Senior R&D Scientist (Molecular Biologist-Microbiologist)

Rachel E. Muir, Ph.D.

** ******* ***. ******* ****, CA 94061

mobile phone: 650-***-****, email: **************@*****.***

Education

Postdoctoral research fellowship in Host-Pathogen Interactions 2003-2008 Dept. of Genetics Stanford University School of Medicine, Palo Alto CA

Postdoctoral advisor: Dr. Man-Wah Tan; Research focus: Elucidating the genetic networks underlying host innate immunity and bacteria pathogenicity using the nematode host model C. elegans

Postdoctoral research project in Bacterial Cell Cycle Regulated Development 2001-2003

Dept. of Chemistry and Biochemistry University of California, Los Angeles CA

Postdoctoral advisor and graduate research mentor: Dr. James W. Gober; Research focus: Prokaryotic cell division cycle and cell cycle regulated development; study of the cell division phenotype of Class II flagellar mutants, identifying the role(s) of the trans-acting regulatory factor FliX

Ph.D. in Biochemistry and Molecular Biology 1995-2001

Dept. of Chemistry and Biochemistry University of California, Los Angeles CA

Graduate mentor: Dr. James W. Gober; Dissertation research: A common regulatory pathway governing flagellar gene expression and cell division in Caulobacter crescentus.

B.S. in Biochemistry and Cell Biology 1991-1995

Dept. of Biology University of California, San Diego, CA

Professional Research Experience

Senior Scientist (7/2021 – 3/2022, 8 mon.)

Strain Engineer R&D, Black Sheep Foods Inc., San Francisco, CA

PCR Operator CLIA lab of Verily Life Sciences (TVC at Google), 3 month contract position with Crowd Staffing contracting agency. Contract spans Jan. 11th, 2021 through April 10th, 2021.

*My paid volunteer work to help the covid-19 testing effort during the pandemic. Valuable exposure to lab automation and working within a clinical lab environment during the emergence of the delta variant.

Senior Scientist (2017, 8 mon.)

Avidocin Technology Platform, AvidBiotics Corp. South San Francisco, CA

Scientist II (2008-2016)

Molecular Biology Microbiology and Protein Expression Dept. of DuPont Industrial

Biosciences (formerly Genencor a Division of Danisco) Palo Alto,

Self-employment and volunteer work

Research Consultant (1/2018 to present), independent contractor serving as a scientific advisor and subject matter expert in the industrial biotechnology R&D life sciences sector. NDA subject ma er: molecular biology, metabolic-engineering, protein-engineering, directed evolution, expression host strain construction, large scale fermentation, phenotypic analysis and membrane effects, isoprenoid biosynthetic pathways. Collaborator: Jeffrey Moseley, Ph.D., Vice-President of Research & Development Phycoil Biotechnology International, 46725 Fremont Blvd, Fremont, CA 94538, ***************@*****.***, 650-***-**** (cell)

Professional Consultant (11/2017 to 1/2019), independent contractor serving as a subject matter expert in the industrial biotechnology R&D life sciences sector relating to intellectual property.

NDA subject ma er: Intellectual property, US patent law, patent council and submission related costs, IP landscape

Collaborator: Rowan Hamilton, PhD, Senior Managing Director, Woodsdale Group

LLC, Redwood City, CA Office, ********@*****.***, (650) 272- 9189 (cell)

Invoice Specialist and Personal Assistant (6/2018 to present) for MPS Construction LLC, Redwood City, CA 94062, General Contractor (owner) Marcus P. Smith, ***************@*****.***, 650-***-**** (cell)

Zum Driver (10/2019 to present) Independent Contractor. Trustline registrant with California Dept. of Social Services. Zum Services, Inc. 275 Shoreline Drive Suite 300,

Redwood City, CA 94065. Zum Support Team www.ridezum.com, *******@*******.***, 855-***-**** (855-RIDE-ZUM).

Parent Volunteer for Kennedy Middle School in Redwood City, CA (3/2018 – 6/2018). I served as a chaperone on field trips, and assisted in the Kennedy School Band and Orchestra’s Spring Concert, 8th grade graduation ceremony and the 8th grade dance.

Prior to that I was a PTA member for Henry Ford Elementary School in Redwood City, CA. I have also taken on volunteer roles with AYSO as a U10 Boys Coach, U8 Boys Asst. Coach, and U8 Boys Parent Referee.

