Robin Nauts - Academia.edu (original) (raw)

Papers by Robin Nauts

Schemes represent a global gene expression response (A) immediately after irradiation; (... more Schemes represent a global gene expression response (A) immediately after irradiation; (B) after 2H and 5H of recovery period. Blue colour, stand for down-regulated genes. Red colour stand for up-regulated genes, Green colour stand for restored expression of the initial silenced genes. (A) The largest changes in transcription occurred upon irradiation, as part of a kind of an “Emergency Response”. Cells displayed a reduced transcription for photosynthesis and energy production (PSII, PSI, ATP), and for carbon and nitrogen metabolism during irradiation. The CO2 fixation via the Calvin-Benson-Bassham cycle (CBB), glycogen biosynthesis (gluconeogenesis) and the tricarboxylic acid cycle (TCA) were repressed. The transcription of the SigE regulator acting as nitrogen-dependent activator for catabolic genes towards glycogen degradation (glycolysis) was induced. Also a re-routing of the metabolic flux to glycolysis and the pentose phosphate pathway (PPP) was seen. A synthesis of carbon storage molecules (PHA) and compatible solutes (trehalose) was seen. The expression of polyamine import (potBC), well known as a group of nitrogen-containing C-compounds which help in cell survival during stress, was recorded. The import of nitrate or cyanate as N-sources was repressed (nrtABCD, cynBD). In parallel also the metabolism of agmatine, a known competitive inhibitor of polyamine transport, was repressed. The cellular protection, detoxification, and repair were enhanced immediately after irradiation. In an effort to maintain the intracellular redox balance while provide sufficient metal-cofactors for enzymes, selective metal export (copA) and import (feoAB, cutA, corA, mtgC, cbiQ1, cbiQ2, znuA) was induced. There was upregulation of isiA gene encoding the CP43’ protein, which is an auxiliary antenna complex, to compensate for the loss of phycobilisomes. This protein may also serve as a chlorophyll storage molecule contributing to the reassembly of reaction centres during recovery. In addition, ROS detoxification was activated via the expression of the peroxiredoxine enzyme (ahpC) and the glutathione synthesis genes. The generation of glutathione starts at T0H via the formation of glutamate from proline by hyuA, from aspartate by aspartate aminotransferase (aat1), from 1-pyrroline-5-carboxylate by (putA), and from 2-oxoglutarate via GLDH (see Fig 8B). Glutamate synthesis via the GS/GOGAT cycle was repressed. The final synthesis of glutathione from glutamate occurred via glutathione (GSH) synthase (gshB), which continued during recovery (see Fig 8B). Chaperones (dnaK1, dnaK2, hspA, cbpA) and proteases (clpB2) were also significantly induced during this stage, to remove damaged proteins. The free amino-acids released from protein degradation, likely lead to the production of urea, and the urease (ureABC) activity, transforming urea to ammonium, was induced. In parallel Arthrospira enhance some genes related to DNA repair system (uvrBCD for nucleotide excision and repair, ruvB resolving holiday junction, and recJ, dnaG and mod genes). The DNA-repair mechanism of Arthrospira included also enzymatic restriction modification (hsdr) and endonucleases. (B) During the later phaseArthrospira cells try to recover from the damage; which lead to a slowly restored expression of the genes related to photosynthesis and energy production, carbon fixation via the CBBn cycle and gluconeogenesis, TCA cycle. Expression of the hydrogenase genes (hypA1, hypB1and hoxW). Metal chaperone proteins HypA and HypB are required for the nickel insertion step of [NiFe]-hydrogenase maturation. In parallel slight reactivation of amino-acid transport (aapJPQ, argGHJ, iaaA) occurred. The genes for import of taurine (tauABC) known as organic sulphur and amino source were highly induced. The restoration of agmatinase, the key enzyme of agmatine hydrolysis was seen in recovery period. ROS detoxification was maintained efficiently via the expression for glutathione biosynthesis (GSH). Few genes related to protein damage clean up (proteases and chaperones) and DNA repair maintained their expression during recovery. The expression of gene cluster arhABCDEF, enriched during recovery, was seen.</p

$Research paper thumbnail of <tex>\beta$</tex>-radiation stress responses on growth and antioxidative defense system in plants : a study with strontium-90 in **Lemna minor**$

