Fostering the Integration of Research with Education (F.I.R.E.)
“Turning the fire of the natural curiosity of students into effective, flexible, and well grounded outcomes will take a concerted effort by many actors. Among them, scientists must play a central role”.


There are many challenges to delivering a high quality education in science, technology and mathematics (STEM fields). For those who do begin to study science, how is it possible to encourage the pursuit of careers in these areas?

At the University of Toledo, steps have been taken to spark interest in scientific learning by linking learning with discovery. Here we describe how the generation of the maize transcription factor ORFeome collection (TFome) has been integrated into a core undergraduate Molecular Genetics Laboratory class. While the class retains more traditional lab sessions devoted to the acquisition of lab skills, an extra module is interspersed over a period of five weeks in which students clone and study novel transcription factors from corn. An outline of this research module is provided below with links to teaching materials that may prove useful to others who wish to adopt this approach at other institutions.



Session 1

Research Objective: Identify a full length cDNA clone for a novel transcription factor (TF) and make a coding sequence clone that is freely available to researchers

Instruction: Students are provided with a lecture on cDNA and the meaning and value of a full length cDNA clone. They then learn to use professional software (Lasergene package from DNASTAR (www.dnastar.com) to search GenBank and evaluate EST collections for flcDNAs (e.g. www.maizecdna.org)

Learning Objectives:

  1. Understand concepts of cDNA library construction and use
  2. Understand concepts of Open Reading Frame and Coding sequences
  3. Understand how to access and search GenBank as a primary resource for genetic information.
  4. Learn the use of DNA analytical software.



Session 2

Research Objective: Isolate plasmid DNA from flcDNA clone and quantify it.

Instruction: Students are taught how to use a kit (Eppendorf Fast-Plasmid) to isolate plasmid DNA and understand the chemistry of each step. They are also instructed on the UV absorption spectrum of DNA and the use of a UV spectrophotometer

Learning Objectives:

  1. Concepts of plasmid DNA and how to isolate it as well as the concept of “plasmid constructs” as tools.
  2. UV absorption spectrum of DNA and its utility in determining DNA concentration and purity
  3. Use of E. coli and sterile technique (to inoculate overnight cultures for plasmid prep)
  4. (Optional) Primer design using Lasergene software.



Session 3

Research Objective: Amplify coding sequences of TF gene by PCR. Analyze gene of interest using online databases and local predictive tools.

Instruction: Students are instructed on the method of PCR and its various uses. Students learn to use bioinformatics software hands on.

Learning Objectives:

  1. PCR as a common and powerful tool for molecular biology studies
  2. Optimization of PCR (often does not work first time).
  3. Performance and analysis of BLAST tools and output.
  4. Use of software to conceptually translate DNA and predict protein properties (such as secondary structure, motif finding, and hydrophobicity).
  5. (Optional) Reading raw DNA trace files to spot sequencing errors.



Session 4

Research Objective: Ligate PCR product into a pENTR/TOPO vector and transform into E. coli.

Instruction: Students are instructed on DNA ligation, Traditional versus TOPO cloning, and methods of DNA uptake by bacteria.

Learning Objectives:

  1. Understand how to perform Recombinant DNA technology – both traditional and current methods
  2. Perform sterile technique, bacterial transformation and Single Colony Purification of transformants



Session 5

Research Objective: Recombine entry clone into a destination vector and transform into E. coli. Complete analysis of DNA insert using bioinformatics tools.

Instruction: Students are instructed on Gateway technology and the range of destination vectors. Students are assisted to complete their computer assignment from previous week which will be incorporated into their final lab reports (30% of grade)

Learning Objectives:

  1. Acquisition of a powerful genetics tool (Gateway technology) derived from lambda phage biology.
  2. Understand a range of molecular biology tools that are employed in research and testing labs.
  3. Writing skills – how to write a proper scientific report
  4. (Optional) – student presentation of their own mini-project


Levels of engagement in research

The professional apprenticeship model.

How three levels of knowledge defined within the laboratory may be interconnected throughout an educational program. From Hanauer et al., Dec 2006 Science 314; 1180-1181. The module described above can serve as a preparation for interest students to pursue higher levels of professional apprenticeship. Students that have taken the course early as an undergraduate are in an excellent position to enter and pursue individual or small group projects in research laboratories (See image below).


In class (1 sememster)

Individual/Group research projects (1 to 3 semesters)

Getting Involved in the Maize TFome Project

Instructors at other institutions are welcome to use any of the materials posted above in their classrooms. The maize TFome project has now advanced to the point at which nearly two thirds (>2000) of all transcription factors (TFs) in corn have been cloned. However about 1000 TFs remain to be cloned.

If you wish to involve your class in cloning some of the remaining genes then please contact John Gray at the University of Toledo (jgray5@utnet.utoledo.edu). You will be assigned accurate gene models and in some cases cDNA that can be used as a template for PCR.

Alternatively laboratories could develop other ORFeome collections for genes other than transcription factors, e.g. families of transport genes, individual biochemical pathway genes, structural protein genes, etc. In these latter cases full length cDNA (flcDNA) clones may be available from the maize flcDNA project collection www.maizecdna.org.