Sharing Laboratory Ideas and Assessments

ASBMB Student Centered Education Conference July 2011

Ann Aguanno, Associate Professor of BiologyMarymount Manhattan College

Benjamin Caldwell, Professor of ChemistryMissouri Western State University

Overview

• Introductions• Two laboratory courses• Student Lab Skills

– Breakout• Specific Lab Activities

– Breakout• Pre and Post-Assessment

– Breakout• Open Discussion

A

Our Schools

Marymount Manhattan College, NYCo Small (1700) liberal arts college, urban, diverse,

academically average student population

Missouri Western State Universityo Medium-sized (6,000), open access admission, diverse,

academically average student population

Your Schools?

•Small liberal arts schools?•PUI?•R1?•HBCU?•Community Colleges?•Other?

•Biochem. vs. Mol Biology?

A

Two Laboratory Courses

Cellular and Molecular Biology (BIOL 240)o Sophomore level courseo Required for all Biology majorso 10-12 students per lecture; 10-12 students per lab section

Biochemistry (CHE 370) o Junior/Senior Level courseo Required for all Biology & Chemistry majorso 48 students per lecture; 16 students per lab section

Cellular & Molecular BiologyLecture Laboratory

Intro to Chemistry and Cells Lab Safety and the Lab ReportEnergy, Catalysis, Biosynthesis Separation of Proteins by Charge (protein structure;

chromatography; micropipette use)Protein Structure and Function Separation of Protein by MW (SDS PAGE)DNA & Chromosomes Nucleosome Structure (chromatin structure; DNA

electrophoresis) DNA Replication, Repair Karyotyping Human Cells (cytogenetics; Microscopy )DNA to Protein Advanced Microscopy/Cell Culture (sterile Technique;

photomicroscopy )Analyzing Genes Intro to Bioinformatics: DNA Sequencing (DNA sequencing

methods; genomics)Control of Gene Expression Cloning, Transformation, Phenotype Assay (microbiology;

transformation; cloning)Cell Cycle and Cell Death Cell Culture (con’t); Insect CellsTissues & Cancer PCR-based DNA Profiling (PCR technology )

Grading: 3 Exams, Primary Literature Analysis, Lab Performance and Reports

Textbook: Essential Cell Biology Alberts, et. al, 3rd Lab Manual: In-HouseTextbook: Reading the Primary Literature , by Gillen

BiochemistryLecture Chapter

• Chemistry in Biological Systems 1  

• Water 2• Amino Acids, Peptides & Proteins

3  • Protein Structure 4  • Enzymes 6  • Carbohydrates 7  • Nucleotides & Nucleic Acids 8

 • Lipids & Membranes 10

& 11  • Principles of Bioenergetics

13  • Intro to Metabolism: Glycolysis,

Kreb’s Cycle, Oxidative Phosphorylation 14, 16, 19

Lab Schedule • Check-in; Pre-Lab Assessment;

Pipette Calibration;• CMC by Fluorescence (Solutions/Graphing)• pH and Buffers• Titration of Amino Acids (reinforce pKa’s)• Protein Quantification (BCA/Bradford)• Gel Filtration Chromatography• Bioinformatics• Mid-term Exam (data analysis/protocols)• Protein Purification Project (Ion Ex.

chrom)• Protein Purification Project (Affinity

chrom.)• Protein Purification Project (SDS-PAGE)• Protein Purification Project (Western Blot)• Enzyme Kinetics (LDH)• Final Exam

704/19/23

Grading: 3-4 Exams + Final, 5-6 quizzes, Questions of the Day,Lab Performance and Reports (20%)

Textbook: Biochemistry, Garrett & Grisham, 4th ed. Lab Manual: In-House

Skills of Incoming Students

• What are the Fundamental Skills? (5 essential)

• Skills Required for Your Laboratory Course– Biochemistry vs. Molecular Biology Courses?

B

Review Group Responses

2:15

Expectations for Our Lab Courses

• CoursesoMATH, MATH, MATH!!! (Level???)o General Biology (1-2 semesters?)o General Chemistry (2 semesters?)o Organic Chemistry (1-2 semester?; coreq ok)oWriting 1 and 2

Expectations for Our Lab Courses

• Basic Skillso Time management, writing, reading, collaborationo Safety, note taking, lab reports, data/graphical

analysis, unit conversion, standards or references, basic statistics

o Handling mass & volume, pipetting, minor instrumentation (e.g. pH, centrifugation, basic spectrophotometry)

o Multiple ways to analyze, threshold, sensitivity, stringency

A

How Assess Incoming Skills?

