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New non-invasive cell imaging method reveals lipid droplet structure

An INRAE-led research coordinated by Marine Froissard, "Cell Différenciation and Polarity" Team in collaboration with Yann Gohon équipe "Dynamics and Structure of Lipid bodies" has developed a new multimodal imaging method that combines different microscopy techniques used at the SOLEIL synchrotron (France) and the ALBA synchrotron (Spain). This method was used to gather complementary information about the composition and structure of lipid droplets in yeast cells. One of its advantages? It does not employ any chemical markers or fixing agents, which can potentially damage cells. The results of this research were published on May 4, 2020, in Journal of Synchrotron Radiation.

The body is made up of different organs, which all have crucial roles. In the same way, the cells of complex organisms are composed of different organelles with distinct functions, ensuring cell viability. Among these organelles are lipid droplets. Lipid droplets have been the focus of intense study because they play a role in several diseases, including diabetes and obesity. The lipids found in the droplets are of interest to the food industry (e.g., for making vegetable oils), the green chemistry industry (e.g., for making biodiesel), and the cosmetics industry (e.g., for making soaps and lotions containing vegetable oils). Diverse lipids are present within the droplets, although triglycerides and cholesterol esters predominate and are responsible for droplet structure. Thus, clarifying the structure and composition of lipid droplets has important practical consequences.

Current methods for studying the internal structure of lipid droplets destroy cells. These methods have led to major discoveries about the structure and composition of individual droplets or droplets observed in sectioned cells. It is now necessary to develop new imaging tools to more comprehensively study how the droplets function and interact with other organelles within intact cells.

A new non-invasive cell imaging method

An INRAE-led research team developed a new non-invasive cell imaging method by adapting and combining two imaging techniques previously used to study plant and animal cells. This new method was employed to study cells of baker's yeast (Saccharomyces cerevisiae).

First, researchers used cryo soft X-ray tomography (employed at the ALBA synchrotron) to analyse yeast cells exposed to ultrarapid freezing (i.e., vitrified yeast cells). This x-ray-based technique makes it possible to study the internal architecture of cells at the nanometric scale (i.e., one billionth of a metre). More specifically, the technique can reveal organelle arrangements and interactions. Lipid droplets strongly absorb x-rays and can thus be clearly seen in the resulting images.

Second, researchers used deep-UV imaging (employed at the SOLEIL synchrotron). This technique does not require any special preliminary procedures and allows researchers to observe living cells at micrometric to nanometric scales (i.e., from one millionth to one billionth of a metre). Consequently, it can be used to observe the dynamics of internal cellular processes. The challenge was to adapt this technique for use on yeast cells, which are 10 times smaller than plant or animal cells.

Revealing the internal structure of cells ten times smaller than plant or animal cells

Cryo soft X-ray tomography showed that the structure of lipid droplets changed depending on their composition. Deep-UV imaging provided information about the structure of and contact between organelles in a living yeast cell at a scale of around 100 nanometres, without the need for any chemical markers. The researchers also developed specific procedures for combining different UV imaging techniques (i.e., based on the transmittance and fluorescence of tryptophan and tyrosine, two amino acids) with a view to studying living cells.

By using cryo soft X-ray tomography and deep-UV imaging in tandem, the researchers were able to obtain complementary information on cells at the micrometric to nanometric scale. The x-ray-based imaging technique can be used to explore the detailed structure of cell organelles. In contrast, the UV-based imaging technique can be used to characterise biological processes within cells (e.g., cell division); determine the fate of molecules that originate from outside the cell; and examine cellular responses to stress. This new non-invasive cell imaging method could also be used to analyse other types of cells, notably plant or animal cells, and could thus prove beneficial to other synchrotron researchers and biologists in general. The method will make it easier to build a new organelle atlas in living cells.

