BIOTECHNOLOGY & YOU a magazine of biotechnology application in healthcare, agriculture, the environment, and industry

Volume 7, Issue No. 2

Diving Into Marine Biotechnology ○○○○○○○○○○○○○○○○○○○○○○○○

BIOTECHNOLOGY & YOU TABLE OF Volume 7, Issue No. 2 Your World/Our World describes the application of T biotechnology to problems facing our world. We C O N N S hope that you find it an interesting way to learn E T about science and engineering. Development by: The Pennsylvania Biotechnology Association, The PBA Education Committee, and Snavely Associates, Ltd. Marine Biotechnology Writing & Editing by: The Writing Company, Cathryn M. Delude and Kenneth W. Mirvis, Ed.D. ○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○○ Design by: Exploring the Diversity Snavely Associates, Ltd. Illustrations by: 3in the Sea Patrick W. Britten Science Advisor: Judy Brown, University of Maryland Center for Marine Biotechnolgy Science Reviewers: The Biotechnology Porthole Dr. Rita Colwell, Dr. Shaojun Du, Dr. William Jones, 4 Dr. Dennis Maeder, Dr. Allen Place, Dr. Frank Robb, Dr. William Straube, Dr. John Stubblefield, Dr. Yonathon Zohar (University of Maryland Biotechnology Institute’s Center of Marine Biotechnology) Special Thanks: The Ocean Superstore The PBA is grateful to the members of the 6 Education Committee for their contributions: John C. Campbell, SmithKline Beecham Kathy Cattell, SmithKline Beecham Ceil M. Ciociola, PRIME, Inc. Jeff Davidson, Pennsylvania Biotechnology Zippy Zebras Association 8 Alan Gardner, SmithKline Beecham Anthony Green, Puresyn, Inc. Mary Ann Mihaly Hegedus, Bioprocessing Resource Center Fertile Turtles Linda C. Hendricks, SmithKline Beecham 10 Daniel M. Keller, Keller Broadcasting Richard Kral Colleen McAndrew, SmithKline Beecham Barbara McHale, Gwynedd Mercy College June Rae Merwin, The West Company Life at the Extremes M. Kay Oluwole 12 Lois H. Peck, Philadelphia College of Pharmacy & Science Jean L. Scholz, University of Pennsylvania P R O F I L E John Tedesco, Brandywine Consultants, Inc. Adam Yorke, SmithKline Beecham 14 Sunny Jiang: Predicting Laurence A. Weinberger, Esquire, Committee Chair Cholera Outbreaks

A C T I V I T Y 15 Taking it to Extremes!

If you would like to make suggestions or comments about Your World/Our World, please contact us at: Internet: [email protected] or write to: Resources Pennsylvania Biotechnology Association 16 1524 W. College Avenue, Suite 206 State College, PA 16801 On the Cover: Deep-sea submersible vessels like the Alvin help us explore the diverse life forms beneath the sea. This and other modern technologies help us study our marine world, combining Copyright 1998, PBA. All rights reserved. research, conservation, and education to understand and protect our earth’s precious natural resource, the ocean. Credits: Cover image, JASON Foundation for Education Page 10, Copyright © 1930 by Ogden Nash Reviewed, reprinted, by permission of Curtis Brown, Ltd Page 13, Reprinted from Journal of Molecular Biology, Vol 270, Figure 10, Lim J-H, Yu Y, Han Y, Cho S, Ahn B, Kim S, Cho Y, “The crystal structure of an Fe-superoxide dismutase from the hyperthermophile Aquifex pyrophilus at 1.9 Å resolution: structural basis for thermostability” pp259-274 (1997), by permission of the publisher Academic Press Limited.

2 Marine Biotechnology INNTTHHEESE E ITYY I SEA EX RSSIT A X P IVVEER P LLOORIN G T H EEDDI Question: RIN G T H What has the oldest, most numerous, most diverse, and least studied life forms on earth? What covers almost three- fourths of our planet but is our greatest untapped resource? Where do creatures thrive in temperatures of 121°C (250°F)? What could provide food to the starving people of the world but is having its supplies endangered by over-

