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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:Ahmed_Abdelsamad|Ahmed Abdelsamad]]
*[[Pecinka_Lab:Pawel_Mikulski|Pawel Mikulski]]
*[[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: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:#C9D3EB;">Selected Publications</font></h3>  
<h3><font style="color:#FF8C00;">Recent Publications</font></h3>  


*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]
*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]  
*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]
*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]
*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]
*Baubec T, Finke A, Mittelsten Scheid O, Pecinka A. Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis. EMBO Reports doi: 10.1002/embr.201337915 (2014). [http://embor.embopress.org/content/early/2014/02/20/embr.201337915 Full text]
*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]
*Pecinka A, Abdelsamad Ahmed, Vu GTH. Hidden genetic nature of epigenetic natural variation in plants. Trends in Plant Science 18:625-632 (2013) [http://www.sciencedirect.com/science/article/pii/S1360138513001453 Full text]  
*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]




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


*[[Maloof_Lab:Publications | see complete list...]]
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<h3><font style="color:red">News</font></h3>
*2014-09-22: Lab field trip to Eltz castle.
*2014-08-12: RNA duplicated genes (retrogenes) are more frequent than expected in Arabidopsis and show transcriptional profile similar to animal retrogenes. Find more in our recent Plant Cell publication [http://www.plantcell.org/content/early/2014/08/12/tpc.114.126011.full.pdf+html Open access PDF]
*2014-03-31: The manuscript "Drugs for Plant Chromosome and Chromatin Research" published in the special issue of Cytogenetic Genome Research [http://www.karger.com/Article/FullText/360774 Full text]


<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]
 
**[http://www-plb.ucdavis.edu/Labs/sinha/TomatoGenome/ GEPR: Elucidating gene networks regulating development in tomato]
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**[[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 13:56, 9 October 2014


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

  • 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
  • Baubec T, Finke A, Mittelsten Scheid O, Pecinka A. Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis. EMBO Reports doi: 10.1002/embr.201337915 (2014). Full text
  • Pecinka A, Abdelsamad Ahmed, Vu GTH. Hidden genetic nature of epigenetic natural variation in plants. Trends in Plant Science 18:625-632 (2013) Full text

News

  • 2014-09-22: Lab field trip to Eltz castle.
  • 2014-08-12: RNA duplicated genes (retrogenes) are more frequent than expected in Arabidopsis and show transcriptional profile similar to animal retrogenes. Find more in our recent Plant Cell publication Open access PDF
  • 2014-03-31: The manuscript "Drugs for Plant Chromosome and Chromatin Research" published in the special issue of Cytogenetic Genome Research Full text




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