The SOLEIL synchrotron and its relationship with INRAE
synchrotron s a large research facility where scientists study matter via its interactions with light. At the SOLEIL synchrotron, researchers can exploit a diversity of spectroscopic methods that utilise a wide range of the electromagnetic spectrum, from the far infrared to UV to hard x-rays.
INRAE is linked to SOLEIL by two engineers, who dedicate themselves to SOLEIL-specific research; a research coordinator; and the scientific advisory board of INRAE users at SOLEIL (the Conseil Scientifique d’Utilisateurs [CSU]). INRAE scientists who want to carry out research at SOLEIL must first send their project proposals to the CSU, which inventories potential projects. It also helps researchers refine their proposals, choose the appropriate program committee, and reduce research overlap. The proposal is then submitted via the Sunset platform. Calls for proposals take place twice a year: the deadlines are February 15 and September 15.

Marine Froissard
Institut Jean-Pierre Bourgin (INRAE, AgroParisTech)
Associated Department: TRANSFORM
Associated Centre :
Ile-de-France - Versailles-Grignon

Référence :
Frédéric Jamme, Bertrand Cinquin, Yann Gohon, Eva Pereiro, Matthieu Réfrégiers et Marine Froissard, Synchrotron multimodal imaging in a whole cell reveals lipid droplet core organization, Journal of Synchrotron radiation, Mai 2020
DOI : https://doi.org/10.1107/S1600577520003847

More information:
Press release INRAE

7th May 2020

First evidence that extracellular nanofilaments manipulate cell shape

Until now, it was thought that the shape of plant cells was determined only by the hydrostatic pressure within the cells exerted against the cell wall. Scientists from the team "Primary cell wall", in collaboration with researchers of the University of Cambridge and the Caltech/Howard Hughes Medical Institute
, have discovered new filamentous structures within plant cell walls that influence cell growth and help build complex three-dimensional cell shapes. Published in Science the 27th February 2020, these results could also have implications in the animal kingdom and in future to be an inspiration for development of new smart materials.

Combining two types of high-performance microscopes, the researchers identified pectin nanofilaments aligned in columns along the edge of the cell walls of plants. The filaments, which are 1,000 times thinner than a human hair, had only ever been synthesised in a lab, but never observed in nature until now.

These revelations about the cell wall structure are crucial for understanding how plants form their complex shapes and will help increase understanding of plant immunity and adaptation to changing environments, and possibly inspire future development of biofuels, agriculture, and even building smart, self-expanding materials.

It might look like a uniform surface of green, but place a typical leaf under a microscope and an intricate patchwork of irregular-shaped cells fitting together perfectly like a jigsaw puzzle is revealed. Each of these cells on the surface of a leaf, called pavement cells, has its own unique shape and continues to expand and change shape as the leaf grows.

The current "textbook" thinking about how these unusual wavy-shaped cells are formed is that the internal pressure within the cell (turgor) pushes against the rigid cell wall that surrounds each cell to define its final shape. Weaker parts of the wall expand further, like air pressure forcing weaker areas of a balloon to expand more.

Published today in the journal Science, researchers from the French National Research Institute for Agriculture, Food and Environment (INRAE) together with scientists from the University of Cambridge and Caltech/Howard Hughes Medical Institute are the first to show the presence of pectin nanofilament structures. Not only did they discover these new structures, they also demonstrated that they actively drive cell shape – and even cell growth – independent of pressure within the cell.

Before the team’s discovery, pectin was considered a disorganised gel-like filling material sitting between the long cellulose fibres in the cell wall. Dr Kalina T. Haas, first author of the paper, who was working at the University of Cambridge at the time and is now an INRAE researcher, explains: “Biochemistry is typically used to study the components of the cell wall, but biochemical analysis disintegrates the cell wall to extract molecules for further study and so we do not get a chance to examine the original structure. Conventional fluorescence microscopes with a resolution of 200 nm aren’t any help either as the cell wall is only 50-100 nm in width and too small for this type of microscope to see its detailed structure. To overcome this, we used two types of cutting-edge microscopy, dSTORM and cryoSEM, which allowed us to keep the cell wall intact. Together, these microscopes revealed that pectins do not form a 'jelly', but create a well organised nanoscaled colonnade (sequence of columns) along the edge of the cell wall.