harvesting and pollution? Plankton Answer: The sea, the sea, the beautiful, Photos Courtesy of JASON Foundation for Education mysterious sea. Diatom The sea remains mysterious because it is so hard to Biotechnology helps us study the explore. It is wide, deep, and dark, with dangerous diverse and beautiful creatures of waves and icebergs on the surface and incredibly the sea. high pressures below. The ocean floor has mountains, canyons, and volcanoes, where Why is this study so valuable temperatures range from below freezing to above to us? Scientists have always boiling. Exploring these areas was impossible until found useful products we developed technologies such as deep-sea produced by living plants and animals. The ocean environ- submersibles, scuba, sonar, lasers, videos, and Blue Slug satellites. Still, studying marine biology remains a ments are completely challenge because so many creatures live in strange, different from our own, and marine creatures probably inaccessible places, and we can’t keep them alive produce a whole different set of useful products – a treasure and thriving in the artificial conditions of a surface chest full! Now researchers are looking to the sea for laboratory. Because of these difficulties, we have everything from a cure for cancer and AIDS to less-polluting probably catalogued fewer than 5% of marine industrial chemicals, and much, much more. organisms, much less studied them in depth. We are alsoimproving our knowledge of the world at Fortunately, biotechnology opens a another large by studying marine creatures. The window on marine life. It allows us to inspect microscopic life in the sea holds clues to the organisms at a molecular and genetic level origin of life on earth – and to global cycles of – and to do so quickly, before oxygen, carbon, and nitrogen. Furthermore, human activity reduces the we share many genes with marine organ- incredible biodiversity isms, so we can learn about ourselves by of life in the sea. studying them. What helps them stay healthy may also help us. Likewise, what hurts them may harm us. This issue of Your World/Our World shows how biotechnology is making the mysteri- ous sea more understandable and useful to us, while also allowing us to protect its precious resources. So put on your snorkel and mask, and dive into our underwater biotechnology laboratory to explore this last earthly frontier.

Your World Our World 3 iotechnology and molecular biology can shed light on the Binnermost life processes of the organisms that live in the sea’s deep, dark, inhospitable places. Here are a few techniques that give us a peek through that porthole. Proteins and Enzymes All organisms produce proteins to build cells and perform the functions of life. Certain proteins, called enzymes, carry out biochemical processes within cells.

Scientists are studying these and other organisms for their scientific and medical value.

Top to bottom, left to right Coral Reefs are to the sea what tropical rain forests are to the land: teeming with species that may have medicinal value, yet vulnerable to destruction by human activity. Puffer Fish secrete a deadly poison that scientists use to study neuromuscular transmission in people. Striped Bass could help feed a hungry world. But they are declining in the wild, and they are hard to breed in fish farms. Genetic Sea Turtles are exposured to research may overcome these difficulties. chemicals that may interfere with (Pages 8 –9.) their egg development. These chemicals may harm mammals as well. The Sea Sponge has defense mechanisms (Pages 10 – 11.) that could someday help you reduce inflammations, fight bacterial and fungal The Squid’s nerve axons serve as a model infections, and perhaps cure cancer. system in neuroscience. (Pages 6 – 7.) Submersible Vessels help us explore the Sharks live in a microbe–infested world,so deep and collect samples for further study. they secrete a steroid disinfectant that kills We can also learn about past climates germs on contact. Some sharks contain a and geological events on earth. substance “squalamine” that cuts off the Thermophiles thrive near the blood supply to tumors and is being tested volcanic heat of these deep-sea vents, for treating cancer. and we might be able to use these Crabs and Shrimp have molecules with unusual organisms for medicine and many uses in every day life and science. industry. (Page 7.) (Pages 12 – 13.)

4 Marine Biotechnology We use the proteins and enzymes as assembling proteins. Variations in Antibodies ingredients in everything from that gene provide a yardstick for When a bacterium or medicines to soap. Analyzing their how closely organisms are related. virus invades your body, chemistry teaches us about their This yardstick gives us a new your immune system roles in the organism’s biology – and panoramic view of the world’s produces an antibody that their potential benefits to us. “family tree.” It also gives us a latches onto that microbe to DNA and Genes shortcut to identifying unstudied destroy it. Scientists use antibod- marine organisms and screening DNA is the informa- ies to “see” a hard-to-detect them for useful products. tion molecule that tells marine microbe: They tag the each organism how to PCR (polymerase antibodies with special labels that develop, giving each cell its chain reaction) identify the microbes when the antibodies lock onto their target. special characteristics. DNA Single fragments of DNA forms genes, which are sequences of are too tiny to manipu- codes that “spell out” the recipes for late in the laboratory. They proteins. We can learn about a need to be amplified just as protein by analyzing its DNA a stereo needs an amplifier to sequence. In addition, we can study make a sound signal loud enough to which genes become active in hear. PCR is a way of making many response to a threat from a predator, exact copies or clones of a tiny Swim through this or a change in temperature and section porthole to see nutrients, or pollution. By tracking of DNA, which can be used for the molecular activity of marine further research. how scientists use organisms, scientists can study their these techniques interaction with the environment Fermentation to stock the Scientists can insert a gene and gain insights into changes in shelves of the global climate and pollution. that produces a valuable marine protein into the ocean superstore Classification DNA of an easy-to-grow We classify organisms bacterium like E. coli on the next page! to tell how they are or a yeast cell. These “workhorse” related to each other. microorganisms then reproduce in Scientists used to focus fermentors and act like mini– on how organisms factories, churning out the protein. looked. If they looked Fermentation allows us to produce similar, they were the valuable natural products even probably related. Genetic compari- when we cannot grow the whole son gives us more accurate classifi- organism – or when we do not want cations. It relies on the fact that all to harvest proteins from a rare organisms share some common creature living in a fragile marine genes, such as a gene involved in ecosystem.

