TY - JOUR TI - Distribution and phenology of Gonolobus suberosus (Apocynaceae, Asclepiadoideae) and its varieties in North America AU - Krings, A. T2 - Vulpia DA - 2006/// PY - 2006/// VL - 5 SP - 24–40 ER - TY - JOUR TI - Four novelties and a lectotypification in Matelea (Apocynaceae, Asclepiadoideae) from Hispaniola AU - Krings, A. T2 - Sida DA - 2006/// PY - 2006/// VL - 22 IS - 2 SP - 941–953 ER - TY - JOUR TI - Notes on types in Apocynaceae – Asclepiadoideae in Cuban herbaria and four lectotypifications in West Indian Gonolobinae AU - Krings, A. AU - Fantz, P.R. T2 - Sida DA - 2006/// PY - 2006/// VL - 22 IS - 1 SP - 533–537 ER - TY - JOUR TI - Cayratia japonica (Vitaceae) new to North Carolina and an updated key to the genera of Vitaceae in the Carolinas AU - Krings, A. AU - Richardson, R.J. T2 - Sida DA - 2006/// PY - 2006/// VL - 22 IS - 1 SP - 813–815 ER - TY - BOOK TI - Manipulation and Expression of Recombinant DNA: A Laboratory Manual AU - Carson, S. AU - Robertson, D. DA - 2006/// PY - 2006/// ET - 2 PB - Academic Press ER - TY - CHAP TI - Phosphoinositide Metabolism: Towards an Understanding of Subcellular Signaling AU - Boss, Wendy F. AU - Davis, Amanda J. AU - Im, Yang Ju AU - Galvão, Rafaelo M. AU - Perera, ImaraY. T2 - Biology of Inositols and Phosphoinositides A2 - Majumber, A.L. A2 - Biswas, B.B. T3 - Subcellular Biochemistry PY - 2006/9/30/ DO - 10.1007/0-387-27600-9_8 SP - 181–205 PB - Springer US SN - 9780387275994 SV - 39 UR - http://dx.doi.org/10.1007/0-387-27600-9_8 ER - TY - JOUR TI - Metabolic engineering of proanthocyanidins through co-expression of anthocyanidin reductase and the PAP1 MYB transcription factor AU - Xie, De-Yu AU - Sharma, Shashi B. AU - Wright, Elane AU - Wang, Zeng-Yu AU - Dixon, Richard A. T2 - The Plant Journal AB - Summary Proanthocyanidins (PAs) and their monomeric building blocks, the (epi)‐flavan‐3‐ols, are plant antioxidants that confer multiple human health benefits. The presence of PAs in forage crops is an important agronomic trait, preventing pasture bloat in ruminant animals. However, many consumed plant materials lack PAs, and there has been little success to date in introducing monomeric or polymeric flavan‐3‐ols de novo into plant tissues for disease prevention by dietary means or development of ‘bloat‐safe’ forages. We report the introduction of PAs into plants by combined expression of a MYB family transcription factor and anthocyanidin reductase for conversion of anthocyanidin into (epi)‐flavan‐3‐ol. Tobacco leaves expressing both transgenes accumulated epicatechin and gallocatechin monomers, and a series of dimers and oligomers consisting primarily of epicatechin units. The levels of PAs reached values that would confer bloat reduction in forage species. Expression of anthocyanidin reductase in anthocyanin‐containing leaves of the forage legume Medicago truncatula resulted in production of a specific subset of PA oligomers. DA - 2006/3// PY - 2006/3// DO - 10.1111/j.1365-313x.2006.02655.x VL - 45 IS - 6 SP - 895-907 LA - en OP - SN - 0960-7412 1365-313X UR - http://dx.doi.org/10.1111/j.1365-313x.2006.02655.x DB - Crossref KW - condensed tannins KW - metabolic engineering KW - transcription factor KW - anthocyanidin reductase ER - TY - JOUR TI - Unraveling the Dynamic Transcriptome AU - Brady, S.M. AU - Long, T.A. AU - Benfey, P.N. T2 - The Plant Cell AB - The advent of large-scale transcriptional profiling techniques signalled a new age in biology. Instead of understanding the expression and action of single genes, the field of transcriptomics allows for the examination of whole transcriptome changes across a variety of biological conditions. These DA - 2006/9// PY - 2006/9// DO - 10.1105/tpc.105.037572 VL - 18 IS - 9 SP - 2101-2111 UR - http://dx.doi.org/10.1105/tpc.105.037572 ER - TY - JOUR TI - Transcription factors and hormones: new insights into plant cell differentiation AU - Long, Terri A AU - Benfey, Philip N T2 - Current Opinion in Cell Biology AB - Plant development is a continuous process, mainly due to the presence of stem cell niches within the root and shoot. The interplay between a host of transcription factors determines whether the cells within the meristem maintain their stem cell state, differentiate into leaves or form secondary meristems, which develop into shoots and flowers. Several recent studies provide new insight into how transcription factors and phytohormones interact within meristems to control cell proliferation and differentiation. DA - 2006/12// PY - 2006/12// DO - 10.1016/j.ceb.2006.09.004 VL - 18 IS - 6 SP - 710-714 J2 - Current Opinion in Cell Biology LA - en OP - SN - 0955-0674 UR - http://dx.doi.org/10.1016/j.ceb.2006.09.004 DB - Crossref ER - TY - JOUR TI - Patenting Applied to Genetic Sequence Information AU - Duval, Manuel AU - Hsieh, Tzung-Fu T2 - Biotechnology and Genetic Engineering Reviews DA - 2006/12// PY - 2006/12// DO - 10.1080/02648725.2006.10648091 VL - 23 IS - 1 SP - 317-330 J2 - Biotechnology and Genetic Engineering Reviews LA - en OP - SN - 0264-8725 2046-5556 UR - http://dx.doi.org/10.1080/02648725.2006.10648091 DB - Crossref ER - TY - JOUR TI - PCR-based screening for insertional mutants. AU - Stepanova, A.N. AU - Alonso, J.M. T2 - Methods in molecular biology (Clifton, N.J.) DA - 2006/// PY - 2006/// VL - 323 SP - 163-172 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33745265233&partnerID=MN8TOARS ER - TY - JOUR TI - The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling AU - Hutchison, Claire E. AU - Li, Jie AU - Argueso, Cristiana AU - Gonzalez, Monica AU - Lee, Eurie AU - Lewis, Michael W. AU - Maxwell, Bridey B. AU - Perdue, Tony D. AU - Schaller, G. Eric AU - Alonso, Jose M. T2 - The Plant Cell Online AB - Arabidopsis thaliana histidine phosphotransfer proteins (AHPs) are similar to bacterial and yeast histidine phosphotransfer proteins (HPts), which act in multistep phosphorelay signaling pathways. A phosphorelay pathway is the current model for cytokinin signaling. To assess the role of AHPs in cytokinin signaling, we isolated T-DNA insertions in the five AHP genes that are predicted to encode functional HPts and constructed multiple insertion mutants, including an ahp1,2,3,4,5 quintuple mutant. Single ahp mutants were indistinguishable from wild-type seedlings in cytokinin response assays. However, various higher-order mutants displayed reduced sensitivity to cytokinin in diverse cytokinin assays, indicating both a positive role for AHPs in cytokinin signaling and functional overlap among the AHPs. In contrast with the other four AHPs, AHP4 may play a negative role in some cytokinin responses. The quintuple ahp mutant showed various abnormalities in growth and development, including reduced fertility, increased seed size, reduced vascular development, and a shortened primary root. These data indicate that most of the AHPs are redundant, positive regulators of cytokinin signaling and affect multiple aspects of plant development. DA - 2006/// PY - 2006/// DO - 10.1105/tpc.106.045674 VL - 18 IS - 11 SP - 3073-3087 ER - TY - JOUR TI - RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis AU - Chen, Jin-Gui AU - Ullah, Hemayet AU - Temple, Brenda AU - Liang, Jiansheng AU - Guo, Jianjun AU - Alonso, José M. AU - Ecker, Joseph R. AU - Jones, Alan M. T2 - Journal of experimental botany AB - The scaffold protein RACK1 (Receptor for Activated CKinase 1) serves as an integrative point for diverse signal transduction pathways. The Arabidopsis genome contains three RACK1 orthologues, however, little is known about their functions. It is reported here that one member of this gene family, RACK1A, previously identified as the Arabidopsis homologue of the tobacco arcA gene, mediates hormone responses and plays a regulatory role in multiple developmental processes. RACK1A expresses ubiquitously in Arabidopsis. Loss-of-function mutations in RACK1A confer defects in multiple developmental processes including seed germination, leaf production, and flowering. rack1a mutants displayed reduced sensitivity to gibberellin and brassinosteroid in seed germination, hypersensitivity to abscisic acid in seed germination and early seedling development, and hyposensitivity to auxin in adventitious and lateral root formation. These results provide the first genetic evidence that RACK1A is involved in multiple signal transduction pathways. DA - 2006/// PY - 2006/// DO - 10.1093/jxb/erl035 VL - 57 IS - 11 SP - 2697-2708 KW - Abscisic acid KW - auxin KW - brassinosteroid KW - flowering KW - gibberellin KW - RACK1 KW - seed germination KW - signal transduction ER - TY - JOUR TI - PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism AU - Lariguet, Patricia AU - Schepens, Isabelle AU - Hodgson, Daniel AU - Pedmale, Ullas V. AU - Trevisan, Martine AU - Kami, Chitose AU - Carbonnel, Matthieu AU - Alonso, José M. AU - Ecker, Joseph R. AU - Liscum, Emmanuel T2 - Proceedings of the National Academy of Sciences AB - Phototropism, or plant growth in response to unidirectional light, is an adaptive response of crucial importance. Lateral differences in low fluence rates of blue light are detected by phototropin 1 (phot1) in Arabidopsis. Only NONPHOTOTROPIC HYPOCOTYL 3 (NPH3) and root phototropism 2, both belonging to the same family of proteins, have been previously identified as phototropin-interacting signal transducers involved in phototropism. PHYTOCHROME KINASE SUBSTRATE (PKS) 1 and PKS2 are two phytochrome signaling components belonging to a small gene family in Arabidopsis (PKS1-PKS4). The strong enhancement of PKS1 expression by blue light and its light induction in the elongation zone of the hypocotyl prompted us to study the function of this gene family during phototropism. Photobiological experiments show that the PKS proteins are critical for hypocotyl phototropism. Furthermore, PKS1 interacts with phot1 and NPH3 in vivo at the plasma membrane and in vitro, indicating that the PKS proteins may function directly with phot1 and NPH3 to mediate phototropism. The phytochromes are known to influence phototropism but the mechanism involved is still unclear. We show that PKS1 induction by a pulse of blue light is phytochrome A-dependent, suggesting that the PKS proteins may provide a molecular link between these two photoreceptor families. DA - 2006/// PY - 2006/// DO - 10.1073/pnas.0603799103 VL - 103 IS - 26 SP - 10134-10139 KW - Arabidopsis thaliana KW - NONPHOTOTROPIC HYPOCCTYL 3 KW - photomorphogenesis photoreceptors ER - TY - CHAP TI - PCR-based screening for insertional mutants AU - Stepanova, Anna N. AU - Alonso, Jose M. T2 - Arabidopsis Protocols PY - 2006/// SP - 163-172 PB - SE - ER - TY - JOUR TI - Molecular mechanisms of ethylene signaling in Arabidopsis AU - Benavente, Larissa M. AU - Alonso, Jose M. T2 - Molecular BioSystems AB - Ethylene is a gaseous plant hormone involved in several important physiological processes throughout a plant's life cycle. Decades of scientific research devoted to deciphering how plants are able to sense and respond to this key molecule have culminated in the establishment of one of the best characterized signal transduction pathways in plants. The ethylene signaling pathway starts with the perception of this gaseous hormone by a family of membrane-anchored receptors followed by a Raf-like kinase CTR1 that is physically associated with the receptors and actively inhibits downstream components of the pathway. A major gap is represented by the mysterious plant protein EIN2 that genetically works downstream of CTR1 and upstream of the key transcription factor EIN3. Transcriptional regulation by EIN3 and EIN3-family members has emerged as a key aspect of ethylene responses. The major components of this transcriptional cascade have been characterized and the involvement of post-transcriptional control by ubiquitination has been determined. Nevertheless, many aspects of this pathway still remain unknown. Recent genomic studies aiming to provide a more comprehensive view of modulation of gene expression have further emphasized the ample role of ethylene in a myriad of cellular processes and particularly in its crosstalk with other important plant hormones. This review aims to serve as a guide to the main scientific discoveries that have shaped the field of ethylene biology in the recent years. DA - 2006/// PY - 2006/// DO - 10.1039/b513874d VL - 2 IS - 3-4 SP - 165 J2 - Mol. BioSyst. LA - en OP - SN - 1742-206X 1742-2051 UR - http://dx.doi.org/10.1039/b513874d DB - Crossref ER - TY - JOUR TI - CDPKs CPK6 and CPK3 function in ABA regulation of guard cell S-type anion-and Ca2+-permeable channels and stomatal closure AU - Mori, Izumi C. AU - Murata, Yoshiyuki AU - Yang, Yingzhen AU - Munemasa, Shintaro AU - Wang, Yong-Fei AU - Andreoli, Shannon AU - Tiriac, Hervé AU - Alonso, Jose M. AU - Harper, Jeffery F. AU - Ecker, Joseph R. T2 - PLoS biology DA - 2006/// PY - 2006/// VL - 4 IS - 10 SP - e327 ER - TY - JOUR TI - Arbuscular Mycorrhizal Assemblages in Native Plant Roots Change in the Presence of Invasive Exotic Grasses AU - Hawkes, Christine V. AU - Belnap, Jayne AU - Carla, D’Antonio AU - Firestone, Mary K. T2 - Plant Soil DA - 2006/3// PY - 2006/3// DO - 10.1007/s11104-005-4826-3 VL - 281 IS - 1-2 SP - 369-380 KW - arbuscular mycorrhizal fungi KW - exotic annual grasses KW - grasslands KW - native perennial grasses KW - plant invasion ER - TY - JOUR TI - DEMETER DNA Glycosylase Establishes MEDEA Polycomb Gene Self-Imprinting by Allele-Specific Demethylation AU - Gehring, Mary AU - Huh, Jin Hoe AU - Hsieh, Tzung-Fu AU - Penterman, Jon AU - Choi, Yeonhee AU - Harada, John J. AU - Goldberg, Robert B. AU - Fischer, Robert L. T2 - Cell AB - MEDEA (MEA) is an Arabidopsis Polycomb group gene that is imprinted in the endosperm. The maternal allele is expressed and the paternal allele is silent. MEA is controlled by DEMETER (DME), a DNA glycosylase required to activate MEA expression, and METHYLTRANSFERASE I (MET1), which maintains CG methylation at the MEA locus. Here we show that DME is responsible for endosperm maternal-allele-specific hypomethylation at the MEA gene. DME can excise 5-methylcytosine in vitro and when expressed in E. coli. Abasic sites opposite 5-methylcytosine inhibit DME activity and might prevent DME from generating double-stranded DNA breaks. Unexpectedly, paternal-allele silencing is not controlled by DNA methylation. Rather, Polycomb group proteins that are expressed from the maternal genome, including MEA, control paternal MEA silencing. Thus, DME establishes MEA imprinting by removing 5-methylcytosine to activate the maternal allele. MEA imprinting is subsequently maintained in the endosperm by maternal MEA silencing the paternal allele. DA - 2006/2// PY - 2006/2// DO - 10.1016/j.cell.2005.12.034 VL - 124 IS - 3 SP - 495-506 J2 - Cell LA - en OP - SN - 0092-8674 UR - http://dx.doi.org/10.1016/j.cell.2005.12.034 DB - Crossref ER - TY - JOUR TI - In situ methods to localize transgenes and transcripts in interphase nuclei: a tool for transgenic plant research AU - Santos, A.P. AU - Wegel, E. AU - Allen, G.C. AU - Thompson, W.F. AU - Stoger, E. AU - Shaw, P. AU - Abranches, R. T2 - Plant Methods AB - Abstract Genetic engineering of commercially important crops has become routine in many laboratories. However, the inability to predict where a transgene will integrate and to efficiently select plants with stable levels of transgenic expression remains a limitation of this technology. Fluorescence in situ hybridization (FISH) is a powerful technique that can be used to visualize transgene integration sites and provide a better understanding of transgene behavior. Studies using FISH to characterize transgene integration have focused primarily on metaphase chromosomes, because the number and position of integration sites on the chromosomes are more easily determined at this stage. However gene (and transgene) expression occurs mainly during interphase. In order to accurately predict the activity of a transgene, it is critical to understand its location and dynamics in the three-dimensional interphase nucleus. We and others have developed in situ methods to visualize transgenes (including single copy genes) and their transcripts during interphase from different tissues and plant species. These techniques reduce the time necessary for characterization of transgene integration by eliminating the need for time-consuming segregation analysis, and extend characterization to the interphase nucleus, thus increasing the likelihood of accurate prediction of transgene activity. Furthermore, this approach is useful for studying nuclear organization and the dynamics of genes and chromatin. C2 - PMC1635696 DA - 2006/// PY - 2006/// DO - 10.1186/1746-4811-2-18 VL - 2 SP - 18 ER - TY - JOUR TI - PATTERNS OF HABITAT USE BY PRIMATES IN EASTERN ECUADOR AU - Sheth, Seema T2 - Theses DA - 2006/6/26/ PY - 2006/6/26/ VL - 41 SP - 146 UR - https://irl.umsl.edu/thesis/41 ER - TY - JOUR TI - Evaluating phylogenetic patterns of threat in Bignonieae (Bignoniaceae) using herbarium data AU - Sheth, Seema N. AU - Jiménez, Iván AU - Consiglio, Trisha K. AU - Lohmann, Lúcia Garcez T2 - Abstracts - Poster DA - 2006/// PY - 2006/// LA - pt-br UR - https://bdpi.usp.br/item/002696357 DB - bdpi.usp.br Y2 - 2019/2/22/ ER - TY - JOUR TI - Two cell-cycle regulated SET-domain proteins interact with proliferating cell nuclear antigen (PCNA) in Arabidopsis AU - Raynaud, Cécile AU - Sozzani, Rosangela AU - Glab, Nathalie AU - Domenichini, Séverine AU - Perennes, Claudette AU - Cella, Rino AU - Kondorosi, Eva AU - Bergounioux, Catherine T2 - The Plant Journal: For Cell and Molecular Biology AB - Summary The proliferating cell nuclear antigen (PCNA) functions as a sliding clamp for DNA polymerase, and is thus a key actor in DNA replication. It is also involved in DNA repair, maintenance of heterochromatic regions throughout replication, cell cycle regulation and programmed cell death. Identification of PCNA partners is therefore necessary for understanding these processes. Here we identify two Arabidopsis SET‐domain proteins that interact with PCNA: ATXR5 and ATXR6. A truncated ATXR5Δex2, incapable of interacting with PCNA, also occurs in planta . ATXR6 , upregulated during the S phase, is upregulated by AtE2F transcription factors, suggesting that it is required for S‐phase progression. The two proteins differ in their subcellular localization: ATXR5 has a dual localization in plastids and in the nucleus, whereas ATXR6 is solely nuclear. This indicates that the two proteins may play different roles in plant cells. However, overexpression of either ATXR5 or ATXR6 causes male sterility because of the degeneration of defined cell types. Taken together, our results suggest that both proteins may play a role in the cell cycle or DNA replication, and that the activity of ATXR5 may be regulated via its subcellular localization. DA - 2006/8// PY - 2006/8// DO - 10.1111/j.1365-313X.2006.02799.x VL - 47 IS - 3 SP - 395-407 J2 - Plant J. LA - eng SN - 0960-7412 DB - PubMed KW - cell cycle KW - S phase KW - AtE2F KW - SET domain KW - proliferating cell nuclear antigen ER - TY - JOUR TI - Interplay between Arabidopsis Activating Factors E2Fb and E2Fa in Cell Cycle Progression and Development AU - Sozzani, Rosangela AU - Maggio, Caterina AU - Varotto, Serena AU - Canova, Sabrina AU - Bergounioux, Catherine AU - Albani, Diego AU - Cella, Rino T2 - Plant Physiology AB - Eukaryotic E2Fs are conserved transcription factors playing crucial and antagonistic roles in several pathways related to cell division, DNA repair, and differentiation. In plants, these processes are strictly intermingled at the growing zone to produce postembryonic development in response to internal signals and environmental cues. Of the six AtE2F proteins found in Arabidopsis (Arabidopsis thaliana), only AtE2Fa and AtE2Fb have been clearly indicated as activators of E2F-responsive genes. AtE2Fa activity was shown to induce S phase and endoreduplication, whereas the function of AtE2Fb and the interrelationship between these two transcription factors was unclear. We have investigated the role played by the AtE2Fb gene during cell cycle and development performing in situ RNA hybridization, immunolocalization of the AtE2Fb protein in planta, and analysis of AtE2Fb promoter activity in transgenic plants. Overexpression of AtE2Fb in transgenic Arabidopsis plants led to striking modifications of the morphology of roots, cotyledons, and leaves that can be ascribed to stimulation of cell division. The accumulation of the AtE2Fb protein