BIOL 3004 is based on the idea of a Course-based Undergraduate Research Experience (CURE). That means the course is created for students to design, conduct, analyze, and communicate a novel biology research project, a core activity of being a biologist and scientist. In this course you will both learn about the subject material of your project and practice the process of being a scientist. Resources and guidance are provided, but the research projects are student led. As the final lab course in the Foundations of Biology series, this is your opportunity to apply the ideas and practices of being a biologist and pursue a research project that interests you.

The Foundations of Biology course sequence and curriculum is unique to the College of Biological Sciences. Further information can be found on the CBS Foundations page.

Prior to enrolling in BIOL3004, it's expected that you have had previous academic experience from biology courses. Whether it be the typical Foundations of Biology pathway (BIOL 1951, 1961 & 2003) or biology credits that transferred into CBS, there are a few core concepts which you should be familiar with.

Biology Basics

• Cell structure of eukaryotes and prokaryotes

• Structure, function and chemical properties of biological molecules (nucleotides, DNA, amino acids, proteins, lipids)

• The basic mechanisms of evolution

• Be able to interpret a phylogeny

• Basic concepts of inheritance and the definition of a gene

• Familiarity with the scientific method and process

Lab-Related Skills

• Unit conversions

• Dilutions and concentration theory

  • Concentration of solutes in solution

  • Dilution using units

  • Dilution using ratio (ie 10X to 1X solution)

  • Dilution with multiple solutes

• Calculating mean and median

• Data analysis with Microsoft Excel (or similar) spreadsheets

• Basic Microscopy – dissecting scopes

• Electronic Balances

• Pipetting

• Microcentrifuge use

• Spectrophotometer (OD₆₀₀) use

Students in BIOL 3004 choose from 4-5 different research areas offered each semester. Most students choose a research area in BIOL 1961 and continue in that area by registering for one of the corresponding sections of BIOL 3004 (where each section is focused on a single area). Some students switch to a new area for BIOL 3004; while this isn't generally recommended, it's fine to switch if you feel like another area would be more appropriate for your skills and interests.

To help you choose a research area that best fits your interests and skills, we have complied a few self-evaluation questions.

Practical skills

• What kind of lab work have you done in past courses and other experiences?

  • Would you like to do something similar in your research project? Or would you like to try something different?

• What kind of lab work have you enjoyed in the past? What would you like to do in the future?

• Are you excited to learn how to conduct research in a particular area of biology?

• Do you like wet lab work (traditional hands-on lab setting) or working on a computer? Both?

Topic interests

• What’s your intended major?

• What sub-fields of biology are you excited about?

Matching a research area with your interests and background

• Of the current projects, Environmental Toxicology and Microbial Evolution are wet lab projects; Computational Microbiology and Global Change Ecology are computationally based.

• Microbial Evolution uses microbiology techniques like streaking bacteria on agar platers and growing liquid cultures of bacteria.

• Environmental Toxicology uses vertebrate organisms (zebrafish). You and your group will be responsible for caring for the fish and designing experiments that meet ethical and scientific standards

• For the computational projects, Computational Microbiology uses command line software and requires writing computer code in R. Global Change Ecology uses graphical interface software like Microsoft Excel and JMP to conduct data analyses. All software is free or provided by the University.

• Computational Microbiology works with published data collected from humans.

• Global Change Ecology uses publicly-available data to address questions related to many kinds of anthropogenic change.

• Microbial Evolution focuses on evolution of antibiotic resistance in microbes, applicable to a range of topics from fundamental evolutionary theory to evolved antibiotic resistance in pathogens.

• Environmental Toxicology focuses on the effects of environmental conditions (especially contaminants) on the development, physiology and/or behavior of fish (as a model vertebrate organism).

Early in the semester (on the first or second day of class) you will form lab groups. After the groups have been established and the general direction of the research project has been discussed, there will be an “Project Plan” assignment that will help you outline the work you'll carry out to answer your research question.

One of the learning objectives of the Foundations laboratories is that students will gain skills and confidence that enable them to work effectively and independently in a research lab. The initial phase of your project work will:

• help you to familiarize yourself with the BIOL3004 lab, with your new group members, and with planning project work together

• give you a chance to practice some basic procedures and skills for working in your research area

• also serve as a good indication for any skills that you may need to develop or ask your TA about!

Do not worry about being a “fish out of water” for the first few weeks if you are just beginning to integrate into CBS. Feel free to cozy up with a group whose project you find interesting. While taking BIOL1961, CBS students already selected a research area and developed a putative project. On the first day of class, don’t expect to walk in with all the prior knowledge your UMN CBS peers have. It can be a very overwhelming experience, but as long as you remain diligent and understand that the transition phase is typically the most difficult for new students, you will be able to find great success in this course and grow as a biologist and member of the CBS community!

