FIVS 316 – BIOTECHNOLOGY & FORENSICS Syllabus - Lecture followed by Laboratory Instructor Information:
Name: Dr. Craig J. Coates Email: ccoates@tamu.edu
Office location: 319 Heep Center Office hours: By Appointment Phone: 979-458-1219
Laboratory TA Information:
Name: Ashleigh M. Faris, Ph.D. Candidate Email: AshMFaris@gmail.com
Office location: Heep 308 & Building 1051 on Agronomy Rd (FLIES) Office hours: By Appointment
Class Information:
Lecture Location: Heep Center, Rm 207 Lecture Meeting days: TR
Lecture Meeting time: 9:35am – 10:50am
Prerequisite: FIVS 308 & FIVS Upper Division Classification. Laboratory Location: Heep Center, Rm 207
Laboratory Meeting Day: Monday
Laboratory Meeting Time: 12:40pm – 3:30pm
Course Description:
This course is designed to illustrate the uses of biotechnology for forensic applications. The students will gain an appreciation and understanding of the underlying molecular biology techniques that are used in a diverse array of settings; including blood analysis, blood typing, DNA fingerprinting and genetic testing. The potential future use of advanced sequencing technologies for forensic applications will be discussed. Additionally, the social, ethical and legal implications of these procedures and applications will be fully considered.
The lecture component is composed of a series of lectures designed to ask and answer questions related to the use of a variety of biotechnology techniques for forensic applications. While each lecture period will address technical aspects and terminology to build base scientific knowledge, time will also be dedicated to discussion of the broader aspects of the impact of biotechnology on forensics and society.
The laboratory component will expose students to techniques utilized in forensic
laboratories to conduct presumptive tests for fluids, isolate DNA, quantify DNA, perform PCR amplifications, analyze a STR profile, perform DNA sequencing and analyze a mtDNA profile. The students will become proficient in the required molecular biology techniques and develop an understanding of the procedures for minimizing
contamination, maintaining accurate records and trouble-shooting their techniques. The assignments will cover topics both related to and outside of the lecture material. The mid-term exams are based on the breadth of biotechnology knowledge and an
understanding of the technology, terminology and forensic applications. The final written paper will describe a future biotechnology application or issue, including a thorough discussion and critique of all options and impacts at social, ethical and legal levels. Prior to the final submission of each paper, each student will give a brief presentation to the class. Each student will also perform a Peer assessment of student papers.
The overall goal is for each student to participate in an intellectual discussion of the use of biotechnology in the forensic field, and be able to make a rationale argument for the scope, potential, and limitations of current and future biotechnology applications for forensic purposes. The laboratory component of the course will provide the students with technical skills and an appreciation and understanding of the molecular biology
techniques utilized in forensic investigations. Course Goals
- Increase the students’ base knowledge of biotechnology techniques and applications for forensics.
- To provide a balanced risk vs. benefit assessment of current and future biotechnology applications from both scientific and social perspectives.
- Allow students to independently assess and critique information provided from a variety of sources.
- Enable students to become effective communicators of this information to others. - Develop laboratory skills and techniques in commonly used molecular biology techniques.
Student Learning Outcomes:
1. Describe biotechnology advances, techniques and biological components of forensic investigations.
Assessment: Assignments, mid-term exam questions.
2. Formulate a balanced position paper on a future topic/issue in forensic biotechnology. Assessment: Final Paper
3. Effectively communicate biotechnology advances to a lay person audience. Assessment: Oral Presentations, Final Paper
4. Understand the scope, application and limitations of forensic biotechnology applications. Assessment: Assignments
5. Develop laboratory technical skills and be able to trouble shoot molecular biology techniques. Assessment: Laboratory Quizzes and Notebook evaluation.
Policies:
Americans with Disabilities Act: The Americans with Disabilities Act (ADA) is a federal anti- discrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires that all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact Disability Services, in Cain Hall, Room B118, or call 845-1637. For additional information visit - http://disability.tamu.edu
Scholastic Dishonesty and Attendance: Student rules governing class attendance and scholastic dishonesty, including plagiarism, can be found on the Texas A&M
University Website, under Student Rules at http://student-rules.tamu.edu/
Aggie Honor Code: An Aggie does not lie, cheat, or steal, or tolerate those who do. Academic misconduct, a violation of the Texas A&M Honor System, involves any of the following: cheating, fabrication, falsification, multiple submission, plagiarism, and complicity. The Honor Council Rules and Procedures can be found at:
http://aggiehonor.tamu.edu
Make-up Exams: These will only be provided for official University sanctioned excused absences. The make-up exams will be oral or written exams at a time and in a format to be determined by the instructor.
Late Assignments: 100% late penalties will be applied to all assignments or quizzes that are not submitted on time.
Course Requirements:
Assessment will be based on assignments, quizzes, mid-term exams, class participation, laboratory notebook evaluation, participation in a peer evaluation process, and a final paper. Total Points = 400. Grading Scale – A = 360-400; B = 320-359; C = 280-319; D = 240-279; F= 0-239.