in these lines was paralleled by an increased expression of E2F-responsive G1/S and G2/M marker genes. These results suggest that AtE2Fa and AtE2Fb have specific expression patterns and play similar but distinct roles during cell cycle progression. DA - 2006/4/1/ PY - 2006/4/1/ DO - 10.1104/pp.106.077990 VL - 140 IS - 4 SP - 1355-1366 LA - en SN - 0032-0889, 1532-2548 UR - http://www.plantphysiol.org/content/140/4/1355 DB - www.plantphysiol.org Y2 - 2019/1/30/ ER - TY - JOUR TI - Quantitative Trait Loci for Root Architecture Traits Correlated with Phosphorus Acquisition in Common Bean AU - Beebe, Stephen E. AU - Rojas-Pierce, Marcela AU - Yan, Xiaolong AU - Blair, Matthew W. AU - Pedraza, Fabio AU - Muñoz, Fernando AU - Tohme, Joe AU - Lynch, Jonathan P. T2 - Crop Science AB - Low soil P availability is a primary constraint to common bean ( Phaseolus vulgaris L.) production in Latin America and Africa. Substantial genotypic variation in bean adaptation to low phosphorus (LP) availability has been linked with root traits that enhance the efficiency of soil foraging. The objectives of this study were to identify quantitative trait loci (QTLs) for P accumulation and associated root architectural traits, to facilitate genetic improvement and to reveal physiological relationships. Eighty‐six F 5.7 recombinant inbred lines (RILs) were developed from a cross between G19833, an Andean landrace with high total P accumulation, and DOR 364, a Mesoamerican cultivar with low total P accumulation in LP conditions. A genetic map constructed with restriction fragment length polymorphisms (RFLPs), microsatellites, and PCR‐based markers covering 1703 centimorgans (cM) total genetic distance and all eleven linkage groups (LGs) was used for QTL analysis. Seventy‐one RILs were evaluated in the field at high phosphorus (HP) and LP for P accumulation, total root length (RL), specific RL, and plant dry weight (DW), while all 86 RILs were evaluated in a hydroponic system in the greenhouse for tap, basal, total, and specific RL and plant DW. Phosphorus accumulation in the field correlated with root parameters measured in the greenhouse. A total of 26 individual QTLs were identified for P accumulation and associated root characters using composite interval mapping (CIM) analysis. Phosphorus accumulation QTLs often coincided with those for basal root development, thus, basal roots appear to be important in P acquisition. Independent QTLs were identified for basal and taproot development, and for specific RL. Distinct QTLs for greater specific RL had positive, null and negative effects on P accumulation. Our results confirm the importance of root structure for LP adaptation and highlight the need for a more detailed understanding of root architectural traits for phenotypic as well as marker‐aided selection of more P‐efficient crops. DA - 2006/// PY - 2006/// DO - 10.2135/cropsci2005.0226 VL - 46 IS - 1 SP - 413 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-32344439116&partnerID=MN8TOARS ER - TY - PAT TI - High efficiency gene targeting in plants AU - Helmer, G. L. AU - Allen, G. C. AU - Thompson, W. F. C2 - 2006/// DA - 2006/// PY - 2006/// ER - TY - JOUR TI - A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide AU - Allen, G. C. AU - Flores-Vergara, M. A. AU - Krasnyanski, S. AU - Kumar, S. AU - Thompson, W. F. T2 - NATURE PROTOCOLS DA - 2006/// PY - 2006/// DO - 10.1038/nprot.2006.384 VL - 1 IS - 5 SP - 2320-2325 SN - 1750-2799 ER - TY - JOUR TI - Positive effect of seed size on seedling survival in fire-prone savannas of Australia, Brazil and West Africa AU - Lahoreau, Gaelle AU - Barot, Sebastien AU - Gignoux, Jacques AU - Hoffmann, William A. AU - Setterfield, Samantha A. AU - Williams, Paul R. T2 - JOURNAL OF TROPICAL ECOLOGY AB - All plant species face a fundamental reproductive trade-off: for a given investment in seed mass, they can produce either many small seeds or few large seeds. Whereas small seeds favour the germination of numerous seedlings, large seeds favour the survival of seedlings in the face of common stresses such as herbivory, drought or shade (Leishman et al. 2000). One mechanism explaining the better survival of large-seeded species is the seedling size effect (SSE) (Westoby et al. 1996): because seeds with large reserves result in bigger seedlings, seedlings from large-seeded species would have better access to light and/or to reliable water supply than seedlings from small-seeded species. DA - 2006/11// PY - 2006/11// DO - 10.1017/S026646740600349X VL - 22 SP - 719-722 SN - 1469-7831 KW - buds KW - resource allocation KW - resprouting KW - root reserves KW - seed mass KW - seedling size ER - TY - JOUR TI - Geminivirus infection up-regulates the expression of two Arabidopsis protein kinases related to yeast SNF1-and mammalian AMPK-activating kinases AU - Shen, Wei AU - Hanley-Bowdoin, Linda T2 - PLANT PHYSIOLOGY AB - Geminivirus Rep-interacting kinase 1 (GRIK1) and GRIK2 constitute a small protein kinase family in Arabidopsis (Arabidopsis thaliana). An earlier study showed that a truncated version of GRIK1 binds to the geminivirus replication protein AL1. We show here both full-length GRIK1 and GRIK2 interact with AL1 in yeast two-hybrid studies. Using specific antibodies, we showed that both Arabidopsis kinases are elevated in infected leaves. Immunoblot analysis of healthy plants revealed that GRIK1 and GRIK2 are highest in young leaf and floral tissues and low or undetectable in mature tissues. Immunohistochemical staining showed that the kinases accumulate in the shoot apical meristem, leaf primordium, and emerging petiole. Unlike the protein patterns, GRIK1 and GRIK2 transcript levels only show a small increase during infection and do not change significantly during development. Treating healthy seedlings and infected leaves with the proteasome inhibitor MG132 resulted in higher GRIK1 and GRIK2 protein levels, whereas treatment with the translation inhibitor cycloheximide reduced both kinases, demonstrating that their accumulation is modulated by posttranscriptional processes. Phylogenetic comparisons indicated that GRIK1, GRIK2, and related kinases from Medicago truncatula and rice (Oryza sativa) are most similar to the yeast kinases PAK1, TOS3, and ELM1 and the mammalian kinase CaMKK, which activate the yeast kinase SNF1 and its mammalian homolog AMPK, respectively. Complementation studies using a PAK1/TOS3/ELM1 triple mutant showed that GRIK1 and GRIK2 can functionally replace the yeast kinases, suggesting that the Arabidopsis kinases mediate one or more processes during early plant development and geminivirus infection by activating SNF1-related kinases. DA - 2006/12// PY - 2006/12// DO - 10.1104/pp.106.088476 VL - 142 IS - 4 SP - 1642-1655 SN - 1532-2548 ER - TY - JOUR TI - Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing AU - Blevins, Todd AU - Rajeswaran, Rajendran AU - Shivaprasad, Padubidri V. AU - Beknazariants, Daria AU - Si-Ammour, Azeddine AU - Park, Hyun-Sook AU - Vazquez, Franck AU - Robertson, Dominique AU - Meins, Frederick, Jr. AU - Hohn, Thomas AU - Pooggin, Mikhail M. T2 - NUCLEIC ACIDS RESEARCH AB - Like other eukaryotes, plants use DICER-LIKE (DCL) proteins as the central enzymes of RNA silencing, which regulates gene expression and mediates defense against viruses. But why do plants like Arabidopsis express four DCLs, a diversity unmatched by other kingdoms? Here we show that two nuclear DNA viruses (geminivirus CaLCuV and pararetrovirus CaMV) and a cytoplasmic RNA tobamovirus ORMV are differentially targeted by subsets of DCLs. DNA virus-derived small interfering RNAs (siRNAs) of specific size classes (21, 22 and 24 nt) are produced by all four DCLs, including DCL1, known to process microRNA precursors. Specifically, DCL1 generates 21 nt siRNAs from the CaMV leader region. In contrast, RNA virus infection is mainly affected by DCL4. While the four DCLs are partially redundant for CaLCuV-induced mRNA degradation, DCL4 in conjunction with RDR6 and HEN1 specifically facilitates extensive virus-induced silencing in new growth. Additionally, we show that CaMV infection impairs processing of endogenous RDR6-derived double-stranded RNA, while ORMV prevents HEN1-mediated methylation of small RNA duplexes, suggesting two novel viral strategies of silencing suppression. Our work highlights the complexity of virus interaction with host silencing pathways and suggests that DCL multiplicity helps mediate plant responses to diverse viral infections. DA - 2006/12// PY - 2006/12// DO - 10.1093/nar/gkl886 VL - 34 IS - 21 SP - 6233-6246 SN - 1362-4962 ER - TY - JOUR TI - Limitations to fruit and seed production by Lysimachia asperulifolia Poir. (Primulaceae), a rare plant species of the Carolinas AU - Franklin, M. A. AU - Stucky, J. M. AU - Wentworth, T. R. AU - Brownie, C. AU - Roulston, T. T2 - JOURNAL OF THE TORREY BOTANICAL SOCIETY AB - Lysimachia asperulifolia Poir., rough–leaf loosestrife, is a federally endangered species that is restricted to longleaf pine savanna – pocosin ecotones in North and South Carolina. Potential causes of the limited fruit and seed production typical of this species and possible effects of prescribed fire on these causes were examined. It was determined that insects rarely visit flowers and that the visitors, Augochlorella spp. and Lasioglossum spp., are not effective pollinators. However, results of artificial pollinations do not support the hypothesis that pollinator limitation alone restricts seed production. Levels of fertility and S allele diversity may vary across natural populations and, combined with ineffective pollination, enforce restricted fruit and seed production. Pollen fertility, amount of flowering, and number of fruits produced in natural populations did not increase following prescribed fire. Restricted seed germination further limits recruitment of genetic variation into populations. Pollinations and propagule dispersal among populations are precluded by habitat fragmentation. Alternative courses of action designed to increase fruit and seed production and seedling recruitment are recommended to those developing loosestrife conservation plans. DA - 2006/// PY - 2006/// DO - 10.3159/1095-5674(2006)133[403:LTFASP]2.0.CO;2 VL - 133 IS - 3 SP - 403-411 SN - 1940-0616 