@article{torbati_totapally_raszynski_osborne_zyl_kalomiris_wolfsdorf_2008, title={Age and Sex Differences in Brain Gene Expression in Neonatal Rats}, volume={39}, ISSN={0174-304X 1439-1899}, url={http://dx.doi.org/10.1055/s-0028-1105923}, DOI={10.1055/s-0028-1105923}, abstractNote={& Gene expression in the central nervous system is highly region-speci fi c. We tested the hypothesis that certain developmental biomarkers could be detected in the whole brain or in cortical, subcortical or cerebellar structures. Brain gene expressions of male and female rats at birth, 3 days, and 10 days of age were measured by micro-array technique ( (cid:1) 10 K genes; n = 9 / category). We found 53 signi fi cantly up-regulated and 8 down-regulated genes at 10 days}, number={04}, journal={Neuropediatrics}, publisher={Georg Thieme Verlag KG}, author={Torbati, D. and Totapally, B. and Raszynski, A. and Osborne, J. and Zyl, L. van and Kalomiris, S. and Wolfsdorf, J.}, year={2008}, month={Aug}, pages={219–225} }
 @article{heller_adomas_li_osborne_van zyl_sederoff_finlay_stenlid_asiegbu_2008, title={Transcriptional analysis of Pinus sylvestris roots challenged with the ectomycorrhizal fungus Laccaria bicolor}, volume={8}, journal={BMC Plant Biology}, author={Heller, G. and Adomas, A. and Li, G. S. and Osborne, J. and Van Zyl, L. and Sederoff, R. and Finlay, R. D. and Stenlid, J. and Asiegbu, F. O.}, year={2008} }
 @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{myburg_morse_amerson_kubisiak_huber_osborne_garcia_nelson_davis_covert_et al._2006, title={Differential gene expression in loblolly pine (Pinus taeda L.) challenged with the fusiform rust fungus, Cronartium quercuum f.sp fusiforme}, volume={68}, ISSN={["0885-5765"]}, DOI={10.1016/j.pmpp.2006.07.002}, abstractNote={Cronartium quercuum f.sp. fusiforme is the pathogen that incites fusiform rust disease of southern pine species. To date, a number of host resistance genes have been mapped. Although genomic mapping studies have provided valuable information on the genetic basis of disease interactions in this pine-rust pathosystem, the interaction at the molecular level is poorly understood. To further our understanding of this interaction, we implemented a microarray study to examine the differential expression of genes in pathogen-challenged progeny of a full-sib loblolly pine family known to be segregating at a single dominant resistance gene (Fr1). Statistical analyses revealed shifts in gene expression that may reflect discrete stages of gall development.}, number={1-3}, journal={PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY}, author={Myburg, Henrietta and Morse, Alison M. and Amerson, Henry V. and Kubisiak, Thomas L. and Huber, Dudley and Osborne, Jason A. and Garcia, Saul A. and Nelson, C. Dana and Davis, John M. and Covert, Sarah F. and et al.}, year={2006}, pages={79–91} }
 @article{zelena_sorochinsky_arnold_zyl_clapham_2005, title={Indications of limited altered gene expression in Pinus sylvestris trees from the Chernobyl region}, volume={84}, ISSN={["1879-1700"]}, DOI={10.1016/j.jenvrad.2005.03.008}, abstractNote={To evaluate the consequences of irradiation on the vegetation of the Chernobyl region, gene expression was compared in morphologically normal and dwarf needles from the same Pinus sylvestris trees in a region where the absorbed dose was 3-5 Gy. To compare the levels of gene expression, arrays consisting of 373 Pinus taeda cDNAs were hybridized with labeled cDNA derived from normal and dwarf needles of P. sylvestris. Twelve genes were significantly (P<0.01) up- or down-regulated between normal and dwarf needles for all five trees taken together. Five of these, related to stress or development, were up- or down-regulated 1.25-1.7-fold in the dwarf needles. There were no significant differences in (137)Cs content in the normal and dwarf needles, or in elongation growth rate of seedlings raised under controlled conditions from seed derived from trees in the region that had received a radiation dose over the range 2-12 Gy.}, number={3}, journal={JOURNAL OF ENVIRONMENTAL RADIOACTIVITY}, author={Zelena, L and Sorochinsky, B and Arnold, S and Zyl, L and Clapham, DH}, year={2005}, pages={363–373} }
 @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} }
