Rozwój idei otwartej nauki na Uniwersytecie w Białymstoku

Artykuł skupia się na rozwoju otwartej nauki w Uniwersytecie w Białymstoku. Nawiązuje do najważniejszych wydarzeń związanych z otwartym dostępem na świecie i w Polsce. Wskazuje na korzyści i problemy wynikające z otwierania wyników pracy naukowej. Przedstawia też decyzje i przedsięwzięcia realizowane w ramach funkcjonowania Repozytorium Uniwersytetu w Białymstoku, będącego centrum działań w zakresie otwartej nauki. Podsumowuje plany dalszych kroków ku otwartości na uczelni, zarówno w sferze otwierania publikacji, jak i danych badawczych, zgodnie z potrzebami i wymaganiami, pojawiającymi się w środowisku [email protected] w BiałymstokuarXiv, https://arxiv.org/ (dostęp: 26.07.2023).Budapest Open Access Initiative, https://www.budapestopenaccessinitiative.org/read/ (dostęp: 26.07.2023).Directorate-General for Research and Innovation, Monitoring of the Open Access Policy by Horizon 2020, 2021, https://research-and-innovation.ec.europa.eu/knowledge-publications-tools-and-data/publications/all-publications/monitoring-open-access-policy-horizon-2020_en (dostęp: 26.07.2023).Gruenpeter N., Otwarte dane badawcze – nowe perspektywy, https://icm.edu.pl/blog/2021/11/12/otwarte-dane-badawcze-nowe-perspektywy (dostęp: 26.07.2023).Harnad S. i in., The Access/Impact Problem and the Green and Gold Roads to Open Access, „Serials Review” 2004, t. 30(4), https://www.sciencedirect.com/science/article/abs/pii/S0098791304001480 (dostęp: 26.07.2023).Narodowe Centrum Nauki, Otwarta nauka, https://www.ncn.gov.pl/finansowanie-nauki/otwarta-nauka (dostęp: 26.07.2023).Polityka Naukowa Państwa, https://www.gov.pl/web/edukacja-i-nauka/polityka-naukowa-panstwa-przyjeta-przez-rade-ministrow (dostęp: 26.07.2023).Ranking Web of Repositories, http://repositories.webometrics.info (dostęp: 26.07.2023).Ruiz-Conde E., Calderon-Martınez A., University Institutional Repositories: Competitive Environment and Their Role as Communication Media of Scientific Knowledge, „Scientometrics” 2014, nr 98, DOI: 10.1007/s11192-013-1159-5 (dostęp: 26.07.2023).Suber P., Open Access Overview: Focusing on Open Access to Peer-Reviewed Research Articles and Their Preprints, http://legacy.earlham.edu/~peters/fos/overview.htm (dostęp: 26.07.2023).Szafrański L., Realizacja polityki otwartego dostępu na przykładzie Uniwersytetu Jagiellońskiego w Krakowie, „Biblioteka” 2022, nr 26(35), s. 343–358, DOI: 10.14746/b.2022.26.12 (dostęp: 26.07.2023).Transparent Ranking: Institutional DATA Repositories by Google Scholar (February 2023), https://repositories.webometrics.info/en/data (dostęp: 26.07.2023).Zarządzenie nr 16 Rektora Uniwersytetu w Białymstoku z dnia l6 maja 2013 r. w sprawie utworzenia Repozytorium Uniwersytetu w Białymstoku, https://docs.uwb.edu.pl/pliki/2013-16-2.pdf (dostęp: 26.07.2023).Zarządzenie nr 17 Rektora Uniwersytetu w Białymstoku z dnia 16 maja 2013 r. w sprawie gromadzenia, przechowywania i udostępniania wersji elektronicznej rozpraw doktorskich dopuszczonych do publicznej obrony na Uniwersytecie w Białymstoku, https://docs.uwb.edu.pl/pliki/2013-17-1.pdf (dostęp: 26.07.2023).738

Pan-Genome Portrait of Bacillus mycoides Provides Insights into the Species Ecology and Evolution

