Honors Proposal: Genetics (Biology III) Proposal: Due to the inherent complexity of the science of genetics and its similarities with other honors classes we propose that it be granted an honors point. Genetics naturally blends the information that students have acquired in their introductory classes in biology, chemistry and math and requires that they apply it using high level critical thinking skills and problem solving strategies. The same skill set is required for success in both honors classes and genetics: independent thinking, multi-dimensional problem solving, good communication skills in both writing and speech, and the ability to read complex text. Genetics is cutting edge science. Students with career goals in the areas of biology and medicine, including forensics, nursing, technicians, bioinformatics, proteomics, pharmacy and similar fields will spend a large portion of their academic and professional careers in the area of genetics. Although all courses should strive to incorporate cross-curricular standards, blending math, literacy, and science; Genetics accomplishes this naturally and at a very high level. In addition, students are presented with scenarios that also factor in ethics and cultural traditions. Genetics students are expected to apply complex content in combination with ethics to analyze and propose solutions for real world problems. Their ability to consider both the moral and the factual side and to express their rationale for possible solutions requires well developed verbal communication. Comparison of Genetics and current Honors Classes Lexile levels: The Genetics textbook has a Lexile measure of 1300 and the Honors Chemistry textbook has Lexile of 1230, and the Honors Biology textbook has a Lexile measure of 1200. The typical reader level for 11-12 grade students is 940-1210. Formal Laboratory Reports: Genetics, Honors Biology, Honors Chemistry all require formal laboratory reports; this is not required in general level core classes or other science electives. Statistical Analysis: Genetics requires the use of probability rules, null hypothesis, Hardy Weinberg Equilibrium, and Chi Square analysis. These statistical methods are also used in AP Biology, AP Statistics, AP Chemistry and to a lesser extent in Honors Biology and AP Psychology. Laboratory: Genetics performs some of the same laboratory activities found in AP Biology, but the labs completed in Genetics are taken several steps further than required in AP Biology. One example is bacterial transformation, in which the steps go beyond the original lab and extract the protein to perform column chromatography. Another example is gel electrophoresis. Students get to experience the process of gel electrophoresis in AP Biology, but in Genetics the students master the process as it is repeated in several different contexts. This allows them to be more familiar with the many uses of electrophoresis including nuclear DNA analysis, mitochondrial DNA analysis, and protein analysis. Protein Synthesis: All Life Science classes learn about protein synthesis. In Genetics students model protein shape and look at the effect of amino acid chemistry on the three dimensional folding of the protein and how this structure affects the function of the protein. This is college level content. Examples Below are examples of a few of the lessons and projects that are conducted that require students to collaborate, think critically, and communicate their new information. These represent typical lessons and demonstrate the complexity of the content of the course. Examples are enclosed. 1. Bioinformatics: (Common Core SL.11-12.4, MP.4, WHST.9-12.7, WHST.9-12.2, RST11.12.8; Next Generation Science Standards: HS-LS1-1, HS-LS3-1, HS-LS4-1, HS-LS4-3.) Bioinformatics is the science of understanding the information encoded in DNA and other biological molecules. This is the intersection of Genetics and Computer Science. We are currently developing more bioinformatics in this class, since this is currently an expanding area of biology. The following is taken from a laboratory entitled Whales, Walruses, and Seals, Oh My: ln this lab activity, we will use sequence information in GenBank (the public repository of known DNA sequences from many species) and bioinformatics software to test hypotheses about the relationships between aquatic mammals (seals, whales, dolphins, walruses, manatees and sea otters) and their potential ancestral relationship to land mammals. We will use a protein that all mammals share: the hemoglobin beta protein. Hemoglobin is a good test molecule since it shows conservation across species (since it carries oxygen in the blood) as well as variation between species. Species with unique challenges such as holding their breath for long underwater dives may have evolved changes in their hemoglobin, which improved their supply of oxygen. ln addition, hemoglobin has been studied by many evolutionary biologists, so sequences are available in GenBank (a public access online genetic database) from many different species. Procedure ln this activity, you will be testing hypotheses about the evolutionary ancestry of different marine mammals. To repeat: you are trying to answer the question "Did marine mammals evolve from a single ancestor who returned to the ocean, or were there distinct return events from separate ancestors?" As a starting point, let's hypothesize that marine mammals have a single common land mammal ancestor... (Additional excerpt attached.) 