CV

EDUCATION

Doctor of Philosophy in Microbiology, Immunology, and Molecular Genetics 2007
UNIVERSITY OF CALIFORNIA, LOS ANGELES, Los Angeles, CA
Dissertation: In Vivo Delivery and Persistence in Mouse of an Episomal Expression Cassette by a Helper Dependent Adenovirus – Epstein-Barr Virus Hybrid Gene Therapy Vector
Advisor: Arnold J Berk, MD

Bachelor of Science in Cell and Molecular Biology, with honors 1997
UNIVERSITY OF CALIFORNIA, LOS ANGELES, Los Angeles, CA

RELEVANT SKILLS

Computational biology / bioinformatics, high-throughput / next-generation sequencing and analysis, RNA-Seq, DNA-Seq, Iso-Seq, transcriptomics, comparative genomics, de novo assembly, structural and functional gene annotation, variant discovery, ChIP-Seq, proteomics, large-scale data management.

Computer / coding experience in Perl, R, Python, SGE, UNIX/LINUX shell scripting, MacOS.

RESEARCH EXPERIENCE

Project Scientist; Department of Chemistry & Biochemistry 2018-present
UNIVERSITY OF CALIFORNIA, LOS ANGELES, Los Angeles, CA
• Discovered that many divergent species of eukaryotic green algae co-express multiple genes on polycistronic mRNA. This finding contradicts the dogma that polycistronic gene expression primarily a feature of prokaryotes. This discovery will facilitate the identification of hundreds of currently unknown genes in algal genomes that are missed by current gene annotation tools that expect only one protein per mRNA.
• Demonstrated that the discovery of polycistronic gene expression in green algae could be leveraged to create bicistronic expression vectors for use in plants and algae. Validated that these vectors produce pairs of proteins, including reporter proteins and selectable markers, of the expected size in vitro, and that these expression vectors could be engineered to alter the relative expression of the downstream and upstream protein.

Associate Specialist; Department of Chemistry & Biochemistry 2014-2018
UNIVERSITY OF CALIFORNIA, LOS ANGELES, Los Angeles, CA
• Created and deployed new software tools designed to facilitate and improve bioinformatics studies in the algal species Chlamydomonas reinhardtii. These include a program to increase the accuracy of RNA-Seq studies by utilizing strain-specific genetic variants, and a program to unambiguously identify and phylogenetically characterize strains based on RNA-Seq data.
• Sequenced and de novo assembled the organellar genomes of C. reinhardtii, and annotated them using transcriptomic data. Used these to study the neglected field of chloroplast and mitochondrial transcription. Discovered poly-NT 3′ tailing of mitochondrial transcripts.
• Collaborated on the development of a high quality genome and transcriptome of the algal species, Chromochloris zofingiensis, with the potential to become an important model organism.

Post-Doctoral Researcher; Department of Chemistry & Biochemistry 2011-2014
UNIVERSITY OF CALIFORNIA, LOS ANGELES, Los Angeles, CA
• Performed extensive comparative genomics study on commonly used laboratory strains of C. reinhardtii.
• Collaborated on RNA-Seq / transcriptomics projects in a variety of species (algae, protozoa, insects) in conjunction with groups at UCLA and a number of outside institutions (UC Davis, Scripps, UC Berkeley, CNRS in France).
• Collaborated in the sequencing of the genomes of a variety of algal and bacterial species.
• Developed and optimized protocols related to high throughput sequencing of DNA and RNA.
• Managed the IT requirements of the group including the deployment of a 22 TB file server for managing the group’s data needs.

Post-Doctoral Researcher; Department of Microbiology, Immunology, & Molecular Genetics 2007-2011
UNIVERSITY OF CALIFORNIA, LOS ANGELES, Los Angeles, CA
• Provided scientific leadership to graduate and undergraduate student researchers. Proactively engaged in inter-laboratory collaborations; took an active interest in both related and unrelated projects, demonstrated techniques, and advised on experimental design.
• Oversight of a project to re-engineer a Sindbis virus replicon to achieve inducible, high-level expression of cytotoxic proteins in human tissue culture.
• Boosted the potential clinical benefit and safety of gene therapy vectors. Employed EBV genetic elements to mediate the long-term persistence of therapeutic vector DNA in target cells both in vitro and in vivo.
• Successfully developed and validated a novel quantitative real-time PCR-based assay for the accurate, reproducible, and rapid titration of virus stocks. Easily scalable and widely applicable to a variety of viruses and gene therapy vectors, including mixed populations.
• Supported the publication efforts of a collaborating laboratory. Devised an innovative PCR-based assay, which addressed reviewers’ concerns and facilitated publication of the work in Genetics.

