Optimizing clearing methods for deeper imaging of fluorescent protein-expressing plant tissues


Attuluri VPS [a], Robert Boisivon H [a]


[a] Hormonal Crosstalk in Plant Development,CEITEC - Masaryk University, Brno, Czech Republic


Tissue clearing methods are growing in popularity due to their improved ability to image deeper while maintaining fluorescence of fluorophores. Although there are many tissue clearing methods present for a long time, new tissue clearing methods were developed to improve the depth of imaging while reducing fluorescence quenching. In broad, the tissue clearing methods are classified into water-based and organic solvent-based methods. Water-based methods (CLARITY, PACT-PARS, CUBIC, Scale) take a long time for clearing while good at preserving fluorescent proteins. On the other hand, organic solvent-based methods (BABB, 3DISCO, FluoClear BABB, Ethanol-ECi, and PEGASOS) achieve tissue clearing in a short amount of time but do not preserve well protein-based fluorescence. Among all these methods, 3DISCO, PACT and CUBIC were reported to be superior for deep tissue imaging. Although all three methods achieve high transparency, 3DISCO is much faster (hours to days instead of weeks). Water-based clearing methods (TDE, Clear See and methods based on Scale) were optimised for plant tissues. However, 3DISCO (or its variants) are yet to be adapted for plants. 3DISCO, being an organic solvent-based method, allows deeper imaging and faster clearing times. In this study, we are trying to adapt 3DISCO to various plant species.

     This work has received funding from European Regional Development Fund-Project “SINGING PLANT“ (No. CZ.02.1.01/0.0/0.0/16_026/0008446).



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9:00 - 17:00


11:00 - 11:15

Welcome address


Danuše Nerudová
Rector, Mendel University in Brno

11:15 - 12:15 Opening Lecture




Dirk Inzé

The pivotal role of Plant Biology in a rapidly changing world

12:15 - 13:15 Keynote Lecture 01




Philip Wigge

Plants in a warming world

13:15 - 14:45  Lunch break & Poster Viewing Sessions
14:45 - 15:15 Talk M01
  George Komis
Conditional and developmental rearrangements of the plant cytoskeleton
15:15 - 15:30 Talk M02
  Antonio Pompeiano
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15:30 - 15:45 Talk M03
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15:45 - 16:00 Talk M04

Tereza Dobisová
Non-invasive in planta Monitoring of Chlorophyll Biosynthesis

16:00 - 16:30 Coffee break
16:30 - 17:30 Keynote Lecture 02



David Alabadí

Upstream and downstream events in DELLA-regulated growth and development

17:30 - 17:45 Talk M05
  Helene Robert Boisivon
Thermomorphogenesis during seed development In Arabidopsis and Brassica napus
17:45 - 18:00 Talk M06
  Sahu Pranav Pankaj 
Understanding the response of Arabidopsis under climate change scenarios
18:00 - 18:15 Talk M07
  Jozef Balla 
Auxin flow-mediated competition between axillary buds fine-tuned by other players
18:15 - 20:00   Welcome party, Poster and student talk session


9:30 - 10:15 Keynote Lecture 03



Peter Hedden

The role of gibberellin signaling in plant responses to abiotic stress

10:15 - 10:45 Talk T01
  Jan Hejátko

Cytokinins control xylem development via NAC SECONDARY WALL THICKENING PROMOTING FACTORs

10:45 - 11:15 Talk T02
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  Barbora Pařízková
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11:30 - 12:00 Coffee break
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Miguel A. Blázquez

An ancestral mechanism for the coordination of transcriptional programs

13:00 - 13:30 Talk T04
  Tomáš Werner
Molecular mechanisms controlling cytokinin homeostasis in the endoplasmic reticulum
13:30 - 14:00 Talk T05
  Radomíra Vaňková
The role of cytokinins in optimal defense to abiotic and biotic stresses as well as pathogen attack strategy
14:00 - 15:30   Lunch break & Poster Viewing Sessions
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Thomas Schmülling

New chapters from cytokinin action in development and stress defense

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Karin Ljung

Auxin-cytokinin metabolism, transport and signaling during lateral root development

17:30 - 18:00 Coffee break
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Aaron Rashotte

Roles of Cytokinin Response Factors in different environmental stress responses

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Mark Stitt

Budgeting carbon in a changing environment: Are plants better than bankers and politicians?


10:00 - 11:00 Keynote Lecture 09



Ondřej Novák

Phytohormone profiling at the cellular and subcellular levels


11:00 - 11:30

 Coffee break
11:30 - 11:45 Talk W01
  Hana Leontovyčová
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11:45 - 12:00 Talk W02
  Parisa Rahimzadeh Karvansara

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12:00 - 12:15 Talk W03
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12:45 - 13:15 Talk W05
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Advanced microscopy for plant developmental and cell biology

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  Miroslav Ovečka

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14:00 - 15:00 Lunch
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Ashverya Laxmi

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16:00 - 17:00 Keynote Lecture 11



Jutta Ludwig-Müller

Plant hormones in biotic interactions


Closing remarks

  Poster P01
Venkata Pardha S. Attuluri
Optimizing clearing methods for deeper imaging of fluorescent protein-expressing plant tissues
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  Kateřina Bělonožníková
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  Poster P09
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  Poster P13
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  Poster P14
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  Poster P15
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  Poster P16
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  Poster P17
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  • Plant abiotic stress
  • Biotic interactions
  • Plant signalling
  • Phytohormones
  • Plant growth and development
  • Global change and sustainable agriculture


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