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Keywords:

  • Matrix;
  • assessment;
  • undergraduate;
  • biochemistry;
  • laboratory;
  • skills

Abstract

  1. Top of page
  2. Abstract
  3. THE BMB SKILLS MATRIX
  4. DEVELOPMENT AND SELECTION OF LABORATORY EXERCISES
  5. SUMMARY
  6. Acknowledgements
  7. REFERENCES

We have designed a skills matrix to be used for developing and assessing undergraduate biochemistry and molecular biology laboratory curricula. We prepared the skills matrix for the Project Kaleidoscope Summer Institute workshop in Snowbird, Utah (July 2001) to help current and developing undergraduate biochemistry and molecular biology program designers to determine which laboratory techniques, skills, and theories to include in a 4-year plan. The skills matrix can be used to evaluate and assess the types of laboratory skills as well as the level at which they are taught in biochemistry and molecular biology curricula. The matrix can foster better communication between faculty in chemistry, biology, math, and physics as they share curricular information. As an example of utility of the skills matrix, we used it to survey several commonly used biochemistry laboratory manuals to evaluate the skills covered in each text.

The authors are not associated with any of the laboratory texts surveyed in this article and do not endorse one text over any of the others.

Developing an appropriate undergraduate program in biochemistry and molecular biology (BMB)11 is a challenging and ever-changing venture. Program curricula must be diligently and rigorously adjusted to reflect the rapid changes and advances in research, technology, methodology, software, and internet resources used by the discipline. New strategies and requirements for assessment make it critical to have available tested methods of evaluating programs and student learning.

A solid BMB program must be built out of core courses offered by biology, chemistry, math, and physics departments. Due to the truly interdisciplinary nature of BMB programs, faculty communication, “ownership” issues, student needs, and campus limitations often dictate, or at least have an impact on, curriculum design and implementation. Luckily, there can be significant flexibility in the number and types of courses offered as long as certain guidelines are maintained. Guidelines to help direct program development and assessment are provided by organizations such as the American Association for Biochemistry and Molecular Biology (ASBMB), the American Chemical Society (ACS) and the International Union of Biochemisty and Molecular Biology [13]. Thus, the development of a BMB program course curriculum, theory, and knowledge is relatively straightforward. However, it is often a more difficult task to plan and develop laboratory strategies and mechanisms to teach students specific techniques and promote laboratory problem-solving skills. Several issues related to laboratory curricula must be considered.

A plan should begin with a statement of the program's goals and objectives. It is impossible to teach all the skills and theories applicable to all of biochemistry and molecular biology in a standard one- or two-semester BMB laboratory sequence [4]; however, programs can select particular areas in which they excel, incorporate departmental strengths, and choose experiences best suited for their student population. For example, many midwestern U. S. schools with strong agriculture departments feature experiments on plant biochemistry. In contrast, programs affiliated with medical schools are more likely to include laboratories relating to human disease. Building on local student needs and faculty expertise is vital to the design and implementation of a strong and sustainable BMB curriculum.

Faculty must determine what basic skills and experiences students should learn in core biology and chemistry courses. The laboratory curriculum should then build on and enhance those goals. If there are curricular gaps in the overall program, such as student research experience, experiments can be developed or added to satisfy those needs. This requires open communication between chemists and biologists, working together toward a common goal. Lack of such cooperation is a common complaint at conferences such as the Project Kaleidoscope (PKAL) (www.pkal.org/) workshops, as well as at national professional society meetings. Departments must share resources and responsibility for course objectives and goals, as well as the benefits of an interdisciplinary program such as biochemistry and molecular biology.

Finally, there are larger issues that also need to be addressed. How does the overall curriculum fit into the campus' goals or strategic plans? What are the ultimate goals of students graduating from this program? Academic departments may have different goals, such as encouraging graduate study and research, workforce development for local or regional industries, professional training in the medical sciences, or preparation of kindergarten-12th grade educators. In some cases, several of these goals may be incorporated into the same curriculum. Additionally, recent developments in biotechnology are forcing many administrators to view biotechnology training programs as lucrative ventures. Some administrators view biotechnology-related programs as signature programs for attracting talented students and funding from outside sources. The strengths or weaknesses of the campus in research and teaching are also critical to the success of BMB programs from an education and funding standpoint.

Guidelines from the ASBMB and ACS for undergraduate programs include discussions about laboratory courses and problem solving skills [1, 2, 46]. In addition to specific skills and techniques, BMB curricula should include laboratory experiences that

  • Incorporate learning of basic theory and laboratory skills;

  • Allow development of critical thinking skills so that students can design appropriate protocols to solve new problems;

  • Reinforce observation and data-recording skills;

  • Include opportunities to communicate results in written and oral form.

