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6. Genetic screening in a Brazilian cohort with inborn errors of immunity

Author

Ferreira, Cristina Santos, Francisco Junior, Ronaldo da Silva, Gerber, Alexandra Lehmkuhl, Guimarães, Ana Paula de Campos, de Carvalho, Flavia Amendola Anisio, dos Reis, Bárbara Carvalho Santos, Pinto-Mariz, Fernanda, de Souza, Monica Soares, de Vasconcelos, Zilton Farias Meira, Goudouris, Ekaterini Simões, and Vasconcelos, Ana Tereza Ribeiro

Published
2023
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7. Assessing whole-exome sequencing data from undiagnosed Brazilian patients to improve the diagnostic yield of inborn errors of immunity

Author

Ferreira, Cristina Santos, da Silva Francisco Junior, Ronaldo, Gerber, Alexandra Lehmkuhl, Guimarães, Ana Paula de Campos, Amendola, Flávia Anisio, Pinto-Mariz, Fernanda, de Souza, Monica Soares, Miranda, Patrícia Carvalho Batista, de Vasconcelos, Zilton Farias Meira, Goudouris, Ekaterini Simões, and Vasconcelos, Ana Tereza Ribeiro

Published
2023
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9. Antimicrobial resistance and genetic background of non-typhoidal Salmonella enterica strains isolated from human infections in São Paulo, Brazil (2000–2019)

Author

Calarga, Aline Parolin, Gontijo, Marco Tulio Pardini, de Almeida, Luiz Gonzaga Paula, de Vasconcelos, Ana Tereza Ribeiro, Nascimento, Leandro Costa, de Moraes Barbosa, Taíse Marongio Cotrim, de Carvalho Perri, Thalita Mara, dos Santos, Silvia Regina, Tiba-Casas, Monique Ribeiro, Marques, Eneida Gonçalves Lemes, Ferreira, Cleide Marques, and Brocchi, Marcelo

Published
2022
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10. Clinical and genetic findings in two siblings with X-Linked agammaglobulinemia and bronchiolitis obliterans: a case report

Author

Francisco Junior, Ronaldo da Silva, de Morais, Guilherme Loss, de Carvalho, Joseane Biso, dos Santos Ferreira, Cristina, Gerber, Alexandra Lehmkuhl, de C Guimarães, Ana Paula, Amendola, Flávia Anisio, Pinto-Mariz, Fernanda, de Vasconcelos, Zilton Farias Meira, Goudouris, Ekaterini Simões, and de Vasconcelos, Ana Tereza Ribeiro

Published
2022
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11. Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans

Author

Lemos, Leandro Nascimento, de Carvalho, Fabíola Marques, Santos, Fernanda Fernandes, Valiatti, Tiago Barcelos, Corsi, Dandara Cassu, de Oliveira Silveira, Alessandro Conrado, Gerber, Alexandra, Guimarães, Ana Paula C., de Oliveira Souza, Cintya, Brasiliense, Danielle Murici, Maia Castelo-Branco, Débora de Souza Collares, Anzai, Eleine Kuroki, Bessa-Neto, Francisco Ozório, de Melo, Gláucia Morgana, de Souza, Gleyce Hellen, Ferraz, Lúcio Fábio Caldas, de Nazaré Miranda Bahia, Márcia, Mattos, Márcia Soares, da Silva, Ramon Giovani Brandão, Veiga, Ruanita, Simionatto, Simone, Monteiro, Walter Aparecido Pimentel, de Oliveira Lima, William Alencar, Kiffer, Carlos Roberto Veiga, Cayô, Rodrigo, Gales, Ana Cristina, and de Vasconcelos, Ana Tereza Ribeiro

Published
2022
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12. Host genetic susceptibility underlying SARS-CoV-2-associated Multisystem Inflammatory Syndrome in Brazilian Children