Bacillus mycoides is poorly known despite its frequent occurrence in a wide variety of environments. To provide direct insight into its ecology and evolutionary history, a comparative investigation of the species pan-genome and the functional gene categorization of 35 isolates obtained from soil samples from northeastern Poland was performed. The pan-genome of these isolates is composed of 20,175 genes and is characterized by a strong predominance of adaptive genes (∼83%), a significant amount of plasmid genes (∼37%), and a great contribution of prophages and insertion sequences. The pan-genome structure and phylodynamic studies had suggested a wide genomic diversity among the isolates, but no correlation between lineages and the bacillus origin was found. Nevertheless, the two B. mycoides populations, one from Białowieża National Park, the last European natural primeval forest with soil classified as organic, and the second from mineral soil samples taken in a farm in Jasienówka, a place with strong anthropogenic pressure, differ significantly in the frequency of genes encoding proteins enabling bacillus adaptation to specific stress conditions and production of a set of compounds, thus facilitating their colonization of various ecological niches. Furthermore, differences in the prevalence of essential stress sigma factors might be an important trail of this process. Due to these numerous adaptive genes, B. mycoides is able to quickly adapt to changing environmental conditions.Izabela Święcicka: [email protected] Fiedoruk - Department of Microbiology, Medical University of Bialystok, Bialystok, PolandJustyna M. Drewnowska - Department of Microbiology, Faculty of Biology, University of Bialystok, Bialystok, PolandJacques Mahillon - Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, BelgiumMonika Zambrzycka - Department of Microbiology, Faculty of Biology, University of Bialystok, Bialystok, PolandIzabela Święcicka - Department of Microbiology, Faculty of Biology, University of Bialystok, Bialystok, Poland; Laboratory of Applied Microbiology, Faculty of Biology, University of Bialystok, Bialystok, PolandSwiecicka I, De Vos P. 2003. Properties of Bacillus thuringiensis isolated from bank voles. J Appl Microbiol 94:60–64. https://doi.org/10.1046/j.1365-2672.2003.01790.x.Ceuppens S, Boon N, Uyttendaele M. 2013. Diversity of Bacillus cereus group strains is reflected in their broad range of pathogenicity and diverse ecological lifestyles. FEMS Microbiol Ecol 84:433–450. https://doi.org/10.1111/1574-6941.12110.Vidic J, Chaix C, Manzano M, Heyndrickx M. 2020. Food sensing: detection of Bacillus cereus spores in dairy products. Biosensors 10:15. https://doi.org/10.3390/bios10030015.Swiecicka I. 2008. Natural occurrence of Bacillus thuringiensis and Bacillus cereus in eukaryotic organisms: a case for symbiosis. Biocontrol Sci Technol 18:221–239. https://doi.org/10.1080/09583150801942334.Mock M, Fouet A. 2001. Anthrax. Annu Rev Microbiol 55:647–671. https://doi.org/10.1146/annurev.micro.55.1.647.Stenfors Arnesen LP, Fagerlund A, Granum PE. 2008. From soil to gut: Bacillus cereus and its food poisoning toxins. FEMS Microbiol Rev 32:579–606. https://doi.org/10.1111/j.1574-6976.2008.00112.x.Drewnowska JM, Stefanska N, Czerniecka M, Zambrowski G, Swiecicka I.2020. Potential enterotoxicity of phylogenetically diverse Bacillus cereus sensu lato soil isolates from different geographical locations. Appl Environ Microbiol 86:e03032-19. https://doi.org/10.1128/AEM.03032-19.Swiecicka I, Bideshi DK, Federici BA. 2008. Novel isolate of Bacillus thuringiensis subsp. thuringiensis that produces a quasicuboidal crystal of Cry1Ab21 toxic to larvae of Trichoplusia ni. Appl Environ Microbiol 74:923–930. https://doi.org/10.1128/AEM.01955-07.Jiménez G, Blanch AR, Tamames J, Rosselló-Mora R. 2013. Complete genome sequence of Bacillus toyonensis BCT-7112T, the active ingredient of the feed additive preparation Toyocerin. Genome Announc 1:e01080-13. https://doi.org/10.1128/genomeA.01080-13.Liu Y, Lai Q, Shao Z. 2018. Genome analysis-based reclassification of Bacillus weihenstephanensis as a later heterotypic synonym of Bacillus mycoides. Int J Syst Evol Microbiol 68:106–112. https://doi.org/10.1099/ijsem.0.002466.Lechner S, Mayr R, Francis K, Prüss BM, Kaplan T, Wiessner-Gunkel E, Stewart GS, Scherer S. 1998. Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. Int J Syst Bacteriol 48:1373–1382. https://doi.org/10.1099/00207713-48-4-1373.Liu Y, Lai Q, Göker M, Meier-Kolthoff JP, Wang M, Sun Y, Wang L, Shao Z. 2015. Genomic insights into the taxonomic status of the Bacillus cereus group. Sci Rep 5:14082. https://doi.org/10.1038/srep14082.Drewnowska JM, Swiecicka I. 2013. Eco-genetic structure of Bacillus cereus sensu lato populations from different environments in Northeastern Poland. PLoS One 8:e80175. https://doi.org/10.1371/journal.pone.0080175.Soufiane B, Côté J-C. 2013. Bacillus weihenstephanensis characteristics are present in Bacillus cereus and Bacillus mycoides strains. FEMS Microbiol Lett 341:127–137. https://doi.org/10.1111/1574-6968.12106.Guinebretière M-H, Thompson FL, Sorokin A, Normand P, Dawyndt P, Ehling-Schulz M, Svensson B, Sanchis V, Nguyen-The C, Heyndrickx M, De Vos P. 2008. Ecological diversification in the Bacillus cereus group. Environ Microbiol 10:851–865. https://doi.org/10.1111/j.1462-2920.2007.01495.x.Swiecicka I, Bartoszewicz M, Kasulyte-Creasey D, Drewnowska JM, Murawska E, Yernazarova A, Lukaszuk E, Mahillon J. 2013. Diversity of thermal ecotypes and potential pathotypes of Bacillus thuringiensis soil isolates. FEMS Microbiol Ecol 85:262–272. https://doi.org/10.1111/1574-6941.12116.Fiedoruk K, Drewnowska JM, Daniluk T, Leszczynska K, Iwaniuk P, Swiecicka I. 2017. Ribosomal background of the Bacillus cereus group thermotypes. Sci Rep 7:46430. https://doi.org/10.1038/srep46430.Drewnowska JM, Fiodor A, Barboza-Corona JE, Swiecicka I. 2020. Chitinolytic activity of phylogenetically diverse Bacillus cereus sensu lato from natural environments. Syst Appl Microbiol 43:126075. https://doi.org/10.1016/j.syapm.2020.126075.Drewnowska JM, Zambrzycka M, Kalska-Szostko B, Fiedoruk K, Swiecicka I. 2015. Melanin-like pigment synthesis by soil Bacillus weihenstephanensis isolates from Northeastern Poland. PLoS One 10:e0125428. https://doi.org/10.1371/journal.pone.0125428.Makart L, Commans F, Gillis A, Mahillon J. 2017. Horizontal transfer of chromosomal markers mediated by the large conjugative plasmid pXO16 from Bacillus thuringiensis serovar israelensis. Plasmid 91:76–81. https://doi.org/10.1016/j.plasmid.2017.04.001.Hu X, Huang D, Ogalo J, Geng P, Yuan Z, Xiong H, Wan X, Sun J. 2020. Application of Bacillus thuringiensis strains with conjugal and mobilizing capability drives gene transmissibility within Bacillus cereus group populations in confined habitats. BMC Microbiol 20:363. https://doi.org/10.1186/s12866-020-02047-4.Swiecicka I, Mahillon J. 2005. The clonal structure of Bacillus thuringiensis isolates from north-east Poland does not correlate with their cry gene diversity. Environ Microbiol 7:34–39. https://doi.org/10.1111/j.1462-2920.2004.00662.xVan der Auwera G, Mahillon J. 2008. Transcriptional analysis of the conjugative plasmid pAW63 from Bacillus thuringiensis. Plasmid 60:190–199. https://doi.org/10.1016/j.plasmid.2008.07.003.Fiedoruk K, Daniluk T, Mahillon J, Leszczynska K, Swiecicka I. 2017. Genetic environment of cry1 genes indicates their common origin. Genome Biol Evol 9:2265–2275. https://doi.org/10.1093/gbe/evx165.Fayad N, Kallassy Awad M, Mahillon J. 2019. Diversity of Bacillus cereus sensu lato mobilome. BMC Genomics 20:436. https://doi.org/10.1186/s12864-019-5764-4.Gillis A, Fayad N, Makart L, Bolotin A, Sorokin A, Kallassy M, Mahillon J. 2018. Role of plasmid plasticity and mobile genetic elements in the entomopathogen Bacillus thuringiensis serovar isrealensis. FEMS Microbiol Rev 42:829–856. https://doi.org/10.1093/femsre/fuy034.Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. 