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| {{Template:Pecinka Lab}} | | {{Template:Pecinka Lab}} |
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| | <h3><font style="color:#31B404;">Research</font></h3> |
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| <h3><font style="color:#9ACD32;">Research</font></h3>
| | The Pecinka lab is hosted by the [http://www.mpipz.mpg.de/10574/koornneef-dpt Department of Plant Breeding and Genetics] at the [http://www.mpipz.mpg.de/2169/en Max Planck Institute for Plant Breeding Research] in Cologne, Germany. |
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| The goal of Pecinka lab is to understand molecular basis of mechanisms shaping plant genomes. We focus in particular on DNA repair and inactivation of repetitive DNA that both have potential to cause large genomic chages. To this end we use model species Arabidopsis thaliana and several other Brassicaceae and analyze them using forward and reverse genetics, molecular, biochemical, cytogenetic and bioinformatic methods.
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| Pecinka lab is hosted by the Department of Plant Breeding and Genetics at the Max Planck Institute for Plant Breeding Research in Cologne, Germany.
| | Our goal is to understand molecular and evolutionary mechanisms shaping plant genomes and epigenomes. We analyze how DNA sequence and chromatin changes are generated by endo- and exogenous factors and how these forces are balanced by the genome repair and epigenetic mechanisms. To this end we use mainly the model plant ''Arabidopsis thaliana'' and several other ''Brassicaceae'' and analyze them by forward and reverse genetics, molecular, biochemical, cytogenetic and bioinformatic methods. |
| | | [[Pecinka_lab:Research | read more...]] |
| Our wiki site is developed under Openwetware, an open access effort to promote the sharing of information among researchers working in biology.
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| [[Pecinka_Lab:Research | read more...]] | |
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| <h3><font style="color:#4169E1;">Lab Members</font></h3> | | <h3><font style="color:#4169E1;">Lab Members</font></h3> |
| | *[[Pecinka_lab:Ales_Pecinka|Ales Pecinka]] |
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| *[[Pecinka_Lab:Ahmed_Abdelsamad|Ahmed Abdelsamad]] | | *[[Pecinka_lab:Heinrich Bente|Heinrich Bente]] |
| *[[Pecinka_Lab:Chun Hsin Liu|Chun Hsin Liu (Phoebe)]] | | *[[Pecinka_lab:Mariana_Diaz|Mariana Andrea Diaz Smoje]] |
| *[[Pecinka_Lab:Ales_Pecinka|Ales Pecinka]] | | *[[Pecinka_lab:Andreas_Finke|Andreas Finke]] |
| *[[Pecinka_Lab:Björn_Pietzenuk|Björn Pietzenuk]] | | *[[Pecinka_lab:Catarine Markus|Catarine Markus]] |
| *[[Pecinka_Lab:Thomas_Piofczyk|Thomas Piofczyk]] | | *[[Pecinka_lab:Kashif Nawaz|Kashif Nawaz]] |
| *[[Pecinka_Lab:Giang Vu|Giang Vu]] | | *[[Pecinka_lab:Anna_Nowicka|Anna Nowicka]] |
| | | *[[Pecinka_lab:Bjoern_Pietzenuk|Björn Pietzenuk]] |
| <h3><font style="color:#4169E1;">Visiting Students</font></h3>
| | *[[Pecinka_lab:Ugur_Ercan|Ugur Ercan]] |
| *[[Pecinka_Lab:Pawel_Mikulski|Pawel Mikulski]] | |
| *[[Pecinka_Lab:Miriam_Schleinitz|Miriam Schleinitz]] | |
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| <h3><font style="color:#4169E1;">Technitians</font></h3> | | <h3><font style="color:#4169E1;">Technitians</font></h3> |
| *[[Pecinka_Lab:Barbara_Eilts|Barbara_Eilts]] | | *[[Pecinka_lab:Barbara_Eilts|Barbara Eilts]] |
| *[[Pecinka_Lab:Petra_Pecinkova|Petra Pecinkova]] | | *[[Pecinka_lab:Petra_Pecinkova|Petra Pecinkova]] |
| | | *[[Pecinka_lab:Valentina_Strizhova|Valentina Strizhova]] |
| <h3><font style="color:#4169E1;">Alumni</font></h3>
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| *[[Pecinka_Lab:Alexander Schott|Alexander Schott]] | |
| *[[Pecinka_Lab:Anastasia Hoffmann|Anastasia Hoffmann]]
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| [[Pecinka_Lab:Alumni|See all former members...]]
