@article{escamez_genetic_2023,
	title = {Genetic markers and tree properties predicting wood biorefining potential in aspen ({Populus} tremula) bioenergy feedstock},
	volume = {16},
	issn = {2731-3654},
	url = {https://doi.org/10.1186/s13068-023-02315-1},
	doi = {10.1186/s13068-023-02315-1},
	abstract = {Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.},
	number = {1},
	urldate = {2023-04-14},
	journal = {Biotechnology for Biofuels and Bioproducts},
	author = {Escamez, Sacha and Robinson, Kathryn M. and Luomaranta, Mikko and Gandla, Madhavi Latha and Mähler, Niklas and Yassin, Zakiya and Grahn, Thomas and Scheepers, Gerhard and Stener, Lars-Göran and Jansson, Stefan and Jönsson, Leif J. and Street, Nathaniel R. and Tuominen, Hannele},
	month = apr,
	year = {2023},
	keywords = {Bioenergy, Biomass, Biorefining, Feedstock recalcitrance, Forest feedstocks, Saccharification},
	pages = {65},
}

Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.

@article{escamez_fluorescence_2021,
	title = {Fluorescence {Lifetime} {Imaging} as an {In} {Situ} and {Label}-{Free} {Readout} for the {Chemical} {Composition} of {Lignin}},
	volume = {9},
	url = {https://doi.org/10.1021/acssuschemeng.1c06780},
	doi = {10/gnr3sb},
	abstract = {Naturally fluorescent polymeric molecules such as collagen, resilin, cutin, suberin, or lignin can serve as renewable sources of bioproducts. Theoretical physics predicts that the fluorescence lifetime of these polymers is related to their chemical composition. We verified this prediction for lignin, a major structural element in plant cell walls that form woody biomass. Lignin is composed of different phenylpropanoid units, and its composition affects its properties, biological functions, and the utilization of wood biomass. We carried out fluorescence lifetime imaging microscopy (FLIM) measurements of wood cell wall lignin in a population of 90 hybrid aspen trees genetically engineered to display differences in cell wall chemistry and structure. We also measured the wood cell wall composition by classical analytical methods in these trees. Using statistical modeling and machine learning algorithms, we identified parameters of fluorescence lifetime that predict the content of S-type and G-type lignin units, the two main types of units in the lignin of angiosperm (flowering) plants. In a first step toward tailoring lignin biosynthesis toward improvement of woody biomass feedstocks, we show how FLIM can reveal the dynamics of lignin biosynthesis in two different biological contexts, including in vivo while lignin is being synthesized in the walls of living cells.},
	number = {51},
	urldate = {2021-12-14},
	journal = {ACS Sustainable Chemistry \& Engineering},
	author = {Escamez, Sacha and Terryn, Christine and Gandla, Madhavi Latha and Yassin, Zakiya and Scheepers, Gerhard and Näsholm, Torgny and Sundman, Ola and Jönsson, Leif J. and Lundberg-Felten, Judith and Tuominen, Hannele and Niittylä, Totte and Paës, Gabriel},
	month = dec,
	year = {2021},
	pages = {17381--17392},
}

Naturally fluorescent polymeric molecules such as collagen, resilin, cutin, suberin, or lignin can serve as renewable sources of bioproducts. Theoretical physics predicts that the fluorescence lifetime of these polymers is related to their chemical composition. We verified this prediction for lignin, a major structural element in plant cell walls that form woody biomass. Lignin is composed of different phenylpropanoid units, and its composition affects its properties, biological functions, and the utilization of wood biomass. We carried out fluorescence lifetime imaging microscopy (FLIM) measurements of wood cell wall lignin in a population of 90 hybrid aspen trees genetically engineered to display differences in cell wall chemistry and structure. We also measured the wood cell wall composition by classical analytical methods in these trees. Using statistical modeling and machine learning algorithms, we identified parameters of fluorescence lifetime that predict the content of S-type and G-type lignin units, the two main types of units in the lignin of angiosperm (flowering) plants. In a first step toward tailoring lignin biosynthesis toward improvement of woody biomass feedstocks, we show how FLIM can reveal the dynamics of lignin biosynthesis in two different biological contexts, including in vivo while lignin is being synthesized in the walls of living cells.

@article{gandla_overexpression_2021,
	title = {Overexpression of vesicle-associated membrane protein {PttVAP27}-17 as a tool to improve biomass production and the overall saccharification yields in {Populus} trees},
	volume = {14},
	issn = {1754-6834},
	url = {https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-021-01895-0},
	doi = {10/gjd7kj},
	abstract = {Abstract
            
              Background
              Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth.
            