• Fundamental Skills?

• Specific Skills Required for Your Course?– Biochemistry vs. Molecular Biology Courses?

A

Review Group Responses

2:45

Learning Goals of Lab CoursesCellular & Molecular Biologyo Communicate and apply fundamentals of cellular &

molecular biologyo Utilize scientific method, critical thinking skills and

problem based-learning techniqueso Perform laboratory- based scientific investigations by

applying the concepts and techniques learned o Apply concepts and techniques learned to current

scientific and medical topicso Present and critique experimental resultso Analyze primary cellular and molecular biology literature

Learning Goals of Lab CoursesBiochemistry

o Demonstrate proficiency in basic biochemistry lab techniqueso Identify connections between experimental design and data

generated from procedureso Differentiate between control and experimental datao Perform mathematic transformations of raw data to useful and

meaningful informationo Generate data in multiple formats (graphs, charts, observations)o Develop conclusions based on objective and logical analysis,

interpretation and evaluation of data and observationso Maintain a laboratory notebook using proper scientific verbage

and notation in order to effectively communicate within the scientific community

o The laboratory experience should also reinforce topics discussed in lecture

Other Learning Goals?

3:00

How To Assess Laboratory Learning Goals?

• 3 methods

How We Assess Laboratory Learning Goals

• Assess Lab Notebooks• Assess Lab Reports • Practica• Exams• Regular Observations of Lab Performance • Oral vs. Written Communication• Pre and Post Test

Example: MWSU Skills Survey Use the following scale, circling the appropriate statement that best matches your feeling about the following laboratory related questions. Strongly Somewhat Neutral/ Somewhat Strongly Disagree Disagree No Opinion Agree Agree

1 2 3 4 5 1. I am able to solve basic mathematic problems that require scientific notation or exponents.

1 2 3 4 5

3. I can accurately determine the correct number of significant digits in a number. 1 2 3 4 5

029.0

3.211.545 x

79. Complete the following mathematical equation, and give your answer with the proper number of significant digits.

a. 4.0 x 105

b. 4.00 x 105

c. 4.00367 x 105

d. 400,367

I understand & can Identify dependent variables 0 0 6 54 40 69

I understand the differences between accuracy & precision 0 0 0 27 73 48

I understand basics of chromatography 0 19 21 29 31 67I can generate a standard curve & determine concentrations of unknowns. 0 6 15 46 33 42

I understand the need for more than 1 type of protein assay 8 13 21 44 15 56

I understand the need for more than 1 type of protein assay 8 27 23 35 6 67

I understand the basic concepts & importance of enzyme kinetics 13 35 27 19 6 73

I understand how electrophoresis is used to separate protein/DNA 8 2 10 23 56 54

Stro

ngly

Disa

gree

Stro

ngly

AgreeSom

ewha

t Disa

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Neutra

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Opini

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b Ta

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Sample survey questions & responses (%) are shown (grey)

Results of task related questions (Far right , yellow) displays overall class performance (% correct).

Sample of pre-course survey at (Spring 2010 results).

Class Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 Q10 Bonus Q's

Average Exam

Score (%)Spring 2010 92.2 76.3 92.5 75.6 66.7 64.4 68.1 80.4 56.3 81.5 70.4 79.2

Spring 2011 95.6 68.0 83.5 75.7 73.2 73.5 68.5 81.4 69.7 84.6 65.2 82.9

Scores represent percentage of students receiving full credit for each question.

However, some areas still requiring improvement (indicated by yellow) include:• Interpreting graphic data (Q’s 2, 6, 9) – graphical/SDS-PAGE results• Comprehension of enzyme assays and kinetics (Q’s 5, 9)• Performing biochemical calculations (Q’s 7, 9)

