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1. Doxing ethics

Author: Naskali, Juhani, Rantanen, Minna M., Rottenkolber, Maria, K. Kimppa, Kai, Naskali, Juhani, Rantanen, Minna M., Rottenkolber, Maria, and K. Kimppa, Kai
Published: 2024

2. Doxing ethics

Author: Naskali, Juhani, Rantanen, Minna M., Rottenkolber, Maria, K. Kimppa, Kai, Naskali, Juhani, Rantanen, Minna M., Rottenkolber, Maria, and K. Kimppa, Kai
Published: 2024

3. Four principles to establish a universal virus taxonomy

Author: Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Vasilakis, Nikos, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos
Abstract: A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes a
Published: 2023

4. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author: Turner, Dann, Shkoporov, Andrey N, Lood, Cédric, Millard, Andrew D, Dutilh, Bas E, Alfenas-Zerbini, Poliane, van Zyl, Leonardo J, Aziz, Ramy K, Oksanen, Hanna M, Poranen, Minna M, Kropinski, Andrew M, Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A, Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, B L, Sullivan, Matthew B, Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, Adriaenssens, Evelien M, Turner, Dann, Shkoporov, Andrey N, Lood, Cédric, Millard, Andrew D, Dutilh, Bas E, Alfenas-Zerbini, Poliane, van Zyl, Leonardo J, Aziz, Ramy K, Oksanen, Hanna M, Poranen, Minna M, Kropinski, Andrew M, Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A, Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, B L, Sullivan, Matthew B, Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, and Adriaenssens, Evelien M
Abstract: This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021-March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
Published: 2023

5. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author: UCL - SST/ELI/ELIM - Applied Microbiology, Turner, Dann, Shkoporov, Andrey N., Lood, Cédric, Millard, Andrew D., Dutilh, Bas E., Alfenas-Zerbini, Poliane, van Zyl, Leonardo J., Aziz, Ramy K., Oksanen, Hanna M., Poranen, Minna M., Kropinski, Andrew M., Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A., Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, BL, Sullivan, Matthew B., Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, Adriaenssens, Evelien M., UCL - SST/ELI/ELIM - Applied Microbiology, Turner, Dann, Shkoporov, Andrey N., Lood, Cédric, Millard, Andrew D., Dutilh, Bas E., Alfenas-Zerbini, Poliane, van Zyl, Leonardo J., Aziz, Ramy K., Oksanen, Hanna M., Poranen, Minna M., Kropinski, Andrew M., Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A., Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, BL, Sullivan, Matthew B., Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, and Adriaenssens, Evelien M.
Abstract: This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
Published: 2023

6. Four principles to establish a universal virus taxonomy.

Author: Simmonds, Peter, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola GA, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Vasilakis, Nikos, Simmonds, Peter, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola GA, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos
Abstract: A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes appa
Published: 2023

7. Consistent centennial-scale change in European sub-Arctic peatland vegetation toward Sphagnum dominance—Implications for carbon sink capacity

Author: Piilo, Sanna R., Väliranta, Minna M., Amesbury, Matt J., Aquino-López, Marco A., Charman, Dan J., Gallego-Sala, Angela, Garneau, Michelle, Koroleva, Natalia, Kärppä, Mai, Laine, Anna M., Sannel, A. Britta K., Tuittila, Eeva-Stiina, Zhang, Hui, Piilo, Sanna R., Väliranta, Minna M., Amesbury, Matt J., Aquino-López, Marco A., Charman, Dan J., Gallego-Sala, Angela, Garneau, Michelle, Koroleva, Natalia, Kärppä, Mai, Laine, Anna M., Sannel, A. Britta K., Tuittila, Eeva-Stiina, and Zhang, Hui
Abstract: Climate warming is leading to permafrost thaw in northern peatlands, and current predictions suggest that thawing will drive greater surface wetness and an increase in methane emissions. Hydrology largely drives peatland vegetation composition, which is a key element in peatland functioning and thus in carbon dynamics. These processes are expected to change. Peatland carbon accumulation is determined by the balance between plant production and peat decomposition. But both processes are expected to accelerate in northern peatlands due to warming, leading to uncertainty in future peatland carbon budgets. Here, we compile a dataset of vegetation changes and apparent carbon accumulation data reconstructed from 33 peat cores collected from 16 sub-arctic peatlands in Fennoscandia and European Russia. The data cover the past two millennia that has undergone prominent changes in climate and a notable increase in annual temperatures toward present times. We show a pattern where European sub-Arctic peatland microhabitats have undergone a habitat change where currently drier habitats dominated by Sphagnum mosses replaced wetter sedge-dominated vegetation and these new habitats have remained relatively stable over the recent decades. Our results suggest an alternative future pathway where sub-arctic peatlands may at least partly sustain dry vegetation and enhance the carbon sink capacity of northern peatlands.
Published: 2023
Full Text: View/download PDF

8. Four principles to establish a universal virus taxonomy

Author: Theoretical Biology and Bioinformatics, Sub Bioinformatics, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Vasilakis, Nikos, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos
Published: 2023

9. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author: Theoretical Biology and Bioinformatics, Sub Bioinformatics, Turner, Dann, Shkoporov, Andrey N, Lood, Cédric, Millard, Andrew D, Dutilh, Bas E, Alfenas-Zerbini, Poliane, van Zyl, Leonardo J, Aziz, Ramy K, Oksanen, Hanna M, Poranen, Minna M, Kropinski, Andrew M, Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A, Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, B L, Sullivan, Matthew B, Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, Adriaenssens, Evelien M, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Turner, Dann, Shkoporov, Andrey N, Lood, Cédric, Millard, Andrew D, Dutilh, Bas E, Alfenas-Zerbini, Poliane, van Zyl, Leonardo J, Aziz, Ramy K, Oksanen, Hanna M, Poranen, Minna M, Kropinski, Andrew M, Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A, Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, B L, Sullivan, Matthew B, Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, and Adriaenssens, Evelien M
Published: 2023

10. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
Full Text: View/download PDF

11. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
Full Text: View/download PDF

12. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
Full Text: View/download PDF

13. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
Full Text: View/download PDF

14. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
Full Text: View/download PDF

15. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
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16. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
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17. Cognitive performance at time of AD diagnosis:a clinically augmented register-based study

Author: Alenius, M. (Minna), Hokkanen, L. (Laura), Koskinen, S. (Sanna), Hallikainen, I. (Ilona), Hänninen, T. (Tuomo), Karrasch, M. (Mira), Raivio, M. M. (Minna M.), Laakkonen, M.-L. (Marja-Liisa), Krüger, J. (Johanna), Suhonen, N.-M. (Noora-Maria), Kivipelto, M. (Miia), Ngandu, T. (Tiia), Alenius, M. (Minna), Hokkanen, L. (Laura), Koskinen, S. (Sanna), Hallikainen, I. (Ilona), Hänninen, T. (Tuomo), Karrasch, M. (Mira), Raivio, M. M. (Minna M.), Laakkonen, M.-L. (Marja-Liisa), Krüger, J. (Johanna), Suhonen, N.-M. (Noora-Maria), Kivipelto, M. (Miia), and Ngandu, T. (Tiia)
Abstract: We aimed to evaluate the feasibility of using real-world register data for identifying persons with mild Alzheimer’s disease (AD) and to describe their cognitive performance at the time of diagnosis. Patients diagnosed with AD during 2010–2013 (aged 60–81 years) were identified from the Finnish national health registers and enlarged with a smaller private sector sample (total n = 1,268). Patients with other disorders impacting cognition were excluded. Detailed clinical and cognitive screening data (the Consortium to Establish a Registry for Alzheimer’s Disease neuropsychological battery [CERAD-nb]) were obtained from local health records. Adequate cognitive data were available for 389 patients with mild AD (31%) of the entire AD group. The main reasons for not including patients in analyses of cognitive performance were AD diagnosis at a moderate/severe stage (n = 266, 21%), AD diagnosis given before full register coverage (n = 152, 12%), and missing CERAD-nb data (n = 139, 11%). The cognitive performance of persons with late-onset AD (n = 284), mixed cerebrovascular disease and AD (n = 51), and other AD subtypes (n = 54) was compared with that of a non-demented sample (n = 1980) from the general population. Compared with the other AD groups, patients with late-onset AD performed the worst in word list recognition, while patients with mixed cerebrovascular disease and AD performed the worst in constructional praxis and clock drawing tests. A combination of national registers and local health records can be used to collect data relevant for cognitive screening; today, the process is laborious, but it could be improved in the future with refined search algorithms and electronic data.
Published: 2022

18. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
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19. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
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20. SUCCOR cone study: conization before radical hysterectomy

Author: Chacon, E, Manzour, N, Zanagnolo, V, Querleu, D, Núñez-Córdoba, J, Martin-Calvo, N, Căpîlna, M, Fagotti, A, Kucukmetin, A, Mom, C, Chakalova, G, Shamistan, A, Gil Moreno, A, Malzoni, M, Narducci, F, Arencibia, O, Raspagliesi, F, Toptas, T, Cibula, D, Kaidarova, D, Meydanli, M, Tavares, M, Golub, D, Perrone, A, Poka, R, Tsolakidis, D, Vujić, G, Jedryka, M, Zusterzeel, P, Beltman, J, Goffin, F, Haidopoulos, D, Haller, H, Jach, R, Yezhova, I, Berlev, I, Bernardino, M, Bharathan, R, Lanner, M, Maenpaa, M, Sukhin, V, Feron, J, Fruscio, R, Kukk, K, Ponce, J, Minguez, J, Vázquez-Vicente, D, Castellanos, T, Boria, F, Alcazar, J, Chiva, L, Chacon, Enrique, Manzour, Nabil, Zanagnolo, Vanna, Querleu, Denis, Núñez-Córdoba, Jorge M, Martin-Calvo, Nerea, Căpîlna, Mihai Emil, Fagotti, Anna, Kucukmetin, Ali, Mom, Constantijne, Chakalova, Galina, Shamistan, Aliyev, Gil Moreno, Antonio, Malzoni, Mario, Narducci, Fabrice, Arencibia, Octavio, Raspagliesi, Francesco, Toptas, Tayfun, Cibula, David, Kaidarova, Dilyara, Meydanli, Mehmet Mutlu, Tavares, Mariana, Golub, Dmytro, Perrone, Anna Myriam, Poka, Robert, Tsolakidis, Dimitrios, Vujić, Goran, Jedryka, Marcin A, Zusterzeel, Petra L M, Beltman, Jogchum Jan, Goffin, Frederic, Haidopoulos, Dimitrios, Haller, Herman, Jach, Robert, Yezhova, Iryna, Berlev, Igor, Bernardino, Margarida, Bharathan, Rasiah, Lanner, Maximilian, Maenpaa, Minna M, Sukhin, Vladyslav, Feron, Jean-Guillaume, Fruscio, Robert, Kukk, Kersti, Ponce, Jordi, Minguez, Jose Angel, Vázquez-Vicente, Daniel, Castellanos, Teresa, Boria, Felix, Alcazar, Juan Luis, Chiva, Luis, Chacon, E, Manzour, N, Zanagnolo, V, Querleu, D, Núñez-Córdoba, J, Martin-Calvo, N, Căpîlna, M, Fagotti, A, Kucukmetin, A, Mom, C, Chakalova, G, Shamistan, A, Gil Moreno, A, Malzoni, M, Narducci, F, Arencibia, O, Raspagliesi, F, Toptas, T, Cibula, D, Kaidarova, D, Meydanli, M, Tavares, M, Golub, D, Perrone, A, Poka, R, Tsolakidis, D, Vujić, G, Jedryka, M, Zusterzeel, P, Beltman, J, Goffin, F, Haidopoulos, D, Haller, H, Jach, R, Yezhova, I, Berlev, I, Bernardino, M, Bharathan, R, Lanner, M, Maenpaa, M, Sukhin, V, Feron, J, Fruscio, R, Kukk, K, Ponce, J, Minguez, J, Vázquez-Vicente, D, Castellanos, T, Boria, F, Alcazar, J, Chiva, L, Chacon, Enrique, Manzour, Nabil, Zanagnolo, Vanna, Querleu, Denis, Núñez-Córdoba, Jorge M, Martin-Calvo, Nerea, Căpîlna, Mihai Emil, Fagotti, Anna, Kucukmetin, Ali, Mom, Constantijne, Chakalova, Galina, Shamistan, Aliyev, Gil Moreno, Antonio, Malzoni, Mario, Narducci, Fabrice, Arencibia, Octavio, Raspagliesi, Francesco, Toptas, Tayfun, Cibula, David, Kaidarova, Dilyara, Meydanli, Mehmet Mutlu, Tavares, Mariana, Golub, Dmytro, Perrone, Anna Myriam, Poka, Robert, Tsolakidis, Dimitrios, Vujić, Goran, Jedryka, Marcin A, Zusterzeel, Petra L M, Beltman, Jogchum Jan, Goffin, Frederic, Haidopoulos, Dimitrios, Haller, Herman, Jach, Robert, Yezhova, Iryna, Berlev, Igor, Bernardino, Margarida, Bharathan, Rasiah, Lanner, Maximilian, Maenpaa, Minna M, Sukhin, Vladyslav, Feron, Jean-Guillaume, Fruscio, Robert, Kukk, Kersti, Ponce, Jordi, Minguez, Jose Angel, Vázquez-Vicente, Daniel, Castellanos, Teresa, Boria, Felix, Alcazar, Juan Luis, and Chiva, Luis
Abstract: OBJECTIVE: To evaluate disease-free survival of cervical conization prior to radical hysterectomy in patients with stage IB1 cervical cancer (International Federation of Gynecology and Obstetrics (FIGO) 2009). METHODS: A multicenter retrospective observational cohort study was conducted including patients from the Surgery in Cervical Cancer Comparing Different Surgical Aproaches in Stage IB1 Cervical Cancer (SUCCOR) database with FIGO 2009 IB1 cervical carcinoma treated with radical hysterectomy between January 1, 2013, and December 31, 2014. We used propensity score matching to minimize the potential allocation biases arising from the retrospective design. Patients who underwent conization but were similar for other measured characteristics were matched 1:1 to patients from the non-cone group using a caliper width ≤0.2 standard deviations of the logit odds of the estimated propensity score. RESULTS: We obtained a weighted cohort of 374 patients (187 patients with prior conization and 187 non-conization patients). We found a 65% reduction in the risk of relapse for patients who had cervical conization prior to radical hysterectomy (hazard ratio (HR) 0.35, 95% confidence interval (CI) 0.16 to 0.75, p=0.007) and a 75% reduction in the risk of death for the same sample (HR 0.25, 95% CI 0.07 to 0.90, p=0.033). In addition, patients who underwent minimally invasive surgery without prior conization had a 5.63 times higher chance of relapse compared with those who had an open approach and previous conization (HR 5.63, 95% CI 1.64 to 19.3, p=0.006). Patients who underwent minimally invasive surgery with prior conization and those who underwent open surgery without prior conization showed no differences in relapse rates compared with those who underwent open surgery with prior cone biopsy (reference) (HR 1.94, 95% CI 0.49 to 7.76, p=0.349 and HR 2.94, 95% CI 0.80 to 10.86, p=0.106 respectively). CONCLUSIONS: In this retrospective study, patients undergoing cervical conizatio
Published: 2022

21. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
Full Text: View/download PDF

22. Norway spruce postglacial recolonization of Fennoscandia

Author: Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, Parducci, Laura, Nota, Kevin, Klaminder, Jonatan, Milesi, Pascal, Bindler, Richard, Nobile, Alessandro, van Steijn, Tamara, Bertilsson, Stefan, Svensson, Brita, Hirota, Shun K., Matsuo, Ayumi, Gunnarsson, Urban, Seppä, Heikki, Väliranta, Minna M., Wohlfarth, Barbara, Suyama, Yoshihisa, and Parducci, Laura
Abstract: Contrasting theories exist regarding how Norway spruce (Picea abies) recolonized Fennoscandia after the last glaciation and both early Holocene establishments from western microrefugia and late Holocene colonization from the east have been postulated. Here, we show that Norway spruce was present in southern Fennoscandia as early as 14.7 ± 0.1 cal. kyr BP and that the millennia-old clonal spruce trees present today in central Sweden likely arrived with an early Holocene migration from the east. Our findings are based on ancient sedimentary DNA from multiple European sites (N = 15) combined with nuclear and mitochondrial DNA analysis of ancient clonal (N = 135) and contemporary spruce forest trees (N = 129) from central Sweden. Our other findings imply that Norway spruce was present shortly after deglaciation at the margins of the Scandinavian Ice Sheet, and support previously disputed finds of pollen in southern Sweden claiming spruce establishment during the Lateglacial.
Published: 2022
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23. Structural Insight into CVB3-VLP Non-Adjuvanted Vaccine.