2. Lab: Secrets of the Rainforest: (Common Core: RI.11-12.3, SL.11-12.1, SL.11-12.4 ; Next Generation Science Standards HS-LS3-1, LS3.A, LS4-1, RST.11-12.9, SL.11-12.5) Secrets of the Rainforest provides a biotechnology experience that takes students on an adventure starting in the rainforest in the Andes, continuing to a biotechnology company engaged in developing new pharmaceutical compounds, and on to the Food and Drug Administration and finally developing a marketing plan to take the protein to market. Objectives: ● Applies the principles of DNA restriction analysis, bacterial transformation, and protein purification ● Introduces students to the world of commercial biotechnology Lab Skills conducted: ● Students must grow a bacterial library ● Students must clone a gene of interest in bacteria ● Students must identify the expressed protein of interest in bacteria ● Students must purify a protein of interest from bacteria using chromatography ● Students will Simulate taking a protein to market How It Works In the hands-on portion of the exercise, students streak out the bacterial library, grow the bacteria, and select the colonies that have acquired the green glowing trait from a background of non-glowing bacteria. A culture of bacteria is grown to scale up production of the green glowing protein, which is then purified by column chromatography. The source of the gene for this fluorescent protein is the bioluminescent jellyfish Aequorea victoria. This practical activity is followed by dry-lab lessons in which the purified green protein is put through the drug discovery process. This includes learning about Food and Drug Administration regulations, animal testing, marketing practices for introducing a new drug, financing, ethical issues, and student presentations. Students examine the needs and viewpoints of advocacy groups, the biotechnology industry, and the FDA. They consider ethical, economic, social, and practical issues, and develop possible strategies for drug development. (Excerpt from manual attached.) 3. Research project (HS-LS3-2, HS-LS3-3, HS-LS4-1) (rubrics attached) Students choose a topic of interest to them such as the genetic cause of a disorder, the use of genetics in a field or profession, or the steps of a specific process such as making a genetically modified organism. To complete their research project students are required to: a. Write an Annotated Bibliography using appropriate resources including at least 2 scientific journals. (Common Core: RST.11-12.1, WHST 11-12.9) b. Teach their content to their class. Presentation options include Photostory, GoAnimate, Powerpoint with Voicethread, Prezi, and Smart Notebook. (Common core: SL.11-12.5, RST.11-12.9) c. Learn and discuss content from their classmates’ presentations. The key to success for students completing this project is reading scientific journal articles, usually current primary research. This is especially necessary for students studying the genetic cause of a particular disorder because such information is usually very new. For students to comprehend the current scientific literature, they must reach a college level of understanding of the genetics at the molecular level. For example, the vast majority of students choose to research a particular disorder. To meet the requirements of the project the student must identify which gene(s) have been mutated and explain how this altered a protein in the cells of the affected individual and then connect that to the trait. They must teach their classmates how a change in the DNA sequence led to the symptoms of the disorder. This means that the students read, present, and discuss genetics at the biochemical, molecular, cellular, and whole body level. 4. Lab: Mitochondrial DNA PCR: (Common Core: WHST.9-12.7, WHST.9-12.1, HS-LS4-1) In this experiment, the polymerase chain reaction (PCR) is used to amplify a small portion of each student’s mitochondrial genome. This experiment allows students to visualize a small region of their own genetic material. Students who are successful are able to send their sample to a lab to have the sequence of their own DNA determined. Once the sequence is returned, a second laboratory this time a bioinformatics laboratory using computers is employed to determine student relationships to each other, other human groups, and even Neanderthals. Summary There are many students who would benefit from the content of this genetics course but miss out on this opportunity because it is not designated as an honors course. We are requesting that the Genetics course be granted an honors point to encourage enrollment in this challenging course for students