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Papers by Krzysztof Treder

Progress in Plant Protection, 2010

Progress in Plant Protection, 2009

Abstract Antimicrobial activity of protein purified from potato cell walls was estimated. The ant... more Abstract Antimicrobial activity of protein purified from potato cell walls was estimated. The antimicrobial protein inhibited growth of bacteria: Erwinia carotovora ssp. carotovora, E. amylovora, Pseudomonas syringae, Clavibacter michiganensis ssp. sepedonicus. Threshold dose of protein active against these bacteria was also estimated.

Progress in Plant Protection, 2009

Abstract The application of the cocktail-ELISA procedure allowed for the detection of PLRV, PVM a... more Abstract The application of the cocktail-ELISA procedure allowed for the detection of PLRV, PVM and PVY in samples 10-fold more diluted than by DAS-ELISA. Dilutions of extracts obtained from PLRV-infected tuber were also tested by IC-RT-PCR and PLRV-specific PCR product was observed even for the most diluted samples.

International Journal of Molecular Sciences, Apr 12, 2023

Contribution in Interactions between Turnip mosaic virus and Arabidopsis thaliana Mutants Lacking... more Contribution in Interactions between Turnip mosaic virus and Arabidopsis thaliana Mutants Lacking Respiratory Burst Oxidase Homologs D and F. Int.

Progress in Plant Protection, 2000

Ionically bound proteins were obtained from potato tuber cell walls by extraction with 1.5 M CaCl... more Ionically bound proteins were obtained from potato tuber cell walls by extraction with 1.5 M CaCl 2. Fractionation of these proteins by exclusion chromatography and isoelectric focusing yields group of proteins with peroxidase activity (45 kD) and bunch of 17-20 kD proteins that display the wide array of isoelectric points. Some of these 17-20 kD proteins suppressed the growth of Erwinia carotovora, Phytophthora infestans and Fusarium sulphureum [Gibberella cyanogena], and were able to agglutinate red blood cells and ...

Progress in Plant Protection, 2009

Studies were conducted to construct a simple method to increase microplate adsorbent capacity to ... more Studies were conducted to construct a simple method to increase microplate adsorbent capacity to improve the sensitivity od the detection of potato viruses by ELISA. Results showed that the microplates washed in laundry detergent resulted in higher ELISA sensitivity. It was revealed that detergent increased adsorbent capacity of microwells. Moreover, reliable recycling of ELISA microplates was possible after washing.

Progress in Plant Protection, 2000

This paper discusses the use of molecular methods (eg RT-PCR, DAS-ELISA and Cocktail-ELISA) for t... more This paper discusses the use of molecular methods (eg RT-PCR, DAS-ELISA and Cocktail-ELISA) for the detection of potato leafroll virus in affected potato plants.

Biuletyn Instytutu Hodowli i Aklimatyzacji Roślin

Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in... more Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in potato, the world’s most important non-cereal crop, the role of the rhizosphere microbiome under drought has been poorly studied. Using a cultivation independent metabarcoding approach, we examined the rhizosphere microbiome of two potato cultivars with different drought tolerance as a function of water regime (continuous versus reduced watering) and manipulation of soil microbial diversity (i.e., natural (NSM), vs. disturbed (DSM) soil microbiome). Water regime and soil pre-treatment showed a significant interaction with bacterial community composition of the drought-sensitive (HERBST) but not the drought-resistant cultivar (MONI). Depending on the cultivar, different taxa responded to reduced watering. Under NSM conditions, these were mostly rhizobiales order representative in MONI, andStreptomyces,Glycomyces,Marmoricola,Aeromicrobium,Mycobacterium, amongst Actinobacteriota, and the r...

Acta Scientiarum Polonorum. Oeconomia

Aim: The aim of this study is to assess the economic viability by calculating the potential profi... more Aim: The aim of this study is to assess the economic viability by calculating the potential profits and expenses for farmers, and to simulate the impact of the application of a microbiological agent on the potato plant in a field trial. The field experiment aimed to identify the role of the biological agent while substituting the synthetic plant fertilization and protection. Methodology: The system dynamics method was applied to the data provided from one planting season of field experiments conducted in the framework of the PotatoMETABiome project. From eleven tested varieties on six different scenario plots, the most economically viable variety – Pasja Pomorska – was tested. The comparative approach was applied to show the results of inoculating potato plants with biological agents and using synthetic pesticides and fertilizers. Results: The results show that the application of biocontrol agents increases the quality and quantity of the potato yield compared to a variant in which ...