Author: Hankaniemi, Minna M, Hankaniemi, Minna M, Baikoghli, Mo A, Stone, Virginia M, Xing, Li, Väätäinen, Outi, Soppela, Saana, Sioofy-Khojine, Amirbabak, Saarinen, Niila VV, Ou, Tingwei, Anson, Brandon, Hyöty, Heikki, Marjomäki, Varpu, Flodström-Tullberg, Malin, Cheng, R Holland, Hytönen, Vesa P, Laitinen, Olli H, Hankaniemi, Minna M, Hankaniemi, Minna M, Baikoghli, Mo A, Stone, Virginia M, Xing, Li, Väätäinen, Outi, Soppela, Saana, Sioofy-Khojine, Amirbabak, Saarinen, Niila VV, Ou, Tingwei, Anson, Brandon, Hyöty, Heikki, Marjomäki, Varpu, Flodström-Tullberg, Malin, Cheng, R Holland, Hytönen, Vesa P, and Laitinen, Olli H
Abstract: Coxsackievirus B (CVB) enteroviruses are common pathogens that can cause acute and chronic myocarditis, dilated cardiomyopathy, aseptic meningitis, and they are hypothesized to be a causal factor in type 1 diabetes. The licensed enterovirus vaccines and those currently in clinical development are traditional inactivated or live attenuated vaccines. Even though these vaccines work well in the prevention of enterovirus diseases, new vaccine technologies, like virus-like particles (VLPs), can offer important advantages in the manufacturing and epitope engineering. We have previously produced VLPs for CVB3 and CVB1 in insect cells. Here, we describe the production of CVB3-VLPs with enhanced production yield and purity using an improved purification method consisting of tangential flow filtration and ion exchange chromatography, which is compatible with industrial scale production. We also resolved the CVB3-VLP structure by Cryo-Electron Microscopy imaging and single particle reconstruction. The VLP diameter is 30.9 nm on average, and it is similar to Coxsackievirus A VLPs and the expanded enterovirus cell-entry intermediate (the 135s particle), which is ~2 nm larger than the mature virion. High neutralizing and total IgG antibody levels, the latter being a predominantly Th2 type (IgG1) phenotype, were detected in C57BL/6J mice immunized with non-adjuvanted CVB3-VLP vaccine. The structural and immunogenic data presented here indicate the potential of this improved methodology to produce highly immunogenic enterovirus VLP-vaccines in the future.
Published: 2020

24. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author: Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
Abstract: In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
Published: 2021

25. Black box of phage-bacterium interactions: exploring alternative phage infection strategies.

Author: Mäntynen, Sari, Mäntynen, Sari, Laanto, Elina, Oksanen, Hanna M, Poranen, Minna M, Díaz-Muñoz, Samuel L, Mäntynen, Sari, Mäntynen, Sari, Laanto, Elina, Oksanen, Hanna M, Poranen, Minna M, and Díaz-Muñoz, Samuel L
Abstract: The canonical lytic-lysogenic binary has been challenged in recent years, as more evidence has emerged on alternative bacteriophage infection strategies. These infection modes are little studied, and yet they appear to be more abundant and ubiquitous in nature than previously recognized, and can play a significant role in the ecology and evolution of their bacterial hosts. In this review, we discuss the extent, causes and consequences of alternative phage lifestyles, and clarify conceptual and terminological confusion to facilitate research progress. We propose distinct definitions for the terms 'pseudolysogeny' and 'productive or non-productive chronic infection', and distinguish them from the carrier state life cycle, which describes a population-level phenomenon. Our review also finds that phages may change their infection modes in response to environmental conditions or the physiological state of the host cell. We outline known molecular mechanisms underlying the alternative phage-host interactions, including specific genetic pathways and their considerable biotechnological potential. Moreover, we discuss potential implications of the alternative phage lifestyles for microbial biology and ecosystem functioning, as well as applied topics such as phage therapy.
Published: 2021

26. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author: Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
Published: 2021

27. Joining European Scientific Forces to Face Pandemics

Author: Vasconcelos, M Helena, Vasconcelos, M Helena, Alcaro, Stefano, Arechavala-Gomeza, Virginia, Baumbach, Jan, Borges, Fernanda, Brevini, Tiziana A L, Rivas, Javier De Las, Devaux, Yvan, Hozak, Pavel, Keinänen-Toivola, Minna M, Lattanzi, Giovanna, Mohr, Thomas, Murovska, Modra, Prusty, Bhupesh K, Quinlan, Roy A, Pérez-Sala, Dolores, Scheibenbogen, Carmen, Schmidt, Harald H H W, Silveira, Isabel, Tieri, Paolo, Tolios, Alexander, Riganti, Chiara, Vasconcelos, M Helena, Vasconcelos, M Helena, Alcaro, Stefano, Arechavala-Gomeza, Virginia, Baumbach, Jan, Borges, Fernanda, Brevini, Tiziana A L, Rivas, Javier De Las, Devaux, Yvan, Hozak, Pavel, Keinänen-Toivola, Minna M, Lattanzi, Giovanna, Mohr, Thomas, Murovska, Modra, Prusty, Bhupesh K, Quinlan, Roy A, Pérez-Sala, Dolores, Scheibenbogen, Carmen, Schmidt, Harald H H W, Silveira, Isabel, Tieri, Paolo, Tolios, Alexander, and Riganti, Chiara
Abstract: Despite the international guidelines on the containment of the coronavirus disease 2019 (COVID-19) pandemic, the European scientific community was not sufficiently prepared to coordinate scientific efforts. To improve preparedness for future pandemics, we have initiated a network of nine European-funded Cooperation in Science and Technology (COST) Actions that can help facilitate inter-, multi-, and trans-disciplinary communication and collaboration.
Published: 2021

28. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author: UCL - SST/ELI/ELIM - Applied Microbiology, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., UCL - SST/ELI/ELIM - Applied Microbiology, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
Abstract: In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
Published: 2021

29. Black box of phage-bacterium interactions: exploring alternative phage infection strategies.

Author: Mäntynen, Sari, Mäntynen, Sari, Laanto, Elina, Oksanen, Hanna M, Poranen, Minna M, Díaz-Muñoz, Samuel L, Mäntynen, Sari, Mäntynen, Sari, Laanto, Elina, Oksanen, Hanna M, Poranen, Minna M, and Díaz-Muñoz, Samuel L
Abstract: The canonical lytic-lysogenic binary has been challenged in recent years, as more evidence has emerged on alternative bacteriophage infection strategies. These infection modes are little studied, and yet they appear to be more abundant and ubiquitous in nature than previously recognized, and can play a significant role in the ecology and evolution of their bacterial hosts. In this review, we discuss the extent, causes and consequences of alternative phage lifestyles, and clarify conceptual and terminological confusion to facilitate research progress. We propose distinct definitions for the terms 'pseudolysogeny' and 'productive or non-productive chronic infection', and distinguish them from the carrier state life cycle, which describes a population-level phenomenon. Our review also finds that phages may change their infection modes in response to environmental conditions or the physiological state of the host cell. We outline known molecular mechanisms underlying the alternative phage-host interactions, including specific genetic pathways and their considerable biotechnological potential. Moreover, we discuss potential implications of the alternative phage lifestyles for microbial biology and ecosystem functioning, as well as applied topics such as phage therapy.
Published: 2021

30. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author: Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
Published: 2021

31. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author: Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
Published: 2021

32. Joining European Scientific Forces to Face Pandemics

Author: Vasconcelos, M Helena, Alcaro, Stefano, Arechavala-Gomeza, Virginia, Baumbach, Jan, Borges, Fernanda, Brevini, Tiziana A L, Rivas, Javier De Las, Devaux, Yvan, Hozak, Pavel, Keinänen-Toivola, Minna M, Lattanzi, Giovanna, Mohr, Thomas, Murovska, Modra, Prusty, Bhupesh K, Quinlan, Roy A, Pérez-Sala, Dolores, Scheibenbogen, Carmen, Schmidt, Harald H H W, Silveira, Isabel, Tieri, Paolo, Tolios, Alexander, Riganti, Chiara, Vasconcelos, M Helena, Alcaro, Stefano, Arechavala-Gomeza, Virginia, Baumbach, Jan, Borges, Fernanda, Brevini, Tiziana A L, Rivas, Javier De Las, Devaux, Yvan, Hozak, Pavel, Keinänen-Toivola, Minna M, Lattanzi, Giovanna, Mohr, Thomas, Murovska, Modra, Prusty, Bhupesh K, Quinlan, Roy A, Pérez-Sala, Dolores, Scheibenbogen, Carmen, Schmidt, Harald H H W, Silveira, Isabel, Tieri, Paolo, Tolios, Alexander, and Riganti, Chiara
Abstract: Despite the international guidelines on the containment of the coronavirus disease 2019 (COVID-19) pandemic, the European scientific community was not sufficiently prepared to coordinate scientific efforts. To improve preparedness for future pandemics, we have initiated a network of nine European-funded Cooperation in Science and Technology (COST) Actions that can help facilitate inter-, multi-, and trans-disciplinary communication and collaboration.
Published: 2021

33. Root-type ferredoxin-NADP+ oxidoreductase isoforms in Arabidopsis thaliana:Expression patterns, location and stress responses

Author: Grabsztunowicz, Magda, Rantala, Marjaana, Ivanauskaite, Aiste, Blomster, Tiina, Koskela, Minna M., Vuorinen, Katariina, Tyystjarvi, Esa, Burow, Meike, Overmyer, Kirk, Mahonen, Ari P., Mulo, Paula, Grabsztunowicz, Magda, Rantala, Marjaana, Ivanauskaite, Aiste, Blomster, Tiina, Koskela, Minna M., Vuorinen, Katariina, Tyystjarvi, Esa, Burow, Meike, Overmyer, Kirk, Mahonen, Ari P., and Mulo, Paula
Abstract: In Arabidopsis, two leaf-type ferredoxin-NADP(+) oxidoreductase (LFNR) isoforms function in photosynthetic electron flow in reduction of NADP(+), while two root-type FNR (RFNR) isoforms catalyse reduction of ferredoxin in non-photosynthetic plastids. As the key to understanding, the function of RFNRs might lie in their spatial and temporal distribution in different plant tissues and cell types, we examined expression of RFNR1 and RFNR2 genes using beta-glucuronidase (GUS) reporter lines and investigated accumulation of distinct RFNR isoforms using a GFP approach and Western blotting upon various stresses. We show that while RFNR1 promoter is active in leaf veins, root tips and in the stele of roots, RFNR2 promoter activity is present in leaf tips and root stele, epidermis and cortex. RFNR1 protein accumulates as a soluble protein within the plastids of root stele cells, while RFNR2 is mainly present in the outer root layers. Ozone treatment of plants enhanced accumulation of RFNR1, whereas low temperature treatment specifically affected RFNR2 accumulation in roots. We further discuss the physiological roles of RFNR1 and RFNR2 based on characterization of rfnr1 and rfnr2 knock-out plants and show that although the function of these proteins is partly redundant, the RFNR proteins are essential for plant development and survival.
Published: 2021

34. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV:update of taxonomy changes in 2021

Author: Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
Abstract: In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
Published: 2021

35. Root-type ferredoxin-NADP+ oxidoreductase isoforms in Arabidopsis thaliana:Expression patterns, location and stress responses

Author: Grabsztunowicz, Magda, Rantala, Marjaana, Ivanauskaite, Aiste, Blomster, Tiina, Koskela, Minna M., Vuorinen, Katariina, Tyystjarvi, Esa, Burow, Meike, Overmyer, Kirk, Mahonen, Ari P., Mulo, Paula, Grabsztunowicz, Magda, Rantala, Marjaana, Ivanauskaite, Aiste, Blomster, Tiina, Koskela, Minna M., Vuorinen, Katariina, Tyystjarvi, Esa, Burow, Meike, Overmyer, Kirk, Mahonen, Ari P., and Mulo, Paula
Abstract: In Arabidopsis, two leaf-type ferredoxin-NADP(+) oxidoreductase (LFNR) isoforms function in photosynthetic electron flow in reduction of NADP(+), while two root-type FNR (RFNR) isoforms catalyse reduction of ferredoxin in non-photosynthetic plastids. As the key to understanding, the function of RFNRs might lie in their spatial and temporal distribution in different plant tissues and cell types, we examined expression of RFNR1 and RFNR2 genes using beta-glucuronidase (GUS) reporter lines and investigated accumulation of distinct RFNR isoforms using a GFP approach and Western blotting upon various stresses. We show that while RFNR1 promoter is active in leaf veins, root tips and in the stele of roots, RFNR2 promoter activity is present in leaf tips and root stele, epidermis and cortex. RFNR1 protein accumulates as a soluble protein within the plastids of root stele cells, while RFNR2 is mainly present in the outer root layers. Ozone treatment of plants enhanced accumulation of RFNR1, whereas low temperature treatment specifically affected RFNR2 accumulation in roots. We further discuss the physiological roles of RFNR1 and RFNR2 based on characterization of rfnr1 and rfnr2 knock-out plants and show that although the function of these proteins is partly redundant, the RFNR proteins are essential for plant development and survival.
Published: 2021

36. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV:update of taxonomy changes in 2021

