Research Gerrit Beemster

Abstract

In addition to the growth promoting interactions between the soil microbiome and plants there is growing evidence that areal plant tissues have their own microbiome of endophytes. Several of these stimulate growth under optimal or limiting conditions, providing a potential for a sustainable enhancement of crop productivity, but how they affect the growing tissues is largely unclear. The aim of the proposed research project is to study the effects of endophytic fungi and bacteria on maize leaf growth regulation under optimal and drought conditions. Endophytic bacteria and fungi isolated from the leaf growth zone of grasses growing in arid conditions will be functionally characterised using a multidisciplinary approach. This will involve culturing and in planta testing of isolates for their effect on leaf growth under optimal and drought conditions. The genome of growth promoting isolates will sequenced, annotated and phylogenetically analysed. Functional analysis of the endophytes in planta will include kinematic analysis of cell division and expansion in the leaf growth zone, flowcytometry, NGS sequencing (plant and endoyphytic mRNA), metabolome analysis and quantification of endophyte numbers under control and drought conditions. The impact of the plant on endophyte development will be tested by comparing the colonisation and growth effects in maize varieties and selected mutants.

Researcher(s)

• Promoter: Beemster Gerrit
• Co-promoter: Abd Elgawad Hamada

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

Microorganisms have been exploited from the earliest times for baking, brewing, and food preservation. More recently, the enormous versatility in biochemical and physiological properties of microbes has been exploited to create new chemicals and nanomaterials, and has led to bio-electrical systems employed for clean energy and waste management. Moreover, it has become clear that humans, animals and plants are greatly influenced by their microbiome, leading to new medical treatments and agricultural applications. Recent progress in molecular biology and genetic engineering provide a window of opportunity for developing new microbiology-based technology. Just as advances in physics and engineering transformed life in the 20th century, rapid progress in (micro)biology is poised to change the world in the decades to come. The Excellence Centre "Microbial Systems Technology" (MST) will assemble and consolidate the expertise in microbial ecology and technology at UAntwerpen, embracing state-of-the-art technologies and interdisciplinary systems biology approaches to better understand microbes and their environment and foster the development of transformational technologies and applications. MST connects recently established research lines across UAntwerpen in the fields of microbial ecology, medical microbial ecology, plant physiology, biomaterials and nanotechnology with essential expertise in Next Generation Sequencing and Bioinformatics. By joining forces, new and exciting developments can be more quickly integrated into research activities, thus catalyzing the development of novel microbial products and processes, including functional food, feed and fertilizers, probiotics, and novel biosensors and bio-electronics applications. This way, MST aims for an essential contribution to the sustainable improvement of human health and the environment.

Researcher(s)

• Promoter: Meysman Filip
• Co-promoter: Beemster Gerrit
• Co-promoter: Laukens Kris
• Co-promoter: Lebeer Sarah
• Co-promoter: Verbruggen Erik
• Co-promoter: Vlaeminck Siegfried

Research team(s)

• Geobiology

Project type(s)

• Research Project

Abstract

Early spring cold is a major limiting factor for maize cultivation in North-Western Europe. Typically, cold spells are only transient and it is known that the capacity of varieties to recover strongly determines their final yield. Nevertheless, in contrast to the direct response to adverse conditions, the mechanisms involved in the recovery of growth have scarcely been studied. This project addresses this critical lack in our knowledge, using an innovative experimental setup where transient exposures to cold are applied at different stages of the development of the 4th leaf of maize lines with contrasting cold tolerance. Advanced phenotyping will be used to quantify the effect on the elongation growth of the leaf, during the cold and upon recovery until the leaf stops growing. Kinematic analysis will be used to quantify the cellular basis of the growth response and recovery. We will determine the molecular changes in the leaf growth zone during the response and recovery phase by means of mRNA sequencing, antioxidant and carbohydrate metabolites analysis and biochemical assays. At the physiological level we will determine the response of photosynthesis and water-relations. Based on this comprehensive and integrated analysis, candidate recovery genes will be identified and mutant and transgenic lines with altered expression of these genes will be acquired and studied in our experimental setup and under field conditions. The obtained knowledge will be scientifically innovative and relevant for plant breeding.