2005. The microbial pan-genome. Curr Opin Genet Dev 15:589–594. https://doi.org/10.1016/j.gde.2005.09.006.Yu J, Zhao J, Song Y, Zhang J, Yu Z, Zhang H, Sun Z. 2018. Comparative genomics of the herbivore gut symbiont Lactobacillus reuteri reveals genetic diversity and lifestyle adaptation. Front Microbiol 9:1151. https://doi.org/10.3389/fmicb.2018.01151.Azarian T, Huang I-T, Hanage WP. 2020. Structure and dynamics of bacterial populations: pangenome ecology, p 115–128. In Tettelin H, Medini D (ed), The pangenome: diversity, dynamics and evolution of genomes. Springer International Publishing, Cham, Switzerland.Laing CR, Whiteside MD, Gannon VPJ. 2017. Pan-genome analyses of the species Salmonella enterica, and identification of genomic markers predictive for species, subspecies, and serovar. Front Microbiol 8:1345. https://doi.org/10.3389/fmicb.2017.01345.Zhang X, Liu Z, Wei G, Yang F, Liu X. 2018. In silico genome-wide analysis reveals the potential links between core genome of Acidithiobacillus thiooxidans and its autotrophic lifestyle. Front Microbiol 9:1255. https://doi.org/10.3389/fmicb.2018.01255.Romaniuk K, Golec P, Dziewit L. 2018. Insight into the diversity and possible role of plasmids in the adaptation of psychrotolerant and metalotolerant Arthrobacter spp. to extreme Antarctic environments. Front Microbiol 9:3144. https://doi.org/10.3389/fmicb.2018.03144.Koskella B, Vos M. 2015. Adaptation in natural microbial populations. Annu Rev Ecol Evol Syst 46:503–522. https://doi.org/10.1146/annurev-ecolsys-112414-054458.Inglin RC, Meile L, Stevens MJA. 2018. Clustering of pan- and core-genome of Lactobacillus provides novel evolutionary insights for differentiation. BMC Genomics 19:284. https://doi.org/10.1186/s12864-018-4601-5.Bazinet AL. 2017. Pan-genome and phylogeny of Bacillus cereus sensu lato. BMC Evol Biol 17:176. https://doi.org/10.1186/s12862-017-1020-1.Nourdin-Galindo G, Sánchez P, Molina CF, Espinoza-Rojas DA, Oliver C, Ruiz P, Vargas-Chacoff L, Cárcamo JG, Figueroa JE, Mancilla M, MaracajaCoutinho V, Yañez AJ. 2017. Comparative pan-genome analysis of Piscirickettsia salmonis reveals genomic divergences within genogroups. Front Cell Infect Microbiol 7:459. https://doi.org/10.3389/fcimb.2017.00459.Collingro A, Tischler P, Weinmaier T, Penz T, Heinz E, Brunham RC, Read TD, Bavoil PM, Sachse K, Kahane S, Friedman MG, Rattei T, Myers GSA, Horn M. 2011. Unity in variety–the pan-genome of the Chlamydiae. Mol Biol Evol 28:3253–3270. https://doi.org/10.1093/molbev/msr161.Kim Y, Koh I, Young Lim M, Chung W-H, Rho M. 2017. Pan-genome analysis of Bacillus for microbiome profiling. Sci Rep 7:10984. https://doi.org/10.1038/s41598-017-11385-9.Hoton FM, Andrup L, Swiecicka I, Mahillon J. 2005. The cereulide genetic determinants of emetic Bacillus cereus are plasmid-borne. Microbiology (Reading) 151:2121–2124. https://doi.org/10.1099/mic.0.28069-0.Murawska E, Fiedoruk K, Swiecicka I. 2014. Modular genetic architecture of the toxigenic plasmid pIS56-63 harboring cry1Ab21 in Bacillus thuringiensis subsp. thuringiensis strain IS5056. Pol J Microbiol 63:147–156. https://doi.org/10.33073/pjm-2014-020.Mahillon J, Chandler M. 1998. Insertion sequences. Microbiol Mol Biol Rev 62:725–774. https://doi.org/10.1128/MMBR.62.3.725-774.1998.Pinto D, da Fonseca RR. 2020. Evolution of the extracytoplasmic function s factor protein family. NAR Genom Bioinform 2:lqz026. https://doi.org/10.1093/nargab/lqz026.Schmidt TR, Scott EJ, Dyer DW. 2011. Whole-genome phylogenies of the family Bacillaceae and expansion of the sigma factor gene family in the Bacillus cereus species-group. BMC Genomics 12:430. https://doi.org/10.1186/1471-2164-12-430.Van Schaik W, Tempelaars MH, Wouters JA, de Vos WM, Abee T. 2004. The alternative sigma factor sB of Bacillus cereus: response to stress and role in heat adaptation. J Bacteriol 186:316–325. https://doi.org/10.1128/JB.186.2.316-325.2004.Fayad N, Kambris Z, El Chamy L, Mahillon J, Kallassy Awad M. 2021. A novel antidipterian Bacillus thuringiensis strain: unusual Cry toxin genes in a high dynamic plasmid environment. Appl Environ Microbiol 87:e02294-20. https://doi.org/10.1128/AEM.02294-20.Carroll LM, Wiedmann M, Kovac J. 2020. Proposal of a taxonomic nomenclature for the Bacillus cereus group which reconciles genomic definitions of bacterial species with clinical and industrial phenotypes. mBio 11: e00034-20. https://doi.org/10.1128/mBio.00034-20.Yoshida K-i, Yamaguchi M, Morinaga T, Kinehara M, Ikeuchi M, Ashida H, Fujita Y. 2008. myo-Inositol catabolism in Bacillus subtilis. J Biol Chem 283:10415–10424. https://doi.org/10.1074/jbc.M708043200.Gonzalez-Uarquin F, Rodehutscord M, Huber K. 2020. myo-Inositol: its metabolism and potential implication for poultry nutrition – a review. Poult Sci 99:893–905. https://doi.org/10.1016/j.psj.2019.10.014.Xin B, Zheng J, Xu Z, Song X, Ruan L, Peng D, Sun M. 2015. The Bacillus cereus group is an excellent reservoir of novel lanthipeptides. Appl Environ Microbiol 81:1765–1774. https://doi.org/10.1128/AEM.03758-14.Wu J, Samara NL, Kuraoka I, Yang W. 2019. Evolution of inosine-specific endonuclease V from bacterial DNase to eukaryotic RNase. Mol Cell 76:44–56. https://doi.org/10.1016/j.molcel.2019.06.046.Caulier S, Nannan C, Gillis A, Licciardi F, Bragard C, Mahillon J. 2019. Overview of the antimicrobial compounds produced by members of the Bacillus subtilis group. Front Microbiol 10:302. https://doi.org/10.3389/fmicb.2019.00302.de la Fuente-Salcido N, Guadalupe Alanís-Guzmán M, Bideshi DK, SalcedoHernández R, Bautista-Justo M, Barboza-Corona JE. 2008. Enhanced synthesis and antimicrobial activities of bacteriocins produced by Mexican strains of Bacillus thuringiensis. Arch Microbiol 190:633–640. https://doi.org/10.1007/s00203-008-0414-2.Abriouel H, Franz CMAP, Omar NB, Gálvez A. 2011. Diversity and applications of Bacillus bacteriocins. FEMS Microbiol Rev 35:201–232. https://doi.org/10.1111/j.1574-6976.2010.00244.x.Raymond B, Wyres KL, Sheppard SK, Ellis RJ, Bonsall MB. 2010. Environmental factors determining the epidemiology and population genetic structure of the Bacillus cereus group in the field. PLoS Pathog 6: e1000905. https://doi.org/10.1371/journal.ppat.1000905.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170.Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, Fookes M, Falush D, Keane JA, Parkhill J. 2015. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691–3693. https://doi.org/10.1093/bioinformatics/btv421.Kaas RS, Friis C, Ussery DW, Aarestrup FM. 2012. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC Genomics 13:577. https://doi.org/10.1186/1471-2164-13-577.Minkin I, Patel A, Kolmogorov M, Vyahhi N, Pham S. 2013. Sibelia: a scalable and comprehensive synteny block generation tool for closely related microbial genomes. p 215–229. In Darling A, Stoye J (ed), Lecture Notes in Computer Science vol 8126. Springer, Berlin, Germany.Jesus TF, Ribeiro-Gonçalves B, Silva DN, Bortolaia V, Ramirez M, Carriço JA. 2019. Plasmid ATLAS: plasmid visual analytics and identification in highthroughput sequencing data. Nucleic Acids Res 47:D188–D194. https://doi.org/10.1093/nar/gky1073.Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS. 2016. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44:W16–W21. https://doi.org/10.1093/nar/gkw387.Xie Z, Tang H. 2017. ISEScan: automated identification of insertion sequence elements in prokaryotic genomes. Bioinformatics 33:3340–3347. https://doi.org/10.1093/bioinformatics/btx433.Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E. 2014. Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol Biol Evol 31:1077–1088. https://doi.org/10.1093/molbev/msu088.Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD, Croucher NJ. 2019. Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Res 29:304–316. https://doi.org/10.1101/gr.241455.118.Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P. 2019. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2 502 viruses. Nucleic Acids Res 47:D309–D314. https://doi.org/10.1093/nar/gky1085Kanehisa M, Sato Y, Morishima K. 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428:726–731. https://doi.org/10.1016/j.jmb.2015.11.006.Murawska E, Fiedoruk K, Bideshi DK, Swiecicka I. 2013. Complete genome sequence of Bacillus thuringiensis subsp. thuringiensis IS50056, an isolate highly toxic to Trichoplusia ni. Genome Announc 21:e0010813. https://doi.org/10.1128/genomeA.00108-13.9111

