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

  • Developed and optimized high-throughput genome engineering tools for S. cerevisiae and Y. lipolytica

  • Developed tools and used automation to perform scaled-down assays to screen metagenomic

    sourced libraries to optimize the activity of enzymes

  • Coordinated a machine-learning campaign to generate libraries predicting top-ranked mutation

    combinations to optimize the activity of complex plant enzymes

  • Designed and performed multiplexed transcriptional fine-tuning to optimize pathways flux and balance

  • Rationally engineered synthetic pathways to discover, balance, and improve rate-limiting steps

  • Wrote reports, patents, and technical developmental plans for customers and other relevant projects

Dry lab, Computational biology

  • 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

  • Analyzed big data sets of WGS from pre-processing to genomics at scale using AWS

  • Wrote standardized notebooks and snakemake pipelines to enable Organism engineers to perform

    ease and fast NGS sequence analysis

  • 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

  • On-boarded tools for metagenomic and genomic assembly, annotation, and analysis using NGS data

  • Analyzed NGS data for characterization of the microbial community composition

  • Performed data mining of antibiotic resistance genes using hidden Markov models

  • Assisted in writing grants around exploring the Brazilian biodiversity and addressing national challenges through sequencing technology

  • 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

  • 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

  • Reprogrammed transcription regulation by rationally engineering the architecture of cis-regulatory elements.

  • Designed new mercury-inducible synthetic promoters recognized by multiple sigma factors and fine-tuned transcription factor-promoter interaction

  • Assembled genetic circuits and analyzed expression through high-throughput fluorescence assays

  • Characterized bioremediation performance of promoters with improved dynamic range

  • 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

  • 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

  • Co-founded, constructed, and managed the first SynBio laboratory from the Brazilian Amazon region

  • 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

  • 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

References available upon request.

Thanks! Gracias! Obrigada!