Progress in Plant Protection, 2021

This paper describes the application of next generation sequencing (NGS) in plant virus research.... more This paper describes the application of next generation sequencing (NGS) in plant virus research. Although NGS has not been routinely used yet, it is increasingly adopted in diagnostics and genomics of phytopathogens. NGS technics enable the simultaneous detection of multiple viruses present in infected material. This makes it possible not only to determine which viruses are present in a single sample but also to determine their concentration and genetic diversity. The simultaneous identification of many viruses, the possibility of early detection of disease outbreaks as well as tracking and monitoring of epidemic development, make NGS a universal research tool that enables not only the detection but also the understanding of molecular mechanisms allowing viruses to adapt to environmental changes (host plant genotype, vector, presence of other pathogens).

The 3\u27-untranslated regions of many plant viral RNAs contain cap-independent translation eleme... more The 3\u27-untranslated regions of many plant viral RNAs contain cap-independent translation elements (CITEs) that drive translation initiation at the 5\u27-end of the mRNA. The barley yellow dwarf virus-like CITE (BTE) stimulates translation by binding the eIF4G subunit of translation initiation factor eIF4F with high affinity. To understand this interaction, we characterized the dynamic structural properties of the BTE, mapped the eIF4G-binding sites on the BTE and identified a region of eIF4G that is crucial for BTE binding. BTE folding involves cooperative uptake of magnesium ions and is driven primarily by charge neutralization. Footprinting experiments revealed that functional eIF4G fragments protect the highly conserved stem-loop I and a downstream bulge. The BTE forms a functional structure in the absence of protein, and the loop that base pairs the 5\u27-untranslated region (5\u27-UTR) remains solventaccessible at high eIF4G concentrations. The region in eIF4G between the eI...

Many plant viral RNA genomes lack a 5 cap, and instead are translated via a cap-independent trans... more Many plant viral RNA genomes lack a 5 cap, and instead are translated via a cap-independent translation element (CITE) in the 3 untranslated region (UTR). The panicum mosaic virus-like CITE (PTE), found in many plant viral RNAs, binds and requires the cap-binding translation initiation factor eIF4E to facilitate translation. eIF4E is structurally conserved between plants and animals, so we tested cap-independent translation efficiency of PTEs of nine plant viruses in plant and mammalian systems. The PTE from thin paspalum asymptomatic virus (TPAV) facilitated efficient cap-independent translation in wheat germ extract, rabbit reticulocyte lysate, HeLa cell lysate, and in oat and mammalian (BHK) cells. Human eIF4E bound the TPAV PTE but not a PTE that did not stimulate cap-independent translation in mammalian extracts or cells. Selective 2-hydroxyl acylation analyzed by primer extension (SHAPE) footprinting revealed that both human and wheat eIF4E protected the conserved guanosine (G)-rich domain in the TPAV PTE pseudoknot. The central G plays a key role, as it was found to be required for translation and protection from SHAPE modification by eIF4E. These results provide insight on how plant viruses gain access to the host's translational machinery, an essential step in infection, and raise the possibility that similar PTE-like mechanisms may exist in mRNAs of mammals or their viruses.

Nucleic Acids Research, 2013

The 3 0-untranslated regions of many plant viral RNAs contain cap-independent translation element... more The 3 0-untranslated regions of many plant viral RNAs contain cap-independent translation elements (CITEs) that drive translation initiation at the 5 0-end of the mRNA. The barley yellow dwarf virus-like CITE (BTE) stimulates translation by binding the eIF4G subunit of translation initiation factor eIF4F with high affinity. To understand this interaction, we characterized the dynamic structural properties of the BTE, mapped the eIF4G-binding sites on the BTE and identified a region of eIF4G that is crucial for BTE binding. BTE folding involves cooperative uptake of magnesium ions and is driven primarily by charge neutralization. Footprinting experiments revealed that functional eIF4G fragments protect the highly conserved stem-loop I and a downstream bulge. The BTE forms a functional structure in the absence of protein, and the loop that base pairs the 5 0-untranslated region (5 0-UTR) remains solventaccessible at high eIF4G concentrations. The region in eIF4G between the eIF4E-binding site and the MIF4G region is required for BTE binding and translation. The data support the model in which the eIF4F complex binds directly to the BTE which base pairs simultaneously to the 5 0-UTR, allowing eIF4F to recruit the 40S ribosomal subunit to the 5 0-end.

