@article{2-s2.0-85148334670,

title = {Potential negative effect of long-term exposure to nitrofurans on bacteria isolated from wastewater},

author = { A. Pacholak and J. Żur and A. Piński and Q.A. Nguyen and M. Ligaj and M. Łuczak and L.D. Nghiem and E. Kaczorek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85148334670&doi=10.1016%2fj.scitotenv.2023.162199&partnerID=40&md5=4f73dc7c51328440a75445282b4b764e},

doi = {10.1016/j.scitotenv.2023.162199},

issn = {00489697},

year  = {2023},

date = {2023-01-01},

journal = {Science of the Total Environment},

volume = {872},

publisher = {Elsevier B.V.},

abstract = {Nitrofurans are broad-spectrum bactericidal agents used in a large quantity for veterinary and human therapy. This study reports the long-term impact of two nitrofuran representatives, nitrofurantoin (NFT) and furaltadone (FTD) on the bacterial strains Sphingobacterium siyangense FTD2, Achromobacter pulmonis NFZ2, and Stenotrophomonas maltophilia FZD2, isolated from a full-scale wastewater treatment plant. Bacterial whole genome sequencing was used for preliminary strains characterization. The metabolomic, electrochemical, and culture methods were applied to understand changes in the bacterial strains after 12-month exposure to nitrofurans. The most significantly altered metabolic pathways were observed in amino acid and sugar metabolism, and aminoacyl-tRNA biosynthesis. Disrupted protein biosynthesis was measured in all strains treated with antibiotics. Prolonged exposure to NFT and FTD also triggered mutagenic effects, affected metabolic activity, and facilitated oxidative stress within the cells. Nitrofuran-induced oxidative stress was evidenced from an elevated activity of catalase and glutathione S-transferases. NFT and FTD elicited similar but not identical responses in all analyzed strains. The results obtained in this study provide new insights into the potential risks of the prolonged presence of antimicrobial compounds in the environment and contribute to a better understanding of the possible impacts of nitrofuran antibiotics on the bacterial cells. © 2023 Elsevier B.V.},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85171835921,

title = {Efficient Agrobacterium-mediated transformation and genome editing of Fagopyrum tataricum},

author = { A. Piński and A. Betekhtin},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85171835921&doi=10.3389%2ffpls.2023.1270150&partnerID=40&md5=ea62185f60b67f1041241e0c54b337bc},

doi = {10.3389/fpls.2023.1270150},

issn = {1664462X},

year  = {2023},

date = {2023-01-01},

journal = {Frontiers in Plant Science},

volume = {14},

publisher = {Frontiers Media SA},

abstract = {Fagopyrum tataricum (L.) Gaertn. is an exceptional crop known for its remarkable health benefits, high levels of beneficial polyphenols and gluten-free properties, making it highly sought-after as a functional food. Its self-fertilisation capability and adaptability to challenging environments further contribute to its potential as a sustainable agricultural option. To harness its unique traits, genetic transformation in F. tataricum is crucial. In this study, we optimised the Agrobacterium-mediated transformation protocol for F. tataricum callus, resulting in a transformation rate of regenerated plants of approximately 20%. The protocol’s effectiveness was confirmed through successful GUS staining, GFP expression, and the generation of albino plants via FtPDS gene inactivation. These results validate the feasibility of genetic manipulation and highlight the potential for trait enhancement in F. tataricum. Copyright © 2023 Pinski and Betekhtin.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85144688398,

title = {Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain Serratia quinivorans KP32 to Fungal Phytopathogens},

author = { D. Chlebek and T.M. Tame and A. Piński and J. Żur and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85144688398&doi=10.3390%2fijms232415561&partnerID=40&md5=8d122b0a287be7d39297e5d8632c6b68},

doi = {10.3390/ijms232415561},

issn = {16616596},

year  = {2022},

date = {2022-01-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {24},

publisher = {MDPI},

abstract = {Fungal phytopathogens are challenging to control due to their penetration into plant tissues. Therefore, plant-colonizing bacteria could serve as an excellent weapon in fighting fungal infections. In this study, we aim to determine the biocontrol potential of the new endophytic strain Serratia quinivorans KP32, isolated from the roots of Petroselinum crispum L.; identify the related mechanisms; and understand the basis of its antagonistic interaction with taxonomically diverse fungi at the molecular level. The KP32 strain presented biological activity against Rhizoctonia solani, Colletotrichum dematium, Fusarium avenaceum, and Sclerotinia sclerotiorum, and its ability to inhibit the growth of the phytopathogens was found to be mediated by a broad spectrum of biocontrol features, such as the production of a number of lytic enzymes (amylases; chitinases; and proteases), siderophores, volatile organic and inorganic compounds, salicylic acid, and N-acyl-homoserine lactones. The higher expression of chitinase (chiA) and genes involved in the biosynthesis of hydrogen cyanide (hcnC), enterobactin (entB), and acetoin (budA) in bacteria exposed to fungal filtrates confirmed that these factors could act in combination, leading to a synergistic inhibitory effect of the strain against phytopathogens. We also confirm the active movement, self-aggregation, exopolysaccharide production, and biofilm formation abilities of the KP32 strain, which are essential for effective plant colonization. Its biological activity and colonization potential indicate that KP32 holds tremendous potential for use as an active biopesticide and plant growth promoter. © 2022 by the authors.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85130260970,

title = {Corrigendum: To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum (Front. Plant Sci., (2021), 12, (768347), 10.3389/fpls.2021.768347)},

author = { N. Borowska-Zuchowska and E. Robaszkiewicz and S. Mykhailyk and J. Wartini and A. Piński and A. Kovaík and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85130260970&doi=10.3389%2ffpls.2022.917940&partnerID=40&md5=9b0bae9c81633dfeba911097fe74aa37},

doi = {10.3389/fpls.2022.917940},

issn = {1664462X},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Plant Science},

