Directions: You will be working in groups (groups can consist of 1- 3 members) to prepare a 41 minute

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Genetic Engineering / Biotechnology

FINAL Presentation – Bio2H 2013-14

Directions: You will be working in groups (groups can consist of 1- 3 members) to prepare a 41 MINUTE presentation on your assigned topic.
TOPIC Selection: Once Groups are formed, we will RANDOMLY draw Topics. Once you have a Topic, it is yours unless another group agrees to Trade with You. If we have fewer groups than topics, I may merge some topics to try to get them all covered. The 8 topics are as follows:
TOPIC 1: Genetic Engineering in Agriculture

 Genetically Engineered (genomic/breeding interventions) Crops for resistance and greater yield / “Frankenfoods” – Processes Involved in Creation - Ex. Round-up Ready seeds or Cocoa Trees breeding intervention (selective breeding)

 Genetically Engineered Livestock/Transgenic Animals Ex. Cattle with Hormones/Proteins, Super Salmon, etc. (Focus is on Producing Greater Yields, Better Enriched Foods, Consumer Products, Proteins in Milk, etc.) – Process Involved

 Examples of GM foods (Genetically Modified) on the market today – Label Regulations

 Myths – Fact vs Fiction of what can be produced

 Use of Genetically Altered Foods for VACCINES/Medicines (Ex. Bananas,Rice)

 Arabidopsis as a Model Organism – What all has this agricultural species been used for in research labs??? Biodegradable Plastics and more…..??? (you can focus on ANY study/studies that Arabidopsis has been the MO for – this could be a whole college course!)

 Cauliflower Mosaic Virus – use of CMV promoter for Genetic Mod – Testing of Product for promoter sequence to ID foods that are Genetically modified – See me about trying to schedule a Saturday to go to Pitt to carry out a GMO Lab that uses this technique!

 Synthetic Meats?? Grown in Petri Dish or Bioreactors??? Popular Science – The Meat Lab – Nov 2013

TOPIC 2: “Central Dogma” – The Human Genome Project AND the other “-OMES”!!!!!!

 History/Completion of the Human Genome Project – When/timeline of completion(History)? Dr. Francis Collins? What has it revealed? Why was it just the START?? How it now ties to ENCODE – ENCyclopedia Of Dna Elements? Good for Introduction with timeline of the other -OMES!

 DNA Sequencing - The process – Many Different Versions? Chain Term Sanger vs Dye Term Sanger using DNA Cycle Sequencing / Dideoxynucleotides – used for HGP. The Next Generation Sequencing – Ex. Ion Torrent sequencer (semi-conductor technology) – how it works! Explain the procedure of How DNA is Sequenced! This is a GREAT area to do an Audience Interactive Activity to Demonstrate the Sequencing Process after teaching the Technique!!! The Dye Terminator Sanger Method is HOW they were able to Sequence the DNA for the Human Genome Project! There are other Sequencing Techniques too (they may get too confusing, so you can be the judge – avoid the early sanger method and stick w/ the dideoxy-method used for the HGP – add on Next Generation Seq only as extra, but be sure to cover method used for HGP)!

 The OTHER “-OMES” Transcriptome? Introme? Exome? Proteome? Interactome? Epigenome? Methylome? Microbiome? = What are they??? Why are they MORE CHALLENGING??? What will they tell us???? You can mention, but don’t go into much detail on the miRnome – it is topic #6. Also the HapMap (Haplotype) and GWAS (Genome Wide Association Studies) Projects!

 Other Organisms with Mapped Genomes and Significance of them???

 Model Organisms used to Study/ID processes of the Central Dogma (Transcripiton/Translation/Post-Transcriptional and Translational Modifications)
TOPIC 3: Microarrays / Biochips / DNA Chips (All terms for the same principle)

How they work!! There are GREAT On-Line Animations / Tutorials for this topic that can be used as part of your presentation. You can even get the audience involved in an enactment/demo of how they work too!!

 Their use in Diagnosis of Genetic Disease (support with one or a few specific examples), Personalized Treatment to Fit each Individual & Ethical Issues for their potential misuse.

 Different types of Array’s and how types reflect specific use (form = function)

 Connection to HapMap (Single Nucleotide Polymorphisms) and GWAS (Genome Wide Association Studies) finding Common Variants/Candidate Genes (Type II Diabetes/Chron’s/etc)

 HINT: Don’t make your ?’s too BROAD, really focus your questions in a step by step manner to cover the KEY Steps of the Technique so you can give your audience a SOLID Explanation of What they are, How they are Made, and How they are used, Different Types, Costs,etc.! You can even make a ? of your presentation a hands on activity to demonstrate the content covered in a previous ? or ?’s (Ex. Can you run an array???? – then have students in class do this!)

