Food from the Sea: Can Biotech Help Feed the World?
Unit Introduction
Earth’s population, at present over six billion people, is projected to grow to ten billion by the year 2050 (see figure below). Fish and other seafood have provided much of the protein needed by the present population, and demand will increase as the population grows. With increasing pressure on depleted wild fish stocks, aquascience and aquaculture technologies must meet an increasingly larger share of that expected demand. An exploding human population will mean increased pollution of coastal and open ocean resources, creating environmental stresses in fish populations that will result in further reduced fishery landings.
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Population growth in third-world countries spills over into developed countries through immigration. Australia, the U.S. and European countries are all experiencing unprecedented immigration rates. |
Worldwide, aquacultural products now account for more than 8.4 million metric tons of finfish, 715,600 metric tons of crustaceans, and 2.9 million metric tons of mollusks grown each year. (One metric ton is equal to 2,204.6 pounds.) Asia, mainly China, is by far the largest aquaculture producer, accounting for 85 percent of the market as compared to only 8 percent for Europe, 2.5 percent for Russia, and 3 percent for North America. Aquaculture is a large and lucrative global business!
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A South Carolina clam aquaculture operation raises both the spat (in open tanks) and the green algae they eat (background cylinders).Image Courtesy: National Oceanic and Atmospheric Administration |
The global economy and worldwide commerce distribute aquaculture products to markets around the world. Some of these products carry foreign pathogens and harmful parasites that can spread quickly, infecting aquacultural stock, with devastating consequences. Existing antibiotics and medicines used to treat fish are becoming less effective as pathogens develop resistance to them. Losses to the United States aquaculture industry from disease outbreaks are more than $3 billion each year. Imagine how many billions of dollars are lost in China and other producers each year because of aquatic disease pathogens and parasites.
This unit will introduce students to fish diseases, organisms important in fish health, and the reasons diseases occur and are spread in fish populations. They will learn about new molecular-based techniques used to diagnose fish diseases, and ways of preventing and treating fish disease. Materials in this unit will also help students explore the risks and benefits of genetic engineering in aquaculture. Ethical questions and environmental threats from the use of biotechnology will be addressed. Finally, students will be introduced to the relatively new but extremely powerful field of bioinformatics to learn how scientists worldwide share information and gain access to genetic databases.
PDF file for this project
IIIA 8. Reading: Marine GEOs: Products in the Pipeline
Background
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Image Courtesy: National Science Foundation |
Because crops like Bt corn and “golden rice” have captured the attention of the mainstream media, many people are aware that some of the crops we eat have been genetically engineered or modified in some way. The use of biotechnology in raising terrestrial food animals has also been in the news. But not many people are aware of the many applications of genetic engineering and other biotechnology techniques to marine organisms. Starting with the field of aquaculture, scientists have modified many marine organisms to encourage faster growth, to use those organisms in bioremediation of contaminated sites, and to produce pharmaceuticals and other substances. This activity asks students to read a comprehensive article about genetically modified marine organisms and then answer some comprehension questions.
PDF file for this project
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How are marine organisms being genetically modified, and for what purposes? |
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Students will understand the many uses of genetic engineering of marine organisms and the potential benefits and drawbacks of the uses of these technologies. |
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Student Work Sheet |
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One class period or homework |
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1. Students will read (either on-screen or in hard copy format) the article Marine GEOs: Products in the Pipeline by A. R. Kapuscinski (Marine Biotechnology Briefs 1, February 2003). Institute for Social, Economic and Ecological Sustainability, University of Minnesota, St. Paul) 2. Students will answer the questions provided on the Student Work Sheet in this chapter. |
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1. What traits are being changed through genetic engineering of aquatic organisms used for human nutrition? 2. What are some of the aquatic organisms which are being genetically engineered? 3. How will these modifications potentially benefit people? 4. What are some concerns people have with genetic engineering of aquatic animals? 5. What roadblocks are there to raising genetically modified organisms for market as seafood products? |
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1. What traits are being changed through genetic engineering of aquatic organisms used for human nutrition? • Reduced dependence on light for growth (plants) Prawns, crayfish, algae, oysters, tilapia, goldfish, salmon, red sea bream, and rainbow trout. • Increased growth rates and improved feed conversion rates Escapement and interbreeding with native populations that may reduce the viability of native species in the natural environment Public distrust of genetically modified food products. Genetically engineered products may be banned by international trading partners, preventing export and limiting the sales of genetically engineered seafood products. |
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Kapuscinski, A.R. 2003. Marine GEOs: Products in the Pipeline. Marine Biotechnology Briefs 1 (February 2003):1-5 plus tables and hotlinks. Institute for Social, Economic and Ecological Sustainability, University of Minnesota, St. Paul. Web site: http://fwcb.cfans.umn.edu/isees/MarineBrief/brief1.htm#text5. Accessed July 2009. |
IIIB 9. Fish Diseases in the Pacific Northwest Region: Student Reading
Background
Just like any other animal, Pacific Northwest salmon and trout are susceptible to diseases caused by bacteria, viruses, and other pathogens. These pathogens are a natural part of any ecosystem. Under normal stream conditions, these fish might harbor the disease organism at low levels but the population may never suffer an outbreak. However, fish exposed to natural or human-caused environmental stress, such as increased water temperatures or turbidity, may have decreased resistance to pathogens, and mortality from diseases may increase. Fish that are exposed to stresses related to various aquaculture methods may also be more susceptible to disease.
Because of the recreational and commercial value of Pacific Northwest salmon and trout species, aquaculture (fish farming) and fish hatchery facilities have been used for over a century to increase and supplement natural production. Salmon farming in saltwater is a minor part of the national aquaculture industry, but it is a valuable economic asset, contributing 11 percent to the total value of all aquaculture products. Farmed salmon now accounts for 80 percent of all salmon sold in the United States.
Over the past several years there has been considerable controversy related to hatchery-raised fish and salmon farming. Compared to natural conditions, hatchery and farming facilities concentrate fish in greater densities in hatchery rearing trays, net pens, and raceways, which can cause stress to the fish. Because of these crowded conditions, epidemics are more likely to occur in hatcheries than in the wild. Importing eggs or fish to a hatchery from other river basins can also increase the risk of introducing diseases to which local fish have little resistance.
Recent advances in the field of marine biotechnology are helping to provide new information about and solutions to the problems of disease and parasite transmission. For example, researchers like Dr. Jerri Bartholomew of Oregon State University’s Department of Microbiology and the Center for Fish Disease Research have been working on the development of a molecular method to detect and measure salmon and trout parasites that cause disease.
Until now, researchers had no quick, easy way to test for the presence of threatening parasites like the myxozoan Ceratomyxa shasta in water samples. This parasite causes a disease that reduces the number of salmon and trout in northwest streams. An analysis of water samples can help identify streams where the parasite is prevalent. Researchers have developed a method using the organism’s own DNA that can detect even 1/1000th of a parasite spore in a water sample.
