Quint Lab: Quint lab journal club: Difference between revisions

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# everybody has to read/prepare the paper!!! → we will discuss the paper figure-by-figure, taking turns in explaining them
# everybody has to read/prepare the paper!!! → we will discuss the paper figure-by-figure, taking turns in explaining them
# keep a critical mind - try to identify the "good and the bad"  
# keep a critical mind - try to identify the "good and the bad"  


{| border="1"
{| border="1"
|+  
|+  
! date!! paper !! link  !! who?
! date!! paper !! link !! who?
|-
 
! 09.12.
|paper ||link || who?
|-
 
! 25.11.
|paper ||link || who?
|-
 
! 11.11.
|paper ||link || who?
|-
 
! 28.10.
| Chaiwanon/Wang ||http://www.sciencedirect.com/science/article/pii/S0960982215002158 Curr Biol 2015|| Carla
|-
 
! 14.10.
|  ||  || Leucorea
|-
 
! 30.09.
| Zhu/Balasubramanian || [http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005085 PLoSG 2015]  || Philipp
|-
 
! 16.09.
| Shen/He Nat.Biotech || [http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3321.html#affil-auth] || Carolin
|-
 
! 02.09.
| Wang et al. 2015, The Plant Cell || http://www.plantcell.org/content/27/4/1128.long  || Usman
|-
 
! 19.08.
| Jang et al. SciRep 2015 || [http://www.nature.com/srep/2015/150710/srep12071/full/srep12071.html SciRep 2015] || Jana
|-
 
! 05.08.
| Sanchez-Bermejo et al. || [http://www.plantphysiol.org/content/early/2015/07/20/pp.15.00942.full.pdf+html?with-ds=yes PP 2015] || Philipp
|-
 
! 22.07.
| Bours et al. 2015 Plant Physiology || [http://www.plantphysiol.org/content/167/2/517.long Plant Physiol 2015] || Wenke
|-
 
! 24.06.
| Yu et al., 2015 J Integr Plant Biol. 2015  || http://onlinelibrary.wiley.com/doi/10.1111/jipb.12363/pdf || Carla
|-
 
! 03.06.
| Shikata et al., 2015 PNAS || http://www.pnas.org/content/111/52/18781.long || philipp
|-
 
! 20.05.
| Bours et al. 2015 Plant Physiology || [http://www.plantphysiol.org/content/167/2/517.long Plant Physiol 2015] || Wenke
|-
 
! 06.05.
|  Soto et al. Plant Science || [http://www.sciencedirect.com/science/article/pii/S0168945214001642] || Julia
|-
 
! 22.04.
| Kaushik et al. 2007 PLoS Biology || [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050146 PLoS B 2007] || Philipp
|-
 
! 08.04.
| Chen et al. PNAS 2014|| [http://www.pnas.org/content/early/2014/12/15/1412274111.abstract PNAS 2014] || Jana
|-
 
! 11.03.
| Foreman et al. 2011 Plant Journal|| [http://hallidaylab.bio.ed.ac.uk/documents/Lightreceptoraction.pdf PJ 2011] || Carla
|-
|-


!12.11.
! 04.03. + lab meeting!
| Gray et al. 1998 PNAS|| [http://www.pnas.org/content/95/12/7197.abstract paper] || Carolin
| |Lee et al. 2014 nature communications|| [http://www.nature.com/ncomms/2014/141117/ncomms6473/full/ncomms6473.html NComm 2014] || Wenke
|-
|-
!
 
|Stavang et al. 2009|| [http://www.ncbi.nlm.nih.gov/pubmed/19686536 paper]|| Carolin
! 11.02.
| Box et al. 2015 Current Biology|| [http://www.sciencedirect.com/science/article/pii/S0960982214014249 CB 2015] || Carla
|-
|-


! 28.01.
| Kurihara et al. 2014 Genes|| [http://www.mdpi.com/2073-4425/5/4/1115/pdf Genes 2014]|| Philipp
|-