with goals in biology or Allied health fields. The honors point will provide that added incentive for taking a course that requires students to work at a college or professional level. At the same time, changing the course to an honors level will not require any increase in rigor, so it should not become less accessible or exclude those who have traditionally taken the course. Common Core Standards referenced above. ELA/Literacy: RST.11-12.1 Cite specific textual evidence to support analysis of science and technical texts, attending to important distinctions the author makes and to any gaps or inconsistencies in the account. RI.11-12.7 Integrate and evaluate multiple sources of information presented in different media or formats (e.g., visually, quantitatively) as well as in words in order to address a question or solve a problem. RST-11.12.8 Evaluate the hypotheses, data, analysis, and conclusions in a science or technical text, verifying the data when possible and corroborating or challenging conclusions with other sources of information. RST.11-12.9 /WHST 11-12.9 Draw evidence from informational texts to support analysis, reflection, and research. SL.11-12.4 Present claims and findings, emphasizing salient points in a focused, coherent manner with relevant evidence, sound valid reasoning, and well-chosen details; use appropriate eye contact, adequate volume, and clear pronunciation. SL. 11-12.5 Make strategic use of digital media (e.g., textual, graphical, audio, visual, and interactive elements) in presentations to enhance understanding of findings, reasoning, and evidence and to add interest. WHST.9-12.7 Conduct short as well as more sustained research projects to answer a question (including a self-generated question) or solve a problem; narrow or broaden the inquiry when appropriate; synthesize multiple sources on the subject, demonstrating understanding of the subject under investigation. WHST.9-12.2 Write informative/explanatory texts, including the narration of historical events, scientific procedures/ experiments, or technical processes. Mathematics: MP.4 Model with mathematics. HSS-IC.A.1 Understand statistics as a process for making inferences about population parameters based on a random sample from that population. HSS-IC.B.6 Evaluate reports based on data. Next Generation Science Standards: HS-LS1-1 Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins which carry out the essential functions of life through systems of specialized cells. HS-LS3.A Heredity: Inheritance and Variation of Traits HS-LS3-1 Ask questions to clarify relationships about the role of DNA and chromosomes in coding the instructions for characteristic traits passed from parents to offspring. HS-LS3-2 Make and defend a claim based on evidence that inheritable genetic variations may result from: (1) new genetic combinations through meiosis, (2) viable errors occurring during replication, and/or (3) mutations caused by environmental factors. HS-LS3-3 Apply concepts of statistics and probability to explain the variation and distribution of expressed traits in a population. HS-LS4-1 Communicate scientific information that common ancestry and biological evolution are supported by multiple lines of empirical evidence. HS-LS4-3 Apply concepts of statistics and probability to support explanations that organisms with an advantageous heritable trait tend to increase in proportion to organisms lacking this trait. 1. Walruses and Whales and Seals, Oh My!! Walruses and whales are both marine mammals. So are dolphins, seals, and manatees. They all have streamlined bodies, legs reduced to flippers, blubber under the skin and other adaptations for survival in the water. Although mammals evolved on land, these species have returned to the sea, or were there different return events and parallel evolution? We can't go back in time to observe what happened, but DNA sequences contain evidence about the relationships of living creatures. From these relationships, we can learn about the evolutionary history of marine mammals. ln this lab activity, we will use sequence information in GenBank (the public repository of known DNA sequences from many species) and bioinformatics software to test hypotheses about the relationships between aquatic mammals (seals, whales, dolphins, walruses, manatees and sea otters) and their potential ancestral relationship to land mammals. We will use a protein that all mammals share: the hemoglobin beta protein. Hemoglobin is a good test molecule since it shows conservation across species (since it carries oxygen in the blood) as well as variation between species. Species with unique challenges such as holding their breath for long underwater dives may have evolved changes in their hemoglobin, which improved their supply of oxygen. ln addition, hemoglobin has been studied by many evolutionary biologists, so sequences are available in GenBank from many different species. Procedure ln this activity, you will be testing hypotheses about the evolutionary ancestry of different marine mammals. To repeat: you are trying to