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| <h3><font style="color:#FF8C00;">Recent Publications</font></h3>
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| *Pecinka A, Mittelsten Scheid O (2012): Stress-induced chromatin changes: A critical view on their heritability. Plant Cell Physiology doi: 10.1093/pcp/pcs044. [http://pcp.oxfordjournals.org/content/early/2012/03/28/pcp.pcs044.abstract]
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| *Alcázar R, Pecinka A, Aarts MGM, Fransz PF, Koornneef M (2012): Signals of speciation within Arabidopsis thaliana in comparison with its relatives. Curr Opin Plant Biol 15:205-211. [http://www.sciencedirect.com/science/article/pii/S1369526612000039]
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| *Pecinka A, Fang W, Rehmsmeier M, Levy AA, Mittelsten Scheid O (2011): Polyploidization increases meiotic recombination frequency in Arabidopsis. BMC Biology 9:24. [http://www.biomedcentral.com/1741-7007/9/24]
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| *Pecinka A, Dinh HQ, Rosa M, Baubec T, Lettner N, Mittelsten Scheid O (2010): Epigenetic control of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell 22: 3118–3129. [http://www.plantcell.org/content/22/9/3118.full]
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| *Pecinka A, Rosa M, Schikora A, Berlinger M, Hirt H, Luschnig C, Mittelsten Scheid O (2009): Transgenerational stress memory is not a general response in Arabidopsis. PLoS One 4:e5202. [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005202]
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| *[[Pecinka_Lab:Publications|see complete list...]]
| | [[Pecinka_lab:People|see complete list...]] |
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| <h3><font style="color:#F8B603;">Announcements</font></h3>
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| *[[Pecinka_Lab:Group_meeting|Group meeting, journal clubs, and seminars]]
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| <h3><font style="color:red">News</font></h3>
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| *2012-06-07: Pecinka lab page runs on OpenWetWare
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| <h3><font style="color:#F8B603;">Publications</font></h3> | | <h3><font style="color:#FF8C00;">Recent Publications</font></h3> |
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| *Kerwin, R. E., Jimenez-Gomez, J. M., Fulop, D., Harmer, S. L., Maloof, J. N. & Kliebenstein, D. J. Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis. Plant Cell 23, 471-485 (2011). [http://dx.doi.org/10.1105/tpc.110.082065] | | *Vu G.T.H., Schmutzer T., Bull F., Cao H.X., Fuchs J., Tran T.D., Jovtchev G., Pistrick K., Stein N., Pecinka A., Neumann P., Novak P., Macas J., Deard P.H., Blattner F.R., Scholz U., Schubert I (2015): Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus. Plant Genome doi:10.3835/plantgenome2015.04.0021 [https://dl.sciencesocieties.org/publications/tpg/articles/0/0/plantgenome2015.04.0021 Open access] |
| | *Rawat V., Abdelsamad A., Pietzenuk B., Seymour D.K., Koenig D., Weigel D., Pecinka A., Schneeberger K. (2015): Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data. PLoS One 10(9):e0137391. [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137391 Open access] |
| | *Cao H.X., Schmutzer T, Scholz U, Pecinka A, Schubert I, Vu G.T.H. (2015): Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species. Frontiers in Microbiology doi: 10.3389/fmicb.2015.00526 [http://journal.frontiersin.org/article/10.3389/fmicb.2015.00526/abstract Open access] |