Author

Santos-Rebouças, Cíntia Barros, Piergiorge, Rafael Mina, dos Santos Ferreira, Cristina, Seixas Zeitel, Raquel de, Gerber, Alexandra Lehmkuhl, Rodrigues, Marta Cristine Felix, Guimarães, Ana Paula de Campos, Silva, Rodrigo Moulin, Fonseca, Adriana Rodrigues, Souza, Rangel Celso, de Souza, Ana Tereza Antunes Monteiro, Rossi, Átila Duque, Porto, Luís Cristóvão de Moraes Sobrino, Cardoso, Cynthia Chester, and de Vasconcelos, Ana Tereza Ribeiro

Published
2022
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14. SARS-CoV-2 Research in Dogs (Canis lupus familiaris) and Felines (Felis silvestris catus) Domiciled in an International Border Region (Paraguay and Brazil).

Author

Rey, Laisa Marina Rosa, Delai, Robson Michael, Batista, Aline Cristiane Cechinel Assing, Ferreira, Leonardo, Santos, Isabela Carvalho dos, Del Vecchio, Marco Aurélio Cunha, Andrade, Ana Cláudia Souza, Teles, Pedro, Pereira, Ulisses de Pádua, Gerber, Alexandra Lehmkuhl, Guimarães, Ana Paula de Campos, Almeida, Luiz Gonzaga Paula de, Lamarca, Alessandra Pavan, Vasconcelos, Ana Tereza Ribeiro de, and Gonçalves, Daniela Dib

Subjects
CATS, COVID-19, SARS-CoV-2 Delta variant, SCIENTIFIC literature, COMMUNICABLE diseases
Abstract

Introduction: COVID-19 is an infectious disease caused by SARS-CoV-2 that has become a serious threat to public health owing to its rapid spread from aerosols from infected people. Despite being considered a strictly human disease, there are reports in the literature about animals with confirmed presence of the virus. Aim: Owing to the scarcity of scientific literature on the potential for infection of animals and their importance for One Health, the objective of this work was to research SARS-CoV-2 RNA in felines (Felis silvestris catus) and dogs (Canis lupus familiaris) domiciled. Materials and Methods: Oropharyngeal swabs were collected from domestic dogs and cats belonging to patients diagnosed with COVID-19 from August to October 2021 and residents of the northwest and west regions of Paraná, Brazil. Results: Of the 34 samples collected, 14 were from dogs and 20 from cats. Three of these samples tested positive in real-time PCR, and two of them were also positive in the immunochromatographic test. After testing positive in real-time PCR, the samples underwent genetic sequencing using the Illumina COVIDSeq test. Of the 34 samples collected, three (9%), all of them female and from the feline species, tested positive in real-time PCR, with two of these (67%) also testing positive in the immunochromatographic test. Regarding sequencing, it was possible to sequence the three samples aligned with the AY.101 lineage, corresponding to the Delta variant. Conclusion: The occurrence of SARS-CoV-2 infection in dogs and cats is seen as an unintended event with significant implications for public health, including its potential transmission to other animal species. Further research is required to enhance our understanding of how this disease spreads among these animals and its broader impact on One Health initiatives. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Uncovering the transcriptional molecular dynamics of shelf life extension and system acquired resistance induction toFusarium pallidoroseumin melon fruits by the use of pulsed-light

Author

Arge, Luis Willian Pacheco, primary, Morais, Guilherme Loss, additional, Carvalho, Joseane Biso, additional, Zocolo, Guilherme Julião, additional, Oster, Andréia Hansen, additional, Vasconcelos, Ana Tereza Ribeiro de, additional, Diniz, Leandro Eugenio Cardamone, additional, Silva, Ebenézer de Oliveira, additional, and Bordallo, Patricia do Nascimento, additional

Published
2024
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16. Transcriptional and Post-Translational Roles of Calcineurin in Cationic Stress and Glycerol Biosynthesis in Cryptococcus neoformans.

