Pecinka lab: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
No edit summary
(35 intermediate revisions by the same user not shown)
Line 5: Line 5:
<h3><font style="color:#31B404;">Research</font></h3>
<h3><font style="color:#31B404;">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 Pecinka lab is hosted by the [http://www.mpipz.mpg.de/2169/en 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.
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. For our research we use ''Arabidopsis thaliana'', several other ''Brassicaceae'', selected crops and analyze them by forward and reverse genetics, molecular, biochemical, cytogenetic and bioinformatic methods.
[[Pecinka_lab:Research | read more...]]
[[Pecinka_lab:Research | read more...]]
|rowspan=2 width=200px style="padding: 5px; background-color: #ffffff; border: 0px solid #4169E1;" |
|rowspan=2 width=200px style="padding: 5px; background-color: #ffffff; border: 0px solid #4169E1;" |
Line 15: Line 15:
*[[Pecinka_lab:Ales_Pecinka|Ales Pecinka]]
*[[Pecinka_lab:Ales_Pecinka|Ales Pecinka]]


*[[Pecinka_lab:Heinrich Bente|Heinrich Bente]]
*[[Pecinka_lab:Mariana_Diaz|Mariana Andrea Diaz Smoje]]
*[[Pecinka_lab:Mariana_Diaz|Mariana Andrea Diaz Smoje]]
*[[Pecinka_lab:Annelotte_van_Dieren|Annelotte van Dieren]]
*[[Pecinka_lab:Andreas_Finke|Andreas Finke]]
*[[Pecinka_lab:Andreas_Finke|Andreas Finke]]
*[[Pecinka_lab:Chun Hsin Liu|Chun Hsin Liu (Phoebe)]]
*[[Pecinka_lab:Karin_Kruska|Karin Kruska]]
*[[Pecinka_lab:Catarine Markus|Catarine Markus]]
*[[Pecinka_lab:Kashif Nawaz|Kashif Nawaz]]
*[[Pecinka_lab:Kashif Nawaz|Kashif Nawaz]]
*[[Pecinka_lab:Bjoern_Pietzenuk|Björn Pietzenuk]]
*[[Pecinka_lab:Fen_Yang|Fen Yang]]
*[[Pecinka_lab:|Fugang Ren]]


<h3><font style="color:#4169E1;">Technitians</font></h3>
<h3><font style="color:#4169E1;">Technitians</font></h3>
Line 43: Line 41:
<h3><font style="color:#FF8C00;">Recent Publications</font></h3>  
<h3><font style="color:#FF8C00;">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].
*Willing E.M., Piofczyk T., Albert A., Winkler J.B., Schneeberger K., Pecinka A. (2016): UVR2 ensures transgenerational genome stability under simulated natural UV-B in ''Arabidopsis thaliana''. Nature Communications 7:13522. doi: 10.1038/ncomms13522. [http://www.nature.com/articles/ncomms13522 Open access]
*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]
*Pietzenuk B., Markus C., Gaubert H., Bagwan N., Merotto A., Bucher E., Pecinka A. (2016): Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. Genome Biology 17:209 DOI: 10.1186/s13059-016-1072-3 [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1072-3 Open access]
*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]
*Baroux C., Pecinka A., Fuchs J., Kreth G., Schubert I., Grossniklaus I. (2016): Non-random chromosome arrangement in triploid endosperm nuclei. Chromosoma doi:10.1007/s00412-016-0578-5 [http://link.springer.com/article/10.1007/s00412-016-0578-5 Open access]
*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]
*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]
 
 
 


*[[Pecinka_lab:Publications|see complete list...]]
*[[Pecinka_lab:Publications|see complete list...]]
Line 56: Line 51:


<h3><font style="color:red">News</font></h3>
<h3><font style="color:red">News</font></h3>
*2015-07-01: Kashif starts his PhD on stress induced chromatin changes.
*2016-12-01: Fast mutation accumulation under natural UV-B without pyrimidine dimer repair. See more in our new paper [http://www.nature.com/articles/ncomms13522 Open access]
*2015-06-18: Phoebe defended her PhD work at University of Cologne. Amazing!
*2016-11-01: Karin and Annelotte start their master works in the group.
*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.  
*2016-10-11: Transposons and heat stress. Read about evolution of heat responsiveness in ''ONSEN'' and other TEs groups in our latest paper [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1072-3 Open access]
*2015-06-15: Ahmed successfully defended his PhD work at University of Göttingen. Congratulations!
*2016-09-15: Fen Yang joins the lab as new PhD student. Welcome in Cologne!
*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]
*2016-08-30: Priscilla successfully defended her B.Sc. work. Congratulations!
 
 




Revision as of 02:06, 14 December 2016


Home      Research      People      Publications      Protocols      Resources      Seminars      Positions      Lab life     


Research

The Pecinka lab is hosted by 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. For our research we use Arabidopsis thaliana, several other Brassicaceae, selected crops and analyze them by forward and reverse genetics, molecular, biochemical, cytogenetic and bioinformatic methods. read more...

Lab Members

Technitians


see complete list...



Recent Publications

  • Willing E.M., Piofczyk T., Albert A., Winkler J.B., Schneeberger K., Pecinka A. (2016): UVR2 ensures transgenerational genome stability under simulated natural UV-B in Arabidopsis thaliana. Nature Communications 7:13522. doi: 10.1038/ncomms13522. Open access
  • Pietzenuk B., Markus C., Gaubert H., Bagwan N., Merotto A., Bucher E., Pecinka A. (2016): Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. Genome Biology 17:209 DOI: 10.1186/s13059-016-1072-3 Open access
  • Baroux C., Pecinka A., Fuchs J., Kreth G., Schubert I., Grossniklaus I. (2016): Non-random chromosome arrangement in triploid endosperm nuclei. Chromosoma doi:10.1007/s00412-016-0578-5 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

News

  • 2016-12-01: Fast mutation accumulation under natural UV-B without pyrimidine dimer repair. See more in our new paper Open access
  • 2016-11-01: Karin and Annelotte start their master works in the group.
  • 2016-10-11: Transposons and heat stress. Read about evolution of heat responsiveness in ONSEN and other TEs groups in our latest paper Open access
  • 2016-09-15: Fen Yang joins the lab as new PhD student. Welcome in Cologne!
  • 2016-08-30: Priscilla successfully defended her B.Sc. work. Congratulations!






Retrieved from "https://openwetware.org/mediawiki/index.php?title=Pecinka_lab&oldid=968022"