Your World Our World 5 SSSuperstoreTheuperstoreuperstore Ocean

elcome to the ocean superstore, the showcase of many present and future products made from marine life. Most of these items weren’t Wactually taken directly from the sea. Rather they were, or will be, “inspired” by products found in the sea. W. Amos, Marine Biology Laboratory W. This sea sponge (Cliona Celata) is just one of many marine organisms that produce proteins and other molecules that may fight inflammation, infection, and even cancer. infections, strengthen or weaken the courtesy of: B. Lies, Marine Biology Laboratory immune system, or fight cancer. They are looking for clues to treat Gianluca Rocco Cone Snail These two venomous animals can wound or even kill deadly infectious diseases such as humans, but their poison also contains ingredients that AIDS, Ebola, and drug-resistant can heal us. Doctors are already using blood pressure medication derived from the rattlesnake’s forms of tuberculosis. poison. Scientists are developing a blood-clotting medication from proteins contained in the cone As you can imagine, searching snail’s venom to treat hemophilia. for new medicines in the vast ocean could take forever if you their preda- simply followed nature’s clues. The Pharmacy Aisle Fortunately, genetic screen- Our oldest medicines were leaves, tors. They ing gives scientists a faster, flowers, and barks, and many defend themselves more precise way to search. modern drugs come from such by producing bad-tasting Suppose you find a species that natural products. Organisms produce or toxic chemicals. Scien- produces a weak anti-cancer proteins, hormones, starches, and tists tested this hypothesis by protein. Perhaps one of its cousins other chemicals to help them survive studying the sponge’s slimy secre- might produce a more potent in their environment. These products tion. Sure enough, it contains toxins protein. How can you find that often have a different effect in human that drive predators away – as well cousin? In the old days, you would beings. For example, the rattlesnake’s as a chemical that reduces inflam- compare their physical structures. poison contains chemicals that lower mation in people. This chemical Today, you compare their genes. blood pressure in people. Until now, prevents the release of an “arachi- The more similar the genes are, the most products used for drugs came donic” (ah-rak-id-on-ik) acid that more likely they produce a product from the land rather than the sea. plays a key role in the biochemical with similar functions. Computers But that may soon change. processes of pain and swelling. Aspirin also works by disrupting the can analyze millions of genes and How do you find new medicines in production of this inflammatory target species with anti–cancer the sea? One way is to follow clues acid. Scientists are adapting the proteins. In this way, you can screen of nature. For example, scientists chemical to develop new anti- thousands of species to find the few noticed that a sponge from the coral inflammatory ointments for treating that may be worth studying further. reefs of the Pacific, Luffrariella bee stings, poison ivy, arthritis, Scientists expect these methods will variabilis, looks good enough to eat, psoriasis, and gout. speed up our search for new medi- but predators leave it alone. Maybe cines from the sea – and fill the the sponge uses the tricks of land Scientists also test the products of pharmacy shelves. plants which can’t run away from marine organisms to see if they stop

6 Marine Biotechnology GRIND & FIND Biotechnology allows us to sample and test huge numbers of marine organisms for useful products. Scientists then reproduce those products synthetically rather than harvesting them directly from the marine environment. Here’s the process for searching for medicinal proteins:

1 2 Extract the proteins Test the proteins to see produced by if they show activity each organism against cancer cells, that is sampled inflammations, and/or using a physical microbial infection. Scientist, Dr. William Jones Scientist, Dr. (perhaps Marine biologist Bill Jones explains how bacterium grinding) or acinetobacter helps clean up oil spills and degrease chemical these shoe parts after they are taken from their molds. procedure.

