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Karen

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Research path

I have a bachelor degree in Biology from Brazil at Unila. There I researched the interaction of two bacteria, Gluconacetobacter diazotrophicus and Azospirillum brasiliensis, and a fungi, Trichoderma harzianum, with the Mate plant, Ilex paraguariensis, under the direction of Cristian A. Rojas and Cleto Peres.

I did my doctorate studies with Hugo Germain and Isabel Desgagne-Penix at UQTR on Transcriptomics and metabolomics of Arabidopsis in response to fungal virulence proteins. Although my PhD program was in Cellular and molecular biology, I did all the analyses of my transcriptomic and metabolomic data. I also developed a R package for selection of reference genes from transcriptomic data (DOI: 10.1186/s12864-019-6426-2), you can access it on Github too. I have collaborated in other projects throughout my PhD doing de novo transcriptome assembly and annotation.

In 2018, I did an internship at Peter Solomon's lab with Megan McDonald, where I used MinIon to sequence the genome of several isolates of the fungus Bipolaris sorokiniana, basecalled the reads and assembled them and finally aligned the new genomes to a reference to study structural changes in the chromosomes.

I was a postdoctoral fellow for one year at Laval University in GENOSCAN project, where I used plant omics for restoration of boreal mining sites. Currently, I am a bioinformatician (postdoctoral fellowship) at the UQTR, working with Dr. Isabel Desgagne-Penix on projects of the Research Chair in Plant Specialized Metabolism and the Partnership Research Chair in Metabolic Engineering of MicroAlgae. In addition to transcriptome assembly and annotation, metabolomics and statistic analyses, I teach lab mates basic bioinformatics.

Education

Doctorate - Cell and Molecular Biology

UQTR

September 2017 - April 2021

Thesis: Unrelated fungal rust candidate effectors act on overlapping plant functions. (2021).

Number of pages: 200.

Supervisors: Hugo Germain, Isabel Desgagné-Penix



Master's - Cell and Molecular Biology

UQTR

September 2016 - August 2017

Fast-track to PhD.

Supervisors: Hugo Germain, Isabel Desgagné-Penix



Bachelor's - Biological Sciences - Ecology and Biodiversity

Universidade Federal da Integração Latino-Americana

April 2011 - July 2016

Thesis: Interaction between Ilex paraguariensis and beneficial microorganisms. (2015).

Number of pages: 59.

Supervisors: Cristian Antonio Rojas, Cleto Kaveski Peres.

Experience

Academic work

Postdoctoral fellowship in Bioinformatics

UQTR

July 2022 - Present

  • Create, update and maintain a database of Amaryllidaceae transcriptomes.
  • Analyse plant and algae metabolome and transcriptome in relation to specialized metabolism.
  • Create tools to improve data analysis in the lab.
  • Supervise students in bioinformatics
  • Teach basic programming skills to lab mates.
  • Teaching
  • Publish research results.


Postdoctoral fellowship in Plant omics

Laval University

May 2021 - June 2022

  • Analyze of genetic structure and diversity of Shea using SNP data.
  • Preparation of protocol for sampling of plants in mining site.
  • DNA extraction from leaves and needles.
  • Analyze of genetic structure and diversity of black spruce using SNP data.


PhD on Cellular and Molecular Biology

Université du Québec à Trois-Rivières

September 2017 - April 2021

  • Designed transcriptomic and metabolomic studies
  • Extracted RNA from Arabidopsis thaliana and analyzed transcriptomic data:
    • Quality control and trimming
    • Transcriptome assembly and read alignment
    • Feature counting
    • Differential expression analysis
    • Transcriptome annotation
    • Results visualization
  • Extracted metabolites from Arabidopsis thaliana and analyze metabolomic data:
    • Annotation of chemical formulas
    • Differential accumulation analysis
    • Results visualization
  • Collaborated in projects analyzing transcriptomic data of plants and fungi, performing statistical analyses and preparing graphics
  • Supervised students, teaching transcriptome assembly and annotation
  • Taught students and professors on the basics of the R language


