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Rui Rocha, Doctorate in Chemical and Biological Engineering by the Faculty of Engineering of the University of Porto; Master¿s in Applied Biology - field of Toxicology and Ecotoxicology by the University of Aveiro and graduate in Applied Biology by the University of Minho. Currently working in the private sector in a Biotech company, is a researcher at CISAS - Center for Research and Development in Agrifood Systems and Sustainability of Instituto Politécnico de Viana do Castelo. Microbiology and Molecular Biology are the main areas of expertise, namely in the development of new rapid microbial diagnostic methods employing nucleic acid mimics, molecular strategies for the determination of authenticity of GI (Geographical Indication) food products and microbiome characterizations recurring to NGS applications. Author/Co-author of 3 Microbial Detection Kits certified by AOAC RI, 13 articles in international peer reviewed scientific journals, 2 book chapters and 1 patent. Co-supervised 1 Master thesis dissertation.
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Identification

Personal identification

Full name
Rui Jorge Alves Rocha

Citation names

  • Rocha, Rui

Author identifiers

Ciência ID
A015-B191-3F19
ORCID iD
0000-0003-3859-2702

Email addresses

  • rru@ipvc.pt (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Microbiology
  • Natural sciences - Biological Sciences - Molecular Biology
  • Agrarian Sciences - Agrarian and Food Biotechnology

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
English Upper intermediate (B2) Advanced (C1) Upper intermediate (B2) Intermediate (B1)
Education
Degree Classification
2013 - 2017
Concluded
 Doctoral Program in Chemical and Biological Engeneering (Doutoramento)
Major in Application of nucleic acid mimics for the detection of microorganisms
Universidade do Porto Faculdade de Engenharia, Portugal
"Optimization of Peptide Nucleic Acid Fluorescence in situ Hybridization (PNA-FISH) for the identification of microorganisms in food matrices" (THESIS/DISSERTATION)
 Aprovado
2009 - 2011
Concluded
 Applied Biology - expertise in Toxicology and Ecotoxicology (Mestrado)
Universidade de Aveiro, Portugal
"Ecotoxicological evaluation of pharmaceuticals on Daphnia magna" (THESIS/DISSERTATION)
 17 valores
2006 - 2009
Concluded
 Applied Biology (Licenciatura)
Universidade do Minho Escola de Ciências, Portugal
"Extraction of quality RNA for application in molecular biology techniques on Quercus suber - building a library of EST's" (THESIS/DISSERTATION)
 16 valores
Affiliation

Science

Category
Host institution 		Employer
2018/06/01 - 2022/01/31 Researcher (Research) Instituto Politécnico de Viana do Castelo, Portugal
Instituto Politécnico de Viana do Castelo Escola Superior de Tecnologia e Gestão, Portugal
2013 - 2017 Researcher (Research) Biomode SA, Portugal
Universidade do Porto Faculdade de Engenharia, Portugal
(...)

Others

Category
Host institution 		Employer
2010/11 - 2011/08 Internship Biomode SA, Portugal
Biomode SA, Portugal
Projects

Grant

Designation Funders
2018/06/01 - 2021/09/30 MobFood – Mobilização de conhecimento científico e tecnológico em resposta aos desafios do mercado Agroalimentar
POCI-01-0247-FEDER-024524
Research Fellow
Instituto Politécnico de Viana do Castelo Escola Superior de Tecnologia e Gestão, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2013/05/01 - 2017/04/30 Optimization of Peptide Nucleic Acid Fluorescence in situ Hybridization (PNA-FISH) for the identification of microorganisms in food matrices
SFRH/BDE/51910/2012
PhD Student Fellow
Universidade do Porto Faculdade de Engenharia, Portugal
 Fundação para a Ciência e a Tecnologia