Lecture Component – 300 Total Points
Assignments (50 Total Points) - There are 5 assignments (10 points each) to be completed.
Mid-term Exams (100 Total Points) - Mid-term exam #1 (50 Points) will cover the material leading up to that exam. Mid-term exam #2 (50 Points) will cover the material following the first exam. Make-up exams will only be given for official University
sanctioned excused absences. The make-ups will be oral or written exams at a time and in a format to be determined by the instructor.
In class participation (30 Total Points) - This will be a combination of attendance, participation in class discussions, and final paper presentations.
Peer Evaluation (15 Total Points) – Each student will perform peer evaluations of student papers.
Final Paper (105 Total Points) – Balanced discussion of future change/issue for forensic biotechnology.
Laboratory Component - 100 Total Points As described in Laboratory Syllabus following. Lecture Schedule:
Week 1
Sep 1 – Central Dogma; Types and Collection of Biological Materials Sep 3 - Blood – antigens, immunoassays, isoenzymes
Week 2
Sep 8 – Blood, Saliva – collection, identification, investigation Sep 10 – Semen – collection, screening, identification techniques Week 3
Sept 15 - DNA – structure, heredity, variability
Sept 17 - RFLPs, PCR – history, technique and use for forensic investigations Week 4
Sept 22 – STRs – development, use, forensic databases Sept 24 – Y-STRs, mtDNA – alternative identifiers Week 5
Sept 29 - In Class Review Oct 1 – 1st Mid-term Exam Week 6
Oct 6 – Quantification of DNA Samples; RNA – collection, variability, information – potential future use in forensic investigations
Oct 8 - SNPs – development, limitations and potential use in forensic investigations Week 7
Oct 13 – New Sequencing Technologies – whole genome sequencing, advances and future applications for forensic investigations. Genetic Testing – history, basis and use of genetic testing procedures for medical and forensic applications.
Oct 15 – DNA Databases – current and future DNA databases and their use for forensic and medical purposes.
Week 8
Oct 20 – Innocence Project Discussion Oct 22 – Innocence Project Discussion Week 9
Oct 27 - In Class Review Oct 29 – 2nd Mid-term Exam Week 10
Nov 3 – Class Discussion of Final Paper Topics and Grading Scheme Nov 5 – Class Discussion of Final Paper Topics and Grading Scheme Week 11
Nov 10 - Presentations # 1-5 Nov 12– Presentations # 6-10 Week 12
Nov 17 – No class due to ESA Meeting Nov 19 – Presentations # 11-15
Week 13
Nov 25 – No Class Week 14
Nov 30 – Monday, 5pm – Draft Papers Due (Submit through eCampus) Dec 1 – Hand out Papers and Grading Forms, Reading and Grading in Class
Week 15
Dec 8 - Grading Sheets due at 9:30am, Class Discussion of Final Papers Dec 11 - 5pm - Papers Due (Submit Through eCampus)
FIVS 316 Forensics & Biotechnology Lab Fall 2015
Monday 12:40-‐3:30pm HPCT 207
Teaching Assistant: Ashleigh M. Faris, PhD Candidate Department of Entomology
Texas A&M University
Office: Heep 308 & Building 1051 on Agronomy Rd (FLIES) Email: AshMFaris@gmail.com
Office Hours: By appointment
Lab Description: Students will be exposed to techniques utilized in forensic laboratories to conduct presumptive tests for fluids, isolate DNA, quantify DNA, perform PCR amplifications, analyze a STR profile, perform DNA sequencing and analyze a mtDNA profile. The students will become proficient in the required molecular biology techniques and develop an understanding of the procedures for minimizing contamination, maintaining accurate records and trouble-‐shooting their techniques.
Student Learning Outcomes:
Upon completion of this lab, students will be able to…
• Generate lab reports in a scientific format that can be used to reproduce the experiment, thoughtfully interpret and discuss results, and provide future direction for further analysis.
• Explain the order in which biological samples should be processed and then analyzed with molecular methods.
• Predict and interpret the likelihood of a random match for a DNA profile in a manner that can be presented in a US court of law.
Prerequisites: GENE 301 or GENE 310 or FIVS 308 or approval of instructor (Dr. Coates). This is a required course for the undergraduate FIVS degree.
Text & Materials: Lab protocols and PowerPoints will be made available prior to lab each week on eCampus. Please come prepared by printing these before lab and bringing them with you to each lab with your lab notebook.
There is no required text for the lab, but one I recommend to help supplement information is (you can get it free by searching online):
Butler, John M. Forensic DNA Typing: Biology, Technology, & Genetics of STR Markers. Second ed. New York City: Elsevier Academic Press, 2008. Print.
Grading: You will keep a detailed notebook, which will be checked throughout the semester. Be sure to keep up with important notes and protocol details in your lab notebook, as you will use these to type up your lab reports. Lab reports will be graded
using the rubric provided on eCampus and should include (at a minimum) an introduction, the lab’s objective/s, materials and methods, results, discussion, and conclusions so that following the student’s notes can reproduce the lab.