Graduate Student Researcher; Department of Microbiology, Immunology, & Molecular Genetics 1999-2007
UNIVERSITY OF CALIFORNIA, LOS ANGELES, Los Angeles, CA
• Successfully demonstrated the benefits of a unique hybrid gene therapy vector over traditional vectors. Engineered this gene delivery tool to include elements from 10 different species of metazoans and viruses for increased safety and efficacy.
• Became the first to achieve in vivo evidence of the superiority of the hybrid vector. Published the results of a long-term study in mouse in which the hybrid achieved 100% delivery of a transgene to mouse hepatocytes following a single intravenous injection.
• Utilized bioluminescent imaging, quantitative PCR, confocal microscopy, and flow cytometry on scores of mice in a year-long study in order to demonstrate that I had achieved sustained, high-level transgene expression.
• Engineered cell lines for the production of gene therapeutics. Dramatically scaled up vector production in these cultured cell lines in order to generate clinical-grade stocks in quantities sufficient for in vivo studies.
• Implemented the required mouse colony from inception; learned all aspects of animal care and maintenance, performed numerous survival surgery procedures, and gained protocol approval from the Animal Research Committee.

Research Assistant 1998-1999
AMGEN INCORPORATED, Thousand Oaks, CA
• Investigated the potential therapeutic application of the human protein leptin.
• Examined biochemical properties and established that homodimerization of leptin nucleated undesirable precipitation of the protein at therapeutically useful concentrations and pH.
• Demonstrated that substitution of two residues in leptin was sufficient to dramatically decrease dimerization, resulting in increased stability and a greater potential for clinical application.

Quality Control Technician 1997-1998
ALPHA THERAPEUTICS INCORPORATED, Los Angeles, CA
• Performed biochemical assays and data analysis on plasma-based therapeutics for quality control in a cGMP/cGLP facility.

