Day
WF add
1 day
15-Jan
16-Jan
Laboratory Exercise
(Instructions for students)
 Print before lab
 Do "Before lab"
assignments in your
notebook or on BioPortal
 Bring to class
Links to required readings
In red: new or substantially revised
Read/watch/do before coming to
class
Teaching notes/To do suggestions for
instructors
in red: To Do for Crima before
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You need to sign into your lab
section in S 315:
Take roll
Show appropriate notebook
Introduce website
Announce homework for next lab
Announce lab policies, absences
1/15: 2:10 with Prof. Pogge
1/16: 10:10 with Prof. Nixon
1/16: 12:10 with Prof. Apollon
17-Jan
Introduction to the lab included
in print package 1, Scientific
method, Protocol writing
 Read: Hillis et al. Principles of Life,
concept 1.5 or Chapter 1 in Knisely
 Read: Laboratory Safety
 Read: Laboratory Notebook
 Bring prepared notebook as
described in above file
 Optional: Check out UC Berkeley's
site on limits of science
 BioPortal quiz on Hillis reading
BioPortal quiz - introduction
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Rewrite exercise: chapter 1 in
Knisely is really good. Include new
homework (see SLO activity) due
1/24
Review Introductory quiz questions
Check notebook at end
Grade open questions on BioPortal
 See “Before coming to lab”
22-Jan
Model cell I included in print
package 1
 See “Before coming to lab”
 Write paragraph as outlined in Model
cell I (after lab)
 Read: Laboratory reports 1 (includes
a rubric used by your instructor)
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Model cell II - included in print
package 1
24-Jan
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Writing lab reports
 Write a brief introduction to our
investigation, use three properly
cited sources – paper copy due in
lab
 Read: Plagiarism
 Author guidelines for PLoS
submissions, includes how to
reference citations.
 Read: Rubric for lab report 1
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Data collection, organization, and
visualization - included in print
package 1
29-Jan
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Check protocol (-2 if not)
Check question (from chemistry they
are used to copy “purpose”
Write homework model 1
Check hypotheses
Go over homework findings
(abstracts). Discuss dependent,
independent, and control variables, as
well as positive and negative control (if
applicable). Refine research question.
Collect homework (4 points)
Assign protocol for investigation next
lab (or do yourself)
Divide file “lab reports in different
parts, assign Knisely, K. Writing in
Biology – free with textbook 1Introduction and quotations), 2 – Title
and results
Write rubrics for 1 and 2
Write intro assignment
Go over introduction, either peer
review or in the form of ppt with bad
and good examples
Carry out experiment
Announce lab report 2 assignment, let
students know we will practice
graphing next lab
Revise lab report 2 write up, include
graphing,
Chymosin I 31-Jan
Chymosin II
 Read: (Micro)Pipettors (you need
this information for the quiz)
 Do: Metric conversion tutorial
 Review Units and Measures if
needed
 Pre-lab pipet, metric conversion
and graphing quiz due on
BioPortal
 Read: Laboratory reports 2 (includes
a rubric used by your instructor)
 Write: Lab report 2: Title and results
– paper copy due in lab or submit
online according to your instructor
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Add graphing exercise to lab
Write graphing quiz for BioPortal
Do graphing exercise
go over pipetting
check “Test your understanding”
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New: Student conferences lab report 2
or peer review or ppt with common
mistakes
Check for data table chymosin I
 Read: Microscopy background
 Read: Chi square of independence
 Pre-lab quiz on microscopes and
chi square due on BioPortal
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 Watch: Video of experiment
(Science)
 Optional: Article summarizing the
research report: Jailbreak rat
(Scientific American)
 Submit revised result section, include
chi square of independence analysis
 You might find it helpful to read p.