volume = {13},

publisher = {Frontiers Media S.A.},

abstract = {In the original article, there was a mistake in Figure 3B as published. The gel lines were marked in an incorrect order. The corrected Figure 3B appears below. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated. Copyright © 2022, Borowska-Zuchowska, Robaszkiewicz, Mykhailyk, Wartini, Pinski, Kovarik and Hasterok.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85121989036,

title = {To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum},

author = { N. Borowska-Zuchowska and E. Robaszkiewicz and S. Mykhailyk and J. Wartini and A. Piński and A. Kovaík and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85121989036&doi=10.3389%2ffpls.2021.768347&partnerID=40&md5=ef4ed95412d5b77ca61c65fd3acb3f58},

doi = {10.3389/fpls.2021.768347},

issn = {1664462X},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in Plant Science},

volume = {12},

publisher = {Frontiers Media S.A.},

abstract = {Nucleolar dominance (ND) is an epigenetic, developmentally regulated phenomenon that describes the selective inactivation of 35S rDNA loci derived from one progenitor of a hybrid or allopolyploid. The presence of ND was documented in an allotetraploid grass, Brachypodium hybridum (genome composition DDSS), which is a polyphyletic species that arose from crosses between two putative ancestors that resembled the modern B. distachyon (DD) and B. stacei (SS). In this work, we investigated the developmental stability of ND in B. hybridum genotype 3-7-2 and compared it with the reference genotype ABR113. We addressed the question of whether the ND is established in generative tissues such as pollen mother cells (PMC). We examined condensation of rDNA chromatin by fluorescence in situ hybridization employing state-of-art confocal microscopy. The transcription of rDNA homeologs was determined by reverse-transcription cleaved amplified polymorphic sequence analysis. In ABR113, the ND was stable in all tissues analyzed (primary and adventitious root; leaf; and spikes). In contrast, the 3-7-2 individuals showed a strong upregulation of the S-genome units in adventitious roots but not in other tissues. Microscopic analysis of the 3-7-2 PMCs revealed extensive decondensation of the D-genome loci and their association with the nucleolus in meiosis. As opposed, the S-genome loci were always highly condensed and localized outside the nucleolus. These results indicate that genotype-specific loss of ND in B. hybridum occurs probably after fertilization during developmental processes. This finding supports our view that B. hybridum is an attractive model to study ND in grasses. Copyright © 2021 Borowska-Zuchowska, Robaszkiewicz, Mykhailyk, Wartini, Pinski, Kovarik and Hasterok.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85117462940,

title = {Non‐targeted metabolite profiling reveals host metabolomic reprogramming during the interaction of black pepper with phytophthora capsici},

author = { D. Kattupalli and A. Piński and S. Sreekumar and A. Usha and A. Girija and M. Beckmann and L.A.J. Mur and S. Eppurathu Vasudevan},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85117462940&doi=10.3390%2fijms222111433&partnerID=40&md5=81a1169457a60165f2e4577ec6828316},

doi = {10.3390/ijms222111433},

issn = {16616596},

year  = {2021},

date = {2021-01-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {21},

publisher = {MDPI},

abstract = {Phytophthora capsici is one of the most destructive pathogens causing quick wilt (foot rot) disease in black pepper (Piper nigrum L.) to which no effective resistance has been defined. To better understand the P. nigrum–P. capsici pathosystem, we employed metabolomic approaches based on flow‐infusion electrospray–high‐resolution mass spectrometry. Changes in the leaf metabolome were assessed in infected and systemic tissues at 24 and 48 hpi. Principal Component Analysis of the derived data indicated that the infected leaves showed a rapid metabolic response by 24 hpi whereas the systemic leaves took 48 hpi to respond to the infection. The major sources of variations between infected leaf and systemic leaf were identified, and enrichment pathway analysis indicated, major shifts in amino acid, tricarboxylic acid cycle, nucleotide and vitamin B6 metabolism upon infection. Moreover, the individual metabolites involved in defensive phytohormone signalling were identified. RT‐qPCR analysis of key salicylate and jasmonate biosynthetic genes indicated a transient reduction of expression at 24 hpi but this increased subsequently. Exogenous application of jasmonate and salicylate reduced P. capsici disease symptoms, but this effect was suppressed with the co‐application of abscisic acid. The results are consistent with abscisic acid reprogramming, sa-licylate and jasmonate defences in infected leaves to facilitate the formation of disease. The augmen-tation of salicylate and jasmonate defences could represent an approach through which quick wilt disease could be controlled in black pepper. © 2021 by the authors. Li-censee MDPI, Basel, Switzerland.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85108074393,

title = {Adaptation of phenol-degrading Pseudomonas putida KB3 to suboptimal growth condition: A focus on degradative rate, membrane properties and expression of xylE and cfaB genes},

author = { A. Nowak and J. Żur-Pińska and A. Piński and G. Pacek and A. Mrozik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108074393&doi=10.1016%2fj.ecoenv.2021.112431&partnerID=40&md5=3d172fd5f8869aa2b2590496396fd4b3},

doi = {10.1016/j.ecoenv.2021.112431},

issn = {01476513},

year  = {2021},

date = {2021-01-01},

journal = {Ecotoxicology and Environmental Safety},

volume = {221},

publisher = {Academic Press},

abstract = {Detailed characterization of new Pseudomonas strains that degrade toxic pollutants is required and utterly necessary before their potential use in environmental microbiology and biotechnology applications. Therefore, phenol degradation by Pseudomonas putida KB3 under suboptimal temperatures, pH, and salinity was examined in this study. Parallelly, adaptive mechanisms of bacteria to stressful growth conditions concerning changes in cell membrane properties during phenol exposure as well as the expression level of genes encoding catechol 2,3-dioxygenase (xylE) and cyclopropane fatty acid synthase (cfaB) were determined. It was found that high salinity and the low temperature had the most significant effect on the growth of bacteria and the rate of phenol utilization. Degradation of phenol (300 mg L−1) proceeded 12-fold and seven-fold longer at 10 °C and 5% NaCl compared to the optimal conditions. The ability of bacteria to degrade phenol was coupled with a relatively high activity of catechol 2,3-dioxygenase. The only factor that inhibited enzyme activity by approximately 80% compared to the control sample was salinity. Fatty acid methyl ester (FAMEs) profiling, membrane permeability measurements, and hydrophobicity tests indicated severe alterations in bacteria membrane properties during phenol degradation in suboptimal growth conditions. The highest values of pH, salinity, and temperature led to a decrease in membrane permeability. FAME analysis showed fatty acid saturation indices and cyclopropane fatty acid participation at high temperature and salinity. Genetic data showed that suboptimal growth conditions primarily resulted in down-regulation of xylE and cfaB gene expression. © 2021 The Authors},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85108404792,

