Marco Alonzo Dueñas

EDUCATION

University of California, Berkeley

University of California, Riverside

RESEARCH EXPERIENCE

Supervised by Dr. Sabeeha Merchant, Berkeley, CA, USA

Department of Plant & Microbial Biology, University of California, Berkeley

Lawrence Berkeley National Laboratory (Affiliate)

Eukaryotic Noncanonical Translation: Dissected the mechanism of eukaryotic polycistronic genes that are widespread and highly conserved within eukaryotic green algae. Used a combination of bioinformatics and genetics to uncover leaky ribosomal scanning as the mechanism driving downstream ORF translation. Used and designed synthetic bicistrons for specific stoichiometric protein output and tunable expression via manipulation of the Kozak-like sequence. Current projects include testing the mechanism in plants for synthetic biology application and bicistronic knockouts to deduce function.

Featured Techniques: Bioinformatics, plasmid design and assembly, DNA extraction, RNA extraction, PCR, Quantitative RT-PCR, algal culturing and transformation, genome manual curation, Ribo-Seq analysis, confocal fluorescence microscopy, reporter assay development, tobacco transient assay.

Lipid Droplet Biogenesis and Designer Lipid Production: Functionally dissected and confirmed subcellular localization of the A. protothecoides Major Lipid Droplet Protein (MLDP), a protein important in the structural formation and biogenesis of lipid droplets. Generated mutants and complement lines to decipher the function of MLDP. Uncovered application of the MLDP as a tool for enhanced targeting of enzymes to the lipid droplet for better sequestration of designer molecules for bioproducts.

Featured Techniques: Plasmid design and assembly, confocal fluorescence microscopy, super resolution microscopy, Fiji analysis, proteomics, lipid extraction and quantification, fatty acid analysis (GC-MS), thin layer chromatography, LC-MS.

Algal Genetic Engineering Toolkit: Genetic toolkit and system development for the oleaginous green alga Auxenochlorella spp. Aided in the assembly of the Auxenochlorella spp. genome and verified the presence of trisomy for the application of an artificial chromosome construction. Current work includes the fluorescent tagging and localization of subcellular compartments to create a protein targeting toolkit.

Featured Techniques: Plasmid design and assembly, promoter cloning, DNA extraction, algal culturing and transformation, confocal fluorescence microscopy.

Artificial Photosynthesis in Algae for Bioproduct Production: In collaboration with the lab of Dr. Robert Jinkerson. Conducted a proof of concept for electro-agriculture by demonstrating that Auxenochlorella symbiontica can grow in waste effluent generated by a two-step electrolysis used to generate CO₂ into acetate more efficiently than biological photosynthesis. A. symbiontica were then genetically engineered to produce the pigment astaxanthin and increased levels of palmitic acid, which serve as high value pigments and palm oil substitutes respectively. Both bioproducts accumulated in strains grown in waste effluent.

Featured Techniques: Plasmid design and assembly, algal culturing and transformation, carotenoid extraction and quantification (HPLC), fatty acid analysis (GC-MS).

Supervised by Dr. Devinder Sandhu, Riverside, CA, USA

USDA ARS George E. Brown Jr. Salinity Laboratory

Department of Botany & Plant Sciences, University of California, Riverside

Almond Salinity Tolerance: Intern and student employee that assisted research on almond salt tolerance genes utilizing the model organism Arabidopsis Thaliana. Contributed to various fieldwork including designing and implementing growing projects as well as surveying the local ecology to ensure experiments can be properly and efficiently conducted. Functionally verified the function of the almond rootstock sodium transporters SOS2 and and HKT1 using complementation in Arabidopsis. Conducted and designed RNA-seq pipeline to identify differential gene expression of almond rootstocks subjected to salinity stress.

Featured Techniques: DNA Extraction, RNA extraction, PCR, gel electrophoresis, ICPOES analysis, crop fieldwork and rootstock cultivation, Arabidopsis transformation, horticulture, hydroponics.

PUBLICATIONS

Featured Publications

1.Dueñas M.A., Craig R.J., Gallaher S.D., Moseley J.L., & Merchant S.S. Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae, Proc. Natl. Acad. Sci. U.S.A. 122 (9) e2417695122, https://doi.org/10.1073/pnas.2417695122 (2025).

2. Craig R.J., Dueñas M.A., Camacho D.J., Gallaher, S.D., Avendaño-Monsalve M.C., Lin Y.T., Blaby-Haas C.E., Moseley J.L., & Merchant S.S. Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella, The Plant Cell, https://doi.org/10.1093/plcell/koaf259 (2025).

Full Publication List

*Authors contributed equally

(newest to oldest)

1. Craig R.J., Dueñas M.A.*, Camacho D.J.*, Gallaher, S.D., Avendaño-Monsalve M.C., Lin Y.T., Blaby-Haas C.E., Moseley J.L., & Merchant S.S. Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella, The Plant Cell, koaf259, https://doi.org/10.1093/plcell/koaf259 (2025).

2. Dueñas M.A., Lin Y.T., Moseley J.L., & Merchant S.S. Transformation Protocol for Targeted Homologous Recombination in Auxenochlorella protothecoides. protocols.io https://dx.doi.org/10.17504/protocols.io.x54v922mql3e/v1 (2025).

3. Dueñas M.A., Craig R.J., Gallaher S.D., Moseley J.L., & Merchant S.S. Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae, Proc. Natl. Acad. Sci. U.S.A. 122 (9) e2417695122, https://doi.org/10.1073/pnas.2417695122 (2025).