Remember, you are doing real scientific research and may be investigating a novel question, and all scientific research generally involves some amount of problem-solving. Not every procedure, whether listed here or one you designed yourself, will work correctly the first time or every time you perform it.

If a procedure does not behave as expected, look back at the notes in your lab notebook, try to determine if something went wrong, and then run the experiment again.

Replication is important in scientific research, and you are not being graded based on whether your experiments worked but on the scientific process itself. And if you find yourself stuck and you are not sure how to progress, talk to a research mentor, a TA, or an instructor and they will try to help.

Research Poster Presentations

The purpose of the posters is to communicate the results of your independent research projects to your fellow BIOL 3004 students, to BIOL 1961 students, and to other interested scientists from outside the course. Every group member is expected to attend one of the poster sessions to present their group’s poster, either alone or in alternation with other members of their team. In addition, each student will be expected to review at least three posters produced by other groups in the course.

These poster sessions serve as a sort of evaluation of each group member’s ability to discuss the results of their project with members of the scientific community who may not be entirely familiar with the scope of their work. Poster sessions are held during one of the final weeks of the semester, and offer the presenter an opportunity to self-reflect on their own ability to verbalize the work they have conducted throughout the semester to an audience.

Research Paper

Writing for publication in peer-reviewed journals serves a very different function than writing a lab report. Lab reports test your understanding and ability to communicate aspects of your experiment to an instructor; generally these experiments have been repeated multiple times and have an expected result, interpretation or outcome. In contrast, a research paper aims to add to the body of knowledge within the scientific community. Research papers use data from experiments and analyses of those data to support the authors’ conclusions.

For this course, you’ll be writing the Introduction, Materials & Methods, Results, and Discussion sections in segments corresponding to the different phases of your lab work. For each portion of the paper, you’ll first submit your draft to Canvas for peer review by classmates, followed by editing (as needed) and a submission to your grad TA for grading and further feedback. Based on feedback you receive on your drafts you'll put all of the pieces together and make further revisions before submitting the final version of your paper at the end of the semester. Allow time for editing and proofreading before you submit your final revised draft!

Why Write a Paper?

• To give you an authentic experience of communicating experimental results in a typical format for biology.

• To challenge you to draw specific conclusions from your data and to defend these conclusions.

• To challenge you to integrate information from a variety of sources to construct and support your conclusions.

• To give you the opportunity to improve your writing through revision based on critiques from your classmates and instructors.

Pro tip for this course: utilize all of the TAs. Whether it be the undergraduate TA lab assistants or the Graduate TA who is in charge of leading your section, make sure to come forward and ask them to address any questions you may have. They are meant to be in lab and in class to serve as resources that you may take advantage of to help your own growth as a biologist.

There will always be TAs at the lab when the lab is open. Each TA has a name tag with a colored sticker on it which represents the Research Area they are most familiar with. Try and utilize the TAs from your research area, but feel free to ask the other TAs as well, especially for general lab questions. They tend to be bombarded with questions from all of the students, but be patient and they will be more than willing to help address any questions or concerns you may have. Personally, I would recommend discussing the “skills checks” with them prior to actually completing those.

Your graduate TA may prove to be the greatest resource for producing a paper and comprehensive poster. Closer to the end of the semester they will typically offer office hours to review your paper prior to turning it in. I would recommend setting time aside, although you may be busy with finals season, because the insight they provide will greatly improve the efficacy of your final paper.

Make sure you have everything planned out prior to working in the lab!

Regardless of which of your team members is going in to the lab to perform different parts of your experiment, make sure you coordinate exactly what you will be doing ahead of time. It will save you valuable time and make this course much more manageable.

Have an open line of communication with your group members.

Using a group messaging app like GroupMe, Google Chat, or iMessage will allow for greater levels of collaboration and will make this process much smoother for everyone involved. You can ask each other questions, coordinate lab times, discuss potential screw-ups, and review each other’s contributions to group assignments. It is also helpful to schedule regular work time as a group. Schedules can be difficult to coordinate, so a scheduling app can be very helpful. Doodle, WhenIsGood, and NeedToMeet all work well.

Make sure to ask questions!

There is an incredible amount of resources for each student, should they not understand certain aspects of this project. Make sure to utilize both your graduate student and undergraduate TAs as much as possible.

Don’t be discouraged during the first few weeks!

It is not uncommon to feel overwhelmed during the beginning of this course, especially if you are not familiar with the background information for this course. Continue to show up on time for class and for lab work, ask questions when you are confused, and talk with your group members who have different strengths from yours - you can help each other figure things out!

This section was created mostly by Michael Dahl, a transfer student who took BIOL3004 and created this guide as part of their honors project.