title = {Comparison of mass spectrometry data and bioinformatics predictions to assess the bona fide localization of proteins identified in cell wall proteomics studies},

author = { A. Piński and D. Roujol and C. Pouzet and L. Bordes and H. San Clemente and L. Hoffmann and E. Jamet},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108404792&doi=10.1016%2fj.plantsci.2021.110979&partnerID=40&md5=fdad76e9e936397e95ba09ae2340722f},

doi = {10.1016/j.plantsci.2021.110979},

issn = {01689452},

year  = {2021},

date = {2021-01-01},

journal = {Plant Science},

volume = {310},

publisher = {Elsevier Ireland Ltd},

abstract = {Plant cell walls have complex architectures made of polysaccharides among which cellulose, hemicelluloses, pectins and cell wall proteins (CWPs). Some CWPs are anchored in the plasma membrane through a glycosylphosphatidylinositol (GPI)-anchor. The secretion pathway is the classical route to reach the extracellular space. Based on experimental data, a canonical signal peptide (SP) has been defined, and bioinformatics tools allowing the prediction of the sub-cellular localization of proteins have been designed. In the same way, the presence of GPI-anchor attachment sites can be predicted using bioinformatics programs. This article aims at comparing the bioinformatics predictions of the sub-cellular localization of proteins assumed to be CWPs to mass spectrometry (MS) data. The sub-cellular localization of a few CWPs exhibiting particular features has been checked by cell biology approaches. Although the prediction of SP length is confirmed in most cases, it is less conclusive for GPI-anchors. Three main observations were done: (i) the variability observed at the N-terminus of a few mature CWPs could play a role in the regulation of their biological activity; (ii) one protein was shown to have a double sub-cellular localization in the cell wall and the chloroplasts; and (iii) peptides were found to be located at the C-terminus of several CWPs previously identified in GPI-anchored proteomes, thus raising the issue of their actual anchoring to the plasma membrane. © 2021 Elsevier B.V.},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85110027459,

title = {3,4‐dehydro‐l‐proline induces programmed cell death in the roots of brachypodium distachyon},

author = { A. Piński and A. Betekhtin and J. Kwaśniewska and Ł. Chajec and E.A. Wolny and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85110027459&doi=10.3390%2fijms22147548&partnerID=40&md5=045642b6770419a71c99a63d6dd94f4c},

doi = {10.3390/ijms22147548},

issn = {16616596},

year  = {2021},

date = {2021-01-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {14},

publisher = {MDPI},

abstract = {As cell wall proteins, the hydroxyproline‐rich glycoproteins (HRGPs) take part in plant growth and various developmental processes. To fulfil their functions, HRGPs, extensins (EXTs) in particular, undergo the hydroxylation of proline by the prolyl‐4‐hydroxylases. The activity of these enzymes can be inhibited with 3,4‐dehydro‐L‐proline (3;4‐DHP), which enables its application to reveal the functions of the HRGPs. Thus, to study the involvement of HRGPs in the development of root hairs and roots, we treated seedlings of Brachypodium distachyon with 250 μM, 500 μM, and 750 μM of 3,4‐DHP. The histological observations showed that the root epidermis cells and the cortex cells beneath them ruptured. The immunostaining experiments using the JIM20 antibody, which recognizes the EXT epitopes, demonstrated the higher abundance of this epitope in the control compared to the treated samples. The transmission electron microscopy analyses revealed morphological and ultrastructural features that are typical for the vacuolar‐type of cell death. Using the TUNEL test (terminal deoxynucleotidyl transferase dUTP nick end labelling), we showed an increase in the number of nuclei with damaged DNA in the roots that had been treated with 3,4‐DHP compared to the control. Finally, an analysis of two metacaspases’ gene activity revealed an increase in their expression in the treated roots. Altogether, our results show that inhibiting the prolyl‐4‐hydroxyl-ases with 3,4‐DHP results in a vacuolar‐type of cell death in roots, thereby highlighting the important role of HRGPs in root hair development and root growth. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85108260977,

title = {Changes in the cell wall proteome of leaves in response to high temperature stress in brachypodium distachyon},

author = { A. Piński and A. Betekhtin and B. Skupien‐rabian and U. Jankowska and E. Jamet and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108260977&doi=10.3390%2fijms22136750&partnerID=40&md5=bd0c6a761d804c4e3473abb1174f406e},

doi = {10.3390/ijms22136750},

issn = {16616596},

year  = {2021},

date = {2021-01-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {13},

publisher = {MDPI},

abstract = {High temperature stress leads to complex changes to plant functionality, which affects, i.a., the cell wall structure and the cell wall protein composition. In this study, the qualitative and quantitative changes in the cell wall proteome of Brachypodium distachyon leaves in response to high (40 °C) temperature stress were characterised. Using a proteomic analysis, 1533 non‐redundant proteins were identified from which 338 cell wall proteins were distinguished. At a high temperature, we identified 46 differentially abundant proteins, and of these, 4 were over‐accumulated and 42 were under‐accumulated. The most significant changes were observed in the proteins acting on the cell wall polysaccharides, specifically, 2 over‐ and 12 under‐accumulated proteins. Based on the qualitative analysis, one cell wall protein was identified that was uniquely present at 40 °C but was absent in the control and 24 proteins that were present in the control but were absent at 40 °C. Overall, the changes in the cell wall proteome at 40 °C suggest a lower protease activity, lignification and an expansion of the cell wall. These results offer a new insight into the changes in the cell wall proteome in response to high temperature. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85092155502,