Author: Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
Abstract: In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
Published: 2021

37. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author: Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, Krupovic, Mart, Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, and Krupovic, Mart
Abstract: This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.
Published: 2020

38. Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases

Author: Seifert, Mona (author), van Nies, Pauline (author), Papini, Flávia S. (author), Arnold, Jamie J. (author), Poranen, Minna M. (author), Cameron, Craig E. (author), Depken, S.M. (author), Dulin, D. (author), Seifert, Mona (author), van Nies, Pauline (author), Papini, Flávia S. (author), Arnold, Jamie J. (author), Poranen, Minna M. (author), Cameron, Craig E. (author), Depken, S.M. (author), and Dulin, D. (author)
Abstract: RNA virus survival depends on efficient viral genome replication, which is performed by the viral RNA dependent RNA polymerase (RdRp). The recent development of high throughput magnetic tweezers has enabled the simultaneous observation of dozens of viral RdRp elongation traces on kilobases long templates, and this has shown that RdRp nucleotide addition kinetics is stochastically interrupted by rare pauses of 1-1000 s duration, of which the short-lived ones (1-10 s) are the temporal signature of a low fidelity catalytic pathway. We present a simple and precise temperature controlled system for magnetic tweezers to characterize the replication kinetics temperature dependence between 25°C and 45°C of RdRps from three RNA viruses, i.e. the double-stranded RNA bacteriophage Φ6, and the positive-sense single-stranded RNA poliovirus (PV) and human rhinovirus C (HRV-C). We found that Φ6 RdRp is largely temperature insensitive, while PV and HRV-C RdRps replication kinetics are activated by temperature. Furthermore, the activation energies we measured for PV RdRp catalytic state corroborate previous estimations from ensemble pre-steady state kinetic studies, further confirming the catalytic origin of the short pauses and their link to temperature independent RdRp fidelity. This work will enable future temperature controlled study of biomolecular complex at the single molecule level., BN/Martin Depken Lab, BN/Nynke Dekker Lab
Published: 2020
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39. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author: Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, Krupovic, Mart, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, and Krupovic, Mart
Published: 2020

40. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author: UCL - SST/ELI/ELIM - Applied Microbiology, Adriaenssens, Evelien M., Sullivan, Matthew B., Knezevic, Petar, van Zyl, Leonardo J., Sarkar, B. L., Dutilh, Bas E., Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I., Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Edwards, Rob A., Kropinski, Andrew M., Petty, Nicola K., Clokie, Martha R. J., Kushkina, Alla I., Morozova, Vera V., Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M., Oksanen, Hanna M., Krupovic, Mart, UCL - SST/ELI/ELIM - Applied Microbiology, Adriaenssens, Evelien M., Sullivan, Matthew B., Knezevic, Petar, van Zyl, Leonardo J., Sarkar, B. L., Dutilh, Bas E., Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I., Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Edwards, Rob A., Kropinski, Andrew M., Petty, Nicola K., Clokie, Martha R. J., Kushkina, Alla I., Morozova, Vera V., Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M., Oksanen, Hanna M., and Krupovic, Mart
Abstract: This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.
Published: 2020

41. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author: Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, Krupovic, Mart, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, and Krupovic, Mart
Published: 2020

42. Spatially varying peatland initiation, Holocene development, carbon accumulation patterns and radiative forcing within a subarctic fen

Author: Piilo, S. R. (Sanna R.), Korhola, A. (Atte), Heiskanen, L. (Lauri), Tuovinen, J.-P. (Juha-Pekka), Aurela, M. (Mika), Juutinen, S. (Sari), Marttila, H. (Hannu), Saari, M. (Markus), Tuittila, E.-S. (Eeva-Stiina), Turunen, J. (Jukka), Väliranta, M. M. (Minna M.), Piilo, S. R. (Sanna R.), Korhola, A. (Atte), Heiskanen, L. (Lauri), Tuovinen, J.-P. (Juha-Pekka), Aurela, M. (Mika), Juutinen, S. (Sari), Marttila, H. (Hannu), Saari, M. (Markus), Tuittila, E.-S. (Eeva-Stiina), Turunen, J. (Jukka), and Väliranta, M. M. (Minna M.)
Abstract: High latitude peatlands act as globally important carbon (C) sinks and are in constant interaction with the atmosphere. Their C storage formed during the Holocene. In the course of time, the aggregate effect of the C fluxes on radiative forcing (RF) typically changes from warming to cooling, but the timing of this shift varies among different peatlands. Here we investigated Holocene peatland development, including vegetation history, vertical peat growth and the lateral expansion of a patterned subarctic fen in northern Finland by means of multiple sampling points. We modelled the Holocene RF by combining knowledge on past vegetation communities based on plant macrofossil stratigraphies and present in situ C flux measurements. The peatland initiated at ca. 9500 calibrated years Before Present (cal yr BP), and its lateral expansion was greatest between ca. 9000 and 7000 cal yr BP. After the early expansion, vertical peat growth proceeded very differently in different parts of the peatland, regulated by internal and external factors. The pronounced surface microtopography, with high strings and wet flarks, started to form only after ca. 1000 cal yr BP. C accumulation within the peatland recorded a high degree of spatial variability throughout its history, including the recent past. We applied two flux scenarios with different interpretation of the initial peatland development phases to estimate the RF induced by C fluxes of the fen. After ca. 4000 cal yr BP, at the latest, the peatland RF has been negative (cooling), mainly driven by C uptake and biomass production, while methane emissions had a lesser role in the total RF. Interestingly, these scenarios suggest that the greatest cooling effect took place around ca. 1000 cal yr BP, after which the surface microtopography established. The study demonstrated that despite the high spatial heterogeneity and idiosyncratic behaviour of the peatland, the RF of the studied fen followed the general development pattern
Published: 2020

43. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author: Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, Krupovic, Mart, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, and Krupovic, Mart
Published: 2020

44. SUCCOR study: an international European cohort observational study comparing minimally invasive surgery versus open abdominal radical hysterectomy in patients with stage IB1 cervical cancer