 @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{yang_zyl_no_loopstra_2004, title={Microarray analysis of genes preferentially expressed in differentiating xylem of loblolly pine (Pinus taeda)}, volume={166}, ISSN={["0168-9452"]}, DOI={10.1016/j.plantsci.2003.12.030}, abstractNote={Wood formation (xylogenesis) is a critical developmental process for all woody land plants. As an initial step to understand the molecular basis for temporal and spatial regulation of xylogenesis and the effect of the expression of individual genes on physical and chemical properties of wood, we compared transcript profiles of differentiating loblolly pine xylem with needles, megagametophytes, and embryos. A microarray containing approximately 1500 ESTs with putative functions of interest, selected from loblolly pine normal wood, compression wood, late wood and planings (deeper cell layers) xylem cDNA libraries, was constructed and screened. Using a P-value = 0.01, 440 genes in the xylem versus megagametophyte, 401 genes in the xylem versus embryo and 191 genes in the xylem versus needle tissue comparisons were identified as differentially expressed genes. Among these, 204 genes in the xylem versus megagametophyte, 178 genes in the xylem versus embryo and 85 genes in the xylem versus needle tissue comparisons were identified as genes preferentially expressed in xylem. Real-time RT-PCR was used to test overall validity of the microarray data.}, number={5}, journal={PLANT SCIENCE}, author={Yang, SH and Zyl, L and No, EG and Loopstra, CA}, year={2004}, month={May}, pages={1185–1195} }
 @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} }
 @article{stasolla_scott_egertsdotter_kadla_d o'malley_sederoff_zyl_2003, title={Analysis of lignin produced by cinnamyl alcohol dehydrogenase-deficient Pinus taeda cultured cells}, volume={41}, ISSN={["0981-9428"]}, DOI={10.1016/S0981-9428(03)00051-2}, abstractNote={Comparative studies were conducted on composition of lignin produced both in vivo and in vitro by cinnamyl alcohol dehydrogenase (CAD)-deficient mutant loblolly pine (Pinus taeda L.). In vivo studies were performed using differentiating xylem obtained from two genotypes of heterozygous (CAD/cad) and two genotypes of homozygous (cad/cad) CAD-deficient mutant trees. In vitro studies were performed using a culture system in which cells, generated from the same genotypes, were induced to produce lignin in culture. Steady state RNA levels and enzyme activity of CAD were dramatically reduced in both xylem and cultured cells obtained from homozygous mutant trees, compared to their heterozygous counterparts. Light microscopic studies showed pronounced differences during the lignin formation between homozygous and heterozygous cells. Phenolic compounds in the heterozygous (CAD/cad) cells were deposited around the cell wall, accumulated preferentially in vacuoles of the homozygous (cad/cad) cells. Differences in lignin composition as revealed by thioacidolysis were also observed. Lignin of both xylem tissue and cultured cells obtained from CAD-deficient homozygotes showed lower levels of coniferyl alcohols and significant enrichments in dihydroconiferyl alcohol (DHCA) and coniferyl aldehyde, compared to their heterozygous counterparts. The striking similarities in lignin composition observed both in vivo and in vitro, open new possibilities for the use of culture systems aimed at revealing the mechanisms controlling lignin biosynthesis, and the formation of DHCA subunits.}, number={5}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, author={Stasolla, C and Scott, J and Egertsdotter, U and Kadla, J and D O'Malley and Sederoff, R and Zyl, L}, year={2003}, month={May}, pages={439–445} }
 @article{watkinson_sioson_vasquez-robinet_shukla_kumar_ellis_heath_ramakrishnan_chevone_watson_et al._2003, title={Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine}, volume={133}, DOI={10.1104/pp.103026914}, number={4}, journal={Plant Physiology}, author={Watkinson, J. I. and Sioson, A. A. and Vasquez-Robinet, C. and Shukla, M. and Kumar, D. and Ellis, M. and Heath, L. S. and Ramakrishnan, N. and Chevone, B. and Watson, L. T. and et al.}, year={2003}, pages={1702–1716} }
 @article{stasolla_zyl_egertsdotter_craig_liu_sederoff_2003, title={The effects of polyethylene glycol on gene expression of developing white spruce somatic embryos}, volume={131}, ISSN={["1532-2548"]}, DOI={10.1104/pp.015214}, abstractNote={Abstract}, number={1}, journal={PLANT PHYSIOLOGY}, author={Stasolla, C and Zyl, L and Egertsdotter, U and Craig, D and Liu, WB and Sederoff, RR}, year={2003}, month={Jan}, pages={49–60} }
 @article{stasolla_zyl_egertsdotter_craig_liu_sederoff_2003, title={Transcript profiles of stress-related genes in developing white spruce (Picea glauca) somatic embryos cultured with polyethylene glycol}, volume={165}, ISSN={["0168-9452"]}, DOI={10.1016/S0168-9452(03)00228-0}, abstractNote={The effect of polyethylene glycol (PEG) on the transcript level of 512 stress-related genes was analyzed by cDNA microarray. Major changes in gene expression between control and PEG-treated embryos were observed during the initial stages of development, upon transfer of the embryogenic tissue on maturation medium, and during the late phases of development, culminating with the generation of cotyledonary embryos. Only small changes in gene expression were observed during the intermediate phases of embryo