! 19.11.
! 14.01.
| Koini et al. 2009 Current Biol|| [http://www.sciencedirect.com/science/article/pii/S0960982209006186 paper]|| Jana
| Dong et al. 2014 Plant Cell|| [http://www.plantcell.org/content/26/9/3630.full?sid=ee416b61-4e54-4030-ab8b-bd862c2ec13c PC 2014]|| Carolin
|-
|-


! 26.11.
! 10.12.
| Franklin et. al. 2011 PNAS|| [http://www.pnas.org/content/108/50/20231.abstract paper]|| Philipp
| Johansen et al. 2014  Nature Comm|| [http://www.nature.com/ncomms/2014/140926/ncomms5848/full/ncomms5848.html NComm 2014]|| Carla
|-
|-


! 05.12. (Friday)
! 05.12. (Friday)
| Toledo-Ortiz et al. 2014 PLOS Genetics|| [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004416 paper]|| Julia
| Toledo-Ortiz et al. 2014 PLOS Genetics|| [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004416 PLoS G 2014]|| Julia
|-
|-


! 10.12.
! 26.11.
| Johansen et al. 2014  Nature Comm|| [http://www.nature.com/ncomms/2014/140926/ncomms5848/full/ncomms5848.html paper ]|| Carla
| Franklin et. al. 2011 PNAS|| [http://www.pnas.org/content/108/50/20231.abstract PNAS 2011]|| Philipp
|-
 
! 19.11.
| Koini et al. 2009 Current Biol|| [http://www.sciencedirect.com/science/article/pii/S0960982209006186 CB 2009]|| Jana
|-
|-


! 17.12.
!12.11.
| Dong et al. 2014 Plant Cell|| [http://www.plantcell.org/content/26/9/3630.full?sid=ee416b61-4e54-4030-ab8b-bd862c2ec13c paper ]|| Carolin
| Gray et al. 1998 PNAS|| [http://www.pnas.org/content/95/12/7197.abstract PNAS 1998] || Carolin
|-
!
|Stavang et al. 2009|| [http://www.ncbi.nlm.nih.gov/pubmed/19686536 PJ 2009]|| Carolin
|-
|-
|}
|}




Line 58: Line 142:
|+  
|+  
! title !! first + last author !! journal
! title !! first + last author !! journal
|-
|''Natural variation in the C-Repeat Binding Factor (CBF) cold response pathway correlates with local adaptation of Arabidopsis ecotypes''
|Gehan et al. ||
[http://onlinelibrary.wiley.com/doi/10.1111/tpj.13027/pdf Plant Journal 2015]
|-
|'''BZR1 interacts with HY5 to mediate brassinosteroid- and light-regulated cotyledon opening in Arabidopsis in darkness'''
|Li and He ||
[http://dx.doi.org/10.1016/j.molp.2015.08.014 Molecular Plant 2015]
|-
|'''Insight into a physiological role of the EC nighttime repressor in the Arabidopsis circadian clock '''
|Mizuno et al. ||
[http://pcp.oxfordjournals.org/content/early/2015/06/23/pcp.pcv094.long PCP 2015]
|-
|'''Natural alleles of a proteasome α 2 subunit gene contribute to thermotolerance and adaptation of African rice'''
|Li et al. ||
[http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3305.html NG 2015]
|-
|'''HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis'''
|Qiu et al. ||
[http://www.plantcell.org/content/early/2015/05/08/tpc.114.136093.abstract?papetoc PC 2015]
|-
|The Transcriptional Regulator BBX19 Promotes Hypocotyl Growth by Facilitating COP1-Mediated EARLY FLOWERING3 Degradation in Arabidopsis
| Wang et al ||
[http://www.plantcell.org/content/early/2015/03/31/tpc.15.00044.abstract PlantCell 2015]
|-
|'''Arabidopsis DET1 degrades HFR1 but stabilizes PIF1 to precisely regulate seed germination'''
| Shi/Deng|| [http://www.pnas.org/content/early/2015/03/05/1502405112.full.pdf+html?with-ds=yes PNAS 2015]
|-
|'''The Coding of Temperature in the Drosophila Brain'''
| Gallio/Zucker|| [http://www.sciencedirect.com/science/article/pii/S0092867411000675 Cell 2011]
|-
|Arabidopsis HFR1 Is a Potential Nuclear Substrate Regulated by the Xanthomonas Type III Effector XopDXcc8004.
| Tan/Yang|| [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117067 P1 2015]
|-
|Climate variation explains a third of global crop yield variability
| Ray/West|| [http://www.nature.com/ncomms/2015/150122/ncomms6989/full/ncomms6989.html NC 2015]
|-
|-