Potential Enterotoxicity of Phylogenetically Diverse Bacillus cereus Sensu Lato Soil Isolates from Different Geographical Locations

Bacillus cereus sensu lato comprises Gram-positive spore-forming bacteria producing toxins associated with foodborne diseases. Three pore-forming enterotoxins, nonhemolytic enterotoxin (Nhe), hemolysin BL (Hbl), and cytotoxin K (CytK), are considered the primary factors in B. cereus sensu lato diarrhea. The aim of this study was to determine the potential risk of enterotoxicity among soil B. cereus sensu lato isolates representing diverse phylogroups and originated from different geographic locations with various climates (Burkina Faso, Kenya, Argentina, Kazakhstan, and Poland). While nheA- and hblA-positive isolates were present among all B. cereus sensu lato populations and distributed across all phylogenetic groups, cytK-2-positive strains predominated in geographic regions with an arid hot climate (Africa) and clustered together on a phylogenetic tree mainly within mesophilic groups III and IV. The highest in vitro cytotoxicity to Caco-2 and HeLa cells was demonstrated by the strains clustered within phylogroups II and IV. Overall, our results suggest that B. cereus sensu lato pathogenicity is a comprehensive process conditioned by many intracellular factors and diverse environmental conditions.Izabela Święcicka - [email protected] Drewnowska - Department of Microbiology, Faculty of Biology, University of Bialystok, Bialystok, PolandNatalia Stefańska - Department of Microbiology, Faculty of Biology, University of Bialystok, Bialystok, PolandMagdalena Czerniecka - Department of Cytobiochemistry, Faculty of Biology, University of Bialystok, Bialystok, Poland; Laboratory of Tissue Culture, Faculty of Biology, University of Bialystok, Bialystok, PolandGrzegorz Zambrowski - Laboratory of Applied Microbiology, University of Bialystok, Bialystok, PolandIzabela Święcicka - Department of Microbiology, Faculty of Biology, University of Bialystok, Bialystok, Poland; Laboratory of Applied Microbiology, University of Bialystok, Bialystok, PolandMock M, Fouet A. 2001. Anthrax. Annu Rev Microbiol 55:647–671. https://doi.org/10.1146/annurev.micro.55.1.647Murawska E, Fiedoruk K, Swiecicka I. 2014. Modular genetic architecture of the toxigenic plasmid pIS56-63 harboring cry1Ab21 in Bacillus thuringiensis subsp. thuringiensis strain IS5056. Pol J Microbiol 63:147–156. https://doi.org/10.33073/pjm-2014-020.Stenfors Arnesen LP, Fagerlund A, Granum PE. 2008. From soil to gut: Bacillus cereus and its food poisoning toxins. FEMS Microbiol Rev 32: 579 – 606. https://doi.org/10.1111/j.1574-6976.2008.00112.x.Dierick K, Van Coillie E, Swiecicka I, Meyfroidt G, Devlieger H, Meulemans A, Hoedemaekers G, Fourie L, Heyndrickx M, Mahillon J. 2005. Fatal family outbreak of Bacillus cereus-associated food poisoning. J Clin Microbiol 43:4277– 4279. https://doi.org/10.1128/JCM.43.8.4277-4279.2005.Swiecicka I, Bideshi DK, Federici BA. 2008. Novel isolate of Bacillus thuringiensis subsp. thuringiensis that produces a quasi-cuboidal crystal of Cry1Ab21 toxic to larvae of Trichoplusia ni. Appl Environ Microbiol 74:923–930. https://doi.org/10.1128/AEM.01955-07.Guinebretiere M-H, Auger S, Galleron N, Contzen M, De Sarrau B, De Buyser M-L, Lamberet G, Fagerlund A, Granum PE, Lereclus D, De Vos P, Nguyen-The C, Sorokin A. 2013. Bacillus cytotoxicus sp. nov. is a novel thermotolerant species of the Bacillus cereus group occasionally associated with food poisoning. Int J Syst Evol Micriobiol 63:31– 40. https://doi.org/10.1099/ijs.0.030627-0.Miller R, Beno SM, Kent DJ, Carroll LM, Martin NM, Boor KJ, Kovac J. 2016. Bacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments. Int J Syst Evol Microbiol 66:4744 – 4753. https://doi.org/10.1099/ijsem.0.001421.Jiménez G, Blanch AR, Tamames J, Rosselló-Mora R. 2013. Complete genome sequence of Bacillus toyonnsis BCT-7112T, the active ingredient of the feed additive preparation Toyocerin. Genome Announc 1:e01080-13. https://doi.org/10.1128/genomeA.01080-13.Lechner S, Mayr R, Francis KP, Prüss BM, Kaplan T, Wiessner-Gunkel E, Stewart GS, Scherer S. 1998. Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. Int J Syst Evol Microbiol 48:1373–1382. https://doi.org/10.1099/00207713-48-4-1373.Nakamura LK. 1998. Bacillus pseudomycoides sp. nov. Int J Syst Evol Microbiol 48:1031–1035. https://doi.org/10.1099/00207713-48-3-1031.Liu Y, Lai Q, Shao Z. 2018. Genome analysis-based reclassification of Bacillus weihenstephanensis as a later heterotypic synonym of Bacillus mycoides. Int J Syst Evol Microbiol 68:106 –112. https://doi.org/10.1099/ijsem.0.002466.Thorsen L, Hansen BM, Nielsen KF, Hendriksen NB, Phipps RK, Budde BB. 2006. Characterization of emetic Bacillus weihenstephanensis, a new cereulide-producing bacterium. Appl Environ Microbiol 72:5118 –5121.https://doi.org/10.1128/AEM.00170-06.Jung MY, Kim JS, Paek WK, Lim J, Lee H, Kim PI, Ma JY, Kim W, Chan YH. 2011. Bacillus manliponensis sp. nov., a new member of the Bacillus cereus group isolated from foreshore tidal flat sediment. J Microbiol 49:1027–1032. https://doi.org/10.1007/s12275-011-1049-6.Jung MY, Paek WK, Park IS, Han JR, Sin Y, Paek J, Rhee MS, Kim H, Song HS, Chang YH. 2010. Bacillus gaemokensis sp. nov., isolated from foreshore tidal flat