Author

Santos, Ronaldo Silva, Martins-Silva, Gabriel, Padilla, Adrián Adolfo Álvarez, Possari, Mateus, Degello, Sérgio Donnantuoni, Bernardes Brustolini, Otávio J., Vasconcelos, Ana Tereza Ribeiro, Vallim, Marcelo Afonso, and Pascon, Renata C.

Subjects
CRYPTOCOCCUS neoformans, GENETIC transcription regulation, COLONIZATION (Ecology), CALCINEURIN, EFFECT of stress on animals
Abstract

Stress management is an adaptive advantage for survival in adverse environments. Pathogens face this challenge during host colonization, requiring an appropriate stress response to establish infection. The fungal pathogen Cryptococcus neoformans undergoes thermal, oxidative, and osmotic stresses in the environment and animal host. Signaling systems controlled by Ras1, Hog1, and calcineurin respond to high temperatures and osmotic stress. Cationic stress caused by Na+, K+, and Li+ can be overcome with glycerol, the preferred osmolyte. Deleting the glycerol phosphate phosphatase gene (GPP2) prevents cells from accumulating glycerol due to a block in the last step of its biosynthetic pathway. Gpp2 accumulates in a phosphorylated form in a cna1Δ strain, and a physical interaction between Gpp2 and Cna1 was found; moreover, the gpp2Δ strain undergoes slow growth and has attenuated virulence in animal models of infection. We provide biochemical evidence that growth in 1 M NaCl increases glycerol content in the wild type, whereas gpp2Δ, cna1Δ, and cnb1Δ mutants fail to accumulate it. The deletion of cnb1Δ or cna1Δ renders yeast cells sensitive to cationic stress, and the Gfp-Gpp2 protein assumes an abnormal localization. We suggest a mechanism in which calcineurin controls Gpp2 at the post-translational level, affecting its localization and activity, leading to glycerol biosynthesis. Also, we showed the transcriptional profile of glycerol-deficient mutants and established the cationic stress response mediated by calcineurin; among the biological processes differentially expressed are carbon utilization, translation, transmembrane transport, glutathione metabolism, oxidative stress response, and transcription regulation. To our knowledge, this is the first time that this transcriptional profile has been described. These results have implications for pathogen stress adaptability. [ABSTRACT FROM AUTHOR]

Published
2024
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17. OntoPPI: Towards Data Formalization on the Prediction of Protein Interactions

Author

Martins, Yasmmin Cortes, Cavalcanti, Maria Cláudia, Arge, Luis Willian Pacheco, Ziviani, Artur, de Vasconcelos, Ana Tereza Ribeiro, Barbosa, Simone Diniz Junqueira, Editorial Board Member, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Garoufallou, Emmanouel, editor, Fallucchi, Francesca, editor, and William De Luca, Ernesto, editor

Published
2019
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19. Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M., Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jérôme, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jønsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, André E. R., Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O., Székely, Tamás, Liu, Yang, Campana, Michael G., Corvelo, André, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Milá, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Ángela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, and Zhang, Guojie

Published
2020
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23. Author Correction: Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M., Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jérôme, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jønsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, André E. R., Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O., Székely, Tamás, Liu, Yang, Campana, Michael G., Corvelo, André, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Milá, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Ángela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, and Zhang, Guojie

Published
2021
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27. Additional file 4 of Host genetic susceptibility underlying SARS-CoV-2-associated Multisystem Inflammatory Syndrome in Brazilian Children

Author

Santos-Rebouças, Cíntia Barros, Piergiorge, Rafael Mina, dos Santos Ferreira, Cristina, Seixas Zeitel, Raquel de, Gerber, Alexandra Lehmkuhl, Rodrigues, Marta Cristine Felix, Guimarães, Ana Paula de Campos, Silva, Rodrigo Moulin, Fonseca, Adriana Rodrigues, Souza, Rangel Celso, de Souza, Ana Tereza Antunes Monteiro, Rossi, Átila Duque, Porto, Luís Cristóvão de Moraes Sobrino, Cardoso, Cynthia Chester, and de Vasconcelos, Ana Tereza Ribeiro

Abstract

Additional file 4: Table S4. Additional very rare variants (MAF < 0.01) found in MIS-C patients. No relevant variants were found in patient EXOC17.

