Podcast Appearance: Toggle Town by Ryan Tomich

I recently met an incredible student from Butte High School, Ryan Tomich, who is interested in making small towns even better through the use of technology. I was fortunate to be a guest on his podcast dedicated to this subject. The questions led me to essentially give a brief summary of my career and also highlighted my recent switch to embracing computational biology in my research and teaching.

Upcoming episodes of this podcast will feature Janet Coe, who will discuss the new Nursing Simulation Lab at Montana Tech. Later, John McKee, will describe his experience with starting a distillery in Butte in Butte, which is aptly called Headframe Spirits.

Next Generation Sequencing 1: Overview Questions

For Biotechnology

Questions to answer while watching this video:

  1. What are the four types of sequencing that will be discussed in this video.
  2. What was the cost of the original human genome sequencing effort?  What was the cost (using Sanger sequencing) immediately after the completion in 2001?
  3. What does it mean that DNA is made of anti-parallel strands?
  4. DNA can be denatured by raising the temperature.  What “R” word did Dr. Chow use as a synonym for annealing the matching strands?
  5. How does a polymerase know what new nucleotide to add to the 3′ hydroxyl group of a growing DNA strand?
  6. What does dNTP stand for?  What are the four types of dNTPs?
  7. What are two ways that a fluorescent terminator differs from the dNTPs?
  8. In a Sanger sequencing-based PCR reaction, how many primers are added?
  9. In a Sanger sequencing-based PCR reaction, which molecules are more common: dNTPs or fluorescent terminators?
  10. What is a typical length of sequence that can be acquired using traditional (Sanger) sequencing?
  11. The Human Genome project used genomes from fewer than 10 people.  How many genomes need to be sequenced to better understand the functions of genes?
  12. Advances in sequencing technology from what company was behind the drops in sequencing costs around the years 2007, 2010, and 2015?
  13. The results from sequencing one stretch of DNA is called a “read”.  How many reads can be obtained from a run on a 384-well plate Sanger sequencing instrument vs. a NovaSeq instrument?
  14. How many gigabases of sequences can be obtained on the Sanger vs. NovaSeq instruments?
  15. What is the cost of sequencing a human genome with the latest Illumina technology (at the time this video was made)?
  16. When showing the different sizes of Illumina flow cells, what was the object that was used as a reference to show scale?
  17. Which spelling do you prefer: adapter or adaptor?
  18. The adaptor sequences have two parts: primer binding sites and capture sequences. 
    1. Once the (denatured) DNA has been loaded into the flow cell, which adaptor sequence part is hybridized to other single-stranded DNA first?
    2. How many copies of the original ssDNA are found in a cluster by the time the sequencing primer is added?
  19. In fluorescent reversible terminator chemistry, which carbon of the ribose sugar is the terminator molecule attached to?
  20. Once the terminator molecule is removed, what functional group resides at that carbon of the ribose sugar?
  21. What is the sequence of the first cluster that Dr. Chow walks through?
  22. What is the limit of the read length for this sequencing approach?
  23. What is the solution for the problem created when two cluster are so close together that they partially overlap?
  24. What is an advantage of switching from 4-color to 2-color chemistry?
  25. What is the pore size in the Oxford Nanopore system’s membranes?
  26. Detectors measure a change in what electrical property as a ssDNA flows through the pore?
  27. How many ssDNA molecules can flow through the pore at the same time?
  28. What features are found on the 3′ carbon and 5′ carbon of the ribose sugar in nucleotides used in PacBio sequencing?
  29. How does a PacBio flow cell limit the number of ssDNA molecules being sequenced at a given position?
  30. Why is a movie created to “watch” the PacBio sequencing, rather than a single image per round like in Illumina sequence technologies?
  31. How does data from PacBio get “corrected” to make up for the 10-15% error rate during the reading of a single stretch of ssDNA?
  32. Why are sequencing technologies that produce long reads beneficial for genome assembly? (3 bullet points for this answer)
  33. Which medical application did you find to be the most interesting? Why?

Current Plan for the Biotechnology Course

This fall, I will be teaching a course titled “Biotechnology: Techniques and Data Analysis” and will use the textbook aptly titled “Biotechnology”.  As I familiarize myself with the book, I have found it difficult to pin down which chapters to cover.  The chapters in the book are as follows:

Chapter 1: Basics of Biotechnology

Chapter 2: DNA, RNA, and Protein

*Chapter 3: Recombinant DNA Technology

*Chapter 4: DNA Synthesis In Vivo and In Vitro

*Chapter 5: RNA-Based Technologies

*Chapter 6: Immune Technology

Chapter 7: Nanobiotechology

*Chapter 8: Genomics and Gene Expression

*Chapter 9: Proteomics

*Chapter 10: Recombinant Proteins

Chapter 11: Protein Engineering

Chapter 12: Environmental Biotechnology

*Chapter 13: Synthetic Biology

Chapter 14: From Cell Phones to Cyborgs

*Chapter 15: Transgenic Plants and Plant Biotechnology

*Chapter 16: Transgenic Animals

Chapter 17: Inherited Defects and Gene Therapy

Chapter 18: Cloning and Stem Cells

Chapter 19: Cancer

Chapter 20: Aging and apoptosis

Chapter 21: Viral and Prion Infections

Chapter 22: Biological Warfare

Chapter 23: Forensic Molecular Biology

*Chapter 24: Bioethics in Biotechnology

(Chapters denoted with an asterisk will be the topics covered in the course.)

One could argue that biotechnology (the modern era at least) started with the development of recombinant DNA technology, so starting with the “Recombinant DNA Technology” chapter is perfect.

Chapters 4, 5, 8, and 9 will essentially walk us through the Central Dogma of Molecular Biology and the techniques that can make use of the cellular processes of this dogma (DNA replication, transcription, and translation).

It might make sense to swap the “Genomics and Gene Expression” topic around with the “Immune Technology” chapter so that we finish up discussing DNA and RNA before moving on to proteins.

Chapter 10’s discussion of “Recombinant Proteins” will see the recombinant DNA technology idea through to its logical conclusion and wrap up the central dogma-centric portion of the course.

The Biotechnology degrees at MSU-Bozeman are split up into three different options: Microbial Systems, Plant Systems, and Animal Systems.  To provide a taste of each of these “systems”, we will cover the chapters on “Synthetic Biology”, “Transgenic Plants and Plant Biotechnology”, and “Transgenic Animals”, respectively.

If time allows, the chapter on “Bioethics in Biotechnology” will be the conclusion of this course.

In total, we are scheduled to cover eleven chapters in the 15-week semester.  From my experience, this should be about the right amount of material but time will tell if it holds true.

Additional assignments will be designed to allow students to explore the remaining topics thus providing some flexibility for students to tailor the course to their interests.