sediment from the Yellow Sea. J Microbiol 48:867– 871. https://doi.org/10.1007/s12275-010-0148-0.Cheng T, Lin P, Jin S, Wu Y, Fu B, Long R, Liu D, Guo Y, Peng L, Xia Q. 2014. Complete genome sequence of Bacillus bombysepticus, a pathogen leading to Bombyx mori Black Chest Septicemia. Genome Announc 2:e00312-14. https://doi.org/10.1128/genomeA.00312-14.Liu B, Liu GH, Hu GP, Sengonca C, Lin NQ, Tang JY, Tang WQ, Lin YZ. 2014. Bacillus bingmayongensis sp. nov., isolated from the pit soil of Emperor Qin’s terra-cotta warriors in China. Antonie Van Leeuwenhoek 105:995. https://doi.org/10.1007/s10482-014-0150-3.Liu Y, Du J, Lai Q, Zeng R, Ye D, Xu J, Shao Z. 2017. Proposal of nine novel species of the Bacillus cereus group. Int J Syst Evol Microbiol 67:2499 –2508. https://doi.org/10.1099/ijsem.0.001821.Castiaux V, Laloux L, Schneider YJ, Mahillon J. 2016. Screening of cytotoxic B. cereus on differentiated Caco-2 cells and in co-culture with mucus-secreting (HT29-MTX) cells. Toxins 8:320. https://doi.org/10.3390/toxins8110320.Jessberger N, Krey VM, Rademacher C, Böhm ME, Mohr AK, Ehling-Schulz M, Scherer S, Märtlbauer E. 2015. From genome to toxicity: a combinatory approach highlights the complexity of enterotoxin production in Bacillus cereus. Front Microbiol 6:560. https://doi.org/10.3389/fmicb.2015.00560.Wijnands LM, Dufrenne JB, Rombouts FM, In ’t Veld PH, van Leusden FM. 2006. Prevalence of potentially pathogenic Bacillus cereus in food commodities in the Netherlands. J Food Prot 69:2587–2594. https://doi.org/10.4315/0362-028X-69.11.2587.Miller RA, Jian J, Beno SM, Wiedmann M, Kovac J. 2018. Intraclade variability in toxin production and cytotoxicity of Bacillus cereus group type strains and dairy-associated isolates. Appl Environ Microbiol 84:e02479-17. https://doi.org/10.1128/AEM.02479-17.Drewnowska JM, Swiecicka I. 2013. Eco-genetic structure of Bacillus cereus sensu lato populations from different environments in northeastern Poland. PLoS One 8:e80175. https://doi.org/10.1371/journal.pone.0080175.Bartoszewicz M, Czyz˙ewska U. 2017. Spores and vegetative cells of phenotypically and genetically diverse Bacillus cereus sensu lato are common bacteria in fresh water of northeastern Poland. Can J Microbiol 63:939 –950. https://doi.org/10.1139/cjm-2017-0337.Da Riol C, Dietrich R, Märtlbauer E, Jessberger N. 2018. Consumed foodstuffs have a crucial impact on the toxic activity of enteropathogenic Bacillus cereus. Front Microbiol 9:1946. https://doi.org/10.3389/fmicb.2018.01946.Tewari A, Abdullah S. 2015. Bacillus cereus food poisoning: international and Indian perspective. J Food Sci Technol 52:2500 –2511. https://doi.org/10.1007/s13197-014-1344-4.Kroten´ MA, Bartoszewicz M, S´wie˛cicka I. 2010. Cereulide and valinomycin, two import ant natural dodecadepsipeptides with ionophoretic activities. Pol J Microbiol 59:3–10. https://doi.org/10.33073/pjm-2010-001.European Food Safety Authority, European Centre for Disease Prevention and Control. 2018. The European Union summary report on trends and sources of zoonoses, zoonotic agents and foodborne outbreaks 2017. EFSA J 16:e05500.Lund T, De Buyser ML, Granum PE. 2000. A new cytotoxin from Bacillus cereus that may cause necrotic enteritis. Mol Microbiol 38:254 –261. https://doi.org/10.1046/j.1365-2958.2000.02147.xFagerlund A, Ween O, Lund T, Hardy SP, Granum PE. 2004. Genetic and functional analysis of the cytK family of genes in Bacillus cereus. Microbiology 150:2689 –2697. https://doi.org/10.1099/mic.0.26975-0Gohar M, Faegri K, Perchat S, Ravnum S, Økstad OA, Gominet M, Kolstø AB, Lereclus D. 2008. The PlcR virulence regulon of Bacillus cereus. PLoS One 3:e2793. https://doi.org/10.1371/journal.pone.0002793Grenha R, Slamti L, Nicaise M, Refes Y, Lereclus D, Nessler S. 2013. Structural basis for the activation mechanism of the PlcR virulence regulator by the quorum-sensing signal peptide PapR. Proc Natl Acad Sci U S A 110:1047–1052. https://doi.org/10.1073/pnas.1213770110.Böhm ME, Huptas C, Krey VM, Scherer S. 2015. Massive horizontal gene transfer, strictly vertical inheritance and ancient duplications differentially shape the evolution of Bacillus cereus enterotoxin operons hbl,cytK and nhe. BMC Evol Biol 15:246. https://doi.org/10.1186/s12862-015-0529-4.Kaminska PS, Yernazarova A, Murawska E, Swiecicki J, Fiedoruk K, Bideshi DK, Swiecicka I. 2014. Comparative analysis of quantitative reverse transcription real-time PCR and commercial enzyme immunoassays for detection of enterotoxigenic Bacillus thuringiensis isolates. FEMS Microbiol Lett 357:34 –39. https://doi.org/10.1111/1574-6968.12503.Swiecicka I, Bartoszewicz M, Kasulyte-Creasey D, Drewnowska JM, Murawska E, Yernazarova A, Lukaszuk E, Mahillon J. 2013. Diversity of thermal ecotypes and potential pathotypes of Bacillus thuringiensis soil isolates. FEMS Microbiol Ecol 85:262–272. https://doi.org/10.1111/1574-6941.12116.Cohan FM. 2017. Transmission in the origins of bacterial diversity, from ecotypes to phyla. Microbiol Spectr 5:MTBP-0014-2016. https://doi.org/10.1128/microbiolspec.MTBP-0014-2016Guinebretière MH, Thompson FL, Sorokin A, Normand P, Dawyndt P, Ehling-Schulz M, Svensson B, Sanchis V, Nguyen-The C, Heyndrickx M,De Vos P. 2008. Ecological diversification in the Bacillus cereus group.Environ Microbiol 10:851– 