Line 66: Line 197:
|Combinatorial Complexity in a Transcriptionally Centered Signaling Hub in Arabidopsis
|Combinatorial Complexity in a Transcriptionally Centered Signaling Hub in Arabidopsis
| Pfeiffer/Quail|| [http://mplant.oxfordjournals.org/content/7/11/1598.full?etoc MP 2014]  
| Pfeiffer/Quail|| [http://mplant.oxfordjournals.org/content/7/11/1598.full?etoc MP 2014]  
|-
!FCA mediates thermal adaptation of stem growth by attenuating auxin action in Arabidopsis
| Lee/Park|| [http://www.nature.com/ncomms/2014/141117/ncomms6473/full/ncomms6473.html NComm 2014]
|-
|-


Line 81: Line 208:


|Differentially Phased Leaf Growth and Movements in Arabidopsis Depend on Coordinated Circadian and Light Regulation
|Differentially Phased Leaf Growth and Movements in Arabidopsis Depend on Coordinated Circadian and Light Regulation
| Dornbusch/Fankhauser| [http://www.plantcell.org/content/26/10/3911.abstract?etoc PC 2014]
| Dornbusch/Fankhauser|| [http://www.plantcell.org/content/26/10/3911.abstract?etoc PC 2014]
|-
 
|Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality
| Shen/Carlborg|| [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004842 PLoS G 2014]
|-
 
|The Arabidopsis thaliana RNA-binding protein FCA regulates thermotolerance by modulating the detoxification of reactive oxygen species
| Lee/Park|| [http://onlinelibrary.wiley.com/doi/10.1111/nph.13079/abstract?campaign=woletoc NP 2014]
|-
 
|Genetic Variation for Life History Sensitivity to Seasonal Warming in Arabidopsis thaliana
| Li/Borevitz|| [http://www.genetics.org/content/196/2/569 G 2014]
|-
 
|Light and COP1 regulate level of overexpressed DET1 protein
| Ly/Schroeder|| [http://www.sciencedirect.com/science/article/pii/S0168945214002817/pdfft?md5=2f72d2097201989bb74a42c6b7fe3b23&pid=1-s2.0-S0168945214002817-main.pdf PS 2015]
|-
 
|Arabidopsis DET1 Represses Photomorphogenesis in part by Negatively Regulating DELLA Protein Abundance in Darkness
| Li/Deng/Chen|| [http://www.cell.com/molecular-plant/pdf/S1674-2052%2814%2900081-1.pdf MP 2015]
|-
 
|Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa
| Yu/He || [http://www.biomedcentral.com/1471-2229/13/208 BMC 2013]
|-
 
|Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature
| Seaton/Halliday || [http://onlinelibrary.wiley.com/doi/10.15252/msb.20145766/abstract MSB 2015]
|-
 
|Cellular auxin homeostasis under high temperature is regulated through a sorting NEXIN1-dependent endosomal trafficking pathway
| Hanzawa/Rahman || [http://www.plantcell.org/content/25/9/3424.long PC 2011]
|-
 
|Negative regulatory roles of DE-ETIOLATED1 in flowering time in Arabidopsis
| Kang et al. || [http://www.nature.com/srep/2015/150512/srep09728/full/srep09728.html SciRep 2015]
|-
 
|Genetic and epigenetic control of plant heat responses
|Liu et al. || [http://journal.frontiersin.org/article/10.3389/fpls.2015.00267/full Front.PlantSci 2015]
|-
 
|CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1
|Zhu et al. || [http://www.nature.com/ncomms/2015/150603/ncomms8245/full/ncomms8245.html NC 2015]
|-
 
