Bio 113 Lab Schedule - Dr. C. Fall 2018

Lab meets either Tuesday at 1:40 pm or Wednesday at 1:30 pm in Wall 104.

Read the safety form. Hard copies for signing will provided for you in lab.

Learning Objectives for Lab Course

List of Protocols Used in Bio113

We will use CATME to facilitate fair assessment of lab group projects.

schedule F18

Your  oral presentation will be divided into four sections: Introduction; Materials and Methods; Results; Discussion. Each person will present one section. The oral presentation must be pledged to indicate that each person made substantial contributions. You will not know which section you are presenting until 1 hour before lab, therefore you should learn all 4 parts.

For the final written lab report, each person must write his or her own (including figure legends), though you may confer about the content. The figures may be shared resources since they were produced as a team. Put your name as the first author and your labmates' names as coauthors.

Grading will be based on these grading rubrics.

Date
Topics
Lab Manual
Word Files
August
21-22

Introduction

1) Safety Issues
2) Submit info to CATME for Team maker
3) Answer 4 Questions

4)
Synthetic Biology Introduction (PDF version)
5)
How to Use a "Pipetman"
6) Lab survey by Dr. Rosemond psswrd = Promoter

Lab Manual Week #1

Practice Calculations

August
28-29

Information & Cells

Before Lab...
1) Answer 4 Questions

2) Create a Registry account (top right "login", apply for new account)

3) Radio show about Synthetic Biology
(7 minutes)

During Lab...
4) Basics of cloning DNA parts
5)
Registry of Parts
6) Read first paper

7) Identify DNA control element to test
8) CATME first week

Lab Manual Week #2

September
4-5

Information & Cells

Before Lab...
1) Answer 4 Questions
2) What is golden gate assembly (GGA)?
Overview and Detailed explanations

During Lab...
3) Identify genetic control element DNA sequence
4) generate oligos from GGA Oligator
5) make a new part on Registry
6) name sequences and email for synthesis
7) one volunteer/group for next Mon. 4:30 pm
in Dr. C's research lab
8) do calculations, steps 1-6
9) CATME peer review

Lab Manual Week #3
September
11-12

Information & Cells

Before Lab...
1) 4:30 pm Monday before lab, boil oligos (one per group)
2) Answer 4 Questions
3) View your receiving plasmid

During Lab...
4) dilute oligos for ligation (step 2 lab manual)
5) do GGA ligation for oligos
6) do paper GGA activity
    + optional review session in lab
7) transform 3 tubes of E. coli
( N and P controls, plus X)
8) design next week's experiments (with controls)
9
) one volunteer/group for next Mon. 4:30 pm, Dr. C's research lab
10) CATME peer review

Lab Manual Week #4
September
18-19

Information & Cells

Before Lab...
1) 4:30 pm Monday before lab, start cells growing (+/- treatment).
2) Watch PCR animation
3) Answer 4 Questions

During Lab...
4) start confirmation PCR, practice loading gel
5) test cells in Synergy machine
6) quantify Synergy data (use Excel)
7) update experience page in Registry
8) CATME peer review

Lab Manual Week #5
September
25-26

Information & Cells

Oral Report Grading Rubric

Before Lab...
1) Answer 4 Questions
2) PCR animation

During Lab...
3) run PCR products on gel (1 kb ladder)
4)
PCR reagents and amplicons
5) prepare for oral presentation (iBOP Bingo)
6) CATME peer review

Lab Manual Week #6

October
2-3

Information & Cells

Oral Report Grading Rubric

Before Lab...
1) Answer 4 Questions
2) prepare oral presentation, assigning email 1 hour before

During Lab...
3) give oral presentation, read peer comments

(iBOP Bingo)
4) choose the next iteration experiment (v2.0)
Research Proposal Template

5) CATME peer review
6) Lab survey #2 by Dr. Rosemond psswrd = Coding Sequence

Lab Manual Week #7
October
9-10

Information & Cells

Fall Break

Week #8
October
16-17

Information & Cells

Before Lab...
1) Evaluate experimental design v2.0
2) Answer 4 Questions

3) View DNA sequencing
4) Answer 4 Questions

During Lab...
5) refine research proposal
(use Research Proposal Template)
6)
generate oligos from GGA Oligator
7) name sequences and email for synthesis
8) submit group research proposal for grading
9) one volunteer/group for next Mon. 4:30 pm, Dr. C's research lab

10) CATME peer review

Lab Manual Week #9

October
23-24

Information & Cells

Before Lab...
1) review GGA and transformation protocols
2) Answer 4 Questions

During Lab...
3) dilute oligos for ligation (calculations last week)
4) do GGA ligation for oligos

5) make a new part on Registry
6) transform 3 tubes of E. coli    (N, P and X DNA)
7) design testing experiments (with controls)
8) one volunteer/group for next Mon. 4:00 pm

9) CATME peer review

Lab Manual Week #10

October
30-31
Information & Cells

Before Lab...
1) review experimental design v2.0

2) Answer 4 Questions

During Lab...
3)  test cells in Synergy machine
4) quantify Synergy data (use Excel)
5) update data in Registry

6) CATME peer review

Lab Manual Week #11
November
6-7
Information & Cells

Before Lab...
1) read through mini-prep protocol
2) Answer 4 Questions

During Lab...
3) miniprep plasmid DNA
4) nanodrop DNA to determine concentration
5) send DNA off to be sequenced

6) Tell your story with data
7) Update your part in the Registry
8) CATME peer review

Lab Manual Week #12

November
13-14
Information & Cells

Written Report Grading Rubric

Before Lab...
1) review how cycle sequencing works
2) Answer 4 Questions

During Lab...
3) analyze sequencing results; use Clustal omega
4) Clustal omega website
   
download your sequences
5) finalize all data from semester-long projects

6) prepare for final graded lab report (each person)
7
) CATME peer review



Lab Manual Week #13
November
20-21
 

Thanksgiving Break

Week #14

November
27-28
Information & Cells

Before Lab...
1) write final lab report

During Lab...
2) submit written lab report for grading (email Word file)
3) Fellowships for you
4) Lab survey #3 for Dr. Rosemond psswerd = Stop Codon
5) Course evaluation (Paper) in lab

Lab Manual Week #15


Practice Calculations

Dr. Campbell's Bio113 Page


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Send comments, questions, and suggestions to: macampbell@davidson.edu