CG A T T A CG A T T A CG A T T A The Cleaning Aisle CG A T T A CG A T T A CG A T T A CG A T T A Check the labels of the soaps and CG A T A T CG A T T A A A T T G detergents in this aisle. Most of them CG A T A T CG A T T A list surfactant as an ingredient. A CG A T T A CG A T T A surfactant reduces the surface CA C G G T 3 C A G T G C A G T G tension of the water at the dirt’s A C G T G surface, loosening the dirt so it can Identify the genes that encode the active proteins, and search for G A G T C be washed away. Certain organisms other organisms with similar genes. Repeat steps 1 and 2 until the T A G C G most effective protein is found. A G C T G produce natural soaps called biosurfactants. One marine microbe named Acinetobacter put on a great show following the 1989 Exxon Valdez oil spill off the Alaskan coast. Its biosurfactant loosened the oil 4 from the sand and rock so the Take a copy of the gene for the most effective protein and insert it into “workhorse” organisms. These workhorses then produce bacteria could break down the oil. the protein when they are grown in large numbers. The proteins Now, Acinetobacter is grown com- are grown first in a small flask, then the whole process is “scaled up,” and the proteins are grown in huge fermentation tanks. mercially to help clean up oil spills. It also has a potential job in another industry. The Nike shoe factory 5 coats the molds for its running shoes Purify the active proteins from the fermentation process and with an oily compound so the plastic prepare them into a final product. shoe parts won’t stick. Afterwards, Thousands of organisms are tested as in steps the parts have to be cleaned. Rather 1 & 2, but VERY FEW go through steps 3-5. than using chemical solvents to dissolve the grease, the company is ice cream. It draws out impurities DNA. It may also create a new type of experimenting with Acinetobacter, from substances, so it helps purify adhesive that hardens under water. the environmentally friendly

materials in research laboratories Dentists could use Shave, Marine Biology Laboratory Photo by P.A. cleaner-upper. and treat drinking water. It absorbs such an The All-Purpose Aisle fat, so it is used in alternative diet adhesive on Many of the foods and drugs in this medicines. New research shows it braces and superstore contain additives derived breaks down the barriers between to glue from shellfish. Their shells contain a cells in the stomach and intestines, teeth back long molecule called chitosan (kite– so it may be used to help your body into the jaw o–san) that is a kind of starch or absorb medicines more completely. It after being Mollusks helped cloak polysaccharide. Chitosan is a gets inside cells, so it may become a knocked out! the ancient Phoenicians molecule of many uses. It acts as a delivery vehicle for gene therapy, in their royal purple robes, thanks to a dye gel and thickening agent in foods like taking “repair” genes into a cell’s derived from their slime.

Your World Our World 7 Fish for a Lifetime ums. The zebrafish is easy to breed in captivity An old saying goes, “Give people a fish and they and matures quickly, so it provides a wonderful can eat for a day. Teach them to fish and they can model for studying both fish reproduction and eat for a lifetime.” As the world’s population developmental biology. Now it is also helping to grows larger, the saying rings truer than ever. Fish solve the striped bass’s reproductive problems provide a healthy, nutritious meal, but the ocean “down on the farm.” is so overfished that many nets come up empty. Model Species: Different Stripes, Pollution in the coastal waters where fish spawn Similar Genes (breed) has also reduced the supply of fish. The zebrafish and the striped bass have Luckily, the aquaculture “fish farm” industry has Marine biologist different stripes, sizes, and life spans. Still, come to the rescue, breeding food fish in captivity Ernest E. Just wrote a they are genetic cousins. They start out to increase their supply. Unfortunately, one land-mark work on fish embryology in 1939. traveling the same developmental path, popular and nutritious food fish – the striped bass The U. S. Postal Service controlled by similar genes. – does not like life in the fish farm. It won’t spawn has honored Dr. Just with a commemora- All vertebrates, from fish to humans, have a in captivity. tive stamp. remarkably similar early development. That’s Scientists are learning why because we all have an almost identical set of “master not by studying the genes” that govern early development. Scientists call these zebrafish. This little fish master genes homeodomain genes because they all share zips around many house- a very similar region, the homeodomain, in their se- hold freshwater aquari- quences. (“Homeo” means “same” in Greek, and a “domain” is a kind of home). You can think of homeodomain genes as highways with toll booths. The highways (genes) are different, but they have an almost identical toll booth section (homeodomain region). Homeodomain genes work like an electri- cal circuit breaker in a house, controlling the action of other genes further down the line. One set of homeodomain genes controls the reproductive pathway. As species develop along this pathway, they acquire different reproductive characteristics. Fish spawn, birds lay eggs in a shell, and mammals have live births. Among fish species, further differences appear in the reproductive wiring. Somewhere down that reproduc- tive circuit is a gene that gets switched off when a striped bass lives in captivity.