865. https://doi.org/10.1111/j.1462-2920.2007.01495.xFiedoruk K, Drewnowska JM, Daniluk T, Leszczynska K, Iwaniuk P, Swiecicka I. 2017. Ribosomal background of the Bacillus cereus group thermotypes. SciRep 7:46430. https://doi.org/10.1038/srep46430.Guinebretière MH, Velge P, Couvert O, Carlin F, Debuyser ML, Nguyen-The C. 2010. Ability to Bacillus cereus group strains to cause food poisoning varies according to phylogenetic affiliation (group I to VII) rather than species affiliation. J Clin Microbiol 48:3388 –3391. https://doi.org/10.1128/JCM.00921-10.Peel MC, Finlayson BL, McMahon TA. 2007. Updated world map of the Köppen-Geiger climate classification. Hydrol Earth Syst Sci 11:1633–1644. https://doi.org/10.5194/hess-11-1633-2007.Slamti L, Lereclus D. 2005. Specificity and polymorphism of the PlcRPapR quorum-sensing system in the Bacillus cereus group. J Bacteriol 187:1182–1187. https://doi.org/10.1128/JB.187.3.1182-1187.2005.Kaminska PS, Yernazarova A, Drewnowska JM, Zambrowski G, Swiecicka I. 2015. The worldwide distribution of genetically and phylogenetically diverse Bacillus cereus isolates harbouring Bacillus anthracis-like plasmids. Environ Microbiol Rep 7:738 –745. https://doi.org/10.1111/1758-2229.12305.Hendriksen NB, Hansen BM, Johansen JE. 2006. Occurrence and pathogenic potential of Bacillus cereus group bacteria in a sandy loam. Antonie Van Leeuwenhoek 89:239 –249. https://doi.org/10.1007/s10482-005-9025-y.Collier FA, Elliot SL, Ellis RJ. 2005. Spatial variation in Bacillus thuringiensis/cereus populations within the phyllosphere of broad-leaved dock (Rumex obtusifolius) and surrounding habitats. FEMS Microbiol Ecol 54:417–425.https://doi.org/10.1016/j.femsec.2005.05.005.Shah N, DuPont HL, Ramsey DJ. 2009. Global etiology of travelers’diarrhea: systematic review from 1973 to the present. Am J Trop Med Hyg 80:609 – 614. https://doi.org/10.4269/ajtmh.2009.80.609.Cohan FM, Perry EB. 2007. A systematic for discovering the fundamental units of bacterial diversity. Curr Biol 17:R373–R386. https://doi.org/10.1016/j.cub.2007.03.032.Slamti L, Lemy C, Henry C, Guillot A, Huillet E, Lereclus D. 2016. CodY regulates the activity of the virulence quorum-sensor PlcR by controlling the import of the signaling peptide PapR in Bacillus thuringiensis. Front Microbiol 6:1501. https://doi.org/10.3389/fmicb.2015.01501.Fagerlund A, Lindbäck T, Granum PE. 2010. Bacillus cereus cytotoxins Hbl, Nhe and CytK are secreted via the Sec translocation pathway. BMC Microbiol 10:304. https://doi.org/10.1186/1471-2180-10-304.Castiaux V, Liu X, Delbrassinne L, Mahillon J. 2015. Is cytotoxin K from Bacillus cereus a bona fide enterotoxin? Int J Food Microbiol 211:79 – 85. https://doi.org/10.1016/j.ijfoodmicro.2015.06.020.Jessberger N, Rademacher C, Krey VM, Dietrich R, Mohr AK, Böhm ME, Scherer S, Ehling-Schulz M, Märtlbauer E. 2017. Simulating intestinal growth conditions enhances toxin production of entheropathogenic Bacillus cereus. Front Microbiol 8:627. https://doi.org/10.3389/fmicb.2017.00627.Bartoszewicz M, Bideshi D, Kraszewska A, Modzelewska E, Swiecicka I. 2009. Natural isolates of Bacillus thuringiensis display genetic and psychrotrophic properties characteristic of Bacillus weihenstephanensis. J Appl Microbiol 106:1967–1975. https://doi.org/10.1111/j.1365-2672.2009.04166.x.Guinebretière MH, Fagerlund A, Granum PE, Nguyen-The C. 2006. Rapid discrimination of cytK-1 and cytK-2 genes in Bacillus cereus strains by a novel duplex PCR system. FEMS Microbiol Lett 259:74 – 80. https://doi.org/10.1111/j.1574-6968.2006.00247.x.Prüß BM, Dietrich R, Nibler B, MäRtlbauer E, Scherer S, 1999. The hemolytic enterotoxin HBL is broadly distributed among species of the Bacillus cereus group. Appl Environ Microbiol 65:5436 –5442. https://doi.org/10.1128/AEM.65.12.5436-5442.1999.Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870 –1874. https://doi.org/10.1093/molbev/msw054.Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carriço JA. 2012. PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics 13:87. https://doi.org/10.1186/1471-2105-13-87.Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG. 2004. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 186:1518 –1530. https://doi.org/10.1128/JB.186.5.1518-1530.2004.Drewnowska JM, Fiodor A, Barboza-Corona JE, Swiecicka I. 4 March 2020. Chitinolytic activity of phylogenetically diverse Bacillus cereus sensu lato from natural environments. Syst Appl Microbiol https://doi.org/10.1016/j.syapm.2020.126075.Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389 –3402. https://doi.org/10.1093/nar/25.17.3389.Reiter L, Kolstø A-B, Piehler AP. 2011. Reference genes for quantitative, reverse-transcription PCR in Bacillus cereus group strains throughout the bacterial life cycle. J Microbiol Methods 86:210 –217. https://doi.org/10.1016/j.mimet.2011.05.006.Pfaffl MW. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45. https://doi.org/10.1093/nar/29.9.e45.Plumb JA, Milroy R, Kaye SB. 1989. Effects of the pH dependence of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide-formazan absorption on chemosensitivity determined by a novel tetrazoliumbased assay. Cancer Res 49:4435– 4440.Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystem Technology (RAST). Nucleic Acids Res 42:D206 –D214. https://doi.org/10.1093/nar/gkt1226.861111