Published
2023
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28. Additional file 2 of Host genetic susceptibility underlying SARS-CoV-2-associated Multisystem Inflammatory Syndrome in Brazilian Children

Author

Santos-Rebouças, Cíntia Barros, Piergiorge, Rafael Mina, dos Santos Ferreira, Cristina, Seixas Zeitel, Raquel de, Gerber, Alexandra Lehmkuhl, Rodrigues, Marta Cristine Felix, Guimarães, Ana Paula de Campos, Silva, Rodrigo Moulin, Fonseca, Adriana Rodrigues, Souza, Rangel Celso, de Souza, Ana Tereza Antunes Monteiro, Rossi, Átila Duque, Porto, Luís Cristóvão de Moraes Sobrino, Cardoso, Cynthia Chester, and de Vasconcelos, Ana Tereza Ribeiro

Abstract

Additional file 2: Table S2. Overview of WES data quality.

Published
2023
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29. Additional file 7 of Host genetic susceptibility underlying SARS-CoV-2-associated Multisystem Inflammatory Syndrome in Brazilian Children

Author

Santos-Rebouças, Cíntia Barros, Piergiorge, Rafael Mina, dos Santos Ferreira, Cristina, Seixas Zeitel, Raquel de, Gerber, Alexandra Lehmkuhl, Rodrigues, Marta Cristine Felix, Guimarães, Ana Paula de Campos, Silva, Rodrigo Moulin, Fonseca, Adriana Rodrigues, Souza, Rangel Celso, de Souza, Ana Tereza Antunes Monteiro, Rossi, Átila Duque, Porto, Luís Cristóvão de Moraes Sobrino, Cardoso, Cynthia Chester, and de Vasconcelos, Ana Tereza Ribeiro

Abstract

Additional file 7: Figure S1. Workflow of the methodology used. Figure S2. Electropherograms obtained by Sanger sequencing, confirming the WES results. Figure S3. Location of the potentially causative variants in the canonical protein forms obtained from the UniProt Platform. The proteins, proportional to size, the positions of the mutations (lollipops), and the coordinates of the domains annotated in Pfam are represented. Variants identified in FREM1, C6, C9, ABCC6, and BSCL2 are contained in the functional domains of their proteins, whereas for the ABCA4 variant, two variants are outside functional domains and one is within it. For POLG, the variant is located outside functional domains. MPO variant was not illustrated, since it is intronic. Figure S4. Highly reliable protein–protein interactions network retrieved from the products of the eight genes studied. The red hexagons represent the genes carrying the variants. The circles represent the interactions obtained through the STRING plugin, with the green circles representing genes already related to the MIS-C phenotype and blue circles representing genes already related to Kawasaki disease. Figure S5. Enrichment analysis through EnrichR tool of the proteins verified in the PPIs network (FDR < 0.05) against the following gene-set libraries: KEGG 2021 (a); Gene Ontology 2021—biological processes (b), molecular function (c), and cellular component (d); Jensen tissues (e); the scRNA-seq database PanglaoDB Augmented 2021 (f); COVID-19-related gene sets 2021 (g). Top ten elements were sorted by adjusted p-value ranking.