            
              Results
              
                In this study, we report on transgenic hybrid aspen (
                Populus tremula
                ×
                tremuloides
                ) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for
                Populus tremula
                ×
                tremuloides
                vesicle-associated membrane protein (VAMP)-associated protein
                PttVAP27-17
                that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20–44\% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26–50\% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24\% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control.
              
            
            
              Conclusions
              The results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {Biotechnology for Biofuels},
	author = {Gandla, Madhavi Latha and Mähler, Niklas and Escamez, Sacha and Skotare, Tomas and Obudulu, Ogonna and Möller, Linus and Abreu, Ilka N. and Bygdell, Joakim and Hertzberg, Magnus and Hvidsten, Torgeir R. and Moritz, Thomas and Wingsle, Gunnar and Trygg, Johan and Tuominen, Hannele and Jönsson, Leif J.},
	month = dec,
	year = {2021},
	pages = {43},
}

Abstract Background Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth. Results In this study, we report on transgenic hybrid aspen ( Populus tremula × tremuloides ) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula × tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20–44% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26–50% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control. Conclusions The results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.

@article{escamez_cell_2020,
	title = {Cell {Death} in {Cells} {Overlying} {Lateral} {Root} {Primordia} {Facilitates} {Organ} {Growth} in {Arabidopsis}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982219315805},
	doi = {10/ggh2vm},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Escamez, Sacha and André, Domenique and Sztojka, Bernadette and Bollhöner, Benjamin and Hall, Hardy and Berthet, Béatrice and Voß, Ute and Lers, Amnon and Maizel, Alexis and Andersson, Magnus and Bennett, Malcolm and Tuominen, Hannele},
	month = feb,
	year = {2020},
	pages = {455--464.e7},
}

@article{lakehal_ethylene_2020,
	title = {{ETHYLENE} {RESPONSE} {FACTOR} 115 integrates jasmonate and cytokinin signaling machineries to repress adventitious rooting in {Arabidopsis}},
	volume = {228},
	copyright = {©2020 The Authors. New Phytologist ©2020 New Phytologist Trust},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16794},
	doi = {10/ghhwk4},
	abstract = {Adventitious root initiation (ARI) is a de novo organogenesis program and a key adaptive trait in plants. Several hormones regulate ARI but the underlying genetic architecture that integrates the hormonal crosstalk governing this process remains largely elusive. In this study, we use genetics, genome editing, transcriptomics, hormone profiling and cell biological approaches to demonstrate a crucial role played by the APETALA2/ETHYLENE RESPONSE FACTOR 115 transcription factor. We demonstrate that ERF115 functions as a repressor of ARI by activating the cytokinin (CK) signaling machinery. We also demonstrate that ERF115 is transcriptionally activated by jasmonate (JA), an oxylipin-derived phytohormone, which represses ARI in NINJA-dependent and independent manners. Our data indicate that NINJA-dependent JA signaling in pericycle cells blocks early events of ARI. Altogether, our results reveal a previously unreported molecular network involving cooperative crosstalk between JA and CK machineries that represses ARI.},
	language = {en},
	number = {5},
	urldate = {2021-06-21},
	journal = {New Phytologist},
	author = {Lakehal, Abdellah and Dob, Asma and Rahneshan, Zahra and Novák, Ondřej and Escamez, Sacha and Alallaq, Sanaria and Strnad, Miroslav and Tuominen, Hannele and Bellini, Catherine},
	year = {2020},
	keywords = {AP2/ERF transcription factors, adventitious rooting, cytokinins, de novo organogenesis, jasmonate},
	pages = {1611--1626},
}

Adventitious root initiation (ARI) is a de novo organogenesis program and a key adaptive trait in plants. Several hormones regulate ARI but the underlying genetic architecture that integrates the hormonal crosstalk governing this process remains largely elusive. In this study, we use genetics, genome editing, transcriptomics, hormone profiling and cell biological approaches to demonstrate a crucial role played by the APETALA2/ETHYLENE RESPONSE FACTOR 115 transcription factor. We demonstrate that ERF115 functions as a repressor of ARI by activating the cytokinin (CK) signaling machinery. We also demonstrate that ERF115 is transcriptionally activated by jasmonate (JA), an oxylipin-derived phytohormone, which represses ARI in NINJA-dependent and independent manners. Our data indicate that NINJA-dependent JA signaling in pericycle cells blocks early events of ARI. Altogether, our results reveal a previously unreported molecular network involving cooperative crosstalk between JA and CK machineries that represses ARI.