development. The transcript levels of several genes involved in cell aging and detoxification mechanisms, including peroxidases and chitinases, were developmentally regulated during the embryogenic process. Major differences in the expression of these genes were observed between control and PEG-treated embryos. Based on their expression profiles, four different clusters of genes involved in stress response mechanisms were identified. The first group of genes, which included several heat shock proteins, was up-regulated in PEG-treated immature embryos. An opposite tendency was observed for a second cluster of genes, which included a glutathione-S-transferase, and a cysteine protease. The third class included genes repressed by PEG in fully developed embryos, whereas a fourth group of genes, which included several heat shock proteins and ubiquitin, was induced in PEG-treated embryos at the end of the culture period. Difference in transcript levels and profiles of several genes involved in cell wall and lignin biosynthesis were also observed between control and PEG-treated embryos.}, number={4}, journal={PLANT SCIENCE}, author={Stasolla, C and Zyl, L and Egertsdotter, U and Craig, D and Liu, WB and Sederoff, RR}, year={2003}, month={Oct}, pages={719–729} }
 @article{zyl_bozhkov_clapham_sederoff_arnold_2003, title={Up, down and up again is a signature global gene expression pattern at the beginning of gymnosperm embryogenesis}, volume={3}, ISSN={["1567-133X"]}, DOI={10.1016/S1567-133X(02)00068-6}, abstractNote={Somatic embryogenesis of a gymnosperm, Picea abies, represents a sequence of specifically regulated developmental stages including proembryogenic mass (PEM), PEM-to-embryo transition, and early and late embryogeny. Here, we report cDNA array analysis of expression patterns of 373 genes in the beginning of P. abies embryo development. The analysis revealed a group of 107 genes (29% of arrayed cDNAs) which were upregulated upon PEM-to-embryo transition, then downregulated during early embryogeny and finally upregulated again at the beginning of late embryogeny. This major gene expression pattern was abrogated in a developmentally arrested cell line that is unable to pass through the PEM-to-embryo transition. Thirty-five genes (9.4% of arrayed cDNAs) were found to be differentially expressed during normal embryonic pattern formation. Among them, 22 genes (5.9% of arrayed cDNAs) were directly associated with embryo pattern formation and can be considered as marker genes for early stages of P. abies embryogenesis. The majority of the marker genes encode for proteins involved in translation and posttranslational modification. Among them, 18 genes displayed the major expression pattern.}, number={1}, journal={GENE EXPRESSION PATTERNS}, author={Zyl, L and Bozhkov, PV and Clapham, DH and Sederoff, RR and Arnold, S}, year={2003}, month={Mar}, pages={83–91} }
 @article{zyl_arnold_bozhkov_chen_egertsdotter_mackay_sederoff_shen_zelena_clapham_2002, title={Heterologous array analysis in Pinaceae: hybridization of Pinus taeda cDNA arrays with cDNA from needles and embryogenic cultures of P-taeda, P-sylvestris or Picea abies}, volume={3}, ISSN={["1532-6268"]}, DOI={10.1002/cfg.199}, abstractNote={Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation betweenPinusandPiceawe have investigated the use of arrays from one genus for studies of gene expression in the other. The partial cDNAs from 384 identifiable genes expressed in differentiating xylem ofPinus taedawere printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures ofPinus taeda,P. sylvestrisandPicea abies, and with labelled cDNA from leaves ofNicotiana tabacum. The Spearman correlation of gene expression for pairs of conifer species was high for needles (r2= 0.78 − 0.86), and somewhat lower for embryogenic cultures (r2= 0.68 − 0.83). The correlation of gene expression for tobacco leaves and needles of each of the three conifer species was lower but sufficiently high (r2= 0.52 − 0.63) to suggest that many partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous probing was further used to identify tissue-specific gene expression over species boundaries. To evaluate the significance of differences in gene expression, conventional parametric tests were compared with permutation tests after four methods of normalization. Permutation tests after Z-normalization provide the highest degree of discrimination but may enhance the probability of type I errors. It is concluded that arrays of cDNA from loblolly pine are useful for studies of gene expression in other pines or spruces.}, number={4}, journal={COMPARATIVE AND FUNCTIONAL GENOMICS}, author={Zyl, L and Arnold, S and Bozhkov, P and Chen, YZ and Egertsdotter, U and MacKay, J and Sederoff, RR and Shen, J and Zelena, L and Clapham, DH}, year={2002}, month={Aug}, pages={306–318} }