answer the question "Did marine mammals evolve from a single ancestor who returned to the ocean, or were there distinct return events from separate ancestors?" As a starting point, let's hypothesize that marine mammals have a single common land mammal ancestor. Part A First, you will explore the relationship of the marine mammals to each other vs. their evolutionary relationship to land mammals. To do this, you will test whether seals and whales are more closely related to each other than either of them are to representative land mammals: dogs (land carnivores) or cows (land herbivores). This exercise will mainly train you in using the bioinformatics software. Part B Second, each pair of students will then develop a cladogram (an evolutionary family tree) which includes a selection of marine mammals and land mammals which represent the major mammalian orders. You will then use this phylogenetic tree to test our hypothesis that all marine mammals have a single common land mammal ancestor. Part A: Finding Amino Acid Sequences 1. First you need to get the sequence data for the hemoglobin protein from our marine and land animals: seals, whales, dogs, and cows. Go to GenBank, a DNA and protein sequence database hosted by the National Center for Biotechnology information (NCBI) in Maryland at: http://www.ncbi.nlm.nih.gov/genbank/ (Note: you can also Google "GenBank" and it will always come up as the first link) 2. The hemoglobin beta gene and protein is known as "HBB" in GenBank. In the "Search" window (top left), select "Protein" from the pull down menu, because we want to compare the amino acid sequence from each animal for this protein. We need to be specific about the identity of each animal, so we will use the harbor seal, the minke whale, Canis familiaris (dog), and Bos taurus (cow). Type in the protein you are looking for and hit "Go". 3. The search result is a page with a lot of information about the protein from this organism. To see the actual amino acid sequence for this protein, click on the "FASTA" link near the top of the page. 4. The FASTA page presents the amino acid sequence of the protein in a coded format using single letters to represent each of the 20 amino acids (A = alanine, M = methionine, p = proline, etc.) Copy the amino acid sequence. You must include the header line, starting from the greater than symbol (>). THIS IS IMPORTANT!! 5. Paste the amino acid sequence into a new Google Docs document. See below (next page). 6. Go back to GenBank and collect the amino acid sequences for the HBB gene from a minke whale, Canis familiaris, and Bos taurus. Paste these sequences onto separate lines in the same Google Docs document as the first sequence. If multiple sequences show up, use the first one. 7. Once you have collected all your sequences, you need to edit the files a bit to make your phylogenetic tree read more clearly. Look at the sequence header at the top of each protein sequence you have copied into the Google Docs document. The species the title that will show up on your tree will be the first line of each set of sequence data following the ">" symbol. So right now, your tree will say things like "gi[122664]sp[P09909.1". That won't make a lot of sense! This header can be edited for clarity, but you MUST preserve the “>” symbol!! You can use the scientific name or the common name to identify your sequence. For example: >harbor_seal VHLTGEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSADAIMGNPKVKAHGKKVLNSFSDG LKNLDNLKGTFAKLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAHKYH Align Your Sequences 1. Open the following link in a new page http://www.ebi.ac.uk/Tools/msa/tcoffee/ This is where you will compare your sequences amino acid by amino acid. 2. Copy and paste your sequences into the box on the T Coffee page. Create Your Tree 1. Click on the "Guide Tree" button at the top of your alignment 2. Once your tree appears, click on the "Show as a Cladogram Tree" button. 2. How Can Jellyfish Shed Light on Biotechnology Education? One of the biggest challenges for those studying molecular biology for the first time has been that many of the events and processes they study are invisible. The Biotechnology Explorer offers a novel solution: a unique gene and its Green Fluorescent Protein (GFP) which glows with a brilliant green color when viewed with the light of an inexpensive hand held ultraviolet lamp. The gene for the fluorescent green protein was originally isolated from a bioluminescent jellyfish. The jellyfish gene has recently been cloned into Bio-Rad’s exclusive pGLO plasmid specifically for use in Biotechnology Explorer kits. Using the pGLO system, students become genetic engineers, transforming bacteria (Bio-Rad Kit 1) and producing and purifying fluorescent recombinant proteins (Bio-Rad Kit 2). They can directly observe the results of gene transfer, gene regulation, gene expression, and the process of protein purification as they are occurring. Bio-Rad’s pGLO system is unique, and generates excitement and creative teaching applications among science educators. Secrets of