Several other factors should also be considered. Laboratory courses should consistently integrate new knowledge and reinforce skills that students already possess. BMB programs should emphasize both quantitative and qualitative aspects of purification and characterization of biomolecules. Experiments should incorporate skill building and should model discovery-based research approaches in the curriculum, wherever possible, particularly if student research experience is limited or not available

THE BMB SKILLS MATRIX

  1. Top of page
  2. Abstract
  3. THE BMB SKILLS MATRIX
  4. DEVELOPMENT AND SELECTION OF LABORATORY EXERCISES
  5. SUMMARY
  6. Acknowledgements
  7. REFERENCES

Because teaching research and laboratory techniques and developing problem solving skills are critical to student development, these elements became areas of focus at the 2001 PKAL workshop. Before coming to the workshop, we created a matrix of skills we believed biochemistry students should have. As part of the workshop, we asked participants which laboratory skills or techniques they felt should be included in a one-semester introductory biochemistry laboratory course. We designed the BMB skills matrix to include a comprehensive list of laboratory skills, organized into categories according to techniques and theory, so it contains elements that are unlikely to be included by every program. Bell et al. [4, 6] have suggested a list of topics that students in an ideal undergraduate biochemistry or molecular life science program would need in order to be well educated in the discipline, and the ASBMB Education and Professional Development Committee recently published recommendations. (More recently, Boyer [7] offered an examination of the topics that ought to be covered specifically in the laboratory curricula of BMB programs, which will be a focus of the education satellite meeting at the 2004 ASBMB meeting.) During the PKAL workshop, participants reviewed Bell's list of topics and commented on the appropriateness of specific laboratory topics and whether they could ever truly be achieved. The responses from workshop attendees were added to the list of laboratory skills and techniques the authors had already assigned to the initial matrix, and the final result is the skills matrix presented here (Table I). Users can reconstruct the skills matrix in a variety of ways, adapting the published format to meet local needs. The matrix file can be accessed online and downloaded as an Excel or portable document file (PDF), and adjusted according to user needs and goals [8].

The BMB skills matrix is designed so that individual programs can evaluate laboratory skills and techniques at several levels. It can be used in the following manner. Each faculty member or department determines which skills, techniques, and theories are taught in relevant courses or laboratories. It can then be determined if a specific matrix element is learned and used as a quantitative or qualitative skill. Faculty must then determine at what level the students must master the technique. If a laboratory technique is presented as theory, one can then ask whether students actually learn the technique and use it once, or whether they use it several times, improving the skill and becoming proficient. For example, most students in biochemistry will learn the theory of mass spectral analysis, but they do not usually perform actual experiments. On the other hand, they will likely perform polyacrylamide gel electrophoresis at least once but will not be very proficient at trouble-shooting the technique. By comparison, by the time BMB majors graduate they should have a good deal of experience and be very proficient at making buffers and reagent solutions, with little direction. According to the matrix, each skill would be designated at one or more different levels of understanding and proficiency. Using the examples above, the use of mass spectral analysis, as described above, might be classified as theoretical and qualitative usage; student exposure to gel electrophoresis might be classified as qualitative and/or quantitative usage, but not at a proficient level; and reagent preparation might be classified as proficient and at a quantitative level.

In some cases, the material will be taught in more than one course, and the level of each experience can be evaluated either in a specific course or throughout the curriculum. For instance, the theory of buffers usually will be introduced in general chemistry courses, but the actual hands-on use of buffers will not be learned until later in courses such as quantitative analysis or introductory biochemistry. This represents a progression from skills that may be described in class but not performed, to experienced but not practiced in lower level laboratories, to skills that are mastered by students in upper-division laboratory courses. In this type of evaluation using the matrix, faculty will follow the thread of skill progression throughout the curriculum.

While completing the BMB skills matrix, faculty will have an opportunity to discuss their experiments and the design of their program with colleagues who are also responsible for developing or assessing the curriculum. In fact, this exercise allows for significant interaction, allowing for the exchange of logic, goals, and the solicitation of ideas. At the University of Michigan-Dearborn, conversations between the chemistry and biology faculty revealed that the biologists were re-teaching water and buffer chemistry. Similarly, some chemists were surprised to find that several advanced biochemistry texts taught the chemistry of water in the first or second chapter. This led to changes in both course and laboratory curricula. This type of interaction can reduce duplication of topics or lead to reinforcement of key concepts. It is also useful to discover that the jargon used by scientists may differ depending on the application. For example, the Greek symbol λ indicates wavelength to chemists and physicists but may indicate a measurement of microliter volume to a molecular biologist. Helping students navigate the cross-disciplinary boundaries is crucial to an integrated curricular design.