PUBLICATIONS

  • Gallaher SD, Craig RJ, Ganesan I, Purvine SO, McCorkle SR, Grimwood J, Strenkert D, Davidi L, Roth MS, Jeffers TL, Lipton MS, Niyogi KK, Schmutz J, Theg SM, Blaby-Haas CE, Merchant SS. Widespread polycistronic gene expression in green algae. Proc Natl Acad Sci U S A. 2021 Feb 16;118(7):e2017714118. doi: 10.1073/pnas.2017714118.
  • Neupert J, Gallaher SD, Lu Y, Strenkert D, Segal N, Barahimipour R, Fitz-Gibbon ST, Schroda M, Merchant SS, Bock R. An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonas. Nat Commun. 2020 Dec 8;11(1):6269. doi: 10.1038/s41467-020-19983-4.
  • Roth MS, Gallaher SD, Westcott DJ, Iwai M, Louie KB, Mueller M, Walter A, Foflonker F, Bowen BP, Ataii NN, Song J, Chen JH, Blaby-Haas CE, Larabell C, Auer M, Northen TR, Merchant SS, Niyogi KK. Regulation of Oxygenic Photosynthesis during Trophic Transitions in the Green Alga Chromochloris zofingiensis. Plant Cell. 2019 Mar;31(3):579-601. doi: 10.1105/tpc.18.00742. Epub 2019 Feb 20.
  • Strenkert D, Schmollinger S, Gallaher SD, Salome PA, Purvine SO, Nicora CD, Mettler-Altmann T, Soubeyrand E, Weber APM, Lipton MS, Basset GJ, Merchant SS. Multiomics resolution of molecular events during a day in the life of Chlamydomonas. Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2374-2383. doi: 10.1073/pnas.1815238116. Epub 2019 Jan 18.
  • Li M, van Zee M, Riche CT, Tofig B, Gallaher SD, Merchant SS, Damoiseaux R, Goda K, Di Carlo D.Small. A Gelatin Microdroplet Platform for High-Throughput Sorting of Hyperproducing Single-Cell-Derived Microalgal Clones.2018 Nov;14(44):e1803315. doi: 10.1002/smll.201803315. Epub 2018 Oct 4.
  • Gallaher SD, Fitz-Gibbon ST, Strenkert D, Purvine SO, Pellegrini M, Merchant SS. High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates. Plant J. 2018 Feb;93(3):545-565.
  • Gallaher SD and Roth MS. RNA Purification from the Unicellular Green Alga, Chromochloris zofingiensis. Bio-protocol. 2018.8(7): e2793.
  • Wittkopp TM, Schmollinger S, Saroussi S, Hu W, Zhang W, Fan Q, Gallaher SD, Leonard MT, Soubeyrand E, Basset GJ, Merchant SS, Grossman AR, Duanmu D, Lagarias JC. Bilin-Dependent Photoacclimation in Chlamydomonas reinhardtii. Plant Cell. 2017 Nov;29(11):2711-2726.
  • Roth MS, Cokus SJ, Gallaher SD, Walter A, Lopez D, Erickson E, Endelman B, Westcott D, Larabell CA, Merchant SS, Pellegrini M, Niyogi KK. Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production. Proc Natl Acad Sci U S A. 2017 May 8.
  • Chambers M, Turki-Judeh W, Kim MW, Chen K, Gallaher SD, Courey AJ. Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activity. BMC Genomics. 2017 Feb 28;18(1):215
  • Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnol Biofuels. 2016 Nov 25;9:258.
  • Lopez D, Hamaji T, Kropat J, De Hoff P, Morselli M, Rubbi L, Fitz-Gibbon S, Gallaher SD, Merchant SS, Umen J, Pellegrini M. Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle. Plant Physiol. 2015 Dec;169(4):2730-43.
  • Gallaher SD, Fitz-Gibbon ST, Glaesener AG, Pellegrini M, Merchant SS. Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies. Plant Cell. 2015 Sep;27(9):2335-52.
  • Hong-Hermesdorf A, Miethke M, Gallaher SD, Kropat J, Dodani SC, Chan J, Barupala D, Domaille DW, Shirasaki DI, Loo JA, Weber PK, Pett-Ridge J, Stemmler TL, Chang CJ, Merchant SS. Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas. Nat Chem Biol. 2015 Mar;11(3):235.
  • Kropat J, Gallaher SD, Urzica EI, Nakamoto SS, Strenkert D, Tottey S, Mason AZ, Merchant SS. Copper economy in Chlamydomonas: prioritized allocation and reallocation of copper to respiration vs. photosynthesis. Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2644-51.
  • Goodenough U, Blaby I, Casero D, Gallaher SD, Goodson C, Johnson S, Lee JH, Merchant SS, Pellegrini M, Roth R, Rusch J, Singh M, Umen JG, Weiss TL, Wulan T. The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii. Eukaryot Cell. 2014 May;13(5):591-613.
  • Blaby IK, Glaesener AG, Mettler T, Fitz-Gibbon ST, Gallaher SD, Liu B, Boyle NR, Kropat J, Stitt M, Johnson S, Benning C, Pellegrini M, Casero D, Merchant SS. Systems-Level Analysis of Nitrogen Starvation-Induced Modifications of Carbon Metabolism in a Chlamydomonas reinhardtii Starchless Mutant. Plant Cell. 2013. Nov;25(11):4305-23.
  • Urzica EI, Vieler A, Hong-Hermesdorf A, Page MD, Casero D, Gallaher SD, Kropat J, Pellegrini M, Benning C, Merchant SS. Remodeling of membrane lipids in iron-starved Chlamydomonas. J Biol Chem. 2013 Oct 18;288(42):30246-58.
  • Gallaher SD, Berk AJ. A rapid Q-PCR titration protocol for adenovirus and helper-dependent adenovirus vectors that produces biologically relevant results. J Virol. Methods. 2013. 192(1-2):28-38.
  • Duanmu D, Casero D, Dent RM, Gallaher S, Yang W, Rockwell NC, Martin SS, Pellegrini M, Niyogi KK, Merchant SS, Grossman AR, Lagarias JC. Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival. Proc Natl Acad Sci U S A. 2013. 110(9):3621-6.
  • Boyle NR, Page MD, Liu B, Blaby IK, Casero D, Kropat J, Cokus SJ, Hong-Hermesdorf A, Shaw J, Karpowicz SJ, Gallaher SD, Johnson S, Benning C, Pellegrini M, Grossman A, Merchant SS. Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J Biol Chem. 2012. 287(19):15811-25.
  • Turlo KA, Gallaher SD, Vora R, Berk AJ, Laski FA, Iruela-Arispe ML. When Cre-mediated Recombination in Mice does not Result in Protein Loss. Genetics. 2010. 186(3):959-67.
  • Gil JS, Gallaher SD, Berk AJ. Delivery of an EBV episome by a self-circularizing helper-dependent adenovirus: long-term transgene expression in immunocompetent mice. Gene Ther. 2010. 17(10):1288-93.
  • Gallaher SD, Gil JS, Dorigo O, Berk AJ. Robust In Vivo Transduction of a Genetically Stable Epstein-Barr Virus Episome to Hepatocytes in Mice by a Hybrid Viral Vector. J Virol. 2009. 83(7):3249-57.
  • Dorigo O, Gil JS, Gallaher SD, Tan BT, Castro MG, Lowenstein PR, Calos MP, Berk AJ. Development of a novel helper dependent adenovirus-Epstein Barr virus hybrid system for the stable transformation of mammalian cells. J Virol. 2004. 78(12):6556-66.