8 Marine Biotechnology Crabby Detectives Human Americans are eating more seafood these days. Naturally, the seafood industry has grown Within these look-alike dramatically – and so embryos, homeodomain has seafood fraud. Some merchants genes program the cells misrepresent common for increasingly specialized fish for more roles in developing tissues. desirable, As these tissues specialize, higher priced species become distinct ones or from each other. they call soy- based products “crab meat.” Fish Others sell illegal seafood, such as whale meat. Now, the same technology that brought DNA fingerprinting into the courtroom can help food inspectors detect the deception. They can take samples of the seafood, extract its DNA or the proteins encoded by the DNA, and find out what species it really is. k messenger in the body. This particular hormone signals repro- Once again, biotechnology helps duction, so without enough of it, fight crime and protects the aver- ▼ The aquaculture industry has the fish does not breed. Now that age citizen! transferred genes into fish to make scientists know more about the them grow bigger than normal, to gene that encodes that hormone, survive in waters colder than their scientists know more about the natural habitats, and to resist gene that encodes that hormone, disease. Scientists keep them in a they can mimic its function by closed system so they won’t breed increasing the hormone level in with wild fish. What might happen if other ways. They are also trying to the fish escaped their farms? Is this make striped bass spawn at an What advantage a risk worth taking in order to earlier age, and even to spawn year ABOU T does aquaculture provide more food for the world? round instead of just once a year. K T

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Eventually, scientists hope to H T stock farming for transfer the zebrafish’s natural the environmental Scientists are trying to coax the switch gene into the striped bass to striped bass to reproduce in captiv- !! resources of a try to correct the reproductive ity. If they can isolate the gene that country? Consider the land, problem from the start. Splicing the water, and feed required to switches off in the striped bass, they zebrafish gene into the site that gets can transfer that gene into the raise farm animals, and the “shut down” in captivity may allow organic waste produced. zebrafish. By observing how that the remaining reproductive circuitry gene affects the zebrafish, scientists to function as normal. If these will learn more about how it behaves efforts succeed, the world will have a in striped bass. much more dependable supply of Scientists already know that in healthy, nutritious food fish. captivity the striped bass does not release enough of a hormone, which is a molecule that acts like a

Your World Our World 9 Research on the diamondback terrapin is shedding light on this mystery. Sea turtles and terrapins are different species, but they are similar Fertile enough that scientists can use terrapins as a model to understand sea turtles better. Turtles Mother Nature’s Enzyme Turtles When the temperature in the diamondback terrapin’s nest is The turtle lives ‘twixt plated decks, above 30°C, all the hatchlings usually become females. Below which practically conceal its sex. 27°C, they will all be males. (The nests in the middle temperature I think it clever of the turtle, range produce a mix.) Higher in such a fix, to be so fertile. temperatures switch on a gene that produces an enzyme called aromatase. Aromatase converts a by Ogden Nash

male hormone (androgen) into the ○○○○○○○○○○○○○○○○○○○○○○○ female hormone estrogen. Estrogen Sea turtles have to be clever to be tells the embryo to develop ovaries fertile – so their species will and become female. At cooler survive. The hatchlings leave their temperatures, the gene for nests on the sand and waddle into aromatase is not switched on, so no the waves to spend their lives at estrogen is produced, and the sea. When it’s time for the female embryos develop into males. to lay her average “litter” of over However, scientists found that some 100 eggs, she returns to her nests kept at the cooler temperature birthplace and builds a nest. are producing females instead of males. To find out why, they coated Al Place, Center of Marine Biotechnology, Baltimore, MD Al Place, Center of Marine Biotechnology, Trouble in the Nest some eggs in cool nests with estro- The diamondback terrapin almost became extinct in Things have gotten tougher for the the early 1900s because it made such a tasty gen. The eggs absorbed the estrogen turtle in recent years. Often, the gourmet soup. Now it is swimming in a soup of man- and developed into females. Even made chemicals. It spends its life in estuaries where female returns to her birthplace to fresh water from rivers and streams mixes with though the embryo cells did not find a house nearby, an RV racing seawater. Most of these rivers and streams carry produce their own estrogen, the pollution, so the diamondback is exposed to more along the sand, and pollution pouring chemicals than animals that live in the open ocean. estrogen from the outside “environ- into the sea. Together, these obstacles ment” had the same effect as natural put many species of turtles in a estrogen would have had. struggle for survival. To make matters worse, the sex ratios of Thus, changing the estrogen levels turtle hatchlings may be out of in the embryos overrides the balance. There are not natural temperature control that enough males! Why not?

