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Claudia has a Ph.D. in Plant Cell Biology (2007) and extensive postdoctoral experience. As an undergraduate, Ph.D. student and Postdoctoral Research Associate, Claudia received 22 years of intense laboratory research training in biological sciences in the UK, Portugal, USA, and France. Claudia has an outstanding training in molecular and cell biology (including plant biology), biochemistry and genetics (including plant genetics), genome editing (CRISPR-Cas), and experience in microbiology and analytical chemistry. Claudia has an h-index of 17 including 7 papers with first/co-first authorship. Currently, Claudia is working as a Senior Research Scientist at InnovPlantProtect CoLab, aiming at developing new and effective protection solutions for specific Mediterranean crops. For over ten years, Claudia was mainly focusing on biomedical research, first at the Institute of Medical Sciences (IMS, University of Aberdeen, UK), and since 2013 at the Cambridge Institute for Medical Research (CIMR, University of Cambridge, UK). At the IMS, Claudia performed multidisciplinary research in Systems Biology (Cell and Molecular Biology, Biochemistry, Genetics, Analytical Chemistry, and Mathematical Modelling) aiming at developing a model of a feedback controller of the antizyme translational recoding, using concepts from enzyme kinetics and control engineering. At the CIMR, in David Ron world-leading research group, Claudia studied protein folding homeostasis in the endoplasmic reticulum (ER) in mammalian cells, specifically the regulation of the ER Hsp70 molecular chaperone BiP. Claudia's main contributions in the last years provided critical advances in the field of proteostasis, allowing for a better understanding of how mammalian cells regulate protein folding homeostasis in the ER, which can play a role in multiple diseases. During her Ph.D., Claudia performed multidisciplinary research in plant molecular and cell biology, and genetics, while studying several signalling pathways (Ca2+, calmodulin and cAMP) and their implications in polarized cell growth using pollen tubes as model system. Supervision: Trained and supervised multiple undergraduate and postgraduate students. Full proficiency in the following laboratory techniques: Molecular biology: extraction and purification of nucleic acids; PCR, RT-PCR, qPCR; molecular cloning; CRISPR-Cas9 genome editing (non-homologous end joining and homology directed repair); site directed mutagenesis; high-throughput genotyping; restriction analysis; agarose and polyacrylamide gel electrophoresis (SDS-PAGE, native PAGE); isoelectric focusing; quantitative Western blotting and dot blotting; capillary electrophoresis. Cell biology: mammalian cell culture (CHO, HEK293, AR42J, HeLa); transient and stable cell transfections (viral transduction and Flp-In T-REx systems); multi-channel flow cytometry analysis and cell sorting; bright field, fluorescence, confocal and scanning electron microscopy; localization of fluorescent fusion proteins and secondary messengers; immunocytochemistry; yeast tetrad dissection; in vivo pharmacological analysis of polarized cell growth; microinjection of living cells. Biochemistry: small-scale production and affinity purification of proteins; protein immunoprecipitation and pull-down assays; proximity dependent biotin identification (BioID); enzyme activity assays; protein-binding assays using fluorescence polarization, fluorescence resonance energy transfer (FRET), and biolayer interferometry (Octet); stable isotope labelling with amino acids in cell culture (SILAC). Other techniques: genetic manipulation and handling of mammalian cells, yeast, bacteria and plants; infectivity assays in plants; electroporation; particle bombardment; basic analytical chemistry techniques (HPLC); FPLC; handling of radioisotopes (3H, 35S); autoradiography and fluorography; ELISA assays; technical writing.
Identification

Personal identification

Full name
Claudia Sofia Rato da Silva

Citation names

  • Rato, Claudia

Author identifiers

Ciência ID
B915-C090-480A
ORCID iD
0000-0002-3971-046X

Addresses

  • InnovPlantProtect, Estrada de Gil Vaz, Apartado 72, 7351-901, Elvas, Elvas, Portugal (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences
  • Natural sciences - Biological Sciences - Plant sciences
  • Agrarian Sciences - Agriculture, Forestry and Fisheries - Plant Breeding and Plant Protection

