Quint Lab:Research

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===genetics of phytohormone responses===
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<h3><font style="color:#F8B603;">let's play</font></h3>
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our knowledge about the mechanisms of signal transduction pathways triggered by plant hormones has dramatically increased within the last decade or so. some pathways, such as auxin signaling seem to be resolved from perception to gene expression. however, the multitude of different responses triggered by the same molecule is as amazing as it is poorly understood. hormone-induced expression of sometimes hundreds of genes seems to be a key aspect of these responses. but which genes or clusters of genes are responsible for which responses? why do ecotypes from different geographical and climatic backgrounds respond differently to the hormone stimulus ... and what are the genetic factors underlying this variation?
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"real science has the potential to not only amaze, but also transform the way one thinks of the world and oneself. this is because the process of science is little different from the deeply resonant, natural processes of play. play enables humans (and other mammals) to discover (and create) relationships and patterns. when one adds rules to play, a game is created. this is science: the process of playing with rules that enables one to reveal previously unseen patterns of relationships that extend our collective understanding of nature." - [http://rsbl.royalsocietypublishing.org/content/7/2/168.long Blackawton et al., 2011, Biology letters]
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[[Image:Auxin signaling.jpg|280px|right]]
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[[Image:Homepic.jpg‎|260px|right]]
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===TIR1-dependent auxin signaling===
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<h3><font style="color:#F8B603;">broad research scope</font></h3>
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to identify novel components of SCF complex regulation and/or auxin signaling we used the f-box protein and auxin receptor mutant ''tir1-1'' for a second site forward genetic screen. in a previous screen in [http://www.cbs.umn.edu/plantbio/faculty/GrayWilliam bill gray's lab] several enhancers of ''tir1-1''-mediated auxin resistance had been identified (see ito and gray, [http://www.ncbi.nlm.nih.gov/pubmed/16877699?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum ''plant physiology'' 2006]; quint et al., [http://www.ncbi.nlm.nih.gov/pubmed/16045473?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum ''plant journal 2005'']; chuang et al., [http://www.ncbi.nlm.nih.gov/pubmed/15208392?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum ''plant cell 2004'']; gray et al., [http://www.ncbi.nlm.nih.gov/pubmed/12782725?ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum ''plant cell 2003'']). Vice versa, we are screening for suppressors of the root growth defect on auxin-supplemented (2,4-D, artificial auxin) media. we identified appr. 15 independent ''tir1-1'' suppressor (''tis'') mutants that restored the wild-type response and are currently cloning the underlying gene/s and charactarize the physiological and genetic features of the mutants.
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'''HOW''' do organisms adapt to the environment and how do they react to different biotic and abiotic stimuli? <br>
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major players in the conversion of such stimuli into cellular responses are hormones acting as signaling molecules.
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our lab is primarily interested in understanding the genetics and molecular biology of [http://en.wikipedia.org/wiki/Auxin auxin] and other [http://en.wikipedia.org/wiki/Plant_hormone plant hormone] responses in the tiny weed [http://en.wikipedia.org/wiki/Arabidopsis_thaliana arabidopsis thaliana] and related [http://en.wikipedia.org/wiki/Brassicaceae brassicaceae]. phytohormones are one of the classic fields in [http://en.wikipedia.org/wiki/Plant_physiology plant physiology] and the past has shown that understanding hormone action in plants bears great potential for agricultural and horticultural applications. by contributing to the current state of knowledge of hormone biology we hope to participate in the advancement of [http://en.wikipedia.org/wiki/Crop_science crop science].
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Secondly, we are fascinated by the mechanisms of [http://en.wikipedia.org/wiki/Molecular_evolution molecular evolution] and how they shape plant life. Learning about the evolutionary history of signaling pathways may help to further our understanding of important developmental processes regulated by these signaling cascades.
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<br>
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we apply mostly [http://en.wikipedia.org/wiki/Genomics genomics] approaches, such as:
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*forward [http://en.wikipedia.org/wiki/Genetic_screen genetic screens] and [http://en.wikipedia.org/wiki/Reverse_genetics reverse genetics]
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*whole genome [http://en.wikipedia.org/wiki/Expression_profiling expression profiling]
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*utilizing natural [http://en.wikipedia.org/wiki/Genetic_variation genetic variation] within the global arabidopsis gene pool
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*[http://en.wikipedia.org/wiki/Quantitative_genetics quantitative genetics] → [http://en.wikipedia.org/wiki/Quantitative_trait_locus qtl] mapping
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*evolutionary and [http://en.wikipedia.org/wiki/Population_genomics population genomics]
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*[http://en.wikipedia.org/wiki/Comparative_genomics comparative genomics]<br>
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[[Image:Natvar.jpg|280px|left]]
[[Image:Natvar.jpg|280px|left]]
===natural variation and quantitative genetics of hormone responses===
===natural variation and quantitative genetics of hormone responses===