In the following study, dose dependent effects on growth and oxidative stress induced by β-radiat... more In the following study, dose dependent effects on growth and oxidative stress induced by β-radiation were examined to gain better insights in the mode of action of β-radiation induced stress in plant species. Radiostrontium (90 Sr) was used to test for β-radiation induced responses in the freshwater macrophyte Lemna minor. The accumulation pattern of 90 Sr was examined for L. minor root and fronds separately over a seven-day time period and was subsequently used in a dynamic dosimetric model to calculate β-radiation dose rates. Exposing L. minor plants for seven days to a 90 Sr activity concentration of 25 up to 25,000 kBq•L −1 resulted in a dose rate between 0.084 ± 0.004 and 97 ± 8 mGy•h −1. After seven days of exposure, root fresh weight showed a dose dependent decrease starting from a dose rate of 9.4 ± 0.5 mGy•h −1. Based on these data, an EDR10 value of 1.5 ± 0.4 mGy•h −1 was estimated for root fresh weight and 52 ± 17 mGy•h −1

Scatter plot showing the differentially expressed genes of Arthrospira</i&gt... more Scatter plot showing the differentially expressed genes of Arthrospira sp. PCC 8005 in response to gamma irradiation plotted accordingly to their change in mRNA concentration (Log2 fold change values), for 3 radiation doses (800, 1600 and 3200 Gy) and 3 time points after radiation (0 hours, 2 hours, 5 hours).</p

This plot visualises whether a certain gene cluster (1–9, on the vertical axis) is conta... more This plot visualises whether a certain gene cluster (1–9, on the vertical axis) is containing a higher number of representatives of a specific COG (21 different COGs, on the horizontal axis) then would be expected by chance. The COG functional category is shown in the vertical direction, the clusters of differentially expressed genes in the horizontal direction. The colour code is according to the 10log value of the corresponding p-value of the GSEA analysis: a p-value of smaller than 1.10–4 (10log-value of 4) results in a colour code red, a p-value of 1 (10log value 0) results in colour code white.</p

The edible cyanobacterium Arthrospira is resistant to ionising radiation. The cellular mecha-nism... more The edible cyanobacterium Arthrospira is resistant to ionising radiation. The cellular mecha-nisms underlying this radiation resistance are, however, still largely unknown. Therefore, additional molecular analysis was performed to investigate how these cells can escape from, protect against, or repair the radiation damage. Arthrospira cells were shortly exposed to different doses of 60Co gamma rays and the dynamic response was investigated by moni-toring its gene expression and cell physiology at different time points after irradiation. The results revealed a fast switch from an active growth state to a kind of 'survival modus ' during which the cells put photosynthesis, carbon and nitrogen assimilation on hold and activate pathways for cellular protection, detoxification, and repair. The higher the radiation dose, the more pronounced this global emergency response is expressed. Genes repressed dur-ing early response, suggested a reduction of photosystem II and I activity ...

Abstract: In the following study, dose dependent effects on growth and oxidative stress induced b... more Abstract: In the following study, dose dependent effects on growth and oxidative stress induced by β-radiation were examined to gain better insights in the mode of action of β-radiation induced stress in plant species. Radiostrontium (90Sr) was used to test for β-radiation induced responses in the freshwater macrophyte Lemna minor. The accumulation pattern of 90Sr was examined for L. minor root and fronds separately over a seven-day time period and was subsequently used in a dynamic dosimetric model to calculate β-radiation dose rates. Exposing L. minor plants for seven days to a 90Sr activity concentration of 25 up to 25,000 kBq·L−1 resulted in a dose rate between 0.084 ± 0.004 and 97 ± 8 mGy·h−1. After seven days of exposure, root fresh weight showed a dose dependent decrease starting from a dose rate of 9.4 ± 0.5 mGy·h−1. Based on these data, an EDR10 value of 1.5 ± 0.4 mGy·h−1 was estimated for root fresh weight and 52 ± 17 mGy·h−1

Biotechnologia. Journal of Biotechnology, Computational Biology and Bionanotechnology, 2013