Researcher(s)

• Promoter: Beemster Gerrit
• Co-promoter: Abd Elgawad Hamada
• Fellow: Lainé Cindy

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

Recent climate change research reveals a novel and significant trend: weather patterns at mid-latitudes, such as in temperate western Europe, are getting more persistent. With respect to rainfall, this means longer droughts, but also longer periods with excessive rain. No comprehensive study has hitherto investigated the ecological consequences of such regime shifts. Can ecosystems adapt, or will the alternation between drought stress and soil water saturation exhaust them? Will this select for communities with novel trait combinations and more volatile species dynamics? And will these novel systems still be robust in the face of further changes in the environment? This study explores the potential impact of the ongoing shift in the frequency of dry/wet cycles at multiple, connected levels of biological organization. It does so in a new, large-scale set-up at UAntwerp built in the framework of the developing European infrastructure for ecosystem research 'AnaEE'. The design simulates changes in rainfall and associated temperature changes in the open air, using a gradient with eight precipitation regimes so that non-linearity and tipping points can be discerned with great precision. The project scope ranges from plants to soil biota such as bacteria and fungi, and from metabolism and genetic regulation assessed with bioinformatics to ecosystem processes. This multi-scale approach explicitly acknowledges the interwoven nature of ecosystems, with knowledge of molecular and cellular changes being instrumental to mechanistically explain the whole-system-scale effects on productivity, greenhouse gas fluxes and biodiversity dynamics. Different experiments are planned each year: (i) year 1 features a gradient in alternating dry/wet cycles, from 1 to 60 days, across a full growing season; (ii) year 2 focuses on legacy effects and the importance of changes of soil communities; (iii) year 3 matches precipitation regimes to corresponding temperature regimes to study the impact of drought-associated warming (an important natural feedback that can greatly increase plant stress). A series of connected, hypothesis-driven measurements is carried out, which will be integrated using structural equation modelling (path analysis) and ecosystem modelling. The project team has successfully collaborated in the past, and the complementary expertise brought together here should yield both significantly increased understanding of key processes as well as new avenues to climate change impact mitigation.

Researcher(s)

• Promoter: Nijs Ivan
• Co-promoter: Asard Han
• Co-promoter: Beemster Gerrit
• Co-promoter: Laukens Kris
• Co-promoter: Verbruggen Erik

Research team(s)

• Plant and Ecosystems (PLECO) - Ecology in a time of change

Project type(s)

• Research Project

Abstract

This project aims to understand the molecular mechanisms underlying the therapeutic effect of cinnamaldehyde (the active constituent of a novel drug of gestational diabetes). We will be using Next Generation Sequencing (NGS), expression analysis and biological interpretation by means of clustering, overrepresentation and pathway analysis. This will also help us to identify new effective signalling molecules.

Researcher(s)

• Promoter: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

Plants need light to grow and how plants regulate growth in response to light is the central theme in this project. Light drives the generation of sugars by photosynthesis and sugars act as signalling molecules that regulate developmental processes including cell division and expansion. Studies on growth regulation by sugars have been done largely in Arabidopsis, but we use the maize leaf due it its larger size that allows to performe analyses of the sugar metabolism, particularly in proliferating and expanding cells that drive growth. Our preliminary data show that shading mature leaves inhibits growth of younger leaves, but shading the mature part of the growing leaf stimulates growth. Also 4 mutations of sugar metabolism genes affect leaf growth. To understand how this regulation works we study to what extent sugar is transported from source leaves and from the mature part of growing leaf (by studying transport of radioactive 11CO2 fed to different leaves. How this sugar regulates leaf growth at cellular (cell division and expansion), metabolic (different sugars and hormones); biochemical (enzyme activities) and transcriptional (mRNA )levels in the growth zone at the base of the leaf. Our combined results will lead to new knowledge about the mechanism linking genetic, molecular, cellular and physiological levels to whole organ growth rates, which can be used to improve the growth of crop species in the context of changing climate conditions.

Researcher(s)

• Promoter: Beemster Gerrit
• Fellow: Abd Elgawad Hamada

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

The major share of research on maize leaf growth focuses on the impact of environmental factors. Despite their importance, these data are limited for the understanding of key regulatory components in leaf growth. Therefore, our laboratory has identified 5 unique long leaf maize lines through screening and selection of chemically mutated maize lines. Consequently, the objective of this project is the characterisation of 3 long leaf mutants to improve our understanding in leaf growth regulation. Firstly, we will try to appoint the (single) mutation that causes the long leaf phenotype. We must validate whether the hypothesised mutation indeed causes the observed long leaf phenotype by selecting/creating an independent line with a mutation in the hypothetical gene. Next to this, we will evaluate whether the mutation affects the expression of certain genes/pathways. Secondly, there is a need for a more extensive examination of the longleaf phenotype. This will be done at the cellular level (where cell division and expansion, both defining leaf growth, will be determined in more detail) and at the whole-plant level. Finally, the outcome of the previous experiments will result in new information on which we can base targeted cellular analyses, metabolite and enzyme measurements.

