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{{Template:Pecinka Lab}}
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<h3><font style="color:#31B404;">Research</font></h3>
<h3><font style="color:#31B404;">Research</font></h3>
The goal of the Pecinka lab is to understand molecular mechanisms shaping plant genomes. To this end we use the model plant ''Arabidopsis thaliana'' and several other ''Brassicaceae'' and analyze them by using forward and reverse genetics, molecular, biochemical, cytogenetic and bioinformatic methods.


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.
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.


Our wiki site was developed under [http://openwetware.org/wiki/Main_Page OpenWetWare], an open access effort to promote sharing of information among biologists.
[[Pecinka_Lab:Research | read more...]]


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...]]
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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]]


*[[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:Chun Hsin Liu|Chun Hsin Liu (Phoebe)]]
*[[Pecinka_Lab:Thomas_Piofczyk|Thomas Piofczyk]]
*[[Pecinka_lab:Catarine Markus|Catarine Markus]]
*[[Pecinka_Lab:Giang Vu|Giang Vu]]
*[[Pecinka_lab:Kashif Nawaz|Kashif Nawaz]]
 
*[[Pecinka_lab:Anna_Nowicka|Anna Nowicka]]
<h3><font style="color:#4169E1;">Visiting Students</font></h3>
*[[Pecinka_lab:Bjoern_Pietzenuk|Björn Pietzenuk]]
*[[Pecinka_Lab:Pawel_Mikulski|Pawel Mikulski]]
*[[Pecinka_Lab:Miriam_Schleinitz|Miriam Schleinitz]]


<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:People|see complete list...]]
[[Pecinka_lab:People|see complete list...]]








[http://www4.clustrmaps.com/user/efef92c9 http://www4.clustrmaps.com/stats/maps-no_clusters/openwetware.org-wiki-Pecinka_Lab-thumb.jpg]


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<h3><font style="color:#FF8C00;">Recent Publications</font></h3>


*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...]]


<h3><font style="color:#FF8C00;">Recent Publications</font></h3>
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*Pecinka A, Mittelsten Scheid O. Stress-induced chromatin changes: A critical view on their heritability. Plant Cell Physiology doi: 10.1093/pcp/pcs044 (2012). [http://pcp.oxfordjournals.org/content/early/2012/03/28/pcp.pcs044.abstract]  
<h3><font style="color:red">News</font></h3>
*Alcázar R, Pecinka A, Aarts MGM, Fransz PF, Koornneef M. Signals of speciation within Arabidopsis thaliana in comparison with its relatives. Curr Opin Plant Biol 15:205-211 (2012). [http://www.sciencedirect.com/science/article/pii/S1369526612000039]
*2015-10-29: Björn successfully defended his PhD work at University of Cologne. Well done!
*Pecinka A, Fang W, Rehmsmeier M, Levy AA, Mittelsten Scheid O. Polyploidization increases meiotic recombination frequency in Arabidopsis. BMC Biology 9:24 (2011). [http://www.biomedcentral.com/1741-7007/9/24]
*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]
*Pecinka A, Dinh HQ, Rosa M, Baubec T, Lettner N, Mittelsten Scheid O. Epigenetic control of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell 22: 3118–3129 (2010). [http://www.plantcell.org/content/22/9/3118.full]
*2015-09-29: 60 km lab bike trip to Ville forest near Cologne. Well done!
*Pecinka A, Rosa M, Schikora A, Berlinger M, Hirt H, Luschnig C, Mittelsten Scheid O. Transgenerational stress memory is not a general response in Arabidopsis. PLoS One 4:e5202 (2009). [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005202]
*2015-09-28: Anna Nowicka joined the lab for her DAAD post-doc.
*2015-09-18: Collaborative paper on the re-annotation of ''Arabidopsis lyrata'' genome was published in PLoS One [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137391 Open access]
*2015-09-04: Pecinka lab was promoted to Max Planck Research group.
*2015-07-16: There is plenty of microbial life inside carnivorous plant traps [http://journal.frontiersin.org/article/10.3389/fmicb.2015.00526/abstract ...]


*[[Pecinka_Lab:Publications|see complete list...]]


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<h3><font style="color:#F8B603;">Seminars</font></h3>
*[[Pecinka_Lab:Group_meeting|Group meeting, journal clubs, and seminars]]
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<h3><font style="color:red">News</font></h3>
*2012-06-07: Pecinka lab website starts to run on the OpenWetWare
*2012-03-28: The review on Stress-Induced Chromatin Changes was published in PCP [http://pcp.oxfordjournals.org/content/early/2012/03/28/pcp.pcs044.abstract]
*2012-01: The review by Alcazar et al. on Signals of speciation in Arabidopsis and its relatives was published in COPB [http://www.sciencedirect.com/science/article/pii/S1369526612000039]
*2011-09: Grant on Epigenetic Control of Repetitive DNA in ''Arabidopsis lyrata'' funded by DFG




Revision as of 14:14, 29 October 2015


Home      Research      People      Publications      Protocols      Resources      Seminars      Positions      Lab life     


Research

The 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. read more...

Lab Members

Technitians


see complete list...



Recent Publications

  • 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 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. 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 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 Open access.
  • see complete list...

News

  • 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 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.
  • 2015-09-18: Collaborative paper on the re-annotation of Arabidopsis lyrata genome was published in PLoS One Open access
  • 2015-09-04: Pecinka lab was promoted to Max Planck Research group.
  • 2015-07-16: There is plenty of microbial life inside carnivorous plant traps ...





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