KW - fruit production KW - habitat fragmentation KW - pan trap sampling KW - pollinator limitation KW - S allele diversity KW - seed germination KW - seed production KW - sterility ER - TY - JOUR TI - Transcriptional and functional analysis of oxalyl-coenzyme A (CoA) decarboxylase and formyl-CoA transferase genes from Lactobacillus acidophilus AU - Azcarate-Peril, MA AU - Bruno-Barcena, JM AU - Hassan, HM AU - Klaenhammer, TR T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - Oxalic acid is found in dietary sources (such as coffee, tea, and chocolate) or is produced by the intestinal microflora from metabolic precursors, like ascorbic acid. In the human intestine, oxalate may combine with calcium, sodium, magnesium, or potassium to form less soluble salts, which can cause pathological disorders such as hyperoxaluria, urolithiasis, and renal failure in humans. In this study, an operon containing genes homologous to a formyl coenzyme A transferase gene (frc) and an oxalyl coenzyme A decarboxylase gene (oxc) was identified in the genome of the probiotic bacterium Lactobacillus acidophilus. Physiological analysis of a mutant harboring a deleted version of the frc gene confirmed that frc expression specifically improves survival in the presence of oxalic acid at pH 3.5 compared with the survival of the wild-type strain. Moreover, the frc mutant was unable to degrade oxalate. These genes, which have not previously been described in lactobacilli, appear to be responsible for oxalate degradation in this organism. Transcriptional analysis using cDNA microarrays and reverse transcription-quantitative PCR revealed that mildly acidic conditions were a prerequisite for frc and oxc transcription. As a consequence, oxalate-dependent induction of these genes occurred only in cells first adapted to subinhibitory concentrations of oxalate and then exposed to pH 5.5. Where genome information was available, other lactic acid bacteria were screened for frc and oxc genes. With the exception of Lactobacillus gasseri and Bifidobacterium lactis, none of the other strains harbored genes for oxalate utilization. DA - 2006/3// PY - 2006/3// DO - 10.1128/AEM.72.3.1891-1899.2006 VL - 72 IS - 3 SP - 1891-1899 SN - 1098-5336 UR - http://europepmc.org/abstract/med/16517636 ER - TY - JOUR TI - The maize Mucronate mutation is a deletion in the 16-kDa gamma-zein gene that induces the unfolded protein response AU - Kim, Cheol Soo AU - Gibbon, Bryan C. AU - Gillikin, Jeffrey W. AU - Larkins, Brian A. AU - Boston, Rebecca S. AU - Jung, Rudolf T2 - PLANT JOURNAL AB - Summary Mucronate ( Mc ) was identified as a dominant maize ( Zea mays L. ) opaque kernel mutation that alters zein storage protein synthesis. Zein protein bodies in Mc endosperm are misshapen and are associated with increased levels of ER Lumenal Binding Protein (BiP). Using GeneCalling TM to profile endosperm RNA transcripts, we identified an aberrant RNA in Mc that encodes the 16‐kDa γ ‐zein protein. The transcript contains a 38‐bp deletion (nucleotides 406–444 after the initiation codon) that creates a frame‐shift mutation and an abnormal sequence for the last 63 amino acids. Genetic mapping revealed the Mc mutation is linked with the locus encoding the 16‐kDa γ ‐zein, and two‐dimensional gel electrophoresis confirmed the 16‐kDa γ ‐zein protein is altered in Mc . The mutant protein exhibited changes in solubility properties and co‐immunoprecipitated with the molecular chaperone, BiP. Transgenic maize plants expressing the Mc 16‐kDa γ ‐zein manifested an opaque kernel phenotype with enhanced levels of BiP in the endosperm, similar to the Mc mutant. Unlike the wild‐type protein, the Mc 16‐kDa γ ‐zein interacted only weakly with the 22‐kDa α ‐zein when expressed in the yeast two‐hybrid system. These results indicate that the Mc phenotype results from a frame‐shift mutation in the gene encoding the 16‐kDa γ ‐zein protein, leading to the unfolded protein response in developing endosperm. DA - 2006/11// PY - 2006/11// DO - 10.1111/j.1365-313X.2006.02884.x VL - 48 IS - 3 SP - 440-451 SN - 0960-7412 KW - unfolded protein response (UPR) KW - endosperm KW - protein body KW - opaque mutant ER - TY - JOUR TI - Testing the paradigms of exotic species invasion in urban riparian forests AU - Vidra, Rebecca L. AU - Shear, Theodore H. AU - Wentworth, Thomas R. T2 - NATURAL AREAS JOURNAL AB - Exotic species research has generated several paradigms about the effects of invasion on native ecosystems and the site characteristics that promote invasibility. We are interested in translating these theoretical paradigms into management recommendations. Using vegetation surveys of urban riparian forests in central North Carolina, we tested the competition and resource availability paradigms. We assessed the association between exotic and native species and identified potential resources that promote invasion. Exotic and native species richness was negatively correlated (r = −0.66, p = 0.0009), conforming to the predictions of the competition paradigm. In particular, native woody species were negatively associated with several exotic growth forms. Two of the most common exotic species, Hedera helix (English ivy) and Microstegium vimineum (Japanese stilt grass), did not co-occur with several native woody plants, suggesting that they may preclude the establishment and regeneration of native woody plant communities. Our results have less direct implications for the resource availability paradigm. There were no correlations between light availability (indexed by canopy cover) and either cover or richness of exotic species. However, exotic species richness was generally positively correlated to soil fertility. These results suggest that the competition and resource availability paradigms are useful for understanding the dynamics of urban riparian forests that are invaded by a suite of exotic species. Removal efforts should focus on two of the most common invasive plants, H. helix and M. vimineum, and native woody plants should be re-established. While soil fertility is difficult to manage at a site level, we urge managers to lobby for strict regulations on nutrient inputs from upstream and adjacent development. DA - 2006/10// PY - 2006/10// DO - 10.3375/0885-8608(2006)26[339:TTPOES]2.0.CO;2 VL - 26 IS - 4 SP - 339-350 SN - 2162-4399 KW - competition KW - exotic species invasion KW - resource availability KW - restoration KW - soil fertility ER - TY - JOUR TI - Peptide aptamers that bind to a geminivirus replication protein interfere with viral replication in plant cells AU - Lopez-Ochoa, Luisa AU - Ramirez-Prado, Jorge AU - Hanley-Bowdoin, Linda T2 - JOURNAL OF VIROLOGY AB - The AL1 protein of tomato golden mosaic virus (TGMV), a member of the geminivirus family, is essential for viral replication in plants. Its N terminus contains three conserved motifs that mediate origin recognition and DNA cleavage during the initiation of rolling-circle replication. We used the N-terminal domain of TGMV AL1 as bait in a yeast two-hybrid screen of a random peptide aptamer library constrained in the active site of the thioredoxin A (TrxA) gene. The screen selected 88 TrxA peptides that also bind to the full-length TGMV AL1 protein. Plant expression cassettes corresponding to the TrxA peptides and a TGMV A replicon encoding AL1 were cotransfected into tobacco protoplasts, and viral DNA replication was monitored by semiquantitative PCR. In these assays, 31 TrxA peptides negatively impacted TGMV DNA accumulation, reducing viral DNA levels to 13 to 64% of those of the wild type. All of the interfering aptamers also bound to the AL1 protein of cabbage leaf curl virus. A comparison of the 20-mer peptides revealed that their sequences are not random. The alignments detected seven potential binding motifs, five of which are more highly represented among the interfering peptides. One motif was present in 18 peptides, suggesting that these peptides interact with a hot spot in the AL1 N terminus. The peptide aptamers characterized in these studies represent new tools for studying AL1 function and can serve as the basis for the development of crops with broad-based resistance to single-stranded DNA viruses. DA - 2006/6// PY - 2006/6// DO - 10.1128/JVI.02698-05 VL - 80 IS - 12 SP - 5841-5853 SN - 1098-5514 ER - TY - JOUR TI - Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1 AU - Kim, Sun A. AU - Punshon, Tracy AU - Lanzirotti, Antonio AU - Li, Liangtao AU - Alonso, Jose M. AU - Ecker, Joseph R. AU - Kaplan, Jerry AU - Guerinot, Mary Lou T2 - SCIENCE AB - Iron deficiency is a major human nutritional problem wherever plant-based diets are common. Using synchrotron x-ray fluorescence microtomography to directly visualize iron in Arabidopsis seeds, we show that iron is localized primarily to the provascular strands of the embryo. This localization is completely abolished when the vacuolar iron uptake transporter VIT1 is disrupted. Vacuolar iron storage is also critical for seedling development because vit1-1 seedlings grow poorly when iron is limiting. We have uncovered a fundamental aspect of seed biology that will ultimately aid the development of nutrient-rich seed, benefiting both human health and agricultural productivity. DA - 2006/11/24/ PY - 2006/11/24/ DO - 10.1126/science.1132563 VL - 314 IS - 5803 SP - 1295-1298 SN - 1095-9203 ER - TY - JOUR TI - A closed loop exponential feeding law: Invariance and global stability analysis AU - Pico-Marco, E AU - Navarro, JL AU - Bruno-Barcena, JM T2 - JOURNAL OF PROCESS CONTROL AB - This article addresses the computation of invariant control laws [A. Fradkov, I. Miroshnik, V. Nikiforov, Nonlinear and Adaptive Control of Complex Systems, Kluwer, 1999] for fed-batch fermenters represented by two standard models. It will be shown how to derive partial state feedbacks that, assuming ideal conditions and perfect model, keep the specific growth rate μ constant provided the initial conditions are adequate. The invariant control law is the closed loop version of the exponential feeding already suggested in several references as shown later. The paper presents an analysis of invariance and a study of global stability within the framework of partial stability. That is, stability with respect to some of the state variables. This