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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:Research | read more...]]
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<h3><font style="color:#C9D3EB;">Lab Members</font></h3>
Our goal is to understand molecular and evolutionary mechanisms shaping plant genomes and epigenomes. We analyze how DNA sequence variation is generated by various mutagenic factors and how these forces are counteracted by the genome repair and maintenance mechanisms. To this end we use 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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*[[Pecinka_Lab:Ahmed_Abdelsamad|Ahmed Abdelsamad]]
<h3><font style="color:#4169E1;">Lab Members</font></h3>
*[[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:#C9D3EB;">Visiting Scholars</font></h3>
*[[Pecinka_lab:Mariana_Diaz|Mariana Andrea Diaz Smoje]]
*[[Pecinka_Lab:Pawel_Mikulski|Pawel Mikulski]]
*[[Pecinka_lab:Andreas_Finke|Andreas Finke]]
*[[Pecinka_lab:Chun Hsin Liu|Chun Hsin Liu (Phoebe)]]
*[[Pecinka_lab:Ales_Pecinka|Ales Pecinka]]
*[[Pecinka_lab:Bjoern_Pietzenuk|Björn Pietzenuk]]
*[[Pecinka_lab:Thomas_Piofczyk|Thomas Piofczyk]]


<h3><font style="color:#C9D3EB;">Alumni</font></h3>
<h3><font style="color:#4169E1;">Technitians</font></h3>
*[[Pecinka_Lab:Alexander Schott|Alexander Schott]]
*[[Pecinka_lab:Barbara_Eilts|Barbara Eilts]]
*[[Pecinka_Lab:Anastasia Hoffmann|Anastasia Hoffmann]]
*[[Pecinka_lab:Petra_Pecinkova|Petra Pecinkova]]
[[Pecinka_Lab:Alumni|See all former members...]]
 
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[[Pecinka_lab:People|see complete list...]]
 
 
 
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<h3><font style="color:#FF8C00;">Recent Publications</font></h3>
 
*Piofczyk T, Jeena G, Pecinka A. 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]
*Abdelsamad A, Pecinka A. Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming. Plant Cell DOI: http:/​/​dx.​doi.​org/​10.​1105/​tpc.​114.​126011 (2014). [http://www.plantcell.org/content/early/2014/08/12/tpc.114.126011.full.pdf+html Open access PDF]
*Pecinka A, Liu C.-H. Drugs for Plant Chromosome and Chromatin Research. Cytogenetic Genome Research DOI: 10.1159/000360774 (2014). [http://www.karger.com/Article/FullText/360774 Full text]
 
 


<h3><font style="color:#C9D3EB;">Selected Publications</font></h3>
*[[Pecinka_lab:Publications|see complete list...]]


*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]
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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]
*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]
*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]
*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]


<h3><font style="color:red">News</font></h3>
*2015-02-10: "Arabis alpina" genome reveals peculiar pattern of DNA methylation. See more in the current Nature Plants paper by Schneeberger lab [http://www.nature.com/articles/nplants201423 Full text]
*2015-02-05: Arabidopsis natural variation in response to UV stress reveals connections to pathogen-like responses. Read more in our Plant Physiology and Biochemistry paper [http://www.sciencedirect.com/science/article/pii/S0981942815000212 Full text]
*2014-10-20: Thomas successfully defended his PhD. Congratulations!
*2014-09-22: Lab field trip to Eltz castle.




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


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<h3><font style="color:#F8B603;">Announcements</font></h3>
 
*[[Maloof_Lab:Group_meeting|Group meeting, journal clubs, and seminars]]
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<h3><font style="color:red">Funding</font></h3>
 
*[http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5338&org=BIO NSF Plant Genome Research Program]
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**[http://www-plb.ucdavis.edu/Labs/sinha/TomatoGenome/ GEPR: Elucidating gene networks regulating development in tomato]
**[[Maloof_Lab:PGRP | Molecular evolutionary genetics of crop and weed responses to
crowding]] (2002-2008)
*[http://www.hfsp.org/ Human Frontier Science Program] (2004-2008)
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Revision as of 11:51, 28 February 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 variation is generated by various mutagenic factors and how these forces are counteracted by the genome repair and maintenance mechanisms. To this end we use 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...


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

Recent Publications

  • Piofczyk T, Jeena G, Pecinka A. 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
  • Abdelsamad A, Pecinka A. Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming. Plant Cell DOI: http:/​/​dx.​doi.​org/​10.​1105/​tpc.​114.​126011 (2014). Open access PDF
  • Pecinka A, Liu C.-H. Drugs for Plant Chromosome and Chromatin Research. Cytogenetic Genome Research DOI: 10.1159/000360774 (2014). Full text

News

  • 2015-02-10: "Arabis alpina" genome reveals peculiar pattern of DNA methylation. See more in the current Nature Plants paper by Schneeberger lab Full text
  • 2015-02-05: Arabidopsis natural variation in response to UV stress reveals connections to pathogen-like responses. Read more in our Plant Physiology and Biochemistry paper Full text
  • 2014-10-20: Thomas successfully defended his PhD. Congratulations!
  • 2014-09-22: Lab field trip to Eltz castle.





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