10 Marine Biotechnology scrambling is especially bad in t if embryos, since fetal cells are WhA extremely sensitive to the signals The debate about global ? that tell them how to develop. In warming is really heating up! If turtles, the effect is powerful enough world temperatures really are to override the temperature control, rising, how might turtles be producing too few males. affected? The Human Connection Why should you care about the determines sex. Some scientists fear turtle’s fertility problems? Well, understand how our that pesticides and other chemicals you may care about the survival of bodies react to in the environment may be jump- endangered species. If there hormones and starting the estrogen reaction in the aren’t enough males, the turtles chemicals at a same way. will soon molecular level. Chemicals Mimicking Hormones become Scientists have extinct. developed systems of cells that Hormones are shaped like keys that produce the same response to can lock into a keyhole or receptor But the turtle’s hormones as a whole organism. on the cell membrane. When a troubles may They can use these systems to test hormone locks into the receptor, it hit closer to the effects of chemicals in the can send a message inside to the home. Other species environment. By studying how DNA. This message tells the DNA to are exposed to the same chemicals turtles are affected, we may find out turn on a certain gene, like turning in the environment. In our mam- how to protect them – and the world on an ignition key to start an engine. mal cousin, the otter, the male at large – from the onslaught of It so happens that many human- reproductive organs decrease in estrogen-mimicking chemicals. made chemicals have a very similar size as the concentration of shape to the estrogen molecule, so pesticides in their bodies in- they “mimic” estrogen in a cell. creases. Perhaps these chemicals There are at least 50 such chemicals have overridden a mechanism in that mimic estrogen. They are used the development of otters. If so, We use so many products in our daily in everything from agriculture to could they be affecting other lives that contribute to estrogen- making plastic and mammals? Some scientists suspect mimicking chemicals in the environ- paper, so they are that human sperm counts have ment: paper, plastic, garden prod- just about declined worldwide because of ucts.... In addition, livestock is often everywhere in the these chemicals. Research into given estrogen to stimulate growth, environment. these issues continues, and you and we absorb that estrogen when These chemicals can follow their development in we eat meat. Do the benefits we get accumulate in animal tissue, where the news. from these products outweigh the they can scramble the genetic One thing is clear: Biotechnology harm we might be doing to other instructions for the cells. This and molecular biology can help us species and ourselves? The Dooming of a Species 90 days later . . . Hey, we're ALL girls! 30˚C I'm gonna be a 27˚C I'm boy! gonna be Uh, oh! a boy! Who will I mate with?

Without enough males, the Below 27ûC, the embryos Estrogen-mimicking species cannot survive. do not produce estrogen chemicals from the environment and should become males. override the temperature control gene, so the embryos become female. Your World Our World 11 Your World Our World 11 Woods Hole Oceanographic Institution Woods

“Black Smoker” and Tube Worms. The mineral rich, super- heated water that spews out of deep-sea vents forms chimneys and supports many colorful creatures and hearty “extremophiles.”

ome aboard a submersible as cal bonds join these amino acids we sink into the freezing together into a three-dimensional Cwater toward the ocean floor. shape, which allows the enzyme to Our lights cut through the blackness interact with cells and molecules. and shine on weird creatures that Thus, the enzyme’s function de- get their energy from minerals in the pends on its structure. Extreme water rather than sunlight. Up ahead conditions, such as high tempera- looms a steaming chimney, spewing ture, acidity, or alkalinity, can break out sulfuric liquids from volcanic the bonds that stabilize an enzyme’s Life at the activity within the earth’s crust. structure. When this happens, the Inside the chimney walls, where it is enzyme no longer functions and 121°C (250°F) and the pressure is may even fall apart. Enzymes from 200 times that at sea level, some extremophiles, however, continue microbes contentedly eat sulfur functioning partly because they while others give off methane gas. have extra stabilizing bonds to hold How do they keep from getting them together. cooked, not to mention crushed to This difference has great commer- death? And why do they choose to cial significance, since we use live there? enzymes to promote chemical In fact, they like these conditions and reactions for industrial and com- would die in less extreme environ- mercial applications. For example, ments like our own. Indeed, their enzymes help convert corn syrup to environment probably resembles our sugar for soft drinks and improve planet when life first began millions the cleaning power of laundry of years ago. We call microbes that detergents. Unfortunately, many still live in such extreme conditions enzymes stop working in the extremophiles. The Greek word extremes of industrial processes. “philo” means “lover”. The ones that But the extremophile enzymes, live in these hot vents are thermo- outfitted with their extra-stable philes. (“Thermós” means “hot” chemical bonds, keep on in Greek.) going ... We learned just how useful the durable enzymes can be from Extra-Stable Enzymes the very first extremophile to be Extremophiles may be very useful to discovered, a thermophile that lives us because they produce enzymes in the hot pools of Yellowstone that act as “survival suits” against National Park. extreme conditions. Hot Bugs in Yellowstone All enzymes consist of building No one thought it was possible for blocks called amino acids. Chemi- organisms to survive in boiling temperatures until a very surprised A bacterial mat at a Yellowstone hot pool teems with scientist discovered the bacterium thermophile organisms. Thermus aquaticus (for “hot water”)