 If you feel you need additional content beyond MicroArray’s, you can also look into Bio-Informatics, New Generation Sequencing (Search: Ion Torrent – Life Technologies – Jonathan Rothberg - Illumina) and RT-PCR!!!

TOPIC 4: Cloning – Value of Clones and other Genetically Altered Organisms in Science!

 SCNT – Somatic Cell Nuclear Transfer (Process of SCNT for Reproductive Cloning and where Therapeutic Cloning Varies – this then ties into Topic 5)

 Successful Reproductive Cloning Experiments – From 1st Cloning experiments (Briggs/King/Gurdon) to Dolly (1st Mammal), Rat, Horse, Dog, Endangered Species? Etc. Why are they cloned????

 Explain outcomes/Successes (rates of success?)!! Are the clones Healthy or do they have problems from the process????? Ex. What are the RISKS of Cloning??? What is seen with the Telomeres/Imprinting/x-Inactivation in clones (are clones really a ”True” clone???) Genome vs. Epigenome?????

 Serial Cloning??? How many times can you clone a clone?

Transgenic Animals and Knockout Animals– What are they and how are they created? How are they used in Research / Industry???

 Xenotransplantation – Cloning of Pigs for Human Organs???? Is it possible?? What are the Risks/Challenges/Outcomes?

 In Vivo Organogenesis / Blastocyst Complementation (Ex. Rat/Mice Pancreas w/ iPSC’s or Human Pancreas in embryo of Pig using Human iPSC’s) – This is NOT the same as Tissue Engineering/Regenerative Medicine with Scaffolds (Topic #5)

 You may also wish to talk about the NEED For ORGANS and current Organ Donation Statistics/Success Rates/etc.

 How far have they gotten with HUMAN Cells / Embryo’s in the SCNT process????? Past Claims with Korean Team (Woo-Suk Hwang & Dr. Gerald Schatten from Pitt) and the controversy / Fraud! First Validated Nuclear Transfer Cloning – June 6, 2013 in Journal Cell???

 Others who have claimed to have Cloned a Human?? Clonaid (Raelians) – Out There???

 SCNT to derive ESC’s is part of Genetic Engineering History – iPSC’s are the FUTURE!

Watch getting too far into iPSC’s since it is part of Topic #5, but you can include it within a Question to point out WHAT the Process is and WHY it is Eliminating the need for SCNT in Humans. Note: SCNT Complications with Oocyte Retrieval, Cost, Teratomas, Ethics

 Synthetic Life?????? J. Craig Venter – What impact has and will this make?????

 Henrietta Lacks – HeLa Cells and their contribution to scientific research - Immortal Cells! You could do an entire presentation on HeLa Cell use and the history of Henrietta Lacks, but keep this to One ? if you decide to include this!

 Be Careful NOT to venture into Therapeutic Cloning – That is another topic!

TOPIC 5: Therapeutic Cloning AND Stem Cell Therapy (Focus on use for Organ/Tissue Replacement)

 Technique of SCNT (Somatic Cell Nuclear Transfer) to provide embryonic stem cells – Do this as a quick overview since Topic 4 already addresses the process of SCNT for Reproductive Cloning – If Topic 4 is not being done by another group, you may have to add more detail – check with me. This would work well incorporated as part of the introduction to save the ?’s for the New Info.

 What are the Different Types of Stem Cells??? Embryonic, Adult (HSC/MSC/ESC/NSC), iPSC’s, Cancer Stem Cells, Amniotic Fetal Stem Cells, and associated Terminology (totipotent, pluripotent, multipotent, differentiation, dedifferentiation, stemness etc.) AND What is the SOURCE/Mode of Isolating each Type??

 Move AWAY from SCNT to creating iPSC’s (Induced Pluripotent Stem Cells) in order to create ORGANS for Transplant or Disease in a Dish Models (Key= Autologous / Self Genetic Match)

 Potential use of Stem Cells to create tissues in order to form or repair ORGANS. Ex. Bladder, Cornea of Eye, Heart, Vessels, etc.

 Jamie Thomson – University of Wisconsin – work with ESC’s and iPSC’s and Yamanaka with iPSC’s (Nobel Prize Yamanaka and Gurdon -2012)

 Use of Adult Stem Cells and/or iPSC’s for Organs / Regenerative Medicine (Ex. Skin from circumcision for bandages, Bone Marrow used to Repair the Human Heart, Pixie Dust Finger Regeneration, and MSC’s for Trachea, Heart Vein, Knee Joints……..!!!!)

