Transcript Sharing Laboratory Ideas and Assessments ASBMB Student

Sharing Laboratory Ideas and
Assessments
ASBMB Student Centered Education Conference July 2011
Ann Aguanno, Associate Professor of Biology
Marymount Manhattan College
Benjamin Caldwell, Professor of Chemistry
Missouri 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, NYC
o Small (1700) liberal arts college, urban, diverse,
academically average student population
Missouri Western State University
o 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 course
o Required for all Biology majors
o 10-12 students per lecture; 10-12 students per lab section
Biochemistry (CHE 370)
o Junior/Senior Level course
o Required for all Biology & Chemistry majors
o 48 students per lecture; 16 students per lab section
Cellular & Molecular Biology
Lecture
Intro to Chemistry and Cells
Energy, Catalysis, Biosynthesis
Protein Structure and Function
DNA & Chromosomes
DNA Replication, Repair
DNA to Protein
Analyzing Genes
Control of Gene Expression
Cell Cycle and Cell Death
Tissues & Cancer
Laboratory
Lab Safety and the Lab Report
Separation of Proteins by Charge (protein structure;
chromatography; micropipette use)
Separation of Protein by MW (SDS PAGE)
Nucleosome Structure (chromatin structure; DNA
electrophoresis)
Karyotyping Human Cells (cytogenetics; Microscopy )
Advanced Microscopy/Cell Culture (sterile Technique;
photomicroscopy )
Intro to Bioinformatics: DNA Sequencing (DNA sequencing
methods; genomics)
Cloning, Transformation, Phenotype Assay (microbiology;
transformation; cloning)
Cell Culture (con’t); Insect Cells
PCR-based DNA Profiling (PCR technology )
Grading: 3 Exams, Primary Literature Analysis, Lab Performance and Reports
Textbook: Essential Cell Biology Alberts, et. al, 3rd
Textbook: Reading the Primary Literature , by Gillen
Lab Manual: In-House
Biochemistry
Lecture
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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
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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
Grading: 3-4 Exams + Final, 5-6 quizzes, Questions of the Day,
Lab Performance and Reports (20%)
Textbook: Biochemistry, Garrett & Grisham, 4th ed.
4/13/2015
Lab Manual: In-House
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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
• Courses
o MATH, MATH, MATH!!! (Level???)
o General Biology (1-2 semesters?)
o General Chemistry (2 semesters?)
o Organic Chemistry (1-2 semester?; coreq ok)
o Writing 1 and 2
Expectations for Our Lab Courses
• Basic Skills
o Time management, writing, reading, collaboration
o 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 Courses
Cellular & Molecular Biology
o Communicate and apply fundamentals of cellular &
molecular biology
o Utilize scientific method, critical thinking skills and
problem based-learning techniques
o Perform laboratory- based scientific investigations by
applying the concepts and techniques learned
o Apply concepts and techniques learned to current
scientific and medical topics
o Present and critique experimental results
o Analyze primary cellular and molecular biology literature
Learning Goals of Lab Courses
Biochemistry
o Demonstrate proficiency in basic biochemistry lab techniques
o Identify connections between experimental design and data
generated from procedures
o Differentiate between control and experimental data
o Perform mathematic transformations of raw data to useful and
meaningful information
o Generate data in multiple formats (graphs, charts, observations)
o Develop conclusions based on objective and logical analysis,
interpretation and evaluation of data and observations
o 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
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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
Disagree
1
Somewhat
Disagree
2
Neutral/ Somewhat
No Opinion
Agree
3
4
Strongly
Agree
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
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
545.1x 21.3

0.029
Sample of pre-course survey at
(Spring 2010 results).
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
67
I 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
Sample survey questions & responses (%) are shown (grey)
Results of task related questions (Far right , yellow) displays overall class performance
(% correct).
Final Exam Results
Scores represent percentage of students receiving full credit for each
question.