Additional Research Training / Academic Work Experience

Postdoctoral Research Fellowship

Bacterial Pathogenesis and Host Innate Immunity 2003-2008

Dept. of Genetics Stanford University School of Medicine, Stanford, CA

Dr. Man-Wah Tan, postdoctoral advisor

Postdoctoral Research

Bacterial Cell Cycle Regulated Development 2001-2003

Dept. of Chemistry and Biochemistry University of California, Los Angeles, CA Dr. James W. Gober, graduate mentor

Graduate Study

Dissertation research 1995-2001: A common regulatory pathway governing flagellar gene expression and cell division in Caulobacter crescentus.

Dept. of Chemistry and Biochemistry University of California, Los Angeles, CA

Teaching Assistant 1996, 1997, 2001 (graduate student)

Metabolic Biochemistry Dept. of Chemistry and Biochemistry UCLA

Teaching Assistant 1995 (undergraduate student)

Structural Biochemistry (Winter) and Cell Biology (Spring) Dept. of Biology

UCSD

Tutor 1994-1995

Undergraduate Tutor Sciences O.A.S.I.S. Tutorial Center UCSD

Research Assistant 1993 lmmuno-Dynamics, Inc. Sorrento Valley, CA

Bibliography

Muir, R. E. and Tan, M. -W. (2008) Virulence of Leucobacter chromiireducens subsp. solipictus to Caenorhabditis elegans: Characterization of a Novel Host-Pathogen Interaction. Appl. Environ. Microbiol. 74: 4185-4198.

Muir, R. E. and Tan, M. -W. (2007) Leucobacter chromiireducens subsp. so/ipictus, subsp. nov., a pigmented bacterium isolated from the nematode Caenorhabditis e/egans and emended description of L. chromiireducens. /JSEM. 57: 2770-2776.

Muir, R. E. and Tan, M. -W. (2006) Evolution of Pathogens in Soil, chapter 8. In The

Evolution of Microbial Pathogens. H. Steven Seifert Northwestern University Medical

School Department of Microbiology-Immunology & Victor J. Dirita University of Michigan Unit for Laboratory Animal Medicine and Department of Microbiology and Immunology (eds.), ASM Press, Washington DC.

Muir, R. E., Easter, J., and Gober, J. W. (2005) The trans-acting flagellar regulatory proteins, FliX and FlbD, play a central role in linking flagellar biogenesis and cytokinesis in Cau/obacter crescentus. Microbiology. 151: 3699- 3711.

Muir, R. E. and Gober, J. W. (2005) Role of Integration Host Factor in the transcriptional activation of flagellar gene expression in Cau/obacter crescentus. J. Bacteriol. 187: 949-960.

Muir, R. E. and Gober, J. W. (2004) Regulation of FlbD activity by flagellum assembly is accomplished through direct interaction with the trans-acting factor, FliX. Mo/. Micro. 54: 715-730.

Muir, R. E. and Gober, J, W. (2002) Mutations in FlbD that relieve the dependency on flagellum assembly alter the temporal and spatial pattern of developmental transcription in Cau/obacter crescentus. Mo/. Micro. 43: 597- 615.

Muir, R. E. and Gober, J. W. (2001) Regulation of late flagellar gene transcription and cell division by flagellum assembly in C. crescentus. Mo/. Micro. 41: 117-130.

Muir, R. E., O'Brien, T. M., and Gober, J. W. (2001) The Cau/obacter crescentus flagellar gene, fliX, encodes a novel trans-acting factor that couples flagellar assembly to transcription. Mo/, Micro. 39: 1623-1637.

ln preparation

Muir, R. E. and Tan, M. -W. (2008) An Elt-3-dependent hypodermal-mediated response is required during Caenorhabditis e/egans innate immune defenses to bacterial infection of the uterus. Prepared for Cellular Microbiol.