To detect myxozoan species like C. shasta before this breakthrough, scientists had to maintain fish in cages along areas of the river suspected to be infectious then return them to the laboratory and wait for months to see if clinical signs appeared. There was no way to quantify the number of infectious spores moving through the water.
This cutting-edge research provides an accurate tool to assess spore levels quickly and allows natural resource managers to develop new and more efficient ways of controlling disease spread. Knowing the distribution pattern of the salmon parasite is critical for testing management actions that might reduce parasite levels and aid in future management decisions.
Salmon and Trout Diseases of Significance
Protozoan Diseases
Ceratomyxa shasta: A protozoan that sometimes can cause widespread mortality in hatchery and wild populations. The parasite infects the intestinal tract of the fish, resulting in tissue necrosis and severe inflammation causing the fish to show a distended stomach and protruding eyes. It eventually leads to death.
Myxobolus cerebralis (whirling disease): Whirling disease is caused by a myxozoan parasite that usually attacks younger fish, damaging the soft spinal cartilage and causing severe deformities. The nervous system of affected fish becomes impaired, and the fish, when startled, circles in a whirling motion, becomes susceptible to predators, and is unable to feed properly. Like C. shasta, M. cerebralis has a complex life cycle involving two hosts: fish (trout or salmon species) and a tiny bottom-dwelling aquatic worm called Tubifex tubifex. When an infected fish dies and decomposes, persistent spores are released into the water; these spores can survive in moist environments for many years. Worms that ingest the Myxobolus spores and become infected release a fragile waterborne spore stage of the parasite that infects the fish, and the cycle begins again.
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Myxobolus cerebratis infected fish. |
Viral Diseases
Infectious hematopoietic (blood forming tissues) necrosis (IHN): The virus that causes IHN attacks the blood forming tissues, such as kidney and spleen, of salmon or steelhead. The fish are more susceptible to IHN when water temperatures are cold. The disease is vertically transmitted, which means that it can be passed from fluids within the gut of female fish to eggs of the next generation. Juvenile salmon mortality can often be very high because of IHN outbreaks.
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Electron micrograph of IHN infection in fish tissue. Rod shapes are viruses.Photo: John Fryer laboratory, Oregon State University |
Bacterial Diseases
Bacterial Kidney Disease (BKD): This chronic bacterial infection is one of the most important diseases of wild and cultured salmonids, particularly in the Pacific Northwest. BKD results from infection by the bacterium Renibacterium salmonarium, which attacks the kidney of salmonids, just as its name implies. This disease can be transmitted “horizontally,” from fish to fish through fecal material, as well as vertically from one generation to the next from a fish to its eggs. It can cause infected salmon or trout to become lethargic, dark-colored, and partially blind and to have abscesses under the skin, which can break open into the water. It’s been shown that these abscesses, as well as fish feces, are responsible for the spread of the bacteria.
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Removing kidney tissue from an IHN-infected fish.Photo: Robert Olson, OSU Hatfield Marine Science Center |
Furunculosis is another bacterial disease that can cause severe problems on salmon farms and in hatcheries. The bacteria become systemic (get into the bloodstream) and can affect all parts of the fish, including the heart, kidneys, and digestive tract. The bacteria multiply in the blood stream, causing the small vessels to burst, releasing the bacteria to spread through surrounding tissues. It also causes boils (furuncles) on the skin of affected fish. Atlantic salmon are more vulnerable to the disease than Pacific salmon. The disease is very infectious and can be transmitted from one fish to another through seawater, where the bacterium that causes the disease can be very long-lived. The main method used to control furunculosis is vaccination, but it is not always effective. Outbreaks of the disease still occur, at which point antibiotics must be used.
Vibriosis is caused by several different strains of bacteria and affects many marine fishes as well as some invertebrates. One of the most important types of vibriosis bacteria of concern to salmon farming in British Columbia is Listonella (Vibrio) anguillarum; a key method of transmission from this pathogen is through the feces of infected fish. The accumulation and dispersal of salmon farm sewage is, therefore, of concern with respect to possible transmission of the disease to wild fish.
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Fish exhibiting infection with vibriosis. Note the frayed tail fins and red abdomen caused by hemorrhaging from the bacterial infection. Both are signs of Vibrio infection.Photo: Robert Olson, OSU Fisheries and Wildlife Department |
Columnaris disease: This is a skin and gill infection caused by the bacteria Flavobacterium columnare. Infected fish form grayish white lesions on the body, head, fins, or gills. It is common in hatcheries but is usually treatable unless warm water temperatures or other stressors are present.
Sea Lice
Sea lice are small crustaceans that can act as parasites for many types of salmon and related species. Sea lice are a major problem for the salmon farming industry. They can result in huge losses, both as a direct result of parasitism, and because they can make the infested salmon more vulnerable to other diseases. While sea lice are naturally occurring in Pacific waters, infected salmon farms can act to amplify the parasite’s population.
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Parasitic copepods (sea lice) attached to the eye of an arrowtooth flounder. |
PDF file for this project
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1. What are the economic costs of these diseases? Consider both wild fish populations and the aquaculture industry. 2. What benefits will be gained if we can control these diseases? 3. What are the environmental benefits to controlling fish diseases? 4. How will people benefit if medicines are developed to control these diseases? |
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1. What are the economic costs of these diseases? Consider both wild fish populations and the aquaculture industry. Fewer fish in the streams for sport fishermen would lead to losses for recreation-related businesses. Aquaculture operations lose significant numbers of fish to diseases, translating into lost revenues. The quantity of fish that can be produced by aquaculture will be significantly increased. The cost of production of seafood would be reduced. Loss of wild fish in streams is significant as we work to preserve wild runs of salmon and trout. Less expensive seafood, more access to recreational fisheries in natural runs of fish. Fish farmers increase production. Consumers can purchase farm-raised fish at a lower price. |
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Center for Fish Disease Research (OSU). http://oregonstate.edu/dept/salmon/. Accessed February 2005. National Marine Fisheries Service. The Net-pen Salmon Farming Industry in the Pacific Northwest, 2001. http://www.nwfsc.noaa.gov/assets/25/4283_06162004_141612_tm49.pdf. Accessed July 2009. OSU News and Communication Services. OSU Researcher Develops new way to detect salmon parasite. http://oregonstate.edu/ua/ncs/archives/2004/dec/osu-researcher-develops-new-way-detect-salmon-parasite. Accessed July 2009. |
IIIB 10. Diagnosing Fish Diseases
Background
My fish has Ich! This is a common complaint from people who keep fish as a hobby. Beyond the hobby trade, disease in aquatic animals is quite an important issue, especially if you own an aquaculture operation. Diseases that can kill the animals can adversely affect the production of the fish or shrimp farm and lower income.
Disease is an unhealthy condition of an aquatic animal that impairs normal physiological functions. It can be caused by poor water-quality management, nutritional imbalance, genetic disorder, physical injury, pollution, and poor sanitation, as well as by pathogenic organisms.
There are two broad categories of fish diseases: infectious and noninfectious. Infectious diseases are caused by pathogenic organisms in the environment or carried by other fish. They are contagious and can possibly be treated with antibiotics and other medicines. Noninfectious diseases are caused by environmental factors, genetic defects, parasites, or nutritional deficiencies. They are not contagious and cannot be treated with medications.
