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In JoVE (2)
- Обработка Лоблолли Пайн PtGen2 кДНК Microarray
- Улучшенный метод выделения РНК из Лоблолли Пайн ( П. taeda L.) и других хвойных пород
Other Publications (4)
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Articles by W. Walter Lorenz in JoVE
JoVE General
Обработка Лоблолли Пайн PtGen2 кДНК Microarray
1Warnell School of Forestry and Natural Resources, University of Georgia (UGA), 2Instituto de Biologia Experimental e Tecnológica, Instituto Tecnologia Química e Biológica UNL, Av. da República
КДНК микрочипов PtGen2 был разработан для изучения экспрессии генов в ладанной сосна,
JoVE General
Улучшенный метод выделения РНК из Лоблолли Пайн ( П. taeda L.) и других хвойных пород
Warnell School of Forestry and Natural Resources, University of Georgia (UGA)
Многие ткани растений, в том числе флоэмы и ксилемы от ладанной сосны (
Other articles by W. Walter Lorenz on PubMed
SAGE Profiling and Demonstration of Differential Gene Expression Along the Axial Developmental Gradient of Lignifying Xylem in Loblolly Pine (Pinus Taeda)
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 used to quantify gene expression in lignifying xylem from a single, 10-year-old loblolly pine (Pinus taeda L.). Two SAGE libraries were generated based on lignifying xylem isolated from either the upper (crown) or lower (base) portions of the trunk. Over 85,000 tags representing a maximum of 27,398 expressed genes were analyzed from the crown wood library, and more than 65,000 tags, representing a maximum of 25,983 expressed genes, were analyzed in the base wood library. Combining these data sets to reflect the sum of genes expressed in lignifying xylem, 150,855 tags were cataloged, representing a maximum of 42,641 different genes. Currently, this study represents the most extensive analysis of its kind in a higher plant and provides a quantitative description of the transcriptome representing the lignifying xylem of a 10-year-old loblolly pine.
SAGE Analysis of Transcriptome Responses in Arabidopsis Roots Exposed to 2,4,6-trinitrotoluene
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 identified overall. The second most highly induced tag (27-fold increase) represented a glutathione S-transferase. Cytochrome P450 enzymes, as well as an ABC transporter and a probable nitroreductase, were highly induced by TNT exposure. Analyses also revealed an oxidative stress response upon TNT exposure. Although some increases were anticipated in light of current models for xenobiotic metabolism in plants, evidence for unsuspected conjugation pathways was also noted. Identifying transcriptome-level responses to TNT exposure will better define the metabolic pathways plants use to detoxify this xenobiotic compound, which should help improve phytoremediation strategies directed at TNT and other nitroaromatic compounds.
Water Stress-responsive Genes in Loblolly Pine (Pinus Taeda) Roots Identified by Analyses of Expressed Sequence Tag Libraries
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 (ESTs) were obtained from both the 3' and 5' ends of 12,918 randomly selected cDNAs generated from root tissues. These ESTs were clustered to identify 6,765 unique transcripts (UniScripts) derived from 6,202 putative unique genes (UniGenes-S). Tentative annotations were assigned on the basis of BLASTX comparisons to the Protein Information Resource Nonredundant Reference (PIR-NREF) database. Expression levels of 42 UniScripts varied with high statistical significance with respect to treatment. Many of them resembled gene products shown to be important for drought tolerance in other species, including dehydrins, endochitinases, cytochrome P450 enzymes, pathogenesis-related proteins and various late-embryogenesis abundant (LEA) gene products. Similarly, expression levels of 110 UniScripts varied with high statistical significance among genotypes, indicating that gene expression patterns in this species are much more dependent on genotype than on treatment. Most of the water stress-induced pine UniScripts that appeared to encode products resembling drought tolerance factors in other species were most highly induced in a single genotype, suggesting that particularly useful adaptive alleles for drought tolerance might exist within the collection of cDNAs characterized from this genotype. Mining and visualizing the complete data set, as well as downloading of both EST and UniScript contig sequences, are possible using MAGIC Gene Discovery at http://fungen.org/genediscovery/.
Microarray Analysis and Scale-free Gene Networks Identify Candidate Regulators in Drought-stressed Roots of Loblolly Pine (P. Taeda L.)
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 were used to identify drought-responsive genes and further characterize the molecular basis of drought tolerance in loblolly pine.