Published
2023
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30. Additional file 6 of Host genetic susceptibility underlying SARS-CoV-2-associated Multisystem Inflammatory Syndrome in Brazilian Children

Author

Santos-Rebouças, Cíntia Barros, Piergiorge, Rafael Mina, dos Santos Ferreira, Cristina, Seixas Zeitel, Raquel de, Gerber, Alexandra Lehmkuhl, Rodrigues, Marta Cristine Felix, Guimarães, Ana Paula de Campos, Silva, Rodrigo Moulin, Fonseca, Adriana Rodrigues, Souza, Rangel Celso, de Souza, Ana Tereza Antunes Monteiro, Rossi, Átila Duque, Porto, Luís Cristóvão de Moraes Sobrino, Cardoso, Cynthia Chester, and de Vasconcelos, Ana Tereza Ribeiro

Abstract

Additional file 6: Table S6. Previous host genetic variants described in patients with MIS-C by whole exome sequencing or immune-gene-panel.

Published
2023
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31. Additional file 3 of Host genetic susceptibility underlying SARS-CoV-2-associated Multisystem Inflammatory Syndrome in Brazilian Children

Author

Santos-Rebouças, Cíntia Barros, Piergiorge, Rafael Mina, dos Santos Ferreira, Cristina, Seixas Zeitel, Raquel de, Gerber, Alexandra Lehmkuhl, Rodrigues, Marta Cristine Felix, Guimarães, Ana Paula de Campos, Silva, Rodrigo Moulin, Fonseca, Adriana Rodrigues, Souza, Rangel Celso, de Souza, Ana Tereza Antunes Monteiro, Rossi, Átila Duque, Porto, Luís Cristóvão de Moraes Sobrino, Cardoso, Cynthia Chester, and de Vasconcelos, Ana Tereza Ribeiro

Abstract

Additional file 3: Table S3. Sequencing metrics to support the call quality of each potentially causative variant.

Published
2023
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32. Additional file 1 of Host genetic susceptibility underlying SARS-CoV-2-associated Multisystem Inflammatory Syndrome in Brazilian Children

Author

Santos-Rebouças, Cíntia Barros, Piergiorge, Rafael Mina, dos Santos Ferreira, Cristina, Seixas Zeitel, Raquel de, Gerber, Alexandra Lehmkuhl, Rodrigues, Marta Cristine Felix, Guimarães, Ana Paula de Campos, Silva, Rodrigo Moulin, Fonseca, Adriana Rodrigues, Souza, Rangel Celso, de Souza, Ana Tereza Antunes Monteiro, Rossi, Átila Duque, Porto, Luís Cristóvão de Moraes Sobrino, Cardoso, Cynthia Chester, and de Vasconcelos, Ana Tereza Ribeiro

Abstract

Additional file 1: Table S1. Genes in which sequence variants or abnormal mRNA expression were previously associated with MIS-C (Lee et al. 2020; Chou et al. 2021; Beckmann et al. 2021; Abolhassani et al. 2022; Vagrecha et al. 2022) and genes for which genome-wide studies found association with Kawasaki disease (Sancho-Shimizu et al. 2021).

Published
2023
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35. Buffy Coat Transcriptomic Analysis Reveals Alterations in Host Cell Protein Synthesis and Cell Cycle in Severe COVID-19 Patients

Author

Cavalcante, Liliane Tavares de Faria, primary, da Fonseca, Guilherme Cordenonsi, additional, Amado Leon, Luciane Almeida, additional, Salvio, Andreza Lemos, additional, Brustolini, Otávio José, additional, Gerber, Alexandra Lehmkuhl, additional, Guimarães, Ana Paula de Campos, additional, Marques, Carla Augusta Barreto, additional, Fernandes, Renan Amphilophio, additional, Ramos Filho, Carlos Henrique Ferreira, additional, Kader, Rafael Lopes, additional, Pimentel Amaro, Marisa, additional, da Costa Gonçalves, João Paulo, additional, Vieira Alves-Leon, Soniza, additional, and Vasconcelos, Ana Tereza Ribeiro, additional

Published
2022
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36. Exploring the Bacteriome and Resistome of Humans and Food-Producing Animals in Brazil

