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AOHS Biotechnology

Lesson 5Model Organisms, Ethnobotany,

and Drug Development

Student Resources

Resource Description

Student Resource 5.1 Note Guide: Model Organisms Used in Biotechnology

Student Resource 5.2 Reading: Model Organisms Used in Biotechnology

Student Resource 5.3 Sample Selection: Plant Bioassay

Student Resource 5.4 Reading: Plant Bioassay Overview

Student Resource 5.5 Anticipation Guide: Pharmacogenomics and Personalized Medicine

Student Resource 5.6 Reading: Pharmacogenomics and Personalized Medicine

Student Resource 5.7 Online Research Guide: Pharmacogenomics and Personalized Medicine

Student Resource 5.8 Conclusion Writing: Plant Bioassay

Student Resource 5.9 Peer Review Rubric: Lab Report Conclusion

Copyright © 2014‒2016 NAF. All rights reserved.

AOHS BiotechnologyLesson 5 Model Organisms, Ethnobotany, and Drug Development

Student Resource 5.1

Note Guide: Model Organisms Used in BiotechnologyStudent Name:_______________________________________________________ Date:___________

Directions: Read the four questions in the table below. As you view the presentation on model organisms, take notes to answer the questions.

Questions Answers from Presentation

What are model organisms?

What characteristics make for a good model organism?



Questions Answers from Presentation

What are the two main ways model organisms are used?

You will be introduced to six model organisms. For each one, list one kind of research that uses that model organism.

1.

2.

3.

4.

5.

6.




Reading: Model Organisms Used in Biotechnology

This presentation describes model organisms and explains how they support the study of biological processes, including basic research as well as drug discovery and development.



The word model has many meanings, but in science, a model is a simplified system that is accessible and easily manipulated. A model organism is an animal, plant, or microbe that can be used to study certain biological processes.

Over the years, a great deal of data has accumulated about such organisms, and that makes them more attractive to study. Model organisms are used to obtain information about other species―including humans.

Many species are used as model organisms. Specific examples include E. coli, yeast, fruit flies, roundworms, mice, and other vertebrates.

Bacteria image courtesy Fabyv07; retrieved from http://commons.wikimedia.org/wiki/File:Bacterias.jpg on 7/3/14. Yeast image courtesy BMC bildes; retrieved from http://commons.wikimedia.org/wiki/File:Yeast_culture_plate.JPG. Drosophila image courtesy Mr. checker; retrieved from http://commons.wikimedia.org/wiki/File:Drosophila_melanogaster.jpg. All three reproduced here under terms of CC BY-SA 3.0 license (http://creativecommons.org/licenses/by-sa/3.0/deed.en).

Caenorhabditis image by NIH; retrieved from http://commons.wikimedia.org/wiki/File:Caenorhabditis_elegans.jpg. Squid image by NOAA; retrieved from http://commons.wikimedia.org/wiki/File:Loligo_pealeii.jpg. Mouse image by NASA; retrieved from http://commons.wikimedia.org/wiki/File:54986main_mouse_med.jpg.


http://commons.wikimedia.org/wiki/File:54986main_mouse_med.jpg

http://commons.wikimedia.org/wiki/File:Loligo_pealeii.jpg

http://commons.wikimedia.org/wiki/File:Caenorhabditis_elegans.jpg

http://creativecommons.org/licenses/by-sa/3.0/deed.en

http://commons.wikimedia.org/wiki/File:Drosophila_melanogaster.jpg

http://commons.wikimedia.org/wiki/File:Yeast_culture_plate.JPG

http://commons.wikimedia.org/wiki/File:Bacterias.jpg


In 1901, fruit flies were identified for their usefulness in genetic research by Charles W. Woodworth of Harvard University. This kind of fruit fly (Drosophila melanogaster) was the subject of genetics experiments housed in Thomas Hunt Morgan’s famous Fly Room. Morgan was awarded a Nobel Prize in 1933, and since then Drosophila has been used for the study of several medical conditions, including Parkinson’s disease, Alzheimer’s, and various types of cancer. This early work in genetics research laid the foundation for modern genetics based on a new understanding of genes and chromosomes in biological science.

Today, most universities and genetic research centers have a fruit fly research department where the flies live in well-controlled stacks of temperature controlled vials.