Biomode SA
Concluded
Outputs

Publications

Book chapter
  1. Azevedo, Andreia S.; Rocha, Rui; Dias, Nicolina. "Flow-FISH Using Nucleic Acid Mimic Probes for the Detection of Bacteria". In Fluorescence In-Situ Hybridization (FISH) for Microbial Cells, edited by Carina Almeida; Nuno Azevedo, 263-277. Springer US, 2021.
    10.1007/978-1-0716-1115-9_17
  2. Rocha, Rui; Almeida, Carina; Azevedo, Nuno F.. Corresponding author: Rocha, Rui. "FISH in Food Samples". In Fluorescence In-Situ Hybridization (FISH) for Microbial Cells, edited by Carina Almeida; Nuno Azevedo, 279-290. Springer US, 2021.
    10.1007/978-1-0716-1115-9_18
Conference abstract
  1. Rocha, Rui; Manuela Vaz-Velho; Pereira Pinto, Ricardo; Fernandes, Paulo; Santos, Joana. "Multiple correspondence analysis of microbiological profiles as markers of authenticity of PDO cheeses". Paper presented in XVI Encontro de Química dos Alimentos, Castelo Branco, 2022.
    Published
Conference poster
  1. Rocha, Rui; Vaz Velho, Manuela; Pereira Pinto, Ricardo; Fernandes, Paulo; Joana Santos. Corresponding author: Rocha, Rui. "Microbiological quality assessment of two Portuguese PDO cheeses - Serra da Estrela and Azeitão.". Paper presented in XVI Encontro de Química dos Alimentos, 2022.
  2. Rocha, Rui; Manuela Vaz Velho; Paulo Fernandes; Joana Santos. "Comparison of Lactic Acid Bacteria content of two Portuguese DOP cheeses - Serra da Estrela and Azeitão". Paper presented in XV Encontro de Química dos Alimentos, 2021.
  3. Rocha, Rui; Nélson Couto; Carla Ramos; Manuela Vaz Velho; Paulo Fernandes. "Microbial characterization of Serra da Estrela PDO cheese". Paper presented in Congress of Microbiology and Biotechnology 2019 - Microbiotec19, 2019.
  4. Oliveira, Ricardo; Rocha, Rui; Sousa, Mário; Cerqueira, Laura; Azevedo, Nuno Filipe; Almeida, Carina. "Rapid identification of Campylobacter spp. using peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) in food samples". Paper presented in V AEICBAS Biomedical Congress - Abel Salazar Biomedical Sciences Institute (ICBAS), Porto, Portugal, 2017.
  5. Rocha, Rui; Carina Almeida; Nuno Azevedo. "Optimization of Peptide Nucleic Acid Fluorescence in situ Hybridization (PNA-FISH) method for the detection of bacteria: the effect of pH, dextran sulfate and probe concentration". Paper presented in 12th International Conference in Chemical and Biological Engineering - CHEMPOR, 2014.
  6. Rocha, Rui; Fernando Gonçalves; Catarina Marques; Bruno Nunes. "Environmental effects of anticholinesterasic therapeutic drugs on a crustacean species, Daphnia magna". Paper presented in 6th World Congress and the 22nd Annual Meeting of the Society of Environmental Toxicology and Chemistry - SETAC, 2012.
Journal article
  1. Mário Sousa; Rui Rocha; Daniela Araújo; Joana Castro; Ana Barbosa; Nuno F. Azevedo; Laura Cerqueira; Carina Almeida. "A New Peptide Nucleic Acid Fluorescence In Situ Hybridization Probe for the Specific Detection of Salmonella Species in Food Matrices". Foodborne Pathogens and Disease 21 (2024): 298-305. http://dx.doi.org/10.1089/fpd.2023.0127.
    Published • 10.1089/fpd.2023.0127
  2. Rui Rocha; Nélson Couto; Ricardo Pereira Pinto; Manuela Vaz Velho; Paulo Fernandes; Joana Santos. "Microbiological Characterization of Protected Designation of Origin Serra da Estrela Cheese". Foods (2023): https://www.mdpi.com/2304-8158/12/10/2008.
    10.3390/foods12102008
  3. Fernandes, P.; Afonso, I.M.; Pereira, J.; Rocha, Rui; Rodrigues, A.S.. "Epiphitic Microbiome of Alvarinho Wine Grapes from Different Geographic Regions in Portugal". Biology 12 2 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85148936918&partnerID=MN8TOARS.
    10.3390/biology12020146
  4. Rocha, Rui; Vaz Velho, Manuela; Santos, Joana; Fernandes, Paulo. "Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing". Microorganisms 9 10 (2021): 2007. http://dx.doi.org/10.3390/microorganisms9102007.