Progress in Plant Protection, 2010

Progress in Plant Protection, 2009

Abstract Antimicrobial activity of protein purified from potato cell walls was estimated. The ant... more Abstract Antimicrobial activity of protein purified from potato cell walls was estimated. The antimicrobial protein inhibited growth of bacteria: Erwinia carotovora ssp. carotovora, E. amylovora, Pseudomonas syringae, Clavibacter michiganensis ssp. sepedonicus. Threshold dose of protein active against these bacteria was also estimated.

Progress in Plant Protection, 2009

Abstract The application of the cocktail-ELISA procedure allowed for the detection of PLRV, PVM a... more Abstract The application of the cocktail-ELISA procedure allowed for the detection of PLRV, PVM and PVY in samples 10-fold more diluted than by DAS-ELISA. Dilutions of extracts obtained from PLRV-infected tuber were also tested by IC-RT-PCR and PLRV-specific PCR product was observed even for the most diluted samples.

International Journal of Molecular Sciences, Apr 12, 2023

Contribution in Interactions between Turnip mosaic virus and Arabidopsis thaliana Mutants Lacking... more Contribution in Interactions between Turnip mosaic virus and Arabidopsis thaliana Mutants Lacking Respiratory Burst Oxidase Homologs D and F. Int.

Progress in Plant Protection, 2000

Ionically bound proteins were obtained from potato tuber cell walls by extraction with 1.5 M CaCl... more Ionically bound proteins were obtained from potato tuber cell walls by extraction with 1.5 M CaCl 2. Fractionation of these proteins by exclusion chromatography and isoelectric focusing yields group of proteins with peroxidase activity (45 kD) and bunch of 17-20 kD proteins that display the wide array of isoelectric points. Some of these 17-20 kD proteins suppressed the growth of Erwinia carotovora, Phytophthora infestans and Fusarium sulphureum [Gibberella cyanogena], and were able to agglutinate red blood cells and ...

Progress in Plant Protection, 2009

Studies were conducted to construct a simple method to increase microplate adsorbent capacity to ... more Studies were conducted to construct a simple method to increase microplate adsorbent capacity to improve the sensitivity od the detection of potato viruses by ELISA. Results showed that the microplates washed in laundry detergent resulted in higher ELISA sensitivity. It was revealed that detergent increased adsorbent capacity of microwells. Moreover, reliable recycling of ELISA microplates was possible after washing.

Progress in Plant Protection, 2000

This paper discusses the use of molecular methods (eg RT-PCR, DAS-ELISA and Cocktail-ELISA) for t... more This paper discusses the use of molecular methods (eg RT-PCR, DAS-ELISA and Cocktail-ELISA) for the detection of potato leafroll virus in affected potato plants.

Biuletyn Instytutu Hodowli i Aklimatyzacji Roślin

Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in... more Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in potato, the world’s most important non-cereal crop, the role of the rhizosphere microbiome under drought has been poorly studied. Using a cultivation independent metabarcoding approach, we examined the rhizosphere microbiome of two potato cultivars with different drought tolerance as a function of water regime (continuous versus reduced watering) and manipulation of soil microbial diversity (i.e., natural (NSM), vs. disturbed (DSM) soil microbiome). Water regime and soil pre-treatment showed a significant interaction with bacterial community composition of the drought-sensitive (HERBST) but not the drought-resistant cultivar (MONI). Depending on the cultivar, different taxa responded to reduced watering. Under NSM conditions, these were mostly rhizobiales order representative in MONI, andStreptomyces,Glycomyces,Marmoricola,Aeromicrobium,Mycobacterium, amongst Actinobacteriota, and the r...

Acta Scientiarum Polonorum. Oeconomia

Aim: The aim of this study is to assess the economic viability by calculating the potential profi... more Aim: The aim of this study is to assess the economic viability by calculating the potential profits and expenses for farmers, and to simulate the impact of the application of a microbiological agent on the potato plant in a field trial. The field experiment aimed to identify the role of the biological agent while substituting the synthetic plant fertilization and protection. Methodology: The system dynamics method was applied to the data provided from one planting season of field experiments conducted in the framework of the PotatoMETABiome project. From eleven tested varieties on six different scenario plots, the most economically viable variety – Pasja Pomorska – was tested. The comparative approach was applied to show the results of inoculating potato plants with biological agents and using synthetic pesticides and fertilizers. Results: The results show that the application of biocontrol agents increases the quality and quantity of the potato yield compared to a variant in which ...