2015 (Active) IP Cases

U.S. Pending Utility Applications: 4

Patent Cooperation Treaty Applications: 1

U.S. Granted Patents: 4

Docket No. Su Ca Application Filing Date Patent Issue Title

b se No. No. Date

Cas Ty

e pe

U.S. UTILITY

APPLICATIONS

NB31596-US CN OR 14/180,075 12-Feb-201 BIOLOGICAL PRODUCTION

T D 4 OF PENTOSE SUGARS

USING RECOMBINANT

CELLS

NB31598-US CN OR 14/175,754 07-Feb-201 COMPOSITIONS AND

T D 4 METHODS FOR IMPROVED

ISOPRENE PRODUCTION

USING TWO TYPES ISPG

ENZYMES

NB31308-US CN OR 13/725,929 09-Jan-201 ENHANCED PRODUCTION

T D 5 OF ISOPRENE USING HOST

CELLS HAVING

DECREASED ISPA

ACTIVITY

NB31604-US NP OR 14/41,6044 20-Jan-201 MICROTITER PLATES FOR

D 5 CONTROLLED RELEASE

(20-Feb-20 OF CULTURE

13) COMPONENTS TO CELL

CULTURES

PATENT

COOPERATION

TREATY

NB40587-WO-PCT PC PCT/US14/07 13-Dec-201 COMPOSITIONS AND

T 153 4 METHODS FOR CONTROL

OF INDUSTRIAL SCALE

PRODUCTION OF

BIO-PRODUCTS

GRANTED PATENTS

NB31596-US NP OR 13/33,5792 22-Dec-201 8,691,5 08-Apr BIOLOGICAL PRODUCTION

D 1 41 -2014 OF PENTOSE SUGARS

USING RECOMBINANT

CELLS

NB31598-US

NP OR 13/335,768 D

22-Dec-201 8,685,7 01-Jun COMPOSITIONS AND

1 02 -2014 METHODS FOR IMPROVED

ISOPRENE PRODUCTION

USING TWO TYPES ISPG

ENZYMES

NB31219-US

NP OR 12/817,134 D

16-Jun-201-******-**-Au IMPROVED ISOPRENE

0 5 g-2013 PRODUCTION USING THE

DXP AND MVA PATHWAY

NB31308-US

NP OR 13/725,929 D

21-Dec-201-******-**-Ma ENHANCED PRODUCTION

2 1 r-2015 OF ISOPRENE USING HOST

CELLS HAVING

DECREASED ISPA

ACTIVITY

Job qualifications to the Senior R&D Research Scientist position

Extensive hands-on experimental laboratory research experience of 20+years and vast in-depth knowledge of modern molecular biology methods and current techniques including droplet digital PCR, real-time q-RT PCR, NGS library preparation and sequencing, design and construction of plasmid transformation vectors, versed in CRISPR based technologies, and bioinformatic tools and other computational tools for bacteria, plant, and various genomics research found at www.softberry.com

Hands-on experience generating and analyzing whole bacterial genome sequence data, transcript profiles and gene expression patterns, protein accumulation assessments across 14-L fermentation time points, and tons and tons of phenotypic studies involving biochemical analysis, microscopy and TEM based morphology characterization, viability studies, and much more as well as application of findings to expression host strain improvements and metabolic pathway and single gene modifications including a range of alterations involving promoters, transcript stability elements, mutations, copy-number, chromosomal location, and varied alleles in efforts to improve host performance, increase product titer, improve product robustness, reduce cell maintenance cost, increase yield on carbon source.

Inventor of an orthogonal expression system for pathway genes that could be used in combination with current popular inducing systems of gene expression and is of lower cost than current methods employed that has the potential of significant savings for the company (please ask me about this)

Demonstrated success working in the fast paced environment at the cutting edge of science and have done so for 10+ years within a large company setting and a smaller start-up environment.

Experience in both the design and in the lab at the bench implementation utilizing of high throughput methods for phenotype screens, mutant hunts, cloning methods, strain generation, and project specific molecular diagnostic tools

Research Mentor for a UCLA Biochemistry Masters student, Genencor summer interns, UCLA and Stanford University undergraduate researchers, as well as juinor to senior colleagues from my professional research career. I enjoy teaching, lab instruction, and training researchers of all ages and experience levels. Needless to say, I have a significant number of years of experience in that realm and am currently looking for a job role that will afford me similar opportunities.