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
French Beginner (A1) Intermediate (B1) Beginner (A1) Intermediate (B1)
Spanish; Castilian Beginner (A1) Intermediate (B1) Beginner (A1) Intermediate (B1)
Education
Degree Classification
2003 - 2007
Concluded
Cell Biology (Doutoramento)
Universidade de Lisboa, Portugal
"Regulation of Pollen Tube Growth by Calmodulin, Cyclic Nucleotides and Cyclic Nucleotide-gated Channels" (THESIS/DISSERTATION)
1997 - 2002
Concluded
Applied Plant Biology (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
Affiliation

Science

Category
Host institution
Employer
2020/02/01 - Current Auxiliary Researcher (Research) InnovPlantProtect, Portugal
2013/05 - 2020/01/31 Postdoc (Research) University of Cambridge Clinical Biochemistry, United Kingdom
Cambridge Institute for Medical Research, United Kingdom
2012/03 - 2013/05 Researcher (Research) European Bioinformatics Institute, United Kingdom
2008/11 - 2011/10 Postdoc (Research) University of Aberdeen Institute of Medical Sciences, United Kingdom
2008/05 - 2008/10 Postdoc (Research) Universidade de Lisboa Faculdade de Ciências, Portugal
2005/09 - 2007/08 Visiting Researcher (Research) University of Nevada Reno, United States
Outputs

Publications

Journal article
  1. Cláudia Rato; Miguel F. Carvalho; Cristina Azevedo; Paula Rodrigues Oblessuc. "Genome editing for resistance against plant pests and pathogens". Transgenic Research 30 4 (2021): 427-459. https://doi.org/10.1007/s11248-021-00262-x.
    10.1007/s11248-021-00262-x
  2. Alisa F. Zyryanova; Kazuhiro Kashiwagi; Claudia Rato; Heather P. Harding; Ana Crespillo-Casado; Luke A. Perera; Ayako Sakamoto; et al. "ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B". Molecular Cell (2021): https://doi.org/10.1016/j.molcel.2020.10.031.
    10.1016/j.molcel.2020.10.031
  3. Steffen Preissler; Claudia Rato; Yahui Yan; Luke A Perera; Aron Czako; David Ron. "Calcium depletion challenges endoplasmic reticulum proteostasis by destabilising BiP-substrate complexes". eLife 9 (2020): https://doi.org/10.7554/eLife.62601.
    10.7554/eLife.62601
  4. Luke A Perera; Claudia Rato; Yahui Yan; Lisa Neidhardt; Stephen H McLaughlin; Randy J Read; Steffen Preissler; David Ron. "An oligomeric state-dependent switch in the ER enzyme FICD regulates AMP ylation and de AMP ylation of BiP". The EMBO Journal 38 21 (2019): https://doi.org/10.15252/embj.2019102177.
    10.15252/embj.2019102177
  5. Milena Vitale; Anush Bakunts; Andrea Orsi; Federica Lari; Laura Tadè; Alberto Danieli; Claudia Rato; et al. "Inadequate BiP availability defines endoplasmic reticulum stress". eLife (2019): https://doi.org/10.7554/eLife.41168.
    10.7554/eLife.41168
  6. Yan, Yahui; Rato, Claudia; Rohland, Lukas; Preissler, Steffen; Ron, David. "MANF antagonizes nucleotide exchange by the endoplasmic reticulum chaperone BiP". Nature Communications 10 1 (2019): http://dx.doi.org/10.1038/s41467-019-08450-4.
    10.1038/s41467-019-08450-4
  7. Amin-Wetzel N; Saunders RA; Kamphuis MJ; Rato C; Preissler S; Harding HP; Ron D. "A J-Protein Co-chaperone Recruits BiP to Monomerize IRE1 and Repress the Unfolded Protein Response.". Cell (2017): http://europepmc.org/abstract/med/29198525.
    10.1016/j.cell.2017.10.040
  8. Preissler S; Rato C; Perera L; Saudek V; Ron D. "FICD acts bifunctionally to AMPylate and de-AMPylate the endoplasmic reticulum chaperone BiP.". Nature structural & molecular biology (2016): http://europepmc.org/abstract/med/27918543.
    10.1038/nsmb.3337
  9. Mitchell A; Chang HY; Daugherty L; Fraser M; Hunter S; Lopez R; McAnulla C; et al. "The InterPro protein families database: the classification resource after 15 years.". (2015): http://europepmc.org/abstract/med/25428371.