Fruit fly image courtesy Andre Karwath; retrieved from http://commons.wikimedia.org/wiki/File:Drosophila_melanogaster_-_side_%28aka%29.jpg on 7/4/14 and reproduced here under terms of CC BY-SA 2.5 license (http://creativecommons.org/licenses/by-sa/2.5/deed.en). Thomas Hunt Morgan image (author unknown) retrieved from http://commons.wikimedia.org/wiki/File:Thomas_Hunt_Morgan.jpg. Fly Room image courtesy American Philosophical Society, Curt Stem Papers; retrieved from http://www.dnalc.org/view/16269-Gallery-10-Columbia-University-Fly-Room-around-1920.html and reproduced here under terms of CC BY-NC-ND 3.0 US license (http://creativecommons.org/licenses/by-nc-nd/3.0/us/).


http://creativecommons.org/licenses/by-nc-nd/3.0/us/

http://creativecommons.org/licenses/by-nc-nd/3.0/us/

http://www.dnalc.org/view/16269-Gallery-10-Columbia-University-Fly-Room-around-1920.html

http://commons.wikimedia.org/wiki/File:Thomas_Hunt_Morgan.jpg


http://commons.wikimedia.org/wiki/File:Drosophila_melanogaster_-_side_(aka).jpg


The basic processes of biology are similar in many different species. For example, the DNA of fruit flies and roundworms works the same as human DNA because the DNA of almost all organisms is based on A, T, C, G nucleotides. Because flies and worms are easier to study than humans, we first learned how DNA works in those species. It turns out that the cells and molecules of humans work in very similar ways to the cells and molecules of all other animals. This means we can learn a lot about humans from studying other species.

Image courtesy Lawrence Berkeley National Laboratory; retrieved from http://www.mc.vanderbilt.edu:8080/reporter/index.html?ID=5626 on 7/4/14. Image included under fair-use guidelines of Title 17, US Code. Copyrights belong to respective owners.


http://www.mc.vanderbilt.edu:8080/reporter/index.html?ID=5626


In basic research, scientists usually begin with a hypothesis they want to test. Using model organisms often allows them to test their hypothesis in a very efficient way, because they can use procedures that other scientists have created for manipulating the genes or cells of a model organism.

In drug development, scientists can begin to understand the biological effects of a potential drug by first studying it in microorganisms. Then, if the results are promising, they can proceed to more complex model organisms and eventually to human trials.

Mouse image by NIH; retrieved from http://commons.wikimedia.org/wiki/File:House_mouse.jpg on 7/14/14. “Knowledge” image from Qiagen website; retrieved from http://biology.kenyon.edu/courses/biol114/Chap08/Chapter_08a.html on 7/14/14 and included under fair-use guidelines of Title 17, US Code. Copyrights belong to respective owners.


http://biology.kenyon.edu/courses/biol114/Chap08/Chapter_08a.html

http://commons.wikimedia.org/wiki/File:House_mouse.jpg


Biotechnologists who work in laboratories generally will conduct research using a wide spectrum of model organisms. These model organisms can range from bacteria like E. coli to large mammals like chimpanzees.

Good scientific method should ensure that animal testing avoids or minimizes discomfort, distress, and pain to the animals. Experiments need to be consistent with sound research design, and appropriate species in appropriate numbers should be used. However, the ethical questions raised by performing research and experiments on model organisms, especially with more complex animals, are subject to debate.

According to the US Department of Agriculture, in animal experiments not including rats, mice, birds, or invertebrates, in 2006 about 670,000 animals (57%) were used in procedures that did not include more than momentary pain or distress. About 420,000 (36%) were used in procedures in which pain or distress was relieved by anesthesia, and 84,000 (7%) were used in studies that would cause pain or distress that would not be relieved.

Agar plates image from NIH; retrieved from http://en.wikipedia.org/wiki/File:Agarplate_redbloodcells.jpg on 7/4/14. Photo by Bill Branson. Mice image from NIH; retrieved from http://commons.wikimedia.org/wiki/File:Knockout_Mice5006-300.jpg. Photo by Maggie Bartlett. All other photos retrieved from Wikimedia Commons and included under fair-use guidelines of Title 17, US Code. Copyrights belong to respective owners.


http://commons.wikimedia.org/wiki/File:Knockout_Mice5006-300.jpg

http://en.wikipedia.org/wiki/File:Agarplate_redbloodcells.jpg


It is important to understand the basic biology characteristics of the most common model organisms. When researchers look for a model organism to use in their studies, they look for several traits. Among these are size, generation time, accessibility, ability to manipulate genetic material, and potential economic benefit.

Yeast, a single-cell eukaryote, is an example of a model organism that has been widely used in genetics and cell biology because it is fast and easy to grow. Yeasts and humans are both eukaryotes: their cells have a nucleus―with a nuclear membrane―containing most of their DNA. Yeast also shares many genes with human cells.

Recent discoveries in cancer research used yeast-based systems in experiments to tell us about mutations that cause cancer.

Fruit fly image: see Slide 3 notes.