The cryo Scanning Electron Microscope (cryoSEM, very low temperature) developed at the Sainsbury Laboratory at the University of Cambridge captured the very first images of these pectin filaments. Dr Raymond Wightman, Imaging Core Facility Manager at the Sainsbury Laboratory, said: “It was in a lab 40 years ago that chemists first demonstrated that pectin might form filaments, but these had never been observed in nature. The cryoSEM provided us with the very first images of pectin as filamentous structures and the super-high resolution light microscope called dSTORM confirmed that what we were seeing was actually pectin structures. No single microscope by itself could have confirmed these results.

Dr Kalina T. Haas and Dr Alexis Peaucelle at INRAE adapted the MRC/LMB’s dSTORM microscope to analyse the leaf cells of Arabidopsis thaliana (thale cress) at a high resolution of 20-40 nm. They found that a single type of chemical change (methyl group removal) in the pectin nanofilament triggers the filaments to swell and expand radially by around 40%. This swelling causes buckling of the cell wall, which then initiates the growth and formation of the unusual wavy-shaped cells.

Dr Peaucelle explained: “This is related to a change in the packaging of pectin polymers inside the nanofilament from a compact to a loose lattice. Such self-expansion of the cell wall components, coupled with their local orientation, can drive the emergence of complex shapes. A computer model found the small change in size that accompanies a modified nanofilament is enough to make the jigsaw puzzle cell shape. Furthermore, these shape changes did not need the force of turgor within the modelled cells.”

Further research will be required to determine what contribution turgor pressure and the cellulose in the cell wall play in determining cell shape. The team think it likely that turgor pressure and cellulose work alongside pectin nanofilaments to help to maintain shape.

Dr Peaucelle continued: “We also found that the puzzle-shape of plant epidermal cells is very ordered. When we sonified the images, we observed that their shapes are organised in waves similar to that produced by a musical instrument. As an example, we used different cells to create notes from a chromatic scale and then play ‘The Blue Danube’ by J. Strauss with them. It is extraordinary that through increasing our understanding of how the epidermal cells form their wavy pattern, we also confirmed that pectin is involved in the growth process. This highlights how little we know about something so vital for sustaining our society as plant growth. I envisage further discoveries in plant and human health will come as more attention is given to the extracellular matrix surrounding cells, thanks to the new generation of high-resolution microscopes. Although animal cells are not surrounded by cell walls, they are surrounded by an extracellular matrix of proteins and sugars, which may similarly guide cell shape.”

Authors conclude, by saying that self-expansion related function may be present in different kingdoms. Other extracellular matrix polysaccharides such as carrageenan of red algae, alginate of brown algae, or even hyaluronic acid in Animalia may play a similar role.

Alexis Peaucelle
Institut Jean-Pierre Bourgin (INRAE, AgroParisTech)
Associated Department: BAP
Associated Centre:
Ile-de-France - Versailles-Grignon

Kalina T. Haas, Raymond Wightman, Elliot M. Meyerowitz et Alexis Peaucelle (2020) Pectin homogalacturonan nanofilament expansion drives morphogenesis in plant epidermal cells, Science, Vol. 367, Issue 6481, pp. 1003-1007
DOI: 10.1126/science.aaz510

More information:
INRAE Press release

Video: Pectin homogalacturonan nanofilament expansion drives morphogenesis in plant epidermal cells.

27th Frebuary 2020
Updated 2nd March 2020

Book: Abscisic Acid in plants

Editors, Mitsunori Seo et
Annie Marion-Poll

Abscisic acid in plants, Volume 92, the latest release in the Advances in Botanical Research series is a compilation of the current state-of-the-art on the topic. Chapters in this new release comprehensively describe latest knowledge on how ABA functions as a plant hormone. They cover topics related to molecular mechanisms as well as the biochemical and chemical aspects of ABA action: hormone biosynthesis, catabolism, transport, perception, signaling in plants, seeds and in response to biotic and abiotic stresses, hormone evolution and chemical biology, and much more.


cover full size

10th December 2019


Plant growth and human diseases: deciphering common regulators

From plant adaptation to the environment to human disease control, the team of Christian Meyer "Nitrogen Use, Transport and signaling" in collaboration with Belgium teams of the Vlaams Instituut voor Biotechnologie (VIB), found common regulators to plants and animals. They show that a mutated protein (YAK1) allow to counteract the effects of another protein (TOR) consequently reducing growth and metabolism. published in Cell Reports, their results open up new perspectives to improve plant growth, human cancer therapy or neurological diseases.