    10.1093/nar/gku1243
  10. Chen R; Rato C; Yan Y; Crespillo-Casado A; Clarke HJ; Harding HP; Marciniak SJ; Read RJ; Ron D. "G-actin provides substrate-specificity to eukaryotic initiation factor 2a holophosphatases.". (2015): http://europepmc.org/abstract/med/25774600.
    10.7554/eLife.04871
  11. Preissler S; Rato C; Chen R; Antrobus R; Ding S; Fearnley IM; Ron D. "AMPylation matches BiP activity to client protein load in the endoplasmic reticulum.". (2015): http://europepmc.org/abstract/med/26673894.
    10.7554/eLife.12621
  12. Tunc-Ozdemir M; Tang C; Ishka MR; Brown E; Groves NR; Myers CT; Rato C; et al. "A cyclic nucleotide-gated channel (CNGC16) in pollen is critical for stress tolerance in pollen reproductive development.". (2013): http://europepmc.org/abstract/med/23370720.
    10.1104/pp.112.206888
  13. Tunc-Ozdemir M; Rato C; Brown E; Rogers S; Mooneyham A; Frietsch S; Myers CT; et al. "Cyclic nucleotide gated channels 7 and 8 are essential for male reproductive fertility.". (2013): http://europepmc.org/abstract/med/23424627.
    10.1371/journal.pone.0055277
  14. Rato C; Amirova SR; Bates DG; Stansfield I; Wallace HM. "Translational recoding as a feedback controller: systems approaches reveal polyamine-specific effects on the antizyme ribosomal frameshift.". (2011): http://europepmc.org/abstract/med/21303766.
    10.1093/nar/gkq1349
  15. Silva PA; Ul-Rehman R; Rato C; Di Sansebastiano GP; Malhó R. "Asymmetric localization of Arabidopsis SYP124 syntaxin at the pollen tube apical and sub-apical zones is involved in tip growth.". (2010): http://europepmc.org/abstract/med/20718953.
    10.1186/1471-2229-10-179
  16. Malhó R; Liu Q; Monteiro D; Rato C; Camacho L; Dinis A. "Signalling pathways in pollen germination and tube growth.". (2006): http://europepmc.org/abstract/med/16937051.
    10.1007/s00709-006-0162-6
  17. Rato C; Monteiro D; Hepler PK; Malhó R. "Calmodulin activity and cAMP signalling modulate growth and apical secretion in pollen tubes.". (2004): http://europepmc.org/abstract/med/15165182.
    10.1111/j.1365-313X.2004.02091.x
  18. Trewavas AJ; Rodrigues C; Rato C; Malhó R. "Cyclic nucleotides: the current dilemma!". (2002): http://europepmc.org/abstract/med/12183181.
    10.1016/S1369-5266(02)00281-9
Activities

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2018/01 - 2018/04 Regulation of FICD activities - an in vivo approach
Supervisor
Cambridge Institute for Medical Research, United Kingdom
2015/08 - 2016/06 Systematic inactivation of known ER-localised co-chaperones of the DNAJ class implicates ERdj4 in selective repression of IRE1 signalling
Co-supervisor
Cambridge Institute for Medical Research, United Kingdom

Event participation

Activity description
Type of event
Event name
Institution / Organization
2010 - 2010 Co-supervised the University of Aberdeen, Scotland team of 2010, a group of undergraduate students participating in The International Genetically Engineered Machine (iGEM) competition organized by MIT, Boston, MA.
Other
The International Genetically Engineered Machine (iGEM) competition organized by MIT, Boston, MA
2009 - 2009 Co-supervised the University of Aberdeen, Scotland team of 2009, a group of undergraduate students participating in The International Genetically Engineered Machine (iGEM) competition organized by MIT, Boston, MA.
Other
The International Genetically Engineered Machine (iGEM) competition organized by MIT, Boston, MA
Distinctions

Award

2006 Postdoctoral fellowship
Fundação para a Ciência e a Tecnologia, Portugal
2003 Ph.D. fellowship
Fundação para a Ciência e a Tecnologia, Portugal