the Rain Forest Secrets of the Rain Forest provides a two-week biotechnology curriculum which takes the students on an adventure starting in the rain forests in the Andes, on to a biotechnology company engaged in developing new pharmaceutical compounds, and finally to the Food and Drug Administration. The adventure begins as Tisha is hiking through the rain forest, looking for unique plant species, when she meets a native boy who tells her about an old medicine man with mysterious green leaves which have the power to treat and cure stomach cancer. The boy gives Tisha a bottle with a few of the leaves which she takes back to Biotex, a fictitious biotechnology company working on developing new compounds to treat human diseases. At Biotex, Tisha notices that the mysterious leaves glow bright green under ultraviolet lights. Other scientists at Biotex determine that the fluorescent green substance is a protein with possible therapeutic powers. During the first week of this curriculum, students play the role of Biotex researchers and learn about removing the DNA that produces the protein from the leaves and inserting it into bacteria cells. Students purify a green fluorescent protein (GFP) from bacteria containing a cloned gene for GFP. The gene is said to come from mysterious fluorescent green leaves which can cure stomach cancer. In the second week (Lessons 7–10) students simulate the real world process of taking this medicinal protein to market as a treatment for stomach cancer. They will examine the needs and viewpoints of advocacy groups, the biotechnology industry, and the Food and Drug Administration (FDA). Given real life scenarios, students will develop possible strategies for problem-solving. This portion simulates true biotechnology in action. In order for students to gain the most from this module, they should know what a gene is and understand the relationship between genes and proteins. It is not necessary for students to understand the details of cloning to be successfully involved in this module. Ron Mardigian Education Programs Manager Bio-Rad Laboratories 1-800-424-6723 ron_mardigian@bio-rad.com 3. Human Genetics Quarter Projects 1. Choose a specific topic such as a genetic disorder, genetics career, or genetic process that interests you. For instance, is there any medical condition in your family or that someone you know has experienced and you would like to know the genetic cause? Have you been interested in knowing what it would take to make a glowing cat or a pig with more human-like organs to use for transplant? Are you curious about the use of stem cells and want to better understand? Get your topic approved by your teacher. 2. Find your sources and produce an annotated bibliography. Follow the librarians recommendations to find at least 5 reliable and appropriate sources of information over your topic. You will produce an annotated bibliography with the guidance of your teacher and librarian and through this process your information will be reviewed and your sources approved. 3. Organize your information into a presentation that you can use to teach your classmates what you have learned about your topic. Appropriate formats include Smart Notebook, Powerpoint (with Voice Thread as an option), GoAnimate, Photostory, Prezi, Windows Movie Maker, and you may suggest other formats. Notice that several options involve voice recordings, which allows students to avoid presenting live. There is still a question and answer session after the presentation plays in the classroom. 4. Write 4 questions that you expect your audience to be able to answer after your presentation. The question should be easily answered in 2 sentences or less. Examples of appropriate questions would be: a. How is this trait or condition inherited? b. What is the heritability of this trait and what environmental factors influence it? c. What are the uses of this technique? d. What questions can be answered using genetics in this field? e. What is the normal job of the protein that causes this genetic disease? f. How does this type of mutation occur? Turn these questions, with answers into your teacher via e-mail or on paper prior to the presentation. 5. Present your topic to class. Review your main points. Answer questions from the audience. 6. Take notes over your classmates’ presentations. 