Biomass Combustion in the Helically Coiled Domestic Boiler Combined with the Equilibrium/Chemical Kinetics CFD Approach

In the face of threats related to energy supply and climate change, the use of biomass is gaining importance, particularly in distributed energy systems. Combustion of biomass, including residue biomass, is considered one of the routes to increase the share of renewables in energy generation. The modeling of gaseous phase reactions remains crucial in predicting the combustion behavior of biomass and pollutant emissions. However, their simulation becomes a challenging task due to the computational cost. This paper presents a numerical analysis of the combustion process of a gas mixture released during biomass decomposition in a domestic 25 kW coil-type boiler. Three types of biogenic fuels were taken into consideration. The work aimed at examining the available tools for modeling gas burning, thus the geometry of the system was limited only to the 2D case. The thermodynamic equilibrium composition of pyrolysis gas was determined and implemented in Ansys to simulate the process. The computational results showed the potential of detailed, but reduced, combustion mechanisms of CH4/CO/H2 mixtures in predicting the main process features. The mechanism involving 85 reactions appeared to be more reliable compared to that comprising 77 reactions, particularly for volatiles with higher H2 content, whilst offering an acceptable calculation time. The burning characteristics obtained for volatiles with less CH4 and more H2 are in good agreement with the real operation conditions reported for the boiler