Journal of Environmental Management, 2021

Pollution of surface waters is a worldwide problem for people and wildlife. Remediation and phyto... more Pollution of surface waters is a worldwide problem for people and wildlife. Remediation and phytoremediation approaches can offer a solution to deal with specific scenarios. Lemna minor, commonly known as duckweed, can absorb and accumulate pollutants in its biomass. To evaluate if L. minor could be applied for phytoremediation purposes, it is necessary to further investigate its remediation capability and to identify which parameters affect the remediation process. Such a model must include both plant growth and pollutant exchange. A remediation model based on a robust experimental study can help to evaluate L. minor as a proper remediation strategy and to predict the outcome of a L. minor based remediation system. To set up this model, this paper focusses on a detailed experimental study and a comprehensive mathematical modelling approach to represent L. minor growth as a function of biomass, temperature, light irradiation and variable nutrient concentrations. The influence of environmental conditions on L. minor growth was studied, by composing 7 days growth curves. Plants were grown under predefined environmental conditions (25°C, 14h photoperiod, 220 μmol m-2 s-1 light intensity and a modified Hoagland solution with 23.94 mg N L-1 and 3.10 mg P L-1 (N:P ratio of 7.73)) as standard for all experiments. The influence of different temperatures (6, 10, 15, 20, 25, 30 and 35°C), light intensities (63, 118, 170, 220 and 262 μmol m-2 s-1), photoperiods (12h and 14h) and N:P ratios (1.18, 3.36, 7.73 and 29.57) were tested in the model. As a result, a growth model was optimised using separate datasets for temperature, light intensity, photoperiod and nutrients and validated by further integrated testing. The growth model is a stable platform for application in phytoremediation of radionuclides in contaminated water, to be extended in future studies with information of pollutant uptake, pollutant-nutrient interactions and transfer to the biomass.

Frontiers in Plant Science, 2021

Previous studies have found indications that exposure to ionising radiation (IR) results in DNA m... more Previous studies have found indications that exposure to ionising radiation (IR) results in DNA methylation changes in plants. However, this phenomenon is yet to be studied across multiple generations. Furthermore, the exact role of these changes in the IR-induced plant response is still far from understood. Here, we study the effect of gamma radiation on DNA methylation and its effect across generations in youngArabidopsisplants. A multigenerational set-up was used in which three generations (Parent, generation 1, and generation 2) of 7-day oldArabidopsis thalianaplants were exposed to either of the different radiation treatments (30, 60, 110, or 430 mGy/h) or to natural background radiation (control condition) for 14 days. The parental generation consisted of previously non-exposed plants, whereas generation 1 and generation 2 plants had already received a similar irradiation in the previous one or two generations, respectively. Directly after exposure the entire methylomes were a...

Plant Physiology and Biochemistry, 2019

The mutants Atnoa1 and Atnia1nia2noa1-2 having a defective chloroplast developmental process, sho... more The mutants Atnoa1 and Atnia1nia2noa1-2 having a defective chloroplast developmental process, showed enhanced chlorophyll levels when they were grown on Murashige and Skoog (MS) medium and on exposure with uranium (U) on Hoagland medium. Thus we hypothesized that these mutants probably produced NO in MS medium and on exposure with U. Wild-type Col-0, Atnoa1, Atnia1nia2noa1-2 plants were cultured on modified Hoagland and 1/10 MS media and NO generation in the roots of these mutants was monitored using NO selective fluorescent dyes, DAF-2DA and Fl2E. Both Atnoa1 and Atnia1nia2noa1-2 triple mutants produced NO as observed by increases in DAF-2T and Fl2E fluorescence when these mutants were grown on MS medium but not on Hoagland medium. In presence of NO scavenger, methylene blue (MB, 200 μM), DAF-2T and Fl2E fluorescence was completely abolished. On the other hand treatment of the plants with 25 μM U triggered NO generation. Utreated Atnoa1 and Atnia1nia2noa1-2 plants upregulated genes (POR B, POR D, CHL D) involved in the chlorophyll biosynthesis. From these results it was concluded that Atnoa1 and Atnia1nia2noa1-2 are conditional NO producers and it appears that NO generation in plants substantially depends on growth medium and NIA1, NIA2 or NOA1 does not appear to be really involved in NO generation in MS medium or after U exposure. Arabidopsis Nitric Oxide Associated 1 (NOA1), also identified as RIF1 (Flores-Perez et al., 2008), was reported initially to encode a protein with NOS activity (Guo et al., 2003). However, subsequent experimental evidences did not support NOA1 dependent catalytic