title = {Degradation of diclofenac by new bacterial strains and its influence on the physiological status of cells},

author = { J. Żur and A. Marchlewicz and A. Piński and U. Guzik and D. Wojcieszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85092155502&doi=10.1016%2fj.jhazmat.2020.124000&partnerID=40&md5=ea0a1291c85c273eacde445aa45e1c1c},

doi = {10.1016/j.jhazmat.2020.124000},

issn = {03043894},

year  = {2021},

date = {2021-01-01},

journal = {Journal of Hazardous Materials},

volume = {403},

publisher = {Elsevier B.V.},

abstract = {Diclofenac (DCF) is one of the most commonly utilized non-steroidal anti-inflammatory drugs (NSAIDs), which is known to pose an ecotoxicological threat. In this study, from activated sludge and contaminated soil, we isolated four new bacterial strains able to degrade DCF under mono-substrate and co-metabolic conditions with glucose supplementation. We found that the effectiveness of DCF removal is strictly strain-specific and the addition of the primary substrate is not always beneficial. To assess the multidirectional influence of DCF on bacterial cells we evaluated the alterations of increasing concentrations of this drug on membrane structure. A significant increase was observed in the content of 17:0 cyclo fatty acid, which is responsible for reduced fluidity and profound changes in membrane rigidity. The cell injury and oxidative stress were assessed with biomarkers used as endpoints of toxicity, i.e. catalase (CAT), superoxide dismutase (SOD), lipids peroxidation (LPX), and both intra- and extracellular alkaline and acid phosphatase activity. Results indicated that DCF induced oxidative stress, frequently intensified by the addition of glucose. However, the response of the microbial cells to the presence of DCF should not be generalized, since the overall picture of the particular alterations greatly varied for each of the examined strains. © 2020 Elsevier B.V.},

note = {9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85096339783,

title = {Genome mining and evaluation of the biocontrol potential of pseudomonas fluorescens brz63, a new endophyte of oilseed rape (Brassica napus l.) against fungal pathogens},

author = { D. Chlebek and A. Piński and J. Żur and J. Michalska and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096339783&doi=10.3390%2fijms21228740&partnerID=40&md5=87d4457488d36bc724971e34dcfdacb3},

doi = {10.3390/ijms21228740},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {22},

pages = {1-21},

publisher = {MDPI AG},

abstract = {Endophytic bacteria hold tremendous potential for use as biocontrol agents. Our study aimed to investigate the biocontrol activity of Pseudomonas fluorescens BRZ63, a new endophyte of oilseed rape (Brassica napus L.) against Rhizoctonia solani W70, Colletotrichum dematium K, Sclerotinia sclerotiorum K2291, and Fusarium avenaceum. In addition, features crucial for biocontrol, plant growth promotion, and colonization were assessed and linked with the genome sequences. The in vitro tests showed that BRZ63 significantly inhibited the mycelium growth of all tested pathogens and stimulated germination and growth of oilseed rape seedlings treated with fungal pathogens. The BRZ63 strain can benefit plants by producing biosurfactants, siderophores, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and ammonia as well as phosphate solubilization. The abilities of exopolysaccharide production, autoaggregation, and biofilm formation additionally underline its potential to plant colonization and hence biocontrol. The effective colonization properties of the BRZ63 strain were confirmed by microscopy observations of EGFP-expressing cells colonizing the root surface and epidermal cells of Arabidopsis thaliana Col-0. Genome mining identified many genes related to the biocontrol process, such as transporters, siderophores, and other secondary metabolites. All analyses revealed that the BRZ63 strain is an excellent endophytic candidate for biocontrol of various plant pathogens and plant growth promotion. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {13},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85090899825,

title = {Diclofenac degradation—enzymes, genetic background and cellular alterations triggered in diclofenac-metabolizing strain pseudomonas moorei KB4},

author = { J. Żur and A. Piński and D. Wojcieszyńska and W. Smułek and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090899825&doi=10.3390%2fijms21186786&partnerID=40&md5=02cb0c3ff66c56b2a75244c5e93fb01b},

doi = {10.3390/ijms21186786},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {18},

pages = {1-22},

publisher = {MDPI AG},

abstract = {Diclofenac (DCF) constitutes one of the most significant ecopollutants detected in various environmental matrices. Biological clean-up technologies that rely on xenobiotics-degrading microorganisms are considered as a valuable alternative for chemical oxidation methods. Up to now, the knowledge about DCF multi-level influence on bacterial cells is fragmentary. In this study, we evaluate the degradation potential and impact of DCF on Pseudomonas moorei KB4 strain. In mono-substrate culture KB4 metabolized 0.5 mg L−1 of DCF, but supplementation with glucose (Glc) and sodium acetate (SA) increased degraded doses up to 1 mg L−1 within 12 days. For all established conditions, 4′-OH-DCF and DCF-lactam were identified. Gene expression analysis revealed the up-regulation of selected genes encoding biotransformation enzymes in the presence of DCF, in both mono-substrate and co-metabolic conditions. The multifactorial analysis of KB4 cell exposure to DCF showed a decrease in the zeta-potential with a simultaneous increase in the cell wall hydrophobicity. Magnified membrane permeability was coupled with the significant increase in the branched (19:0 anteiso) and cyclopropane (17:0 cyclo) fatty acid accompanied with reduced amounts of unsaturated ones. DCF injures the cells which is expressed by raised activities of acid and alkaline phosphatases as well as formation of lipids peroxidation products (LPX). The elevated activity of superoxide dismutase (SOD) and catalase (CAT) testified that DCF induced oxidative stress. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85087866006,

title = {Comparative genomics of stenotrophomonas maltophilia and stenotrophomonas rhizophila revealed characteristic features of both species},

author = { A. Piński and J. Żur and R. Hasterok and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85087866006&doi=10.3390%2fijms21144922&partnerID=40&md5=d3558a7364b4d6e0f87930ba3345b45d},

doi = {10.3390/ijms21144922},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {14},