    10.3390/microorganisms9102007
  5. Fernandes, Paulo Alexandre da Costa; Ferreira, Fernando Alberto da Conceição; Morais, Orlando Miguel; Ramos, Carla Maria Taxa; Fernandes, Élia Maria Raposo; Rocha, Susana Andreia Alves da; Rocha, Rui; et al. "Performance of saliva as a specimen to detect SARS-CoV-2". Journal of Clinical Virology 142 (2021): 104913. http://dx.doi.org/10.1016/j.jcv.2021.104913.
    10.1016/j.jcv.2021.104913
  6. Rocha, Rui; Sousa, José M.; Cerqueira, Laura; Vieira, Maria J.; Almeida, Carina; Azevedo, Nuno F.. "Development and application of Peptide Nucleic Acid Fluorescence in situ Hybridization for the specific detection of Listeria monocytogenes". Food Microbiology 80 (2019): 1-8. http://dx.doi.org/10.1016/j.fm.2018.12.009.
    10.1016/j.fm.2018.12.009
  7. Sousa, J. Mário; Rocha, Rui; Cerqueira, Laura; Almeida, Carina; Azevedo, Nuno F.; Bastin, Benjamin; Bird, Patrick; et al. "Validation of Biomode S.A. Probe4CronobacterTM for the Identification of Cronobacter spp.". Journal of AOAC International 102 3 (2019): 855-864. http://dx.doi.org/10.5740/jaoacint.18-0328.
    10.5740/jaoacint.18-0328
  8. Rocha, Rui; Almeida, Carina; Azevedo, Nuno F.. "Influence of the fixation/permeabilization step on peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria". PLOS ONE 13 5 (2018): e0196522. http://dx.doi.org/10.1371/journal.pone.0196522.
    10.1371/journal.pone.0196522
  9. Mendes, Luzia; Rocha, Rui; Azevedo, Andreia S.; Henriques, Mariana; Pinto, Miguel G.; Azevedo, Nuno F.. "#126. Nova estratégia para detetar e localizar patogénicos periodontais: a técnica de PNA-FISH". Revista Portuguesa de Estomatologia, Medicina Dentária e Cirurgia Maxilofacial 57 (2016): 52. http://dx.doi.org/10.1016/j.rpemd.2016.10.123.
    10.1016/j.rpemd.2016.10.123
  10. Mendes, Luzia; Rocha, Rui; Azevedo, Andreia Sofia; Ferreira, Catarina; Henriques, Mariana; Pinto, Miguel Gonçalves; Azevedo, Nuno Filipe. "Novel strategy to detect and locate periodontal pathogens: The PNA-FISH technique". Microbiological Research 192 (2016): 185-191. http://dx.doi.org/10.1016/j.micres.2016.07.002.
    Published • 10.1016/j.micres.2016.07.002
  11. Rocha, Rui; Santos, Rita S.; Madureira, Pedro; Almeida, Carina; Azevedo, Nuno F.. "Optimization of peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria: The effect of pH, dextran sulfate and probe concentration". Journal of Biotechnology 226 (2016): 1-7. http://dx.doi.org/10.1016/j.jbiotec.2016.03.047.
    10.1016/j.jbiotec.2016.03.047
  12. Rocha, Rui; Gonçalves, F.; Marques, C.; Nunes, B.. "Environmental effects of anticholinesterasic therapeutic drugs on a crustacean species, Daphnia magna". Environmental Science and Pollution Research 21 6 (2013): 4418-4429. http://dx.doi.org/10.1007/s11356-013-2339-9.
    10.1007/s11356-013-2339-9
  13. Almeida, C.; Sousa, J. M.; Rocha, Rui; Cerqueira, L.; Fanning, S.; Azevedo, N. F.; Vieira, M. J.. "Detection of Escherichia coli O157 by Peptide Nucleic Acid FluorescenceIn SituHybridization (PNA-FISH) and Comparison to a Standard Culture Method". Applied and Environmental Microbiology 79 20 (2013): 6293-6300. http://dx.doi.org/10.1128/aem.01009-13.
    Published • 10.1128/aem.01009-13
Newsletter article
  1. Rocha, Rui; Carina Almeida; Nuno Azevedo. "Metodologias para a identificação de microrganismos patogénicos em amostras alimentares: a técnica de PNA-FISH", Boletim de Biotecnologia, 2015
Thesis / Dissertation
  1. Rocha, Rui. "Optimization of Peptide Nucleic Acid Fluorescence in situ Hybridization (PNA-FISH) for the identification of microorganisms in food matrices". PhD, 2017.
  2. Rocha, Rui. "Toxicity of terapeutic anticolinesterasic drugs in Daphnia magna". Master, 2011.