Infectious diseases can be divided into four categories:
1. Parasitic. Parasites obtain their food from their hosts, causing stress and poor health in the host organism that leads to an increased susceptibility to other diseases.
While many people think of worms when parasites are mentioned, parasitic infections are often caused by microscopic protozoans. These organisms occur naturally in the aquatic environment and infest and attack the skin, eyes, mouth, gills and intestinal cavities of aquatic organisms, resulting in severe irritation, decreased appetite, loss of vigor, weight loss, and eventual death. Most protozoan outbreaks can be treated with chemicals such as magnesium sulfate or acetic acid.
2. Bacterial. Bacteria are microscopic single celled organisms that exist everywhere life does. Diseases caused by bacteria are often internal infections that can be treated with medicated antibiotic feeds. Typical signs are hemorrhagic ulcers or sores on the body and around the eyes and mouth, deteriorating skin, and protruding eyes.
3. Viral. Viruses are much smaller than bacteria, so tiny and simple they can be observed only with an electron microscope. They live and reproduce in living cells so they cannot be treated with chemicals because the chemicals would also kill the host cells. Viruses can survive outside the body for extended periods of time and some can even survive freezing and drying. It is not always possible to differentiate infections caused by viruses and bacteria without special and expensive laboratory tests. Viral diseases are the most difficult to diagnose and few antiviral vaccines exist. Vaccines can prevent viral infections in aquatic organisms by building up their immune antibodies, but the only effective way to treat viral infections is to remove the diseased fish from the population to prevent the disease from spreading to other individuals.
4. Fungal. Fungal spores are common in aquatic environments but are usually not a problem in healthy fish. When fish are attacked and weakened by other pathogens or parasites, fungi will colonize damaged tissue, and a white cottony growth will appear. Most fungal infections can be treated with hydrogen peroxide.
Fish are constantly surrounded by all of these potential pathogens in their aquatic environment. In nature, sick fish are quickly removed from the population by predators, and fish are much less crowded than those grown in captivity. In aquaculture systems, fish are stocked in high densities, resulting in stressful conditions that can lead to disease and parasitic problems that spread quickly. Disease is a relationship between a pathogen, a host, and the environment. Serious disease problems occur only when all three factors are present:
- A susceptible host
- A host-specific pathogen
- An environment that is favorable to the disease state
Diseases affect many aquacultured species, including
- Cultured food fishes—catfish, tilapia, rainbow trout, salmon, shrimp, shellfish
- Fish cultured for bait—flathead minnows, goldfish, crawfish, golden shiners
- Fish for stocking ponds and sport fishing—mullet, trout, channel catfish, bass
- Ornamental species—goldfish, angelfish, guppies, platys, swordtails
Diseases in natural ecosystems occur under a number of conditions including
- High host population densities—A more stressful environment leads to lowered immunity and increased disease and parasite problems.
- Unusual temperatures—Can cause stress that results in weakened and unhealthy fish populations
- Environmental stressors—Unfavorable pH levels, high ammonia or nitrite levels, high turbidity, and algae blooms that deplete dissolved oxygen levels
- Introduced pathogens—Native fish populations lack immunity to the introduced pathogens.
Many factors affect how an aquatic organism resists disease. Fish possess four natural protective barriers against infection:
- Mucus—This slime coat creates a physical barrier that limits the entry of disease. It contains enzymes and antibodies that can kill invading pathogens. When this mucus is wiped off during capture or transport, disease pathogens can more readily infect the fish.
- Scales and skin—They function as strong protective barriers against injury. When rough handling breaks off scales, an entry point is opened for bacteria and other organisms to attack the fish.
- Inflammation—This is a cellular protective response to an invading pathogen that protects fish by creating an internal barrier that walls off and attempts to destroy the invading protein pathogen.
- Antibodies—Just as in humans, antibodies are immune response molecules that naturally respond to invading pathogens. When a fish is affected by a pathogen for the first time, the fish will produce antigens, which are antibodies that protect the organism from future infection by the same organism. Nonlethal exposure to various pathogens is essential for a fish to produce antigens that create a competent immune response system.
The most important fish pathogens are:
- Protozoan parasites—Organisms from the phylum Protozoa. These are mainly aquatic, microscopic, single-celled animals that are parasitic in nature. A common freshwater disease called Ich is caused by the protozoan Ichthyophthirius multifiliis.
- Microsporidian parasites—Microscopic, fungal, spore-producing organisms
- Myxozoan parasites—Metazoan spore-forming parasites that have a two-host life cycle
- Parasitic crustaceans—Anchor parasites that attach themselves to host organisms, causing lesions and fungal entry points. They can also live in the gills, mouths, and body cavities of affected fish.
- Tapeworms—Small worms that live inside the intestinal body cavities and flesh of fish and cause loss of appetite, inactivity, and weight loss. Are very unsightly and make fish unfit for market.
- Trematodes—Ectoparasitic flukes that live on the bodies of fish, causing discomfort and entry points for bacterial and fungal infections. All warm-water fish are susceptible.
- Bacterial pathogens—Disease-causing bacteria
- Viral pathogens—Disease-causing viruses
Fish health begins with prevention of disease rather than treatment. Once disease breaks out in aquaculture systems, salvaging the sick fish is difficult. The goal of culturing fish, crustaceans, and shellfish is to reduce stress through wise management practices. Stress is any condition that causes an aquatic animal to be unable to maintain normal physiology because of factors beyond its natural tolerance level. Some common stressors include poor water quality, pollution, improper diet, animal waste, crowded population densities, pathogenic microorganisms, internal and external microscopic parasites, temperature, light, low dissolved oxygen levels, rough handling, and shipping.
By conducting a general dissection of a fish, we may find parasites or other evidence of disease.
Introduced hosts—Fish new to an environment often lack resistance to local pathogens and parasites.
PDF file for this project
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How can aquaculturists identify sick fish that should be quarantined or treated? |
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Students will |
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A copy of the document Basic Methods of Fish Examination (III. Methods Fish Examination), included on this CD for each group of students
A reference book or web site that shows the external and internal anatomy of a fish. Examples include http://fishanatomy.net/ and http://www.iowas.co.uk/fish%20anatomy.html .
Scalpels
Dissecting scissors
Latex gloves
Small butcher knife
Alcohol and a burner for sterilizing tools
Iiodophor or other disinfectants for cleaning the work surface
Paper towels
Glass microscope slides and coverslips
Fixatives (formaldehyde or alcohol)
Bacteriological media
Containers for samples
Pencils and pens for labeling
Compound microscope with at least a low- and medium-power objective lens
Fresh dead fish—can be obtained from a supermarket or fish market, but be sure that the fish is whole and not gutted
One class period
1. Divide students into teams.
2. Provide fresh dead fish for dissection and examination and tools for the dissection and a copy of the document Basic Methods of Fish Examination (III. Methods Fish Examination), developed by Dr. Jerri Bartholomew. This guide has been adapted for use in high school biology labs but follows many of the same protocols that fisheries scientists use to conduct fish necropsies. Note that standardization of protocols is commonly used in science to reduce variables that could alter the results of an investigation.
