@article{2-s2.0-85149460033,

title = {Structure of the lipopolysaccharide O-antigen of endophytic Pseudomonas sp. strain L1},

author = { A. Choma and Z. Kaczyński and I. Komaniecka and A. Swatek and K. Kasperkiewicz and M. Pawlik and Z. Piotrowska-Seget},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85149460033&doi=10.1016%2fj.carres.2023.108779&partnerID=40&md5=1de182885720d739852b026656a7d36f},

doi = {10.1016/j.carres.2023.108779},

issn = {00086215},

year  = {2023},

date = {2023-01-01},

journal = {Carbohydrate Research},

volume = {525},

publisher = {Elsevier Ltd},

abstract = {The O-specific polysaccharide (OPS) was isolated from the lipopolysaccharide of Pseudomonas sp. Strain L1, the endophytic bacteria of Lolium perenne (ryegrass) plants growing in soil in an industrial area in the Silesia region (Zabrze; Southern Poland). The high-molecular-weight O-PS fraction liberated from Pseudomonas sp. L1 lipopolysaccharide by mild acid hydrolysis was studied using chemical methods, MALDI-TOF mass spectrometry, and 1D and 2D NMR spectroscopy techniques. It was found that the O-specific polysaccharide was built of tetrasaccharide repeating units composed of D-FucpN, D-Fucp4N, and two D-QuipN residues. The following structure of the O-PS of Pseudomonas sp. Strain L1 was established: [Formula presented] © 2023},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85147428219,

title = {Structure of the lipopolysaccharide O-antigen of Serratia spp. strains 10.1WK and 1XS plant endophytes isolated from O. biennis and L. corniculatus},

author = { A. Swatek and Z. Kaczyński and K. Kasperkiewicz and M. Pawlik and I. Komaniecka and A. Choma},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85147428219&doi=10.1016%2fj.carres.2023.108760&partnerID=40&md5=f8d1964e9ef0a34346bd78de7eb5d2ab},

doi = {10.1016/j.carres.2023.108760},

issn = {00086215},

year  = {2023},

date = {2023-01-01},

journal = {Carbohydrate Research},

volume = {524},

publisher = {Elsevier Ltd},

abstract = {O-specific polysaccharides (O-PSs) isolated from lipopolysaccharides of Serratia spp., strains 10.1WK and 1XS, which are endophytic bacteria of Oenothera biennis (common evening-primrose) and Lotus corniculatus (bird's-foot trefoil), plants growing on a petroleum hydrocarbon polluted site in the Silesia region, were investigated. The high-molecular-weight O-PS fractions liberated from lipopolysaccharides by mild acid hydrolysis were studied using chemical methods, MALDI-TOF mass spectrometry, and a set of 1D and 2D NMR spectroscopy techniques. It was found that both O-specific polysaccharides were built of an identical trisaccharide repeating unit composed of D-Rhap and D-Manp residues. The following structure of the O-PSs of Serratia spp. strains 10.1WK and 1XS was established: →4)-α-D-Rhap-(1 → 3)-β-D-Manp-(1 → 4)-β-D-Rhap–(1→ © 2023 Elsevier Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85132818018,

title = {Outer Membrane Vesicles as Mediators of Plant–Bacterial Interactions},

author = { M. Rudnicka and M. Noszczyńska and M. Malicka and K. Kasperkiewicz and M. Pawlik and Z. Piotrowska-Seget},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85132818018&doi=10.3389%2ffmicb.2022.902181&partnerID=40&md5=46f103a6c4d53db69a0da7d9312fbd41},

doi = {10.3389/fmicb.2022.902181},

issn = {1664302X},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Microbiology},

volume = {13},

publisher = {Frontiers Media S.A.},

abstract = {Plants have co-evolved with diverse microorganisms that have developed different mechanisms of direct and indirect interactions with their host. Recently, greater attention has been paid to a direct “message” delivery pathway from bacteria to plants, mediated by the outer membrane vesicles (OMVs). OMVs produced by Gram-negative bacteria play significant roles in multiple interactions with other bacteria within the same community, the environment, and colonized hosts. The combined forces of innovative technologies and experience in the area of plant–bacterial interactions have put pressure on a detailed examination of the OMVs composition, the routes of their delivery to plant cells, and their significance in pathogenesis, protection, and plant growth promotion. This review synthesizes the available knowledge on OMVs in the context of possible mechanisms of interactions between OMVs, bacteria, and plant cells. OMVs are considered to be potential stimulators of the plant immune system, holding potential for application in plant bioprotection. Copyright © 2022 Rudnicka, Noszczyńska, Malicka, Kasperkiewicz, Pawlik and Piotrowska-Seget.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85127813319,

