I am an enthusiastic scientist interested in synthetic and computational biology to explore the power of biodiversity. My passion for deciphering and engineering the complex regulatory network in cells has driven me to develop projects from the rational design of biosensors and transcriptional promoters fine-tuning; to genomics and metagenomics towards environmental biotechnology; and the metabolic engineering and reprogramming of yeast through automation, AI, and high-throughput systems at Ginkgo Bioworks. I am currently Doctoral Student at the Joinet Program of Bioengineering of the University of California, Berkeley & San Francisco. I am excited to work at the intersection of metagenomics, machine-learning, and synbio to mine, design, and predict genetic novelty.
Maria C. T. Astolfi
Education
2021-2026 (current)
University of California, Berkeley & San Francisco
California, USA
2015-2018
Federal University of Amazonas, Brazil
Amazonas, Brazil
Doctor of Philosophy (Ph.D.)
Joint Program in Bioengineering
Bachelor of Technology (B.Tech) in Biotechnology
Thesis: Building a BioBrick toolbox for genome engineering in E. coli using CRISPR/Cas9
Advisor: Professor Dr. Jerusa A. Q. A. Faria
Professional experience
2021-2021
2019-2021
2019
Ginkgo Bioworks
Boston, Massachusetts, USA
2018
Synthetic and Systems Biology Lab, University of São Paulo
Ribeirão Preto, São Paulo, Brazil
Organism Engineer II
Organism Engineer I
Organism Engineering Associate
Metabolic engineering of yeast for sweetener biosynthesis using automation and AI
Manager: Dr. Matthew D. McMahon, Program Director
Wet lab, Strain engineering
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Developed and optimized high-throughput genome engineering tools for S. cerevisiae and Y. lipolytica
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Developed tools and used automation to perform scaled-down assays to screen metagenomic
sourced libraries to optimize the activity of enzymes
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Coordinated a machine-learning campaign to generate libraries predicting top-ranked mutation
combinations to optimize the activity of complex plant enzymes
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Designed and performed multiplexed transcriptional fine-tuning to optimize pathways flux and balance
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Rationally engineered synthetic pathways to discover, balance, and improve rate-limiting steps
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Wrote reports, patents, and technical developmental plans for customers and other relevant projects
Dry lab, Computational biology
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Developed pipelines for the analysis of next-generation sequencing data from E. coli, S. cerevisiae, and Y. lipolytica WGS aiming at deciphering genomic diversity of production strains
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Analyzed big data sets of WGS from pre-processing to genomics at scale using AWS
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Wrote standardized notebooks and snakemake pipelines to enable Organism engineers to perform
ease and fast NGS sequence analysis
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Trained PhD-level engineers on introduction to NGS sequence analysis and data science
Research Associate, Bioinformatics
Decoding the web of the antibiotic resistance and mobile elements network in microbiomes
Advisor: Professor Dr. Rafael Silva-Rocha
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On-boarded tools for metagenomic and genomic assembly, annotation, and analysis using NGS data
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Analyzed NGS data for characterization of the microbial community composition
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Performed data mining of antibiotic resistance genes using hidden Markov models
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Assisted in writing grants around exploring the Brazilian biodiversity and addressing national challenges through sequencing technology
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Designed BioBricks for fast and easy genome engineering of E. coli by developing an AND logic gate driving the expression of Cas9 and a red-lambda_recA operon
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Characterized genome engineering efficiency through high-throughput fluorescence and β-galactosidase assays integrating GFP and knocking-out lacZ using 96-well plates
2017
Synthetic Biology Lab of Amazonas, Federal University of Amazonas
Amazonas, Brazil
Principal Instructor, Amazonas_Brazil iGEM team
A BioBrick toolbox for standardized genome engineering using CRISPR/Cas9 machinery
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Reprogrammed transcription regulation by rationally engineering the architecture of cis-regulatory elements.