Extremes Photo courtesy of Judy Brown

12 Marine Biotechnology process was quite slow and expen- When you dive to BOU sive. Today, scientists use the A T the bottom of a

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keeps working through repeated heat H pressure in The deep-sea vents occur where T water comes in contact with hot cycles and quickly produces millions your ears. How magma beneath the earth’s crust. of copies of DNA. This technique, can you scuba called “PCR” or the “polymerase ! dive! so much deeper without The hot water dissolves minerals and metals, mixes with gases, and chain reaction,” has automated DNA ruining your ears? bursts to the surface. The dissolved replication and revolutionized all metals precipitate as they meet the areas of biotechnology and genetic freezing water of the ocean, forming research. chimneys. These chimneys are gold Scientists are studying the mines, containing gold, silver, and structure of other Archaea other precious metals. Some extremophile enzymes to Many extremophiles belong to a countries would like to mine these The learn more about their chimneys for their metals. But unique properties. They branch of life called Archaea. The same word “Archaea” comes from the marine biologists claim the volcanic hope to find other same root as “archaeology,” which genetic value of the forces form amazing applications extremophiles around these the Yellowstone that will bring more is the study of ancient things. vents is worth more than their hot pools and technological Scientists think that Archaea are so weight in gold. Is it worth deep-sea vents, breakthroughs. ancient that they evolved when the endangering the ecosystem and the same extremo For example, earth as we know it was still that could prove so -philes live in both places. extremophiles forming. But we did not know Thus, although the hot pools valuable tomorrow to gain can protect Archaea existed before scientists are not marine (ocean water), wealth today? and repair studied the Yellowstone hot pools. marine biologists use Yellowstone Once people began to look for as an extremophile laboratory their DNA from heat and such life forms, however, they found because it is so much more them everywhere, not just in accessible than acid. Perhaps extreme environments. In fact, deep-sea vents. their enzymes can be tailored Archaea may be the most common living in a Yellowstone hot pool to protect us from organisms in the ocean. in the 1960s. Today, this “hot bug” is DNA damage caused by toxic When Archaea were first discov- quite a celebrity. One of its enzymes pollutants, radiation, and other ered, scientists did not agree on is used to sustain a chemical reaction harmful elements. This protection how to classify them. Biotechnology that happens naturally in cells: the could prevent cancer and other solved the dispute. Analysis of their replication or copying of DNA. A cell diseases. So now, when scientists go genes showed that about one half uses an enzyme called “polymerase” “shopping” for new genes to develop of their genes are completely to copy the DNA. Scientists were medicines and industrial products, unknown to us. Many of these using the polymerase from an they check out the “catalog” of unusual genes probably build their ordinary bacterium to copy DNA in extremophile genes and proteins, survival suits for their extreme the laboratory. To do so, they heated and they look to the oceans! environments. ▼ the DNA sample over and over to make copies in a process called thermal cycling. However, the enzymes only made one copy and then stopped working because the heat broke down their structure. More enzymes had to be added for each

Photo courtesy of Sandra Nykerk cycle, so the Journal of Molecular Biology, author Lim J-H, et al Journal of Molecular Biology, Superoxide dismutase from Aquifer pyrophilus. Red Superoxide dismutase from Mycoplasm tuberculosis blue colors show bonds that hold the enzyme that is unstable even at 70oC. There are far fewer of together at temperatures up to 100oC. the red and blue bonds holding the enzme together. Marine biologist Judy Brown collects samples from a hot pool in Yellowstone.

