The INDEPTH Academy is a training facility developed by INDEPTH to deliver multimedia resources to inform how the spatial organisation of nuclear DNA is critical in the adaptation to environmental stresses.
Many of these resources can be found on the INDEPTH Academy YouTube Channel.
INDEPTH Academy outputs include:
– Short webinar teaching resources that introduce functional domains of the nucleus (such as the nucleolus of nuclear envelope) and explore how chromatin dynamics influence gene expression
– Masterclass tutorials in which technical experts will lead discussion-led sessions on experimental techniques that are important for study of the plant nucleus
– Standardised Protocols that are linked to INDEPTH member research activities
– Expert talks from the 2021 Society of Expeimental Biology (SEB) Main Meeting (online) within a special INDEPTH session on ‘Dynamic organization of the nucleus across kingdoms”. These talks can be viewed on the Society of Experimental Biology YouTube Channel here.
INDEPTH Academy Masterclass Tutorials
Vicente Rubio: MASS SPECTROMETRY METHODS TO INVESTIGATE PROTEIN-PROTEIN INTERACTIONS
Mariusz Czarnocki-Cieciura: BIOPHYSICAL METHODS TO INVESTIGATE PROTEIN-PROTEIN INTERACTIONS
Celia Baroux on the ‘Spatial analysis of nuclear signal distribution using Imaris and DataViz’
Dimiter Prodanov and Sumit Vohra introduce their Active Segmentation tool for plant image analysis.
Christophe Tatout provides a detailed description of NucleusJ 2.0 with Q+A
Stefanie Rosa provides a detailed description of smFISH with extended Q+A
Professor Hank Bass from Florida State University is hosting the INDEPTH Image Repository through the OMERO software. https://doi.org/10.24384/cqrx-5f97
INDEPTH Academy Teaching Webinars
Francesca Lopez talks to the SciencePhile about ‘Genetic Engineering and Editing the Code Of Life?’
Danny Geelen discusses the effect of temperature on sexual reproduction
Dr Christian Chevalier introduces ‘DNA-dependent fruit growth in tomato: the role of endoreduplication
Dr Kriton Kalantidis introduces the fascinating biology of Virioids, smallest-known pathogens.
Dr Celia Baroux introduces the background and state of the art in the knowledge about Linker Histone in plants.
Dr Geraint Parry introduces the Plant Nuclear Pore Complex. https://doi.org/10.24384/crg5-8×04
Dr Monica Pradillo introducing the Role of Chromatin Domains on Plant Meiosis. https://doi.org/10.24384/tnrm-mz90
Dr Frederic Pontvianne introduces the Function of the Plant Nucleolus. https://doi.org/10.24384/zn4x-0468
Francesca Lopez discusses gene dosing of ribosomal RNA and her INDEPTH STSMs
Emilia Cepowska discusses her STSM work on Gene Loops in Stress Memory in Arabidopsis
Gianluca Teano discusses his research on the role of Histone 1 in chromatin organisation, which has benefited from his participation in two STSMs.
INDEPTH Academy Expert Protocols
Protocol for Hi-C Chromosome Confirmation Capture. This method is adapted from research in the labs of Chang Liu and Silin Zhong. https://doi.org/10.24384/39fw-jm66
Protocol for Single Molecular Fluorescent In Situ Hybridisation. This method is adapted from research in Stefanie Rosa’s lab and provides instructions for this powerful technique for analysis of gene expression https://doi.org/10.24384/4h9v-ar37
Protocol for Localising Total mRNA in Plant Cells . This method is adapted by Geraint Parry for a selection of published methodologies https://doi.org/10.24384/m5dm-he87
Protocol for Fluorescence Activated Nuclear Sorting (FANS) for RNA extraction, DNA extraction or Chromatin Immunoprecipitation. This method is adapted from protocols developed in Ortrun Mittelsten Scheid’s lab https://doi.org/10.24384/fvmf-km57
Protocol for Localising Total mRNA in Plant Cells . This Protocol for Isolation of Plant Nucleolus. This method is adapted from protocols by Frederic Pontvianne. https://doi.org/10.24384/ycxk-1685
Protocol for Assay for Transposase-Accessible Chromatin (ATAC-seq ). This method is adapted from a variety of protocols from the labs of Roger Deal and Kenneth Berendzen https://doi.org/10.24384/y5pn-8a86
Protocol for Membrane Yeast Two-Hybrid (MYTH) for analysis of targeted interactions or identification of novel interactors. This method is adapted from a variety of protocols, in particular from the lab of Christophe Tatout. https://doi.org/10.24384/4zmm-x149