title = {Ceftazidime/Avibactam and Other Commonly Used Antibiotics Activity Against Enterobacterales and Pseudomonas aeruginosa Isolated in Poland in 2015–2019},

author = { P. Zalas-Wiȩcek and M. Prażyńska and Ł. Pojnar and A. Pałka and D. Żabicka and M. Orczykowska and A. Polak and B. Możejko-Pastewka and E.A. Głowacka and I. Pieniążek and M. Pawlik and M. Grys and M. Bogiel},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85127813319&doi=10.2147%2fIDR.S344165&partnerID=40&md5=e7d52f22ddf39b74efc6e296cce3f713},

doi = {10.2147/IDR.S344165},

issn = {11786973},

year  = {2022},

date = {2022-01-01},

journal = {Infection and Drug Resistance},

volume = {15},

pages = {1289-1304},

publisher = {Dove Medical Press Ltd},

abstract = {Purpose: Infections caused by resistant Gram-negative bacteria are becoming increasingly common and now pose a serious public health threat worldwide, because they are difficult to treat due to few treatment options and they are associated with high morbidity and mortality. The combination of ceftazidime with the beta-lactamase inhibitor avibactam – seems to be the right choice in this situation. The aim of the study was to evaluate the activity of ceftazidime/avibactam and other commonly used antibiotics against Enterobacterales and Pseudomonas aeruginosa strains isolated within last years in Poland. Patients and Methods: This study analyzed the antibiotic susceptibility of 1607 Enterobacterales isolates and 543 nonfermenting P. aeruginosa strains collected between 2015 and 2019 in 4 medical laboratories participating in the ATLAS (Antimicrobial Testing Leadership And Surveillance) program in Poland. Unduplicated clinically significant Enterobacterales and P. aeruginosa strains were collected from patients with respiratory, skin and musculoskeletal, genitourinary, abdominal, bloodstream or other infections (ear; eye). Results: The ceftazidime/avibactam combination demonstrates the highest activity against Enterobacterales (98.9%), in both adults and children, including strains presenting MDR (multidrug-resistant) (97.5%) and ESBL (extended spectrum β-lactamase) (96.3%) phenotypes. The activity of ceftazidime/avibactam increased to 100% when only MBL (metallo-β-lactamase)-negative subset of Enterobacterales was considered. This combination also achieved the second highest activity result (89.3%) after colistin in P. aeruginosa, including isolates of MDR (65.9%) and carbapenem-resistant (CR) phenotypes (54.8%). When MBL-positive isolates were excluded, susceptibility rate of P. aeruginosa increased to 94.7%. It is worth to note that susceptibility of the examined P. aeruginosa strains to ceftazidime/avibactam was very high in children (93.3%), especially in a pediatric intensive care unit (94.2%). Conclusion: Enterobacterales and P. aeruginosa included in this analysis presented high susceptibility rates to ceftazidime/avibactam. Ceftazidime/avibactam showed the highest activity against Enterobacterales strains among all antibiotics studied, both for the total population as well as for MDR phenotype and ESBL phenotype. Ceftazidime/avibactam also achieved the second highest activity result against P. aeruginosa strains (including MDR and CR phenotypes). These results are much higher when excluding MBL-positive isolates that exhibit intrinsic resistance to ceftazidime/avibactam. © 2022 Zalas-Więcek et al.},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85110012338,

title = {CNN-Based Classifier as an Offline Trigger for the CREDO Experiment},

author = { M. Piekarczyk and O. Bar and Ł. Bibrzycki and M. Niedźwiecki and K. Rzecki and S. Stuglik and T. Andersen and N.M. Budnev and D.E. Alvarez-Castillo and K.A. Cheminant and D. Góra and A.C. Gupta and B. Hnatyk and P. Homola and R. Kamiński and M. Kasztelan and M. Knap and P. Kovács and B. Łozowski and J. Miszczyk and A. Mozgova and V. Nazari and M. Pawlik and M. Rosas and O. Sushchov and K. Smelcerz and K. Smolek and J. Stasielak and T. Wibig and K.W. Woźniak and J. Zamora-Saa},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85110012338&doi=10.3390%2fs21144804&partnerID=40&md5=543533453ac0e083b0c8cab96ea651cc},