@article{zhang_pirin2_2020,
	title = {{PIRIN2} suppresses {S}‐type lignin accumulation in a noncell‐autonomous manner in {Arabidopsis} xylem elements},
	volume = {225},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.16271},
	doi = {10.1111/nph.16271},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Zhang, Bo and Sztojka, Bernadette and Escamez, Sacha and Vanholme, Ruben and Hedenström, Mattias and Wang, Yin and Turumtay, Halbay and Gorzsás, András and Boerjan, Wout and Tuominen, Hannele},
	month = mar,
	year = {2020},
	pages = {1923--1935},
}

@article{zhang_chromatin-modifying_2020,
	title = {The chromatin-modifying protein {HUB2} is involved in the regulation of lignin composition in xylem vessels},
	volume = {71},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/71/18/5484/5849544},
	doi = {10.1093/jxb/eraa264},
	abstract = {Abstract
            PIRIN2 (PRN2) was earlier reported to suppress syringyl (S)-type lignin accumulation of xylem vessels of Arabidopsis thaliana. In the present study, we report yeast two-hybrid results supporting the interaction of PRN2 with HISTONE MONOUBIQUITINATION2 (HUB2) in Arabidopsis. HUB2 has been previously implicated in several plant developmental processes, but not in lignification. Interaction between PRN2 and HUB2 was verified by β-galactosidase enzymatic and co-immunoprecipitation assays. HUB2 promoted the deposition of S-type lignin in the secondary cell walls of both stem and hypocotyl tissues, as analysed by pyrolysis-GC/MS. Chemical fingerprinting of individual xylem vessel cell walls by Raman and Fourier transform infrared microspectroscopy supported the function of HUB2 in lignin deposition. These results, together with a genetic analysis of the hub2 prn2 double mutant, support the antagonistic function of PRN2 and HUB2 in deposition of S-type lignin. Transcriptome analyses indicated the opposite regulation of the S-type lignin biosynthetic gene FERULATE-5-HYDROXYLASE1 by PRN2 and HUB2 as the underlying mechanism. PRN2 and HUB2 promoter activities co-localized in cells neighbouring the xylem vessel elements, suggesting that the S-type lignin-promoting function of HUB2 is antagonized by PRN2 for the benefit of the guaiacyl (G)-type lignin enrichment of the neighbouring xylem vessel elements.},
	language = {en},
	number = {18},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Zhang, Bo and Sztojka, Bernadette and Seyfferth, Carolin and Escamez, Sacha and Miskolczi, Pál and Chantreau, Maxime and Bakó, László and Delhomme, Nicolas and Gorzsás, András and Bhalerao, Rishikesh P. and Tuominen, Hannele},
	editor = {Turner, Simon},
	month = sep,
	year = {2020},
	pages = {5484--5494},
}

Abstract PIRIN2 (PRN2) was earlier reported to suppress syringyl (S)-type lignin accumulation of xylem vessels of Arabidopsis thaliana. In the present study, we report yeast two-hybrid results supporting the interaction of PRN2 with HISTONE MONOUBIQUITINATION2 (HUB2) in Arabidopsis. HUB2 has been previously implicated in several plant developmental processes, but not in lignification. Interaction between PRN2 and HUB2 was verified by β-galactosidase enzymatic and co-immunoprecipitation assays. HUB2 promoted the deposition of S-type lignin in the secondary cell walls of both stem and hypocotyl tissues, as analysed by pyrolysis-GC/MS. Chemical fingerprinting of individual xylem vessel cell walls by Raman and Fourier transform infrared microspectroscopy supported the function of HUB2 in lignin deposition. These results, together with a genetic analysis of the hub2 prn2 double mutant, support the antagonistic function of PRN2 and HUB2 in deposition of S-type lignin. Transcriptome analyses indicated the opposite regulation of the S-type lignin biosynthetic gene FERULATE-5-HYDROXYLASE1 by PRN2 and HUB2 as the underlying mechanism. PRN2 and HUB2 promoter activities co-localized in cells neighbouring the xylem vessel elements, suggesting that the S-type lignin-promoting function of HUB2 is antagonized by PRN2 for the benefit of the guaiacyl (G)-type lignin enrichment of the neighbouring xylem vessel elements.