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we have revealed extensive natural variation for auxin responses in the root in world-wide arabidopsis ecotype collections (delker et al., [http://www.ncbi.nlm.nih.gov/pubmed/18299888?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum planta 2008]) and could recently determine the first quantitative trait loci (QTLs) involved in the inheritance of this genetic variation. the question that arises is which genes are underlying the QTLs and what are the allelic variants responsible for the variation? to address these questions we are fine-mapping the target intervals and make use of the vast genetic resources of ''arabidopsis thaliana'' to come up with a reasonable number of candidate genes that can be tested for their ability to functionally complement the differences in auxin response.  
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'''quantitative genetics'''<br>
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we have observed that ecotypes with a high degree of auxin insensitivity in the root do not necessarily display the same insensitivity in other organs like the hypocotyl. hence, it is
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we have revealed extensive natural variation for auxin responses in the root in world-wide arabidopsis ecotype collections (see delker et al., [http://www.ncbi.nlm.nih.gov/pubmed/18299888?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Planta 2008]). classic genetics tells us that this variation is most likely inherited in a quantitative genetic manner. We are therefore pursuing QTL and association mapping approaches to understand the genetics underlying this variation. Furthermore, we are making an effort to clone selected QTLs with strong effects on auxin-related phenotypes.<br>
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likely that the various factors responsible for this variation are downstream components and we are therefore also interested in transcriptional differences in response to auxin between ecotypes.
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'''population genetics'''<br>
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a possible reason for such natural variation on the physiological level maybe sequence polymorphisms in auxin-associated genes. extensive molecular population genetic analyses allow us to derive selection signatures for the respective gene classes and identify candidate genes which may be the driving forces behind the variation detected.<br>
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'''transcriptional networks'''<br>
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[[Image:Thlaspi arvense Blüte1 crop compressed.jpg|280px|right]]another possible effect contributing to the variation detected are differences on the transcriptional auxin responses between ecotypes. we have observed extensive variation in auxin-induced gene regulation between ecotypes and are using network approaches to understand the causative factors and derive hypotheses thereon (see delker et al., [http://www.ncbi.nlm.nih.gov/pubmed/20622145 Plant Cell 2010]).
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'''evolutionary insights'''<br>
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from an evolutionary perspective it will be important to learn about the differences in auxin responses on the physiological and the transcriptional level between species. Comparison of inter-species with intra-species variation may shed new light on the evolutionary development of the auxin response pathway(s). We are using closely related [http://en.wikipedia.org/wiki/Brassicaceae brassicaceae] species such as thlaspi arvense in this picture for this type of analysis which - in addition to the evolutionary perspective - is most interesting for possible future knowledge transfer to agronomically important species from that family.  
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[[Image:FBP_GFP.gif|150px|right]]‎
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===f-box proteins===
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===evo-devo===
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the evolutionary conserved f-box motifs can be found in various organisms ranging from fungi, insects, fish, and mammals to plants. f-box proteins are subunits of SCF-type E3 ubiquitin ligases and selectively recruit target proteins via their protein-protein interaction domain for ubiquitination and subsequent proteasomal degradation. therefore, this system represents a straight forward mechanism for simple regulation of signal transduction pathways by removal of target proteins. furthermore, the members of the TIR1 f-box protein family in arabidopsis perceive auxinic compounds and thereby constitute a previously unknown novel class of intracellular receptors for small molecules in eukaryotes. the arabidopsis genome encodes appr. 700 f-box proteins which makes this gene superfamily one of the largest in eukaryotes. however, a biological function has been assigned to less than 30 genes/proteins of the 700 members. a major reason for this seems to be functional redundancy due to evolutionary emergence by gene duplication which disqualifies forward genetics as the approach of choice for the characterization of f-box proteins in plants. we are applying reverse genetic approaches to biologically characterize two subfamilies of f-box proteins
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[[Image:Hourglass_mosaic.jpg|100px|right]]
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to place them into the regulatory networks in which they are active.
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for one, we are interested in the evolutionary history of gene families that are involved in important signaling cascades, such as the ubiquitin-proteasome system (see schumann et al. [http://www.ncbi.nlm.nih.gov/pubmed/21119043 ''plant physiology 2011'']). furthermore, we are developing ways to utilize whole genome transcriptional information for evolutionary approaches in close collaboration with the lab of [http://www.informatik.uni-halle.de/arbeitsgruppen/bioinformatik/mitarbeiterinnen/grosse/?lang=en ivo grosse]. by applying phylotranscriptomics – the combination of [http://en.wikipedia.org/wiki/Phylogenetics phylogenetics] and [http://en.wikipedia.org/wiki/Transcriptomics transcriptomics] – to developmental series such as embryogenesis, we are able to trace the evolutionary path across a complete developmental process.  
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Revision as of 02:34, 6 December 2012