 Biodegradable Scaffolds for Organs (Decellularization Process in connection to Tissue Engineering/Regeneration)

 iPSC’s for Sickle Cell, Parkinson’s, ALS, MD, Type1Diabetes, SCID, Retinitis Pigmentosa

 Organoids????? Nature August 8th 2013 – Generation of Inner Ear sensory epithelia via 3-D culture “Oraganoid” – Indiana University Other Examples: Man Made Teeth, Optic Cup, Liver, and Cerebral Organoids

 Dr. Atala / Wake Forest Institute for Regenerative Medicine.- Regenerative Pharmacology

 Human Embryome Project – find all 220 sets of signals!!!

TOPIC 6: RNAi – RNA Interference: The miRNome and Gene Control!!!

 History of Discovery / Nobel Prize Physiology & Medicine 2006– background of Fire/Mello and their Research and what this has meant to the scientific community – their work with C. elegans (simple roundworms as the MO)

 What is RNAi?? Terminology – Types Involved (sncRNA, dsRNA, ssRNA, shRNA, miRNA, siRNA, etc)  How Does it Work??? Interference with Translation (On/OFF Switch) – Mechanism (Enzymes used in pathway – DICER, RISC, Ago, etc.) = Gene Control Mechanism that overrides the Promoter Control (even if coding gene ON with Promoter, can still act on mRNA transcript to turn OFF)

 Two Mechanisms: siRNA and miRNA – How do they differ??

 Applications for Disease – Give Specific Examples of how it can be used (current research results – HIV, SARS, Huntington Disease, Certain Cancers etc.)

 Use in Hypertrophic cardiomyopathy (HCM) – HHMI Investigator Christine Seidman – study in mice

 Natural Examples of RNAi in our bodies to see how they work / why they exist (Ex. ONCO-miR’s = miRNA’s that can act on Tumor Supressor Genes – Ex. Chronic Lymphocytic Leukemia)

lnc RNA’s (long Non-Coding) and lincRNA (Long Intergenic Non-Coding) Gene Control = another form of RNA CONTROL!!!

 If SHORT on Information, you can add “PNA’s” to your topic. PNA = Peptide Nucleic Acids – What are they and How are they being used???

TOPIC 7: Pharmaceutical Products and Gene Therapy (Treatment/Potential Cures for Genetic Diseases)

 Pharmaceutical Products produced by Recombinant DNA technology in a host Organism. Ex. Insulin & Interferon in Bacteria, Clotting Factor, Human Growth Hormone, etc. Be sure to expand on what we discussed in class! What other examples???

RNA based drugs / Ribozymes / Exon Skipping Drugs – Clinical Trials/Problems/Potential/etc.

 Gene Therapy Invivo (insert gene directly into person / transfection) or Ex-Vivo (Extract WBC’s, Insert Gene, allow mitosis to occur, insert back)

 What are some of the Vector’s being used in Gene Therapy (Ex adeno-associated virus, lentivirus, naked plasmid, artificial chromosomes, liposome) and How are they being used??? What are some potential problems with their use? NOTE: There is a great Vector Toolbox Animation Site used by students in the past for research!

 Use of Gene Therapy to cure / prevent / treat genetic diseases Ex. SCID’s (using moloney retrovirus – Exvivo), Hemophilia B, Duchenne & Becker Muscular Dystrophy, Deafness, Blindness, Huntington Disease, Adrenoleukodystrophy (ALD)

 Leber Congenital Amaurosis Type 2 – LCA2 – RPE65 Gene with AAV vector – Nov 2009

 PCSK9 gene???? Why is it a hot target for pharmaceutical companies??

 RNAi’s – This is actually another topic (#6), but can be incorporated under Gene Therapy – focus on the details of a specific use / therapy with RNAi’s for this – Ex. siRNA gene Silencing to turn off the Huntingtin Gene

 Genetic Medicine VS Genomic Medicine (New trend to use Microarray’s/SNP’s to treat multifactoral/polygenic diseases)

 Regenerative Pharmacology – Disease in a Dish Models (May overlap Topic #5, but OK)

 Additional Resources: Genomic Medicine – Holiday Lecture 2013 AND “The Forever Fix” – Gene Therapy book by Ricki Lewis

TOPIC 8: From the Fertilization Process and Fetal Origins to Designer Babies and Aging –What does it mean to Future Generations!

 Using knowledge of Genetics to Create Children with Desired Traits and Desired Gender – Uses for ENHANCEMENT

 Fetal Origins (Time Oct 2010 and CNN Toxic America) – Environmental Effects on Fetal Dev/Epigenome Connection/Epigenetic Inheritance (Agouti Mice / Human - Swedish Study / Dr. Perera at Columbia)

 IVF and ICSI – The process and how it is connected to Designer Babies! What do they do with unused Embryo’s??