@article{wessels_ap2erf_2019,
	title = {An {AP2}/{ERF} transcription factor {ERF139} coordinates xylem cell expansion and secondary cell wall deposition},
	volume = {224},
	issn = {0028-646X, 1469-8137},
	shorttitle = {An {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.15960},
	doi = {10/gjcsfs},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Wessels, Bernard and Seyfferth, Carolin and Escamez, Sacha and Vain, Thomas and Antos, Kamil and Vahala, Jorma and Delhomme, Nicolas and Kangasjärvi, Jaakko and Eder, Michaela and Felten, Judith and Tuominen, Hannele},
	month = dec,
	year = {2019},
	pages = {1585--1599},
}

@article{escamez_extracellular_2019,
	title = {Extracellular peptide {Kratos} restricts cell death during vascular development and stress in {Arabidopsis}},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/70/7/2199/5308826},
	doi = {10/gjd42p},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Escamez, Sacha and Stael, Simon and Vainonen, Julia P and Willems, Patrick and Jin, Huiting and Kimura, Sachie and Van Breusegem, Frank and Gevaert, Kris and Wrzaczek, Michael and Tuominen, Hannele},
	month = apr,
	year = {2019},
	pages = {2199--2210},
}

@article{escamez_collection_2017,
	title = {A collection of genetically engineered {Populus} trees reveals wood biomass traits that predict glucose yield from enzymatic hydrolysis},
	volume = {7},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-017-16013-0},
	doi = {10/gcmn8b},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Escamez, Sacha and Latha Gandla, Madhavi and Derba-Maceluch, Marta and Lundqvist, Sven-Olof and Mellerowicz, Ewa J. and Jönsson, Leif J. and Tuominen, Hannele},
	month = dec,
	year = {2017},
	pages = {15798},
}

@article{escamez_contribution_2017,
	title = {Contribution of cellular autolysis to tissular functions during plant development},
	volume = {35},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526616302126},
	doi = {10.1016/j.pbi.2016.11.017},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Escamez, Sacha and Tuominen, Hannele},
	month = feb,
	year = {2017},
	pages = {124--130},
}

@article{salojarvi_genome_2017,
	title = {Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch},
	volume = {49},
	issn = {1061-4036, 1546-1718},
	url = {http://www.nature.com/articles/ng.3862},
	doi = {10/f96grj},
	abstract = {Abstract
            
              Silver birch (
              Betula pendula
              ) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred
              B. pendula
              individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes
              PHYC
              and
              FRS10
              correlated with latitude and longitude and temperature, and with precipitation for
              PHYC
              . Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes
              KAK
              and
              MED5A
              .},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Nature Genetics},
	author = {Salojärvi, Jarkko and Smolander, Olli-Pekka and Nieminen, Kaisa and Rajaraman, Sitaram and Safronov, Omid and Safdari, Pezhman and Lamminmäki, Airi and Immanen, Juha and Lan, Tianying and Tanskanen, Jaakko and Rastas, Pasi and Amiryousefi, Ali and Jayaprakash, Balamuralikrishna and Kammonen, Juhana I and Hagqvist, Risto and Eswaran, Gugan and Ahonen, Viivi Helena and Serra, Juan Alonso and Asiegbu, Fred O and de Dios Barajas-Lopez, Juan and Blande, Daniel and Blokhina, Olga and Blomster, Tiina and Broholm, Suvi and Brosché, Mikael and Cui, Fuqiang and Dardick, Chris and Ehonen, Sanna E and Elomaa, Paula and Escamez, Sacha and Fagerstedt, Kurt V and Fujii, Hiroaki and Gauthier, Adrien and Gollan, Peter J and Halimaa, Pauliina and Heino, Pekka I and Himanen, Kristiina and Hollender, Courtney and Kangasjärvi, Saijaliisa and Kauppinen, Leila and Kelleher, Colin T and Kontunen-Soppela, Sari and Koskinen, J Patrik and Kovalchuk, Andriy and Kärenlampi, Sirpa O and Kärkönen, Anna K and Lim, Kean-Jin and Leppälä, Johanna and Macpherson, Lee and Mikola, Juha and Mouhu, Katriina and Mähönen, Ari Pekka and Niinemets, Ülo and Oksanen, Elina and Overmyer, Kirk and Palva, E Tapio and Pazouki, Leila and Pennanen, Ville and Puhakainen, Tuula and Poczai, Péter and Possen, Boy J H M and Punkkinen, Matleena and Rahikainen, Moona M and Rousi, Matti and Ruonala, Raili and van der Schoot, Christiaan and Shapiguzov, Alexey and Sierla, Maija and Sipilä, Timo P and Sutela, Suvi and Teeri, Teemu H and Tervahauta, Arja I and Vaattovaara, Aleksia and Vahala, Jorma and Vetchinnikova, Lidia and Welling, Annikki and Wrzaczek, Michael and Xu, Enjun and Paulin, Lars G and Schulman, Alan H and Lascoux, Martin and Albert, Victor A and Auvinen, Petri and Helariutta, Ykä and Kangasjärvi, Jaakko},
	month = jun,
	year = {2017},
	pages = {904--912},
}

Abstract Silver birch ( Betula pendula ) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC . Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A .

