1. Single-cell RNA sequencing (scRNA-seq) in Arabidopsis thaliana

As sessile by nature, plants are constantly exposed to a variety of environmental stresses such asdrought, extreme temperatures, heavy metals, salinity, pollutants, and nutrient deprivation. These abiotic stresses cause various imbalances at the cellular, molecular, physiological, and developmental levels and therefore have detrimental effects on growth and development and reduce the productivity of crops worldwide. However, plants appear to adapt or acclimatize by modulating or altering themselves at the genomic, transcriptomic, proteomic and metabolomic levels. Several studies have been conducted using bulk methods to elucidate the molecular mechanisms of abiotic stress.

Although these approaches have remarkably contributed to improve our understanding the effects of abiotic stresses and tolerance mechanisms in plants, the information obtained from bulk methods is limited. Especially, due to heterogeneity in tissues, the detection of differentially expressed genes in cell type is very limited by bulk methods. In addition, it is not possible to detect rare cell types in these methods. Fortunately, single-cell sequencing techniques enable expression profiles on a cell basis, solves heterogeneous problem, obtain high-resolution transcriptomic data, and allow the analysis of cell types with high resolution.

In our study, for the first time in the literature, single-cell RNA sequencing was performed in Arabidopsis thaliana root cells exposed to abiotic stress. We obtained single-cell transcriptomes from protoplasts of more than 25,000 Arabidopsis root cells. Major cell types including root cap, columella, cortex, quiescent center, endodermis, and trichoblast their changes in expression profiles depending on abiotic stress were identified.

2. Vaccine production in Nicotiana benthamiana

Virus-like particles (VLP) are an innovative vaccine type that can provide protection from virus variants that evolve over time by allowing more than one different antigen to be obtained in the same production process. Although mammalian cell lines are one of the most preferred expression systems for VLP production, in case of clinical material production, there are disadvantages such as low protein yield, high production cost, long expression time and the possibility of contamination of cell lines with human pathogens. Among the emerging new recombinant-based vaccine development platforms, plants have become one of the most remarkable approaches with their ability to produce high-scale protein in safe and with low cost in a short time. It is stated that the cost of the plant system is 0.1% of the cost of the mammalian cell line. Moreover, in recent years, plant-based vaccine development studies have moved from the research dimension to the industrial level. The aim of the proposed project is to produce a VLP-based 2nd generation vaccine candidate on the plant platform. Thus, it is expected that the multi-epitope vaccine candidate will have an effect on viral escapes caused by mutations and provide an effective immune response in the host.

3. New transfection method with peptides for recombinat production

In this project, by means of transfection of formed the complex including vector DNA with an entry peptide to Nicotiana benthamiana leaves without protoplast isolation, it is aimed to produce the important intermediate metabolites having high antioxidant capacity in Nicotiana benthamiana leaves. By combining the vector and Cell Penetrating Peptide components in vitro and by introducing directly into the plant cell without protoplast isolation, very rapid recombinant production without obstacles to GMO can be used in plant technology and agriculture..

4. Boron biology in plants

Boron toxicity induces sulfate transporters at transcriptional level in Arabidopsis thaliana

Boron toxicity induces sulfate transporters at transcriptional level in Arabidopsis thaliana
Figure. Relative expression levels of sulfate transporters in the root tissues of A. thaliana in response to toxic B. C: Control, 1B: 1 mM H3BO3 , 3B: 3mM H3BO3 . 1;1: SULTR1;1, 1;2: SULTR1;2, 1;3: SULTR1;3, 2;1: SULTR2;1, 2;2: SULTR2;2, 3;1: SULTR3;1, 3;2: SULTR3;2, 3;3: SULTR3;3, 3;4: SULTR3;4, 3;5: SULTR3;5, 4;1: SULTR4;1, 4;2: SULTR4;2. 5;1: SULTR5;1, 5;2: SULTR5;2. Values represent mean ± SEM (n = 3). An asterisk above the bars represents significant differences between control and B-toxicity treated samples (p ≤ 0.05).
The involvement of the induction of anthocyanin biosynthesis and transport in toxic boron responsive regulation in Arabidopsis thaliana
The involvement of the induction of anthocyanin biosynthesis and transport in toxic boron responsive regulation in Arabidopsis thaliana
Figure. Fifteen-day-old WT and slim1 mutant Arabidopsis thaliana seedlings exposed to control (C) and toxic B treatments. WT and slim1 mutant Arabidopsis thaliana seeds were sown on the left and right sides of plates, respectively. A) WT seeds were directly sown into medium including 100 μM H3BO3 (C), 1 mM H3BO3 (1B(D)), 2 mM H3BO3 (2B(D)), and 3 mM H3BO3 (3B(D)); however, slim1 mutant seeds were directly sown into medium including C, 1B(D), and 2B(D) conditions because they did not tolerate the 3B(D) treatment. B) In order to increase the toxic B concentration applied to slim1 mutant Arabidopsis thaliana, 3B and 5B were applied to WT (for comparison) and slim1 mutant Arabidopsis thaliana at seedling stage. In fact, they were grown under control condition for 11 days and were transferred to medium including 3 mM H3BO3 (3B(T)) and 5 mM H3BO3 (5B(T)) for 4 days.