 Checking the Fetal Genome: Amniocentesis, CVS, PGD, Blastocoel Cavity DNA analysis, Fetal DNA in Maternal Serum

 The Science of Genetic Disease Screening: PGD, FISH, SNP/CNP + Why??? Examples of HOW and Actual Cases

 The Science of Sex Selection/Screening: Microsort, Ericsson, etc + Why???

 iPSC’s Potential – Creating Spermatids from Skin (male infertility fix) or Oocytes (female infertility fix) – Egg Engineers – nature, August 22, 2013 pg 392

 Human Embryome Project – find all 220 sets of signals to alter stem cell differentiation!!!

 Oocyte Stem Cells – Women can procreate forever! Nature Medicine – March 2012

 What genes, along with gender, are at the forefront of this topic?? Note: Complication due to Multifactoral Genes/Polygenes etc????

 Actual Applications/Documented Cases = Families using these techniques to have a designed child / pre-selected child to save a child! AKA: Survivor Siblings

 Longevity – Anti-Aging Drugs = mammalian TOR – Telomeres – etc?????

Presentations will go in the order that the topics are listed in!!!!!

(The only adjustment will be if a Group with Seniors NEEDS to present sooner due to graduation or if there is a Sporting Even Competition we must work around – Track and Crew??)

You will be given a brief amount of CLASS LIBRARY time to DO INITIAL RESEARCH on your topic and to get as much CURRENT INFORMATION as you can. The Information that I gave under each topic is just to GENERATE ideas and provide a direction for your research. You DO NOT have to use all of the examples that I gave, but they will be helpful in starting your search. Between the initial RESEARCH DAYS and the PRESENTATIONS, I will give a few additional class days so that your groups can assess what has been done and what needs to be done. Since this is YOUR FINAL for THE CLASS, you will need to complete the MAJORITY of the Research/Compilation on your OWN TIME. You will have plenty of time to set up meetings with your group. You are always welcome to meet in my room or go to the after school library hours.

You will NOT need to include a Bibliography – I trust you to use credible cites. Your Book has some basic info to reference, but you must expand your research to Online Sites, Journals, Personal Contacts, GUC Notes, etc!
Requirements of Presentation:
1. Your group will be responsible for teaching a full 41 MINUTE Class Period on the assigned topic.
2. Each group member will be responsible for addressing ONE or TWO QUESTIONS on the topic (See SPECIFICS #2 – it Matches the Grading RUBRIC) NOTE: Single Member Groups will follow a 2 member group format!
3. You must START off the presentation with an INTRODUCTION that describes the topic AND engages your audience, but also shows signs of research/new content (See SPECIFICS #2 for this)
4. You must END the presentation with a CONCLUSION. The conclusion must FOCUS on the ETHICS of your topic (unless that was the focus of one of your Questions). You should also end with a defined statement on what your topic may mean to us in the future??!!??!! (See SPECIFICS #2 for this)