@incollection{de_lucas_quick_2017,
	address = {New York, NY},
	title = {Quick {Histochemical} {Staining} {Methods} to {Detect} {Cell} {Death} in {Xylem} {Elements} of {Plant} {Tissues}},
	volume = {1544},
	isbn = {978-1-4939-6720-9 978-1-4939-6722-3},
	url = {http://link.springer.com/10.1007/978-1-4939-6722-3_3},
	urldate = {2021-06-07},
	booktitle = {Xylem},
	publisher = {Springer New York},
	author = {Escamez, Sacha and Bollhöner, Benjamin and Tuominen, Hannele},
	editor = {de Lucas, Miguel and Etchhells, J. Peter},
	year = {2017},
	doi = {10.1007/978-1-4939-6722-3_3},
	note = {Series Title: Methods in Molecular Biology},
	pages = {27--36},
}

@article{escamez_metacaspase9_2016,
	title = {{METACASPASE9} modulates autophagy to confine cell death to the target cells during \textit{{Arabidopsis}} vascular xylem differentiation},
	volume = {5},
	issn = {2046-6390},
	url = {https://journals.biologists.com/bio/article/5/2/122/643/METACASPASE9-modulates-autophagy-to-confine-cell},
	doi = {10.1242/bio.015529},
	abstract = {ABSTRACT
            We uncovered that the level of autophagy in plant cells undergoing programmed cell death determines the fate of the surrounding cells. Our approach consisted of using Arabidopsis thaliana cell cultures capable of differentiating into two different cell types: vascular tracheary elements (TEs) that undergo programmed cell death (PCD) and protoplast autolysis, and parenchymatic non-TEs that remain alive. The TE cell type displayed higher levels of autophagy when expression of the TE-specific METACASPASE9 (MC9) was reduced using RNAi (MC9-RNAi). Misregulation of autophagy in the MC9-RNAi TEs coincided with ectopic death of the non-TEs, implying the existence of an autophagy-dependent intercellular signalling from within the TEs towards the non-TEs. Viability of the non-TEs was restored when AUTOPHAGY2 (ATG2) was downregulated specifically in MC9-RNAi TEs, demonstrating the importance of autophagy in the spatial confinement of cell death. Our results suggest that other eukaryotic cells undergoing PCD might also need to tightly regulate their level of autophagy to avoid detrimental consequences for the surrounding cells.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Biology Open},
	author = {Escamez, Sacha and André, Domenique and Zhang, Bo and Bollhöner, Benjamin and Pesquet, Edouard and Tuominen, Hannele},
	month = feb,
	year = {2016},
	pages = {122--129},
}

ABSTRACT We uncovered that the level of autophagy in plant cells undergoing programmed cell death determines the fate of the surrounding cells. Our approach consisted of using Arabidopsis thaliana cell cultures capable of differentiating into two different cell types: vascular tracheary elements (TEs) that undergo programmed cell death (PCD) and protoplast autolysis, and parenchymatic non-TEs that remain alive. The TE cell type displayed higher levels of autophagy when expression of the TE-specific METACASPASE9 (MC9) was reduced using RNAi (MC9-RNAi). Misregulation of autophagy in the MC9-RNAi TEs coincided with ectopic death of the non-TEs, implying the existence of an autophagy-dependent intercellular signalling from within the TEs towards the non-TEs. Viability of the non-TEs was restored when AUTOPHAGY2 (ATG2) was downregulated specifically in MC9-RNAi TEs, demonstrating the importance of autophagy in the spatial confinement of cell death. Our results suggest that other eukaryotic cells undergoing PCD might also need to tightly regulate their level of autophagy to avoid detrimental consequences for the surrounding cells.