4. Kaundal A., Sandhu D., Singh V., Dueñas, M.A., Acharya B.R., Nelson B. Ferreira, Litt A. Transgenic expression of Prunus persica Salt Overly Sensitive 2 (PpSOS2) in atsos2 mutant imparts salt tolerance in Arabidopsis. ACS Agricultural Science and Technology. 2(1):153-164, https://doi.org/10.1021/acsagscitech.1c00276 (2022).

5. Acharya B., Sandhu D., Dueñas C., Dueñas M.A. et al. Morphological, physiological, biochemical, and transcriptome studies reveal the importance of transporters and stress signaling pathways during salinity stress in Prunus. Scientific reports vol. 12,1 1274, doi:10.1038/s41598-022-05202-164 (2022).

6. Kaundal A., Sandhu D., Dueñas M.A., Ferreira JFS. Expression of the high-affinity K+ transporter 1 (PpHKT1) gene from almond rootstock ‘Nemaguard’ improved salt tolerance of transgenic Arabidopsis. PloS one vol. 14,3 e0214473, doi: 10.1371/journal.pone.0214473 (2019).

Manuscripts in progress

1. Dueñas M.A., Lin Y.T., Camacho D.J., Yu N.J., Moseley J.L., Merchant S.S. Functional Analysis of the Auxenochlorella Major Lipid Droplet Protein for Oil Droplet Biogenesis and Designer Lipid Sequestration. Manuscript in progress.

2. Dueñas M.A., Lin Y.T., Moseley J.L., Merchant S.S. Production of Cyclopropane fatty acids in Auxenochlorella Protothecoides to produce sustainable aviation fuels. Work in progress.

3. Le, D., Dueñas M.A., Moseley J.L., Merchant S.S, Jinkerson, R.E. Practical application of Green algae for use in electro-agriculture. Manuscript in preparation.

4. Lin, Y.T., Kosina, S., Dueñas, M.A., Moseley J.L., Merchant, S.S. Engineering Auxenochlorella protothecoides triacylglycerides to mimic the fatty acid composition and regioisomeric structure of human milk fat. Manuscript in preparation.

5. Avendaño-Monsalve M.C., Dueñas M.A., Moseley J.L., Merchant S.S. A cell atlas and subcellular localization toolkit in Auxenochlorella. Work in progress.

FELLOWSHIPS & SCHOLARSHIPS

PRESENTATIONS

Ottawa, Canada,

TBD

Berkeley, USA

“Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae”

Pomona, USA

“Functional analysis of the Auxenochlorella protothecoides Major Lipid Droplet Protein for oil droplet biogenesis and designer lipid sequestration”

San Francisco, USA

“Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae”

Berkeley, USA

“Tunable leaky ribosomal scanning governs translation of polycistronic genes in green algae”

Poster Presentations

Munster, Germany

“Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae” & “Functional analysis of the Auxenochlorella protothecoides Major Lipid Droplet Protein for oil droplet biogenesis and designer lipid sequestration”

San Francisco, USA,

“Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae”

Pomona, USA

“Functional analysis of the Auxenochlorella protothecoides Major Lipid Droplet Protein for oil droplet biogenesis and designer lipid sequestration”

San Francisco, USA

“Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae”

Barcelona, Spain

“Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae”

Berkeley, USA

“Utilizing Polycistronic Expression in Auxenochlorella protothecoides to mimic the lipid composition of Human Milk Fat”

Riverside, USA

“Expression of the high-affinity K+ transporter 1 (PpHKT1) gene from almond rootstock ‘Nemaguard’ improved salt tolerance of transgenic Arabidopsis”

SPOTLIGHTS

Not Lost in Translation: Algae Show How to Make Two Proteins from One Messenger RNA

Algae show how to make two proteins from one messenger RNA

Focus on: PhD candidate Marco Dueñas

TEACHING EXPERIENCE

Teaching Assistant (TA)

University of California, Berkeley

Head graduate student instructor

University of California, Berkeley

Recognized as an outstanding graduate student instructor, which is given to the top 10 percent of graduate student instructors recognized for outstanding work in teaching on the Berkeley campus.

Grader Positions

Instructor: Norma Cecilia Martinez-Gomez

Instructor: Anastasios Melis & Yangnan Gu

Instructor: Anastasios Melis

RESEARCH MENTORSHIP

INDUSTRY EXPERIENCE

Berkeley Alt: Meat Lab, CA, USA

Sutardja Center for Entrepreneurship and Technology (SCET), University of California, Berkeley

Seaweed for Alternative Protein Project: Research, develop, and propose alternative protein sources and extraction from seaweed. This included the viability of seaweed utility, extraction methods, and financial viability as a protein source, in addition to brainstorming for product development.

Featured Techniques: Literature search, market exploration, product development, focus group presentation.

EXTRACURRICULARS & OUTREACH

Current lead organizer for monthly seminar series with the topic of RNA research. Responsibilities include organizing speaker talks, coordinating labs on hosting schedule, and acquiring funding for the supergroup via fellowship applications.

Current graduate student chair in charge of running weekly seminars for the PMB students and postdocs, which include info sessions, practice talks, and networking opportunities.

Graduate student assistant for the Amgen Scholars program, a 10-week summer research opportunity for undergraduate students in the U.S. who are interested in science or engineering careers. Responsibilities included organizing and leading workshops on applying to graduate school, one on one peer mentoring, and conducting social activities for students in Berkeley. Participated in Summer 2024 & Summer 2025.

Judge panelist for EBI Internship application hosted at UC Berkeley

Volunteer speaker for the UCR MARC U STAR program, which aims to increase diversity in STEM research via outreach, guest seminars, activities, and sharing the benefits of engaging in undergraduate research.

LANGUAGES

English- Native proficiency

Spanish- Native proficiency

Chinese (Mandarin)– Elementary proficiency