There are dozens of different model organisms used in biotechnology today. The right model organism to use depends on the research project you want to do. In order to choose the right model organism for an experiment, you have to understand the basic biology of different model organisms.

What do all these organisms have in common? They all grow and mature quickly, are relatively simple and inexpensive to work with, and are widely available for use in experiments.

E. coli image courtesy Eric Erbe (colorized by Christopher Pooley); retrieved from http://commons.wikimedia.org/wiki/File:E_coli_at_10000x.jpg on 7/4/14. Yeast image from National Institute of General Medical Sciences; retrieved from http://www.nigms.nih.gov/Education/Pages/modelorg_factsheet.aspx. Worm image from NIH; retrieved from http://commons.wikimedia.org/wiki/File:Caenorhabditis_elegans.jpg. Fruit fly image: see slide 3 notes. Mouse image courtesy of Rama; retrieved from http://en.wikipedia.org/wiki/File:Lab_mouse_mg_3308.jpg and included here under terms of the CeCILL (http://en.wikipedia.org/wiki/CeCILL).


http://en.wikipedia.org/wiki/CeCILL

http://en.wikipedia.org/wiki/File:Lab_mouse_mg_3308.jpg


http://www.nigms.nih.gov/Education/Pages/modelorg_factsheet.aspx

http://commons.wikimedia.org/wiki/File:E_coli_at_10000x.jpg


Escherichia coli bacteria are very common bacteria that are at home in your intestines. All bacteria, including E. coli, are organisms that consist of single prokaryotic cells. Even though bacteria cells are simpler than the cells of most other organisms, they carry out many of the same cell processes.

Several strains of E. coli are used as model organisms and have proven invaluable in the study of the functions and genetics of fundamental cell processes. E. coli is easy to grow and maintain, and its entire DNA sequence is known. Another important aspect of E. coli is its rapid cell division rate. Each E. coli cell can divide every 30 minutes to produce a new generation, enabling rapid adaptation to the environment.

However, E. coli cells differ from human cells. Human (and yeast) cells are eukaryotes. By contrast E.coli (bacteria) is a prokaryote. The prokaryotic nuclear body, or nucleoid, lacks a nuclear membrane. Therefore, it is not a good model for studying cell nuclei.

Bacteria image: see slide 2 notes. Cell diagram courtesy of Mariana Ruiz Villarreal (LadyofHats); retrieved from http://commons.wikimedia.org/wiki/File:Average_prokaryote_cell-_en.svg on 7/14/14.



The strain of yeast used as a model organism is the same strain of baker’s yeast that is used to make bread rise. Like E. coli, yeast is a single-celled organism that is easy to grow and maintain, and its entire DNA sequence is known. However, its cells are eukaryotic cells, the same kind of complex cells found in plants and animals. In fact, at least 31% of human genes are similar to genes found in yeast. This is because, as a eukaryote, yeast carries out many of the same basic cellular processes that other eukaryotes do, including humans. Yeast has been used for many kinds of research, in particular the study of the fundamental genetic instructions that tell cells when to grow and divide.

Yeast image: see Slide 2 notes. Yeast drawing courtesy of Gary E. Kaiser; retrieved from http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit4/fungi/u1fig35.html on 7/14/14 and included under fair-use guidelines of Title 17, US Code. Copyrights belong to respective owners.


http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit4/fungi/u1fig35.html


Roundworms are the most common organisms found on Earth. The roundworm used as a model organism, C. elegans, is a transparent multicellular organism about 1 mm in length. Easy to grow and maintain, C. elegans undergoes development from a one-cell zygote to an adult organism with 959 cells in just three days. If development took a longer period of time, it would not be useful as a model organism. C. elegans was the first multicellular organism to have its DNA sequence completely determined. In particular, the genes that control development and programmed cell death are well understood in C. elegans. Development is invariant, which means that cell division and programmed cell death from zygote (fertilized egg) to adult occurs in exactly the same way in all individuals. This allows deviations from normal anatomy and development to be easily detected. In addition, C. elegans is also the only organism to have had all its nerve processes identified and traced, leading to a nerve diagram.

Worms image courtesy Alexander Soloviev (http://lysozyme.co.uk); retrieved from http://snowbio.wikispaces.com/C.+elegans+(nematode) on 7/4/14 and included under fair-use guidelines of Title 17, US Code. Copyrights belong to respective owners.


http://snowbio.wikispaces.com/C.+elegans+(nematode)

http://lysozyme.co.uk/


The fruit fly is a small invertebrate insect that has a long history of use in the lab. It is easy to grow and maintain. Early research with Drosophila melanogaster led to pivotal discoveries about chromosomes and mechanisms of development. D. melanogaster has only four pairs of chromosomes, and they are easily seen with a microscope. Their DNA sequence is completely known, and about 75% of fruit fly genes are similar to human genes.