Class
Q1
Spring
92.2
2010
Spring
95.6
2011
Average
Exam
Score (%)
Q2
Q3
Q4
Q5
Q6
Q7
Q8
Q9
Bonus
Q10
Q's
76.3
92.5
75.6
66.7
64.4
68.1
80.4
56.3
81.5
70.4
79.2
68.0
83.5
75.7
73.2
73.5
68.5
81.4
69.7
84.6
65.2
82.9
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)
Lab Skills
– Skills necessary
– Theory/background on experimental
procedures
– Data analysis
– Instrumentation exposure
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WHEN SKILL IS LEARNED AND LEVEL
BMB SKILLS
Adapted from BMBEd
Vol. 32, No. 1, pp. 11–16, 2004
LAB TECHNIQUES
Lab skills
Lower Level
Courses
Theory
Usage
Proficiency
Upper Level
Theory
Usage
Competence
TYPE
BMB Courses
The
ory
Usa
ge
Competenc
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Qua
ntitativ
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Qual
itativ
e
Acid/Base chemistry
• Review of matrix and discussion
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
4/13/2015
Cloning
and Selection
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WHEN SKILL IS LEARNED AND LEVEL
BMB SKILLS
Lower Level
Courses
Adapted from BMBEd
Vol. 32, No. 1, pp. 11–16, 2004
LAB TECHNIQUES
The
ory
Usag
e
Proficienc
y
Acid/Base chemistry
C111
C120
C120
C120
Upper Level
BMB Courses
Theor
y
Usag
e
Compete
nce
Theor
y
C321
C370
C321
C370
C321
C370
C321
C370
Affinity techniques
C370
C426
370
Amino acid analysis
C370
cDNA
Cell Culture-Aseptic/Sterile
Techniques
B215
B215
B215
B215
Cell Culture: Adherents vs.
suspension
B205
B215
B205
B215
Cell Culture-Bactierial/insects
B215
B215
Cell Culture-Mamallian
Centrifugation-high speed
B215
B215
Centrifugation-separation and ppt
Centrifugation-subcellular fractionation
Centrifugation-ultraspeed
B215
B215
B421
TYPE
Usag
e
Compete
nce
Qua
ntitativ
e
Quali
tativ
e
X
C370
C370
X
B313
B313
X
B421
B421
B215
B421
B215
B421
B421
B390
B421
B390
B421
B390
B421
B431
X
X
B215
B390
B390
B390,
B421
B205
B215
B390
B411
B421
B390
B411
B421
B390
B411
B421
B205
B215
B390
B421
B205
B215
B390
B421
B390
B421
X
X
B390
B390
B390
B421
B390
B421
B390
B421
B390
B421
X
X
B411
B411
C370
C370
C370
C370
C370
C370
C370
C370
C370
C470
C370
X
X
C370
C370
X
X
X
C370
Characterization of carbohydrates
Characterization of lipids
Characterization of proteins
C370
C370
Chromatography-Affinity
C370
C370
X
X
X
Lab Performance Rubric
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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?
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3:30
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
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Lab Skills Course at MMC (BIOL 251)
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Lab Skills
Course
(BIOL 251)
What do you folks do?
Lab Skills
Make it an everyday activity
EVERYDAY CHECKLIST
GENERAL LAB ITEMS
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Did you make a schedule for when you will be working and in the lab?
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Do you have proper PPE?
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Did you check your email?
TISSUE CULTURE
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Did you check to see if any notes were left for you?
•Did you check Tissue Culture?
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Did you make a list for yourself of task for day
•Did you look at your cells under
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Are these tasks in order of importance
microscope ?
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Did you have the proper background and readings for task?
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Did you prepare all reagents and materials for experiment day before? •Did you check for contamination in
incubator?
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Did you write out the protocol in your lab book?
•Did you check the CO2 tanks?
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Did you write in your lab notebook?
•Full/leaking/at right PSI
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Did you clean up after the experiment
– Cleaned dishes/bench paper/ put away reagents and instruments •Did you check the incubator?
•Temp/CO2 input
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Did you print out a copy of results and put in results binder
•Did you check to see if you have all
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Did you put results in lab notebook
materials under hood/ stocked in TC
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Did you restock supplies used
•Did you do all TC chores
– Pipet tips/ autoclaved deionized water/ pipettes
•Did you check Tissue Culture before you
– If you used the last one did you report it?
locked up for night?
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Did you properly label all reagents?
•Incubator on at right settings/ no leaks/
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Did you properly store all reagents?
UV LIGHT ON?
– Rm temp/ 4°/-20°
•Are the proper signs on the door for TC
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Is your work space clean and clear?
•Did you put out the garbage
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Did you make a list of tasks for the next day?
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Did you prepare all reagents materials and lab notebook for tasks next
day?
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Did you put out the lab garbage?
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Did you lock the lab?
Acid into water
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Did you say goodbye?
DNA runs to red
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WORDS OF WISDOM
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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
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Reinforcement or Redundancy?
• Compare Syllabi
• Communicate
B
Reinforcement or Redundancy?
MMC Cell/Molec Lab (240)
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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
Biochemistry (441)
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Reinforcement or Redundancy?
MWSU Biochemistry Lab (370)
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Molec Cell Bio Lab (115)
Pre-Lab Assessment
Pipette Calibration
CMC by Fluorescence
pH and Buffers
Titration of Amino Acids
Protein Quantification (BCA/Bradford)
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
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B
Other Things to Consider
• Peer Mentors
• Teaching Assistants
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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