Author: Chiva, L, Zanagnolo, V, Querleu, D, Martin-Calvo, N, Arévalo-Serrano, J, Căpîlna, M, Fagotti, A, Kucukmetin, A, Mom, C, Chakalova, G, Aliyev, S, Malzoni, M, Narducci, F, Arencibia, O, Raspagliesi, F, Toptas, T, Cibula, D, Kaidarova, D, Meydanli, M, Tavares, M, Golub, D, Perrone, A, Poka, R, Tsolakidis, D, Vujić, G, Jedryka, M, Zusterzeel, P, Beltman, J, Goffin, F, Haidopoulos, D, Haller, H, Jach, R, Yezhova, I, Berlev, I, Bernardino, M, Bharathan, R, Lanner, M, Maenpaa, M, Sukhin, V, Feron, J, Fruscio, R, Kukk, K, Ponce, J, Minguez, J, Vázquez-Vicente, D, Castellanos, T, Chacon, E, Alcazar, J, Chiva, Luis, Zanagnolo, Vanna, Querleu, Denis, Martin-Calvo, Nerea, Arévalo-Serrano, Juan, Căpîlna, Mihai Emil, Fagotti, Anna, Kucukmetin, Ali, Mom, Constantijne, Chakalova, Galina, Aliyev, Shamistan, Malzoni, Mario, Narducci, Fabrice, Arencibia, Octavio, Raspagliesi, Francesco, Toptas, Tayfun, Cibula, David, Kaidarova, Dilyara, Meydanli, Mehmet Mutlu, Tavares, Mariana, Golub, Dmytro, Perrone, Anna Myriam, Poka, Robert, Tsolakidis, Dimitrios, Vujić, Goran, Jedryka, Marcin A, Zusterzeel, Petra L M, Beltman, Jogchum Jan, Goffin, Frederic, Haidopoulos, Dimitrios, Haller, Herman, Jach, Robert, Yezhova, Iryna, Berlev, Igor, Bernardino, Margarida, Bharathan, Rasiah, Lanner, Maximilian, Maenpaa, Minna M, Sukhin, Vladyslav, Feron, Jean-Guillaume, Fruscio, Robert, Kukk, Kersti, Ponce, Jordi, Minguez, Jose Angel, Vázquez-Vicente, Daniel, Castellanos, Teresa, Chacon, Enrique, Alcazar, Juan Luis, Chiva, L, Zanagnolo, V, Querleu, D, Martin-Calvo, N, Arévalo-Serrano, J, Căpîlna, M, Fagotti, A, Kucukmetin, A, Mom, C, Chakalova, G, Aliyev, S, Malzoni, M, Narducci, F, Arencibia, O, Raspagliesi, F, Toptas, T, Cibula, D, Kaidarova, D, Meydanli, M, Tavares, M, Golub, D, Perrone, A, Poka, R, Tsolakidis, D, Vujić, G, Jedryka, M, Zusterzeel, P, Beltman, J, Goffin, F, Haidopoulos, D, Haller, H, Jach, R, Yezhova, I, Berlev, I, Bernardino, M, Bharathan, R, Lanner, M, Maenpaa, M, Sukhin, V, Feron, J, Fruscio, R, Kukk, K, Ponce, J, Minguez, J, Vázquez-Vicente, D, Castellanos, T, Chacon, E, Alcazar, J, Chiva, Luis, Zanagnolo, Vanna, Querleu, Denis, Martin-Calvo, Nerea, Arévalo-Serrano, Juan, Căpîlna, Mihai Emil, Fagotti, Anna, Kucukmetin, Ali, Mom, Constantijne, Chakalova, Galina, Aliyev, Shamistan, Malzoni, Mario, Narducci, Fabrice, Arencibia, Octavio, Raspagliesi, Francesco, Toptas, Tayfun, Cibula, David, Kaidarova, Dilyara, Meydanli, Mehmet Mutlu, Tavares, Mariana, Golub, Dmytro, Perrone, Anna Myriam, Poka, Robert, Tsolakidis, Dimitrios, Vujić, Goran, Jedryka, Marcin A, Zusterzeel, Petra L M, Beltman, Jogchum Jan, Goffin, Frederic, Haidopoulos, Dimitrios, Haller, Herman, Jach, Robert, Yezhova, Iryna, Berlev, Igor, Bernardino, Margarida, Bharathan, Rasiah, Lanner, Maximilian, Maenpaa, Minna M, Sukhin, Vladyslav, Feron, Jean-Guillaume, Fruscio, Robert, Kukk, Kersti, Ponce, Jordi, Minguez, Jose Angel, Vázquez-Vicente, Daniel, Castellanos, Teresa, Chacon, Enrique, and Alcazar, Juan Luis
Abstract: Background: Minimally invasive surgery in cervical cancer has demonstrated in recent publications worse outcomes than open surgery. The primary objective of the SUCCOR study, a European, multicenter, retrospective, observational cohort study was to evaluate disease-free survival in patients with stage IB1 (FIGO 2009) cervical cancer undergoing open vs minimally invasive radical hysterectomy. As a secondary objective, we aimed to investigate the association between protective surgical maneuvers and the risk of relapse. Methods: We obtained data from 1272 patients that underwent a radical hysterectomy by open or minimally invasive surgery for stage IB1 cervical cancer (FIGO 2009) from January 2013 to December 2014. After applying all the inclusion-exclusion criteria, we used an inverse probability weighting to construct a weighted cohort of 693 patients to compare outcomes (minimally invasive surgery vs open). The first endpoint compared disease-free survival at 4.5 years in both groups. Secondary endpoints compared overall survival among groups and the impact of the use of a uterine manipulator and protective closure of the colpotomy over the tumor in the minimally invasive surgery group. Results: Mean age was 48.3 years (range; 23-83) while the mean BMI was 25.7 kg/m2 (range; 15-49). The risk of recurrence for patients who underwent minimally invasive surgery was twice as high as that in the open surgery group (HR, 2.07; 95% CI, 1.35 to 3.15; P=0.001). Similarly, the risk of death was 2.42-times higher than in the open surgery group (HR, 2.45; 95% CI, 1.30 to 4.60, P=0.005). Patients that underwent minimally invasive surgery using a uterine manipulator had a 2.76-times higher hazard of relapse (HR, 2.76; 95% CI, 1.75 to 4.33; P<0.001) and those without the use of a uterine manipulator had similar disease-free-survival to the open surgery group (HR, 1.58; 95% CI, 0.79 to 3.15; P=0.20). Moreover, patients that underwent minimally invasive surgery with protective va
Published: 2020