enables us to treat the case with Haldane-like or non-monotonous kinetics. DA - 2006/4// PY - 2006/4// DO - 10.1016/j.jprocont.2005.06.014 VL - 16 IS - 4 SP - 395-402 SN - 1873-2771 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-29144509840&partnerID=MN8TOARS KW - fed-batch bioreactors KW - exponential feeding law KW - partial stability KW - Monod and Haldane kinetics ER - TY - JOUR TI - Ancestral chloroplast polymorphism and historical secondary contact in a broad hybrid zone of Aesculus (Sapindaceae) AU - Modliszewski, JL AU - Thomas, DT AU - Fan, CZ AU - Crawford, DJ AU - DePamphilis, CW AU - Xiang, QY T2 - AMERICAN JOURNAL OF BOTANY AB - Knowledge regarding the origin and maintenance of hybrid zones is critical for understanding the evolutionary outcomes of natural hybridization. To evaluate the contribution of historical contact vs. long‐distance gene flow in the formation of a broad hybrid zone in central and northern Georgia that involves Aesculus pavia , A. sylvatica , and A. flava , three cpDNA regions ( matK , trnD‐trnT , and trnH‐trnK ) were analyzed. The maternal inheritance of cpDNA in Aesculus was confirmed via sequencing of matK from progeny of controlled crosses. Restriction site analyses identified 21 unique haplotypes among 248 individuals representing 29 populations from parental species and hybrids. Haplotypes were sequenced for all cpDNA regions. Restriction site and sequence data were subjected to phylogeographic and population genetic analyses. Considerable cpDNA variation was detected in the hybrid zone, as well as ancestral cpDNA polymorphism; furthermore, the distribution of haplotypes indicates limited interpopulation gene flow via seeds. The genealogy and structure of genetic variation further support the historical presence of A. pavia in the Piedmont, although they are at present locally extinct. In conjunction with previous allozyme studies, the cpDNA data suggest that the hybrid zone originated through historical local gene flow, yet is maintained by periodic long‐distance pollen dispersal. DA - 2006/3// PY - 2006/3// DO - 10.3732/ajb.93.3.377 VL - 93 IS - 3 SP - 377-388 SN - 1537-2197 KW - Aesculus KW - cpDNA inheritance KW - hybrid zone KW - phylogeography KW - Pleistocene KW - Sapindaceae KW - secondary contact KW - southeastern United States ER - TY - JOUR TI - An oxidoreductase is involved in cercosporin degradation by the bacterium Xanthomonas campestris pv. zinniae AU - Taylor, Tanya V. AU - Mitchell, Thomas K. AU - Daub, Margaret E. T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT The polyketide toxin cercosporin plays a key role in pathogenesis by fungal species of the genus Cercospora . The bacterium Xanthomonas campestris pv. zinniae is able to rapidly degrade this toxin. Growth of X. campestris pv. zinniae strains in cercosporin-containing medium leads to the breakdown of cercosporin and to the formation of xanosporic acid, a nontoxic breakdown product. Five non-cercosporin-degrading mutants of a strain that rapidly degrades cercosporin (XCZ-3) were generated by ethyl methanesulfonate mutagenesis and were then transformed with a genomic library from the wild-type strain. All five mutants were complemented with the same genomic clone, which encoded a putative transcriptional regulator and an oxidoreductase. Simultaneous expression of these two genes was necessary to complement the mutant phenotype. Sequence analysis of the mutants showed that all five mutants had point mutations in the oxidoreductase gene and no mutations in the regulator. Quantitative reverse transcription-PCR (RT-PCR) showed that the expression of both of these genes in the wild-type strain is upregulated after exposure to cercosporin. Both the oxidoreductase and transcriptional regulator genes were transformed into three non-cercosporin-degrading bacteria to determine if they are sufficient for cercosporin degradation. Quantitative RT-PCR analysis confirmed that the oxidoreductase was expressed in all transconjugants. However, none of the transconjugants were able to degrade cercosporin, suggesting that additional factors are required for cercosporin degradation. Further study of cercosporin degradation in X. campestris pv. zinniae may allow for the engineering of Cercospora -resistant plants by using a suite of genes. DA - 2006/9// PY - 2006/9// DO - 10.1128/AEM.00483-06 VL - 72 IS - 9 SP - 6070-6078 SN - 1098-5336 ER - TY - JOUR TI - Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis AU - Alonso, Jose AU - Ecker, Joseph R. T2 - Nature Reviews Genetics DA - 2006/// PY - 2006/// DO - 10.1038/nrg1893 VL - 7 IS - 7 SP - 524-536 ER - TY - JOUR TI - Endoplasmic reticulum targeted GFP reveals ER organization in tobacco NT-1 cells during cell division AU - Gupton, S. L. AU - Collings, D. A. AU - Allen, N. S. T2 - PLANT PHYSIOLOGY AND BIOCHEMISTRY AB - The endoplasmic reticulum (ER) of plant cells undergoes a drastic reorganization during cell division. In tobacco NT-1 cells that stably express a GFP construct targeted to the ER, we have mapped the reorganization of ER that occurs during mitosis and cytokinesis with confocal laser scanning microscopy. During division, the ER and nuclear envelope do not vesiculate. Instead, tubules of ER accumulate around the chromosomes after the nuclear envelope breaks down, with these tubules aligning parallel to the microtubules of the mitotic spindle. In cytokinesis, the phragmoplast is particularly rich in ER, and the transnuclear channels and invaginations present in many interphase cells appear to develop from ER tubules trapped in the developing phragmoplast. Drug studies, using oryzalin and latrunculin to disrupt the microtubules and actin microfilaments, respectively, demonstrate that during division, the arrangement of ER is controlled by microtubules and not by actin, which is the reverse of the situation in interphase cells. DA - 2006/// PY - 2006/// DO - 10.1016/j.plaphy.2006.03.003 VL - 44 IS - 2-3 SP - 95-105 SN - 0981-9428 KW - actin microfilaments KW - cell division KW - endoplasmic reticulum KW - green fluorescent protein KW - microtubules KW - nuclear envelope KW - nuclear invaginations ER - TY - JOUR TI - Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis AU - Rudella, Andrea AU - Friso, Giulia AU - Alonso, Jose M. AU - Ecker, Joseph R. AU - Wijk, Klaas J. T2 - PLANT CELL AB - Plastids contain tetradecameric Clp protease core complexes, with five ClpP Ser-type proteases, four nonproteolytic ClpR, and two associated ClpS proteins. Accumulation of total ClpPRS complex decreased twofold to threefold in an Arabidopsis thaliana T-DNA insertion mutant in CLPR2 designated clpr2-1. Differential stable isotope labeling of the ClpPRS complex with iTRAQ revealed a fivefold reduction in assembled ClpR2 accumulation and twofold to fivefold reductions in the other subunits. A ClpR2:(his)(6) fusion protein that incorporated into the chloroplast ClpPRS complex fully complemented clpr2-1. The reduced accumulation of the ClpPRS protease complex led to a pale-green phenotype with delayed shoot development, smaller chloroplasts, decreased thylakoid accumulation, and increased plastoglobule accumulation. Stromal ClpC1 and 2 were both recruited to the thylakoid surface in clpr2-1. The thylakoid membrane of clpr2-1 showed increased carotenoid content, partial inactivation of photosystem II, and upregulated thylakoid proteases and stromal chaperones, suggesting an imbalance in chloroplast protein homeostasis and a well-coordinated network of proteolysis and chaperone activities. Interestingly, a subpopulation of PsaF and several light-harvesting complex II proteins accumulated in the thylakoid with unprocessed chloroplast transit peptides. We conclude that ClpR2 cannot be functionally replaced by other ClpP/R homologues and that the ClpPRS complex is central to chloroplast biogenesis, thylakoid protein homeostasis, and plant development. DA - 2006/7// PY - 2006/7// DO - 10.1105/tpc.106.042861 VL - 18 IS - 7 SP - 1704-1721 SN - 1532-298X ER - TY - JOUR TI - Polycations globally enhance binding of 14-3-3 omega to target proteins in spinach leaves AU - Shen, Wei AU - Huber, Steven C. T2 - PLANT AND CELL PHYSIOLOGY AB - The binding of 14-3-3ω to phosphorylated nitrate reductase (pNR) is stimulated by cations such as Mg2+ or spermine, and decreased by 5′-AMP. In order to determine whether binding to other cellular proteins is affected similarly, far-Western overlays of extracts prepared from light- or dark-treated spinach (Spinacia oleracea) leaves were performed using digoxigenin (DIG)-labeled Arabidopsis 14-3-3ω. When separated by SDS–PAGE, approximately 25 proteins of >35 kDa could be resolved that interacted with DIG-labeled 14-3-3ω in the absence of added cations. The presence of 5 mM Mg2+ or 0.5 mM spermine enhanced binding to most of the target proteins to a maximum of about a doubling of the observed binding. In most cases, the binding was dependent on phosphorylation of the target protein, whereas that was not necessarily the case for binding to target proteins that were unaffected by polycations. The extent of stimulation varied among the target proteins, but there was no indication that the nature of the cation activator (e.g. Mg2+ vs. spermine4+) altered the specificity for target proteins. In addition, binding of DIG-labeled 14-3-3ω to some, but not all, target proteins was reduced by 5 mM 5′-AMP. Interestingly, light/dark treatment of spinach leaves affected the subsequent binding of DIG-labeled 14-3-3ω in the overlay assay to only a few of the target proteins, one of which was identified as NADH:nitrate reductase. Overall, the results suggest that the binding of 14-3-3s to targets in addition to pNR may also be regulated by polycations and 5′-AMP. DA - 2006/6// PY - 2006/6// DO - 10.1093/pcp/pcj050 VL - 47 IS - 6 SP - 764-771 SN - 1471-9053 KW - divalent cations KW - far-Western overlay KW - nitrate reductase KW - 14-3-3 protein KW - spermine KW - Spinacia oleracea ER - TY - JOUR TI - Interrelationships between p-coumaric acid, evapotranspiration, soil water content, and leaf expansion AU - Blum, Udo AU - Gerig, Thomas M. T2 - JOURNAL OF CHEMICAL ECOLOGY DA - 2006/8// PY - 2006/8// DO - 10.1007/s10886-006-9111-2 VL - 32 IS - 8 SP - 1817-1834 SN - 1573-1561 KW - cucumber seedlings KW - p-coumaric acid KW - evaporation KW - evapotranspiration leaf area expansion KW - soil water content KW - soil solution concentrations inhibition and recovery KW - negative feedback regulation KW - allelopathy KW - competition ER - TY - JOUR TI - Propane and n-butane oxidation by Pseudomonas putida GPo1 AU - Johnson, EL AU - Hyman, MR T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - Propane and n-butane inhibit methyl tertiary butyl ether oxidation by n-alkane-grown Pseudomonas putida GPo1. Here we demonstrate that these gases are oxidized by this strain and support cell growth. Both gases induced alkane hydroxylase activity and appear to be oxidized by the same enzyme system used for the oxidation of n-octane. DA - 2006/1// PY - 2006/1// DO - 10.1128/aem.72.1.950-952.2006 VL - 72 IS - 1 SP - 950-952 SN - 1098-5336 UR - https://europepmc.org/articles/PMC1352225 ER - TY - PCOMM TI - Women in ecology - Authors reply AU - Damschen, E. I. AU - Rosenfeld, K. M. AU - Wyer, M. AU - Murphy-Medley, D. AU - Wentworth, T. R. AU - Haddad, N. M. DA - 2006/// PY - 2006/// SP - 10 ER - TY - JOUR TI - Screening of thermophilic anaerobic bacteria for solid substrate cultivation on lignocellulosic substrates AU - Chinn, MS AU - Nokes, SE AU - Strobel, HJ T2 - BIOTECHNOLOGY PROGRESS AB - Interest in solid substrate cultivation (SSC) techniques is gaining for biochemical production from renewable resources; however, heat and mass transfer problems may limit application of this technique. The use of anaerobic thermophiles in SSC offers a unique solution to overcoming these challenges. The production potential of nine thermophilic anaerobic bacteria was examined on corn stover, sugar cane bagasse, paper pulp sludge, and wheat bran in submerged liquid cultivation (SmC) and SSC. Production of acetate, ethanol, and lactate was measured over a 10 day period, and total product concentrations were used to compare the performance of different organism-substrate combinations using the two cultivation methods. Overall microbial activity in SmC and SSC was dependent on the organism and growth substrate. Clostridium thermocellum strains JW20, LQRI, and 27405 performed significantly better in SSC when grown on sugar cane bagasse and paper pulp sludge, producing at least 70 and 170 mM of total products, respectively. Growth of C. thermocellum strains in SSC on paper pulp sludge proved to be most favorable, generating at least twice the concentration of total products produced in SmC (p-value < 0.05). Clostridium thermolacticum TC21 demonstrated growth on all substrates producing 30-80 and 60-116 mM of total product in SmC and SSC, respectively. Bacterial species with optimal growth temperatures of 70 degrees C grew best on wheat bran in SmC, producing total product concentrations of 45-75 mM. For some of the organism-substrate combinations total end product concentrations in SSC exceeded those in SmC, indicating that SSC may be a promising alternative for microbial activity and value-added biochemical production. DA - 2006/// PY - 2006/// DO - 10.1021/bp050163x VL - 22 IS - 1 SP - 53-59 SN - 1520-6033 ER - TY - JOUR TI - SEUSS and LEUNIG regulate cell proliferation, vascular development and organ polarity in Arabidopsis petals AU - Franks, Robert G. AU - Liu, Zhongchi AU - Fischer, Robert L. T2 - PLANTA DA - 2006/9// PY - 2006/9// DO - 10.1007/s00425-006-0264-6 VL - 224 IS - 4 SP - 801-811 SN - 0032-0935 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33745961426&partnerID=MN8TOARS KW - adaxial KW - FILAMENTOUS FLOWER KW - GRAMINIFOLIA KW - PHABULOSA KW - STYLOSA KW - YABBY ER - TY - JOUR TI - Electromagnetic fields (900 MHz) evoke consistent molecular responses in tomato plants AU - Roux, David AU - Vian, Alain AU - Girard, Sebastien AU - Bonnet, Pierre AU - Paladian, Francoise AU - Davies, Eric AU - Ledoigt, Gerard T2 - PHYSIOLOGIA PLANTARUM AB - Although the effects of high-frequency electromagnetic fields on biological systems have been studied frequently, unequivocal results have rarely been obtained, primarily because suitably controlled experiments could not be performed. In the present work, tomato plants were exposed to a homogeneous and isotropic field (900 MHz) using a mode stirred reverberation chamber, and the stress-related transcripts (calmodulin, protease inhibitor and chloroplast mRNA-binding protein) were assayed by real-time quantitative PCR. Exposure to an electromagnetic field induced a biphasic response, in which the levels of all three transcripts increased four- to six-fold 15 min after the end of electromagnetic stimulation, dropped to close to initial levels by 30 min, and then increased again at 60 min. We deliberately focused on the very early molecular responses to high-frequency electromagnetic fields in order to minimize secondary effects. The development and increased use of wireless communication technologies in recent years have aroused suspicion that there may be hazardous effects of High-Frequency (HF) Electromagnetic Fields (HF-EMFs) on living systems, including humans (Elwood 2003). A wide range of EM signals emitted by the global system for mobile phone (GSM) networks are mixed in urban areas locally displaying an HF-EM environment with amplitudes of several volts per meter. Frequently, mobile phones or mobile phone-like devices are used for eletromagnetic exposure experiments (Dasdag et al. 2003, Haarala et al. 2003, Irmak et al. 2002, Weisbrot et al. 2003), as are other emitting devices, such as transversal electromagnetic cells (Marinelli et al. 2004), parallel plate resonators (Mashevich et al. 2003), wave guides (Czyz et al. 2004) and anechoic chambers (Gos et al. 2000). We utilized a Mode Stirred Reverberation Chamber (MSRC), since it has recently been recognized in the IEC 61000-4-21 standard (IEC 2003) as a stimulation device. The main advantages of the MSRC are that it provides protection from environmental EMF and creates a statistically isotropic and homogeneous EMF similar to that found in urban environments (Otterskog and Madsén 2003), ensuring that experiments are directly related to the sole variable, that of EMF exposure. The majority of EMF studies, especially in epidemiology, have led to highly conflicting conclusions (Elwood 2003; Levin 2003). For example, human behaviors such as cognitive performance (Haarala et al. 2003) and comportment (D'Andrea et al. 2003) did not yield conclusive results, because of the difficulty in evaluating psychology-related parameters. Similar kinds of problem have been encountered with animals (mainly rabbit and rat by Irmak et al. 2002 and Dasdag et al. 2003), due to the stress generated by the experimental protocol. Data obtained from culture of immunity-related cells (Aldinucci et al. 2003; Marinelli et al. 2004; Mashevich et al. 2003) are the most convincing: they show effects of HF-EMF at the cellular or molecular level (such as decrease in DNA stability, Ca2+ movement, deregulation of apoptosis). However, an intact organism is preferable to cultured cells, since the former maintains its full potential for signal perception, transduction and response. With this in mind, we focused our attention on the tomato plant (Lycopersicon esculentum), the model system for studying plant responses to environmental stresses such as wounding, in order to circumvent any psychological factors and to allow control of all potential environmental variables (i.e. light, temperature, nutrients, handling) that may modulate perception of, or response to, the EMF stimulus. Plants, notably flax, have already given noteworthy results in response to HF-EMF (Tafforeau et al. 2002, 2004, 2006). Many studies focused on animal behavior and cancer have furnished contradictory results because of the difficulty in identifying relevant parameters that are measurable in a rapid and repeatable manner. This contrasts with experiments associated with clearly defined parameters such as oxidative stress (Irmak et al. 2002), gene expression (Czyz et al. 2004), Ca2+ movement (Aldinucci et al. 2003), genomic stability (Marinelli et al. 2004), or heat shock proteins (Weisbrot et al. 2003), which generate reproducible data. However, many of these studies measured responses after hours (Marinelli et al. 2004), days (Mashevich et al. 2003) or even months (Dasdag et al. 2003) following the electromagnetic stimulus. In striking contrast, we were interested in the very rapid molecular responses following electromagnetic stimulation, in order to minimize side effects and the possible influence of other factors. To do this, we measured changes in the abundance of three previously identified wound-induced transcripts that are known to play a role in the early events of plant responses to stress. Here we show that a non-thermal HF-EMF (900 MHz, 5 V m−1) is able to evoke rapid accumulation of these transcripts. Future work will be directed towards the global analysis of microwave-induced gene expression (microarrays) and comparison with other stresses. Tomato plants (Lycopersicon esculentum cv. VFN-8) were grown inside a plywood custom-made culture chamber for 3 weeks (until the fourth terminal leaf appears). A controlled hydroponic system was used for culture with a light/dark photoperiod of 16 : 8 h, 26 : 21°C (150 μmol m−2 s−1 light intensity, Mazdafluor blanc industrie, Mazda-Philips, Paris, France). The MSRC is a system with several essential components constructed especially to give reproducible EMF stimulation (Fig. 1). It consists of: a large room with a double-layered steel wall, acting as a Faraday cage and protecting experiments from environmental electromagnetic pollution; an antenna to generate the EMF; movable blades to stir the EMF so that it is statistically homogeneous and isotropic in a determined working volume; and a control panel to generate the appropriate EMF with the following characteristics: frequency, 900 MHz non-modulated; amplitude, 5 V m−1(average signal amplitude of a GSM telephone) and 40 V m−1 (close to the French legal emission limit); duration, 2–10 min (within the duration of a GSM phone call). The culture chambers containing plants were placed in the working volume of the MSRC 24 h prior to EMF exposure, to avoid possible stress responses due to the moving procedure. The wooden culture chamber