BIOL345 Advanced DNA Methods Spring 2010

Text: Butler, JM. 2005. Forensic DNA Typing. Elsevier Academic Press, Oxford.

Instructor: Dr. Ted Nuttall E-mail: tnuttall@lhup.edu

Office: Ulmer Hall 307 Web Site: www.lhup.edu/tnuttall/

Phone: 484-2058 Office Hours: M 11- 12 am; T 1-2; R 10-12

Agenda:

First half of the semester: DNA Sequencing (using AFDIL protocols)

Isolate DNA, PCR amplify multiple fragments of mtDNA, sequence analysis on 310 Genetic Analyzer

Book chapter 10-11, 12-14

Second half of the semester: Genotyping (using Profiler Plus)

Isolate DNA, PCR amplify multiple loci, fragment analysis on 310 Genetic Analyzer

Book chapters 1-7, 12-15

Exams: Exam I will be during the last week in February

Exam 2 will be held during finals week: 2-3:30pm, Tuesday, May 4

Report: Oral presentation and Poster presentation

Poster: Rough draft due March 19 (30pts), Final due April 9 (10pts)

Bring to Class: Text book, Notebook for general note-taking, Dedicated lab notebook (spiral bound, leave in lab), Sharpie (extra fine is best), Calculator, Gloves, blue book for MCJ (metacognative journal).

Reasonable Accommodations: Students with disabilities are encouraged to discuss requests for reasonable accommodations with me at the beginning of the semester. In order for accommodations to be provided, your disability must be verified by Dr. Reynol Junco, Director of Disability Services for Students, 104 Russell Hall, 484-2926.

Email: All email correspondences will be made to campus email addresses only. Please be sure to use your LHU account and check it.

Exams & Quizzes: All exams must be taken on schedule. No make-up exams will be given unless prior arrangements with me are made as far in advance of the exam as possible. Only official LHU excuses are acceptable. All quizzes will begin a few minutes after the beginning of class, and may be unannounced. Some may include finding information in your lab manual. Be on time! No make-up quizzes will be given.

BIOL345 Advanced DNA Methods Spring 2010

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Cheating: Please don't! If you are caught cheating (this includes plagiarism) you will receive a zero on that assignment or exam. If you are caught a second time, you will immediately fail the class. Read the Academic Honesty policy in the student handbook. Cheating is an insult to everyone who studies hard and works honestly.

Laboratory conduct: Do not play around with equipment or supplies—they are expensive and sometimes dangerous! Stealing or intentionally misusing/breaking supplies or equipment will result in suspension from the class. Additionally, intentional classroom disruptions will not be tolerated—please be courteous to your fellow students.

Grading: (The actual total may be different due to extra quizzes in lab.)

Exam 1 100pts

Exam 2 100pts

Lab notebook 20pts

MCJ 10pts

Quizzes 40pts

Report 60pts (poster = 40 and oral = 20)

TOTAL 330pts

Exams may contain hands-on tasks, such as genotype/sequence interpretation, instrument use, and problem solving.

PLANNING

Genotyping Labs:

FTA paper 1hr (to dry)

DNA IQ isolation lab 2 hr

Wash FTA sample for PCR 0.5hr

PCR setup and Run (profiler plus) 1hr (includes overview)

Load and run 310 2hr

Clean up 310 0.5hr

Genescan hands-on 2hr (half class at a time-1 hr)

Genotyper hands-on 2hr (half class at a time-1 hr)

Genotyping Lectures: Students read chap 1, 2

DNA isolation, Quantitation 1hr Chap 3

PCR multiplex, issues 1hr Chap 4

Capillary electrophoresis, etc. 1hr Chap 11, 12

310 operation, data collection overview 1hr Chap 13, 14

Running samples on the 310 1hr

Genescan, raw data analysis overview 1hr

Biology of STR 1hr Chap 5