Graduate Trainee

Australian National University

August 2018 - October 2018

  • Extracted DNA from the fungus Bipolaris sorokiniana for long-read sequencing
  • Prepared and sequenced libraries on Oxford Nanopore MinIon
  • Assembled genomes of different isolates of Bipolaris sorokiniana (wheat and barley pathogen) with Canu
  • Prepared graphical visualization of genome structure


Undergraduate intern

Bela Vista Biological Refuge

March 2016 - July 2016

  • Studied conservation and reproductive biology of the harpy eagle and managed their nutrition
  • Studied behavior ecology of wild cats and capuchin monkeys and applied techniques of environment enrichment.
  • Managed the nutrition of the animals in captivity


Undergraduate intern

Université du Québec à Trois-Rivières

June 2015 - September 2015

  • Extracted and quantified proteins from Arabidopsis thaliana and Nicotiana benthamiana plants
  • Performed Western blot and coimmunoprecipitation
  • Performed Chromatin Immunoprecipition with Arabidopsis thaliana plants




Leadership

President

Centre SEVE’s International Partnership Committee

January 2021 - December 2021

  • Directed the deliberations, maintained order and decorum, received the proposals and submitted them to the assembly
  • Ensured that the CSIPC schedule runs smoothly and helped each of the other sectors if necessary.
  • Represented the committee during each of the activities in which CSIPC participated.
  • Called the vote and proclaimed the result, and signed the official documents.


Mentor

Mitacs

May - September (2017 and 2018)

  • Helped Mitacs Globalink interns arrive to the city, register to the university and open bank accounts.
  • Helped Mitacs Globalink interns adapt to the new environment
  • Organized social events for the interns
  • Wrote reports to Mitacs


Communication committee

Biology Students’ Center Hydrochaeris hydrochaeris (CEBHy) – Universidade Federal da Integração Latino-Americana

March 2014 - July 2014

  • Announced activities and meetings and published documents of the Students’ Center to all the members.


Skills



Soft skills

Fast learner

Critical thinking

Creative

Mentoring

Good written and oral communication

Willing to accept feedback

Willingness to learn



Informatics

  • MS Office
  • R and Bioconductor
  • High performance computing
  • Unix
  • Markdown
  • HTML
  • CSS
  • Python
  • SQL
  • Latex


Languages

Language Read Write Speak Understand Native
English Fluent Advanced Fluent Fluent
French Fluent Intermediary Advanced Fluent
Portuguese Fluent Fluent Fluent Fluent Yes
Spanish Fluent Fluent Advanced Fluent

Publications

Papers

2024

Liyanage, N.S, Awwad, F., dos Santos, K.C.G., Jayawardena, T.U., Merindol, N. & Desgagné-Penix, I. Navigating Amaryllidaceae Alkaloids: Bridging Gaps and Charting Biosynthetic Territories – A Comprehensive Review. Journal of Experimental Botany, erae187. DOI: 10.1093/jxb/erae187

Bucknell, A., Wilson, H., dos Santos, K.C.G., Simpfendorfer, S., Milgate, A., Germain, H., Solomon, P., Bentham, A. & McDonald, M. Sanctuary: A Starship transposon facilitating the movement of the virulence factor ToxA in fungal wheat pathogens. bioRxiv. DOI: 10.1101/2024.03.04.583430

2023

Koirala, M., dos Santos, K.C.G., Gélinas, S.-E., Ricard, S., Karimzadegan, V., Lamichhane, B., Liyanage, N.S., Merindol, N. & Desgagné-Penix, I. Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus. Phytochemistry, 216: 113883. DOI: 10.1016/j.phytochem.2023.113883

