ANG 6462L (Section 9738) BIOLOGICAL ANTHROPOLOGY LABORATORY

Molecular Anthropology section

 

Prof. Connie J. Mulligan

 

Class meets in B304 Turlington for lectures and B103 Turlington for labs

Class time: Fri, 9:35-1:40

 

Contact information:

B119 Turlington Hall

(352)392-2253, ext 248 (office), ext 247 (lab)

mulligan@anthro.ufl.edu

Office/lab hours: Mon and Wed, 10:30-12:00

 

Teaching assistant – Amy Non

B103 Turlington Hall

392-2253, ext 247

 

 

Course objectives: The purpose of the first half of the course is to provide hands-on experience with the latest molecular techniques as applied to questions of anthropological and human genetic interest (the second half of the course is taught by Prof. John Krigbaum and involves stable isotope analysis).  Students will isolate their own DNA from hair and buccal samples and generate DNA sequence data using an automated DNA analysis system.  Data will be analyzed using current computer algorithm and software packages that are widely available.

 

Reading and course format:  The main reference for the course is Molecular Systematics, 2nd edition, eds. Hillis, Moritz, and Mable (select chapters are available as a course packet from Orange and Blue Textbooks, 309 NW 13th St, 375-2707).  Experiments for each class will be posted on the course webpage.  Students are expected to have studied the reading material and experiments before class in order to intelligently discuss the material and conduct the scheduled experiments.  Students are encouraged to find articles of interest for discussion in class (inform instructor of such articles so that reading and discussion can be arranged).

 

Course format will consist of brief lectures to discuss the day’s experiments (B304 Turlington Hall) followed by performance of the day’s experiments (B103 Turlington Hall).  The exact time devoted to lecture and lab work will vary depending on the specific experiments, but will always involve more lab work than lecture.

 

Grading: Final grades for the molecular genetic section of the course will contribute 50% to your final grade for the course and will be determined by the following four categories: 1) daily laboratory experiments and experiment summaries/lab notebooks (100 pts), 2) quizzes (100 pts), 3) homework exercises (100 pts), and 4) a final paper (100 pts).  Grades will be based on the following point percentages: 90-100%=A, 87-89%=B+, 80-86%=B, 77-79%=C+, 70-76%=C, 67-69%=D+, 60-66%=D, < 59%=E.

-                      Experiment summaries in the form of a lab notebook (detailing objectives, methods, and summary of results) must be turned in at the end of each lab class.  All details necessary to conduct the experiments, without any additional documentation, must be included in the weekly summaries.  Missed experiments will be rescheduled solely at the discretion of the instructor and only with advance notice.

-                      At the beginning of each class, a quiz will be given based on the reading material and lab experiments for the day.  A total of five quizzes will be given.  Missed quizzes cannot be made up.

-                      Two exercises involving the analysis of data from the literature or unpublished work will be assigned.  Exercises will be due one week after they are assigned with no exceptions. 

-                      A final paper (~4-5 pages, single-spaced) will be prepared based on a summation of the experiments, results, and analyses conducted in class.  The paper will be written in the format of a research paper including title, abstract, introduction, materials and methods, results, discussions, and references.

 

Useful websites:

Although basic molecular biological concepts will be reviewed, some knowledge of DNA structure, Mendelian genetics, and molecular biology is expected (such as Intro Bio, BCS 2011).  Useful information is provided by several websites:

http://www.clas.ufl.edu/users/mulligan/Webpage/BioAnthLab.2005/BioAnthLabhome.html - website for class

http://www.uflib.ufl.edu/ej/ - UF database of available electronic journals (may only be available from a campus computer)

http://www.ncbi.nlm.nih.gov/PubMed - National Library of Medicine database of over 11 million journal articles dating back to the 1960s

http://www.genome.gov/glossary.cfm – NIH-maintained glossary of genetic terms

http://medical.webends.com - Online medical dictionary

http://www.genomesonline.org/ - status of genome sequencing projects

http://www.stanford.edu/group/morrinst/hgdp.html – Human Genome Diversity Project (dated, good for historical perspective)

 

Class attendance policy: Because the class meets only one time per week and because the class format is mainly laboratory work, it is impossible to make up missed classes by borrowing notes, etc.  Therefore, students are required to attend all classes.  Missed experiments will be rescheduled solely at the discretion of the instructor and only with advance notice.  Computers are allowed in class for taking notes, but are not allowed during exams.  Class discussions/lectures cannot be recorded in any manner without special permission.

