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3. Women in the European Virus Bioinformatics Center

Author

Hufsky, Franziska, Abecasis, Ana, Agudelo-Romero, Patricia, Bletsa, Magda, Brown, Katherine, Claus, Claudia, Deinhardt-Emmer, Stefanie, Deng, Li, Friedel, Caroline C, Gismondi, María Inés, Kostaki, Evangelia Georgia, Kühnert, Denise, Kulkarni-Kale, Urmila, Metzner, Karin J, Meyer, Irmtraud M, Miozzi, Laura, Nishimura, Luca, Paraskevopoulou, Sofia, Pérez-Cataluña, Alba, Rahlff, Janina, Thomson, Emma, Tumescheit, Charlotte, van der Hoek, Lia, Van Espen, Lore, Vandamme, Anne-Mieke, Zaheri, Maryam, Zuckerman, Neta, Marz, Manja, Hufsky, Franziska [0000-0002-9489-3182], Abecasis, Ana [0000-0002-3903-5265], Agudelo-Romero, Patricia [0000-0002-3703-4111], Bletsa, Magda [0000-0003-3184-6618], Brown, Katherine [0000-0002-8400-6922], Claus, Claudia [0000-0003-4962-6568], Deinhardt-Emmer, Stefanie [0000-0003-4495-4052], Deng, Li [0000-0003-0225-0663], Friedel, Caroline C [0000-0003-3569-4877], Gismondi, María Inés [0000-0002-2566-1169], Kostaki, Evangelia Georgia [0000-0002-3346-0930], Kühnert, Denise [0000-0002-5657-018X], Kulkarni-Kale, Urmila [0000-0002-1168-2479], Metzner, Karin J [0000-0003-4862-1503], Meyer, Irmtraud M [0000-0002-4048-3479], Miozzi, Laura [0000-0003-0410-8230], Nishimura, Luca [0000-0003-2144-7867], Paraskevopoulou, Sofia [0000-0003-2608-2596], Pérez-Cataluña, Alba [0000-0002-4784-8346], Rahlff, Janina [0000-0002-2132-2709], Thomson, Emma [0000-0003-1482-0889], Tumescheit, Charlotte [0000-0002-7563-5575], van der Hoek, Lia [0000-0003-2803-642X], Van Espen, Lore [0000-0002-3870-4551], Vandamme, Anne-Mieke [0000-0002-6594-2766], Zaheri, Maryam [0000-0003-2777-835X], Zuckerman, Neta [0000-0001-6074-2100], Marz, Manja [0000-0003-4783-8823], Apollo - University of Cambridge Repository, Medical Microbiology and Infection Prevention, AII - Infectious diseases, University of Zurich, Hufsky, Franziska, and Marz, Manja

Subjects
10028 Institute of Medical Virology, virus evolution, virus discovery, Cancer Research, viral ecology, Virus Bioinformatics, Big Data, Networking, Virus Discovery, Virus Evolution, Viral Infection, Transcriptomics, Emerging Viruses, Epidemiology, Viral Ecology, networking, virus bioinformatics, Computational Biology, 610 Medicine & health, 2725 Infectious Diseases, Research Personnel, Europe, emerging viruses, transcriptomics, big data, Viruses, 2406 Virology, 570 Life sciences, biology, Humans, epidemiology, Female, viral infection
Abstract

Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics. ispartof: VIRUSES-BASEL vol:14 issue:7 ispartof: location:Switzerland status: published