doi = {10.3390/s21144804},

issn = {14248220},

year  = {2021},

date = {2021-01-01},

journal = {Sensors},

volume = {21},

number = {14},

publisher = {MDPI},

abstract = {Gamification is known to enhance users’ participation in education and research projects that follow the citizen science paradigm. The Cosmic Ray Extremely Distributed Observatory (CREDO) experiment is designed for the large-scale study of various radiation forms that contin-uously reach the Earth from space, collectively known as cosmic rays. The CREDO Detector app relies on a network of involved users and is now working worldwide across phones and other CMOS sensor-equipped devices. To broaden the user base and activate current users, CREDO extensively uses the gamification solutions like the periodical Particle Hunters Competition. However, the adverse effect of gamification is that the number of artefacts, i.e., signals unrelated to cosmic ray detection or openly related to cheating, substantially increases. To tag the artefacts appearing in the CREDO database we propose the method based on machine learning. The approach involves training the Convolutional Neural Network (CNN) to recognise the morphological difference between signals and artefacts. As a result we obtain the CNN-based trigger which is able to mimic the signal vs. artefact assignments of human annotators as closely as possible. To enhance the method, the input image signal is adaptively thresholded and then transformed using Daubechies wavelets. In this exploratory study, we use wavelet transforms to amplify distinctive image features. As a result, we obtain a very good recognition ratio of almost 99% for both signal and artefacts. The proposed solution allows eliminating the manual supervision of the competition process. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85096223947,

title = {Cosmic-ray extremely distributed observatory},

author = { B. Łozowski and P. Homola and D. Beznosko and G. Bhatta and Ł. Bibrzycki and M. Borczyńska and Ł. Bratek and N.M. Budnev and D. Burakowski and D.E. Alvarez-Castillo and K.A. Cheminant and A. Ćwikła and P. Dam-O and N. Dhital and A.R. Duffy and P. Głownia and K. Gorzkiewicz and D. Góra and A.C. Gupta and Z. Hlávková and M. Homola and J. Jałocha and R. Kamiński and M. Karbowiak and M. Kasztelan and R. Kierepko and M. Knap and P. Kovács and S. Kuliński and M. Magryś and M.V. Medvedev and J. Mędrala and J.W. Mietelski and J. Miszczyk and A. Mozgova and A. Napolitano and V. Nazari and Y.J. Ng and M. Niedźwiecki and C. Oancea and B. Ogan and G. Opiła and K. Oziomek and M. Pawlik and M. Piekarczyk and B. Poncyljusz and J. Pryga and M. Rosas and K. Rzecki and J. Zamora-Saa and K. Smelcerz and Authors. Other},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096223947&doi=10.3390%2fsym12111835&partnerID=40&md5=c7667f4387be3746f9e1408982698e98},

doi = {10.3390/sym12111835},

issn = {20738994},

year  = {2020},

date = {2020-01-01},

journal = {Symmetry},

volume = {12},

number = {11},

pages = {1-55},

publisher = {MDPI AG},

abstract = {The Cosmic-Ray Extremely Distributed Observatory (CREDO) is a newly formed, global collaboration dedicated to observing and studying cosmic rays (CR) and cosmic-ray ensembles (CRE): groups of at least two CR with a common primary interaction vertex or the same parent particle. The CREDO program embraces testing known CR and CRE scenarios, and preparing to observe unexpected physics, it is also suitable for multi-messenger and multi-mission applications. Perfectly matched to CREDO capabilities, CRE could be formed both within classical models (e.g.; as products of photon–photon interactions), and exotic scenarios (e.g.; as results of decay of Super-Heavy Dark Matter particles). Their fronts might be significantly extended in space and time, and they might include cosmic rays of energies spanning the whole cosmic-ray energy spectrum, with a footprint composed of at least two extensive air showers with correlated arrival directions and arrival times. As the CRE are predominantly expected to be spread over large areas and, due to the expected wide energy range of the contributing particles, such a CRE detection might only be feasible when using all available cosmic-ray infrastructure collectively, i.e., as a globally extended network of detectors. Thus, with this review article, the CREDO Collaboration invites the astroparticle physics community to actively join or to contribute to the research dedicated to CRE and, in particular, to pool together cosmic-ray data to support specific CRE detection strategies. © 2020, MDPI AG. All rights reserved. 