2021

Rahman, M.S, Madina, M.H.,Plourde, M.B., dos Santos, K.C.G., Huang, X., Zhang, Y, Laliberté, J.-F., Germain, H. The fungal effector Mlp37347 alters plasmodesmata fluxes and enhances susceptibility to pathogen. Microorganisms (2021), 9(6): 1232. DOI: 10.3390/microorganisms9061232

dos Santos, K.C.G., Pelletier, G., Séguin, A. Guillemette, F., Hawkes, J., Desgagné-Penix, I. & Germain, H. Unrelated fungal rust candidate effectors act on overlapping plant functions. Microorganisms (2021), 9(5): 996. DOI: 10.3390/microorganisms9050996.

2020

dos Santos, K.C.G., Desgagné-Penix, I. & Germain, H. Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis. BMC Genomics (2020), 21(35). DOI: 10.1186/s12864-019-6426-2

2019

Fradj, N., dos Santos, K.C.G., Montigny, N., Awwad, F., Boumghar, Y., Germain, H., Desgagné-Penix, I. RNA-Seq de novo assembly and differential transcriptome analysis of Chaga (Inonotus obliquus) cultured with different betulin sources and the regulation of genes involved in terpenoid biosynthesis. International Journal of Molecular Sciences (2019), 20(18): 4334. DOI: 10.3390/ijms20184334

Lorrain, C., Gonçalves dos Santos, K.C., Germain, H., Hecker, A. and Duplessis, S. Advances in understanding obligate biotrophy in rust fungi. New Phytologist (2019), 222: 1190-1206. DOI: 10.1111/nph.15641

2018

dos Santos, K.C.G., McDonald, M. High molecular weight DNA extraction for long read sequencing v1. Protocols.io (2018), DOI: 10.17504/protocols.io.uppevmn

Ahmed, M.B., Santos, K.C.G.d., Sanchez, I.B., Petre, B., Lorrain, C., Plourde, M.B., Duplessis, S., Desgagné-Penix, I, Germain, H. A rust fungal effector binds plant DNA and modulates transcription. Scientific Reports (2018), 8, 14718, DOI: 10.1038/s41598-018-32825-0

2013

dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; C.A. Rojas. Gluconacetobacter diazotrophicus enhances growth initial stages of Ilex paraguariensis development. II Conferência Iberoamericana de Interaçoes Benéficas Microorganismos-Planta-Ambiente (IBEMPA) (2013), p.450-451 (Extended abstract).

Oral presentations

2020

dos Santos, K.C.G., Desgagné-Penix, I. & Germain, H. 2017. Impact of fungal virulence proteins on in plants. Conferences Webs du Centre SÉVE (online).

2017

dos Santos, K.C.G., Desgagné-Penix, I. & Germain, H. 2017. Transcriptomic and metabolomic analysis of the alteration of physiological processes in a collection of transgenic plants expressing fungal effectors. Journées du Centre SÉVE, Orford, Canada

2014

dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; Rojas, C.A. 2014. Análise da interação endofítica de microorganismos benéficos e a erva-mate. III Encontro de Iniciação Científica da Unila “Pesquisa no século XXI: desafios e possibilidades”. In: Anais do III Encontro de Iniciação Científica da Unila “Pesquisa no século XXI: desafios e possibilidades”, p.135, Foz do Iguaçu, Brazil.

2013

dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; Rojas, C.A. 2013. Evaluación de la respuesta de la yerba mate a la inoculación con microorganismos potencialmente benéficos. II Congreso Paraguayo de Recursos Naturales y Medio Ambiente, Asunción, Paraguay.

dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; Rojas, C.A. 2013. Avaliação da Resposta da Erva-mate à Inoculação com Microorganismos Potencialmetne Benéficos. II Encontro de Iniciação Científica da Unila “Resultados em debate”. In: Anais do 2º Encontro de Iniciação Científica da Unila “Resultados em debate”, p.55-56, Foz do Iguaçu, Brazil.