I have a range of scientific writing experience including IP and patent examples, SOP, safety manuals, BSL2 instructional powerpoint training slide set, ergonomics site policy, audit guidelines for PPE and ergonomics assessments, data figures, conference posters, project meeting reports, seminar talks, collaboration communications, scientific journal publications, etc. I also have many years of presenting data in both casual and formal settings. and took on a previous role at Genencor / Du Pont Industrial Biosciences as a scientific liaison representing R&D for our research collaborators and business partners

Technical skill set:

PCR, ddPCR, qRT-PCR, real time PCR, cDNA, DNA/RNA purification, sequencing and NGS and RNAseq and microarray and cDNA-PCR gene expression profiling, northern blot, southern blot, western blot etc., transcriptomics, genomics, proteomics, metabolomics. metabolic engineering, recombinant protein expression, protein purification, protein activity assays, stability assays, transcription, translation, mRNA half-life, post translational modification, design and use of in vivo and in vitro reporter assays, protein engineering, genomic modification, transduction, electro- and chemical transformation, competent cells, Cloning restriction digest T4 ligation, Gibson Assembly, Topo, Gateway, PAGE, FACS, ELISA, immuno-blot, 2D- gels, native gels, silver stain, use of P32 and S35 in southern blots protein labeling stability studies south-western blots phage library screens, phage display, plasmid libraries and libraries and expression constructs of all sorts, synthetic biology, meta genomics, Primer design, microscopy, immunofluorescence microscopy, fermentation, bacteria cultures, host modification, BSL2, bacteriophage, SPR BIACORE. In vivo and in vitro protein-protein interaction, protein-DNA interaction, FISH, strain collection, strain preservation, SEL library design construction and screening, mutagenesis, selective pressure screens, protein evolution, microbial genetics, C. elegans genetics, computational software tools (see www.softberry.com), membrane preparation, biochemical separation and assessment of extra-cellular, intra-cellular, periplasmic fractions/fractionation, lipid profile, BIOLOG, antimicrobics, antibody and phage and purocin/monocin work: titer specificity efficacy purify stability propagation, patent writing, teaching, lab instruction, research mentorship environment health and safety Officer, Ergonomics trainee

Summary:

R&D Senior Scientist – Strain Engineer, first R&D hire for Black Sheep Foods Inc. (2021-2022); small start-up company of 10-15 employees in San Francisco working within the food technology sector. Responsible for putting together a BSL1 lab space, building an R&D department, designing and implementing the strain engineering group project plan; research focused on the development of a fermentation process for the large scale production of a subset of mid-length branched chain fatty acids (BCFAs) known to be of the primary flavor compounds contributing to the smell and taste of ground lamb. Proof of Principle work spanning the first 12-18 months including IP filings covered minimal strain engineering of bacterial and algal hosts, corresponding upstream molecular biology / synthetic biology efforts and assay development (microbial physiology, protein biochemistry, analytical chemistry) to assess host potential to support the production of commercially viable titer of the desired BCFAs as either free fatty acids or incorporation into TAGs.

PCR Operator CLIA lab of Verily Life Sciences

Role description:

Handle and perform COVID-19 RT-PCR based diagnostic testing on clinical specimenin a CLIA environment.

Run automated liquid handling systems, RT-qPCR, QS5, KingFisher and otherinstruments as required in the lab.

Maintain sample and process records in LIMS.

Maintain instrumentation and appropriate documentation as required in the la.b

R&D Senior Scientist – Molecular Biology and Microbiology serving Avidocin Technology platform for Avidbiotics Corp (2017; small start-up company of 12-15 employees in South San Francisco); R&D Scientist II – Molecular Biology, Microbiology, and Protein Expression Dept. for Dupont Industrial Biosciences (2008-2016; formally Genencor, currently Dowdupont; very large multinational corporation); research career of 20+ years including work experience in both academic and industrial biotechnology settings; academic research spans graduate training as a molecular biologist conducted in a BSL2 microbiology / microbial genetics / molecular genetics laboratory (model system: asymmetrically dividing bacterium Caulobacter crescentus) within the biochemistry dept. of UCLA through a post-doctoral fellowship spent in a BSL2 C. elegans genetics and innate immunity / microbial pathogenesis laboratory (studied host-pathogen interactions using the nematode as a model host for bacterial infection) within the Genetics Dept. of Stanford University School of Medicine; professional research career spent entirely within the industrial biotechnology hub of the bay area.

Participated in the fields of molecular biology, biochemistry, microbiology, and genetics. Significant research efforts conducted in the areas of functional genomics, comparative genomics, transcriptomics, proteomics, and to a lesser extent metabolomics. Some experience using bioinformatics, metagenomics, and synthetic biology approaches. Research focus in general was on gene expression with work primarily geared toward elucidation of genetic networks, signal transduction and metabolic/physiological/stress response pathways and often involved comparing genomes and mining genomes for genes of interest. Learnings resulted in further understanding of the prokaryotic cell cycle-, inherent-, and environmental-governed gene expression, as well as understanding eukaryotic host innate immune response and microbial pathogenesis regulated behavior (aka virulence response) at the molecular level.