| | *Liu C-H, Finke A, Diaz M, Rozhon W, Poppenberger B, Baubec T, Pecinka A. (2015): Repair of DNA Damage Induced by the Cytidine Analog Zebularine Requires ATR and ATM in Arabidopsis. Plant Cell doi/10.1105/tpc.114.135467 [http://www.plantcell.org/content/early/2015/05/28/tpc.114.135467.full.pdf+html Open access]. |
| | *[[Pecinka_lab:Publications|see complete list...]] |
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| *Chang, C. S., Maloof, J. N. & Wu, S. H. COP1-mediated degradation of BBX22/LZF1 optimizes seedling development in Arabidopsis. Plant Physiol (2011). [http://dx.doi.org/10.1104/pp.111.175042]
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| *Nozue, K., Harmer, S. L. & Maloof, J. N. Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PIF5 as a modulator of auxin signaling in Arabidopsis. Plant Physiol (2011). [http://dx.doi.org/10.1104/pp.111.172684] | | <h3><font style="color:red">News</font></h3> |
| | *2016-02-01: Heinrich selected to join Mittelsten Scheid lab at GMI Vienna as new Ph.D. student. Congratulations! |
| | *2016-01-01: Happy and successful new year 2016. |
| | *2015-12-20: Lab visit to the Christmas market |
| | *2015-10-29: Björn successfully defended his PhD work at University of Cologne. Well done! |
| | *2015-10-21: Reveal the secrets of minute carnivorous plant genome [https://dl.sciencesocieties.org/publications/tpg/articles/0/0/plantgenome2015.04.0021 Open access] |
| | *2015-09-29: 60 km lab bike trip to Ville forest near Cologne. Well done! |
| | *2015-09-28: Anna Nowicka joined the lab for her DAAD post-doc. |
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| *Kim, K., Shin, J., Lee, S. H., Kweon, H. S., Maloof, J. N. & Choi, G. Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors. Proc Natl Acad Sci U S A 108, 1729-1734 (2011). [http://dx.doi.org/10.1073/pnas.1011066108]
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| *Maloof, J. N. Recent advances in regulation of flowering. F1000 Biol Rep 2, (2010). [http://dx.doi.org/10.3410/B2-9]
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| *Brock, M. T., Dechaine, J. M., Iniguez-Luy, F. L., Maloof, J. N., Stinchcombe, J. R. & Weinig, C. Floral Genetic Architecture: An Examination of QTL Architecture Underlying Floral (Co)Variation Across Environments. Genetics 186, 1451-1465 (2010). [http://dx.doi.org/10.1534/genetics.110.119982]
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| *Brock, M. T., Maloof, J. N. & Weinig, C. Genes underlying quantitative variation in ecologically important traits: PIF4 (phytochrome interacting factor 4) is associated with variation in internode length, flowering time, and fruit set in Arabidopsis thaliana. Mol Ecol 19, 1187-1199 (2010). [http://dx.doi.org/10.1111/j.1365-294X.2010.04538.x]
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| *Jiménez-Gómez, J. M., Wallace, A. D. & Maloof, J. N. Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis. PLoS Genet 6, (2010). [http://dx.doi.org/10.1371/journal.pgen.1001100]
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| *Jimenez-Gomez, J. M. & Maloof, J. N. Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol 9, 85 (2009). [http://dx.doi.org/10.1186/1471-2229-9-85]
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| *Jiménez-Gómez, J. M. & Maloof, J. N. Plant research accelerates along the (bio)informatics superhighway: symposium on plant sensing, response and adaptation to the environment. EMBO Rep 10, 568-572 (2009). [http://dx.doi.org/10.1038/embor.2009.116]
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| *Schwartz, C., Balasubramanian, S., Warthmann, N., Michael, T. P., Lempe, J., Sureshkumar, S., Kobayashi, Y., Maloof, J. N., Borevitz, J. O., Chory, J. & Weigel, D. Cis-regulatory Changes at FLOWERING LOCUS T Mediate Natural Variation in Flowering Responses of Arabidopsis thaliana. Genetics 183, 723-32, 1SI-7SI (2009). [http://dx.doi.org/10.1534/genetics.109.104984]