Authors: Homola, P.; Beznosko, D.; Bhatta, G.; Bibrzycki, Ł.; Borczyńska, M.; Bratek, Ł.; Budnev, N.M.; Burakowski, D.; Alvarez-Castillo, D.E.; Cheminant, K.A.; Ćwikła, A.; Dam-O, P.; Dhital, N.; Duffy, A.R.; Głownia, P.; Gorzkiewicz, K.; Góra, D.; Gupta, A.C.; Hlávková, Z.; Homola, M.; Jałocha, J.; Kamiński, R.; Karbowiak, M.; Kasztelan, M.; Kierepko, R.; Knap, M.; Kovács, P.; Kuliński, S.; Łozowski, B.; Magryś, M.; Medvedev, M.V.; Mędrala, J.; Mietelski, J.W.; Miszczyk, J.; Mozgova, A.; Napolitano, A.; Nazari, V.; Ng, Y.J.; Niedźwiecki, M.; Oancea, C.; Ogan, B.; Opiła, G.; Oziomek, K.; Pawlik, M.; Piekarczyk, M.; Poncyljusz, B.; Pryga, J.; Rosas, M.; Rzecki, K.; Zamora-Saa, J.; Smelcerz, K.; Smolek, K.; Stanek, W.; Stasielak, J.; Stuglik, S.; Sulma, J.; Sushchov, O.; Svanidze, M.; Tam, K.M.; Tursunov, A.; Vaquero, J.M.; Wibig, T.; Woźniak, K.W.},

note = {20},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85090893280,

title = {Comparison of two inoculation methods of endophytic bacteria to enhance phytodegradation efficacy of an aged petroleum hydrocarbons polluted soil},

author = { M. Pawlik and T. Płociniczak and S. Thijs and I. Pintelon and J. Vangronsveld and Z. Piotrowska-Seget},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090893280&doi=10.3390%2fagronomy10081196&partnerID=40&md5=f2f787ff1be30dda008aa9d732e2907f},

doi = {10.3390/agronomy10081196},

issn = {20734395},

year  = {2020},

date = {2020-01-01},

journal = {Agronomy},

volume = {10},

number = {8},

publisher = {MDPI AG},

abstract = {Endophyte-enhanced phytodegradation is a promising technology to clean up polluted soils. To improve the success rate of this nature-based remediation approach, it is important to advance the inoculation method as this has been shown to strongly affect the final outcome. However, studies evaluating inoculation strategies and their effect on hydrocarbon degradation are limited. This study aims to investigate two different manners of endophyte inoculation in Lolium perenne growing in an aged petroleum hydrocarbon polluted soil: (1) direct soil inoculation (SI), and (2) pre-inoculation of the caryopses followed by soil inoculation (PI). Different endophytic bacterial strains, Rhodococcus erythropolis 5WK and Rhizobium sp. 10WK, were applied individually as well as in combination. Depending on the method of inoculation, the petroleum hydrocarbon (PHC) degradation potential was significantly different. The highest PHC removal was achieved after pre-inoculation of ryegrass caryopses with a consortium of both bacterial strains. Moreover, both strains established in the aged-polluted soil and could also colonize the roots and shoots of L. perenne. Importantly, used endophytes showed the selective colonization of the environment compartments. Our findings show that the method of inoculation determines the efficiency of the phytodegradation process, especially the rate of PHC degradation. This study provides valuable information for choosing the most cost-effective and beneficial means to optimize phytodegradation. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).},

note = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85021779386,

title = {Hydrocarbon degradation potential and plant growth-promoting activity of culturable endophytic bacteria of Lotus corniculatus and Oenothera biennis from a long-term polluted site},

author = { M. Pawlik and B. Cania and S. Thijs and J. Vangronsveld and Z. Piotrowska-Seget},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021779386&doi=10.1007%2fs11356-017-9496-1&partnerID=40&md5=61028a54082d5dbe39342dba80f99a81},

doi = {10.1007/s11356-017-9496-1},

issn = {09441344},

year  = {2017},

date = {2017-01-01},

journal = {Environmental Science and Pollution Research},

volume = {24},

number = {24},

pages = {19640-19652},

publisher = {Springer Verlag},

abstract = {Many endophytic bacteria exert beneficial effects on their host, but still little is known about the bacteria associated with plants growing in areas heavily polluted by hydrocarbons. The aim of the study was characterization of culturable hydrocarbon-degrading endophytic bacteria associated with Lotus corniculatus L. and Oenothera biennis L. collected in long-term petroleum hydrocarbon-polluted site using culture-dependent and molecular approaches. A total of 26 hydrocarbon-degrading endophytes from these plants were isolated. Phylogenetic analyses classified the isolates into the phyla Proteobacteria and Actinobacteria. The majority of strains belonged to the genera Rhizobium, Pseudomonas, Stenotrophomonas, and Rhodococcus. More than 90% of the isolates could grow on medium with diesel oil, approximately 20% could use n-hexadecane as a sole carbon and energy source. PCR analysis revealed that 40% of the isolates possessed the P450 gene encoding for cytochrome P450-type alkane hydroxylase (CYP153). In in vitro tests, all endophytic strains demonstrated a wide range of plant growth-promoting traits such as production of indole-3-acetic acid, hydrogen cyanide, siderophores, and phosphate solubilization. More than 40% of the bacteria carried the gene encoding for the 1-aminocyclopropane-1-carboxylic acid deaminase (acdS). Our study shows that the diversity of endophytic bacterial communities in tested plants was different. The results revealed also that the investigated plants were colonized by endophytic bacteria possessing plant growth-promoting features and a clear potential to degrade hydrocarbons. The properties of isolated endophytes indicate that they have the high potential to improve phytoremediation of petroleum hydrocarbon-polluted soils. © 2017, The Author(s).},

