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<h3><font style="color:#31B404;">Research</font></h3>


<h3><font style="color:#F8B603;">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.


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.


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...]]
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<h3><font style="color:#4169E1;">Lab Members</font></h3>
 
*[[Pecinka_lab:Heinrich Bente|Heinrich Bente]]
*[[Pecinka_lab:Mariana_Diaz|Mariana Andrea Diaz Smoje]]
*[[Pecinka_lab:Andreas_Finke|Andreas Finke]]
*[[Pecinka_lab:Chun Hsin Liu|Chun Hsin Liu (Phoebe)]]
*[[Pecinka_lab:Catarine Markus|Catarine Markus]]
*[[Pecinka_lab:Ales_Pecinka|Ales Pecinka]]
*[[Pecinka_lab:Bjoern_Pietzenuk|Björn Pietzenuk]]
 
<h3><font style="color:#4169E1;">Technitians</font></h3>
*[[Pecinka_lab:Barbara_Eilts|Barbara Eilts]]
*[[Pecinka_lab:Petra_Pecinkova|Petra Pecinkova]]
 
 
[[Pecinka_lab:People|see complete list...]]


Our wiki site is developed under Openwetware, an open access effort to promote the sharing of information among researchers working in biology.
[[Pecinka_Lab:Research | read more...]]
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<h3><font style="color:#4169E1;">Lab Members</font></h3>


*[[Pecinka_Lab:Ahmed_Abdelsamad|Ahmed Abdelsamad]]
*[[Pecinka_Lab:Chun Hsin Liu|Chun Hsin Liu (Phoebe)]]
*[[Pecinka_Lab:Ales_Pecinka|Ales Pecinka]]
*[[Pecinka_Lab:Petra_Pecinkova|Petra Pecinkova]]
*[[Pecinka_Lab:Björn_Pietzenuk|Björn Pietzenuk]]
*[[Pecinka_Lab:Thomas_Piofczyk|Thomas Piofczyk]]
*[[Pecinka_Lab:Giang Vu|Giang Vu]]


<h3><font style="color:#4169E1;">Visiting Scholars</font></h3>
*[[Pecinka_Lab:Pawel_Mikulski|Pawel Mikulski]]


<h3><font style="color:#4169E1;">Alumni</font></h3>
|-
*[[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>


<h3><font style="color:#C9D3EB;">Recent Publications</font></h3>
*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 PDF].
*Baranauskė S, Mickutė M, Plotnikova A, Finke A, Venclovas Č, Klimašauskas S, Vilkaitis G. (2015): Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins. Nucleic Acids Research 43:2802-2812 [http://nar.oxfordjournals.org/content/43/5/2802.long Full text]
*Willing, Rawat et al. (2015): Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants 1:1-7 [http://www.nature.com/articles/nplants201423 Full text]
*Piofczyk T, Jeena G, Pecinka A. (2015): Arabidopsis thaliana natural variation reveals connections between UV radiation stress and plant pathogen-like defense responses. Plant Physiology Biochemistry DOI: 10.1016/j.plaphy.2015.01.011 (2015) [http://www.sciencedirect.com/science/article/pii/S0981942815000212 Full text]


*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]
*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]
*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]
*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]
*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]


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


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<h3><font style="color:#F8B603;">Announcements</font></h3>
*[[Pecinka_lab:Publications|see complete list...]]
*[[Pecinka_Lab:Group_meeting|Group meeting, journal clubs, and seminars]]
 
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<h3><font style="color:red">News</font></h3>
<h3><font style="color:red">News</font></h3>
*[http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5338&org=BIO NSF Plant Genome Research Program]
*2015-06-18: Phoebe defended her PhD work at University of Cologne. Amazing!
**[http://www-plb.ucdavis.edu/Labs/sinha/TomatoGenome/ GEPR: Elucidating gene networks regulating development in tomato]
*2015-06: Thomas leaving the lab after 4.5 years, Henrich starting his masters and Catarine joining the group for one year of her PhD.  
**[[Maloof_Lab:PGRP | Molecular evolutionary genetics of crop and weed responses to
*2015-06-15: Ahmed successfully defended his PhD work at University of Göttingen. Congratulations!
crowding]] (2002-2008)
*2015-06: Not only DNA demethylation - cytidine analog zebularine triggers DNA damage response in Arabidopsis. Read more in our recent Plant Cell paper [http://www.plantcell.org/content/early/2015/05/28/tpc.114.135467.full.pdf+html PDF]
*[http://www.hfsp.org/ Human Frontier Science Program] (2004-2008)
*2015-05: Andreas co-authored on the paper showing physical interaction between specific miRNA components. Congratulations! [http://nar.oxfordjournals.org/content/43/5/2802 Full text]
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[http://www4.clustrmaps.com/user/60a714c2 http://www4.clustrmaps.com/stats/maps-no_clusters/malooflab.openwetware.org--thumb.jpg]
 
 
 
 
 
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Revision as of 12:45, 18 June 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

  • 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 PDF.
  • Baranauskė S, Mickutė M, Plotnikova A, Finke A, Venclovas Č, Klimašauskas S, Vilkaitis G. (2015): Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins. Nucleic Acids Research 43:2802-2812 Full text
  • Willing, Rawat et al. (2015): Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants 1:1-7 Full text
  • Piofczyk T, Jeena G, Pecinka A. (2015): Arabidopsis thaliana natural variation reveals connections between UV radiation stress and plant pathogen-like defense responses. Plant Physiology Biochemistry DOI: 10.1016/j.plaphy.2015.01.011 (2015) Full text

News

  • 2015-06-18: Phoebe defended her PhD work at University of Cologne. Amazing!
  • 2015-06: Thomas leaving the lab after 4.5 years, Henrich starting his masters and Catarine joining the group for one year of her PhD.
  • 2015-06-15: Ahmed successfully defended his PhD work at University of Göttingen. Congratulations!
  • 2015-06: Not only DNA demethylation - cytidine analog zebularine triggers DNA damage response in Arabidopsis. Read more in our recent Plant Cell paper PDF
  • 2015-05: Andreas co-authored on the paper showing physical interaction between specific miRNA components. Congratulations! Full text





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