Researcher(s)

• Promoter: Beemster Gerrit
• Fellow: Sprangers Katrien

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

Pollution with cadmium (Cd) caused by historical industrial activity is a serious problem in the Campine region of Belgium. Cd inhibits plant growth and understanding this response may facilitate the growth of plants on polluted soils, its accumulation in and harvest of Cd-containing plant biomass. From a scientific point of view, the response of plant growth to Cd exposure is interesting, as it perturbs specific regulatory mechanisms, including cell cycle regulation, cell wall chemistry and redox regulation. Thereby, the role of these processes in organ growth regulation can be unravelled. By studying the maize leaf growth zone we can combine kinematic analyses of cell division and expansion rates with molecular and physiological studies that are not feasible in the model species Arabidopsis. Using both short- and long-term Cd exposure allows us to unravel signalling events and regulatory interactions in growth regulation. The effects on cell division will be further analysed by flowcytometry and on expansion by measuring cell wall extensibility. The underlying molecular mechanisms will be studied in each zone (division, elongation and maturation) at the transcriptome, metabolite and enzyme levels. Initially, wild-type maize lines are used. Based on the obtained results, mutants perturbed in key pathways will be studied. All data will be integrated using bio-informatics, so that a holistic view of growth regulation in general and its response to Cd in particular is obtained.

Researcher(s)

• Promoter: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

In a recent screen of segregating mutant lines in the field, our laboratory identified 35 maize mutants with an increased leaf size. I have confirmed 5 of these with the strongest phenotype under controlled growth room conditions. Unlike other model species the maize leaf growth zone is large enough to harvest samples across the gradient of dividing, expanding and mature cells for a wide range of molecular and physiological analyses. Therefore these mutants provide a unique opportunity to generate new insights into the mechanisms by which plants regulate organ growth. The objective of this project is to mechanistically understand the phenotype of 3 of these mutants by: -Mapping the mutation that causes the longleaf phenotype. To validate whether the identified mutations indeed cause the observed longleaf phenotype we will select/create independent lines with a mutation in the same gene. -Perform genome-wide transcriptome analysis to identify which genes and pathways are affected by the mutation. -Determine the cellular basis (cell division and expansion) of the phenotype and study the effect of the mutation on other parts of the plant. -Perform physiological, metabolite and enzyme measurements focusing on specific regulatory pathways identified by the above analyses. The obtained results will give us a more integrated understanding of the key regulatory processes in leaf growth and size determination.

Researcher(s)

• Promoter: Beemster Gerrit
• Fellow: Sprangers Katrien

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

Native rice cultivars of Argentina show strong difference in cold tolerance. In the context of her running PhD project, the candidate has shown that this is related to differences in physiological parameters, particularly related to photosynthesis and water use efficiency. Currently, she is performing a transcriptome analysis and a metabolite analysis to investigate differences in gene expression and selected metabolic pathways between lines with contrasting cold tolerance. The proposed project at the UA aims to complement these analyses with a kinematic analysis of cell division and expansion in the growing rice leaves of contrasting lines growing under optimal and cold conditions to understand the cellular basis of the growth effects and subsequently perform a proteome analysis of the leaf growth zone using the iTraq approach recently established in the host group.

Researcher(s)

• Promoter: Beemster Gerrit
• Fellow: Gazquez Ayelén

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

This project represents a formal research agreement between UA and on the other hand Erasmus Mundus. UA provides Erasmus Mundus research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

The project will further investigate the collection of 10 new maize mutants, which all have increased leaf size phenotypes under field and growth chamber conditions. The overall aim is to identify the mechanisms underlying the observed phenotype at the leaf, whole plant and crop level.

Researcher(s)

• Promoter: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

The aim of this project is to develop a next generation sequencing (NGS) platform to advance in a collaborative way biological and medical research within the Antwerp research community. The consortium involves more than 16 research groups in various disciplines of medicine, biology and biomedical informatics. The goals are to identify new genes and mutations in various rare Mendelian disorders, to achieve more insights in the genetic causes of cancer and to unravel more precisely the genetic determinants of infectious diseases. This new knowledge will improve both the diagnosis and management of these human diseases. The project will also focus on the interaction between environment and genes. More specifically, the effect of environmental stressors on genetic variation in aquatic organisms, the effect of teratogenic factors on embryonic development in vertebrates and the effects of environmental conditions on growth in maize and Arabidopsis lines will be studied. The analysis of the large amount of genomic and transcriptomic data, generated by the various research groups, will be coordinated by the recently founded UZA/UA bioinformatics group Biomina

Researcher(s)

• Promoter: Mortier Geert
• Co-promoter: Beemster Gerrit
• Co-promoter: Blust Ronny
• Co-promoter: Goossens Herman
• Co-promoter: Knapen Dries
• Co-promoter: Laukens Kris
• Co-promoter: Peeters Marc
• Co-promoter: Van Hul Wim
• Co-promoter: Vrints Christiaan

Research team(s)

Project type(s)

• Research Project

Abstract

In this network, we want to investigate how root and shoot influence each other and how this interaction contributes to the development of the plant. Such an intergrated approoach represents a realistic potential to identify major plant growth controlling components, therefore we aim to transfer this knowledge to the crop species maize.

