@article{adomas_heller_li_olson_chu_osborne_craig_van zyl_wolfinger_sederoff_et al._2007, title={Trranscript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion}, volume={27}, ISSN={["1758-4469"]}, DOI={10.1093/treephys/27.10.1441}, abstractNote={The mechanisms underlying defence reactions to a pathogen attack, though well studied in crop plants, are poorly understood in conifers. To analyze changes in gene transcript abundance in Pinus sylvestris L. root tissues infected by Heterobasidion annosum (Fr.) Bref. s.l., a cDNA microarray containing 2109 ESTs from P. taeda L. was used. Mixed model statistical analysis identified 179 expressed sequence tags differentially expressed at 1, 5 or 15 days post inoculation. In general, the total number of genes differentially expressed during the infection increased over time. The most abundant group of genes up-regulated upon infection coded for enzymes involved in metabolism (phenylpropanoid pathway) and defence-related proteins with antimicrobial properties. A class III peroxidase responsible for lignin biosynthesis and cell wall thickening had increased transcript abundance at all measurement times. Real-time RT-PCR verified the microarray results with high reproducibility. The similarity of the expression profiling pattern observed in this pathosystem to those documented in crop pathology suggests that angiosperms and gymnosperms use similar genetic programs in responding to invasive growth by microbial pathogens.}, number={10}, journal={TREE PHYSIOLOGY}, author={Adomas, Aleksandra and Heller, Gregory and Li, Guosheng and Olson, Ake and Chu, Tzu-Ming and Osborne, Jason and Craig, Deborah and Van Zyl, Len and Wolfinger, Russ and Sederoff, Ron and et al.}, year={2007}, month={Oct}, pages={1441–1458} }
 @article{wadenback_clapham_craig_sederoff_peter_von arnold_egertsdotter_2005, title={Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays}, volume={6}, number={61}, journal={BMC Genomics}, author={Wadenback, J. and Clapham, D. H. and Craig, D. and Sederoff, R. and Peter, G. F. and Von Arnold, S. and Egertsdotter, U.}, year={2005} }
 @article{brinker_zyl_liu_craig_sederoff_clapham_arnold_2004, title={Microarray analyses of gene expression during adventitious root development in Pinus contorta (1[w])}, volume={135}, ISSN={["1532-2548"]}, DOI={10.1104/pp.103.032235}, abstractNote={Abstract}, number={3}, journal={PLANT PHYSIOLOGY}, author={Brinker, M and Zyl, L and Liu, WB and Craig, D and Sederoff, RR and Clapham, DH and Arnold, S}, year={2004}, month={Jul}, pages={1526–1539} }
 @article{stasolla_belmonte_zyl_craig_liu_yeung_sederoff_2004, title={The effect of reduced glutathione on morphology and gene expression of white spruce (Picea glauca) somatic embryos}, volume={55}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/erh074}, abstractNote={Inclusions of reduced glutathione (GSH) in the maturation medium increased the conversion frequency of white spruce somatic embryos without the need of a partial drying treatment (PDT). This beneficial effect was the result of major alterations in morphology and gene expression during the maturation period. Compared with control embryos, GSH-treated embryos showed a differential accumulation of storage products, i.e. preferential deposition of starch, the reduced formation of protein bodies, and increased vacuolation of cells. These morphological changes correlated with extensive alterations of gene expression occurring throughout the maturation period. The transcript profiles of stage-specific embryos matured with or without GSH were analysed using a DNA microarray containing 2 178 cDNAs from loblolly pine (Pinus taeda). The efficiency of heterologous hybridization between spruce and pine species on microarrays has previously been documented. The results indicate that several genes involved in a variety of signal regulatory pathways were differentially expressed in developing GSH- treated embryos. The transcript levels of many genes involved in carbohydrate metabolism and protein synthesis were altered by the presence of GSH and denoted differences in physiology between treatments. Extensive changes in the expression of genes participating in hormone synthesis, nucleotide metabolism, and meristem formation were also observed and related to the post-embryonic performance of the embryos.}, number={397}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Stasolla, C and Belmonte, MF and Zyl, L and Craig, DL and Liu, WB and Yeung, EC and Sederoff, RR}, year={2004}, month={Mar}, pages={695–709} }
 @article{stasolla_bozhkov_chu_van zyl_egertsdotter_suarez_craig_wolfinger_von arnold_sederoff_2004, title={Variation an transcript abundance during somatic embryogenesis in gymnosperms}, volume={24}, ISSN={["1758-4469"]}, DOI={10.1093/treephys/24.10.1073}, abstractNote={Somatic embryogenesis of Norway spruce (Picea abies L.) is a versatile model system to study molecular mechanisms regulating embryo development because it proceeds through defined developmental stages corresponding to specific culture treatments. Normal embryonic development involves early differentiation of proembryogenic masses (PEMs) into somatic embryos, followed by early and late embryogeny leading to the formation of mature cotyledonary embryos. In some cell lines there is a developmental arrest at the PEM-somatic embryo transition. To learn more about the molecular mechanisms regulating embryogenesis, we compared the transcript profiles of two normal lines and one developmentally arrested line. Ribonucleic acid, extracted from these cell lines at successive developmental stages, was analyzed on DNA microarrays containing 2178 expressed sequence tags (ESTs) (corresponding to 2110 unique cDNAs) from loblolly pine (Pinus taeda L.). Hybridization between spruce and pine species on microarrays has been shown to be effective (van Zyl et al. 2002, Stasolla et al. 2003). In contrast to the developmentally arrested line, the early phases of normal embryo development are characterized by a precise pattern of gene expression, i.e., repression followed by induction. Comparison of transcript levels between successive stages of embryogenesis allowed us to identify several genes that showed unique expression responses during normal development. Several of these genes encode proteins involved in detoxification processes, methionine synthesis and utilization, and carbohydrate metabolism. The potential role of these genes in embryo development is discussed.}, number={10}, journal={TREE PHYSIOLOGY}, author={Stasolla, C and Bozhkov, PV and Chu, TM and Van Zyl, L and Egertsdotter, U and Suarez, MF and Craig, D and Wolfinger, RD and Von Arnold, S and Sederoff, RR}, year={2004}, month={Oct}, pages={1073–1085} }