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Designed new mercury-inducible synthetic promoters recognized by multiple sigma factors and fine-tuned transcription factor-promoter interaction
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Assembled genetic circuits and analyzed expression through high-throughput fluorescence assays
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Characterized bioremediation performance of promoters with improved dynamic range
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Improved bioremediation and scaled the process to 10L bioreactors
2015 - 2017
National Council for Scientific and Technological Development, Ministry of Science and Technology, Brazil
Amazonas, Brazil
National Research Fellow
Designing and fine-tuning synthetic promoters to improve mercury bioremediation in E. coli
Advisor: Professor Dr. Carlos G. Nunes-Silva
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Assisted on the design of constructs to engineer the beta-oxidation pathway by knocking down the gene encoding the transcriptional repressor (fadR) and overexpressing genes encoding the membrane transporters (fadD and fadL)
2015 - 2017
Synthetic Biology Lab of Amazonas, Federal University of Amazonas
Amazonas, Brazil
High-school iGEMer, Manaus_Amazonas-Brazil iGEM team
Optimizing beta-oxidation in S. putrefaciens to transform oil waste into renewable energy
Advisor: Professor Dr. Carlos G. Nunes-Silva
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Co-founded, constructed, and managed the first SynBio laboratory from the Brazilian Amazon region
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Wrote grants for the development of synthetic biology in the region and raised governmental, public, and private funding through partnerships with Google, the Secretary for Environmental and Sustainable Development, Amazonas State House, Natura, and other top companies and institutions
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Led and mentored several projects from design to execution, managed students in biological engineering applied to Amazonian demands, collaborated in the training of +50 students
2013 - 2018
Co-founder
Synthetic Biology Lab of Amazonas, Federal University of Amazonas
Amazonas, Brazil
Awards & grants
Person of the month. Sustainability Magazine, Página22 | Brazil
Top 100 young leaders transforming Latin America bioeconomy | ALLBIOTECH | Mexico
International grant, Bioinformatics | ICGEB | United Nations IDO | Triste, Italy
Silver Medalist | iGEM Foundation | Boston, USA
Best Molecular Biology Project | University of São Paulo | São Paulo, Brazil
Honorable Mention | Research and Innovation Division | University of Amazonas | Amazonas, Brazil
Silver Medalist | iGEM Foundation | Boston, USA
Grand Prize Award | TECNOx Competition | Buenos Aires, Argentina
Public Engagement Award | TECNOx Competition | Buenos Aires, Argentina
Scientific Scholar Fellowship | Amazonas Research Foundation (FAPEAM) | Amazonas, Brazil
National Research Fellowship Grant | Ministry of Science and Technology | Brasília, Brazil
Gold Medalist | iGEM Foundation | Boston, USA
Dean’s Merit Award | University of Amazonas | Amazonas, Brazil
Bronze Medalist | iGEM Regional Jamboree | Santiago, Chile
Latin American Best Presentation | iGEM Regional Jamboree | Santiago, Chile
2021
2020
2018
2017
2016
2016
2016
2016
2016
2016
2015
2014
2014
2013
2013
Productions
Invited Reviewer, Applied and Environmental Microbiology, American Society for Microbiology.
A method for engineering synthetic promoters for tight regulation of heterologous genes in Escherichia coli (translated title). Inventor: Moreira D., Astolfi M., Pinto K., Astolfi-Filho S. BR10201900047. Brazilian National Institute of Property.
Astolfi M. et al. Draft genome sequence of the novel Enterobacter cloacae strain amazonensis, a highly heavy metal-resistant bacterium from a contaminated stream in Amazonas, Brazil. Genome announcements, ASM Journals.
2021
2019
2018
Selected talks
Invited: Perspectivas del futuro de la biotecnología | Sociedad Estudiantil de Biotecnología y Bioingeniería de Yucatán | Yucatán, México.
Invited: Ginkgo Bioworks: making biology easier to engineer with software and hardware automation | Congreso Biogénesis | Congreso Nacional de Biotecnología | Acapulco, México.