Published
2022

6. Women in the European Virus Bioinformatics Center

Author

Hufsky, Franziska; https://orcid.org/0000-0002-9489-3182, Abecasis, Ana; https://orcid.org/0000-0002-3903-5265, Agudelo-Romero, Patricia; https://orcid.org/0000-0002-3703-4111, Bletsa, Magda; https://orcid.org/0000-0003-3184-6618, Brown, Katherine; https://orcid.org/0000-0002-8400-6922, Claus, Claudia; https://orcid.org/0000-0003-4962-6568, Deinhardt-Emmer, Stefanie; https://orcid.org/0000-0003-4495-4052, Deng, Li; https://orcid.org/0000-0003-0225-0663, Friedel, Caroline C; https://orcid.org/0000-0003-3569-4877, Gismondi, María Inés; https://orcid.org/0000-0002-2566-1169, Kostaki, Evangelia Georgia; https://orcid.org/0000-0002-3346-0930, Kühnert, Denise; https://orcid.org/0000-0002-5657-018X, Kulkarni-Kale, Urmila; https://orcid.org/0000-0002-1168-2479, Metzner, Karin J; https://orcid.org/0000-0003-4862-1503, Meyer, Irmtraud M; https://orcid.org/0000-0002-4048-3479, Miozzi, Laura; https://orcid.org/0000-0003-0410-8230, Nishimura, Luca; https://orcid.org/0000-0003-2144-7867, Paraskevopoulou, Sofia; https://orcid.org/0000-0003-2608-2596, Pérez-Cataluña, Alba; https://orcid.org/0000-0002-4784-8346, Rahlff, Janina; https://orcid.org/0000-0002-2132-2709, Thomson, Emma; https://orcid.org/0000-0003-1482-0889, Tumescheit, Charlotte; https://orcid.org/0000-0002-7563-5575, van der Hoek, Lia; https://orcid.org/0000-0003-2803-642X, Van Espen, Lore; https://orcid.org/0000-0002-3870-4551, Vandamme, Anne-Mieke; https://orcid.org/0000-0002-6594-2766, Zaheri, Maryam; https://orcid.org/0000-0003-2777-835X, Zuckerman, Neta; https://orcid.org/0000-0001-6074-2100, Marz, Manja; https://orcid.org/0000-0003-4783-8823, Hufsky, Franziska; https://orcid.org/0000-0002-9489-3182, Abecasis, Ana; https://orcid.org/0000-0002-3903-5265, Agudelo-Romero, Patricia; https://orcid.org/0000-0002-3703-4111, Bletsa, Magda; https://orcid.org/0000-0003-3184-6618, Brown, Katherine; https://orcid.org/0000-0002-8400-6922, Claus, Claudia; https://orcid.org/0000-0003-4962-6568, Deinhardt-Emmer, Stefanie; https://orcid.org/0000-0003-4495-4052, Deng, Li; https://orcid.org/0000-0003-0225-0663, Friedel, Caroline C; https://orcid.org/0000-0003-3569-4877, Gismondi, María Inés; https://orcid.org/0000-0002-2566-1169, Kostaki, Evangelia Georgia; https://orcid.org/0000-0002-3346-0930, Kühnert, Denise; https://orcid.org/0000-0002-5657-018X, Kulkarni-Kale, Urmila; https://orcid.org/0000-0002-1168-2479, Metzner, Karin J; https://orcid.org/0000-0003-4862-1503, Meyer, Irmtraud M; https://orcid.org/0000-0002-4048-3479, Miozzi, Laura; https://orcid.org/0000-0003-0410-8230, Nishimura, Luca; https://orcid.org/0000-0003-2144-7867, Paraskevopoulou, Sofia; https://orcid.org/0000-0003-2608-2596, Pérez-Cataluña, Alba; https://orcid.org/0000-0002-4784-8346, Rahlff, Janina; https://orcid.org/0000-0002-2132-2709, Thomson, Emma; https://orcid.org/0000-0003-1482-0889, Tumescheit, Charlotte; https://orcid.org/0000-0002-7563-5575, van der Hoek, Lia; https://orcid.org/0000-0003-2803-642X, Van Espen, Lore; https://orcid.org/0000-0002-3870-4551, Vandamme, Anne-Mieke; https://orcid.org/0000-0002-6594-2766, Zaheri, Maryam; https://orcid.org/0000-0003-2777-835X, Zuckerman, Neta; https://orcid.org/0000-0001-6074-2100, and Marz, Manja; https://orcid.org/0000-0003-4783-8823

Abstract

Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.