Within the R&D industrial biotechnology arena, relevant findings were applied in efforts to improve metabolic engineering, pathway engineering, protein engineering and expression host engineering of commercial platform strains. Most project work involved hands-on molecular biology and microbiology skill sets applied in product development expression host improvement / host engineering, and 14-L scale fermentation and process development project goals (PCR, cloning, sequencing, plasmid design and construction, comparative genome-genome mining-bioinformatics-metagenomics work, synthetic biology combo. with functional genomics, protein engineering, host strain construction, chromosomal alterations “genetic engineering”, mutagenesis and selected mutagenesis screens, host strain phenotypic-viability-stability-performance-maintenance studies, microscopy, gene/pathway library generation and screens, protein purification, antibody projects, ELISA, westerns, enzyme activity assays, mass spec., q-RT PCR, RNA-seq, transcript profiles/microarrays, NGS sample preparation, literature research etc.). Though primary contribution as experimentalist was to upstream efforts, work experience within biotech. industry includes substantial fermentation efforts performed at bench scale using numerous methods to replicate large scale performance in the lab (microferm, dasgip, slow-release plates, specialty high OD flasks), numerous satellite ferms off 14-Ltime points, viability assessments, and much much work involved in phenotypic studies of 14-L runs involving SOP generation and hands-on sampling of the 14-L vessel inside the fermentation lab, a lot of microscope time and FACS analysis, some biochemical assays including preparing samples for outsourced material determinations, metabolomics work, generation of transcript profiles, genome sequencing, transmission electron microscopy samples, protein expression and stability assessments, plasmid retention, mutation frequency and mutant hunts, and likely more. Many projects involved development of project/product specific diagnostic assays for quantitation and quality assessment of large-scale time points. Some projects required participation in bench scale recovery studies, 14-L scale recovery work performed in the recovery lab and BSL2 lab, and process/formulation development work.

Products of projects included the volatile natural product 5-carbon alkene isoprene, MegaDalton sized multipeptide-containing complexes called Avidocins, and various leghemoglobins derived from cyanobacteria genes and other gram-negative bacterial orfs encoding putative alleles of the heme-containing protein.

Extensive contribution to experimental design and hands-on experimental bench research. Senior level scientist contributor to the design and implementation of: project plan and management, data-driven revamping of project plan, project timelines, project goals and milestones, project staffing, go / no-go decisions, recognized achievements of team members, R&D representative liaison for project partner business teams, head of troubleshooting / brainstorming efforts, data presentation at formal quarterly project meetings, senior member on scientific panel for collaboration projects, generating and presenting meeting reports, training junior team members in the lab, inviting project specific and company-wide seminar speakers of expertise, coordinating third party research efforts securing NDA, MTA and necessary regulatory affairs assessments and permits, IP generation, patent example writing, coordinating patent application and updates with project lawyers and outside council, assisting in project team building social functions and entertaining collaborators on-site. As senior level scientist represented the company at scientific conferences and afforded the opportunity to attend work related and self-betterment seminars, classes, training exercises, and conferences.

Proven problem-solving skills. Leadership training: Lab to Leadership course, Edward Tufte seminar on informational graphics, IP & patent writing course, and professional coaching. Leadership work experience: collaboration manager, technical lead scientist Molecular Biologist / Microbiologist on cross-disciplinary project teams, cross-site subproject leader, task manager, environmental health and safety coordinator/officer, summer inter mentor, coached junior colleagues in the lab and at the desk through job promotions, new hirer go-to colleague/friend, hiring committee member, academic author, IP inventor, SOP author, research presentation / seminar speaker, BSL2 laboratory safety instructor, teaching assistant, life sciences tutor, on-site events committee member, and social events planner for on-site and off-site company-wide events and retreats.

Lively, open minded, enthusiastic, approachable research scientist that enjoys working with team members of all ages and levels of research experience in a collaborative effort toward solving the task(s) at hand. Have been described as a creative scientist that works well with others, is a positive mentor and subject matter expert mentor, has a knack for finding answers in the literature, can relate to the young colleagues while capable of communicating efficiently to the higher ups and easily adapts others’ ideas into the work plan where ever and as often as possible (not one with a need for sole credit, but one who rather enjoys a team victory and shared success.)

Contact this candidate