Works (30)
Updated: April 4th, 2024 13:39
2024 article
Cell-material interactions in 3D bioprinted plant cells
Madison, I., Tahir, M., Broeck, L. V., Phan, L., Horn, T., & Sozzani, R. (2024, February 1).
TL;DR:
A study in which 3D bioprinting parameters, such as needle gauge, extrusion pressure, and scaffold type, were all tested in 3D bioprinted Tobacco BY-2 cells revealed an optimal range of extrusion pressures and needle gauges that resulted in an optimum cell viability.
(via Semantic Scholar)
doi.org (repository)
Source: ORCID
Added: February 2, 2024
2023 journal article
Functional annotation of proteins for signaling network inference in non-model species
Nature Communications, 14(1).
TL;DR:
A multi-layer neural network that determines protein functionality directly from the protein sequence is developed that shows generalization and scalability and extends to Oryza sativa, Zea mays, Sorghum bicolor, and Triticum aestivum.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, Crossref
Added: September 5, 2023
2023 article proceedings
Optimal Brain Dissection in Dense Autoencoders: Towards Determining Feature Importance in -Omics Data
Presented at the 2023 IEEE 5th International Conference on BioInspired Processing (BIP).
Event: 2023 IEEE 5th International Conference on BioInspired Processing (BIP)
TL;DR:
This paper introduced Optimal Brain Dissection (OBD), an innovative methodology designed to examine the importance of first-layer connections in a biology-inspired autoencoder, aiming to understand the relative importance of connections for autoencoder performance.
(via Semantic Scholar)
Sources: ORCID, Crossref
Added: January 25, 2024
2023 article
Phosphate starvation: response mechanisms and solutions
Madison, I., Gillan, L., Peace, J., Gabrieli, F., Broeck, L., Jones, J. L., & Sozzani, R. (2023, August 23). (D. Ort, Ed.). JOURNAL OF EXPERIMENTAL BOTANY, Vol. 8.
Ed(s): D. Ort
author keywords: Nutrient uptake; nutrient sensing; phosphorus; Pi
TL;DR:
This review describes regulatory mechanisms used by specific tissues in the root apical meristem to sense and uptake phosphate from the rhizosphere and overviews the major mechanism of plant systemic phosphate starvation responses.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
Sources: ORCID, Web Of Science
Added: September 18, 2023
2023 conference paper
Prediction and functional characterization of transcriptional activation domains
Mahatma, S., Broeck, L. V., Morffy, N., Staller, M. V., Strader, L. C., & Sozzani, R. (2023, March 22).
TL;DR:
This work used an unsupervised learning approach to classify the ADs into 10 subclasses, which can be explored for AA specificity and AD functionality, and shed light on the non-linear properties of ADs.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2024
2023 article
Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation
Gaudinier, A., Broeck, L. V., Moreno-Risueño, M., Rodriguez-Medina, J., Sozzani, R., & Brady, S. M. (2023, December 6).
TL;DR:
Linking the N time course transcriptomics, LR mutant phenotypes, and cell-type specific single cell profiling, these approaches provide multiple lines of evidence to find and test the roles of TFs that are involved in early root patterning responses to N conditions.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2024
2023 article
The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice
Beretta, V. M., Franchini, E., Din, I. U., Lacchini, E., Broeck, L., Sozzani, R., … Kater, M. M. (2023, April 21). PLANT JOURNAL, Vol. 4.
author keywords: Oryza sativa; transcription factor; inflorescence architecture; meristem identity; transcriptome analysis; CRISPR mutants; gene regulatory network; ALOG
TL;DR:
The spatio-temporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of OsHOX14 suggests that the proposed GRN indeed serves as a valuable resource for the identification of new players involved in rice inflorescence development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: May 9, 2023
2022 article
Establishing a reproducible approach for the controllable deposition and maintenance of plants cells with 3D bioprinting
Broeck, L. V., Schwartz, M. F., Krishnamoorthy, S., Spurney, R. J., Tahir, M. A., Melvin, C., … Sozzani, R. (2022, March 27). (Vol. 3). Vol. 3.
TL;DR:
The framework of 3D bioprinting with plant cells to study cell viability, cell division, and cell identity is established and the identity of isolated cells of Arabidopsis roots expressing endodermal markers maintained longer periods of time.