Published
2022

8. Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina

Author

Torres, Carolina, primary, Mojsiejczuk, Laura, additional, Acuña, Dolores, additional, Alexay, Sofía, additional, Amadio, Ariel, additional, Aulicino, Paula, additional, Debat, Humberto, additional, Fay, Fabián, additional, Fernández, Franco, additional, Giri, Adriana A., additional, Goya, Stephanie, additional, König, Guido, additional, Lucero, Horacio, additional, Nabaes Jodar, Mercedes, additional, Pianciola, Luis, additional, Sfalcin, Javier A., additional, Acevedo, Raúl M., additional, Bengoa Luoni, Sofía, additional, Bolatti, Elisa M., additional, Brusés, Bettina, additional, Cacciabue, Marco, additional, Casal, Pablo E., additional, Cerri, Agustina, additional, Chouhy, Diego, additional, Dus Santos, María José, additional, Eberhardt, María Florencia, additional, Fernandez, Ailen, additional, Fernández, Paula del Carmen, additional, Fernández Do Porto, Darío, additional, Formichelli, Laura, additional, Gismondi, María Inés, additional, Irazoqui, Matías, additional, Campos, Melina Lorenzini, additional, Lusso, Silvina, additional, Marquez, Nathalie, additional, Muñoz, Marianne, additional, Mussin, Javier, additional, Natale, Mónica, additional, Oria, Griselda, additional, Pisano, María Belén, additional, Posner, Victoria, additional, Puebla, Andrea, additional, Re, Viviana, additional, Sosa, Ezequiel, additional, Villanova, Gabriela V., additional, Zaiat, Jonathan, additional, Zunino, Sebastián, additional, Acevedo, María Elina, additional, Acosta, Julián, additional, Alvarez Lopez, Cristina, additional, Álvarez, María Laura, additional, Angeleri, Patricia, additional, Angelletti, Andrés, additional, Arca, Manuel, additional, Ayala, Natalia A., additional, Barbas, Gabriela, additional, Bertone, Ana, additional, Bonnet, Agustina, additional, Bourlot, Ignacio, additional, Cabassi, Victoria, additional, Castello, Alejandro, additional, Castro, Gonzalo, additional, Cavatorta, Ana Laura, additional, Ceriani, Carolina, additional, Cimmino, Carlos, additional, Cipelli, Julián, additional, Colmeiro, María, additional, Cordero, Andrés, additional, Cristina, Carolina, additional, Di Bella, Sofia, additional, Dolcini, Guillermina, additional, Ercole, Regina, additional, Espasandin, Yesica, additional, Espul, Carlos, additional, Falaschi, Andrea, additional, Fernandez Moll, Facundo, additional, Foussal, María Delia, additional, Gatelli, Andrea, additional, Goñi, Sandra, additional, Jofré, María Estela, additional, Jaramillo, José, additional, Labarta, Natalia, additional, Lacaze, María Agustina, additional, Larreche, Rocio, additional, Leiva, Viviana, additional, Levin, Gustavo, additional, Luczak, Erica, additional, Mandile, Marcelo, additional, Marino, Gioia, additional, Massone, Carla, additional, Mazzeo, Melina, additional, Medina, Carla, additional, Monaco, Belén, additional, Montoto, Luciana, additional, Mugna, Viviana, additional, Musto, Alejandra, additional, Nadalich, Victoria, additional, Nieto, María Victoria, additional, Ojeda, Guillermo, additional, Piedrabuena, Andrea C., additional, Pintos, Carolina, additional, Pozzati, Marcia, additional, Rahhal, Marilina, additional, Rechimont, Claudia, additional, Remes Lenicov, Federico, additional, Rompato, Gabriela, additional, Seery, Vanesa, additional, Siri, Leticia, additional, Spina, Julieta, additional, Streitenberger, Cintia, additional, Suárez, Ariel, additional, Suárez, Jorgelina, additional, Sujansky, Paula, additional, Talia, Juan Manuel, additional, Theaux, Clara, additional, Thomas, Guillermo, additional, Ticeira, Marina, additional, Tittarelli, Estefanía, additional, Toro, Rosana, additional, Uez, Osvaldo, additional, Zaffanella, María Belén, additional, Ziehm, Cecilia, additional, and Zubieta, Martin, additional