3. Have students follow the protocols outlined in the guide for examining and sampling their fish for diseases and parasites.
Each fish will likely have different parasites or disease problems.
1. What parasites were found in your fish? Location and description will suffice.
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2. What evidence of diseases did you find (such as enlarged organs, frayed fins, discolored liver)?
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3. How do you think scientists can address the problem of controlling fish diseases and parasites?
Each fish will likely have different parasites or disease problems.
1. What parasites were found in your fish? Location and description will suffice.
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Answers will vary
2. What evidence of diseases did you find (such as enlarged organs, frayed fins, discolored liver)?
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Answers will vary. Although the fish used in this exercise may not have any diseases, students should be evaluated on their critical dissection and examination of the specimen and should not be marked down if they exaggerate the disease evidence they provide in answer to this question.
3. How do you think scientists can address the problem of controlling fish diseases and parasites?
Development of medicines, chemical treatments to control parasites, biotech applications to develop vaccines, disrupting the life cycle of parasites
None
IIIC 11. Community Meeting: Addressing an Outbreak of Shrimp Disease
Background
Shrimp aquaculture is a prime example of how our food production and harvesting is moving from complex natural systems to monoculture. These monocultures are susceptible to serious disease problems and can also have significant impacts on natural populations. The rapid worldwide spread of several shrimp diseases has focused attention on these issues and disease spread has become one of the most pressing issues in aquaculture today.
Viral diseases seriously affect shrimp aquaculture on a worldwide scale. Although these viruses are also found in nature, the high stocking densities in aquaculture facilities can create viral outbreaks that infect aquaculture facilities rapidly, and drastically reduce production and profitability. For an aquaculture system to be productive and sustainable, disease prevention is essential, both in the hatchery and grow-out phase (the period of time to rear shrimp to market size). Diseases create an urgent need for quick solution. To analyze the problem, scientists use a methodical approach to identify modes of transmission and develop methods of control. This all takes time, but the need is urgent as production drops and farms become economically nonviable. Humans are not susceptible to these viruses, and transmission from shrimp to humans has never been known to occur.
Another pressing concern is the spread of disease from the aquaculture facility into native populations of shrimp and other crustaceans. There are various ways in which viral diseases are transmitted to native populations. Shrimp packing plants process imported shrimp and may discharge contaminated effluents into estuaries, spreading the disease to native populations of shrimp and crabs and increasing the risk of virus transmission to other shrimp farms in the area. Transmission can occur when gulls or other birds scavenge landfills for shrimp remains and drop or regurgitate undigested infected material into nearby waters. Disease can spread to other farms if farms draw water from a contaminated estuary. Another potential transmission pathway is through contamination of frozen shrimp used as bait for coastal fishing. Bait shrimp may be eaten by wild shrimp or crabs, creating immediate risk for those populations. The same risk to wild crawfish exists when frozen imported shrimp are used for bait in inland fresh waters. Also, ballast water exchange may be a significant pathway for shrimp virus transmission to wild stock.
There are methods of control if disposal of shrimp waste by seafood plants is done properly. Heating the waste to kill the viruses before disposal is a simple way to kill the virus.
Using biotechnological tools, aquaculturists can monitor the health of their shrimp stock before the onset of clinical signs of the virus. These tools enable the aquaculturists to make sound management decisions, including protecting broodstock and preventing the spread of diseases from farm to farm. Detection of viral disease can also help prevent the spread of viruses to native species in close proximity to shrimp pond effluent.
There are four important viruses that infect shrimp. White spot syndrome (WSSV) first shows up as shell spotting from abnormal deposits of calcium salts, and occasionally a reddish discoloration under the shell. When farmed shrimp are infected, they become lethargic, stop feeding, swim slowly near the pond surface, and eventually sink to the bottom and die. Because WSSV spreads through the hemolymph (the fluid that bathes the cells and fills the body cavity in arthropods, which have an open circulatory system), infection can be detected by taking hemolymph samples.
Taura Syndrome (TSV) was first discovered in shrimp farms in Ecuador and quickly spread throughout North and South America. It has now spread into Asia. IHHNV, infectious hypodermal hematopoietic necrosis, is yet another virus that causes mass mortalities in shrimp facilities. The fourth shrimp virus is Yellow Head Virus, or YHV. Each virus has a unique life cycle. All are of concern and can impede the ecologically safe expansion of the aquaculture industry.
PDF file for this project
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How will your community respond to a viral outbreak at your local shrimp farm? |
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Students will understand the threat of viral disease to shrimp farms and brainstorm potential solutions to the problem. |
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Literature and Internet search results on shrimp diseases and basic dynamics of shrimp farming |
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Two class days: one preparatory day for introduction of topic and student research and one day for conducting community meeting |
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Day 1 1. Assign students to represent the following interest groups: a. Shrimp farmer whose shrimp stock has been diagnosed with a disease Students will research disease in aquaculture facilities (especially shrimp farms) from the perspective of these interest groups. Students should focus on the question, “How will your community respond to a viral outbreak at your local shrimp farm?” keeping in mind the particular interest group they represent. They will present their results in the form of a community meeting at which a solution to the problem of disease outbreak will be sought. Students who represent research scientists should determine how biotechnology can play a role in identifying and treating the shrimp disease. 1. Allow a day for research and preparation of posters or visuals. Use the references given below to gather information about the problem and develop positions for the group they represent. 2. Judge(s) should establish basic rules for presentation, the order in which groups will present, and a list of judging criteria. Day 2 1. Each group should be given 4 to 5 minutes to present their opinion with supporting evidence regarding what should be done about the disease outbreak. Allow each group to present without interruption. 2. A final 5-minute session for questions between groups is optional. 3. Judge will tally score for each group and determine the best action for the community based on the information presented. |
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1. What insights did you gain into shrimp farming from your research and debate? 2. What do you think about the future of shrimp farming? 3. What do you think about the impact of shrimp farming on the environment? 4. What was the most persuasive argument presented by one of the presenting groups other than your own? Were you convinced by that argument? Why or why not? |
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Student answers will vary |
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Aquatic Enterprise. http://www.shrimpcare.com. Accessed May 2005. Clay, B. 1998. Shrimp Aquaculture and the Environment. Scientific American. June 1988. http://www.sciamdigital.com/index.cfm?fa=Products.ViewIssuePreview&ARTICLEID_CHAR=F73F5DA8-4CFC-4879-93EF-ACAF5BBB077 . Accessed July 2009. Schering-Plough Animal Health Aquaculture. www.spaquaculture.com/default.aspx. Accessed July 2009. World Organization for Animal Health, Aquatic Animal Disease: http://www.oie.int/fdc/fdc_new/eng/diseases/en_diseases.htm. Accessed July 2009. World Wildlife Fund. Aquaculture- Shrimp. http://www.worldwildlife.org/what/globalmarkets/aquaculture/dialogues-shrimp.html . Accessed July 2009. |
IIIC 12. Identification of White Spot Syndrome Virus in Shrimp Using PCR
Background
White spot syndrome virus (WSSV) was first identified as a major economic and ecological threat in Taiwan in 1992. The virus rapidly spread throughout Asia until finally reaching the Western hemisphere in 1995. From the Western hemisphere the virus continued to travel through Central and South America (van Hulten 2001).