Progress in Plant Protection, 2021

This paper describes the application of next generation sequencing (NGS) in plant virus research.... more This paper describes the application of next generation sequencing (NGS) in plant virus research. Although NGS has not been routinely used yet, it is increasingly adopted in diagnostics and genomics of phytopathogens. NGS technics enable the simultaneous detection of multiple viruses present in infected material. This makes it possible not only to determine which viruses are present in a single sample but also to determine their concentration and genetic diversity. The simultaneous identification of many viruses, the possibility of early detection of disease outbreaks as well as tracking and monitoring of epidemic development, make NGS a universal research tool that enables not only the detection but also the understanding of molecular mechanisms allowing viruses to adapt to environmental changes (host plant genotype, vector, presence of other pathogens).

The 3\u27-untranslated regions of many plant viral RNAs contain cap-independent translation eleme... more The 3\u27-untranslated regions of many plant viral RNAs contain cap-independent translation elements (CITEs) that drive translation initiation at the 5\u27-end of the mRNA. The barley yellow dwarf virus-like CITE (BTE) stimulates translation by binding the eIF4G subunit of translation initiation factor eIF4F with high affinity. To understand this interaction, we characterized the dynamic structural properties of the BTE, mapped the eIF4G-binding sites on the BTE and identified a region of eIF4G that is crucial for BTE binding. BTE folding involves cooperative uptake of magnesium ions and is driven primarily by charge neutralization. Footprinting experiments revealed that functional eIF4G fragments protect the highly conserved stem-loop I and a downstream bulge. The BTE forms a functional structure in the absence of protein, and the loop that base pairs the 5\u27-untranslated region (5\u27-UTR) remains solventaccessible at high eIF4G concentrations. The region in eIF4G between the eI...

Many plant viral RNA genomes lack a 5 cap, and instead are translated via a cap-independent trans... more Many plant viral RNA genomes lack a 5 cap, and instead are translated via a cap-independent translation element (CITE) in the 3 untranslated region (UTR). The panicum mosaic virus-like CITE (PTE), found in many plant viral RNAs, binds and requires the cap-binding translation initiation factor eIF4E to facilitate translation. eIF4E is structurally conserved between plants and animals, so we tested cap-independent translation efficiency of PTEs of nine plant viruses in plant and mammalian systems. The PTE from thin paspalum asymptomatic virus (TPAV) facilitated efficient cap-independent translation in wheat germ extract, rabbit reticulocyte lysate, HeLa cell lysate, and in oat and mammalian (BHK) cells. Human eIF4E bound the TPAV PTE but not a PTE that did not stimulate cap-independent translation in mammalian extracts or cells. Selective 2-hydroxyl acylation analyzed by primer extension (SHAPE) footprinting revealed that both human and wheat eIF4E protected the conserved guanosine (G)-rich domain in the TPAV PTE pseudoknot. The central G plays a key role, as it was found to be required for translation and protection from SHAPE modification by eIF4E. These results provide insight on how plant viruses gain access to the host's translational machinery, an essential step in infection, and raise the possibility that similar PTE-like mechanisms may exist in mRNAs of mammals or their viruses.

Nucleic Acids Research, 2013

The 3 0-untranslated regions of many plant viral RNAs contain cap-independent translation element... more The 3 0-untranslated regions of many plant viral RNAs contain cap-independent translation elements (CITEs) that drive translation initiation at the 5 0-end of the mRNA. The barley yellow dwarf virus-like CITE (BTE) stimulates translation by binding the eIF4G subunit of translation initiation factor eIF4F with high affinity. To understand this interaction, we characterized the dynamic structural properties of the BTE, mapped the eIF4G-binding sites on the BTE and identified a region of eIF4G that is crucial for BTE binding. BTE folding involves cooperative uptake of magnesium ions and is driven primarily by charge neutralization. Footprinting experiments revealed that functional eIF4G fragments protect the highly conserved stem-loop I and a downstream bulge. The BTE forms a functional structure in the absence of protein, and the loop that base pairs the 5 0-untranslated region (5 0-UTR) remains solventaccessible at high eIF4G concentrations. The region in eIF4G between the eIF4E-binding site and the MIF4G region is required for BTE binding and translation. The data support the model in which the eIF4F complex binds directly to the BTE which base pairs simultaneously to the 5 0-UTR, allowing eIF4F to recruit the 40S ribosomal subunit to the 5 0-end.