Invited: Rebuilding the future and reinventing industry with biology | HUBTalks | The HUB Innovation Institute | Rio de Janeiro, Brazil
Invited: Engineering bacterial transcriptional regulation towards environmental and industrial applications | 7th Brazilian Biotech Congress and 2nd Biotech Ibero-American Congress | Brasilia, Brazil
Invited: The building blocks of synthetic biology in Brazil | Brazilian SynBio Conference | São Paulo, Brazil Invited: Genetic engineering: reprogramming the living world | Campus Party Brasil | Brasília, Brazil
Engineering a mercury biosensor and bioremediator device through synthetic biology | iGEM Competition | Boston, USA
An innovative approach to Hg bioremediation in E. coli | TECNOx Competition | Buenos Aires, Argentina Designing synthetic promoters towards living machines improvement | CONIC | Amazonas, Brazil 2015
Invited: Challenges and proposals for the development of the Amazon region | Amazonian Biological Sciences Conference | Amazonas, Brazil
2021
2021
2020
2018
2018
2017
2016
2016
2015
2014
Teaching experience
Workshops
Invited: Making biology easier to engineer using automation at Ginkgo Bioworks. Brazilian Synthetic Biology Symposium. Brazil.
Invited: NGS sequence analysis. Ginkgo Bioworks. Boston, USA.
Invited: Data science for high-throughput large-scale biological data. Ginkgo Bioworks. Boston, USA.
Invited: Foundations of synthetic biology. Federal University of Goiás. Goiânia, Brazil.
Invited: Synthetic biology approaches to reprogram gene regulation in bacteria. Federal University of Amazonas. Amazonas, Brazil.
Courses
Invited Speaker, Special topics in Synthetic Biology. University of Campinas (UNICAMP). São Paulo, Brazil. Invited Speaker, BTC0139 Biotechnology: Career and Global Market. Federal University for Latin American Integration. Institute of Life and Nature Sciences. Bachelor of Biotechnology. Brazil, Argentina, and Paraguay.
Teaching Assistant, IBB269 Molecular Biology. Federal University of Amazonas. Institute of Biological Sciences. Bachelor of Biotechnology. Brazil.
2021
2020
2020
2018
2017
2021
2020
2017
Selected leadership & community building
Founder | iGEM Academy
Coordinator of Education | iGEM Design League
Co-founder | SynBio Brasil | Brazilian Synthetic Biology Association
Founder and Host | iGEM & Ginkgo Challenge: How can we make biology easier to engineer?
Leader, Latin American Bioeconomy | ALLBIOTECH | Mexico
Mentor and Organizer | BioHack: the Brazilian Synthetic Biology Hackathon | São Paulo, Brazil
Judge and mentor | iGEM Foundation | Boston, US
Co-founder | SynBio Amazonas | Amazonas, Brazil
Skills
Software | Major: Bash and unix environment | Learning: Python and R | Parts mining: HMMER | Microbial community: 2013 Metaphlan2, QIIME | Assembly & annotation: trimmomatic, Velvet, MetaVelvet, SPAdes, MetaSPAdes, Prokka, RAST, MG-RAST, bowtie2| Motif finding: MEME | Database building: RegulonDB, Uniprot, NCBI | Network visualization: CytoScape | Data science: Tableau, ggplot, seaborn
Hosts | Escherichia coli WT MG1655, DH5ɑ, DH10B, JM110, BL21(DE3), S. cerevisiae, Yarrowia lipolytica, Enterobacter cloacae amazonensis, Shewanella putrefaciens, Chromobacterium violaceum
Molecular Biology | High-throughput screening and automation: 96-well plate, 384-well plate, Hamilton STARplus, and Echo | Yeast genome editing: HDR, NHEJ, CRISPR/Cas9, Cre/LoxP | E. coli recombineering: CRISPR/Cas9, lambda-red | Parts and genetic circuits rational design | Fine-tuning dynamic range of E. coli promoters | Cloning: traditional digestion-ligation, 3A Assembly, Golden Gate, Gibson Assembly | Fluorescence assays: plate reader, flow cytometry | Error-prone PCR | Functional metagenomics | Transformation: Y. lipolytica, E. coli, S. cerevisiae, C. violaceum | Conjugation: E. coli, S. putrefaciens | RNA diagnostics: SARS-CoV-2 RT-qPCR, NGS library prep for Swab-Seq