WSSV has the potential to infect cultured shrimp and incur a mortality rate of 100 percent of the population within 3 to 10 days. The potentially fatal virus has been found to be a threat not only to all shrimp species, but also to other marine and freshwater crustaceans, such as crab and crayfish. Densely stocked systems are at a greater risk of contracting WSSV because of the high stress levels in the system (van Hulten 2001). The threat of the virus spreading from farms into coastal waters and infecting other crustaceans is of great concern.
The white-spot baculovirus is a large, enveloped, rod-shaped to somewhat elliptical non-occluded virus consisting of double-stranded DNA. The WSSV is extremely virulent, and it attacks primarily tissue cells, including ectodermic and mesodermal tissues, connective tissues of organs, nervous tissues, muscle, lymphoids, and hematopoetic tissue. Stomach, gills, antennal glands, heart, and eyes are also affected, resulting in the total lysis of the cells.
WSSV belongs to a new virus family known as Nimaviridae. Its genome is about 300,000 base pairs in length, based on analysis of different isolates. The virions contain one nucleocapsid with 5 major proteins and at least 13 minor proteins (Witeveldt et al. 2004).
This activity applies biotechnology techniques to the diagnosis of WSSV in shrimp. Diagnostic kits obtained from DiagXotics use DNA extraction and PCR to detect the virus in shrimp tissues.
NOTE: DNA can be isolated successfully from hemolymph or tissue with the following method or by using an extraction kit. Hemolymph is the liquid that fills the entire interior (hemocoel) of the body and bathes all cells in organisms with open circulatory systems.
NOTE: This activity uses a kit and equipment that may be beyond the budget of most high school science classrooms. Some companies are often willing to donate materials at a discount or free for educational purposes.
PDF file for this project
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How can biotechnology methods be used to identify WSSV in shrimp? |
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Students will use commercially developed kits that apply biotechnology procedures to identify diseases in farmed animals. |
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Frozen or fresh shrimp Materials required to complete the activity but not supplied in the kits |
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4 to 5 class periods of at least 45 minutes. For longer laboratory blocks, days 1 and 2 or days 2 and 3 could be combined. Day 1: Introduction to PCR and background information |
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Extracting Shrimp DNA 1. DNA can be extracted from the pleopods and tail tissue of shrimp. Dissect a fresh or frozen shrimp using scalpels, forceps, and scissors down the ventral side. Either mince 10–20 mg of tissue finely with scalpel or grind in a mortar prechilled with liquid nitrogen. 2. Transfer tissue to a microfuge tube containing 600 μl of ice-cold cell lysis buffer. Homogenize the suspension quickly with 30–50 strokes of a microfuge pestle. 3. Add 3 µl of Proteinase K (20 mg/ml) to the extracted tissue and lysis buffer. 4. Incubate at 55oC for at least 3 hours but no longer than 16 hours to increase yield of genomic DNA. 5. Allow to cool to room temperature and add 3 µl of 4 mg/ml DNase-free RNase . 6. Incubate the digest at 37 oC for 60 minutes. 7. Add 200 µl of potassium acetate solution (5 M potassium acetate, 11.5 ml of glacial acetic acid, 28.5 ml of water) to precipitate out the protein. Mix the contents of the tube vigorously by vortexing for 20 seconds. 8. Pellet the precipitated protein/SDS complex by centrifugation at maximum speed for 3 minutes at 4 oC in a microfuge. (If a pellet of protein is not visible at the bottom of the tube, incubate the lysate for 5 minutes on ice and repeat centrifugation.) 9. Transfer the supernatant to a fresh microfuge tube containing 600 µl of isopropanol. Mix well and then recover the precipitate of DNA by centrifuging the tube at maximum speed for 1 minute at room temperature in a microfuge. 10. Remove the supernatant by aspiration and add 600 µl of ethanol to the clean DNA pellet. Invert the tube several times and centrifuge the tube at maximum speed for 1 minute at room temperature in a microfuge. 11. Carefully remove the supernatant by aspiration and allow the DNA pellet to air dry for 15 minutes. 12. The precipitated DNA should be preserved in 100 µl TE (pH 7.6) until concentrations and purity can be determined by use of a spectrophotometer and run on a 1% agarose gel. (Method is modified from Protocol #6, Rapid Isolation of Mammalian DNA, Molecular Cloning: A laboratory Manual . Accessed May 2005.) Polymerase Chain Reaction |
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1. What is white spot shrimp virus and why is it a threat to the shrimp aquaculture industry? 2. How can PCR be used to detect WSSV? 3. What advantages does PCR have over other methods of disease detection? 4. Summarize how PCR works. |
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1. What is white spot shrimp virus and why is it a threat to the shrimp aquaculture industry? WSSV is a large, enveloped, rod-shaped to somewhat elliptical non-occluded virus consisting of double-stranded DNA. The WSSV is extremely virulent. WSSV has the potential to infect cultured shrimp and incur a mortality rate of 100 percent of the population within 3 to 10 days. The potentially fatal virus has not only been found to be a threat to all shrimp species, but also to some other marine and freshwater crustaceans such as crab and crayfish. 2. How can PCR be used to detect WSSV? PCR can be used to detect small quantities of the viral genome present in infected shrimp. 3. What advantages would PCR have over other methods of disease detection? PCR is fast, reliable, and very sensitive. It can be used to detect the presence of virus before signs of infection are obvious. 4. Summarize how PCR works. PCR works as a “molecular photocopier” for the genetic material of all organisms. Using the natural function of a DNA-copying enzyme known as DNA polymerase, PCR can be used to generate unlimited copies of any specified fragment of DNA. The DNA to be copied can be present in minute quantities in living tissues, ancient tissues, or complex mixtures such as blood, hair, and processed foods. A PCR amplification reaction requires source DNA containing the sequence of interest (as few as one copy), two unique single-stranded DNA primers that bracket the desired sequence, deoxyribonucleotides (the building blocks of DNA), and Taq DNA polymerase (an enzyme that helps to build DNA strands, taken from the thermophilic organism Thermus aquaticus). Different phases of the reaction take place at three temperatures that facilitate the synthesis of new copies of the desired DNA sequence. At 95°C, the double-stranded source (or template) DNA is denatured into single strands. Then, at 55°C, the primers bind (anneal) to complementary sequences on the template DNA that bracket the sequence to be amplified. Last, at 72°C, the Taq DNA polymerase adds deoxyribonucleotides in sequence to the primer as it builds a complementary strand to the template DNA (extension). This cycle is repeated until a very large number of copies are obtained. The reaction is usually carried out in a machine called a thermal cycler that quickly changes the temperature of the reaction mixture among the three necessary temperatures. |