pages = {1-20},

publisher = {MDPI AG},

abstract = {Although Stenotrophomonas maltophilia strains are efficient biocontrol agents, their field applications have raised concerns due to their possible threat to human health. The non-pathogenic Stenotrophomonas rhizophila species, which is closely related to S. maltophilia, has been proposed as an alternative. However, knowledge regarding the genetics of S. rhizophila is limited. Thus, the aim of the study was to define any genetic differences between the species and to characterise their ability to promote the growth of plant hosts as well as to enhance phytoremediation efficiency. We compared 37 strains that belong to both species using the tools of comparative genomics and identified 96 genetic features that are unique to S. maltophilia (e.g.; chitin-binding protein; mechanosensitive channels of small conductance and KGG repeat-containing stress-induced protein) and 59 that are unique to S. rhizophila (e.g.; glucosylglycerol-phosphate synthase; cold shock protein with the DUF1294 domain; and pteridine-dependent dioxygenase-like protein). The strains from both species have a high potential for biocontrol, which is mainly related to the production of keratinases (KerSMD and KerSMF), proteinases and chitinases. Plant growth promotion traits are attributed to the biosynthesis of siderophores, spermidine, osmoprotectants such as trehalose and glucosylglycerol, which is unique to S. rhizophila. In eight out of 37 analysed strains, the genes that are required to degrade protocatechuate were present. While our results show genetic differences between the two species, they had a similar growth promotion potential. Considering the information above, S. rhizophila constitutes a promising alternative for S. maltophilia for use in agricultural biotechnology. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85085871596,

title = {A CRISPR/Cas9-Based Mutagenesis Protocol for Brachypodium distachyon and Its Allopolyploid Relative, Brachypodium hybridum},

author = { K. Hus and A. Betekhtin and A. Piński and M. Rojek-Jelonek and E. Grzebelus and C. Nibau and M. Gao and K.E. Jaeger and G. Jenkins and J.H. Doonan and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85085871596&doi=10.3389%2ffpls.2020.00614&partnerID=40&md5=b86deda01a9059410a6d9ffe28faed8e},

doi = {10.3389/fpls.2020.00614},

issn = {1664462X},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Plant Science},

volume = {11},

publisher = {Frontiers Media S.A.},

abstract = {The CRISPR/Cas9 system enables precise genome editing and is a useful tool for functional genomic studies. Here we report a detailed protocol for targeted genome editing in the model grass Brachypodium distachyon and its allotetraploid relative B. hybridum, describing gRNA design, a transient protoplast assay to test gRNA efficiency, Agrobacterium-mediated transformation and the selection and analysis of regenerated plants. In B. distachyon, we targeted the gene encoding phytoene desaturase (PDS), which is a crucial enzyme in the chlorophyll biosynthesis pathway. The albino phenotype of mutants obtained confirmed the effectiveness of the protocol for functional gene analysis. Additionally, we targeted two genes related to cell wall maintenance, encoding a fasciclin-like arabinogalactan protein (FLA) and a pectin methylesterase (PME), also in B. distachyon. Two genes encoding cyclin-dependent kinases (CDKG1 and CDKG2), which may be involved in DNA recombination were targeted in both B. distachyon and B. hybridum. Cas9 activity induces mainly insertions or deletions, resulting in frameshift mutations that, may lead to premature stop codons. Because of the close phylogenetic relationship between Brachypodium species and key temperate cereals and forage grasses, this protocol should be easily adapted to target genes underpinning agronomically important traits. © Copyright © 2020 Hus, Betekhtin, Pinski, Rojek-Jelonek, Grzebelus, Nibau, Gao, Jaeger, Jenkins, Doonan and Hasterok.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85084456097,

title = {Effects of low concentration of selected analgesics and successive bioaugmentation of the activated sludge on its activity and metabolic diversity},

author = { J. Żur and J. Michalska and A. Piński and A. Mrozik and A. Nowak},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85084456097&doi=10.3390%2fW12041133&partnerID=40&md5=90f5b4c6b8ccf903e458fdb6e230e0c4},

doi = {10.3390/W12041133},

issn = {20734441},

year  = {2020},

date = {2020-01-01},

journal = {Water (Switzerland)},

volume = {12},

number = {4},

publisher = {MDPI AG},

abstract = {In this study, we evaluated the impact of the successive bioaugmentation of the activated sludge (AS) with the defined bacterial consortium on the activity and functional capacity of the AS microorganisms. In parallel, the removal of low concentrations of the selected non-steroidal anti-inflammatory drugs (ibuprofen; naproxen; diclofenac) and analgesic paracetamol was studied. We found that the addition of the bacterial consortium consisting of three pharmaceuticals-degrading strains Bacillus thuringiensis B1 (2015b), Stenotrophomonas maltophilia KB2, and Pseudomonas moorei KB4 into the AS did not cause any significant changes in the biomass abundance and metabolic activity of the AS microorganisms. Although, the successive bioaugmentation of the AS caused a slight increase in the metabolic diversity, the intensity of carbohydrates usage, and metabolic richness. Microorganisms in the bioaugmented and non-bioaugmented AS were able to degrade the mixture of the analyzed drugs with similar efficiency, however, diclofenac was removed more effectively in the bioaugmented AS. Several metabolites were identified and efficiently utilized, with the exception of 4-OH diclofenac. Two new diclofenac-degrading strains assigned as Serratia proteamaculans AS4 and Rahnella bruchi AS7 were isolated from the diclofenac-treated AS. © 2020 by the authors.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85083227042,

title = {Genome mining revealed a high biosynthetic potential for antifungal streptomyces sp. S-2 isolated from black soot},

author = { P. Siupka and A. Piński and D. Babicka and Z. Piotrowska-Seget},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85083227042&doi=10.3390%2fijms21072558&partnerID=40&md5=8d03614905f0d09dac5423ffa3cca837},

doi = {10.3390/ijms21072558},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {7},