Author

de Carvalho, Fabíola Marques, primary, Valiatti, Tiago Barcelos, additional, Santos, Fernanda Fernandes, additional, Silveira, Alessandro Conrado de Oliveira, additional, Guimarães, Ana Paula C., additional, Gerber, Alexandra Lehmkuhl, additional, Souza, Cintya de Oliveira, additional, Cassu Corsi, Dandara, additional, Brasiliense, Danielle Murici, additional, Castelo-Branco, Débora de Souza Collares Maia, additional, Anzai, Eleine Kuroki, additional, Bessa-Neto, Francisco Ozório, additional, Guedes, Glaucia Morgana de Melo, additional, de Souza, Gleyce Hellen de Almeida, additional, Lemos, Leandro Nascimento, additional, Ferraz, Lúcio Fábio Caldas, additional, Bahia, Márcia de Nazaré Miranda, additional, Vaz, Márcia Soares Mattos, additional, da Silva, Ramon Giovani Brandão, additional, Veiga, Ruanita, additional, Simionatto, Simone, additional, Monteiro, Walter Aparecido Pimentel, additional, Lima, William Alencar de Oliveira, additional, Kiffer, Carlos Roberto Veiga, additional, Campos Pignatari, Antonio Carlos, additional, Cayô, Rodrigo, additional, de Vasconcelos, Ana Tereza Ribeiro, additional, and Gales, Ana Cristina, additional

Published
2022
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38. Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal

Author

Seabra, Sofia S.G., Libin, Pieter, Theys, Kristof, Zhukova, Anna, Potter, Barney, Nebenzahl-Guimaraes, Hanna, Gorbalenya, Alexander A.E., Sidorov, I.A., Pimentel, Victor, Pingarilho, Marta, De Vasconcelos, Ana Tereza Ribeiro, Dellicour, Simon, Khouri, Ricardo, Gascuel, Olivier, Vandamme, Anne-Mieke, Baele, Guy, Cuypers, Lize, Abecasis, Ana A.B., Seabra, Sofia S.G., Libin, Pieter, Theys, Kristof, Zhukova, Anna, Potter, Barney, Nebenzahl-Guimaraes, Hanna, Gorbalenya, Alexander A.E., Sidorov, I.A., Pimentel, Victor, Pingarilho, Marta, De Vasconcelos, Ana Tereza Ribeiro, Dellicour, Simon, Khouri, Ricardo, Gascuel, Olivier, Vandamme, Anne-Mieke, Baele, Guy, Cuypers, Lize, and Abecasis, Ana A.B.

Abstract

The Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classification system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolutionary dynamics analyses, which included recombination and phylogenetic analyses, within-and between-group pairwise genetic distances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized 'African' and 'Asian' genotypes, respectively. Within ZB, two subgroups, ZB.1 and ZB.2, represent the Asiatic and the American (and Oceania) lineages, respe, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2022

39. (m, n)-mer—a simple statistical feature for sequence classification.

Author

Andrade, Amanda Araújo Serrão de, Grivet, Marco, Brustolini, Otávio, and Vasconcelos, Ana Tereza Ribeiro

Subjects
FEATURE extraction, COMPUTATIONAL biology, SCIENTIFIC community, MACHINE learning, NUCLEOTIDES
Abstract

Summary The (m , n)-mer is a simple alternative classification feature based on conditional probability distributions. In this application note, we compared k -mer and (m , n)-mer frequency features in 11 distinct datasets used for binary, multiclass and clustering classifications. Our findings show that the (m , n)-mer frequency features are related to the highest performance metrics and often statistically outperformed the k -mers. Here, the (m , n)-mer frequencies improved performance for classifying smaller sequence lengths (as short as 300 bp) and yielded higher metrics when using short values of k (ranging from 2 to 4). Therefore, we present the (m , n)-mers frequencies to the scientific community as a feature that seems to be quite effective in identifying complex discriminatory patterns and classifying polyphyletic sequence groups. Availability and implementation The (m , n)-mer algorithm is released as an R package within the CRAN project (https://cran.r-project.org/web/packages/mnmer) and is also available at https://github.com/labinfo-lncc/mnmer. Supplementary information Supplementary data are available at Bioinformatics Advances online. [ABSTRACT FROM AUTHOR]

Published
2023
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40. PPIntegrator: semantic integrative system for protein–protein interaction and application for host–pathogen datasets.

