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AOHS Biotechnology

Lesson 5 Model Organisms, Ethnobotany,

and Drug Development

Teacher Resources

Resource Description

Teacher Resource 5.1 Supplement: Plant Bioassay

Teacher Resource 5.2 Presentation 1 and Notes: Model Organisms Used in Biotechnology (includes separate PowerPoint file)

Teacher Resource 5.3 Presentation 2 and Notes: Plant Bioassay Overview (includes separate PowerPoint file)

Teacher Resource 5.4 Rubric: Lab Report Conclusion

Teacher Resource 5.5 Presentation 3: Model Organisms, Ethnobotany, and Pharmacogenomics Game Show (separate PowerPoint file)

Teacher Resource 5.6 Quiz: Model Organisms, Ethnobotany, and Pharmacogenomics

Teacher Resource 5.7 Answer Key: Model Organisms, Ethnobotany, and Pharmacogenomics Quiz

Teacher Resource 5.8 Key Vocabulary: Model Organisms, Ethnobotany, and Drug Development

Teacher Resource 5.9 Bibliography: Model Organisms, Ethnobotany, and Drug Development

Copyright © 2014‒2016 NAF. All rights reserved.

AOHS BiotechnologyLesson 5 Model Organisms, Ethnobotany, and Drug Development

Teacher Resource 5.1

Supplement: Plant Bioassay This resource works in tandem with Lab Resource 5.1, Procedure: Plant Bioassay, where the equipment needed and the instructions for the lab are provided for both the teacher and student. This supplement explains how to prepare for the lab.

OverviewThis guide describes the materials and setup for carrying out a bioassay to test a plant extract for antibacterial and antifungal activity. The model organisms E. coli and yeast are used in the bioassay.

Ideally students work in pairs. If supplies or space are limited, groups of three or four will also work.

Advance Preparation1. Order the E. coli bacteria so that it arrives one or two days before the lesson begins. When it

arrives, prepare E. coli starter plates. To do so, you will need to have on hand LB powder, agar, petri dishes (one dish per four students), heat source, the E. coli, and an inoculating loop. Prepare the LB broth agar and pour it into the petri dishes as described in Part 1 and Part 2 of the Lab Resource 5.1 Procedure: Plant Bioassay. Streak the dishes with E. coli, tape them shut, turn them upside down, and incubate at 37°C. Check on the plates over two days to make sure that the bacteria colonies are growing. When colonies are visible on the dishes, store them in Ziploc bags in the refrigerator until students use them for Part 3 of the lab.

2. You should also prepare some extra LB and YPD plates in case a team has problems pouring all their plates. Prepare the LB broth agar and the YPD broth agar and pour it into the petri dishes as described in Part 1 and Part 2 of the Lab Resource 5.1 Procedure: Plant Bioassay.

3. Prepare the filter paper assay discs prior to Part 6: Running the Bioassay. Use a standard single hole punch to punch out small discs from the filter paper. Students will need six filter paper discs for each sample. Collect the punched out discs in small containers for each group; extra microfuge tubes or empty petri dishes work well.

4. Review disposal requirements for microorganisms and set up appropriate disposal protocols. The best way to dispose of cultures is to pressure sterilize them in a heat-stable biohazard bag. If autoclaves or pressure cookers are not available or large enough to make this convenient, an alternative is to bleach the equipment in a 20% bleach (household) solution (1 part bleach and 4 parts water). Let equipment soak overnight before disposing of it. Please note that the bleach solution is corrosive and needs to be thoroughly removed afterwards. In addition, the plates can be incinerated if access to an incinerator is available.

5. Collect some plant samples in case some students do not bring one.

Equipment Setup

Part 1Set up separate stations with balance, flasks, and reagents for the LB culture media preparation and the YPD culture media preparation. Set up the autoclave or pressure cookers.



Sterilize the work areas and set up separate stations with three petri dishes. Note: Parts 1 and 2 of the lab need to occur on subsequent days so that the sterilizing of the media in the autoclave or pressure cooker can continue after class is over, before Part 2 the next day.

Part 2Liquefy the bottles of agar broth, prepared during Part 1, in a hot water bath before class.

Part 3Set up separate stations for streaking the plates with the E. coli and yeast grown in the culture tubes.

Part 4Set up separate stations with chopping and grinding tools.




Presentation 1 Notes: Model Organisms Used in Biotechnology

Before you show this presentation, use the text accompanying each slide to develop presentation notes. Writing the notes yourself enables you to approach the subject matter in a way that is comfortable to you and engaging for your students. Make this presentation as interactive as possible by stopping frequently to ask questions and encourage class discussion.