7. At the end of the presentations period, students take an open note quiz over all the presentations. Genetics Quarter Project Rubrics (Students choose one of three categories below for each project.) Objective: Students will research a topic in the field of genetics, such as a genetic disorder, the genetics of a specific trait, the steps of a genetic process, or the use of genetics in a particular field, and teach their new knowledge to their classmates. Option 1: Genetics of a disorder (Ex: Alzheimer, Schizophrenia, Muscular Dystrophy, Diabetes, etc.) Presentation Points Topic: __________________________________ Total # Slides: ________ Possible Introduction Topic/Title Slide Captures audience attention (statistics, dramatic images, an explanation about why you chose this topic) Background information What? (symptoms/description of trait(s) When? (onset in early childhood, adolescence, adulthood? Lifespan?) Who? (gender or ethnic differences if applicable) Information has a logical flow and is easy to follow Information is explained in easy-to-understand terms, in speaker’s own words (not read from science source directly) Enough details provided to give audience a clear understanding of the topic Speaker is teaching audience about their chosen topic Review main points with class (your 5 questions) Presentation is neat and contains few grammatical errors References included in APA format (minimum 5, last slide) Presentation is completed on time save in i-drive in class folder or e-mail to jessica.rowe@fhsdschools.org 5 questions over your topic turned in to class folder by due date Points Earned (15 pts) (15 pts) (10 pts) (5 pts) (15 pts) Content (Unique requirements for each category/topic type) 1. Genetics of a trait or disorder Specific gene(s) are identified, location on a chromosome, type of mutation variety in the population normal function of the protein explained effect of the mutation explained in reference to protein explain the effect in the cell (what is different due to the mutation(s)?) Link between the gene, protein, and symptoms clearly explained Ongoing research, treatments, and/or unanswered questions are identified. Adequate information is given for the audience to gain a clear understanding of how the gene(s) determine the trait. Points Possible (30 pts) (5 pts) (5 pts) Points Earned Option 2: Uses of Genetics in a field or profession (Examples: Zoology, Archeology, Military, Forensics) Presentation Topic: __________________________________ Total # Slides: ________ Introduction Topic/Title Slide Captures attention of audience Background information What question is genetics used to answer in the field? What are the applications/significance of the field? Who works in the field? What education, training, or background is required? Information has a logical flow and is easy to follow Enough details provided to give audience a clear understanding of the topic Information is explained in easy-to-understand terms, in speaker’s own words (not read from science source directly) Speaker is teaching audience about their chosen topic Review main points with class (your 5 questions) Presentation is neat and contains few grammatical errors References included in APA format (minimum 5) Presentation is completed on time save in i-drive in class folder or e-mail to jessica.rowe@fhsdschools.org 5 questions over your topic turned in to class folder by due date Points Possible Points Earned (15 pts) (15 pts) (10 pts) (5 pts) (15 pts) Content (Unique requirements for each category/topic type) Uses of Genetics in a field or profession The relevance or importance of genetics for this profession is explained. Specific techniques or genetic knowledge used in the field/profession are explained to audience Education, background, or training required for profession Salary and daily tasks for a person working in this profession Processes, equipment, techniques Vocabulary specific to the field is used and explained Explanation of data/results generated in this profession Adequate information is given for the audience to gain a clear understanding of how genetics is used in the identified field or profession. Points Possible (10 pts) (20 pts) Points Earned (10 pts) Option 3 – Genetic Process (Examples: Genetic Engineering, Gene Therapy, DNA Sequencing, Epigenetics, Gene regulation) Presentation Points Points Topic: __________________________________ Total # Slides: ________ Possible Earned Introduction Topic/Title Slide Background information What is the purpose/goal of the process? What are the applications of the process? Who works in the field? (15 pts) Information has a logical flow and is easy to follow Enough details provided to give audience a clear understanding of the topic Information is explained in easy-to-understand terms, in speaker’s own words (15 pts) (not read from science source directly) Speaker is teaching audience about their chosen topic Review main points with class (your 5 questions) Presentation is neat and contains few grammatical errors References included in APA format (minimum 5) Presentation is completed on time save in i-drive in class folder or e-mail to jessica.rowe@fhsdschools.org 5 questions over your topic turned in to class folder by due date (10 pts) (5 pts) (15 pts) Content (Unique requirements for each category/topic type) 2. Genetic Process The purpose and uses of the process are identified and clearly explained The process Step-by-step description of the process Explain each step (how it works and why it is important) Equipment or materials used in the process Source of samples or materials Explanation of the data/results generated by the process The outcome of the process is clear and ways to interpret or test for the desired outcome are explained. Points Possible (10 pts) (20 pts) (10 pts) Points Earned