Final Exam Results

22

Lab Skills

– Skills necessary – Theory/background on experimental

procedures– Data analysis– Instrumentation exposure

04/19/23 23

Lab skills

• Review of matrix and discussion

BMB SKILLS Adapted from BMBEd

Vol. 32, No. 1, pp. 11–16, 2004

WHEN SKILL IS LEARNED AND LEVEL TYPE

Lower Level Courses Upper Level BMB Courses

Quanti-tative

Quali-

tativeLAB TECHNIQUES Theory

Usage

Proficiency

Theory

Usage

Competence

Theory

Usage

Competence

Acid/Base chemistry                      

Affinity techniques                      

Amino acid analysis                      

cDNA                      

Cell Culture-Aseptic/Sterile Techniques                      

Cell Culture: Adherents vs. suspension                      

Cell Culture-Bactierial/insects                      

Cell Culture-Mamallian                      

Centrifugation-high speed                      

Centrifugation-separation and ppt                      

Centrifugation-subcellular fractionation                      

Centrifugation-ultraspeed                      

Characterization of carbohydrates                      

Characterization of lipids                      

Characterization of proteins                      

Chromatography-Affinity                      

Chromatography-ion exchange                      

Chromatography-size exclusion                      

Chromatography-HPLC                      

Cloning and Selection                      

Dialysis and Desalting                      

DNA array                      

DNA digests                      

Electrophoresis-DNA.RNA, agarose                      

Electrophoresis-proteins, PAGE                      

Enzyme kinetics                      

Fluorescence/ fluorimetry                      

Gene expression/transcription                      

Immunocytochemistry-Blots-Northern                      

Immunocytochemistry-Blots-Southern                      

Immunocytochemistry-Blots-Western                      

Immunocytochemistry-Immunoprecipitation                      

Immunocytochemistry-Immnofluorescence                      

Immunocytochemistry- In Situ Hybridization                      

Ligand-binding, ELISA                      

Membranes                      

Microscopy - light                      

Microscopy - phase                      

Microscopy - fluorescence                      

BMB SKILLS Adapted from BMBEd

Vol. 32, No. 1, pp. 11–16, 2004

WHEN SKILL IS LEARNED AND LEVEL TYPE

Lower Level Courses Upper Level BMB Courses

Quanti-tative

Quali-

tativeLAB TECHNIQUES

Theory

Usage

Proficiency

Theory

Usage

Competence

Theory

Usage

Competence

Acid/Base chemistry

C111 C120 C120 C120

C321 C370

C321 C370

C321 C370

C321 C370     X  

Affinity techniques      C370 C426 370   C370 C370      X

Amino acid analysis       C370     B313 B313     X

cDNA B215 B215    B421 B421 B421B215 B421

B215 B421 B421 X X

Cell Culture-Aseptic/Sterile Techniques

B215 B215 B215 B390 B390

B390, B421

B390 B421

B390 B421

B390 B421 B431  X

Cell Culture: Adherents vs. suspension

B205B215

B205 B215

B205 B215

B390 B411 B421

B390 B411B421

B390 B411 B421

B205 B215 B390 B421

B205 B215B390 B421

B390 B421 X X

Cell Culture-Bactierial/insectsB215 B215 B390 B390

B390 B421

 B390 B421

B390 B421

 B390 B421  X X 

Cell Culture-Mamallian        B411 B411            X 

Centrifugation-high speed B215 B215 C370 C370   C370 C370     X

Centrifugation-separation and ppt       C370 C370           X 

Centrifugation-subcellular fractionation

B215 B215 C370 C370   C370 C370     X

Centrifugation-ultraspeed       C370               

Characterization of carbohydrates                      

Characterization of lipids                      

Characterization of proteins       C370 C370  C370 C470 C370   X X

Chromatography-Affinity       C370 C370           X 

Chromatography-ion exchange      C370 C426    

C370 C426       X 

Chromatography-size exclusion       C370 C370   C370 C370

       X

Chromatography-HPLC       C426 C426          X  X

Lab Performance Rubric • Does student arrive on time?• Does student have all required lab materials?

– Notebook– Manual– Lab coat– Goggles• Can student answer questions regarding the day’s lab activity?• Can student perform methods associated with day’s activity?• Does student set up their experiment independently?• Does student use time well?• Does student write in notebook• Does student ask questions that they should already know the answers

to?• Does student critique/evaluate their results effectively?• Can student troubleshoot?• Can the student explain to other students?• Does the student clean up their bench and store materials correctly?

A3:30

How much do students NEED to know?

• How to pour gels vs. precast (time vs. $$)

• Kits vs. preparing solutions/reagents ahead of lab time

• Using TA’s to prep?