Journal of Environmental Radioactivity, 2018

The long-term radiological impact to the environment of the nuclear accidents in Chernobyl and Fu... more The long-term radiological impact to the environment of the nuclear accidents in Chernobyl and Fukushima is still under discussion. In the course of spring of 2016 we sampled two Brassicacea plants, Arabidopsis thaliana and Capsella bursa-pastoris native to Ukraine and Japan, respectively, alongside a gradient of radiation within the exclusion and difficult to return zones of Chernobyl (CEZ) and Fukushima (FEZ). Ambient dose rates were similar for both sampling gradients ranging from 0.5 to 80 μGy/h at plant height. The hypothesis was tested whether a history of several generations of plants growing in enhanced radiation exposure conditions would have led to changes in genome-wide DNA methylation. However, no differences were found in the global percentage of 5-methylated cytosines in Capsella bursa pastoris plants sampled in FEZ. On the other hand a significant decrease in whole genome methylation percentage in Arabidopsis thaliana plants was found in CEZ mainly governed by the highest exposed plants. These data support a link between exposure to changed environmental conditions and changes genome methylation. In addition to methylation the activity concentration of different radionuclides, 137 Cs, 90 Sr, 241 Am and Pu-238,239,240 for CEZ and 137, 134 Cs for FEZ, was analysed in both soil and plant samples. The ratio of 5.6 between 137 Cs compared to 134 Cs was as expected five years after the FEZ accident. For CEZ 137 Cs is the most abundant polluting radionuclide in soil followed by 90 Sr. Whereas 241 Am and Pu-isotopes are only marginally present. In the plant tissue, however, higher levels of Sr than Cs were retrieved due to a high uptake of 90 Sr in the plants. The 90 Sr transfer factors ranged in CEZ from 5 to 20 (kg/kg) depending on the locality. Based on the activity concentrations of the different radionuclides the ERICA tool was used to estimate the total dose rates to the plants. It was found that for FEZ the doses was mainly contributable to the external Cs-isotopes and as such estimated total dose rates (0.13-38 μGy/h) were in the same range as the ambient measured dose rates. In strong contrast this was not true for CEZ where the total dose rate was mainly due to high uptake of the 90 Sr leading to dose rates ranging from 1 to 370 μGy/h. Hence our data clearly indicate that not taking into account the internal contamination in CEZ will lead to considerable underestimation of the doses to the plants. Additionally they show that it is hard to compare the two nuclear accidental sites and one of the main reasons is the difference in contamination profile.

Environmental and Experimental Botany, 2019

The responses and recovery after gamma irradiation are highly dependent on leaf age at the time o... more The responses and recovery after gamma irradiation are highly dependent on leaf age at the time of exposure in rice (Oryza sativa L.

Journal of Environmental Radioactivity, 2019

Ectomycorrhizal (EM) fungi form symbioses with dominant tree families in boreal, temperate and tr... more Ectomycorrhizal (EM) fungi form symbioses with dominant tree families in boreal, temperate and tropical ecosystems and are important drivers of ecosystem function. EM fungal hyphae extend over a large area making them susceptible to enhanced radiation levels from naturally occurring or anthropogenically originating radioisotopes in the rhizosphere. In this study, the in-vitro effects of ionizing radiation on the growth and biomass of EM fungi Suillus luteus, S. bovinus and Rhizopogon luteolus were investigated. EM fungal cultures were exposed to gamma radiation from a 137 Cs source for 137 h in darkness at 21°C at dose rates of 404, 108.5 and 54.9 mGy h −1 resulting in total absorbed doses of 55.21, 14.82 and 7.50 Gy respectively. Cultures grown in the dark at 21°C but not exposed to the 137 Cs source served as the control. Our results show that EM fungi vary in their sensitivity to ionizing radiation. EM fungi used in this study produced melanin and reactive oxygen species scavenging enzymes such as catalase and superoxide dismutase as a response to ionizing radiation.

$Research paper thumbnail of {"__content__"=>"Potential of four aquatic plant species to remove Co from contaminated water under changing experimental conditions.", "sup"=>{"__content__"=>"60"}}$

Environmental science and pollution research international, Jan 20, 2018

This study aimed to compare the potential of Lemna minor, Spirodela sp., Eichhornia crassipes and... more This study aimed to compare the potential of Lemna minor, Spirodela sp., Eichhornia crassipes and Pistia stratiotes to remove Co from a realistic aquatic environment. Although all four plant species performed similarly well after 3 days of exposure to 50 kBq LCo, Lemna minor and Spirodela sp. came forward as having higher Co removal potential. This conclusion is, in first instance, based on the high Co removal percentage obtained after a short contact time (e.g. more than 95% could be removed after 6 h by Spirodela sp.). Additionally, Lemna minor and Spirodela sp. accumulated a high amount of Co per gram of biomass. For example, Lemna minor accumulated over three times more Co per gram of biomass compared to Pistia stratiotes and Eichhornia crassipes. Both plants also performed well in the pH range 5-9. We used Lemna minor to test the influence of the initial Co concentration (10, 50, 100 and 200 kBq LCo) on its phytoremediation capacity but no differences could be observed in remov...