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Hoang, T., M. Barchiesis, S. Y. Lee, C. P. Keenan, and G. E. Marsden. 2002. Influences of light intensity and photoperiod on moulting and growth of Penaeus merguiensis cultured under laboratory conditions. Australia: Elsevier Science B.V. Kanna R., G. Kalagayan, D. Godin, and G. Hagino. 1991. Juvenile Production. In Intensive Shrimp Production Technology, the Oceanic Institute Shrimp Manual (pp.71–80). Honolulu: Oceanic Institute. Molecular Cloning: A Laboratory Manual http://www.molecularcloning.com. Accessed May 2005 Mickolos, D. A., and G. A. Freyer. 2003. DNA Science: First Course, second edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. Oceanic Institute. 2001. Oceanic Institute Annual Report 2001 (pp. 13–14). Oceanic Institute, Honolulu. Van Hulten, Marielle. 2001. Virion composition and genomics of white spot syndrome virus of shrimp. Wageningen University dissertation. Vaughn, R. 1995. Aquaculture Science. Delmar Publishers, New York. White Spot Disease United States. http://www.aphis.usda.gov/vs/ceah/cei/taf/iw_2004_files/domestic/wsd_us_0404_files/wsd_us_0404.htm . Accessed July 2009. Witeveldt, J., C. Cifuentes, J. Vlak, and M. van Hulten. 2004. Protection of Penaeus monodon against white spot syndrome virus by oral vaccination. J. Virology 78:2057–2061. Wyban, J. and J. Sweeney. 1991. Intensive Shrimp Production Technology, the Oceanic Institute Shrimp Manual. Oceanic Institute, Honolulu. |
IIIE 14. Using Bioinformatics to Research Shrimp Disease
Background
In the 21st century, biology is undergoing a transformation from being a purely lab-based science to being an information-based science. Advances in DNA-based technologies, such as genome sequencing, have led to an explosion of genetic information being generated by the scientific community. Biology, computer science, and information technology have merged into the new field of bioinformatics to solve the problems associated with storing, organizing, indexing, viewing, and analyzing the mind-boggling volume of data. It is routine now for scientists to search databases and perform extensive Web-based searches as they analyze results, formulate specific hypotheses, and design new experiments.
By helping scientists in many different disciplines advance their understanding of basic biological processes, the rapidly emerging field of bioinformatics is leading to advances in the diagnosis, treatment, and prevention of many diseases affecting humans and other organisms. Scientists studying marine pathogens use the same bioinformatics tools as scientists studying human diseases.
Aquaculture products such as shrimp are a significant source of protein in many countries. Some of these products carry foreign pathogens and harmful parasites that are harmless to humans, but that in a global marketplace can spread quickly, infecting aquaculture and wild stocks around the world, with devastating consequences. White spot syndrome virus (WSSV) is one disease that threatens the global shrimp industry. WSSV has the potential to infect cultured shrimp and incur a mortality rate of 100 percent of the population within 3 to 10 days. The potentially fatal virus has been found to be a threat not only to all shrimp species, but also to some freshwater crustaceans such as crab and crayfish. The threat of the virus spreading from farms into coastal waters and infecting other crustaceans is of great concern.
Using bioinformatics tools, what kind of genetic sequence information can be gathered on white spot syndrome virus? Discover how the sequences can open doors to more information about this virus and the species of shrimp it infects. This activity will teach students to locate a DNA sequence in a database and learn a little about how genetic information is posted for other scientists to use. Using discoveries from other scientists around the world, they can begin to understand how the viral DNA compares to DNA sequences in other organisms. While it sounds challenging, there are no wrong answers here—only information to be gathered and analyzed.
BLAST, basic local alignment search tool, is a computer-based system that allows scientists to enter DNA sequences and compare them to other sequences stored in a large database. Results of a BLAST search may tell scientists what species the DNA came from, what other genes encode proteins similar to the ones they entered, or a wealth of other information.
To conduct a BLAST search, at least two sequences must be input: a query sequence (also called the target sequence) and a sequence database. BLAST will find subsequences from the query that are similar to a subsequence in the database. The query sequence, which may be as long as one thousand nucleotides, is compared to a database that contains several billion nucleotides. The BLAST Web server is hosted by the National Center for Biotechnology Information (NCBI). Anyone with a Web browser can perform similar searches against constantly updated databases of protein and DNA sequences. Newly sequenced organisms are constantly being added to the database. This activity will guide students through an actual BLAST search.
Students will first locate a WSSV sequence in the Entrez function of the NCBI Web site and then run a BLAST search using that sequence.
PDF file for this project
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What information on specific gene sequences can be gathered from the NCBI BLAST Web site? |
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Students will explore the BLAST section of the NCBI Web site to learn about resources that can be |
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Computer with Internet access |
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One class period |
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Part 1: Obtaining a Gene Sequence from the Entrez Function of NCBI Web Site 1. Go to the NCBI Web site http://www.ncbi.nlm.nih.gov/. 2. First you will use the Entrez function of the site to search for a WSSV DNA sequence. To search for a sequence, select “Entrez Home” located on right side of the page under "Hot Spots." 3. In the Entrez window, click on “GenBank” on the top bar to open a nucleotide databank that provides access to many sequences. How many bases are stored in GenBank (the first paragraph indicates how many)? 4. Change the pulldown search menu to "Nucleotide." Enter the letters “WSSV” in the search box and click on GO. 5. The page that opens will display a list of numbers. Each number corresponds to a scientific paper about the shrimp virus. What are the first five papers dealing with WSSV? Open one paper and list one author. In which country was the study conducted? 6. The genetic sequence for a part of the WSSV genome will be visible at the bottom of the page. Cut and paste the sequence information into a Word document. Accuracy is critical as this sequence will be used in the next part of the activity. Part 2: Performing a BLAST Search 1. Go to the NCBI Web site, http://www.ncbi.nlm.nih.gov/. 2. Click on “BLAST,” which appears on the menu across the top of the page. 3. The BLAST section of interest is nucleotides only. Select the "nucleotide blast" program under "Basic BLAST." 