Fruit flies produce a new generation every 10 days and have large numbers of offspring. They have a transparent embryo. All of these features make D. melanogaster a great model system for studying development and embryogenesis, which is the process of embryo formation. Since they reproduce sexually, they inherit one allele for each trait from each parent, making them valuable in studying genetics. About 75% of known human disease genes have a recognizable match in the genome of fruit flies and 50% of fly protein sequences have mammalian homologs or similar sequences.

Drosophilia image: see Slide 2 notes. Chromosomes diagram courtesy of Dixi; retrieved from http://php.med.unsw.edu.au/embryology/index.php?title=File:Drosophila_chromosomes.png on 7/14/14 and included here under terms of the CC BY-SA 3.0 license (http://creativecommons.org/licenses/by-sa/3.0/deed.en).



http://php.med.unsw.edu.au/embryology/index.php?title=File:Drosophila_chromosomes.png


Squids are invertebrates and cephalopods. The cephalopods are a group of animals with large, complex brains that carry out a wide range of behaviors, including learning and memory. Cephalopod model organisms, including Loligo pealei, have been used extensively to study normal nerve function, memory, memory loss, and dementia.

L. pealei is an invaluable model organism for the study of nerve function because it has a giant axon, or nerve fiber, that is nearly 1 mm in diameter. This makes it about a thousand times larger than mammalian axons. The axon controls the water jet propulsion system in the squid. The axon and the electrical signals that it transmits can be easily examined and measured using probes and other devices.

Since they are sea-dwelling animals, squid for research are obtained from marine laboratories specially designed to breed and care for them. Loligo pealei take about 5 months to reach maturity.

Image retrieved from http://www.devbio.biology.gatech.edu/?page_id=803 on 7/4/14 and included here under fair-use guidelines Title 17, US Code. Copyrights belong to respective owners.


http://www.devbio.biology.gatech.edu/?page_id=803


Strains of the common mouse are extensively used for research and the development of drug therapies. The cost of maintenance of Mus musculus is low and the mice can quickly multiply, reproducing as often as every six weeks. Like humans, M. musculus is a vertebrate and mammal, and therefore has similar anatomy, physiology, and genetics. Over 95% of mouse genes are similar to human genes. Mice give birth to live young, nurse their young, are warm blooded, and have relatively large brains for a given body size (in general they have more capacity for learned behavior and are more flexible in behavior than nonmammals). Research on M. musculus is particularly applicable to human diseases, as the mice are prone to many of the same diseases and even addictions that afflict humans. The M. musculus model organism is used in the study of cystic fibrosis, cancers, glaucoma, diabetes, epilepsy, heart disease, atherosclerosis, hypertension, obesity, Down Syndrome, Alzheimer's, muscular dystrophy, Lou Gehrig's disease, AIDS, Huntington's disease, anxiety, aggressive behavior, alcoholism, and drug addiction.

Image retrieved from http://mcgbiology.wikispaces.com/Rat+Red on 7/4/14 and included here under fair-use guidelines of Title 17, US Code. Copyrights belong to respective owners.


http://mcgbiology.wikispaces.com/Rat+Red


Regardless of their genetic or experimental advantages and disadvantages, certain species are chosen as model organisms because they occupy an important position in the evolutionary tree or because some quality of their genome makes them ideal to study. The field of biotechnology would literally not exist without model organisms.

Image retrieved from http://ehp.niehs.nih.gov/121-a250 on 7/4/14. Copyright Bill Sanderson/Science Source.


http://ehp.niehs.nih.gov/121-a250



Sample Selection: Plant BioassayStudent Name:_______________________________________________________ Date:___________

Part A: Sample Collection

Directions: Collect a plant sample that you predict will have antibacterial or antifungal activity. Record the work you did to collect your sample in your lab notebook.

Your sample must meet the following criteria:

The sample must be from a plant. Note that many foods, including spices, herbs, vegetables, and fruits, are parts of plants.

The sample must be uniform in composition, not mixes of different plants or different parts of the same plant.

The amount of the sample should fill a large spoon.

The sample must be carefully stored in a small plastic bag.

You must have a reason for your sample selection. For example, you might choose a plant because it is used in a home remedy, or you might choose the peel of an orange because you have noticed that many cleaning agents have a strong citrus odor.

You must have permission from a parent or guardian if you obtain the sample from a yard or from your kitchen.

You must have permission from your teacher if you obtain the sample from a school yard or garden.

Using your reason for choosing the plant as a starting point, state a hypothesis for the effect of your sample in the plant bioassay. Be sure to include your reason as support for your hypothesis. After you have written your hypothesis, add this resource to your lab notebook.