Published
2021
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9. Women in the European Virus Bioinformatics Center

Author

Hufsky, Franziska, Abecasis, Ana, Agudelo-Romero, Patricia, Bletsa, Magda, Brown, Katherine, Claus, Claudia, Deinhardt-Emmer, Stefanie, Deng, Li, Friedel, Caroline C., Gismondi, María Inés, Kostaki, Evangelia Georgia, Kühnert, Denise, Kulkarni-Kale, Urmila, Metzner, Karin J., Meyer, Irmtraud M., Miozzi, Laura, Nishimura, Luca, Paraskevopoulou, Sofia, Pérez-Cataluña, Alba, Rahlff, Janina, Thomson, Emma, Tumescheit, Charlotte, van der Hoek, Lia, Van Espen, Lore, Vandamme, Anne-Mieke, Zaheri, Maryam, Zuckerman, Neta, and Marz, Manja

Subjects
Commentary, virus bioinformatics, big data, networking, virus discovery, virus evolution, viral infection, transcriptomics, emerging viruses, epidemiology, viral ecology, ddc
Published
2021

10. Isolation of endophytic bacteria from the medicinal, forestal and ornamental tree Handroanthus impetiginosus.

Author

Yarte, Mauro Enrique, Gismondi, María Inés, Llorente, Berta Elizabet, and Larraburu, Ezequiel Enrique

Subjects
ENDOPHYTIC bacteria, ORNAMENTAL trees, RHIZOBIUM, FERTILIZERS, INDOLE compounds, TREE growth, NITROGEN compounds, PESTICIDES
Abstract

Plant interactions with endophytic bacteria produce mutual benefits and contribute to environmental sustainability. Handroanthus impetiginosus (Mart. ex DC.) Mattos 'pink lapacho' (syn. Tabebuia impetiginosa, Bignoniaceae) is a medicinal, ornamental and forestal native tree from South and Mesoamerica. Plant growth promoting bacteria (PGPB) isolated from pink lapacho are scarcely described. The aim of this work was to isolate and characterize native endophytic bacteria from pink lapacho. Ten bacterial strains were isolated from leaves and six from roots of naturally growing trees in Luján (Central-Eastern region of Argentina). Endophytes were identified as Bacillus, Paenibacillus, Pseudomonas, Rhizobium, Rummeliibacillus and Methylobacterium genera, according to 16S rRNA gene sequencing and phylogenetic analysis. In the present study, a strain of the Rummelibacillus genus (L14) has been first ever reported as endophyte. This strain was capable of growing in Nfb medium and exhibited zinc solubilization ability. A high percentage of strains showed PGPB traits; namely 88% fixed nitrogen, 63% solubilized zinc, 69% solubilized phosphate and 63% produced indole compounds such as IAA. Most strains were salt tolerant that confer them a potential competitive advantage to survive in saline conditions. To the best of our knowledge, this is the first study reporting an approach to assess the diversity of cultivable endophytic bacteria of H. impetiginosus tree and its plant growth promoting capacity. The knowledge about this kind of associations could contribute to environmental sustainability by developing effective biofertilizers that minimize the use of chemical fertilizers and pesticides. [ABSTRACT FROM AUTHOR]

Published
2022
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15. A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing.

Author

Cacciabue, Marco, Currá, Anabella, Carrillo, Elisa, König, Guido, and Gismondi, María Inés

Subjects
NUCLEOTIDE sequencing, FOOT & mouth disease, VIRAL variation, VIRUS diseases, VIRAL genomes, RNA viruses
Abstract

Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity. However, the analysis of next-generation sequencing data might be challenging for researchers who have never approached the study of viral quasispecies by this methodology. In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data. The guide includes a complete analysis pipeline along with user-friendly descriptions of software and file formats. In addition, we assessed the feasibility of the workflow proposed by analyzing a set of foot-and-mouth disease viruses (FMDV) with different degrees of variability. This guide introduces the analysis of quasispecies of FMDV and other viruses through this kind of approach. [ABSTRACT FROM AUTHOR]