note = {34},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85019267226,

title = {Improvement of phytoremediation of an aged petroleum hydrocarbon-contaminated soil by Rhodococcus erythropolis CD 106 strain},

author = { T. Płociniczak and E. Fic and M. Pacwa-Płociniczak and M. Pawlik and Z. Piotrowska-Seget},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85019267226&doi=10.1080%2f15226514.2016.1278420&partnerID=40&md5=2ccee0f9bdf71f304543948e2d5fd67f},

doi = {10.1080/15226514.2016.1278420},

issn = {15226514},

year  = {2017},

date = {2017-01-01},

journal = {International Journal of Phytoremediation},

volume = {19},

number = {7},

pages = {614-620},

publisher = {Taylor and Francis Inc.},

abstract = {The aim of this study was to assess the impact of soil inoculation with the Rhodococcus erythropolis CD 106 strain on the effectiveness of the phytoremediation of an aged hydrocarbon-contaminated [approx. 1% total petroleum hydrocarbon (TPH)] soil using ryegrass (Lolium perenne). The introduction of CD 106 into the soil significantly increased the biomass of ryegrass and the removal of hydrocarbons in planted soil. The fresh weight of the shoots and roots of plants inoculated with CD 106 increased by 49% and 30%, respectively. After 210 days of the experiment, the concentration of TPH was reduced by 31.2%, whereas in the planted, non-inoculated soil, it was reduced by 16.8%. By contrast, the concentration of petroleum hydrocarbon decreased by 18.7% in non-planted soil bioaugmented with the CD 106 strain. The rifampicin-resistant CD 106 strain survived after inoculation into soil and was detected in the soil during the entire experimental period, but the number of CD 106 cells decreased constantly during the enhanced phytoremediation and bioaugmentation experiments. The plant growth-promoting and hydrocarbon-degrading properties of CD 106, which are connected with its long-term survival and limited impact on autochthonous microflora, make this strain a good candidate for improving the phytoremediation efficiency of soil contaminated with hydrocarbons. © 2017 Taylor & Francis Group, LLC.},

note = {20},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84942428396,

title = {Endophytic bacteria and their role in environmental microbiology, medicine and industry [Bakterie endofityczne i ich znaczenie w mikrobiologii s̈rodowiskowej, medycynie i przemys̈le]},

author = { M. Pawlik and T. Płociniczak and Z. Piotrowska-Seget},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84942428396&partnerID=40&md5=05709f76f31dd8658cc135b2bf0a4e0a},

issn = {00794252},

year  = {2015},

date = {2015-01-01},

journal = {Postepy Mikrobiologii},

volume = {54},

number = {2},

pages = {115-122},

publisher = {Polish Society of Microbiologists},

abstract = {Endophytic bacteria have been known for more than 120 years. They live inside plant tissues without causing any apparent symptoms of disease or negative effects on the host. Each of the nearly 300 000 plant species that exist on the earth is host to one or more endophytes. Only a few of these plants have ever been completely studied relative to their endophytic biology. Consequently, the opportunity to find new and beneficial endophytic microorganisms among the diversity of plants in different ecosystems is considerable. During the long co-evolutionary process with their hosts, endophytes have developed many significant and novel characteristics. The relationships between plants and endophytic bacteria are very close. The endophytes which reside inside plant tissues can be classified as 'obligate' or 'facultative'. The first group is strictly dependent on the host plant for their growth and survival and transmission to other plants. The second group has a stage in their life cycle in which they are able to exist outside the host plant. Recent studies have shown that endophytes accelerate the adaptation of plants to unbalanced environmental conditions such as saline soil, drought, stress caused by pesticides, heavy metals or hydrocarbons. Therefore, the exploitation of the interaction of plant endophytes for the remediation of contaminated soils is a promising area; however, role of these microorganisms is still unclear.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}