Example: My hypothesis is that the fruit from my aunt's tree has antibacterial properties because she rubs it on cuts to cure them.

Hypothesis



Part B: Sample IdentificationDirections: You will be looking up information about your plant sample. Add the resource to your lab notebook when you are done with this part of the experiment.

1. Use books and Internet resources (below) to try and find the scientific name of your plant and what is known about its antibacterial and antifungal activity. If you can't find your exact plant, try to at least determine what general category of plants it belongs to. Record the information here.

Example: "My bark sample came from a tree I believe to be a Knotareal Pine. The scientific name for Knotareal Pine is Cedrus imaginarius. I made this identification because the shape and height of the tree I sampled matches the description and picture of Cedrus imaginarius provided at http://plants.usda.gov/classification/CedrusImaginarius, and because this species is said to be very common in this area. I could not find any specific information about the antifungal or antibacterial properties of the bark, but one source (http://local.lore/bark) claims that Native Americans used it to treat wounds, which is also what my grandmother told me."

2. Using the permanent marker to label a collection bag. Include the following information: the scientific name of your plant, where the sample was collected, and the date it was collected.

3. Place a small piece of your plant sample into the collection bag and add it to your notebook. Keep the rest of your plant sample to use in the bioassay.

Internet Resourceshttp://biology.burke.washington.edu/herbarium/imagecollection.php?Page=plantkey.php

http://plants.usda.gov/classification.html

Using a search engine such as Google, do an online search using the phrase "common plants of [your state or region]" and consider using those resources.


http://plants.usda.gov/classification.html

http://biology.burke.washington.edu/herbarium/imagecollection.php?Page=plantkey.php

http://local.lore/bark

http://plants.usda.gov/classification/CedrusImaginarius



Reading: Plant Bioassay Overview

This presentation explains how bioassays work and how the plant bioassay will be carried out.



Many diseases are due to bacterial or fungal infections. Treatments for these diseases often use compounds that kill bacteria or fungi. A compound that kills bacteria in the body is considered an antibiotic, whereas a compound that kills fungi in the body is an antifungal compound.

Diseases caused by viruses, like the common cold, cannot be treated with antibiotics or antifungals.

Bacteria image courtesy of Dartmouth Electron Microscope Facility. Retrieved from http:// www.nisenet.org/sites/default/files/catalog/uploads/12615/cholera_bacteria_nise.jpg on 6/25/14 and included here under fair-use guidelines of Title 17, US Code. Fungus image retrieved from http :// bioweb.uwlax.edu/bio203/s2008/miller_melo/Disease.htm on 6/25/14 and included here under fair-use guidelines of Title 17, US Code. Copyrights belong to respective owners.


http://bioweb.uwlax.edu/bio203/s2008/miller_melo/Disease.htm



http://www.nisenet.org/sites/default/files/catalog/uploads/12615/cholera_bacteria_nise.jpg

http://www.nisenet.org/sites/default/files/catalog/uploads/12615/cholera_bacteria_nise.jpg


A bioassay determines the impact of a compound by measuring its effects on living organisms. You can use a bioassay to see if a compound, such as a plant extract, has antibiotic properties. In that kind of bioassay, the plant extract is placed in the middle of a petri dish stocked with bacteria. If the plant extract kills the bacteria, there will be an empty area surrounding the plant extract. The stronger the effect of the extract, the bigger the blank area will be. If the plant extract does not have any antibiotic properties, then the bacteria will completely fill the dish.

The initial discovery of penicillin was made because of an accidental bioassay, when a mold containing penicillin happened to get into a petri dish with bacteria.

A bioassay can be used to test for antifungal properties by using a fungus in place of the bacteria.

Image courtesy of Jim Deacon. Retrieved from http://archive.bio.ed.ac.uk/jdeacon/microbes/penicill.htm on 6/25/14 and included here under fair-use guidelines of Title 17, US Code. Copyrights belong to respective owners.


http://archive.bio.ed.ac.uk/jdeacon/microbes/penicill.htm


You will use a bioassay to see if your plant sample has any antibiotic (bacteria-killing) or antifungal (fungus-killing) properties. It is possible for a plant extract to have both antibiotic and antifungal effects. Other compounds may be an antibiotic but not an antifungal, or vice versa. Some compounds are neither antibiotics nor antifungals.

In the images here, the first petri dish shows that the plant sample has an antimicrobial (in this case, antibiotic) effect on the bacteria. The second petri dish shows no effect on the fungus.

Images courtesy of Jim Deacon. Retrieved from http :// archive.bio.ed.ac.uk/jdeacon/microbes/penicill.htm on 6/25/14 and included here under fair-use guidelines of Title 17, US Code. Copyrights belong to respective owners.