4. The new BLAST window will have an “Enter Query Sequence” box near the top. Cut and paste the WSSV sequence you found earlier into the search window. It is critical that the WSSV genetic sequence be copied correctly. To insure accuracy, cut and paste the sequence, with the numbers, into the search box. 5. Below the SEARCH box there are many changes that can be made to search parameters and other options, but those can be explored at another time. Only two adjustments will be made to the search parameters at this time. Look carefully at the menu. Use the drop down database menu in the "Search Set" section to change the "Human genomic plus transcript (Human G + T)" to “Non-human, non-mouse ESTs (est_others).” The “nr” refers to nucleotide results. The “est_others” refers to expressed tag sequences that are small parts of larger genes that have not been entirely identified yet, and “others” refers to organisms other than human and mouse. 6. Finally, scroll to the bottom to “BLAST” for results. Hit the BLAST button. The results page may take a minute or two. It depends on how many other researchers are chasing after any number of the millions of sequences on the NCBI site at the same time this search is being conducted. 7. A Nucleotide Sequence page will appear. View a page that shows several other sequences from the data bank that have a high similarity to the WSSV sequence. If your result reads “No significant similarities found,” copy a second WSSV sequence and try again. 8. The Query ID number in the upper left side of the page denotes the search identification number. Use the mouse to move the cursor over the graph. The graph displays how numerically close the sequence came to others in the databank. Each line can be selected, and the following information on that sequence will appear: • The sequence alignment comparison |
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1. Why is it important that a database of all genetic sequences be created? 2. What kinds of information can researchers get from being able to search and align 3. What does “est_others” mean? How about “est_mouse”? What can we learn from incomplete sequences? 4. How has the ability to sequence genes and blend computer technology with life sciences affected scientists’ ability to conduct research? 5. How many bases are stored in GenBank? 6. What are the first five articles listed that deal with white spot syndrome virus? Give only the title of the article. 1. 7. List one author of the first paper 8. In what country was the study conducted? 9. What is the Query ID number? 10. Locate the graph of the comparison (pass cursor over the box to the left) to be sure all information appears. What is the Line One information? Click on the line to show nucleotide alignments (this feature shows the genes that the query 11. How many gaps and misalignments are there in the sequence? 12. What is the genus or species of the organism? 13. What is the sequence access number (the “gi” number) that allows location of the sequence at a later date? 14. What is the genetic source of the information? 1 DNA or 1 RNA (Check one) |
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1. Why is it important that a database of all genetic sequences be created? A database of all genetic sequences allows scientists to look at the degree of similarity among disparate genetic information from huge numbers of different organisms. This information is important in many types of research, including examining the genetic basis of disease and disease resistance. This database also allows researchers to look at the “relatedness” of different populations of the same organism and allows scientists to post discoveries in a place where they can be easily accessed by any researcher in the world. This allows scientific 2. What kinds of information can researchers get from being able to search and align sequences? They can see how closely related one gene in an organism is to another. This allows scientists to look at how certain genes may have evolved over time. It also allows scientists to compare genetic sequences of one organism with another in a user-friendly program. 3. What does “est_others” mean? How about “est_mouse”? What can we learn from incomplete sequences? The term “est_others” means expressed tag sequences (small, incomplete sequences) of newly discovered genes in organisms other than humans or mice. The term “est_mouse” means the partially expressed tag sequences of all of the mouse genes that have been discovered so far. Newly discovered sequences can be compared to all mouse sequences to look for differences. A partial sequence may be completed by another researcher’s lab in another part of the world. 4. How has the ability to sequence genes and blend computer technology with life sciences affected scientists’ ability to conduct research? Unprecedented speed and enhanced collaboration are facilitated by computers. We cannot even begin to grasp the impact computers have had on scientific research. Research has been able to move at lightning speed, and projects such as the Human Genome Project are living proof. Without computer capabilities, the Human Genome Project would have taken many, many years. Only through the development of computer programs that can rapidly analyze and organize sequence data was the blueprint of human life able to be determined. BLAST Search Questions: 89 billion in GenBank, 108 billion in the WGS division as of August 2009 6. What are the first five articles listed that deal with white spot syndrome virus? Give only the title of the article. Paper titles will look similar to these: 1. GQ328029 Shrimp white spot syndrome virus isolate 03 VP28 gene, complete cds 2. GQ328028 Shrimp white spot syndrome virus isolate 03 VP19 gene, complete cds 3. Shrimp white spot syndrome virus isolate SDDL18/04 envelope protein VP19 (VP19) gene, complete cds 4. Shrimp white spot syndrome virus isolate SDDL18/04 envelope protein VP28 (VP28) gene, complete cds 5. Shrimp white spot syndrome virus unkonwn mRNA 7. List one author of the first paper 8. In what country was the study conducted? After running the sequence through the BLAST search, look for the following features and answer the questions. Answers will vary, depending on results of each search. 9. What is the Query ID number? 10. Locate the graph of the comparison (pass cursor over the box to the left) to be sure all information appears. What is the Line One information? Click on the line to show nucleotide alignments (this feature shows the genes that the query 11. How many gaps and misalignments are there in the sequence? 12. What is the genus or species of the organism? 13. What is the sequence access number (the “gi” number) that allows location of the sequence at a later date? 14. What is the genetic source of the information? 1 DNA or 1 RNA (Check one) |
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IIIE 15. Navigating the National Center for Biotechnology Information (NCBI) Web Site
Background
The National Center for Biotechnology Information (NCBI) was organized in 1988 to help researchers organize and obtain genetic information. Through the use of mathematics and computer programming, DNA data can now be stored and used by scientists to advance their genetic work. The NCBI site allows scientists to align their genetic sequences with those that have already been entered into the site. This speedy analysis greatly enhances their research because millions of sequences can be matched to help decode DNA sequences. The Web site has many other functions, such as being able to show gene locations on the chromosome and models of the 3-D structure of proteins encoded by specific DNA sequences.