had no major influence on the EMF characteristics (homogeneity and isotropy) received. In control (i.e. ‘shielding') experiments, plants were placed in the culture chamber enclosed in a polymer mesh covered with aluminum foil to prevent exposure to EMF (Vian et al., 2006). In all cases, the fourth leaf of control and treated plants was harvested at the appropriate time and immediately frozen in liquid nitrogen. A single plant was used for each point of the kinetic, and the experiments were independently repeated at least three times. The plants were discarded after tissue collection. The MSRC equipment especially designed to generate homogeneous and isotropic HF-EMF. mRNA extraction was performed using Tri-reagent (Sigma), and the ‘advantage RT-for-PCR kit’ (BD Biosciences) was used for cDNA synthesis, both according to the manufacturer’s instructions. Amplifications were conducted on an iCycler iQ (Bio-Rad) with the qPCR Mastermix Plus for SYBR Green I (Eurogentec). The abundance of targeted genes transcripts was normalized to actin mRNA and set relative to the control plant (C, not exposed, harvested before electromagnetic exposure) according to the 2-ΔΔCT method (Livak and Schmittgen, 2001). The accession numbers of targeted genes are: actin, BM956640; calmodulin-N6, Y14764; chloroplast mRNA-binding protein (cmbp), AF106660; and proteinase inhibitor (pin2), AY129402. Exposure of tomato plants to an EMF of 900 MHz, 5 V m−1 for 10 min led to changes in abundance of all three stress-related transcripts, calmodulin-N6, cmbp and pin2 (Fig. 2, black bars). Calmodulin-N6 (Fig. 2A) and cmbp mRNA (Fig. 2B) accumulated strongly (5.5- and 6.6-fold respectively) by 15 min, declined to levels indistinguishable from those in the shielded plants at 30 min, and showed somewhat weaker accumulation at 60 min (5.3- and 5.1-fold respectively). The pin2 transcript gave slightly smaller responses, 4.2-fold at 15 min and 3.4-fold at 60 min (Fig. 2C). When plants were totally shielded from the EMF in the aluminum-enclosed culture chamber, the accumulation of mRNA was strongly reduced (Fig. 2. white bars), verifying that the responses did, indeed, result from EMF exposure. Abundance of stress-related transcripts after exposure to EMF. Tomato plants were grown as described in Materials and methods and transferred into the MSRC 24 h prior experiment: EMF exposure for 10 min at 900 MHz (black bars), or shielding from exposure (white bars). At different times after exposure, RNA was isolated; the amount of transcript encoding calmodulin-N6 (A), cmbp (B) and pin2 (C) was quantified by RT-qPCR and normalized to the amount of the housekeeping transcript, actin. Values are expressed relative to the control (not exposed plant) value. Bars represent mean values ± SEM from at least three independent experiments. In order to determine if there was a dose–response relationship between the EMF applied and the amount of transcript accumulated, we subjected plants to the dose used in Fig. 2 (5 V m−1 for 10 min), a dose of higher amplitude (40 V m−1 for 10 min), a dose of shorter duration (5 V m−1 for 2 min), and no dose (shielded plants), and measured pin2 mRNA accumulation (Fig. 3). Furthermore, to determine how rapidly transcript accumulation occurs, plants were also harvested immediately (0 min) and 5 min after EMF exposure. Transcript accumulation was essentially identical at the two higher doses (Fig. 3, black bars and gray bars), being about five-fold at 15 min and four-fold at 60 min, but there was no transcript accumulation at the low dose (Fig. 3, hatched bars) or in the shielded plants (Fig. 3, white bars). No transcript accumulation occurred prior to 15 min (Fig. 3). Abundance of pin2 transcripts after exposure to different amplitude/duration of EMF. Conditions are the same as Fig. 2. pin2 transcript were measured and EMF was applied at 40 V m−1 for 10 min (black bars); 5 V m−1 for 10 min (gray bars), or 5 V m−1 for 2 min (hatched bars), or the plants were not exposed (shielded) (white bars). The purpose of this study was to determine whether short exposure (10 min) of a plant to low-level (5 V m−1) HF-EMF (900 MHz), similar to that used in cell phones, could evoke a rapid biological response at the molecular level in tomato plants. We think that EMF could constitute a genuine environmental stimulus/stress for tomato plants, insofar as it evokes rapid and strong molecular responses – the accumulation of stress-related transcripts. Our results tend to show a direct relationship between HF-EMF exposure of tomato plants and responses at the level of gene expression. Although not identical, the kinetics and amplitudes (three- to seven-fold increases) of the targeted transcripts showed striking similarities with the previously described physiologic responses following injurious treatments such as leaf flaming or electrical stimulation (Stankovic and Davies 1997, Vian et al. 1999). Accordingly, we propose here that HF-EMF exposure may constitute an environmental stimulus for the tomato plants. Calmodulin is the major cell Ca2+ receptor and plays a central role in the early events of cell stress responses (Yang and Poovaiah 2003), while cmbp and pin2 are expressed after wounding (flaming, insect bite) (Vian et al. 1999, Zhang et al. 2004). The fact that they all accumulate rapidly indicates that plant stress response pathways are affected by HF-EMF. Surprisingly, all transcripts showed the maximum accumulation at the same time point (15 min after the end of the electromagnetic exposure), and had the same accumulation profile (two distinct peaks separated by a sharp decrease). These similarities (in terms of kinetics and amplitude) indicate the existence of a primary signal able to trigger the molecular response. Such biphasic accumulation of stress transcripts has been observed before in response to flame wounding (Peña-Cortès et al. 1995) and has led to various hypotheses concerning the nature of the primary signal: chemical, hydraulic or electrical, or a combination of these (Davies and Stankovic, 2006). Indeed, it is quite possible that three distinct signals are involved: the first stimulating the initial synthesis of the transcripts; the second evoking their degradation; and the third stimulating the later burst of synthesis. The interaction between EMF and the biological sample is not yet understood (Lacy-Hulbert 1998). Frequently, it appears that most of the observed biological responses are due to a ‘thermal’ effect (D’Andrea et al. 2003, Meltz 2003). The energy used here in the electromagnetic exposure was very low (close to 0.1 W dissipated in 200 m3) and did not produce any thermal effect. It is important to note that duration (10 min), amplitude (5 V m−1), homogeneity and isotropy of the EMF exposure were representative of a standard mobile phone emission. The shielding experiments showed reduced accumulation of the tested transcripts (Fig. 2). This result could also indicate a slower plant response to the remaining EMF (0.5 V m−1) present in the aluminum enclosed culture chamber. This interpretation may explain the consistent accumulation of cmbp transcripts (particularly at 30 min) in the shielded chamber. The amplitude of 40 V m−1 is close to the maximum authorized emission of GSM base antennae according to International Commission on Non-Ionizing Radiation Protection guidelines (ICNIRP 1998). Surprisingly, no significant differences occurred in the kinetics or levels of pin2 mRNA accumulation between 5 V m−1 and 40 V m−1 exposure (Fig. 3). Interestingly, decreasing the duration of exposure to EMF (from 10 to 2 min), at a fixed amplitude of 5 V m−1, suppressed the molecular response (Fig. 3). There is therefore no direct link between the amplitude of the stimulation and the amplitude of the plant response. These results suggest the concept of an ‘all-or-nothing’ response, which is characteristic of the action potential (AP), the only ‘genuine’ electrical signal found in plants (Bowles 1995, Davies 2006). However, the propagation of a variation potential (VP), produced after an injurious stimulation, could also be implicated. Specific investigations using electrophysiological methods would be required to determine this. Preliminary results indicate that a rapid signal is actually transmitted through the plant after local stimulation (data not shown). Our results concerning calmodulin-N6 suggest that variations in cytoplasmic and membrane-neighboring Ca2+ concentrations are early events in plant responses to EMF stimuli. The EMF could interact with moving charges or charged species (Levin 2003) such as hydrogen ions, which are implicated in various biological processes. Moreover, HF-EMF may lead to ion movement, directly or indirectly, and particularly near the plasma membrane (Lacy-Hulbert et al. 1998), and this could initiate the biological response. This ‘ionic’ explanation is particularly attractive when considering the ionic (Ca2+, Cl−, K+) nature of the plant AP (Davies 2006, Davies and Stankovic 2006). This work suggests the existence of a formal connection between HF-EMF exposure of intact plants and very rapid molecular responses. Assuming that a stress response is really demonstrated, actual damage could occur, but this has not yet been proven (the HF-EMF does not cause any obvious physical tissue damage). The basic claim that low-intensity HF-EMF actually causes a measurable reaction in plant should not be underestimated, or overestimated. In particular, the relevance of these observations to other biological systems must not be overstated. Finally, the ultimate goal of this work is to use microarrays to identify the similarities and differences between microwave-induced genes and those induced by injurious treatments such as flame wounding (Stankovic and Davies 1997, Vian et al. 1999). Edited by C. Guy Acknowledgements – This work was supported in part by grant RTM0005 ‘Effets biologiques et sanitaires de la radiotéléphonie mobile’ awarded to G. Ledoigt by the Ministère déléguéà l’Enseignement supérieur et à la Recherche. The authors thank R. Rechat and L. Chastaing (Blaise Pascal university technical service) for the construction of the culture chamber. DA - 2006/10// PY - 2006/10// DO - 10.1111/j.1399-3054.2006.00740.x VL - 128 IS - 2 SP - 283-288 SN - 1399-3054 ER - TY - JOUR TI - A universal role for inositol 1,4,5-trisphosphate-mediated signaling in plant gravitropism AU - Perera, IY AU - Hung, CY AU - Brady, S AU - Muday, GK AU - Boss, WF T2 - PLANT PHYSIOLOGY AB - Inositol 1,4,5-trisphosphate (InsP3) has been implicated in the early signaling events of plants linking gravity sensing to the initiation of the gravitropic response. However, at present, the contribution of the phosphoinositide signaling pathway in plant gravitropism is not well understood. To delineate the role of InsP3 in plant gravitropism, we generated Arabidopsis (Arabidopsis thaliana) plants constitutively expressing the human type I inositol polyphosphate 5-phosphatase (InsP 5-ptase), an enzyme that specifically hydrolyzes InsP3. The transgenic plants show no significant differences in growth and life cycle compared to wild-type plants, although basal InsP3 levels are reduced by greater than 90% compared to wild-type plants. With gravistimulation, InsP3 levels in inflorescence stems of transgenic plants show no detectable change, whereas in wild-type plant inflorescences, InsP3 levels increase approximately 3-fold within the first 5 to 15 min of gravistimulation, preceding visible bending. Furthermore, gravitropic bending of the roots, hypocotyls, and inflorescence stems of the InsP 5-ptase transgenic plants is reduced by approximately 30% compared with the wild type. Additionally, the cold memory response of the transgenic plants is attenuated, indicating that InsP3 contributes to gravisignaling in the cold. The transgenic roots were shown to have altered calcium sensitivity in controlling gravitropic response, a reduction in basipetal indole-3-acetic acid transport, and a delay in the asymmetric auxin-induced beta-glucuronidase expression with gravistimulation as compared to the controls. The compromised gravitropic response in all the major axes of growth in the transgenic Arabidopsis plants reveals a universal role for InsP3 in the gravity signal transduction cascade of plants. DA - 2006/2// PY - 2006/2// DO - 10.1104/pp.105.075119 VL - 140 IS - 2 SP - 746-760 SN - 1532-2548 ER - TY - JOUR TI - Relative activity of a tobacco hybrid expressing high levels of a tobacco anionic peroxidase and maize ribosome-inactivating protein against Helicoverpa zea and Lasioderma serricorne AU - Dowd, PF AU - Holmes, RA AU - Pinkerton, TS AU - Johnson, ET AU - Lagrimini, LM AU - Boston, RS T2 - JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY AB - Tobacco (Nicotiana tabacum) plants grown from seed obtained by crossing a tobacco line that expressed an activated maize ribosome-inactivating protein (RIP) with a line that overexpressed tobacco anionic peroxidase were tested for their effects on corn earworm Helicoverpa zea and cigarette beetle Lasioderma serricorne larvae as compared to the wild-type plant cross. Significant feeding reductions were noted for transgenic plants expressing both resistance proteins as compared to wild-type plants for both H. zea and L. serricorne. Significant increases in mortality were also noted for those insects fed on the transgenic cross as compared to wild-type plants in some cases. Levels of both peroxidase and maize RIP were significantly higher in transgenic as compared to wild-type plants (which did not produce maize RIP). The degree of feeding was significantly negatively correlated with the level of RIP or peroxidase individually. Keywords: Helicoverpa; Lasioderma; peroxidase; ribosome-inactivating protein; insect resistance; transgenic DA - 2006/4/5/ PY - 2006/4/5/ DO - 10.1021/jf058180p VL - 54 IS - 7 SP - 2629-2634 SN - 1520-5118 KW - Helicoverpa KW - Lasioderma KW - peroxidase KW - ribosome-inactivating protein KW - insect resistance KW - transgenic ER - TY - JOUR TI - Phenotypic variation and natural selection at Catsup, a pleiotropic quantitative trait gene in Drosphila AU - Carbone, Mary Anna AU - Jordan, Katherine W. AU - Lyman, Richard F. AU - Harbison, Susan T. AU - Leips, Jeff AU - Morgan, Theodore J. AU - DeLuca, Maria AU - Awadalla, Philip AU - Mackay, Trudy F. C. T2 - CURRENT BIOLOGY AB - Quantitative traits are shaped by networks of pleiotropic genes [1Mackay T.F.C. The genetic architecture of quantitative traits.Annu. Rev. Genet. 2001; 35: 303-339Crossref PubMed Scopus (753) Google Scholar]. To understand the mechanisms that maintain genetic variation for quantitative traits in natural populations and to predict responses to artificial and natural selection, we must evaluate pleiotropic effects of underlying quantitative trait genes and define functional allelic variation at the level of quantitative trait nucleotides (QTNs). Catecholamines up (Catsup), which encodes a negative regulator of tyrosine hydroxylase [2Stathakis D.G. Burton D.Y. McIvor W.E. Krishnakumar S. Wright T.R. O'Donnell J.M. The Catecholamines up (Catsup) protein of Drosophila melanogaster functions as a negative regulator of tyrosine hydroxylase activity.Genetics. 1999; 153: 361-382Crossref PubMed Google Scholar], the rate-limiting step in the synthesis of the neurotransmitter dopamine, is a pleiotropic quantitative trait gene in Drosophila melanogaster [2Stathakis D.G. Burton D.Y. McIvor W.E. Krishnakumar S. Wright T.R. O'Donnell J.M. The Catecholamines up (Catsup) protein of Drosophila melanogaster functions as a negative regulator of tyrosine hydroxylase activity.Genetics. 1999; 153: 361-382Crossref PubMed Google Scholar, 3O'Donnell J.M. Wang Z. Chaudhuri A. Effects of perturbation of catecholamine regulation on resistance of Drosophila melanogaster to environmental stress.in: Blau N. Thony B. Pterins, Folates, and Related Biogenic Amines. SPS Publications, Heilbronn2004: 94-100Google Scholar, 4Mackay T.F.C. Roshina N.V. Leips J.W. Pasyukova E.G. Complex genetic architecture of Drosophila longevity.in: Masaro E.J. Austad S.N. Handbook of the Biology of Aging. Sixth Edition. Elsevier Press, Burlington2005: 181-216Crossref Scopus (24) Google Scholar]. We used association mapping to determine whether the same or different QTNs at Catsup are associated with naturally occurring variation in multiple quantitative traits. We sequenced 169 Catsup alleles from a single population and detected 33 polymorphisms with little linkage disequilibrium (LD). Different molecular polymorphisms in Catsup are independently associated with variation in longevity, locomotor behavior, and sensory bristle number. Most of these polymorphisms are potentially functional variants in protein coding regions, have large effects, and are not common. Thus, Catsup is a pleiotropic quantitative trait gene, but individual QTNs do not have pleiotropic effects. Molecular population genetic analyses of Catsup sequences are consistent with balancing selection maintaining multiple functional polymorphisms. DA - 2006/5/9/ PY - 2006/5/9/ DO - 10.1016/j.cub.2006.03.051 VL - 16 IS - 9 SP - 912-919 SN - 1879-0445 ER - TY - JOUR TI - Gene targeting in plants: fingers on the move AU - Kumar, S AU - Allen, GC AU - Thompson, WF T2 - TRENDS IN PLANT SCIENCE AB - Zinc-finger endonucleases (ZFNs) make targeted double-stranded breaks in genomic DNA and, thus, stimulate recombination and repair processes at specific sites. ZFNs can now be harnessed to stimulate homologous recombination and gene targeting in plants, which represents a major step towards modifying the plant genome more precisely. ZFN-mediated gene targeting is likely to become a powerful tool for genome research and genetic engineering. DA - 2006/4// PY - 2006/4// DO - 10.1016/j.tplants.2006.02.002 VL - 11 IS - 4 SP - 159-161 SN - 1360-1385 ER - TY - JOUR TI - Species Level Phylogeny of the Genus Cornus (Cornaceae) Based on Molecular and Morphological Evidence-Implications for Taxonomy and Tertiary Intercontinental Migration AU - Xiang, Qiu-Yun (Jenny) AU - Thomas, David T. AU - Zhang, Wenheng AU - Manchester, Steven R. AU - Murrell, Zack T2 - Taxon AB - Abstract DNA sequences were generated for matK and ITS for 68 and 103 samples of Cornus to reconstruct a species level phylogeny of the genus. The results support the monophyly of most subgenera, except subg. Kraniopsis and subg. Cornus. Subgenus Kraniopsis was suggested to exclude C. peruviana from South America and subg. Afrocrania and subg. Sinocornus were nested within subg. Cornus. Four major clades corresponding to groups also recognizable by morphological differences were revealed: the big‐bracted dogwoods (BB) including subg. Cynoxylon, subg. Syncarpea, and subg. Discocrania, the dwarf dogwoods (DW) including subg. Arctocrania, the cornelian cherries (CC) including subg. Cornus, subg. Sinocornus, and subg. Afrocrania, and the blue‐ or white‐fruited dogwoods (BW) including subg. Kraniopsis, subg. Mesomora, and subg. Yinquania. This finding is consistent with previous studies with more limited sampling. The single South American species C. peruviana was found to be sister to the Asian C. oblonga of subg. Yinquania, adding a fourth intercontinental disjunction in the genus that was previously unknown. Species relationships within the subgenera were clearly resolved except for the relatively large subg. Syncarpea and subg. Kraniopsis. Phylogenetic analyses of total evidence combining morphology, matK, ITS, and previously published rbcL and 26S rDNA sequences resolved the relationships among subgenera as (BW(CC(BB, DW))). Biogeographic analyses using DIVA with or without fossils resulted in different inferences of biogeographic history of the genus, indicating the importance of fossil data in biogeographic analyses. The phylogeny based on the total evidence tree including fossils supports an origin and early Tertiary diversification of Cornus in Europe and multiple trans‐Atlantic migrations between Europe and North America by the early Tertiary. It also supports that distribution of the few species in the southern hemisphere was not ancestral, but a result of migration from the north. This evidence rejects a previous hypothesis of a southern hemispheric origin of the genus. DA - 2006/2/1/ PY - 2006/2/1/ DO - 10.2307/25065525 VL - 55 IS - 1 SP - 9 LA - en SN - 00400262 UR - http://doi.wiley.com/10.2307/25065525 DB - Crossref Y2 - 2019/1/29/ KW - biogeography KW - Cornus KW - Cornaceae KW - ITS KW - matK KW - morphology KW - phylogeny ER -