Your bioassay has three main parts:

• One part is preparing the petri dishes with the bacterial (E. coli) and fungal (yeast) colonies.

• Another part is extracting the compounds from your plant sample. You’ll do this by chopping up the plant and then soaking it in alcohol. This frees the chemicals in the plant and puts them into solution so that they can act on the bacteria and fungi.

• The final part of the experiment is to place the plant extract into the petri dishes with E. coli and yeast.



If your plant extract has antibiotic or antifungal properties, it should produce a “zone of inhibition” around the plant extract, where there are no colonies of E. coli or yeast. The size of the zone of inhibition indicates the approximate strength of the plant extract.

Image courtesy of Jim Deacon. Retrieved from http:// archive.bio.ed.ac.uk/jdeacon/microbes/penicill.htm on 6/25/14 and included here under fair-use guidelines of Title 17, US Code. Copyrights belong to respective owners.





But what happens if you don’t see any bacteria at all? This could mean one of two things. One possibility is that the plant extract is a really strong antibiotic and prevented any bacterial growth. Another possibility is that something went wrong in the experiment and caused the lack of bacteria.

For example, maybe the main container of E. coli accidentally got too warm while being shipped, and all the bacteria died before they even got to your school. Or maybe you made a mistake in mixing up the agar, and the bacteria did not have enough food to grow. If so, then you really don’t know whether your plant extract is an antibiotic or not.

Is there a way you can figure out whether something went wrong with the experimental procedure? By checking the growth in your positive and negative control plates, you can better determine what actually happened.





In an experiment, control samples are used to test whether the experimental procedure is working the way it should. For example, the negative control for your bioassay is to use a paper disc with no plant extract added to it. Without any plant extract, there is nothing to inhibit the growth of bacteria or fungus. The expectation, then, is that you should see growth in the negative control dishes.

• If the negative control has bacteria or fungus, that means the procedure worked.

• If there are no bacteria or fungus in the negative control, then something besides the plant extract killed them. There was probably a mistake in the procedure. The other possibility is that the paper itself kills bacteria or fungus, but this is unlikely.





The positive control for your bioassay is to use a known antibiotic and antifungal compound on a bacteria plate.

• If the positive control has no zone of inhibition, it means there is a problem with the procedure, since the known antibiotic should have killed some bacteria.

• If the positive control does have a zone of inhibition, it confirms the procedure is working as expected.

Using both negative and positive controls makes it easier to tell if the result is due to your independent variable (in this case, your plant extract) or some problem with the procedure. Using controls in an experiment is vitally important for doing good science.





Your bioassay will use six different paper discs combinations to determine whether your plant extract has antibiotic and/or antifungal properties.

Two of these will be test discs: one with your plant extract and yeast, one with your plant extract and E. coli.

Then there are two negative controls: one has yeast and a plain paper disc (no plant extract), one has E. coli and a plain paper disc (no plant extract).

Then there are two positive controls: one has yeast and a paper disc soaked in iodine (no plant extract), one has E. coli and a paper disc soaked in iodine (no plant extract).



The simplest way to test your five paper discs would be to use six different petri dishes, one per disc. However, using six petri dishes would require a lot of agar. Instead, you can do the experiment more efficiently by putting three paper discs into the same petri dish. That way the experiment can be done using only two petri dishes instead of six.

This is a common issue in biotechnology: what is the most efficient way to do an experiment? The goal is to design experiments that provide the information you need in a fast and inexpensive manner. Finding ways to do the same experiment while using fewer supplies (such as agar) is important in biotech labs in order to avoid wasting money.





The kind of bioassays that you will be doing are a key step in the development of potential therapeutic drugs. If a plant extract has no impact on bacteria in a petri dish, it is unlikely (though not impossible) that the compound will kill bacteria in people. The same is true for killing fungi. Bioassays, then, are a powerful tool for drug development in biotechnology.

Drug development is not the only use for bioassays. For example, they can be used to test whether environmental samples might be toxic to life forms. By learning how to carry out a bioassay, you are learning an important biotechnology skill with many applications.