DEVELOPMENT AND SELECTION OF LABORATORY EXERCISES

  1. Top of page
  2. Abstract
  3. THE BMB SKILLS MATRIX
  4. DEVELOPMENT AND SELECTION OF LABORATORY EXERCISES
  5. SUMMARY
  6. Acknowledgements
  7. REFERENCES

There are many sources for laboratory exercises—Biochemistry and Molecular Biology Education journal being one primary source. It is not an uncommon practice for laboratory instructors, or even departments, to write laboratory manuals for their courses or use exercises available on the web, including sites such as the digital library projects [9, 10]. BMB programs might simply choose one of several available laboratory texts. A commercially prepared laboratory manual offers the advantages of an outlined series of experiments, lists of reagents needed for each experiment, detailed introductory information, theoretical background, and references.

Many of the participants at the 2001 PKAL conference were considering, or in the process of developing, a new biochemistry program. In preparation for the PKAL workshop, we decided to review the content of four popular, commercially available biochemistry laboratory texts [1114] to determine what topics, techniques, and laboratory skills the authors included in their texts. Our intent was not to review the laboratory texts, surveyed in this article, for correctness, accuracy, or reliability. Instead, we surveyed the topics presented in each text against the BMB skills matrix to compare which topics are presented in these commercial texts. If a matrix category is described in some detail, the category is indicated by an X, even if it was not directly involved in an experiment in the text (Table II). Hopefully, this analysis and comparison will help in the selection of biochemistry laboratory manuals that might meet the programmatic needs and goals of those considering new biochemistry programs, as well as those seeking to evaluate or alter their laboratory curriculum. Although Table I can be applied to BMB programs, Table II is generally more applicable to biochemistry laboratories.

SUMMARY

  1. Top of page
  2. Abstract
  3. THE BMB SKILLS MATRIX
  4. DEVELOPMENT AND SELECTION OF LABORATORY EXERCISES
  5. SUMMARY
  6. Acknowledgements
  7. REFERENCES

The BMB skills matrix (Table I) can be used for the development of a new BMB program and for the indirect assessment of an existing one. The matrix can be resorted and adjusted as needed for specific departments, as desired. A copy of the matrix list or matrix comparative study (Tables I and II) can be accessed online and downloaded as an Excel or a PDF file [8]. The BMB skills matrix has also been adapted to address the needs of those looking for a commercially available laboratory text for an introductory biochemistry laboratory course. We believe that one or both of these tools will be useful to faculty or departments developing BMB curricula, and to departments wishing to evaluate and assess the effectiveness of their current programs.

Table Table I. Biochemistry and molecular biology laboratory assessment matrix
Thumbnail image of
Table Table II. Comparison of BMB skills and commercial text books
BMB skills
  • a

    a X indicates the topic is covered to some degree.

 Boyer [11F]Switzer & Garrity [12]Ninfa & Ballou [13]O'Farrel & Ranello [14]
Laboratory techniques    
    Acid/Base chemistry XXX
    Affinity techniquesXaXX 
    Amino acid analysisXX  
    Blots-Northern    
    Blots-Southern    
    Blots-Western XXX
    Centrifugation-high-speedXX X
    Centrifugation separation and pptXXXX
    Centrifugation-ultraspeedX   
    Characterization of carbohydratesXX  
    Characterization of lipidsXX  
    Characterization of proteinsXXXX
    Chromatography-affinityXXXX
    Chromatography-ion exchangeX XX
    Chromatography-size exclusionX XX
    Cloning and selection XXX
    Dialysis and desaltingX X 
    DNA array    
    DNA digestsXXXX
    Electrophoresis-DNA, RNA, agaroseXXX 
    Electrophoresis-proteins, PAGEXXXX
    Enzyme kineticsXXXX
    Fluorescence/fluorimetryX X 
    IR    
    Ligand-binding, ELISAXXX 
    Membranes X  
    NMR    
    PCR XXX
    Pipetting-micropettesX XX
    Pipetting-traditionalX X 
    Purification of bacterial DNAXXX 
    Purification of carbohydrates    
    Purification of eukaryotic DNA    
    Purification of lipidsXX  
    Purification of proteinsXXXX
    RadioisotopesXX  
    Re-Dox, electron transferXX  
    Reagents and solutionsXXX 
    Recombinant DNA XXX
    Sequence determination-DNA    
    Sequence determination-peptidesXX  
    Site directed-mutagenesis    
    Small molecule characterizationX   
    Spectroscopy-spec 21XXXX
    Spectroscopy-UV/VisXXXX
    Sterile techniques-growing bacteria    
    Sterile techniques-solutions & plates X  
    Group work    
Knowledge acquisition    
    Literature searchesX   
    NCBI databases XX 
Experimental design and protocol    
    Perform work using literature    
    Perform work using kits    
    Design appropriate controls    
    Design and prepare experiments    
    Writing a grant proposal    
Data keeping    
    Notebooks (legal)XXXX
    Electronic    
    Spreadsheet    
    Share data    
Communicating results    
    Lab reportX   
    Journal-style article    
    Poster    
    Dept, local or national conference    
Types of experiments    
    Skill buildingXXXX
    DiscoveryX  X
    Research    