@incollection{gunawardena_life_2015,
	address = {Cham},
	title = {Life {Beyond} {Death}: {The} {Formation} of {Xylem} {Sap} {Conduits}},
	isbn = {978-3-319-21032-2 978-3-319-21033-9},
	shorttitle = {Life {Beyond} {Death}},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Plant {Programmed} {Cell} {Death}},
	publisher = {Springer International Publishing},
	author = {Ménard, Delphine and Escamez, Sacha and Tuominen, Hannele and Pesquet, Edouard},
	editor = {Gunawardena, Arunika N. and McCabe, Paul F.},
	year = {2015},
	pages = {55--76},
}

@article{escamez_programmes_2014,
	title = {Programmes of cell death and autolysis in tracheary elements: when a suicidal cell arranges its own corpse removal},
	volume = {65},
	issn = {1460-2431, 0022-0957},
	shorttitle = {Programmes of cell death and autolysis in tracheary elements},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/eru057},
	doi = {10/f234sm},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Escamez, Sacha and Tuominen, Hannele},
	month = mar,
	year = {2014},
	pages = {1313--1321},
}

@article{pesquet_non-cell-autonomous_2013,
	title = {Non-{Cell}-{Autonomous} {Postmortem} {Lignification} of {Tracheary} {Elements} in \textit{{Zinnia} elegans}},
	volume = {25},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/25/4/1314/6100539},
	doi = {10/f22bdv},
	abstract = {Abstract
            Postmortem lignification of xylem tracheary elements (TEs) has been debated for decades. Here, we provide evidence in Zinnia elegans  TE cell cultures, using pharmacological inhibitors and in intact Z. elegans plants using Fourier transform infrared microspectroscopy, that TE lignification occurs postmortem (i.e., after TE programmed cell death). In situ RT-PCR verified expression of the lignin monomer biosynthetic cinnamoyl CoA reductase and cinnamyl alcohol dehydrogenase in not only the lignifying TEs but also in the unlignified non-TE cells of Z. elegans  TE cell cultures and in living, parenchymatic xylem cells that surround TEs in stems. These cells were also shown to have the capacity to synthesize and transport lignin monomers and reactive oxygen species to the cell walls of dead TEs. Differential gene expression analysis in Z. elegans  TE cell cultures and concomitant functional analysis in Arabidopsis thaliana resulted in identification of several genes that were expressed in the non-TE cells and that affected lignin chemistry on the basis of pyrolysis–gas chromatography/mass spectrometry analysis. These data suggest that living, parenchymatic xylem cells contribute to TE lignification in a non-cell-autonomous manner, thus enabling the postmortem lignification of TEs.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Pesquet, Edouard and Zhang, Bo and Gorzsás, András and Puhakainen, Tuula and Serk, Henrik and Escamez, Sacha and Barbier, Odile and Gerber, Lorenz and Courtois-Moreau, Charleen and Alatalo, Edward and Paulin, Lars and Kangasjärvi, Jaakko and Sundberg, Björn and Goffner, Deborah and Tuominen, Hannele},
	month = may,
	year = {2013},
	pages = {1314--1328},
}

Abstract Postmortem lignification of xylem tracheary elements (TEs) has been debated for decades. Here, we provide evidence in Zinnia elegans  TE cell cultures, using pharmacological inhibitors and in intact Z. elegans plants using Fourier transform infrared microspectroscopy, that TE lignification occurs postmortem (i.e., after TE programmed cell death). In situ RT-PCR verified expression of the lignin monomer biosynthetic cinnamoyl CoA reductase and cinnamyl alcohol dehydrogenase in not only the lignifying TEs but also in the unlignified non-TE cells of Z. elegans  TE cell cultures and in living, parenchymatic xylem cells that surround TEs in stems. These cells were also shown to have the capacity to synthesize and transport lignin monomers and reactive oxygen species to the cell walls of dead TEs. Differential gene expression analysis in Z. elegans  TE cell cultures and concomitant functional analysis in Arabidopsis thaliana resulted in identification of several genes that were expressed in the non-TE cells and that affected lignin chemistry on the basis of pyrolysis–gas chromatography/mass spectrometry analysis. These data suggest that living, parenchymatic xylem cells contribute to TE lignification in a non-cell-autonomous manner, thus enabling the postmortem lignification of TEs.

@article{dhooghe_sulphur_2013,
	title = {Sulphur limitation provokes physiological and leaf proteome changes in oilseed rape that lead to perturbation of sulphur, carbon and oxidative metabolisms},
	volume = {13},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-13-23},
	doi = {10/gbcv4c},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {D’Hooghe, Philippe and Escamez, Sacha and Trouverie, Jacques and Avice, Jean-Christophe},
	year = {2013},
	pages = {23},
}