Published
2020
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24. Epstein barr virus associated pediatric nasopharyngeal carcinoma: Its correlation with p53 and <TOGGLE>bcl</TOGGLE>-2 expression

Author

Preciado, María Victoria, Chabay, Paola A., Matteo, Elena N. De, Gismondi, María Inés, Rey, Guadalupe, and Zubizarreta, Pedro

Abstract

Pediatric nasopharyngeal carcinoma (NPC) is relatively rare. The Epstein Barr virus (EBV) association with the oncogenesis of NPC is well established. Apoptosis-related proteins, p53 and bcl-2, have also been described in adult NPC pathogenesis. From 1988 to 1998, 16 patients with NPC were treated at R. Gutierrez Children's Hospital and the National J.P. Garrahan Pediatric Hospital. Their median age was 12 years (range 8–20), 2 females and 14 males. The presence of p53, bcl-2 and latent membrane protein-1 (LMP-1) of EBV expression was studied by immunohistochemistry and Epstein Barr encoded RNAs (EBERs) by in situ hybridization in tissue sections from formalin-fixed, paraffin-embedded NPC biopsies EBV presence and LMP-1 expression in epithelial tumor cells were detected in all the biopsies studied. p53 was expressed in 13/16 NPCs, but the frequency of positive malignant cells differed from case to case, ranging from less than 25 to 100% with heterogeneous staining intensity. Bcl-2 positive staining in tumor epithelial cells was detected in 2/16; whereas 10/16 cases showed bcl-2 positivity in infiltrating lymphocytes. Although our series is small, we conclude that the pathogenesis of pediatric NPC as a multistep process may well involve EBV infection. This leads to LMP-1 expression and p53 overexpression in epithelial tumor cells, whereas bc-2 seems unrelated to the development of this disorder. Med. Pediatr. Oncol. 2002;38:345–348. © 2002 Wiley-Liss, Inc.

Published
2002
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25. Differential replication of Foot-and-mouth disease viruses in mice determine lethality.

Author

García-Núñez, María Soledad, Marrero, Rubén, Cacciabue, Marco, Currá, Anabella, Molinari, Paula, Gismondi, María Inés, Delgado, Fernando, Rieder, Elizabeth, and Carrillo, Elisa

Subjects
*FOOT & mouth disease virus, *CAPSIDS
Abstract

Adult C57BL/6J mice have been used to study Foot-and-mouth disease virus (FMDV) biology. In this work, two variants of an FMDV A/Arg/01 strain exhibiting differential pathogenicity in adult mice were identified and characterized: a non-lethal virus (A01NL) caused mild signs of disease, whereas a lethal virus (A01L) caused death within 24–48 h independently of the dose used. Both viruses caused a systemic infection with pathological changes in the exocrine pancreas. Virus A01L reached higher viral loads in plasma and organs of inoculated mice as well as increased replication in an ovine kidney cell line. Complete consensus sequences revealed 6 non-synonymous changes between A01L and A10NL genomes that might be linked to replication differences, as suggested by in silico prediction studies. Our results highlight the biological significance of discrete genomic variations and reinforce the usefulness of this animal model to study viral determinants of lethality. [ABSTRACT FROM AUTHOR]

Published
2017
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26. Women in the European Virus Bioinformatics Center.

Author

Hufsky F, Abecasis A, Agudelo-Romero P, Bletsa M, Brown K, Claus C, Deinhardt-Emmer S, Deng L, Friedel CC, Gismondi MI, Kostaki EG, Kühnert D, Kulkarni-Kale U, Metzner KJ, Meyer IM, Miozzi L, Nishimura L, Paraskevopoulou S, Pérez-Cataluña A, Rahlff J, Thomson E, Tumescheit C, van der Hoek L, Van Espen L, Vandamme AM, Zaheri M, Zuckerman N, and Marz M

Subjects
Europe, Female, Humans, Computational Biology, Research Personnel statistics & numerical data, Viruses genetics
Abstract

Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.

Published
2022
Full Text
View/download PDF

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