(via Semantic Scholar)
Source: ORCID
Added: October 21, 2022
2022 journal article
Establishing a reproducible approach to study cellular functions of plant cells with 3D bioprinting
Science Advances.
MeSH headings : Arabidopsis / genetics; Bioprinting; Cell Survival; Plant Cells; Printing, Three-Dimensional; Tissue Engineering / methods; Tissue Scaffolds
TL;DR:
A framework for 3D biop printing plant cells to study cell viability, cell division, and cell identity is established and the cell cycle reentry of bioprinted cells for which the timing coincides with the induction of core cell cycle genes and regeneration-related genes are shown.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: ORCID
Added: October 21, 2022
2022 article
Functional annotation of proteins for signaling network inference in non-model species
Broeck, L. V., Bhosale, D., Song, K., Lima, C. F., Ashley, M., Zhu, T., … Sozzani, R. (2022, November 11).
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: January 25, 2024
2022 journal article
Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation
PLANT CELL, 34(1), 535–556.
MeSH headings : Capsicum / genetics; Capsicum / physiology; Gene Expression Regulation, Plant / physiology; Gene Regulatory Networks; Homeodomain Proteins / genetics; Homeodomain Proteins / metabolism; Solanum lycopersicum / genetics; Solanum lycopersicum / physiology; Plant Proteins / genetics; Plant Proteins / metabolism
TL;DR:
A model system with Solanum lycopersicum ‘tomato’ and Capsicum annuum ‘pepper’ heterografting is developed, which expresses signs of anatomical junction failure within the first week of grafting, and SlWOX4 is the first gene to be functionally implicated in vegetable crop grafting.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: ORCID, Web Of Science
Added: February 7, 2022
2021 journal article
A hybrid model connecting regulatory interactions with stem cell divisions in the root
Quantitative Plant Biology, 2.
TL;DR:
This work proposes a non-cell autonomous role for WOX5 in the cortex endodermis initial (CEI) and identifies a regulator, ANGUSTIFOLIA (AN3)/GRF-INTERACTING FACTOR 1, that coordinates CEI divisions.
(via Semantic Scholar)
Source: ORCID
Added: April 13, 2021
2021 journal article
Analysis of the transcriptomic, metabolomic, and gene regulatory responses to <i>Puccinia sorghi in maize
Molecular Plant Pathology, 22(4), 465–479.
author keywords: common rust; gene regulatory network; maize; Puccinia sorghi; RNA‐ Seq
MeSH headings : Gene Expression Profiling; Host-Pathogen Interactions; Metabolome; Metabolomics; Plant Diseases / microbiology; Plant Proteins / genetics; Plant Proteins / metabolism; Puccinia / physiology; Transcriptome; Zea mays / genetics; Zea mays / microbiology
TL;DR:
A number of transcription factors including WRKY53, BHLH124, NKD1, BZIP84, and MYB100 were identified as potentially important signalling hubs in the resistance‐specific response of P. sorghi.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
3. Good Health and Well-being
(OpenAlex)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID, Crossref
Added: March 1, 2021
2021 review
Divide and Conquer: The Initiation and Proliferation of Meristems
[Review of ]. CRITICAL REVIEWS IN PLANT SCIENCES, 40(2), 147–156.
Contributors: L. Broeck n
author keywords: Founder cells; meristem initiation; meristem maintenance; procambium; root apical meristem; shoot apical meristem
TL;DR:
This review focuses on the various plant meristems, how cells within theseMeristems maintain their identity, and particularly the molecular players that regulate stem cell maintenance, including pericycle and rachis founder cells.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: ORCID, Web Of Science
Added: May 10, 2021
2021 article
Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation
Thomas, H., Broeck, L. V., Spurney, R., Sozzani, R., & Frank, M. (2021, February 27). (Vol. 2). Vol. 2.
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: ORCID
Added: October 21, 2022
2021 article
The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice
Franchini, E., Beretta, V. M., Din, I. U., Lacchini, E., Broeck, L. V., Sozzani, R., … Kater, M. M. (2021, May 3). (Vol. 5). Vol. 5.
TL;DR:
The spatio-temporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of the homeodomain-leucine zipper transcription factor gene OsHOX14 suggest that the proposed GRN indeed serves as a valuable resource for the identification of new players involved in rice inflorescence development.
(via Semantic Scholar)
Source: ORCID
Added: October 21, 2022
2021 journal article
Tissue Regeneration with Hydrogel Encapsulation: A Review of Developments in Plants and Animals
BioDesign Research.