Lab Reports (70 points total): Lab reports are to be typed in 12 point font with standard margins, in a readable and openable word document (file should end in .doc or .docx). Reports are due on the following dates at the start of the lab period and should be submitted electronically to me at ashmfaris@gmail.com. An example report and rubric can be found on eCampus. The example if to provide formatting ideas, reports will be graded strictly by the rubric.
Lab Report Due Dates:
• Report 1: September 14, 2015 • Report 2: October 5, 2015 • Report 3: October 26, 2015 • Report 4: November 30, 2015 • Report 5: December 7, 2015
Quizzes (30 points total): There will be two quizzes, each worth 15 points. Quizzes will cover lab PowerPoints, procedures, and protocols covered up to the date the quiz is given. Quiz Dates: • Quiz 1: October 12 • Quiz 2: November 2 Grading Scheme:
Lab is worth 100 points out of the 400 available for the course (lecture is worth 300 points). Quizzes are worth 30 points and lab reports are worth 14 points each (for a total of 70 points).
Attendance & Make-‐Up Policy: Attendance is required in order to receive credit for the lab. Due to time constraints and that labs build off one another, no make-‐up labs will be given. However, should you have a University Approved Absence (http://student-‐ rules.tamu.edu/rule07 -‐ http://student-‐rules.tamu.edu/rule07), you will be permitted to make-‐up the missed assignment/lab write-‐up/quiz and receive credit so long as the lab write-‐up/quiz is submitted within 1 week of the approved, missed date. Any write up/quiz not completed 1 week from the approved absence will result in a “0” given. Contact myself and Dr. Coates immediately for missed assignments and plans for their submission. Should an emergency come up (and if you are able to) that prevents you from making lab, contact me immediately by email at ashmfaris@gmail.com.
Late Assignment Policy: Late assignments will lose one full grade (A downgraded to a B, etc.) per day, starting at the beginning of the course on the due date of an assignment. Therefore, after 24 hours from the due date and start of class time (12:40pm), one letter grade (10 points) will be deducted from your assignment grade. After 4 days from assignment due date no credit will be received.
Estimated Schedule of Classroom Activities (Schedule and assignments are subject to change; you are responsible for keeping track of updates to the schedule):
Lab Topic Assignment/Quiz/Report Due
1: August 31 Introduction, Lab Safety, Lab Notebooks, & Reports 2: September 7 Pipetting Techniques & Presumptive Tests
3: September 14 DNA Extraction Pre-‐lab Questions Lab Report 1 (Presumptive Tests) 4: September 21 Quantification & PCR Amplification
5: September 28 PCR Product Clean-‐Up, Digestion, Gel Electrophoresis, & RFLP Analysis
6: October 5 mtDNA Extraction for STR Analysis
Lab Report 2 (DNA extraction,
quantification, amplification, clean-‐up, digestion, gel electrophoresis, & RFLP analysis)
7: October 12 Quantification & mtDNA STR Amplification Quiz 1 8: October 19 STR Analysis & Primer Design
9: October 26 mtDNA HVI Amplification Lab Report 3 (mtDNA extraction, STR amplification, STR analysis)
10: November 2 Nested PCR for HVI Quiz 2
11: November 9 PCR Clean Up for Sequencing & Sequencing Rxn.
12: November 16 Lab does not meet due to ESA Read Ch. 22 in Butler on Mixture Analysis 13: November 23 Sequencing Analysis & Mixtures Case Study Intro.
14: November 30 Mixtures Case Study & Lab Notebook Evaluations Lab Report 4 (HVI Amplification, Nested PCR, Clean-‐up, Sequencing Reaction, & Sequence Analysis)
15: December 7 Redefined Day: Attend Friday Classes Lab Report 5 (Mixtures)
Teaching Laboratory Safety
The department of Entomology is committed to the safety of all students and employees participating in teaching laboratories. To ensure that a safe environment is maintained in our teaching laboratories, it is expected that all students will adhere to general safety guidelines and emergency procedures, as well as course-‐specific and activity-‐specific safety instructions provided by faculty and teaching assistants. Laboratory safety and emergency procedures will be reviewed during the first class period and you will be asked to sign your acknowledgement of these instructions before attending further classes in this course.
Americans with Disabilities Act (ADA) Policy
The Americans with Disabilities Act (ADA) is a federal anti-‐discrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires that all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact the Department of Student Life, Services for Students with Disabilities, in Cain Hall or call 845-‐1637.
Academic Integrity Statement
“An Aggie does not lie, cheat, or steal or tolerate those who do.”
Upon accepting admission to Texas A&M University, a student immediately assumes a commitment to uphold the Honor Code, to accept responsibility for learning and to follow the philosophy and rules of the Honor System. Students will be require to state their commitment on examinations, research papers, and other academic work. Ignorance of the rules does not exclude any member of the Texas A&M University community from the requirements or the processes of the Honor System. For additional information please visit: www.tamu.edu/aggiehonor.