 
|'''The spliceosome assembly factor GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms.'''
| Schlaen et al. || [http://www.pnas.org/content/early/2015/07/08/1504541112.full.pdf PNAS 2015]
|-
 
|The effect of temperature on the male and female recombination landscape of barley
|Phillips et al. ||
[http://onlinelibrary.wiley.com/doi/10.1111/nph.13548/pdf NP 2015]
|-
 
|Phosphorylation of CONSTANS and its COP1-dependent degradation during photoperiodic flowering of Arabidopsis
|Sarid-Krebs et al. || [http://onlinelibrary.wiley.com/doi/10.1111/tpj.13022/abstract PJ 2015]
|-
 
|'''The EC Night-Time Repressor Plays a Crucial Role in Modulating Circadian Clock Transcriptional Circuitry by Conservatively Double-Checking Both Warm-Night and Night-Time-Light Signals in a Synergistic Manner in Arabidopsis thaliana'''
|Mizuno et al. || [http://pcp.oxfordjournals.org/content/55/12/2139.long PP 2014]
|-
|-
|SHW1 Interacts with HY5 and COP1, and Promotes COP1-mediated Degradation of HY5 During Arabidopsis Seedling Development
|Srivastava et al. || [http://www.ncbi.nlm.nih.gov/pubmed/26474641 PP 2015]
|-
|Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M.
| Lutz et al. || [http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005588 PG 2015]
|-
|}
|}

Latest revision as of 06:26, 29 October 2015

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Quint lab journal club

Wednesday 10 am

person responsible for the respective date has to

  1. give a short introduction into the topic
  2. state the aims of the paper/work presented
  3. state the rationale for choosing the paper

but keep in mind:

  1. everybody has to read/prepare the paper!!! → we will discuss the paper figure-by-figure, taking turns in explaining them
  2. keep a critical mind - try to identify the "good and the bad"
date paper link who?
09.12. paper link who?
25.11. paper link who?
11.11. paper link who?
28.10. Chaiwanon/Wang http://www.sciencedirect.com/science/article/pii/S0960982215002158 Curr Biol 2015 Carla
14.10. Leucorea
30.09. Zhu/Balasubramanian PLoSG 2015 Philipp
16.09. Shen/He Nat.Biotech [1] Carolin
02.09. Wang et al. 2015, The Plant Cell http://www.plantcell.org/content/27/4/1128.long Usman
19.08. Jang et al. SciRep 2015 SciRep 2015 Jana
05.08. Sanchez-Bermejo et al. PP 2015 Philipp
22.07. Bours et al. 2015 Plant Physiology Plant Physiol 2015 Wenke
24.06. Yu et al., 2015 J Integr Plant Biol. 2015 http://onlinelibrary.wiley.com/doi/10.1111/jipb.12363/pdf Carla
03.06. Shikata et al., 2015 PNAS http://www.pnas.org/content/111/52/18781.long philipp
20.05. Bours et al. 2015 Plant Physiology Plant Physiol 2015 Wenke
06.05. Soto et al. Plant Science [2] Julia
22.04. Kaushik et al. 2007 PLoS Biology PLoS B 2007 Philipp
08.04. Chen et al. PNAS 2014 PNAS 2014 Jana
11.03. Foreman et al. 2011 Plant Journal PJ 2011 Carla
04.03. + lab meeting! Lee et al. 2014 nature communications NComm 2014 Wenke
11.02. Box et al. 2015 Current Biology CB 2015 Carla
28.01. Kurihara et al. 2014 Genes Genes 2014 Philipp
14.01. Dong et al. 2014 Plant Cell PC 2014 Carolin
10.12. Johansen et al. 2014 Nature Comm NComm 2014 Carla
05.12. (Friday) Toledo-Ortiz et al. 2014 PLOS Genetics PLoS G 2014 Julia
26.11. Franklin et. al. 2011 PNAS PNAS 2011 Philipp
19.11. Koini et al. 2009 Current Biol CB 2009 Jana
12.11. Gray et al. 1998 PNAS PNAS 1998 Carolin
Stavang et al. 2009 PJ 2009 Carolin



papers we might want to talk about in the future:

title first + last author journal
Natural variation in the C-Repeat Binding Factor (CBF) cold response pathway correlates with local adaptation of Arabidopsis ecotypes Gehan et al.