Disposal of Waste from Tattoo and Beauty Parlors in Poland: A Survey-Based Analysis on Epidemiological Safety

Appropriate waste management is increasingly relevant due to environmental and infectious disease transmission concerns. An anonymous observational cross-sectional study was conducted from 2013–2017 of 262 tattooists and 824 beauticians throughout Poland. Knowledge, attitudes, behavior, and compliance with blood-borne infection controls and correct waste disposal were assessed. Tattooists correctly addressed hazardous waste significantly more often than did beauticians (83.3% vs. 44.8%). Medical waste was collected by a specialist company in 90.1% of tattoo parlors and 63.3%of beauty parlors. Tattooists correctly used and disposed of sharps more frequently than beauticians (93.1% vs. 68.9%); however, 46.4% of beauticians and 12.4% of tattooists discarded waste into municipal trash, including sharps (27.1% and 2.6%, respectively). Incorrect collection and labeling of biological waste present occupational risk to waste disposal personnel. Education and instructional controls could improve health safety in this industry. Biological waste management processes are restrictive for medical services and liberal for beauty services, an industry for which they should also be applied more comprehensively

Assessment of Epidemiological Safety in the Cosmetic Service Industry in Poland: A Cross-Sectional Questionnaire Study

The variety of current cosmetic procedures has increased the potential risks of adverse events and infections. In a nationwide cross-sectional study (2013–2015), we assessed the aspects of infection risk in cosmetic services. An anonymous voluntary questionnaire survey was conducted among 813 employees of cosmetic establishments in Poland. The establishments were selected from a register of service providers. The survey was conducted by employees of the State Sanitary Inspectorate during an audit, and the results showed that cosmetic providers were not fully prepared for risk assessment in terms of occupational exposure or infection transmission. The majority of the respondents (84%) reportedly washed the salon tools. Some establishments did not perform any decontamination (2%) or sterilization (~13%) procedures. Occupational punctures or lacerations occurred from needles, ampoules-syringes, or razors. Most respondents had attended professional training or studied medical textbooks. Approximately 1.7% of the respondents had not updated their knowledge, and 5% gained knowledge from unauthorized sources.The project’s results impacted a variety of innovations and improvements in the field of public health. The results were used to update the national education program (2012–2017); more attention has been directed toward effective education in infection prevention, general hygiene, and post-exposure procedures. Moreover, the study’s results were grounds for the introduction of legislative modifications in the field of epidemiological safety standards for cosmetic services in Poland

On the trails of ancient and modern Polish: A jubilee book dedicated to Professor Danuta Bieńkowska

Na publikację składają się teksty bardzo zróżnicowane pod względem podejmowanych tematów i stosowanej metodologii. Jest to specyfiką tomów jubileuszowych, które w pewien sposób scala odniesienie do osoby jubilata. W tym przypadku wszystkie teksty dobrze wkomponowują się w całość, tworzą zbiór niejednorodny, lecz ciekawy i oryginalny. Autorzy nawiązują do poruszanych przez jubilata tematów, twórczo je rozwijając lub z nimi polemizując. Pod tym względem osoba Jubilatki, Profesor Danuty Bieńkowskiej, jest gwarantem, że opisywane w publikacji zagadnienia nie mają marginalnego dla nauki charakteru. Tomem zainteresują się przede wszystkim badacze Biblii, jednak krąg potencjalnych odbiorców będzie oczywiście zdecydowanie szerszy ze względu na inne poruszane tu zagadnienia: kwestie normatywne, językoznawczo zorientowaną stylistykę, synchroniczne i diachroniczne badania nad polszczyzną. Z recenzji dr hab. Anetty Luto-Kamińskie

Regnare Gubernare Administrare: Z dziejów administracji, sądownictwa i nauki prawa (t. 2)

Prace dedykowane profesorowi Jerzemu Malcowi z okazji 40-lecia pracy naukowe