publisher = {MDPI AG},

abstract = {The increasing resistance of fungal pathogens has heightened the necessity of searching for new organisms and compounds to combat their spread. Streptomyces are bacteria that are well-known for the production of many antibiotics. To find novel antibiotic agents, researchers have turned to previously neglected and extreme environments. Here, we isolated a new strain, Streptomyces sp. S-2, for the first time, from black soot after hard coal combustion (collected from an in-use household chimney). We examined its antifungal properties against plant pathogens and against fungi that potentially pose threat to human health (Fusarium avenaceum; Aspergillus niger and the environmental isolates Trichoderma citrinoviridae Cin-9; Nigrospora oryzae sp. roseF7; and Curvularia coatesieae sp. junF9). Furthermore, we obtained the genome sequence of S-2 and examined its potential for secondary metabolites production using anti-SMASH software. The S-2 strain shows activity against all of the tested fungi. Genome mining elucidated a vast number of biosynthetic gene clusters (55), which distinguish this strain from closely related strains. The majority of the predicted clusters were assigned to non-ribosomal peptide synthetases or type 1 polyketide synthetases, groups known to produce compounds with antimicrobial activity. A high number of the gene clusters showed no, or low similarity to those in the database, raising the possibility that S-2 could be a producer of novel antibiotics. Future studies on Streptomyces sp. S-2 will elucidate its full biotechnological potential. © 2020 by the authors.},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85079226601,

title = {A whole-cell immobilization system on bacterial cellulose for the paracetamol-degrading Pseudomonas moorei KB4 strain},

author = { J. Żur and A. Piński and J. Michalska and K.T. Hupert-Kocurek and A. Nowak and D. Wojcieszyńska and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079226601&doi=10.1016%2fj.ibiod.2020.104919&partnerID=40&md5=83d05c44cb2a78963ef96e3d769f2088},

doi = {10.1016/j.ibiod.2020.104919},

issn = {09648305},

year  = {2020},

date = {2020-01-01},

journal = {International Biodeterioration and Biodegradation},

volume = {149},

publisher = {Elsevier Ltd},

abstract = {Microorganisms with a high natural ability to degrade xenobiotics, which are usually characterized by a diverse metabolism and unique features, can be used as natural biocatalysts in wastewater treatment or bioaugmentation processes. The immobilization of such strains greatly increases their stability and degradation properties. The most critical issues in designing whole-cell immobilization systems are selecting the suitable carrier and determining the bacterial features that will promote effective immobilization. In this study, we immobilized the paracetamol-degrading Pseudomonas moorei KB4 strain on the bacterial cellulose disks that were produced by Komagataeibacter xylinus E-89370. The KB4 strain immobilized on the cellulose degraded 150 mg L−1 of paracetamol in three series of 50 mg L−1 in each cycle. The average protein concentration and dehydrogenase activity increased after the degradation of each dose. The specific activity (U mg−1 of protein) of the main enzymes involved in the degradation pathway was 0.22 for deaminase, 5.1 for acylamidohydrolase and 3.49 for ring-cleavage hydroquinone 1,2-dioxygenase. The relative expression level of the genes encoding deaminases and acylamidohydrolases increased in the presence of paracetamol, though more prominently in the immobilized than in the free cells. © 2020 Elsevier Ltd},

note = {19},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85082558569,

title = {Analysis of the bioaugmentation potential of Pseudomonas putida OR45a and Pseudomonas putida KB3 in the sequencing batch reactors fed with the phenolic landfill leachate},

author = { J. Michalska and A. Piński and J. Żur and A. Mrozik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85082558569&doi=10.3390%2fw12030906&partnerID=40&md5=67a6b3c06ffeeb8d282ff6659fcac256},

doi = {10.3390/w12030906},

issn = {20734441},

year  = {2020},

date = {2020-01-01},

journal = {Water (Switzerland)},

volume = {12},

number = {3},

publisher = {MDPI AG},

abstract = {The treatment of landfill leachate could be challenging for the biological wastewater treatment systems due to its high toxicity and the presence of poorly biodegradable contaminants. In this study, the bioaugmentation technology was successfully applied in sequencing batch reactors (SBRs) fed with the phenolic landfill leachate by inoculation of the activated sludge (AS) with two phenol-degrading Pseudomonas putida OR45a and Pseudomonas putida KB3 strains. According to the results, the SBRs bioaugmented with Pseudomonas strains withstood the increasing concentrations of the leachate. This resulted in the higher removal efficiency of the chemical oxygen demand (COD) of 79-86%, ammonia nitrogen of 87-88% and phenolic compounds of 85-96% as compared to 45%, 64%, and 50% for the noninoculated SBR. Simultaneously, the bioaugmentation of the AS allowed to maintain the high enzymatic activity of dehydrogenases, nonspecific esterases, and catalase in this ecosystem, which contributed to the higher functional capacity of indigenous microorganisms than in the noninoculated AS. Herein, the stress level experienced by the microorganisms in the SBRs fed with the leachate computed based on the cellular ATP measurements showed that the abundance of exogenous Pseudomonas strains in the bioreactors contributed to the reduction in effluent toxicity, which was reflected by a decrease in the stress biomass index to 32-45% as compared to the nonbioaugmented AS (76%). © 2020 by the authors.},

note = {9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85079488590,

title = {Selecting bacteria candidates for the bioaugmentation of activated sludge to improve the aerobic treatment of landfill leachate},

author = { J. Michalska and A. Piński and J. Żur and A. Mrozik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079488590&doi=10.3390%2fw12010140&partnerID=40&md5=55858d2eb6135c7439f0d8ad67055693},