Plant Journal 2015

BZR1 interacts with HY5 to mediate brassinosteroid- and light-regulated cotyledon opening in Arabidopsis in darkness Li and He

Molecular Plant 2015

Insight into a physiological role of the EC nighttime repressor in the Arabidopsis circadian clock Mizuno et al.

PCP 2015

Natural alleles of a proteasome α 2 subunit gene contribute to thermotolerance and adaptation of African rice Li et al.

NG 2015

HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis Qiu et al.

PC 2015

The Transcriptional Regulator BBX19 Promotes Hypocotyl Growth by Facilitating COP1-Mediated EARLY FLOWERING3 Degradation in Arabidopsis Wang et al

PlantCell 2015

Arabidopsis DET1 degrades HFR1 but stabilizes PIF1 to precisely regulate seed germination Shi/Deng PNAS 2015
The Coding of Temperature in the Drosophila Brain Gallio/Zucker Cell 2011
Arabidopsis HFR1 Is a Potential Nuclear Substrate Regulated by the Xanthomonas Type III Effector XopDXcc8004. Tan/Yang P1 2015
Climate variation explains a third of global crop yield variability Ray/West NC 2015
Plasticity to simulated shade is associated with altitude in structured populations of Arabidopsis thaliana Botto PCE 2014
Combinatorial Complexity in a Transcriptionally Centered Signaling Hub in Arabidopsis Pfeiffer/Quail MP 2014
BR-dependent phosphorylation modulates PIF4 transcriptional activity and shapes diurnal hypocotyl growth Bernardo-Garcia/Prat GD 2014
UV-B-Responsive Association of the Arabidopsis bZIP Transcription Factor ELONGATED HYPOCOTYL5 with Target Genes, Including Its Own Promoter Binkert/Ulm PC 2014 + feature
Differentially Phased Leaf Growth and Movements in Arabidopsis Depend on Coordinated Circadian and Light Regulation Dornbusch/Fankhauser PC 2014
Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality Shen/Carlborg PLoS G 2014
The Arabidopsis thaliana RNA-binding protein FCA regulates thermotolerance by modulating the detoxification of reactive oxygen species Lee/Park NP 2014
Genetic Variation for Life History Sensitivity to Seasonal Warming in Arabidopsis thaliana Li/Borevitz G 2014
Light and COP1 regulate level of overexpressed DET1 protein Ly/Schroeder PS 2015
Arabidopsis DET1 Represses Photomorphogenesis in part by Negatively Regulating DELLA Protein Abundance in Darkness Li/Deng/Chen MP 2015
Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa Yu/He BMC 2013
Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature Seaton/Halliday MSB 2015
Cellular auxin homeostasis under high temperature is regulated through a sorting NEXIN1-dependent endosomal trafficking pathway Hanzawa/Rahman PC 2011
Negative regulatory roles of DE-ETIOLATED1 in flowering time in Arabidopsis Kang et al. SciRep 2015
Genetic and epigenetic control of plant heat responses Liu et al. Front.PlantSci 2015
CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1 Zhu et al. NC 2015
The spliceosome assembly factor GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms. Schlaen et al. PNAS 2015
The effect of temperature on the male and female recombination landscape of barley Phillips et al.

NP 2015

Phosphorylation of CONSTANS and its COP1-dependent degradation during photoperiodic flowering of Arabidopsis Sarid-Krebs et al. PJ 2015
The EC Night-Time Repressor Plays a Crucial Role in Modulating Circadian Clock Transcriptional Circuitry by Conservatively Double-Checking Both Warm-Night and Night-Time-Light Signals in a Synergistic Manner in Arabidopsis thaliana Mizuno et al. PP 2014
SHW1 Interacts with HY5 and COP1, and Promotes COP1-mediated Degradation of HY5 During Arabidopsis Seedling Development Srivastava et al. PP 2015
Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M. Lutz et al. PG 2015
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