50363361.
On or before Jul 29, 2011 this sequence version replaced gi:50363326, gi:50363327, gi:50363328, gi:50363325.
On or before Jul 29, 2011 this sequence version replaced gi:50363336, gi:50363337, gi:50363335.
Ferroxidase activity was detected in a laccase-like multicopper oxidase (LMCO) produced in transgenic tobacco cells expressing an LMCO cDNA (Ltlacc2.2) cloned from yellow-poplar (Liriodendron tulipifera). This marks the first report of ferroxidase activity associated with a plant laccase and suggests that some members of this plant enzyme family ma...
Transcriptional profiling in plants using SAGE has so far been limited mostly to a handful of important model systems: Arabidopsis, rice, maize, tobacco and pine. However, the technique has been used to study a great diversity of plant responses, including pathogen resistance, environmental and nutritional stress responses, and the metabolism of to...
Ferroxidase activity was detected in a laccase-like multicopper oxidase (LMCO) produced in transgenic tobacco cells expressing an LMCO cDNA (Lt/acc2.2) cloned from yellow-poplar (Liriodendron tulipifera). This marks the first report of ferroxidase activity associated with a plant laccase and suggests that some members of this plant enzyme family ma...
Serial analysis of gene expression was used to profile transcript levels in Arabidopsis roots and assess their responses to 2,4,6-trinitrotoluene (TNT) exposure. SAGE libraries representing control and TNT-exposed seedling root transcripts were constructed, and each was sequenced to a depth of roughly 32,000 tags. More than 19,000 unique tags were...
Wood formation has been studied extensively at the cellular and biochemical levels, but remains poorly understood with respect to gene expression and regulation. As a first step toward identifying genes specifically involved in wood formation and characterizing their roles in determining wood quality, serial analysis of gene expression (SAGE) was u...
Wood formation has been studied extensively at the cellular and biochemical levels, but remains poorly understood with respect to gene expression and regulation. As a first step toward identifying genes specifically involved in wood formation and characterizing their roles in deter-mining wood quality, serial analysis of gene expression (SAGE) was...
Wood formation has been studied extensively at the cellular and biochemical levels, but remains poorly understood with respect to gene expression and regulation. As a first step toward identifying genes specifically involved in wood formation and characterizing their roles in determining wood quality, serial analysis of gene expression (SAGE) was u...
A gene (yacK) encoding a putative multicopper oxidase (MCO) was cloned from Escherichia coli, and the expressed enzyme was demonstrated to exhibit phenoloxidase and ferroxidase activities. The purified protein contained
six copper atoms per polypeptide chain and displayed optical and electron paramagnetic resonance (EPR) spectra consistent
with the...
A new chromogenic substrate for laccases and peroxidases, 1,8-diaminonapthalene, was used to detect phenoloxidase activity in gels after SDS-PAGE. This substrate has several advantages over other widely used phenoloxidase stains in that it is inexpensive, and the oxidized product has both high molar absorptivity and very low solubility. Furthermore...
The past year has seen the fruits of biotechnological manipulation of forest trees approach commercial application. Advances in somatic embryogenesis have brought mass clonal propagation of the top commercial trees closer to reality, and efficient gene transfer systems have been developed for a number of conifers and hardwoods. Radical alterations...
Hydrogen peroxide is required for a variety of physiological processes associated with plant cell wall biosynthesis. Several recent studies have suggested that starch-KI could be used as an effective histochemical stain for studying the spatial and temporal regulation of H2O2 production during plant development. In this study, we found that detecti...
Four closely related cDNA clones encoding laccase isoenzymes from xylem tissues of yellow-poplar (Ltlacc2.1-4) were identified and sequenced. The inferred yellow-poplar laccase gene products were highly related to one another (79-91% at the amino acid level) and showed significant similarity to other blue copper oxidases, especially with respect to...
A sweetgum (Liquidambar styraciflua) nodule culture system was developed and integrated with genetic transformation by microprojectile bombardment. Nodule cultures
were established from seedling hypocotyls and proliferated in liquid medium containing 0.1 mg (0.45 µM) thidiazuron (TDZ) per 1 and 0.01 mg (0.045 µM) 2,4-dichlorophenoxyacetic acid (2,4...
Forest Products Biotechnology
edited by Alan Bruce and John W. Palfreyman, Taylor & Francis, 1998. UK£49.95 hbk (xi+326 pages) ISBN 0 74840 415 5
Lignin is formed via the oxidative polymerization of monolignols within the plant cell wall matrix. Peroxidases, which are abundant in virtually all cell walls, can oxidize the monolignols in the presence of H2O2, and have long been held to be the principal catalysts for this reaction. Recent evidence shows, however, that laccases (p-diphenol: O2 o...
It was recently shown that the white rot basidiomycete Pycnoporus cinnabarinus secretes an unusual set of phenoloxidases when it is grown under conditions that stimulate ligninolysis (C. Eggert, U. Temp, and K.-E. L. Eriksson, Appl. Environ. Microbiol. 62:1151-1158, 1996). In this report we describe the results of a cloning and structural analysis...
The forest products industry has traditionally viewed trees as merely a raw, and more or less immutable, natural resource. However, unlike such inanimate resources as metallic ores, trees have the potential to be modified genetically, essentially transmuting lead into gold. Increasingly, modern alchemists are applying the tools of biotechnology in...
The cloning, sequencing, and expression in E. coli of a gene from the hyperthermophile, Thermatoga maritima, encoding a thermostable xylanase is reported. The enzyme is active at 100°C for several hours and efficient in releasing lignin from kraft pulp. Comparison of the T. maritima recombinant enzyme with a commercially available xylanase, Pulpzym...
Lignin peroxidase is generally considered to be a primary catalyst for oxidative depolymerization of lignin by white-rot fungi. However, some white-rot fungi lack lignin peroxidase. Instead, many produce laccase, even though the redox potentials of known laccases are too low to directly oxidize the non-phenolic components of lignin. Pycnoporus cinn...
The phenoxazinone chromophore occurs in a variety of biological systems, including numerous pigments and certain antibiotics. It also appears to form as part of a mechanism to protect mammalian tissue from oxidative damage. During cultivation of the basidiomycete, Pycnoporus cinnabarinus, a red pigment was observed to accumulate in the culture medi...
Cerium is becoming an increasingly popular reagent for histochemical localization of oxidases and phosphatases because it combines directly with reaction products to form fine precipitates of electron-dense materials that can be easily detected using transmission electron microscopy or laser confocal scanning microscopy. We used epi-polarization mi...
Indirect ELISA was used to quantify (+)-abscisic acid (ABA) in developing zygotic embryo and megagametophyte tissues from
two loblolly pine (Pinus taeda L.) mother trees. On a dry weight basis, embryonic and megagametophytic ABA concentrations were highest during early development
and decreased steadily to their lowest values at cone ripening. Embr...
Questions
Question (1)
This is a question I frequently pose to graduate students for their oral examinations or thesis defense. Its purpose is to remind them that the definition varies considerably depending on whether you were trained primarily as a geneticist, biochemist, molecular biologist or a bioinformatician. With the increasing accessibility of next-gen sequencing data for researchers from all these disciplines it is ever more important that we define the parameters for what constitutes a "gene" in any conversation where these disciplines overlap. In that spirit, it may be a worthy exercise to start a thread to which researchers contribute their personal working definitions for what constitutes a gene. The differences and commonalities should prove informative for those who are trying to wrap their heads around the concept.
