Chapter 1: Getting Started
How to begin
kathleef
Welcome to Genetic Engineering 2024
Welcome to BISC 357. We hope you will find it interesting and enjoyable. This short chapter will get you started and introduce you to the learning goals and aims of the course. It will also help you understand where to look for more information and how to use the course website most efficiently.
Learning goals of this course:
- Perform the basic techniques covered (as described in the lab manual)
- Explain the techniques-understanding the techniques and how they work is what gives you an edge in the job market. Anyone can pipet according to instructions.
- Select the best technique for a particular experiment and justify why it is the best choice
- Given results from experiments and the appropriate controls, interpret what the results tell us, including troubleshooting (can we trust the results and why or why not?)
- Design constructs for particular purposes, given the genes and vectors available
- Perform simple bioinformatic searches for construct design to address a variety of research questions
Course Structure
Following is a description of the course components and the grading scheme.
Lectures (10%)
The lectures are held in AQ 3149, M/W/F at 10:30 am. I have requested that they be recorded, both video and audio. There will be clicker questions asked during the lectures. These serve a variety of purposes. They help me to see if I’ve been clear. They help you to see if you understood the material. And, they sometimes provide practice in interpreting results or doing important calculations. The clickers are worth 10% of your total grade. You get a point for showing up and pressing buttons to answer the questions and then one point for every correct button you press. I have set the total clicker points at 85%; that is, if you earn 85% or more of the points you could have earned answering the clicker questions, you will get 10/10. This compensates for possibly missing one or two lectures.
Labs (35%)
Labs are held in SSB 8121. If you have taken 303, it is the smaller lab beside the 303 lab. There is no lab in the first week of classes. The lab schedule will be on your canvas course site.
Pre-Lab Quizzes:
Surprise pre-lab quizzes will be held every week at the beginning of the lab. They test whether you have read the lab handout and understand the basics of what we are doing. So, it is not: how many µl of 5M NaCl are we adding at step 3 of the procedure, but rather: why do we add salt before the precipitation step in our DNA isolation? Hopefully you can see the difference between these two questions. There will also be calculations in most quizzes. If we have 200 µl of RNA at 53 ng/µl how much RNA total have we isolated? These quizzes will be worth 10% of your overall grade and I will drop the lowest grade from the quizzes before calculating your quiz mark for the semester.
Lab Worksheets:
In several of the labs there are worksheets to complete. These help you understand the planning of experiments, how to predict outcomes and probe your understanding of the techniques we are using. Many students hate these worksheets but admit that they force you to really understand the work we are doing. They are also worth 10% of the grade.
Post-lab quizzes:
About every two weeks (the schedule is posted on Canvas) there are quizzes that ensure you understood what we did in the previous labs and what your results mean. The schedule is posted on Canvas and the quizzes are worth 10% of the grade. Please attend to the deadlines as these are FIRM. Since the answers will be available the day after the quizzes are due, we cannot accept late one for credit. Meeting deadlines is an important employment skill.
LabArchives.
We are using an online lab notebook platform through Lab Archives. In each notebook there will be a lab handout, that you should read in advance of the lab and some questions about the experiment and your results that must be answered by the Sunday following your lab (every week). We will grade (in random order) a subset of these every week. So you need to complete the questions every week. Answering them soon after finishing the lab helps cement the understanding in your mind. The questions are worth 5% of your grade. So don’t panic if you miss one week but try to always have them done on time.
Bioinformatics assignments 15% (subject to some adjustment)
We want to give you some experience using various online tools to help you find out what a gene does, find the open reading frame in a genomic sequence, design primers to amplify an insert for a construct (for various purposes), and so on.
These are the assignments you will do (with guidance and instructions):
- Annotation of a plant gene (eukaryotic).
- Design of oligonucleotides for a CRISPR construct to knock out a gene in a plant model organism.
- Design of primers for an RNAi or overexpression construct for the gene from assignment 2
- Design of transcriptional and translational fusion reporter constructs for the gene in assignment 2 (different for each pair of students; note that for different genes you may need to select different cloning methods)
Each of the assignments will be introduced via a recording, that takes you through the steps of the search or design. We will spend some Friday lectures going over the instructions together as well, to try to head off any technical issues that could arise.
Midterm: 15%
The midterm will cover the lab and lecture material from weeks 1 through 6. The kinds of questions will be similar to quiz and lab worksheet questions. Some of it will be focused directly on what you’ve been doing in the lab. I will post some practice midterm questions and other review material closer to the date of the midterm.