Author

Martins, Yasmmin Côrtes, Ziviani, Artur, Costa, Maiana de Oliveira Cerqueira e, Cavalcanti, Maria Cláudia Reis, Nicolás, Marisa Fabiana, and Vasconcelos, Ana Tereza Ribeiro de

Subjects
PROTEIN-protein interactions, HOST-parasite relationships, SEMANTIC Web, KNOWLEDGE graphs, INTERNETWORKING
Abstract

Summary Semantic web standards have shown importance in the last 20 years in promoting data formalization and interlinking between the existing knowledge graphs. In this context, several ontologies and data integration initiatives have emerged in recent years for the biological area, such as the broadly used Gene Ontology that contains metadata to annotate gene function and subcellular location. Another important subject in the biological area is protein–protein interactions (PPIs) which have applications like protein function inference. Current PPI databases have heterogeneous exportation methods that challenge their integration and analysis. Presently, several initiatives of ontologies covering some concepts of the PPI domain are available to promote interoperability across datasets. However, the efforts to stimulate guidelines for automatic semantic data integration and analysis for PPIs in these datasets are limited. Here, we present PPIntegrator, a system that semantically describes data related to protein interactions. We also introduce an enrichment pipeline to generate, predict and validate new potential host–pathogen datasets by transitivity analysis. PPIntegrator contains a data preparation module to organize data from three reference databases and a triplification and data fusion module to describe the provenance information and results. This work provides an overview of the PPIntegrator system applied to integrate and compare host–pathogen PPI datasets from four bacterial species using our proposed transitivity analysis pipeline. We also demonstrated some critical queries to analyze this kind of data and highlight the importance and usage of the semantic data generated by our system. Availability and implementation https://github.com/YasCoMa/ppintegrator , https://github.com/YasCoMa/ppi%5fvalidation%5fprocess and https://github.com/YasCoMa/predprin. [ABSTRACT FROM AUTHOR]

Published
2023
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41. Identification and characterisation of SARS-CoV-2 and Human alphaherpesvirus 1 from a productive coinfection in a fatal COVID-19 case

Author

Herlinger, Alice Laschuk, Monteiro, Fábio Luís Lima, D’arc, Mirela, Moreira, Filipe Romero Rebello, Westgarth, Harrison James, Galliez, Rafael Mello, Mariani, Diana, da Costa, Luciana Jesus, de Almeida, Luiz Gonzaga Paula, Voloch, Carolina Moreira, Melo, Adriana Suely de Oliveira, Aguiar, Renato Santana de, dos Santos, André Felipe Andrade, Castiñeiras, Terezinha Marta Pereira Pinto, de Vasconcelos, Ana Tereza Ribeiro, João Filho, Esaú Custódio, Escosteguy, Claudia Caminha, Ferreira Junior, Orlando da Costa, Tanuri, Amilcar, and Higa, Luiza Mendonça