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Contents

let's play

"real science has the potential to not only amaze, but also transform the way one thinks of the world and oneself. this is because the process of science is little different from the deeply resonant, natural processes of play. play enables humans (and other mammals) to discover (and create) relationships and patterns. when one adds rules to play, a game is created. this is science: the process of playing with rules that enables one to reveal previously unseen patterns of relationships that extend our collective understanding of nature." - Blackawton et al., 2011, Biology letters

broad research scope

HOW do organisms adapt to the environment and how do they react to different biotic and abiotic stimuli?
major players in the conversion of such stimuli into cellular responses are hormones acting as signaling molecules. our lab is primarily interested in understanding the genetics and molecular biology of auxin and other plant hormone responses in the tiny weed arabidopsis thaliana and related brassicaceae. phytohormones are one of the classic fields in plant physiology and the past has shown that understanding hormone action in plants bears great potential for agricultural and horticultural applications. by contributing to the current state of knowledge of hormone biology we hope to participate in the advancement of crop science.

Secondly, we are fascinated by the mechanisms of molecular evolution and how they shape plant life. Learning about the evolutionary history of signaling pathways may help to further our understanding of important developmental processes regulated by these signaling cascades.
we apply mostly genomics approaches, such as:

natural variation and quantitative genetics of hormone responses

quantitative genetics
we have revealed extensive natural variation for auxin responses in the root in world-wide arabidopsis ecotype collections (see delker et al., Planta 2008). classic genetics tells us that this variation is most likely inherited in a quantitative genetic manner. We are therefore pursuing QTL and association mapping approaches to understand the genetics underlying this variation. Furthermore, we are making an effort to clone selected QTLs with strong effects on auxin-related phenotypes.


population genetics
a possible reason for such natural variation on the physiological level maybe sequence polymorphisms in auxin-associated genes. extensive molecular population genetic analyses allow us to derive selection signatures for the respective gene classes and identify candidate genes which may be the driving forces behind the variation detected.


transcriptional networks

another possible effect contributing to the variation detected are differences on the transcriptional auxin responses between ecotypes. we have observed extensive variation in auxin-induced gene regulation between ecotypes and are using network approaches to understand the causative factors and derive hypotheses thereon (see delker et al., Plant Cell 2010).


evolutionary insights
from an evolutionary perspective it will be important to learn about the differences in auxin responses on the physiological and the transcriptional level between species. Comparison of inter-species with intra-species variation may shed new light on the evolutionary development of the auxin response pathway(s). We are using closely related brassicaceae species such as thlaspi arvense in this picture for this type of analysis which - in addition to the evolutionary perspective - is most interesting for possible future knowledge transfer to agronomically important species from that family.

evo-devo

for one, we are interested in the evolutionary history of gene families that are involved in important signaling cascades, such as the ubiquitin-proteasome system (see schumann et al. plant physiology 2011). furthermore, we are developing ways to utilize whole genome transcriptional information for evolutionary approaches in close collaboration with the lab of ivo grosse. by applying phylotranscriptomics – the combination of phylogenetics and transcriptomics – to developmental series such as embryogenesis, we are able to trace the evolutionary path across a complete developmental process.

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