TL;DR:
A background into the adoption of hydrogel encapsulation methods in the study of mammalian cells is provided, some key findings that may aid with the adopters' adoption are highlighted, and key findings of studies that have utilized these methods in plant sciences are discussed.
(via Semantic Scholar)
Source: ORCID
Added: April 8, 2022
2020 journal article
Accessing Legacy Phosphorus in Soils
Soil Systems, 4(4), 74.
author keywords: legacy phosphorus; speciation; transformation; accessibility
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: ORCID, Crossref
Added: December 23, 2020
2020 journal article
Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling
Frontiers in Genetics, 11.
author keywords: gene regulatory network; network properties; network inference; machine learning; experimental methodologies
TL;DR:
This review provides examples of experimental methodologies commonly used to identify regulatory interactions and generate GRNs, and describes network inference techniques that leverage gene expression data to predict regulatory interactions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: ORCID, Web Of Science, Crossref
Added: July 13, 2020
2020 journal article
Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big
Annual Review of Plant Biology, 71(1), 789–816.
author keywords: Forster resonance energy transfer; scanning fluorescent correlation spectroscopy; microfluid devices; light sheet microscopy; imaging of macroscopic traits; multiscale imaging techniques
MeSH headings : Biology; Plant Development; Plants
TL;DR:
New imaging modalities are presented and how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale are reviewed to enable unprecedented systems-level computational modeling.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID, Crossref
Added: September 14, 2020
2020 journal article
Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division
Proceedings of the National Academy of Sciences, 117(26), 15332–15342.
author keywords: protein complex stoichiometry; intercellular protein movement; mathematical modeling; expression dynamics; transcription factor
MeSH headings : Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / chemistry; Arabidopsis Proteins / metabolism; Biomarkers; Cell Differentiation; Gene Expression Regulation, Plant / physiology; Models, Biological; Mutation; Stem Cells / physiology; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
It is suggested that SHR-SCR protein complex stoichiometry and regulation of SHR transcription modulate the division timing of two different specialized cell types in the root stem cell niche.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: ORCID, Crossref
Added: September 14, 2020
2020 journal article
tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks
PLANT JOURNAL, 101(3), 716–730.
author keywords: Arabidopsis thaliana; gene regulatory network inference; graphical user interface; RNA sequencing processing; stem cell maintenance; technical advance
MeSH headings : Algorithms; Arabidopsis / genetics; Bayes Theorem; Computational Biology; Gene Expression Regulation, Plant; Gene Regulatory Networks / genetics; Genome, Plant / genetics; Sequence Analysis, RNA; Transcriptome
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: ORCID, Web Of Science
Added: December 9, 2019
2018 journal article
Early mannitol-triggered changes in the Arabidopsis leaf (phospho)proteome reveal growth regulators.
Journal of Experimental Botany, 8.
author keywords: AHA2; Arabidopsis thaliana; CRRSP38; leaf growth; mild osmotic stress; phosphoproteome; signalling
MeSH headings : Arabidopsis / drug effects; Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; Mannitol / pharmacology; Phosphoproteins / metabolism; Plant Growth Regulators / metabolism; Plant Leaves / drug effects; Plant Leaves / metabolism; Proteome / drug effects; Proteome / metabolism
TL;DR:
Early changes in the Arabidopsis leaf proteome and phosphoproteome are captured upon mild mannitol stress and AHA2 and CRRSP38 are identified as novel regulators of shoot growth under osmotic stress.
(via Semantic Scholar)
Source: ORCID
Added: October 21, 2022
2018 journal article
The Pivotal Role of Ethylene in Plant Growth.
Trends in Plant Science, 4.
MeSH headings : Ethylenes / metabolism; Plant Development; Plant Growth Regulators / physiology; Plant Leaves / growth & development
TL;DR:
This review focuses on how ethylene regulates shoot growth, with an emphasis on leaves, and alters the expression of ethylene response factors (ERFs) provides a new strategy for targeted ethylene-response engineering.