• Other

B

How To Hone Basic Lab skills

• Incorporate into Course (BIOL 240)– Pipetting Activity, Solution Making– Spectrophotometry Activity– pH Exercise– Casting and Running gels– Sterile Technique– Instrumentation Principals

• Lab Skills Course at MMC (BIOL 251)

A

Lab Skills Course

(BIOL 251)

What do you folks do?

Lab Skills

Make it an everyday activity

EVERYDAY CHECKLISTGENERAL LAB ITEMS• Did you make a schedule for when you will be working and in the lab?• Do you have proper PPE?• Did you check your email?• Did you check to see if any notes were left for you?• Did you make a list for yourself of task for day• Are these tasks in order of importance• Did you have the proper background and readings for task?• Did you prepare all reagents and materials for experiment day

before?• Did you write out the protocol in your lab book?• Did you write in your lab notebook?• Did you clean up after the experiment

– Cleaned dishes/bench paper/ put away reagents and instruments• Did you print out a copy of results and put in results binder• Did you put results in lab notebook• Did you restock supplies used

– Pipet tips/ autoclaved deionized water/ pipettes– If you used the last one did you report it?

• Did you properly label all reagents?• Did you properly store all reagents?

– Rm temp/ 4°/-20°• Is your work space clean and clear?• Did you make a list of tasks for the next day?• Did you prepare all reagents materials and lab notebook for tasks next

day?• Did you put out the lab garbage?• Did you lock the lab?• Did you say goodbye?

TISSUE CULTURE •Did you check Tissue Culture?

•Did you look at your cells under microscope ?•Did you check for contamination in incubator?•Did you check the CO2 tanks?•Full/leaking/at right PSI•Did you check the incubator?•Temp/CO2 input•Did you check to see if you have all materials under hood/ stocked in TC•Did you do all TC chores

•Did you check Tissue Culture before you locked up for night?

•Incubator on at right settings/ no leaks/ UV LIGHT ON?•Are the proper signs on the door for TC•Did you put out the garbage

Acid into waterDNA runs to red A

WORDS OF WISDOM• Make a schedule and stick to it• Do not eat in the lab• Don’t get too comfortable • Make a list of tasks and arrange them in order of importance• Do not put off small tasks or they will never get done• Do TC in the morning when you are bright and awake• Write out complete protocol in lab notebook day before experiment• Make sure all reagents are out/prepared the day before experiment• Unlock doors and return keys • Do not keep common lab materials in 611• Clean up before you leave each night• Haste makes waste (take it slow)• Make time in week to read primary lit papers• Go to lab meetings with results printed or ready to be easily displayed• Go to lab meetings prepared to discuss issues and topics • Be honest, don’t say you did something when you didn’t• Be honest when you feel overwhelmed • It takes time to place orders (make sure you have all materials)• You know it when you can explain it to someone else• Explain it in different ways• mg/ml= ug/ul• Thawing on ice may take a while; take that into account • Give yourself a time frame then double it to get something done

A

Reinforcement or Redundancy?

• Compare Syllabi• Communicate

B

Reinforcement or Redundancy?

MMC Cell/Molec Lab (240) Biochemistry (441)

• Lab Safety and the Lab Report • Separation of Proteins by Charge • Separation of Protein by MW • Nucleosome Structure • Karyotyping Human Cells• Advanced Microscopy/Cell Culture• Intro to Bioinformatics: DNA Sequencing • Cloning, Transformation, Phenotype Assay• Cell Culture (con’t); Insect Cells• PCR-based DNA Profiling

A

Reinforcement or Redundancy?

MWSU Biochemistry Lab (370) Molec Cell Bio Lab (115)• Pre-Lab Assessment • Pipette Calibration • CMC by Fluorescence• pH and Buffers• Titration of Amino Acids• Protein Quantification (BCA/Bradford) (Lowry)• Gel Filtration Chromatography• Bioinformatics• Protein Purification Project (Ion Ex. chrom)• Protein Purification Project (Affinity chrom.)• Protein Purification Project (SDS-PAGE) • Protein Purification Project (Western Blot) • Enzyme Kinetics

B

Other Things to Consider

• Peer Mentors• Teaching Assistants

• Buy or make Lab Manual?• How much student prep? • Kits?• Cost?• Waste Handling/Safety• Resources

A

Example Lab Activities

• www.Drop-box.com

• Share your Lab ideas, experiments, exercises, etc…

• Register, let Ben know – share folder

Good Resources

Open Discussion