doi = {10.3390/w12010140},

issn = {20734441},

year  = {2020},

date = {2020-01-01},

journal = {Water (Switzerland)},

volume = {12},

number = {1},

publisher = {MDPI AG},

abstract = {In this study, a multifaceted approach for selecting the suitable candidates for bioaugmentation of activated sludge (AS) that supports leachate treatment was used. To determine the exploitation of 10 bacterial strains isolated from the various matrices for inoculating the AS contaminated with the Kalina pond leachate (KPL), their degradative potential was analyzed along with their aptitude to synthesize compounds improving remediation of pollutants in wastewater and ability to incorporate into the AS flocs. Based on their capability to degrade aromatic compounds (primarily catechol; phenol; and cresols) at a concentration of 1 mg/mL and survive in 12.5% of the KPL, Pseudomonas putida OR45a and P. putida KB3 can be considered to be the best candidates for bioaugmentation of the AS among all of the bacteria tested. Genomic analyses of these two strains revealed the presence of the genes encoding enzymes related to the metabolism of aromatic compounds. Additionally, both microorganisms exhibited a high hydrophobic propensity (above 50%) and an ability to produce biosurfactants as well as high resistance to ammonium (above 600 g/mL) and heavy metals (especially chromium). These properties enable the exploitation of both bacterial strains in the bioremediation of the AS contaminated with the KPL. © 2020 by the authors.},

note = {19},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85061604241,

title = {Stability and instability processes in the calli of Fagopyrum tataricum that have different morphogenic potentials},

author = { A. Betekhtin and A. Piński and A. Milewska-Hendel and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85061604241&doi=10.1007%2fs11240-019-01575-w&partnerID=40&md5=645591d8a95ce3e965e098b879213554},

doi = {10.1007/s11240-019-01575-w},

issn = {01676857},

year  = {2019},

date = {2019-01-01},

journal = {Plant Cell, Tissue and Organ Culture},

volume = {137},

number = {2},

pages = {343-357},

publisher = {Springer Netherlands},

abstract = {The morphogenic callus (MC) of Fagopyrum tataricum contains a large amount of flavonoids, especially rutin, and exhibits a high level of antioxidant activity. A non-morphogenic callus (NC) may appear on the surface of the MC after two to three years of cultivation and is then subjected to a consistently high level of oxidative stress. The elucidation of the molecular background of this instability is essential for gaining a better understanding of the somaclonal variation mechanisms in tissue cultures that have different morphogenic potentials. Thus, in this study we show that continuous oxidative stress in a NC might be connected with a rapid senescence process and as a result, in the upregulation of the genes that are connected with the telomere complexity, ethylene biosynthesis and the expression of DNA methyltransferases. Moreover, we analysed the presence of the hydroxyproline-rich glycoproteins in the calli and demonstrated the differences between the MC and NC. The LM2 antibody can be useful as a marker of the cells in the MC that are embryogenically determined, while the MAC207 antibody seems to be a positive marker of a MC as its signal was absent in the NC. This study also provides the first report on the effect of trichostatin A on the DNA methyltransferases and demethylases in a MC. © 2019, The Author(s).},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85066960172,

title = {Hydroxyproline-rich glycoproteins as markers of temperature stress in the leaves of brachypodium distachyon},

author = { A. Piński and A. Betekhtin and K. Sala and K. Godel-Jędrychowska and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85066960172&doi=10.3390%2fijms20102571&partnerID=40&md5=83367841b3aa36bbcbe19816364135ad},

doi = {10.3390/ijms20102571},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {10},

publisher = {MDPI AG},

abstract = {Plants frequently encounter diverse abiotic stresses, one of which is environmental thermal stress. To cope with these stresses, plants have developed a range of mechanisms, including altering the cell wall architecture, which is facilitated by the arabinogalactan proteins (AGP) and extensins (EXT). In order to characterise the localisation of the epitopes of the AGP and EXT, which are induced by the stress connected with a low (4◦ C) or a high (40◦ C) temperature, in the leaves of Brachypodium distachyon, we performed immunohistochemical analyses using the antibodies that bind to selected AGP (JIM8; JIM13; JIM16; LM2 and MAC207), pectin/AGP (LM6) as well as EXT (JIM11; JIM12 and JIM20). The analyses of the epitopes of the AGP indicated their presence in the phloem and in the inner bundle sheath (JIM8; JIM13; JIM16 and LM2). The JIM16 epitope was less abundant in the leaves from the low or high temperature compared to the control leaves. The LM2 epitope was more abundant in the leaves that had been subjected to the high temperatures. In the case of JIM13 and MAC207, no changes were observed at the different temperatures. The epitopes of the EXT were primarily observed in the mesophyll and xylem cells of the major vascular bundle (JIM11; JIM12 and JIM20) and no correlation was observed between the presence of the epitopes and the temperature stress. We also analysed changes in the level of transcript accumulation of some of the genes encoding EXT, EXT-like receptor kinases and AGP in the response to the temperature stress. In both cases, although we observed the upregulation of the genes encoding AGP in stressed plants, the changes were more pronounced at the high temperature. Similar changes were observed in the expression profiles of the EXT and EXT-like receptor kinase genes. Our findings may be relevant for genetic engineering of plants with increased resistance to the temperature stress. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85065116283,

title = {Defining the genetic basis of plant–endophytic bacteria interactions},

author = { A. Piński and A. Betekhtin and K.T. Hupert-Kocurek and L.A.J. Mur and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85065116283&doi=10.3390%2fijms20081947&partnerID=40&md5=96b5990897aec8304bac8977b991dff7},

doi = {10.3390/ijms20081947},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {8},

publisher = {MDPI AG},

abstract = {Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as ‘omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {52},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85057991726,

title = {Cell wall epitopes and endoploidy as reporters of embryogenic potential in brachypodium distachyon callus culture},

author = { A. Betekhtin and M. Rojek-Jelonek and K. Nowak and A. Piński and A. Milewska-Hendel and E.U. Kurczyńska and J.H. Doonan and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85057991726&doi=10.3390%2fijms19123811&partnerID=40&md5=a019f7df04ed76fd5a1440b62abca7ae},

doi = {10.3390/ijms19123811},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {12},