Researcher(s)

• Promoter: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

This project represents a formal research agreement between UA and on the other hand Erasmus Mundus. UA provides Erasmus Mundus research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

Developmental processes involve a complex network of interactions between multiple regulatory processes that traditionally are studied separately. We propose a systems biology approach, whereby experimental biologists closely interact with mathematical modellers, to unravel the functional relationships between auxin signalling, cell division and expansion and whole leaf morphogenesis.

Researcher(s)

• Promoter: Beemster Gerrit
• Co-promoter: Broeckhove Jan
• Co-promoter: Prinsen Els
• Co-promoter: Vanroose Wim
• Co-promoter: Vissenberg Kris

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

The MOMEVIP partners will integrate competences in ecology, physiology, biochemistry, molecular biology, functional genomics and bioinformatics to improve knowledge about the molecular and metabolic bases of VIP biosynthesis, and the functions of VIP (isoprene, monoterpenes and sesquiterpenes, collectively) in plant protection, per se and when interacting with other defensive pathways.

Researcher(s)

• Promoter: Asard Han
• Co-promoter: Beemster Gerrit
• Co-promoter: Janssens Ivan
• Co-promoter: Nijs Ivan

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

system to investigate the molecular and cellular basis of plant growth responses to drought. By means of kinematic analysis we found that cell division in the basal 2 cm and cell expansion in the next 5 cm are inhibited. In this project we propose to perform a genome-wide study of the molecular changes associated with this inhibition of the growth process and, additionally, we will specifically focus on redox homeostasis. The genome-wide analysis involves a microarray and a proteome study, where we will sample meristem, elongation zone and mature tissue under control conditions and different levels of drought. For the redox studies we will use the spatial gradient along the leaf to measure redox capacity, the level of the major antioxidants and the expression level and activity of key regulatory enzymes. This will be done in wild-type plants subjected to different levels of stress and in mutants that are defective in redox enzymes. All essential equipment and personnel for the proposed experiments is available in the research group, only consumables are needed to be able to execute them.

Researcher(s)

• Promoter: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

This project represents a formal research agreement between UA and on the other hand EU. UA provides EU research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

We will functionally analyze Zea mays mutants for their response to abiotic stress conditions. This will be done using kinematic analysis of cell division and expansion and RT-PCR expression analysis.

Researcher(s)

• Promoter: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

The aim of the project is to develop a 3-D mathematic simulation model of inter-actions at the molecular, cellular and organ level during leaf growth in Arabidopsis thaliana. We will start from an existing 2-D model of vascular development that was build in the previous research group of the Promotor. This model will be extended to include multiple cell layers and modules for cell division and expansion.

Researcher(s)

• Promoter: Beemster Gerrit
• Co-promoter: Broeckhove Jan
• Co-promoter: Vanroose Wim

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

The aim of this project is to identify and functionally characterize new genes and regulatory pathways that play a role in the response of Arabidopsis thaliana to drought stress. In collaboration with the Vision lab we will develop an automated image analysis platform that will allow quantification of number, composition and size of cells in cleared leaves of 75 Arabidopsis genotypes. The most promising lines will be analyzed in more detail.

Researcher(s)

• Promoter: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

The role of the growth regulating plant hormone auxin in the response to abiotic stresses such as drought has hardly been investigated to date. Based on micro-array data we have strong indications that the expression of 45 auxin response genes is specific for dividing cells and is strongly affected by drought. In this project mutants for these genes will be isolated and tested for their effect on growth under optimal and drought conditions.

Researcher(s)

• Promoter: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project type(s)

• Research Project

Abstract

The research plan "Systems biology of organ growth" refers to the enormous importance of plant growth for society and economy (among others a source of renewable energy). The question is how it is possible that plants on the one hand can respond strongly and in a very predictable way to genetic variations and environmental conditions and on the other hand generate a morphology that is characteristic enough for each species that taxonomy can be based on it. The systems-biology approach will be worked out with a strong emphasis on the role of cell division and expansion. The research plan aims to enable a complete quantitative description of phenotypes caused by genetic or environmental perturbations and to transfer this knowledge into dynamic and mechanistic simulation models in which new hypotheses can be rigorously tested and to apply the obtained insight to improve the crop species maize.

Researcher(s)

• Promoter: Beemster Gerrit
• Fellow: Beemster Gerrit

Research team(s)

• Integrated Molecular Plant Physiology Research (IMPRES)

Project website

Project type(s)

• Research Project