39-40 in Writing in Biology
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5-Feb
7-Feb
12-Feb
14-Feb
Introduction to microscopy
Introduction to chi square test of
independence
Scientific literature I
No lab
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Shorten microscope background
Write chi square of independence,
tailored to investigation
Add chi square questions to quiz
Check chymosin II graphs (or do
during notebook eval)
check article, paragraph numbers,
underlined words, definitions
Assign topics for bioethics
Bioethics
 Optional: TED talk by Paul Root
Wolfe on an astonishing series of
recent bio-engineering experiments
 Bioethics Presentation due
 Bioethics talking points
 Personal reflection
 Bioethics quote
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check quote (I do gallery walk) and
have students present on their topic
 Watch: Mitosis animation
 Read laboratory report 3 (discussion
and abstract)
 Submit discussion/abstract for
investigation
 Read: Principles of Life pp. 128-132
 BioPortal quiz on mitosis
 Read: Principles of Life pp. 134-141
 Read chi square background
 BioPortal quiz on meiosis
 Read: How City College and E. coli
got their amylase - by Dr. Sheri
Miraglia
 Revise entire lab report incorporating
peer and instructor feedback submit
all drafts
 Read: Centrifuges (you need this
information for the quiz)
 Pre-lab quiz on centrifuges due on
BioPortal
 See “Before coming to class
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New: Peer review discussion and
abstract and/or instructor conferences
or ppt with good/bad examples
19-Feb
21-Feb
26-Feb
Mitosis
Meiosis, Chi square
Amylase
28-Feb
Rewrite qui square to distinguish from
independence
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check arguments for hypotheses
check test your understanding
check protocol
Genetics, Chi square goodness of
fit
 Read: Chi square background
 Read: Hilis, Principles of Life,
Appendix B
 Pre-lab quiz on BioPortal
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Introduce aseptic assignment
Could aseptic intro be take-home?
Write assignment part for aseptic prelab
 Bring two abstract pertaining to
aseptic investigation that can serve
as background information
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Lab midterm exam
Notebook due
Lab exam: justify your choice of
abstracts
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Discuss variables
Discuss data collection
Make sure enough data for statistical
analysis
Write review questions for
bioinformatics
5-Mar
7-Mar
12-Mar
Aseptic techniques
14-Mar
Bioinformatics online lab, we will do
this in class together
Read up to "Questions to answer",
answer discussion questions in
your notebook.
 See “Before coming to class”
 After class: Review: Bioinformatics
Power Point Presentation adapted
from Alexandra Schnoes
 Watch: PCR animation (you need
this information for the quiz).
 Pre-lab quiz on PCR due
PCR I
19-Mar
PCR II
21-Mar
 Watch: Electrophoresis animation
 Read: Introduction to electrophoresis
 Pre-lab quiz on electrophoresis
due
 Full report on Aseptic lab is due,
including chi square of
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independence, paper copy
2-Apr
4-Apr
9-Apr
11-Apr
Scientific literature II
 See “Before coming to class”
 Article: Quantifying the Integration of
Quorum-Sensing Signals with
Single-Cell Resolution
 Read: Synopsis: Going With the
Glow: How Bacteria Integrate
Molecular Signals to Synchronize
Bioluminescence
 TED talk by Bonnie Bassler (we will
watch this together in lab)
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New: Instructor – student conferences
on lab report
 See “Before coming to class”
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Check table with reagents and
protocol
Rewrite procedures
Check test your understanding
Pre-lab quiz autoinduction
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Check protocol
GE I
Autoinduction
Check autoinduction results
GE II
 Watch: Lux operon animation
 If you loved Dr. Bassler's TED talk,
you might want to check out Dr.
Bassler's longer seminars
(Bioseminar, HHMI Holiday Lecture)
 Revised lab report due
 See “Before coming to class”
 Review: Introduction to
electrophoresis
 See “Before coming to class”
Lifestyle analysis take home
16-Apr
18-Apr
 Familiarize yourself with this online
diet and exercise analysis tool
 Nutritional research sites: e.g.,
American Society of Nutritional
Sciences and Harvard School of
Public Health
 Discussion forum essay practice
 In a group of 3-4 students, choose
one of the articles below. Note that
often there are easier articles about
the articles available. Do a search!
Write discussion forum questions
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Introduce oral presentation
Talk about group work
Review available articles
 Lifestyle quiz on BioPortal
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Check protocol and material list
grade nutrition quiz
prepare sign up sheet for
presentations
write quiz on chaper 8 Knisely
GE II)
Scientific literature 3, preparation
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4/23
Check GE III results
Cardiovascular system lab
Sign up for presentation topic
BioPortal quiz on oral presentations
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425
No lab
 Pre-lab quiz on BioPortal
(Re)write quiz on drug and the brain
4/30
Drugs and the brain
 Pre lab quiz on oral presentation
5/2
ELISA
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5/7
Scientific Literature 3 - Student
presentations I
Presentation rubric
(adjust to 32 points total)
+ 8 for participation in discussion
and assessments
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5/9
5/14
Student presentations II
Review for final
Lab final
Lab notebook due
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Rewrite presentation rubric?
Rewrite instructions for sci lit III,
emphasize reflection part