Intellectual property

Patent
  1. Carina Almeida; Mário Sousa; Rocha, Rui; Laura Cerqueira; Maria João Vieira; Nuno Azevedo. 2014. "Peptide nucleic acid probe, kit and method for detecting and/or quantifying Escherichia coli 0157:H7 and respective uses".
    Granted/Issued

Other

Other output
  1. Probe4Salmonella Test Kit Certification by AOAC RI. This method has been evaluated in the AOAC® Performance Tested MethodsSM Program, and found to perform as stated by the manufacturer contingent to the comments contained in the manuscript. This certificate means that an AOAC® Certification Mark License Agreement has been executed which authorizes the manufacturer to display the AOAC Performance Tested SM certification mark.. 2018. De Sousa, José Mário; Rocha, Rui; Cerqueira, Laura; Almeida, Carina; Azevedo, Nuno Filipe.
  2. Probe4Monocytogenes Test Kit Certification by AOAC RI. This method has been evaluated in the AOAC® Performance Tested MethodsSM Program, and found to perform as stated by the manufacturer contingent to the comments contained in the manuscript. This certificate means that an AOAC® Certification Mark License Agreement has been executed which authorizes the manufacturer to display the AOAC Performance Tested SM certification mark. 2017. Rocha, Rui; De Sousa, José Mário; Cerqueira, Laura; Almeida, Carina; Azevedo, Nuno Filipe.
  3. Probe4Cronobacter Test Kit Certification by AOAC RI. first product in the world certified by AOAC for Cronocbacter Evaluation under the AOAC® PTM Program, and found to perform as stated by the manufacturer contingent to the comments contained in the manuscript. This certificate means that an AOAC® Certification Mark License Agreement has been executed which authorizes the manufacturer to display the AOAC Performance Tested SM certification mark;. 2017. Rocha, Rui; De Sousa, José Mário; Cerqueira, Laura; Almeida, Carina; Azevedo, Nuno Filipe.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2021/09/05 Application of microsatellite high resolution melting analysis for the discrimination of Alcobaça PGI Golden Delicious apples XV Encontro de Química dos Alimentos
(Funchal, Portugal)
2019/07 Characterization of Portuguese pear varieties using microsatellite high resolution melting analysis 12th Iberoamerican Congress of Food Engineering - CIBIA
Algarve University (Faro, Portugal)
2017/03 Development and application of Peptide Nucleic Acid Fluorescence in situ Hybridization for the specific detection of Listeria monocytogenes International Association for Food Protection European Symposium on Food Safety
International Association for Food Protection (Belgium)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2015 - 2016 Development and Validation of a PNA-FISH method for Vibrio detection
Co-supervisor
 Bioengineering (Master)
Universidade do Minho Centro de Engenharia Biológica, Portugal