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.

Presentation notes



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.

Presentation notes


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:Drosophila_melanogaster.jpg

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

Presentation notes


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://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:Thomas_Hunt_Morgan.jpg


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

Presentation notes


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

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.

Presentation notes


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

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

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

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.

Presentation notes


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

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

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

Presentation 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).

Presentation notes


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

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

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

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.

Presentation notes


http://commons.wikimedia.org/wiki/File:Average_prokaryote_cell-_en.svg

http://commons.wikimedia.org/wiki/File:Average_prokaryote_cell-_en.svg


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.

Presentation notes


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

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.

Presentation notes


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).

Presentation notes



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

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.

Presentation notes


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.

Presentation notes


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.

Presentation notes


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



Presentation 2 Notes: Plant Bioassay OverviewBefore you show this presentation, use the text accompanying each slide to develop presentation notes. Writing the notes yourself enables you to approach the subject matter in a way that is comfortable to you and engaging for your students. Make this presentation as interactive as possible by stopping frequently to ask questions and encourage class discussion.

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

Presentation notes



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/1261 5/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.

Presentation notes


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





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.

Presentation notes


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.

Presentation notes






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.

Presentation notes



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.

Presentation notes





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.


Presentation notes




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.


Presentation notes




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.


Presentation notes




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).

Presentation notes



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.


Presentation notes




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_elega ns.jpg . Mouse image by NASA; retrieved from http :// commons.wikimedia.org/wiki/File:54986main_mouse_ med.jpg.

Presentation notes












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





Rubric: Lab Report Conclusion

Section Exemplary Solid Developing Needs Attention

Conclusion

Part 1: Results with Evidence and Explanation

Presents data results from experiment.

Clearly explains what was learned from positive and negative controls.

Clearly describes trends and inconsistencies in the data.

Proposes possible reasons for inconsistencies.

Addresses whether the results supported or refuted the hypothesis.

If the hypothesis was not supported, the author proposes an explanation.


Explains what was learned from positive and negative controls.

Describes trends and inconsistencies in the data.

Proposes possible reasons for inconsistencies.

Addresses whether the results supported or refuted the hypothesis.


Poorly explains what was learned from positive and negative controls.

Poorly describes trends and inconsistencies in the data.

Does not address whether the results supported or refuted the hypothesis.


Does not describe data results from positive and negative controls.

Does not describe trends and inconsistencies in the data.

Does not address whether the results supported or refuted the hypothesis.

Conclusion

Part 2: Possible Errors

Identifies two or more probable sources of error.

Explains how errors might have affected the results.

Describes modifications to the experiment to reduce errors, and explains why the modifications would reduce error.

Identifies two or more probable sources of error.


Describes modifications to the experiment to reduce errors.

Identifies one or more probable sources of error.


Identifies insignificant or improbable sources of error.



Section Exemplary Solid Developing Needs Attention

Conclusion

Part 3: Potential Applications

Proposes one or more viable practical applications for the knowledge gained from the experiment.

Identifies people who would be interested in the experimental results.

Identifies reasons why people would be interested in the experimental results.


Identifies people who would be interested in the experimental results.


Does not propose a viable practical application.




Quiz: Model Organisms, Ethnobotany, and Pharmacogenomics

Directions: Answer the following questions in complete sentences.

1. List a model organism that would be suited for each of the following areas of study.

a. Nervous system

b. Cell processes

c. Human disease

d. Growth and development

2. Organisms need to have certain characteristics to be a good model organism in the laboratory. List two of those characteristics.

3. A scientist is examining the transportation of a compound across a cell wall. The findings must be applicable to human cells. Which model organism should the scientist use and why?

4. Explain why pharmacogenomics is referred to as personalized medicine.

5. Describe the two methods by which new drugs are discovered.

6. Explain the purpose of a negative control and positive control in a bioassay experiment.



7. An ethnobotanist learns that a paste made from a plant may be effective against a skin rash. The entire plant—stem, leaves, and root—are boiled to make the paste and the paste appears to be effective after being applied three days in a row. You have obtained the plant from the ethnobotanist and you will determine if there is an effective compound, and the part of the plant that contains the compound. Briefly describe the experiment you would do using mice model organisms that have the skin rash.