publisher = {MDPI AG},

abstract = {Effective regeneration of callus tissue into embryos and then into whole plants is essential for plant biotechnology. The embryonic potential is often low and can further decrease with time in culture, which limits the utilisation of calli for transformation procedures and in vitro propagation. In this study, we show that the loss of embryogenic potential in callus cultures of Brachypodium distachyon is progressive over time. Flow cytometry analyses indicated endoploidy levels increased in 60-and 90-day-old calli with effective loss of the 2C DNA content peak in the latter. Analysis of indolic compounds content revealed a decrease in 60-and 90-day-old calli compared to either freshly isolated explants or 30-day-old calli. Immunohistochemical analysis revealed a decrease in arabinogalactan proteins (AGP) signal with the time of culture, but extensin (EXT) epitopes either increased (JIM12 epitopes) or decreased (JIM11 epitopes). The transcript accumulation levels of AGPs and EXTs confirmed these results, with most of AGP and EXT transcripts gradually decreasing. Some chimeric EXT transcripts significantly increased on the 30th day of culture, perhaps because of an increased embryogenic potential. Selected somatic embryogenesis-related genes and cyclins demonstrated a gradual decrease of transcript accumulation for YUCCA (YUC), AINTEGUMENTA-LIKE (AIL), BABY BOOM (BBM), and CLAVATA (CLV3) genes, as well as for most of the cyclins, starting from the 30th day of culture. Notably, WUSCHEL (WUS) transcript was detectable only on the 30th and 60th day and was not detectable in the zygotic embryos and in 90-day-old calli. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85048822480,

title = {Organic micropollutants paracetamol and ibuprofen—toxicity, biodegradation, and genetic background of their utilization by bacteria},

author = { J. Żur and A. Piński and A. Marchlewicz and K.T. Hupert-Kocurek and D. Wojcieszyńska and U. Guzik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85048822480&doi=10.1007%2fs11356-018-2517-x&partnerID=40&md5=bed6633cc8ff497e87e086da67cbead2},

doi = {10.1007/s11356-018-2517-x},

issn = {09441344},

year  = {2018},

date = {2018-01-01},

journal = {Environmental Science and Pollution Research},

volume = {25},

number = {22},

pages = {21498-21524},

publisher = {Springer Verlag},

abstract = {Currently, analgesics and nonsteroidal anti-inflammatory drugs (NSAIDs) are classified as one of the most emerging group of xenobiotics and have been detected in various natural matrices. Among them, monocyclic paracetamol and ibuprofen, widely used to treat mild and moderate pain are the most popular. Since long-term adverse effects of these xenobiotics and their biological and pharmacokinetic activity especially at environmentally relevant concentrations are better understood, degradation of such contaminants has become a major concern. Moreover, to date, conventional wastewater treatment plants (WWTPs) are not fully adapted to remove that kind of micropollutants. Bioremediation processes, which utilize bacterial strains with increased degradation abilities, seem to be a promising alternative to the chemical methods used so far. Nevertheless, despite the wide prevalence of paracetamol and ibuprofen in the environment, toxicity and mechanism of their microbial degradation as well as genetic background of these processes remain not fully characterized. In this review, we described the current state of knowledge about toxicity and biodegradation mechanisms of paracetamol and ibuprofen and provided bioinformatics analysis concerning the genetic bases of these xenobiotics decomposition. © 2018, The Author(s).},

note = {90},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85021369406,

title = {Genomic analysis of plant-associated bacteria and their potential in enhancing phytoremediation efficiency},

author = { A. Piński and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021369406&doi=10.12911%2f22998993%2f74281&partnerID=40&md5=072bd8a796ca987e1fc16e2af5c5e52f},

doi = {10.12911/22998993/74281},

issn = {2081139X},

year  = {2017},

date = {2017-01-01},

journal = {Journal of Ecological Engineering},

volume = {18},

number = {4},

pages = {152-159},

publisher = {Polish Society of Ecological Engineering (PTIE)},

abstract = {Phytoremediation is an emerging technology that uses plants in order to cleanup pollutants including xenobiotics and heavy metals from soil, water and air. Inoculation of plants with plant growth promoting endophytic and rhizospheric bacteria can enhance efficiency of phytoremediation. Genomic analysis of four plant-associated strains belonging to the Stenotrophomonas maltophilia species revealed the presence of genes encoding proteins involved in plant growth promotion, biocontrol of phytopathogens, biodegradation of xenobiotics, heavy metals resistance and plant-bacteria-environment interaction. The results of this analysis suggest great potential of bacteria belonging to Stenotrophomonas maltophilia species in enhancing phytoremediation efficiency.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85011672972,

title = {Genetic basis of endophytic bacteria-plant interactions [Genetyczne podłoze oddziałyawń bakterii endofitycznych z roslinami]},

author = { A. Piński and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85011672972&partnerID=40&md5=118d5da7c4e1d1f3c9c3477fb256b068},

issn = {00794252},

year  = {2016},

date = {2016-01-01},

journal = {Postepy Mikrobiologii},

volume = {55},

number = {4},

pages = {404-412},

publisher = {Polish Society of Microbiologists},

abstract = {Bacterial endophytes promote plant growth through colonization of the internal tissues of the plant without external signs of infection or negative effects on their host. Although endophytic bacteria enter the plant through the primary and lateral root hair cells, root cracks and wounds, they are found at many sites in the plants, such as stems, leaves, seeds, and xylem. The colonization of plant tissues comprises: host recognition, chemotactic migration of endophyte towards root exudates, adhesion to the surface of the root, penetration of the epidermidis and finally adaptation to a new environment. The distinctive features of endophytic bacteria are their flagellar motility, secretion of the cell-wall degrading enzymes (CWDEs) and biofilm-forming ability. It is postulated that endophytic bacteria capable of colonizing plants should contain at least a minimum set of genes responsible for their endophytic behavior. Among them, genes involved in chemotaxis and adhesion processes, secretion and translocation of effector proteins as well as genes which facilitate survival in reactiveoxygen rich environment can be distinguished. An important group of genes are the ones which encode regulatory proteins involved in the control of gene expression at the transcriptional level. However, in establishing an endophytic association with plants, species-specific gene-functions seem to be involved. Identification of genes responsible for endophytic behavior will increase our knowledge about the genetic aspects of plant-endophyte interactions and enable to fully exploit their potential.},

note = {2},

keywords = {},

pubstate = {published},

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