Subjects
SARS-CoV-2, viruses, coronavirus, COVID-19, HSV-1, coinfection
Abstract

BACKGROUND During routine Coronavirus disease 2019 (COVID-19) diagnosis, an unusually high viral load was detected by reverse transcription real-time polymerase chain reaction (RT-qPCR) in a nasopharyngeal swab sample collected from a patient with respiratory and neurological symptoms who rapidly succumbed to the disease. Therefore we sought to characterise the infection. OBJECTIVES We aimed to determine and characterise the etiological agent responsible for the poor outcome. METHODS Classical virological methods, such as plaque assay and plaque reduction neutralisation test combined with amplicon-based sequencing, as well as a viral metagenomic approach, were performed to characterise the etiological agents of the infection. FINDINGS Plaque assay revealed two distinct plaque phenotypes, suggesting either the presence of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains or a productive coinfection of two different species of virus. Amplicon-based sequencing did not support the presence of any SARS-CoV-2 genetic variants that would explain the high viral load and suggested the presence of a single SARS-CoV-2 strain. Nonetheless, the viral metagenomic analysis revealed that Coronaviridae and Herpesviridae were the predominant virus families within the sample. This finding was confirmed by a plaque reduction neutralisation test and PCR. MAIN CONCLUSIONS We characterised a productive coinfection of SARS-CoV-2 and Herpes simplex virus 1 (HSV-1) in a patient with severe symptoms that succumbed to the disease. Although we cannot establish the causal relationship between the coinfection and the severity of the clinical case, this work serves as a warning for future studies focused on the interplay between SARS-CoV-2 and HSV-1 coinfection and COVID-19 severity.

Published
2022

43. Unfolding of a COVID-19 Transmission Wave in a Cluster of Highly Vulnerable Individuals in Rio De Janeiro – a Spatial Populational-Based Serosurvey

Author

Coelho, Lara E., primary, Luz, Paula Mendes, additional, Pires, Débora Castanheira, additional, Jalil, Emília M., additional, Perazzo, Hugo, additional, Torres, Thiago Silva, additional, Cardoso, Sandra Wagner, additional, Peixoto, Eduardo Mesquita, additional, Nazer, Sandro, additional, Massad, Eduardo, additional, Silveira, Mariangela Freitas, additional, Barros, Fernando C., additional, Vasconcelos, Ana Tereza Ribeiro, additional, Costa, Carlos Alberto Moraes, additional, Amancio, Rodrigo Teixeira, additional, Villela, Daniel Antunes Maciel, additional, Pereira, Tiago, additional, Goedert, Guilherme T., additional, Santos, Cleber Vinicius Brito, additional, Rodrigues, Nadia Cristina Pinheiro, additional, Grinsztejn, Beatriz, additional, Veloso, Valdiléa G., additional, and Struchiner, Claudio Jose, additional

Published
2022
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47. Cellular Growth Arrest and Efflux Pumps Are Associated With Antibiotic Persisters in Streptococcus pyogenes Induced in Biofilm-Like Environments

Author

Martini, Caroline Lopes, primary, Coronado, Amada Zambrana, additional, Melo, Maria Celeste Nunes, additional, Gobbi, Clarice Neffa, additional, Lopez, Úrsula Santos, additional, de Mattos, Marcos Correa, additional, Amorim, Thais Tavares, additional, Botelho, Ana Maria Nunes, additional, Vasconcelos, Ana Tereza Ribeiro, additional, Almeida, Luiz Gonzaga Paula, additional, Planet, Paul J., additional, Zingali, Russolina Benedeta, additional, Figueiredo, Agnes Marie Sá, additional, and Ferreira-Carvalho, Bernadete Teixeira, additional

Published
2021
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50. Whole-exome sequencing reveals insights into genetic susceptibility to Congenital Zika Syndrome

Author

Borda, Victor, primary, da Silva Francisco Junior, Ronaldo, additional, Carvalho, Joseane B., additional, Morais, Guilherme L., additional, Duque Rossi, Átila, additional, Pezzuto, Paula, additional, Azevedo, Girlene S., additional, Schamber-Reis, Bruno L., additional, Portari, Elyzabeth A., additional, Melo, Adriana, additional, Moreira, Maria Elisabeth L., additional, Guida, Letícia C., additional, Cunha, Daniela P., additional, Gomes, Leonardo, additional, Vasconcelos, Zilton F. M., additional, Faucz, Fabio R., additional, Tanuri, Amilcar, additional, Stratakis, Constantine A., additional, Aguiar, Renato S., additional, Cardoso, Cynthia Chester, additional, and Vasconcelos, Ana Tereza Ribeiro de, additional

Published
2021
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