Environmental Pollution, 2017

Genetic and epigenetic changes were investigated in chronically irradiated Scots pine (Pinus sylv... more Genetic and epigenetic changes were investigated in chronically irradiated Scots pine (Pinus sylvestris L.) populations from territories that were heavily contaminated by radionuclides as result of the Chernobyl Nuclear Power Plant accident. In comparison to the reference site, the genetic diversity revealed by electrophoretic mobility of AFLPs was found to be significantly higher at the radioactively contaminated areas. In addition, the genome of pine trees was significantly hypermethylated at 4 of the 7 affected sites.

Plant Science, 2017

minor plants chronically exposed to ionising radiation: RNA-seq analysis indicates a dose rate de... more minor plants chronically exposed to ionising radiation: RNA-seq analysis indicates a dose rate dependent shift from acclimation to survival strategies, Plant Science

Journal of Environmental Radioactivity, 2016

When the environment gets contaminated with gamma emitting substances, plants that grow in these ... more When the environment gets contaminated with gamma emitting substances, plants that grow in these contaminated areas are almost always exposed to gamma radiation during consecutive generations. Therefore it is important to evaluate the gamma induced stress response in plants in and between generations. The objective of this research is to reveal differences at the level of the antioxidative stress response between generations with a different radiation history. An experiment was conducted in which 7-days old Arabidopsis thaliana plants were exposed for 14 days to four different gamma dose rates: 22 mGy/h, 38 mGy/h, 86 mGy/h and 457 mGy/h. Two different plant groups were used: plants that were not exposed to gamma radiation before (P0) and plants that received the aforementioned gamma treatment during their previous generation (S1). Growth, the concentration of the antioxidants ascorbate and glutathione, a number of antioxidative enzyme activities and their gene transcript levels were analysed. A dose-rate dependent induction was seen for catalase (CAT) and guaiacol peroxidase (GPX) in the roots and for syringaldazine peroxidase (SPX) in the shoots. Differences between the two generations were observed for CAT and GPX in the roots, where a significantly higher activity of these ROS detoxifying enzymes was observed in the S1 generation. For SPX in the shoots, a dose dependent upregulation was observed in the P0 generation. However, high SPX activities were present for all doses in the S1 generation. These differences in enzyme activity between generations for SPX and GPX and the involvement of these enzymes in cell wall biosynthesis, suggest an important role for cell wall strengthening in the response to gamma irradiation.

PLOS ONE, 2015

The edible cyanobacterium Arthrospira is resistant to ionising radiation. The cellular mechanisms... more The edible cyanobacterium Arthrospira is resistant to ionising radiation. The cellular mechanisms underlying this radiation resistance are, however, still largely unknown. Therefore, additional molecular analysis was performed to investigate how these cells can escape from, protect against, or repair the radiation damage. Arthrospira cells were shortly exposed to different doses of 60 Co gamma rays and the dynamic response was investigated by monitoring its gene expression and cell physiology at different time points after irradiation. The results revealed a fast switch from an active growth state to a kind of 'survival modus' during which the cells put photosynthesis, carbon and nitrogen assimilation on hold and activate pathways for cellular protection, detoxification, and repair. The higher the radiation dose, the more pronounced this global emergency response is expressed. Genes repressed during early response, suggested a reduction of photosystem II and I activity and reduced tricarboxylic acid (TCA) and Calvin-Benson-Bassham (CBB) cycles, combined with an activation of the pentose phosphate pathway (PPP). For reactive oxygen species detoxification and restoration of the redox balance in Arthrospira cells, the results suggested a powerful contribution of the antioxidant molecule glutathione. The repair mechanisms of Arthrospira cells that were immediately switched on, involve mainly proteases for damaged protein removal, single strand DNA repair and restriction modification systems, while recA was not induced. Additionally, the exposed cells showed significant increased expression of arh genes, coding for a novel group of protein of unknown function, also seen in our previous irradiation studies. This observation confirms our hypothesis that arh genes are key elements in radiation resistance of Arthrospira, requiring further investigation. This study provides new insights into phasic response and the cellular pathways involved in the radiation resistance of microbial cells, in particularly for photosynthetic organisms as the cyanobacterium Arthrospira.

International Journal of Molecular Sciences, 2015