Pill bottle image courtesy Vanderbilt University Medical Center website; retrieved from http:// www.mc.vanderbilt.edu/root/vumc.php?site=CAPNAH&doc=29724 on 6/25/14 and included here under fair-use guidelines of Title 17, US Code. Petri dish image courtesy of Jim Deacon; retrieved from http://archive.bio.ed.ac.uk/jdeacon/microbes/penicill.htm on 6/25/14 and included here under fair-use guidelines of Title 17, US Code. Copyrights belong to respective owners. Roundworm image by National Institutes of Health; retrieved from http:// commons.wikimedia.org/wiki/File:Caenorhabditis_elegans.jpg . Mouse image by NASA; retrieved from http :// commons.wikimedia.org/wiki/File:54986main_mouse_med.jpg .








http://www.mc.vanderbilt.edu/root/vumc.php?site=CAPNAH&doc=29724

http://www.mc.vanderbilt.edu/root/vumc.php?site=CAPNAH&doc=29724



Anticipation Guide: Pharmacogenomics and Personalized Medicine

Student Name:_______________________________________________________ Date:___________

Directions: For each of the statements below, circle “I agree” if you think the statement is accurate or “I disagree” if you disagree with the statement. Write one reason to explain your guess.

All people react the same way to a pharmaceutical drug.

My guess: I agree I disagree

My reason:

I learned:

DNA testing of a patient can be used to determine the effectiveness of a pharmaceutical drug.


My reason:

I learned:

Genes do not affect how a person reacts to a pharmaceutical drug.


My reason:

I learned:




Reading: Pharmacogenomics and Personalized Medicine

Directions: Complete the reading below. Return to the anticipation guide in Student Resource 5.11 when you have finished reading and record what you learned.

What is pharmacogenomics?Pharmacogenomics uses information about a person's genetic makeup, or genome, to choose the drugs and drug doses that are likely to work best for that particular person. This new field combines the science of how drugs work, called pharmacology, with the science of the human genome, called genomics.

Health professionals take blood samples from patients with the same condition. DNA is purified from the blood and placed on a profiling chip. The chip tests for gene variants that expect a response to a drug used to treat the condition. Depending on which genetic variants they have, patients may have a good response, no response, or bad side effects. The drug is only given to people who are likely to have a good response.

Why is pharmacogenomics a part of biotechnology? The pharmacogenomics branch of biotechnology has its roots in pharmacogenetics, a discipline that is already about 50 years old. In the past researchers usually looked at a single gene that could be defective



in how it metabolized a drug in the body. But now we have much more complex information about genes through the study of the human genome. We now understand that each drug interacts with numerous proteins in each gene. Pharmacogenomics analyzes how genetic makeup affects an individual's response to drugs based on this much broader understanding of human genetics.

The goal of pharmacogenomics research is to develop a genetic basis to optimize drug therapy with respect to a patient’s individual genotype in order to get the best therapeutic effect along with minimal adverse effects. This research will lead to the expansion of a personalized form of medical treatment in which drugs and drug combinations are optimized for each individual's unique genetic makeup based on genetic testing. This branch of medicine is called personalized medicine. The larger field of biotechnology study, which includes personalized medicine, is called pharmacogenomics.

What are some applications for pharmacogenomics in medicine? In pharmacogenomics, scientists and doctors work with much larger amounts of information about genetic variation on a drug’s response in patients. By correlating a patient’s individual genetics with a drug’s efficacy (effectiveness) or toxicity (harmful effects), a doctor can offer the best form of personalized medicine possible for individuals. This is very important, because it means patients can be treated safely, faster, and in a more cost-effective manner.

Pharmacogenomics has applications in illnesses like cancer, cardiovascular disorders, depression, bipolar disorder, attention deficit disorders, HIV, tuberculosis, asthma, and diabetes.

For example in cancer treatment, pharmacogenomics tests are used to identify which patients are most likely to respond to certain cancer drugs. In cardiovascular disorders, the main concern of pharmacogenomics is the response to drugs that thin the blood or regulate heart rate or lower cholesterol. Pharmacogenomics may also help to quickly identify the best drugs to treat people with certain mental health disorders. For example some patients with depression do not respond to the first drug they are given, so doctors have to try another drug. A drug for depression takes weeks to take its full effect, so a patient’s depression may grow worse during the time spent searching for a drug that helps. Now doctors will have the tools to more exactly prescribe the right medication for a person’s health condition.

Pharmacogenomics is also known as companion diagnostics, meaning genetic testing is being bundled with drugs. There are currently over 120 US Food and Drug Administration approved drugs that include pharmacogenomic biomarkers in their labels.

What is in the future of personalized medicine? Advances in personalized medicine rely on technology that confirms a patient's fundamental biology, DNA, RNA, or protein, which ultimately leads to confirming disease. For example, personalized medicine techniques such as genome sequencing, can reveal mutations in the DNA code that lead to diseases ranging from cystic fibrosis to cancer. Another method, called RNA-seq, can show which RNAs are involved with specific diseases. Unlike DNA, levels of RNA change in response to the environment. Therefore, sequencing RNA can reveal a broader understanding of a person’s state of health. Methods of RNA-seq are very similar to genome sequencing.