Found in animals, plants, fungi and yeasts, the protein « Target Of Rapamycin » (TOR) control many key biological processes as cell proliferation and metabolic activities. TOR is an enzyme of kinase type; it means that this enzyme adds a phosphate on aminoacids of target proteins to regulate its activity or stabilize it.

TOR activity is increased in numerous human cancers and its inhibitors can reduce the proliferation of cancers. Among them, the most famous is rapamycin, an antibiotic discovered in the 70s and produced by a bacterium found in the Easter Islands (Rapa Nui).

In plants TOR regulates growth and yield of defense against pathogens. Scientists shown that genetic mutations of TOR affecting the activity of the protein reduce drastically growth and slow down the development.

TOR's hammer

Scientists of the IJPB team of Christian Meyer "Nitrogen Use, Transport and signaling" in collaboration with Belgium teams, used the model plant Arabidopsis thaliana to identify new mutations suppressing the growth and allowing to compensate TOR defects. Thanks to this strategy another kinase, YAK1 (Yet Another Kinase 1) also existing in yeast, was identified. The mutated YAK1 allow to plants already affected in TOR activity to recover a bigger size and a better growth. The metabolic disturbances linked to the inactivation of TOR are also decreased. Then, YAK1 inactivation by TOR seams to be necessary to activate the plant growth.

Homologues of the YAK1 kinase do exit in animals. In human notably, those homologues (including DYRK1A) are involved among others in symptoms of trisomy 21 or autism.

A better understanding of links between TOR and YAK1 could improve cultivated plants adaptation performances to the environment, but also therapies of human diseases linked to cell proliferation (as cancers) or to neurological development. Indeed, a hight proportion of genes involved in human cancers do also exist in Arabidopsis and cell processes associated to cell proliferation are very similars, for example, in response to some pathogens.


Wild type Arabidopsis plants (top left) show a very reduced growth when the LST8 protein, a component of the TOR complex, is mutated (top right). Extra mutations of the kiinase YAK1 supress partially defects of the plant growth and development (bottom left and right). The YAK1 kinase is located in the nucleus and cytoplasm of vegetal cells (in the center, detection of a protein fusion between YAK1 and a fluorescent marker). Photos IINRA, Céline Forzani

  A model of the relationship between TOR, YAK1 and growth in plants. RAPTOR, LST8 and TOR proteins are components of the TORC1 complex in Eucaryotes. the reversed T corresponds to an inhibition. copyright INRA

Communiqué de presse INRA 06/06/19

Christian Meyer (01 30 83 30 67)
Institut Jean-Pierre Bourgin (INRA, AgroParisTech ; ERL CNRS)
Associated Department:
Plant Biology and Breeding
Associated Centre:

Contact(s) press:
Inra Press Room (01 42 75 91 86)

Mutations of the AtYAK1 kinase suppress TOR deficiency in Arabidopsis. Céline Forzanni, Gustavo T. Duarte, Jelle Van Leene, Gilles Clément, Stéphanie Huguet, Christine Paysant-Le Roux, Raphaël Mercier, Geert De Jaeger, Anne-Sophie Leprince, Christian Meyer. Cell Reports. 18 juin 2019. doi: 10.1016/j.celrep.2019.05.074

24th June 2019


Monday 9th March 2020, 2:00 pm


Invited Speaker IJPB/SPS
Prof. Farhah ASSAAD
Technical University of Munich, Germany
Allocation decisions in Arabidopsis thaliana
Invited by :
Registration compulsory except for INRAE Versailles members up to 06/03/20 15h00


Seminars location except other indications

Amphitheatre, Building 10
INRA Centre de Versailles-Grignon
Route de St Cyr (RD10)
F-78026 Versailles Cedex


Page Intranet séminaires IJPB


Workshop Sugar Allocation in Plants

The organization of the Workshop is postponed taking into account the health situation.

