Bio 113 COVID19 Lab Schedule - Dr. C. Spring 2020

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

Lab Safety Guidelines and Agreement. 

Learning Objectives for Lab Course

List of Protocols Used in Bio113

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

schedule

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
January
14 - 15

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) GenBio-MAPS pre-survey (~20 minutes)

Lab Manual Week #1

Practice Calculations - optional

January
20 - 21

No Lab - MLK Week
January
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) Read p
Clone Red paper
    (view J119137 in Registry)

6) Find a promoter to test (PubMed)
7) CATME first week

Lab Manual Week #2

February
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

February
11-12

Information & Cells

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

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
February
18-19

Information & Cells

Before Lab...
1) 4:30 pm Monday before lab, start cells growing
  
(1 person per group; +/- 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
February
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

March
3 - 4

Spring Break
March
  10 - 11

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

Lab Manual Week #7
March
17 - 18
Information & Cells Adjust to new situation

March
24 - 25

Information & Cells

Lab Group Preparation
1) View DNA sequencing
2) Review GGA method
3) Answer 4 Questions week 8 Lab Manual

Remote Lab Group Work
5) refine research proposal
(use Research Proposal Template)
6)
generate oligos from GGA Oligator
7) name sequences and email Dr. C.
8) submit group research proposal for grading

10) CATME peer review


Lab Manual Week #8

March 31 -
April 1
Information & Cells

Lab Group Preparation
1) View DNA sequencing
2) Review GGA method
3) Review Your Graded Research Proposal
4) Answer 4 Questions week 9 Lab Manual

Remote Lab Group Work
5) Read through methods
6) Dr. C. will anneal oligos, GGA, transform, plate
7) Data sent by email in PPT photos.

8) Discuss results with your group, find colonies to be picked. Circle them in PPT file and email to Dr. C. (1/group)
9) Choose one clone (X1, X2 or X3) from version 1 to test --> email your choice (1/group)
10) Dr. C. will grow overnight for Synergy and miniprep isolation of plasmid DNA
11) CATME peer review


Lab Manual Week #9
April
7 - 8
Information & Cells

Lab Group Preparation
1) Read through Lab Manuals for Weeks 10 & 11
2) Answer 4Qs

Remote Lab Group Work
3) Generate a graph from Synergy Data
4) read through miniprep method
5) read through nanodrop method
6) Use Nanodrop DNA concentration to calculate how to prepare DNA for sequencing

7) Dr. C. will send DNA off for sequencing
8) Update your part in the Registry
9) CATME peer review


Lab Manual Week #10

Lab Manual Week #11

April
14 - 15
 

Easter Week


April
20 - 21
Information & Cells

Lab Report Template

Lab Group Preparation
1) review how cycle sequencing works
2) Answer 4 Questions

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

6) prepare for final solo lab report
7) download FinchTV for chromat viewing
8
) CATME peer review

Lab Manual Week #12



April
28 - 29
Information & Cells

Lab Group Preparation
1) write solo lab report (may share group figures)

Due 5 pm eastern normal lab day
2) submit written lab report for grading (email Word file)
3) Fellowships for you (recording link here)
4) Course evaluation (found in Moodle) ~15 min
5) Bio assessment (if last intro bio course) ~20 min

Lab Manual Week #13


Practice Calculations

Dr. Campbell's Bio113 Page


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