1. As a GROUP, you should gather as much information as possible. Once you have all looked over the information, come up with a direction you would like to take your topic in. You will probably find enough information that you could teach weeks on your topic, so you will have to BE SELECTIVE and choose what interests you the most. Don’t try to tackle something too big – focus your questions!!! Be sure to Follow the RUBRIC FORMAT for your Group Size!
2. Each group member should then formulate TWO QUESTIONS that they would like to address and answer based on the information found.
IN GROUPS OF FOUR (Not permitted 2013 due to class sizes): Two group members will only formulate ONE QUESTION because they will then be doing EITHER the INTRODUCTION or the CONCLUSION. The other group members will formulate TWO QUESTIONS. The Introduction & Conclusion should be VERY INFORMATIVE / Detailed (It should actually address a ? itself) since each will be the soul responsibility of 1 of the group members. For the Introduction, an activity, demo, or Q/A engagement would work well!! I am Looking For more than stating your topic and the order of your presentation for an introduction – I want something that Informs/ENGAGES/Captures your audience and is equivalent in value / information to the other Questions!!!
IN GROUPS OF TWO or THREE: EACH group member will formulate TWO QUESTIONS and the group can JOINTLY work on the INTRODUCTION and CONCLUSION. Since Each Group Member already has 2 ?’s to present, the Introduction and Conclusion can be Shared By ALL Members (or done by just one if that is what your group chooses). It should still be INFORMATIVE/show evidence of research and new content, because it does carry the SAME point value as an individual ? –an activity, demo, or Q/A session can be part of the intro!! I am Looking For more than stating your topic and the order of your presentation for an introduction – I want something that ENGAGES/Captures your audience and is equivalent in value to the other Questions!!! In the past, some groups have even done an animoto intro.
NOTE: The Intro., Individual ?’s, and Conclusion will Act as Your OUTLINE for the Presentation. You will be responsible for Specifically STATING each of the QUESTIONS clearly in your presentation and then answering them. It is ESSENTIAL to Follow this Set-Up since it MATCHES the GRADING RUBRIC!!! (See Grading Rubric for your group size)
3. Each Group MUST compile all of the questions onto a handout for the class so that they can use it to take notes on during your presentation. This sheet should include the following titles in BOLD with space for NOTES after each: INTRODUCTION, ? #1-XXXXXXX, ?#2-XXXXXXX, ?#3-XXXXXXX, ?etc., Conclusion. /Be sure to also LIST the Group Members NAME next to their ?/Intro/Conc. I will run class set copies of this for you as long as I have it 2 DAYS PRIOR to your presentation. This goes for any Handouts you would like me to make copies of!!!
4. You must be sure to get feedback from your audience to be sure that they are paying attention. EACH MEMBER of your group must generate a minimum of 3 Audience Feedback Questions that will be asked pertaining to the Intro, ?’s, or Conc. that you present. Be creative on how and when you ask the questions – Make it a game, do it after each new ?/sub-topic is presented, do it at the end of the whole presentation, give rewards (try to make it a Healthy Treat), make it a test, etc. Be Creative!! (I will keep track of the audience and record every time a student answers a ? – all students must answer at least 2 questions during all of the presentations or 5pts/unanswered ? will be deducted from their individual score on their Presentation!! Note: IF absent, your chance to answer ?’s drops – Seniors are excluded!!) These Audience Feedback ?’s are NOT your MAIN ?’s that establish your outline. They are being included to ensure audience participation and will be part of each group member’s individual score.
The Actual Presentation:
1. Must fit the FULL 41 minute class period.
2. ALL group members must PRESENT their OWN Intro/ QUESTION(S)/Conc according to Specifics #2 = Also SEE your RUBRIC!!!!
3. Each group MUST PROVIDE a HANDOUT for the CLASS with the required information. (See Specifics #3)
4. Each group MUST PROVIDE the TEACHER with the SAME HANDOUT, but also INCLUDE the ANSWERS + Which Group Member is Presenting Each ?/Intro/Conc!!! This will allow me to focus on your presentation and also have a hard copy to review afterwards. The Answers should be a BULLETED List of the key points, NOT a script of your presentation!!!!
5. You must also INCLUDE a minimum of 2 VISUAL-AIDS along with the ? HANDOUT. (This could include diagram handouts, props, models, photos, video clips, etc.) There will be a specific scoring category for this!!! This is 2 for the Entire Group! If you need to use CANDY in a demonstration, it is acceptable under our Health Guidelines since it is being used in an educational manner. Ex. Colored M&M’s for a MicroArray Demo, Pull Apart Twizlers for DNA Demo, etc. The MORE VISUALS the BETTER as long as they ENHANCE your presentation!

6. BE CREATIVE!!!!!! You may present on the Promethean Board using PowerPoint, Photostory, Animoto along with the option of using the white board, posters, TV/Movie or Documentary Clips, etc. It is up to your group to choose the way you feel most comfortable with. You can also use a variety if some group members prefer one way to another. NOTE: If you do use PowerPoint DO NOT just place up your notes and read them to us!!!!!!!!!

7. You will be provided with a grading rubric to SUPPORT the IMPORTANCE of Following my instructions on HOW to organize your presentation. The RUBRIC Grading Format strictly follows the Set-Up of your presentation.
8. See me if a GROUP MEMBER is NOT pulling their weight!! I will ask for ALL Group Members to do CHECK-POINT Evaluations to also keep me informed on who is and is NOT Contributing! Be HONEST!!!!!!!!!!
NOTE: Do NOT wait until the Day Of your Presentation (OR, after your Presentation) to tell me this!!!!! IT will be too late to make any adjustments – I need to know as soon as possible so that we can take appropriate actions.
Also, There is an area of the grade where you get to score your group members on a scale of 1-10 for their contributions to the group. Be sure to be honest – it will be done anonymously after your presentation.


START YOUR PRE-RESEARCH ASAP!!! I will give you a DATE when I need your group to turn in an OUTLINE of your INTRO/?’s/CONC so that I can give you my feedback and suggestions to make sure you are on the right track! At that point, you can still make changes, but I want to be sure you are all following the proper format and that all group members know what individual parts they are responsible for.

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