Aaron Trippe discusses the changes and challenges of working with the PacBio Sequel since 2016. He discusses improvements in the technology since 2016 and has advice for user who would like to utilize this service.

Aaron Trippe, our long-time PacBio technician, stands next to the CGRB’s Pacific Biosciences Sequel.

Q1: How long have you been running the PacBio sequencing service at the CGRB?

The CGRB was one of the early adopters of the Sequel, the second phase of long read genomic sequencing technology from Pacific Biosciences.  It arrived here on campus in August of 2016.  Since then the technology has made significant improvements to the user-interface, and has tremendously increased read lengths and output. 

Q2: You started up the PacBio sequencing service at the CGRB. What has been the most challenging aspect about developing this service?

Aside from the continually changing and evolving technology, one of the most challenging aspects of the service is getting everything you feed the machine to produce optimal results.  One of the advantages of the technology is that you are sequencing native DNA, but that also makes it challenging when working with an organism that traditionally is difficult to work with and considered problematic.  Finding ways to produce super clean and high molecular weight DNA from just about everything is probably the largest hurdle to working with the technology as a service provider.  The keys to success are definitely within the sample quality.  Having pure, high molecular weight DNA is essential to take advantage of the long read aspect of the technology, and is directly correlated to the quality of the sequencing output.

Q3: What type(s) of project(s) would you recommend to use PacBio’s long read technology?

The technology is great for just about any sequencing application.  With the long reads, you have access to regions of DNA that were not previously accessible due to repetitive regions in genomic DNA.  There is enough output to multiplex several microbial genomes on a single SMRT Cell.  Complete sequences of multiplexed amplicons using Circular Consensus Sequencing for high fidelity reads of shorter inserts. With the read lengths exceeding that of RNA transcripts, Isoform sequencing using the Iso-seq application is also available for obtaining complete transcripts.

Q4: Favorite or most interesting project you’ve worked on?

Since managing the PacBio Sequel, I’ve gotten to work with plants, animals (vertebrates/invertebrates), fungi, bacteria, and insects for the local scientific community, and beyond.  I can’t say that I have had a favorite organism, and they have all been interesting projects, but overcoming challenges with successful results always feels rewarding.

For more information please visit the CGRB website: https://cgrb.oregonstate.edu/core/pacbio

Note: We wish Aaron the best as he purses a new opportunity and are grateful he was able to develop a successful PacBio Service at the CGRB! For future sequencing inquires please contact Katie Carter.

Close up of a PacBio SMRT cell.

Friday, September 20, 2019 CH2M HILL Alumni Center

Congratulations to our winners! To all the participants and presenters, another thank you for your contributions. We look forward to welcoming the CGRB Community to the 2020 Spring Conference on April 24, 2020.

Undergraduate Poster: Kelsey Shimoda “Altering metabolic gene expression in fruit flies: effects on longevity and brain aging”
Graduate Poster:             Benjamin Americus “Elegant Infection Machines: Nematocyst diversification within Myxozoa”
                                           Daniel Schneck “Phenotypic and transcriptional responses to different light regimes in allopatric populations of Tigriopus californicus”
                                            Manoj Gurung “Lactobacilli ameliorate western diet induced diabetes by preventing hepatic mitochondrial damage”
                                            Miranda Leek “A Biochemical and Biophysical Investigation into the Pathological Gain-of-Function of Nitrated Hsp90”
                                            Rebecca Veitch “Exposure to Light at Night Alters DNA Methylation and Expression of Proliferative and DNA Damage Repair Genes”
Post-Doc Poster :               Allie Graham “Independent losses of the Hypoxia-Inducible Factor (HIF) Pathway within Crustacea”
Lightning Talks:                 Eileen Chow “Daily blue light exposure accelerates aging in Drosophila melanogaster”

Raffle drawing for voting in all categories:             1st place – Miranda Leek
                                                                                       2nd place – Alexandre Sathler

8:00Registration & refreshments (Poster & sponsor setup) 
8:50Brett Tyler, Director, CGRB
Introduction, CGRB update
9:15Andrew Annalora, Environmental and Molecular Toxicology
Exploring Splice Variant Biology in Nuclear Receptor and Cytochrome P450 Genes
9:40Ed Kelly, University of Washington
Tissue Chips for Human Disease Modeling
10:50Lightning Talks Moderated by Jeff Anderson
Featuring: Martin Pearce, Stephanie Bollmann, Benjamin Americus, Evan Carpenter, Eileen Chow, Lauren Chan, Nolan Newman, Alexandra Weisberg
11:35Felipe Barreto, Integrative Biology
Genomics in the Tidepool: Functional and Population Genetics of Adaptation and Speciation in a Tiny Crustacean
12:00Kevin Brown, Pharmaceutical Sciences and Chemical, Biological, and Environmental Engineering
Adventures in Complex Systems
1:25Afua Nyarko, Biochemistry & Biophysics
Selectivity and Specificity in Cancer Regulatory Proteins
1:50Daniel Liefwalker, Oregon Health and Science University 
Therapeutic strategies targeting c-MYC
2:30Lightning Talks
Moderated by Jeff Anderson
Featuring: Armando Alcazar Magana, Christine Tataru, Sarah Alto, Anh Ha, Heather Forsythe, Kayla Jara, Rebecca France, Rachel Franklin
3:45Morgan Giers, Chemical, Biological, and Environmental Engineering
Regenerating the Intervertebral Disc: Developing Effective Therapies in a Nutrient Limited Environment  
4:10Doris Taylor, Texas Heart Institute
Building Solutions for Heart Disease: A 2019 Update
5:00-7:30Poster Session Reception, Sponsor Displays


Jaga Giebultowicz, Department of Integrative Biology
Craig Marcus, Environmental and Molecular Toxicology
Jeff Anderson, Department of Botany and Plant Pathology
Viviana Perez, Department of Biochemistry and Biophysics

Fall Term 2019
October 9, 2019Marilyn Roossinck
The Pennsylvania State University
Lessons in Virus Ecology from Forty Years of Research
Host: Jerri Bartholomew
October 23, 2019Ran Blekhman
The University of Minnesota
Population and Functional Genomics of Host-Microbiome Interactions
Host: Tom Sharpton
November 6, 2019Mark Farman
UC Davis
Telomeric transposons: major drivers of fungal genome evolution and guards against genome change
Host: Michael Freitag
December 4, 2019Carolina Tropini
The University of British Columbia
Physical perturbations to the gut microbiota during health and disease
Host: Natalia Shulzhenko
Winter Term 2020
January 8, 2020Chris Hittinger
University of Wisconsin-Madison
Host: Joey Spatafora
Genomic and metabolic evolution across budding yeasts
January 22, 2020Audrey Gasch
University of Wisconsin-Madison
Host: Michael Freitag
The genetic basis of aneuploidy tolerance in wild yeast
February 19, 2020Jill Banfield
UC Berkeley
Host: Steve Giovannoni
March 4, 2020Josh Cuperus
University of Washington
Host: Molly Megraw, John Fowler
Spring Term 2020
April 1, 2020Pankaj Kapahi
USC Leonard Davis
Host: Jaga Giebultowicz
April 15, 2020Jose Dinneny
Stanford University
Host: John Fowler
May 13, 2020TBD
May 27, 2020TBD