Answer Key: Model Organisms, Ethnobotany, and Pharmacogenomics Quiz

1. List a model organism that would be suited for each of the following areas of study.

a. Nervous system Squid

b. Cell processes E. coli OR yeast

c. Human disease Mice

d. Growth and development Roundworms OR fruit flies

2. Organisms need to have certain characteristics to be a good model organism in the laboratory. List two of those characteristics.

Any two of the following: well studied by other scientists, easy to keep in the laboratory, short generation time (reproduces quickly), has biological attributes that make it easy to study the system of interest.

3. A scientist is examining the transportation of a compound across a cell wall. The findings must be applicable to human cells. Which model organism should the scientist use and why?

Yeast should be used as it is a model for the study of cell processes. Yeast cells are more similar to human cells than are E. coli cells.

4. Explain why pharmacogenomics is referred to as personalized medicine.

Pharmacogenomics is part of personalized medicine because it uses information specific to a particular individual, such as that person’s DNA sequence, the genetics of the person’s cancer, or the DNA sequences of the population of infectious agent to customize treatment.

5. Describe the two methods by which new drugs are discovered.

By screening naturally occurring or known compounds and by creating new compounds using synthetic chemistry.

6. Explain the purpose of a negative control and positive control in a bioassay experiment.

The negative control is used to ensure that the conditions of the experimental protocol minus the test compound do not affect the growth of the microorganisms. The positive control is used to ensure that the microorganisms are behaving as expected by using a compound that has a known effect on the microorganisms.



7. An ethnobotanist learns that a paste made from a plant may be effective against a skin rash. The entire plant—stem, leaves, and root—are boiled to make the paste and the paste appears to be effective after being applied three days in a row. You have obtained the plant from the ethnobotanist and you will determine if there is an effective compound, and the part of the plant that contains the compound. Briefly describe the experiment you would do using mice model organisms that have the skin rash.

Boil each part of the plant separately and then prepare the paste. Prepare a negative control that is made the same way as the experimental paste minus the plant ingredients. Prepare a positive control using a paste that is known to have some effect on the rash. Apply the paste made of three plant parts and the two control pastes to a group of mice with the rash, using the method and amount of paste. Repeat the applications for three days and take photographs of the rash each day to keep a record of the effect of each paste.




Key Vocabulary: Model Organisms, Ethnobotany, and Drug Development

Term Definition

agar A compound that is used to solidify culture medium, which provides a semisolid surface for microorganism growth.

bacteria A microorganism that is used in many biotechnology applications. The bacteria found in the human intestine, Escherichia coli, is a model organism.

bioassay A test to determine the biological activity of a substance.

culture medium A liquid or solid that supports growth of microorganisms. There are many kinds of media formulated for specific microorganisms. LB media feeds E. coli and YPD media feeds yeast. Specific substances are sometimes added to media to enable cell selection and gene activation.

DNA (deoxyribonucleic acid)

The nucleic acid that is the genetic material determining the makeup of all living cells and many viruses. It consists of two long strands of nucleotides linked together in a structure resembling a ladder twisted into a spiral.

ethnobotany A field of study that combines the study of plants with the study of anthropology and that is concerned with accumulation of cultural knowledge of health and natural remedies.

gene A section of DNA that encodes the instructions for making a specific protein. Genes can determine distinct traits, and they are passed down from parents to offspring.

homolog Something that is homologous, or similar in position, structure, or evolutionary origin but not necessarily in function.

hypothesis A predicted experimental outcome that will be supported or refuted by experimental data.

medicinal chemistry A discipline with a focus on synthetic chemistry and the broad goal of creating new drug products.



Term Definition

metabolism The chemical reactions that take place within cells in order to provide them with energy.

microorganism Species of organisms visible only under a microscope, often unicellular; includes bacteria and yeast.

model organism A nonhuman species that is well suited for, and commonly used in, used research to study particular biological processes. Examples of model organisms are E. coli bacteria, baker’s yeast, roundworms, fruit flies, squid, and mice.

negative control In an experiment, a sample or group where no effect is expected. Used to detect experimental error and/or to establish a baseline for other results. An example is giving placebo (sugar) pills to one group and a drug to another group. The placebo pills would be the negative control.

petri dish A small shallow covered dish that is filled with an agar nutrient culture medium and used to grow microorganisms.

pharmacogenomics A field of study that combines the study of drugs and the study of genomics and that is concerned with developing drug therapies that compensate for genetic differences in patients. Also known as personalized medicine.

positive control In an experiment, a sample or group where a known effect is expected, used to detect failures in the procedure.

proteins Large biological molecules, or macromolecules, consisting of one or more long chains of amino acid residues.

secondary metabolite A compound produced by a plant during metabolism that does not contribute to growth, development, or reproduction but that can defend the plant from other organisms.

sterile technique A set of procedures that protects lab workers and products from contamination by microorganisms.

synthetic chemistry The process of making more complex chemical compounds from simpler substances.

yeast A microorganism, technically considered a fungus, used in biotechnology as a model organism or to ferment products.