Final Exam: 25%
Students always ask if the final is cumulative and it is but not the way you think. All the material in the course is related to all the other material in the course. If you don’t understand how genes work, and restriction enzymes and DNA preps and PCR, or even just nucleic acid basics, then you’re going to have a hard time with the final exam even though the final will be focused on techniques and topics from the second half of the course. Because it is all related, and the course is a “building” course; every new topic is built on the foundation of the previous material. Without a solid foundation of understanding of the first 6 chapters or so of material, you will have only a shaky understanding of the later material.
The exams are somewhat de-emphasized because being a good scientist is more about designing experiments, interpreting data, coming up with new ideas to test and working with others, rather than memorizing stuff for a timed test. However, there will be exams because they are a proxy for your basic understanding of concepts you should know if you plan to be a genetic engineer. They are the types of concepts you should not have to look up if you are working in the field.
How this book is structured
This book serves as a textbook; it is a set of course notes. I’ve tried to keep the chapters fairly short and to stick to the basics you need to know. It is designed specifically for this course, so it is I think preferable to a textbook. Most textbooks do not really cover the material with this practical focus. And it is entirely free, another advantage.
This text provides – I hope- enough background information for a reasonable understanding of the course concepts. If ever you have additional questions or require clarification please email me or one of the TAs. I have included a number of extra resources on the course CANVAS site for those who need more information and there are other resources I could also post if people want more. Just let me know.
Each chapter – or at least most of them – has some interactive components. I would like to make more if I have time. These can help you test your understanding as you are reading through the sections. If you have suggestions for good self-test questions or other activities for any of the chapters, please let me know. Bonus points could be involved.
I have embedded into each section some relatively short recorded lectures from previous course offerings. They are optional but I think many students will find them useful. One warning though: I haven’t got time to redo these recordings so some of them refer to lab simulations. These are from the 2020 offering of the course when the course was entirely online. You can ignore those references-the rest of the information is still valid. I have been checking through the chapters to ensure that links are live etc but if you find anything that doesn’t work, please let me know right away so I can fix it. I don’t have a “student” view option for this book so I can’t tell if there are issues for the students.
Navigating the course website:
I have put links to all the course material (lecture notes, quizzes, bioinformatics assignments etc) on the homepage of our Canvas site. That should help you navigate the website. It will contain links to the chapters to read (in this primer) each week, and a handout to read in advance of the weekly lab sessions. It will also have a link to the post-lab quizzes and to the bioinformatics assignments for that week as well. I will also have weekly modules containing a checklist of everything that needs to be done in that week, which I hope will help you stay on track.
I am always updating the course so it is being rebuilt as we proceed through the semester. Text reading and some of the materials for labs and lectures will come available a week or two in advance. Ideally we would like to have materials ready further in advance but this is probably not realistic.
Tips for success:
I recommend trying to keep up with the course; if you fall behind it is very difficult to catch up. And all the new material is based on the assumption that you understood the material that came before it. This is a building course. Ensure that you read all the primer material and watch the videos embedded in the chapters. Try the self-test questions. There are not as many of these yet as I would like but I’m planning to add more as I am able. Think of yourself as a scientist in training as you proceed through the course. I read a paper a couple of years ago and it described the most important characteristics of some top scientists. Try to think of what these characteristics are.
As you read, don’t just look at the words. Actually think about what the words mean. This probably sounds stupidly obvious but it isn’t. Many people read while thinking about something else and don’t take in any of the actual meaning of what they’ve read. At the end of each section, write a quick summary for yourself. What was/were the main point(s) of that section? If it is a process like DNA sequencing, see if you can draw it for yourself. Being able to draw something is a good way to demonstrate that you understand it. When you draw something involving DNA or RNA I strongly suggest including some nucleotides in your drawing. It makes it much easier to see things like complementary base pairing. Don’t forget to always label the 3′ and 5′ ends of the nucleic acids also.
Ask yourself how the section you’ve just read relates to the previous ones. Ask questions about it. If PCR primers will bind the wrong sequences at low temperatures, can we use that to make changes in a DNA sequence? Or how can we avoid primer mismatches? Or why do DNA polymerases require a primer while RNA polymerases don’t? Even if you don’t immediately answer the question, you will be truly engaging with the material.
Finally, sometimes the concepts or material will be difficult to grasp. The way I explain it may not make sense to you. Talk to your TAs, and watch the posted videos and any supplementary materials available. These may be easier for you to follow. But also, be aware that when learning something new there is bound to be frustration and confusion and if you want a career in science be prepared to be confused a lot of the time. The two most important features of successful scientists may not be what you think. According to the article I read, the first is curiosity; wondering how things work, being interested in exploring the world, enjoying testing ideas and interpreting the results you get. The second is persistence. You are bound to have set backs and frustrations and not giving up the first time something becomes difficult is very important. Persistence even when things are difficult was something I had to work on personally in my career so I can tell you from my own experience that it is important. Frankly if you aren’t experiencing any confusion or struggle you are likely not learning much, if anything.