PDF file for this project
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What is bioinformatics? What resources are available on the NCBI Web site? |
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Students will learn about the new field of bioinformatics and the many resources now available to scientists and educators on the NCBI Web site. |
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Student work sheet “Exploring NCBI” |
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One class period |
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Go to: http://www.ncbi.nlm.nih.gov/. Follow these instructions and complete the work sheet “Exploring NCBI” included here. Although the amount of information available on this Web site may appear overwhelming, this activity will focus on only a few aspects of the NCBI Web site. This work sheet will provide a guide to the field of bioinformatics and to the process of finding a gene (gene mining) and analyzing and understanding the accompanying information. 1. Read through the explanation of what NCBI does, found under “What does NCBI do?” on the home page. 2. A left sidebar menu of links allows access to a variety of information used in biotechnology research. Select the link “About NCBI.” In the new window, select “NCBI at a Glance." This will open a window displaying several menu items. 3. Read the “Our Mission” section, including the “General Introduction,” “Creating NCBI,” and “Basic Research” sections. Pay special attention to the “Basic Research” information. Go back to “NCBI at a Glance” (hit the “back” button). Select the “Programs and Activities” menu item. Another section titled “Basic Research” and “Databases and Software” will appear. Read through both of these sections. 4. The next steps will guide you through the process of locating a gene (DNA sequence) in the database and understanding how it fits into the process of finding cures for disease in animals and humans. Go back to “NCBI at a Glance.” Select the link “A Story of Discovery.” Pay special attention to “Discovery of Disease Genes.” How does NCBI help identify new genes that code for proteins that may cure diseases? What is “GenBank” and how is it different from a bank that deals with money? How are gene discovery and NCBI helping to find cures for diseases? |
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1. What is the field of bioinformatics? 2. What does NCBI do? 3. What is the mission of NCBI? 4. What are some of NCBI’s programs and activities? 5. How have computers changed biological research? 6. What is a story of discovery through NCBI resources? 7. How are gene discovery and NCBI helping to find cures for diseases? |
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1. What is bioinformatics? The merger of biotechnology and information technology with the goal of revealing new insights and principles in biology 3. What is the mission of NCBI? As a national resource for molecular biology information, NCBI’s mission is to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. More specifically, the NCBI has been charged with creating automated systems for storing and analyzing knowledge about molecular biology, biochemistry, and genetics; facilitating the use of such databases and software by the research and medical community; coordinating efforts to gather biotechnology information both nationally and internationally; and performing research into advanced methods of computer-based information processing for analyzing the structure and function of biologically important molecules. 4. What are some of NCBI’s programs and activities? Basic Research—Scientists from various disciplines from molecular biologist to computer scientists work at NCBI to study fundamental biomedical problems. Some of the problems they address include detection and analysis of gene organization, repeating sequence patterns, protein domains and structural elements, creation of a gene map of the human genome, and mathematical modeling of the kinetics of HIV infection. NCBI scientists also collaborate with numerous institutions and academic institutions. GenBank is DNA sequence database. NSBI scientists build the database from sequences submitted by individual laboratories and by data exchange with the international nucleotide sequence databases. NCBI supports and distributes a variety of databases for the medical and scientific communities. Entrez is NCBI’s search and retrieval system that provides users with integrated access to sequence, mapping, taxonomy, and structural data and graphical views of sequences and chromosome maps. BLAST is a program that executes sequence searches against the entire DNA database in less than 15 seconds. NCBI also has e-mail servers that provide an alternative way to access the databases for text searching or sequence-similarity searching. 5. How have computers changed biological research? Computers have greatly accelerated scientists’ ability to analyze, store, compare, and share data, especially DNA sequences. Computer software helps scientists model DNA and protein structure. Collaboration between scientists is faster as research information can be shared over the Internet. 6. What is a story of discovery through NCBI resources? • NCBI resources helped researchers identify genes that cause diseases. 7. How are gene discovery and NCBI helping to find cures for diseases? One example of gene discovery: the HNPCC gene that causes colorectal cancer was identified using NCBI gene bank resources. This information has been used to develop blood tests to identify carriers and initiate medical care to save lives. |
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IIIE 16. The NCBI PubMed: Accessing Scientific Publications
Background
Accessing the scientific results of other researchers is an essential component of a successful research program. Scientists are constantly reading and analyzing results published by other researchers to find clues to their own research puzzles. PubMed is an Internet-based service of the National Library of Medicine that provides scientists access to over 14 million citations from MEDLINE and additional life sciences journals. PubMed is one of the many resources and databases developed and maintained by the National Center for Biotechnology Information to promote a better understanding of the molecular processes that affect human health and disease.
This activity will direct students through the steps to locate scientific publications.
PDF file for this project
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How do researchers search for scientific papers that may be relevant to their area of research? |
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Students will |
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Computers with Internet access |
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30 minutes |
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Go to http://www.ncbi.nlm.nih.gov/. Use the student work sheet to accompany these instructions. Select the link “PubMed” in the upper left corner. This is a scientific library that stores millions of scientific publications from all over the world and makes them instantly accessible. Some publications are abstracts only and those publications need to be purchased, but some are free publications that can be printed out. 1. Enter “cancer” in the search box and hit return. This is a search by subject. This search method is used to find general information quickly. How many hits do you get on this subject? Look carefully. What are the top five articles? Write them down on the student work sheet. How can you narrow the number of search results you get back? 2. Enter “coral” in the search box and hit return. How many hits do you get? Record the references for the top five articles. 3. Search by author. Enter “Leong J C” in the menu box and hit the search button (sometimes listed as Leong J A). This author is a well-known virologist who has been doing research on fish viruses for many years. Locate two papers by Jo-Ann C. Leong. What are the titles? Confirm the author. Use the reference section of one of the papers to open another paper by Leong. What is this new title? 4. Now perform a PubMed search on a topic of marine biotechnolgy research you are interested in, for example a specific fish disease or natural product derived from a marine organism. Describe your search criteria and your results. |
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1. What number was listed for the number of citations hits on the subject of cancer? 2. Number of entries, or hits, for the “coral” search: ________ 3. Locate two articles by Jo-Ann Leong 4. Under reference section, locate another paper by JA Leong. Title:____________________________________________________________ 5.Now perform a PubMed search on a topic of marine biotech research you are interested in, for example, a specific fish disease or natural product derived from a marine organism. Describe your search criteria and your results. 6. How do you think NCBI pub med services would be of benefit to scientists? |
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1. How many citations (entries) on the subject of Cancer?: 1,695,347; The number may vary with each search. This may vary with each search as the database changes. 2,656; the number may vary with each search . Articles will vary with each search. 1. Misumi I ,Vella AT, Leong JA, Nakanishi T, Schreck CB 2. Alonso M,Kim CH, Johnson MC, Pressley M, Leong JA, The NV gene of snakehead rhabdovirus (SHRV) is not required for pathogenesis, and a heterologous glycoprotein can be incorporated into the SHRV envelope. J Virol. 2004 Jun;78(11):5875–82. Confirm the author. If the publications originated at Oregon State University or the Hawaii Institute of Marine Biology the author JA Leong is the JoAnn Leong you searched for. All this information can be located on one Web site that lists biotechnology research papers. A computer search makes it easy for scientists to locate scientific papers by topic. This method is so much easier and faster than searching through libraries or journals to find the same articles. |
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IIIF 18. Exploring the Risks and Benefits of Biotechnology in Aquaculture
Background
Controversies are stirring throughout the U.S. and other nations over the application of biotech innovations to food production and genetic modification of organisms. While biotech has provided tools that have helped scientists make tremendous strides forward in research and medical and consumer product development, how these tools and advances are used raises many societal and ethical questions. Public fears center around making changes to organisms at the genetic level with little information about the long-range ecological and health effects these changes might bring. The most ardent controversies center on genetically modified foods and the effects they might have on the general population. In this activity, students will explore some of the risks and benefits of the use of these technologies from the perspective of various “stakeholder” groups.
PDF file for this project
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What are the arguments for and against using biotechnology techniques in aquaculture settings? |
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Students will explore concerns about applying biotechnology to food production and develop their own arguments for or against its use and application in aquaculture. |
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Computers with Internet access |
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Two class periods with independent research as homework |
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1. View the video Harvest of Fear, a PBS/NOVA production that explores issues related to genetically modified foods. Purchase the video here or view the content on the PBS website for the video here. Have students read the article “Marine GEOs: Products in the Pipeline” (IIIA8) 2. Break the class into small groups. Individuals in each group will take on the roles of: a. Marine biotechnology researcher studying fish diseases in aquaculture settings 3. One or more students in each group can represent each of these stakeholder perspectives. Allow the students time to conduct some Web-based research on the ethical and social issues raised by the video and this activity. • What are the key concerns and motivations of each stakeholder? 5. Each team then presents their main points of their discussion to the entire class. 6. Extension or supplemental activities could include preparing flyers or posters advocating each point of view, preparing research papers on these topics, or having students interview actual members of these stakeholder groups (scientists, aquaculture facility managers, consumers). |
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