PhD Topics

1. Plant signaling at the crossroads of biotic and abiotic interactions

Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.

Consultant: Mgr. Martin Černý, Ph.D.

Keywords: abiotic stress, biotic stress, multifactorial stress, signaling pathways, transcriptomics, proteomics, metabolomics, lipidomics, hormonomics

Plants have evolved elaborated mechanisms that enable them to sense and respond to changes in environmental conditions. These mechanisms involve abiotic and biotic stimuli triggering wide arrays of signals initiating developmental processes and stress responses that are regulated and coordinated by common integrative pathways. Heat, cold, drought, flooding, pathogens, all these factors have shown devastating effects on crop plant productions in the past, leading to famines or even mass extinctions. Traditional approaches in plant molecular biology rely on a detailed analysis of a single stressor, but this is seldom the case in the natural environment. A combination of biotic and abiotic stress can be more challenging than each of these factors separately. On the other hand, mild stress can promote plans' resistance and make it more resilient to the next stressor. Here, we will analyze in details both of these pathways, employing the state-of-the-art mass spectrometry for multi-omics analyses, including proteomics, metabolomics, lipidomics and hormonomics profiling.

2. Cold-light interaction in Arabidopsis cold acclimation: ontogenic and phyllotactic perspective

Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.

Consultant: Mgr. Martin Černý, Ph.D.

Keywords: cold acclimation, light, frost tolerance, multifactorial stress, signaling pathways, plant hormones, phyllotaxy, ontogenesis, Arabidopsis thaliana, transcriptomics, proteomics, metabolomics, lipidomics

Distribution of a given plant species reflects its ability to acclimate to different natural environmental conditions. Plant acclimation to cold is of high importance because of recent raise of abundance of temperature extremes. We propose to use a suite of omics approaches to deepen our understanding of cold adaptation in a model plant Arabidopsis thaliana. As light intensity is often low during cold acclimation, we will compare cold responses in plants exposed to standard and low light intensities. To address roles of phyllotaxy and ontogenesis, the cold responses will be analyzed in leaves 6 and 14 when their cells are completing cell proliferation stage and in leaf 6 when its cells complete cell expansion and differentiation stage. Based on the data obtained, we will construct and experimentally validate a mechanistic model of plant response to combined cold and low light stress. The validated model will deepen our knowledge of molecular circuits governing plant plasticity which underlies ability of a particular species to colonize distinct climatic zones.

3. The impact of changing environmental conditions on seed germination and early plant development: Omics analyses

Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.

Consultant: Mgr. Martin Černý, Ph.D.

Keywords: seed germination, plant development, Hordeum vulgare, transcriptomics, proteomics, metabolomics, lipidomics, hormonomics

Seed germination and early plant development is a crucial phase of plants' life. Its progress is governed by multiple internal and external stimuli and has a serious impact on a plant's survival and vitality. Here, we will employ a model crop plant Hordeum vulgare, and study its early development via multi-omics approaches, including proteomics, metabolomics, lipidomics, hormonomics and transcriptomics. We will analyze seed steep water composition and individual developmental stages of germinating barley. We will evaluate the effects of simulated adverse environmental conditions and identify key elements responsible for the perception of abiotic and biotic inputs.

4. Metabolic regulation of chromatin modifications and gene expression

Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.

Consultant: Pavel Kerchev, Ph.D.

Keywords: plant stress tolerance, genome editing, epigenetics, proteomics, metabolomics, mass spectrometry, LC-MS, GC-MS

Plant survival under adverse environmental conditions relies on flexible mechanisms for reprogramming of gene expression. The structure of chromatin, the assembly of DNA with histone proteins, provides an extra layer of a control over gene expression which is exerted through a plethora of chemical modifications of histones. This proposed project will study how histone modifying enzymes and metabolism interact to alter chromatin structure and contribute to plant stress tolerance. We will use state-of-the-art mass spectrometry and next-generation sequencing to follow the dynamics of histone modifications, metabolic pathways and gene expression under stress and process the acquired data using bioinformatics approaches. This will help us to identify important molecular mechanisms which will be employed to generate plants with improved stress tolerance using molecular biology tools and genome editing (CRISPR-Cas9).

5. Abscisic acid – cytokinin crosstalk in regulation of plant development

Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.

Consultant: Mgr. Jan Novák, Ph.D.

Keywords: abscisic acid, cytokinin, plant development, transcriptomics, proteomics, metabolomics, lipidomics

Plant hormones are important regulators of plant development through an entire plant lifespan. Plant hormones abscisic acid and cytokinin have been implicated in regulation of various aspects of plant development, and responses to abiotic and biotic stresses. Recently, data on interactions of abscisic acid and cytokinin signaling have emerged. However, the topic is far from being understood. Here, a suit of multi-omics analyses (including transcriptome, proteome, metabolome, lipidome and hormonome profiling) will be employed to decipher molecular circuits involved in abscisic acid – cytokinin crosstalk in regulation of Arabidopsis development in response to various environmental cues.