INRAE, Versailles

Plant biomass production and crop quality is the result of a number of processes. One major process is how sugars are allocated over the different organs after carbon fixation and assimilation in the leaves by photosynthesis. It depends on a steady-state balance between consumption, storage and long-distance transport at the level of the cell and the organ. It is also intricately related to sugar metabolism and homeostasis. It is also characterized by the trade-offs of plant energetic and primary metabolism, therefore plant growth, with the responses to the environment. The most recent discoveries of key factors acting in the regulation of sugar allocation have recently shed light on the role of sugars transport in plant adaptation to a range of abiotic and biotic stresses. The objective of this workshop is to bring together researchers, students and plant breeders to discuss the latest advances and their applications in this domain.

Organized at Versailles, by IJPB (Institut Jean Pierre Bourgin) - INRAE Versailles and EBI (Ecologie et Biologie des Interactions, CNRS/Université de Poitiers) Team SEVE (Laboratory CNRS-University, Transport de sucres et réponses des plantes aux contraintes abiotiques) - University of Poitiers.

This workshop follows up a serie of events that have been organized by the same co-organizers at Poitiers (Le phloème dans tous ses états”, 2004, 2012), with the support of the SFBV (Société Française de Biologie Végétale).

Scientific Committee
Dr. Sylvie Dinant, Senior Scientist, INRAE, IJPB Versailles
Dr. Rémi Lemoine, Senior Scientist, CNRS, Université de Poitiers
Dr. Nathalie Pourtau, Assistant Professor, Université de Poitiers

Scientific Committee IJPB:
Prof. Catherine Bellini
Dr. Fabien Chardon
Dr. Rozenn Le Hir
Dr. Françoise Vilaine

Local Organization Committee:
Beate Hoffman
Laurence Bill
Corine Enard, IJPB
Nazneen Badroudine, IJPB
Maria-Jesus Lacruz, IJPB
Stéphane Raude, IJPB
Philippe Porée, INRAE Versailles
Gisèle Cordillot (SFBV)

Contact and more information Workshop Sugar Allocation in Plants website

13th july 2020


ZELCOR Summer School 2020

Due to the COVID-19 situation, the Zelcor Summer School is cancelled in July.
We hope to reschedule it later and will keep you informed.

6-10 juillet 2020

INRAE, Versailles

Bolstered by the success of the 1st Zelcor summer school (Wageningen, 2018), Zelcor consortium offers a second edition on the topic: “Zero waste biorefineries: value chain approach, methods and processes for lignin up-grading”.

This international event organized by INRAE will be held in Versailles (France) from 6th to 10th July.
It targets a mixed public of academic and private partners (total of 50 participants) with the objective to favor interactions between scientific research and industry. The programme includes lectures dedicated to the latest advances in plant cell wall knowledge and biorefinery technologies (4 ½ days), lab training on analytical technics or tutorials on sustainability assessment (1 day), visit of a biorefinery site (1 day), and work in group on study cases (2 ½ days).

The last day sessions jointly organized with the Saclay Plant Science summer school will allow all the participants to benefit from the lectures of two invited speakers involved in cellulosic ethanol value chains and to share their poster and project presentations.


Scientific Committee IJPB :
Stéphanie Baumberger
Herman Höfte
Matthieu Reymond
Helen North

lLocal Committee :
Corine Enard, IJPB
Marie-Jeanne Sellier, SPS, INRAE Versailles
Maria-Jesus Lacruz, IJPB
Philippe Porée, INRAE Versailles
Stéphanie Zimmermann, IJPB, INRAE, Versailles
Stéphane Raude, IJPB

Contact and more information ZELCOR Summer School 2020 website

10th February 2020


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