(via Semantic Scholar)
Source: ORCID
Added: October 21, 2022
2017 dataset
E-MTAB-6205 - The expression profiles of 31 transcription factors in wild-type Col-0 plants upon mild osmotic stress, including 10 time points and different leaf tissues
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6205
Source: ORCID
Added: October 21, 2022
2017 dataset
E-MTAB-6209 - The expression profiles of 30 transcription factors in 17 inducible gain-of-function lines after activation of overexpression, including 5 time points
https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6209
Source: ORCID
Added: October 21, 2022
2017 journal article
From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress
Molecular Systems Biology, 13(12), 961.
author keywords: growth regulation; mild osmotic stress; short-term stress response; transcription factors; transcriptional network
MeSH headings : Adaptation, Physiological / drug effects; Adaptation, Physiological / genetics; Arabidopsis / drug effects; Arabidopsis / genetics; Gene Expression Profiling; Gene Expression Regulation, Plant / drug effects; Gene Regulatory Networks / drug effects; Genes, Plant; Gibberellins / biosynthesis; Gibberellins / metabolism; Mannitol / pharmacology; Osmotic Pressure / physiology; Phenotype; Plant Leaves / drug effects; Plant Leaves / genetics; Plant Leaves / growth & development; Plants, Genetically Modified; Stochastic Processes; Stress, Physiological / drug effects; Stress, Physiological / genetics; Transcription Factors / metabolism; Transcription, Genetic / drug effects
TL;DR:
This study investigated a complex, highly interconnected network of 20 Arabidopsis transcription factors at the basis of leaf growth inhibition upon mild osmotic stress, resulting in the identification of a core network, composed of ERF6, ERF8, ERf9,ERF59, and ERF98, which is responsible for most transcriptional connections.
(via Semantic Scholar)
Source: ORCID
Added: October 21, 2022
2017 journal article
Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought.
Plant, Cell & Environment, 2.
author keywords: leaf growth regulation; mild drought response; time-course transcriptomics
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; Circadian Clocks / genetics; Droughts; Gene Expression Profiling; Gene Expression Regulation, Plant; Plant Leaves / genetics; Plant Leaves / growth & development; RNA, Messenger / genetics; RNA, Messenger / metabolism; Real-Time Polymerase Chain Reaction; Sequence Analysis, RNA; Stress, Physiological / genetics; Time Factors; Transcriptome / genetics
TL;DR:
It is found that growth and transcriptome responses to drought are highly dynamic and time of day strongly affected the extent, specificity, and in certain cases even direction of drought-induced changes in gene expression.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: ORCID
Added: October 21, 2022
2016 journal article
RALFL34 regulates formative cell divisions in Arabidopsis pericycle during lateral root initiation.
Journal of Experimental Botany, 8.
author keywords: Arabidopsis thaliana; ERF; GATA23; lateral root initiation; RAPID ALKALINIZATION FACTOR (RALF)
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cell Division; Gene Expression Regulation, Plant; Peptide Hormones / genetics; Peptide Hormones / metabolism; Plant Roots / genetics; Plant Roots / growth & development; Plant Roots / metabolism; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
The role of RALFL34 is described during early events in lateral root development, and its specific importance in orchestrating formative cell divisions in the pericycle is demonstrated.
(via Semantic Scholar)
Source: ORCID
Added: October 21, 2022
2015 journal article
The ETHYLENE RESPONSE FACTORs ERF6 and ERF11 Antagonistically Regulate Mannitol-Induced Growth Inhibition in Arabidopsis.
Plant Physiology, 9.
MeSH headings : Amino Acids, Cyclic / pharmacology; Arabidopsis / drug effects; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis / physiology; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Dexamethasone / pharmacology; Ethylenes / metabolism; Gene Expression Regulation, Plant / drug effects; Mannitol / adverse effects; Plant Growth Regulators / metabolism; Plant Leaves / drug effects; Plant Leaves / genetics; Plant Leaves / growth & development; Plant Leaves / physiology; Promoter Regions, Genetic / genetics; Repressor Proteins / genetics; Repressor Proteins / metabolism; Signal Transduction; Stress, Physiological; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
It is demonstrated that dynamic mechanisms exist to fine-tune the stress response and that ERF11 counteracts ERF6 to maintain a balance between plant growth and stress defense.
(via Semantic Scholar)
Source: ORCID
Added: October 21, 2022
Employment
Updated: May 6th, 2020 05:18
North Carolina State University Raleigh, North Carolina, US
Plant Microbial and Biology
2013 - 2018
VIB Gent, BE
PhD student
PSB
Education
Updated: October 15th, 2019 16:01
2008 - 2013
Universiteit Gent Gent, BE
Master of Science in Biochemistry and Biotechnology
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