Acknowledgements

  1. Top of page
  2. Abstract
  3. THE BMB SKILLS MATRIX
  4. DEVELOPMENT AND SELECTION OF LABORATORY EXERCISES
  5. SUMMARY
  6. Acknowledgements
  7. REFERENCES

We thank Rodney Boyer (Hope College, Holland, MI), Ellis Bell (University of Richmond, Richmond, VA), Fred Rudolph (recently deceased; Rice University, Houston, TX) and Kazem Mostafapour (University of Michigan, Dearborn, MI) for additions and suggestions for the matrix. We thank Jeanne Narum and the Project Kaleidoscope staff for all their work in organizing the Summer Institute, where much of the discussion concerning the organization and content of skills matrix occurred. Specifically, we thank all 2001 PKAL BMB workshop attendees for their valuable input and assistance. We also thank Dr. Keith Rhodes (Missouri Western State College, St. Joseph, MO) for comments and suggestions regarding the manuscript.

  • 1

    The abbreviations used are: BMB, biochemistry and molecular biology; ASBMB, American Association for Biochemistry and Molecular Biology; ACS, American Chemical Society; PKAL, Project Kaleidoscope.

REFERENCES

  1. Top of page
  2. Abstract
  3. THE BMB SKILLS MATRIX
  4. DEVELOPMENT AND SELECTION OF LABORATORY EXERCISES
  5. SUMMARY
  6. Acknowledgements
  7. REFERENCES
  • 1
    American Society for Biochemistry and Molecular Biology (2003) Website, www.ASBMB.org/.
  • 2
    American Chemical Society (2003) Website, www.acs.org/.
  • 3
    International Union of Biochemistry and Molecular Biology (2003) Website, www.iubmb.unibe.ch/.
  • 4
    E. Bell (2001) The future of education in the molecular life sciences, Nat. Rev. Mol. Cell Biol. 2, 221225.
  • 5
    R. Boyer (1999) Does biochemistry have a core? ASBMB News VIII, 6, 1012.
  • 6
    J. G. Voet, E. Bell, R. Boyer, J. Boyle, M. O'Leary, J. K. Zimmerman (2003) Recommended curriculum for a program in biochemistry and molecular biology, Biochem. Mol. Biol. Educ. 31, 161162.
  • 7
    R. Boyer (2003) Concepts and skills in the biochemistry/molecular biology lab, Biochem. Mol. Biol. Educ. 31, 102105.
  • 7
    B. Caldwell, C. Rohlman, M. Benore-Parsons (2003) A curriculum skills matrix for development and assessment of undergraduate biochemistry and molecular biology laboratory programs, Website, curie.umd.umich.edu/parsons/.
  • 9
    University of Leeds (2003) Virtual labs, Website, www.tlsu.leeds.ac.uk/courses/bioc2060/proteinlab102/ProteinLab.html.
  • 10
    American Society for Microbiology (2003) Digital resources, Website, www.microbelibrary.org/.
  • 11
    R.Boyer (2000) Modern Experimental Biochemistry, 3rd ed., Benjamin Cummings, San Francisco, CA.
  • 12
    R. L. Switzer, L. F. Garrity (1999) Experimental Biochemistry, 3rd ed., W. H. Freeman and Co., New York.
  • 13
    A. J. Ninfa, D. P. Ballou (1998) Fundamental Laboratory Approaches for Biochemistry and Biotechnology, Fitzgerald Science Press, Bethesda, MD.
  • 14
    S. O. Farrell and R. T. Ranallo (2000) Experiments in Biochemistry: A Hands-on Approach, Harcourt Brace and Co., Philadelphia, PA.