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| *Balasubramanian, S., Schwartz, C., Singh, A., Warthmann, N., Kim, M. C., Maloof, J. N., Loudet, O., Trainer, G. T., Dabi, T., Borevitz, J. O., Chory, J. & Weigel, D. QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines. PLoS ONE 4, e4318 (2009). [http://dx.doi.org/10.1371/journal.pone.0004318]
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| *Covington, M. F., Maloof, J. N., Straume, M., Kay, S. A. & Harmer, S. L. Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol 9, R130 (2008). [http://dx.doi.org/10.1186/gb-2008-9-8-r130]
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| *Filiault, D. L., Wessinger, C. A., Dinneny, J. R., Lutes, J., Borevitz, J. O., Weigel, D., Chory, J. & Maloof, J. N. Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. Proc Natl Acad Sci U S A 105, 3157-3162 (2008). [http://dx.doi.org/10.1073/pnas.0712174105]
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| *Weinig, C., Johnston, J. A., Willis, C. G. & Maloof, J. N. Antagonistic multilevel selection on size and architecture in variable density settings. Evolution 61, 58-67 (2007). [http://dx.doi.org/10.1111/j.1558-5646.2007.00005.x]
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| *Nozue, K., Covington, M. F., Duek, P. D., Lorrain, S., Fankhauser, C., Harmer, S. L. & Maloof, J. N. Rhythmic growth explained by coincidence between internal and external cues. Nature 448, 358-361 (2007). [http://dx.doi.org/10.1038/nature05946]
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| *Maloof, J. N. Small but not forgotten. Heredity 96, 1-2 (2006). [http://dx.doi.org/10.1038/sj.hdy.6800708]
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| *Balasubramanian, S., Sureshkumar, S., Agrawal, M., Michael, T. P., Wessinger, C., Maloof, J. N., Clark, R., Warthmann, N., Chory, J. & Weigel, D. The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat Genet 38, 711-715 (2006). [http://dx.doi.org/10.1038/ng1818]
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| *Nozue, K. & Maloof, J. N. Diurnal regulation of plant growth. Plant Cell Environ 29, 396-408 (2006).
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| *Lu, L., Lee, Y. R., Pan, R., Maloof, J. N. & Liu, B. An internal motor kinesin is associated with the Golgi apparatus and plays a role in trichome morphogenesis in Arabidopsis. Mol Biol Cell 16, 811-823 (2005). [http://dx.doi.org/10.1091/mbc.E04-05-0400]
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| *Maloof, J. N. Plant development: slowing root growth naturally. Curr Biol 14, R395-R396 (2004). [http://dx.doi.org/10.1016/j.cub.2004.05.016]
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| *Wolyn, D. J., Borevitz, J. O., Loudet, O., Schwartz, C., Maloof, J., Ecker, J. R., Berry, C. C. & Chory, J. Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana. Genetics 167, 907-917 (2004). [http://dx.doi.org/10.1534/genetics.103.024810]
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| *Maloof, J. N. Genomic approaches to analyzing natural variation in Arabidopsis thaliana. Curr Opin Genet Dev 13, 576-582 (2003).
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| *Maloof, J. N. QTL for plant growth and morphology. Curr Opin Plant Biol 6, 85-90 (2003).
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| *Nemhauser, J. L., Maloof, J. N. & Chory, J. Building integrated models of plant growth and development. Plant Physiol 132, 436-439 (2003). [http://dx.doi.org/10.1104/pp.102.017061]
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