Personalized medicine can also be used to predict a person’s risk for a particular disease, based on one or several genes. This approach uses the same sequencing technology to focus on the evaluation of disease risk, allowing the physician to initiate preventive treatment before the disease presents itself in the patient. For example, if it is found that a DNA mutation increases a person’s risk of developing type 2 diabetes, this individual can begin lifestyle changes that will lessen his or her chances of developing type 2 diabetes later in life.


http://en.wikipedia.org/wiki/Type_2_Diabetes

http://en.wikipedia.org/wiki/Type_2_Diabetes

http://en.wikipedia.org/wiki/RNA-seq

http://en.wikipedia.org/wiki/Biomarker

http://en.wikipedia.org/wiki/Food_and_Drug_Administration

http://en.wikipedia.org/wiki/Cardio_vascular_disorder

http://en.wikipedia.org/wiki/Cancer_drugs

http://en.wikipedia.org/wiki/Cancer_treatment

http://en.wikipedia.org/wiki/Genetics

http://en.wikipedia.org/wiki/Adverse_effect_(medicine)

http://en.wikipedia.org/wiki/Genotype


Text materials adapted from the following sources:

Berlin, D.S. et al. “DNATwist: A Web-Based Tool for Teaching Middle and High School Students about Pharmacogenomics.” PubMed, www.ncbi.nlm.nih.gov/pubmed/20305671 (accessed June 10, 2015)

Sadee, Dr. Wolfgang, “What Is Pharmacogenetics, Pharmacogenomics and Clinical Evaluation?” American Association of Pharmaceutical Scientists, http://www.aaps.org/News/What_Is_Pharmacogenetics,_Pharmacogenomics_and_Clinical_Evaluation_/ (accessed June 10, 2015)

“Genes, Genomes and Personalized Medicine.” MSOE Center for BioMolecular Modeling, http://cbm.msoe.edu/teacherWorkshops/ggpm.php (accessed June 10, 2015)

“Personalized Medicine.” Wikipedia, http://en.wikipedia.org/wiki/Personalized_medicine (accessed June 10, 2015) (This article correlates with other scientific sources.)


http://en.wikipedia.org/wiki/Personalized_medicine

http://cbm.msoe.edu/teacherWorkshops/ggpm.php

http://www.aaps.org/News/What_Is_Pharmacogenetics,_Pharmacogenomics_and_Clinical_Evaluation_/

http://www.ncbi.nlm.nih.gov/pubmed/20305671



Online Research Guide: Pharmacogenomics and Personalized Medicine

Student Names:_______________________________________________________ Date:___________

Directions: You are a physician, and your patient has questions about why he or she is being tested to determine if a therapeutic drug will work for him or her. Work with a partner to answer the patient's questions by consulting the Internet resources listed below. Your teacher will tell you which disease your patient has before you begin.

Disease my patient has:

Questions from the patient:

1. What drug is usually prescribed for my disease?

2. Can I start taking the drug right away?

3. Why do I need to be tested before I can take a drug?

4. What is the test you will perform, and what information will you learn from it?

Suggested websites: http://publications.nigms.nih.gov/medsforyou/ http://publications.nigms.nih.gov/insidelifescience/genes-guide-prescriptions.html http://learn.genetics.utah.edu/content/pharma/


http://learn.genetics.utah.edu/content/pharma/

http://publications.nigms.nih.gov/insidelifescience/genes-guide-prescriptions.html

http://publications.nigms.nih.gov/medsforyou/



Conclusion Writing: Plant Bioassay Student Names:_______________________________________________________ Date:___________

Write a Conclusion Directions: Write a conclusion for the plant bioassay. The conclusion should have three parts―Part 1: Results with Evidence and an Explanation; Part 2: Possible Errors; and Part 3: Potential Applications. Use Teacher Resource 5.4, Rubric: Lab Report Conclusion, which your teacher provided as guidance. Use the space below to make initial notes.

Part 1: Results with Evidence and Explanation

Part 2: Possible Errors

Part 3: Potential Applications




Peer Review Rubric: Lab Report ConclusionStudent Names:_______________________________________________________ Date:___________

Directions: Use Teacher Resource 5.4, Rubric: Lab Report Conclusion, to review your partner’s lab report conclusion (Student Resource 5.8). Circle the level of proficiency in column 2 and give an explanation for your evaluation in the last column.

Name of Classmate Who Wrote the Report: _________________________________________

Section Level of Proficiency(circle one)

Explanation

Conclusion

Part 1: Results with Evidence and Explanation

Exemplary Solid Developing Needs attention

Conclusion

Part 2: Possible Errors


Conclusion

Part 3: Potential Applications



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