 

Accommodations for students with disabilities: If you require accommodation due to a disability, please make an appointment during my office hours so that we may discuss your needs.  Students requesting classroom accommodation must first register with the Dean of Students Office.  The Dean of Students Office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodation.

 

Academic honesty: As a result of completing the registration form at the University of Florida, every student has signed the following statement: “I understand that the University of Florida expects its students to be honest in all their academic work.  I agree to adhere to this commitment to academic honesty and understand that my failure to comply with this commitment may result in disciplinary action up to and including expulsion from the University.”  An excellent website that explains plagiarism (provides a definition and many useful examples) is http://www.csubak.edu/ssric/Modules/Other/plagiarism.htm.  All students are encouraged to read this material at least once.  In addition, the university has recently implemented the world’s leading plagiarism prevention service to ensure that any instances of plagiarism are detected and investigated.

 

UF Counseling Services: On-campus services are available for students having personal problems or lacking clear career and academic goals.  They include:

  1. University Counseling Center, 301 Peabody Hall, 392-1575, personal and career counseling
  2. Student Mental Health, Student Health Care Center, 392-1171, personal counseling
  3. Sexual Assault Recovery Services (SARS), Student Health Care Center, 392-1161, sexual assault counseling
  4. Career Resource Center, Reitz Union, 392-1601, career development assistance and counseling

 

Course schedule:

 

August 26 -       Lecture - Syllabus, structure and goals of the course, background on molecular genetics.

                        Video - "The Gene Hunters"

 

                        Lab

                        - Begin DNA extraction from hair and buccal (cheek) samples

 

September 2 -   Reading material and lecture

-  Course webpage - http://www.clas.ufl.edu/users/mulligan/Webpage/BioAnthLab.2005/Safetylinks.html

o        Lab safety, lab etiquette, and measurement techniques’ and ‘Lab safety checklist’ links

o        Skim Laboratory Safety Manual and Chemical Hygiene Program on same webpage.  Additional websites for lab safety and the Bloodborne Pathogen Program are also listed on the webpage.

-  Course packet

o        Forensics and Mitochondrial DNA, Budowle et al., 2003, Annu Rev Genomics Hum Genet, 4:119-141.

o        Molecular Systematics, Chpts  2, and 7 (read Chpt 7 closely) – Intro, Project design and PCR

 

                        Lab

-  Finish DNA extractions

-  Set up DNA amplification reaction (PCR)

-  Pour agarose gel

                 

Exercise #1: Identify genetic markers suitable for discriminating yourself from others in the general population and from others in the class.

 

 

September 9 -   Reading material and lecture

-  Course packet - Molecular Systematics - Chpts 7 (read it again) and 8 (pp 249-282) – PCR and Analysis of DNA fragments

 

                        Lab

-  Gel electrophoresis of amplification reactions

-  Purification of amplification products (Qiagen kits)

-  Pour agarose gel

 

                        Exercise #1 due

 

September 16 -  Reading material and lecture

-  Course packet

o        Molecular Systematics – Chpt 9 – Sequencing and cloning (skip the protocols)

o        Ice Ages and the mitochondrial DNA chronology of human dispersal: A review, Forster, 2004, Phil Trans R Soc Lond B, 359:255-264

 

                        Lab

-  Quantitate amplification products (on agarose gel)

-  Set up cycle sequencing reactions

 

                        Exercise #2 – Sequence analysis problem

 

September 23 -  Reading material and lecture

-  Molecular Systematics – Chpt 11 – Phylogenetic inference (pp 407-446)

 

                        Lab

-  Purify cycle sequencing reactions

-  Load cycle sequencing reactions on CEQ 8000 Automated DNA Analysis System

 

                        Exercise #2 due

 

 

September 30 -  Reading material and lecture

-  Course packet

o        Molecular Systematics – Chpt 12 – Applications of molecular systematics

o        Are Human Still Evolving? Science, 2005, 309:234-237

 

                        Lab

-  Edit and align DNA sequences

-  Analyze sequence data – phylogenetic, etc analysis

 

 

October 7 -       Homecoming – no class

 

 

October 14 -     Final papers due.  Hand in to Dr. Mulligan.

                       

                        - First day of stable isotopes section of class