Term Definition

zones of inhibition Clear circles around discs soaked with compounds that are placed on an agar surface that is streaked with microorganisms. The circles indicate that the compound has prevented microorganism growth.




Bibliography: Model Organisms, Ethnobotany, and Drug Development

The following sources were used in the preparation of this lesson and may be useful for your reference or as classroom resources. We check and update the URLs annually to ensure that they continue to be useful.

PrintDaugherty, Ellyn. Biotechnology Science for the New Millennium. Saint Paul, MN: Paradigm Publishing, 2007.

Daugherty, Ellyn. Biotechnology Science for the New Millennium Laboratory Manual. Saint Paul, MN: Paradigm Publishing, 2007.

Endersby, Jim. A Guinea Pig's History of Biology. Cambridge, MA: Harvard University Press, 2009.

Henderson, Jenny, and Stephen Knutton. Biotechnology in Schools: A Handbook for Teachers. Bristol, PA: Open University Press, 1990.

Pressley, Brian. Introduction to Biotechnology. Portland: ME: J. Weston Walch, 2010.

OnlineBotstein, David, Steven A. Chervitz, and J. Michael Cherry. "Yeast as a Model Organism." http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039837/ (accessed March 7, 2016).

De Beer, Josef, and Elrina Whitlock. “Indigenous Knowledge in the Life Sciences Classroom: Put on Your de Bono Hats!” The American Biology Teacher, April 2009, https://www.nabt.org/websites/institution/File/pdfs/american_biology_teacher/2009/April/071-04-0209.pdf (accessed March 7, 2016).

Dutchen, Stephanie. “Living Laboratories: How Model Organisms Advance Science.” Live Science, June 1, 2011, http://www.livescience.com/14382-model-organisms-slime-mold-yeast-bacteria.html (accessed March 7, 2016)

“Drosophila melanogaster.” Wikipedia, http://en.wikipedia.org/wiki/Drosophila_melanogaster (accessed March 7, 2016).

Grant, Philip, Yali Zheng, and Harish C. Pant. “Squid (Loligo pealei) Giant Fiber System: A Model for Studying Neurodegeneration and Dementia?” The Biological Bulletin, June 2006, http://www.biolbull.org/content/210/3/318.full (accessed March 7, 2016).

Liu, Shijun, and Laurie Usinger. “All About Agar.” Science Buddies, http://www.sciencebuddies.org/science-fair-projects/project_ideas/MicroBio_Agar.shtml (accessed March 7, 2016).

National Institutes of Health. Model Organisms for Biomedical Research. http://www.nih.gov/science/models/ (accessed March 7, 2016).

Rubin Gerald.M., and Edward B. Lewis. "A Brief History of Drosophila's Contributions to Genome Research." Science 287:2216‒2218,.http://web.mit.edu/HST.160/www/DrosophilaGenomeResearch.pdf (accessed March 7, 2016).


http://web.mit.edu/HST.160/www/DrosophilaGenomeResearch.pdf

http://www.nih.gov/science/models/

http://www.sciencebuddies.org/science-fair-projects/project_ideas/MicroBio_Agar.shtml

http://www.biolbull.org/content/210/3/318.full

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

http://www.livescience.com/14382-model-organisms-slime-mold-yeast-bacteria.html

https://www.nabt.org/websites/institution/File/pdfs/american_biology_teacher/2009/April/071-04-0209.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039837/


Spencer, Geoff. “Background on Mouse as a Model Organism.” National Human Genome Research Institute, https://www.genome.gov/10005834 (accessed March 7, 2016).

The Marine Biological Laboratory. "The Long-Finned Squid." http://hermes.mbl.edu/publications/pub_archive/Loligo/squid/index.html (accessed March 7, 2016).

“Using Model Organisms to Study Health and Disease.” National Institute of General Medical Sciences, http://www.nigms.nih.gov/Education/Pages/modelorg_factsheet.aspx (accessed March 7, 2016).



http://hermes.mbl.edu/publications/pub_archive/Loligo/squid/index.html

https://www.genome.gov/10005834

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