45. Joining European Scientific Forces to Face Pandemics

Author: European Commission, Instituto de Salud Carlos III, Ikerbasque Basque Foundation for Science, Carraresi Foundation, Regione Lombardia, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Consejo Superior de Investigaciones Científicas (España), Fundação para a Ciência e a Tecnologia (Portugal), Associazione Italiana per la Ricerca sul Cancro, PharmaMar, Fonds National de la Recherche Luxembourg, Ministère de l’Enseignement Supérieur et de la Recherche (Luxembourg), Fondation Coeur - Daniel Wagner, Vasconcelos, M. Helena, Alcaro, Stefano, Arechavala-Gameza, Virginia, Baumbach, Jan, Borges, Fernanda, Brevini, Tiziana A. L., De Las Rivas, Javier, Devaux, Yvan, Hozak, Pavel, Keinänen-Toivola, Minna M., Lattanzi, Giovanna, Mohr, Thomas, Murovska, Modra, Prusty, Bhupesh K., Quinlan, Roy A., Pérez-Sala, Dolores, Scheibenbogen, Carmen, Schmidt, Harald H.H.W., Silveira, Isabel, Tieri, Paolo, Tolios, Alexander, Riganti, Chiara, European Commission, Instituto de Salud Carlos III, Ikerbasque Basque Foundation for Science, Carraresi Foundation, Regione Lombardia, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Consejo Superior de Investigaciones Científicas (España), Fundação para a Ciência e a Tecnologia (Portugal), Associazione Italiana per la Ricerca sul Cancro, PharmaMar, Fonds National de la Recherche Luxembourg, Ministère de l’Enseignement Supérieur et de la Recherche (Luxembourg), Fondation Coeur - Daniel Wagner, Vasconcelos, M. Helena, Alcaro, Stefano, Arechavala-Gameza, Virginia, Baumbach, Jan, Borges, Fernanda, Brevini, Tiziana A. L., De Las Rivas, Javier, Devaux, Yvan, Hozak, Pavel, Keinänen-Toivola, Minna M., Lattanzi, Giovanna, Mohr, Thomas, Murovska, Modra, Prusty, Bhupesh K., Quinlan, Roy A., Pérez-Sala, Dolores, Scheibenbogen, Carmen, Schmidt, Harald H.H.W., Silveira, Isabel, Tieri, Paolo, Tolios, Alexander, and Riganti, Chiara
Abstract: Despite the international guidelines on the containment of the coronavirus disease 2019 (COVID-19) pandemic, the European scientific community was not sufficiently prepared to coordinate scientific efforts. To improve preparedness for future pandemics, we have initiated a network of nine European-funded Cooperation in Science and Technology (COST) Actions that can help facilitate inter-, multi-, and trans-disciplinary communication and collaboration.
Published: 2020

46. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Author: Parducci, Laura, Alsos, Inger Greve, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Valiranta, Minna M., Slotte, Tanja, Wohlfarth, Barbara, Parducci, Laura, Alsos, Inger Greve, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Valiranta, Minna M., Slotte, Tanja, and Wohlfarth, Barbara
Abstract: The lake sediments of Hasseldala Port in south-east Sweden provide an archive of local and regional environmental conditions similar to 14.5-9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerod (14.1-12.7 ka BP), Younger Dryas (12.7-11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerod; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach.
Published: 2019
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47. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Author: Parducci, Laura, Alsos, Inger Greve, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Valiranta, Minna M., Slotte, Tanja, Wohlfarth, Barbara, Parducci, Laura, Alsos, Inger Greve, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Valiranta, Minna M., Slotte, Tanja, and Wohlfarth, Barbara
Abstract: The lake sediments of Hasseldala Port in south-east Sweden provide an archive of local and regional environmental conditions similar to 14.5-9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerod (14.1-12.7 ka BP), Younger Dryas (12.7-11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerod; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach.
Published: 2019
Full Text: View/download PDF

48. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Author: Parducci, Laura, Alsos, Inger Greve, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Valiranta, Minna M., Slotte, Tanja, Wohlfarth, Barbara, Parducci, Laura, Alsos, Inger Greve, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Valiranta, Minna M., Slotte, Tanja, and Wohlfarth, Barbara
Abstract: The lake sediments of Hasseldala Port in south-east Sweden provide an archive of local and regional environmental conditions similar to 14.5-9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerod (14.1-12.7 ka BP), Younger Dryas (12.7-11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerod; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach.
Published: 2019
Full Text: View/download PDF

49. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Author: Parducci, Laura, Greve Alsos, Inger, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Väliranta, Minna M., Slotte, Tanja, Wohlfarth, Barbara, Parducci, Laura, Greve Alsos, Inger, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Väliranta, Minna M., Slotte, Tanja, and Wohlfarth, Barbara
Abstract: The lake sediments of Hasseldala Port in south-east Sweden provide an archive of local and regional environmental conditions similar to 14.5-9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerod (14.1-12.7 ka BP), Younger Dryas (12.7-11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerod; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach.
Published: 2019
Full Text: View/download PDF

50. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Author: Parducci, Laura, Alsos, Inger Greve, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Valiranta, Minna M., Slotte, Tanja, Wohlfarth, Barbara, Parducci, Laura, Alsos, Inger Greve, Unneberg, Per, Pedersen, Mikkel W., Han, Lu, Lammers, Youri, Salonen, J. Sakari, Valiranta, Minna M., Slotte, Tanja, and Wohlfarth, Barbara
Abstract: The lake sediments of Hasseldala Port in south-east Sweden provide an archive of local and regional environmental conditions similar to 14.5-9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerod (14.1-12.7 ka BP), Younger Dryas (12.7-11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerod; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach.
Published: 2019
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