Montana State University

Department of Cell Biology & Neuroscience

Montana State University
P.O. Box 173148
Bozeman, MT 59717-3148

Tel: (406) 994-5120
Fax: (406) 994-7077
Location: 510 Leon Johnson Hall

Department Chair

Frances Lefcort, Ph.D.



BIOB 476R: Gene Construction

Students in BIOB 476R: Gene Construction
Gene construction in action

Professor: Dr. Thom Hughes

Create new genes

This is a hands on laboratory course in which we design and build new genes. The intention is for students to get a real feeling for the practice and art of doing molecular biology.

Discovery in action

This is a course for upper level undergraduates who want to apply what they have learned in biochemistry, genetics, and cell biology.

Cloning scheme
Cloning strategy    

Life in the lab

The course starts at 6 pm three times each week and goes until everyone is done. The students who get the most out of the course are curious, like to do experiments, and are willing to work long hours in an evening course. 




Biology 467: Gene Construction

Instructor: Dr. Thomas Hughes

227 Cooley. Phone 994 5395. Email:

Gene Construction is an upper level course for students who want hands on experience creating their own synthetic genes and plasmids. This course combines lectures, small group discussions, and real lab work to give students an experience in what real molecular biology research looks and feels like.

This is a creative class (with a “research” or R designation in the catalog). It involves student inspired projects to create real, testable constructs in recombinant DNA.

Outcomes: Students who have mastered the class can work independently to-

  • Design their own DNA constructs encoding complex, hybrid gene products that produce chimeric proteins with the aid of commonly used software packages.
  • Design their own cloning strategy to build the constructs.
  • Create PCR primers sufficient to amplify the different coding regions and plasmid components.
  • Amplify DNA regions and isolate the DNA, set up and trouble shoot ligation independent cloning reactions.
  • Critique the lab work and notebooks of colleagues to constructively help them find solutions.
  • Test and improve prototypes.
  • Read and interpret the methods section of biomedical research papers that use molecular approaches to create novel plasmids, coding regions, and heterologous expression systems.

Prerequisites: An advanced biochemistry course at the very least is required for this course. Examples are BIOB 425 or BCH 380 here at MSU.

Classes: Will all be in the teaching lab on the first floor of Leon Johnson. Class starts at 6 pm and finishes when necessary on Monday, Tuesday, and Wednesday nights.

Lectures: The first few weeks will involve lectures and examples so that everyone in the class feels comfortable with the theory of DNA manipulation and gene synthesis. These lectures will typically be an hour in length. This will be followed by tutorials and sample projects on the computer with modern molecular biology software.

Laboratory work: The vast majority of the class will involve real lab work starting at 6 pm and continuing until students go home, hopefully by 9 pm.

Grading: It is necessary to give grades at this university. It is believed by some that they are useful in motivating the student to learn more. We will do this, while trying to minimize the negative side effects of grading. This particular course involves real research, real lab work, and real creativity. It is an opportunity for each student see new things, learn new skills, and advance their own inquiry.

In any research setting, the laboratory notebook is a critical tool for the biologist. In this class it will be what each student hands in at the end of the course for a grade. Should a student feel that their final grade is inappropriate, they can ask for a re-review, in which case their notebook will be graded anonymously by another faculty member with many decades of molecular biology experience.

Once the notebooks are all graded, they will be returned to the students with the hope that at least some will continue to use them in future research endeavors. Every year at least one student from this course has gone on to pursue their Ph.D. in biomedical research, while others have gone on the medical school, the biotechnology sector, or advanced degrees in engineering.

The notebook is where we record our every thought, it is where we do all of our math, it is where we plan reactions, and it is where we document our results. The laboratory notebook is the foundation of an intellectual property claim. The notebook need not be perfect; it will inevitably contain stains from solutions, crossed out reactions that were a bad idea, and often diagrams and cartoons. It should however, be interpretable by others, and it should clearly document the successes and failures of the semester. The notebook will be graded on the content, addressing the following questions:

  • Has the student sought to creatively solve a problem?
  • Are there pictures, diagrams, and descriptions of the “plan”?
  • Has the student worked out a plausible strategy for creating a new DNA construct?
  • Has the student done real experiments, seeking to create something truly new?
  • When faced with adversity, and results that were not anticipated, has the student been able to troubleshoot the experiment and isolate what isn’t working?
  • Is the notebook legible enough someone else can reproduce the experiment of the day, and identify mistakes that may have occurred?

Things that will not be graded include:

  • Did the experiment work.
  • Is the notebook perfect.
  • Are all the words spelled correctly.
  • Is the math always right?

The results: Each group will have it’s own Wiki site on which they can post notes to one another., post results, and post files. Should we get to the point that we have produced useful plasmids, we will share these by depositing them with the not-for-profit plasmid repository Addgene.

Campus ToolsStudent E-MailDesire2LearnMy InfoIT ResourcesMy Passwords