Poster presentations

2022

dos Santos, K.C.G., Porth, I., Villareal, J.C. & Khasa, D. 2022. Génomique des populations végétales dans les zones minières boréales canadiennes. Colloque du CEN Edition 2022. Québec, Canada. (online)

2021

dos Santos, K.C.G., Porth, I., Villareal, J.C. & Khasa, D. 2021. Plant population genomics in Canadian boreal mining areas. Concours d’affiches scientifiques étudiantes 2021 du Centre SÈVE. Canada. (online)

2020

dos Santos, K.C.G., Pelletier, G., Séguin, A. Guillemette, F., Hawkes, J., Desgagné-Penix, I. & Germain, H. Differential alteration of plant functions by homologous fungal candidate effectors. Concours d’affiches scientifiques étudiantes 2020 du Centre SÈVE (online).

dos Santos, K.C.G., Desgagné-Penix, I. & Germain, H. 2020. Étude des plantes exprimant des protéines de virulence de la rouille du peuplier. Contest of scientific Posters - UQTR, Trois-Rivières, Canada.

2019

dos Santos, K.C.G., Desgagné-Penix, I. & Germain, H. 2019. Transcriptomics and metabolomics of Arabidopsis expressing effectors from the poplar rust. Réunion conjointe Centre SÉVE-SPPQ, Bromont, Canada.

dos Santos, K.C.G., Desgagné-Penix, I. & Germain, H. 2019. Effectors from poplar rust modulate Arabidopsis transcriptome. IS-MPMI 2019, Glasgow, United Kingdom.

dos Santos, K.C.G., Desgagné-Penix, I. & Germain, H. 2019. Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis. Plant Canada 2019, Guelph, Canada.

dos Santos, K.C.G., Desgagné-Penix, I. & Germain, H. 2019. Facteurs de virulence fongique modulent le transcriptome d’Arabidopsis. Contest of scientific Posters - UQTR, Trois-Rivières, Canada.

2018

dos Santos, K.C.G., Desgagné-Penix, I. & Germain, H. 2018. Analysis of transcriptomic alterations in a collection of transgenic plants expressing fungal effectors. Plant Biology 2018, Montreal, Canada.

dos Santos, K.C.G., Desgagné-Penix, I. & Germain, H. 2018. Analysis of transcriptomic alterations in a collection of transgenic plants expressing fungal effectors. Contest of scientific Posters - UQTR, Trois-Rivières, Canada.

2017

dos Santos, K.C.G., Desgagné-Penix, I. & Germain, H. 2017. Transcriptomic and metabolomic analysis of the alteration of physiological processes in a collection of transgenic plants expressing fungal effectors. Contest of scientific posters - UQTR, Trois-Rivières, Canada.

2014

dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; Rojas, C.A. 2014. Promoción del crecimiento de Ilex paraguariensis mediada por Gluconacetobacter diazotrophicus y su relación con el metabolismo del nitrógeno. In: Memorias del VI Congreso Sudamericano de Yerba Mate y II Simposio Internacional de Yerba-Mate y Salud, Montevideo, Uruguay.

dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; C.A. Rojas. 2014. Análise da interação endofítica de microorganismos benéficos e a erva-mate. III Encontro de Iniciação Científica da Unila “Pesquisa no século XXI: desafios e possibilidades”, Foz do Iguaçu, Brazil.

2013

dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; Rojas, C.A. 2013. Evaluación de la respuesta de la yerba mate a la inoculación con microorganismos potencialmente benéficos. IV Congreso de Agrobiotecnología, Propiedad Intelectual y Políticas Públicas, Posadas, Argentina.

dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; Rojas, C.A. 2013. Avaliação da Resposta da Erva-mate à Inoculação com Microorganismos Potencialmente Benéficos. II Encontro de Iniciação Científica da Unila “Resultados em debate”, Foz do Iguaçu, Brazil.