Your World Our World 13 Sunny Jiang

Sunny Jiang uses biotechnology to understand the relationship between cholera outbreaks and weather patterns. In her spare time, she trains for marathons.

unny became interested in tests. Sometimes the bacterium will marine science when she was not grow in cultures, so laboratories Sin middle school in China. cannot detect it. Also, many strains “We lived on a harbor and I loved don’t carry the form of the gene that the beauty of the animals and the causes disease. So even if we detect blue colors of the sea water,” Sunny the bacterium, we still don’t know if it muses. She planned to major in will cause disease. Luckily, we can use marine environmental science in biotechnology to overcome these college. However, her parents problems.” In one method, the wanted her to become a doctor, so scientists run water through a filter to she studied pre-medicine with a collect all the bacteria. They attach major in biochemistry at the Nankai specially tagged V. cholerae antibodies University in Tainjin. “In China it is that allow them to detect that bacte- traditional for parents to influence rium in the water. Then, they use the career choices of their children,” PCR and other techniques to analyze Sunny laughs. “But I still wanted to this bacterium to see if it is a disease- follow my dream, so I accepted a causing strain. graduate fellowship at the University Sunny’s team studies samples of V. of South Florida.” cholerae collected from outbreak Sunny earned her Ph.D. and now areas around the world. They isolate works in a research laboratory at the and culture disease-causing strains of University of Maryland Biotechnology the bacterium and compare their Institute’s Center of Marine Biotech- genetic structure to strains in other nology. This research team uses areas. This analysis may show that a

Profile: biotechnology to study how global disease-causing strain is moving into weather patterns such as El Niño a new area. “If it is, we can warn the contribute to the spread of cholera. people there to take preventive Cholera is a life-threatening disease measures, such as boiling or filtering carried by a waterborne bacterium their water,” Sunny explains. “We’re Vibrio cholerae. Cholera outbreaks also trying to link the presence of V. often occur during the summer in cholerae in water samples with areas near stagnant estuaries (bays). changes in the water’s characteris- The El Niño weather pattern distrib- tics, such as its salinity, temperature, utes more warm, moist air around and levels of plankton. We use the globe, affecting the circulation satellite data to help get these and temperatures of estuary waters. measurements. It’s really cool to These changes may increase the combine technology from space with numbers of V. cholerae and make genetic analysis of marine organisms them more deadly. to save human lives!” “People might not know that the cholera bacterium is in their water until the disease strikes,” Sunny This Coastal Zone Color Scanner image of the Bay of Bengal in India , shows a plankton bloom associated explains. “That’s because it’s hard to with cholera a outbreak. detect using standard water quality

Background photo courtsey of: CZCS Project, NASA Goddard Space Flight Center.

14 Marine Biotechnology ACTIVITY:ACTIVITY:I

Location What They Love Name Example Sea ice cold Psychrophile Polaromonas he ocean contains many environments that vacuolata are completely different from our own: to Deep-sea vent heat Thermophile Pyrolobus start with, it’s salty. In many places, it’s way fumarii T Deep sea pressure Barophile Colwellia too cold for our comfort, but organisms from hadeliensis whales to algae to microbes call it “home sweet Sulfuric spring acid Acidophile Sulfolobus home.” Others find the high pressure at the ocean acidocaldarius Soda lake alkali Alkaliphile Natronobacterium floor cozy. But extremophiles don’t just live in the gregoryi sea. The chart to the right shows some of the Saltern salt Halophile Haloferax volcanii places they like. Cliffs rocks Lithotroph Thiobacillus ferrooxidans In this activity, you will recreate some of these Desert dryness Xerophile Xeromycees extreme conditions and see how they affect the bisporus proteins in a “normophile” cell. You will use a cell that is big enough to see without special equip- ment: a chicken egg. Could this cell survive in an Hypotheses extreme environment? What do you think will happen to Materials the proteins in a raw egg when they • 5 raw eggs, cracked open carefully so the yolk are exposed to those five extremes? remains intact Do you think the proteins can protect themselves from damage? • 5 bowls or cups to hold the raw eggs and the liquids below Can they repair the damage once they are removed from the extreme About 10 ml of the following: condition? • A 9% solution of salt (9 grams salt to 100 ml water); Experiment and Find Out Develop a way to test your • A 9% solution of bleach (pH 12) hypotheses using the materials • Vinegar (acetic acid, pH 4.5) suggested. Write up your proce- • Boiling water dure, record your data, and Freezer develop a theory about the nature of normophile Focus proteins. How can you simulate the following extreme conditions: high salinity, alkalinity (high pH), acidity (low pH), extreme cold, and extreme heat?

YourYour World World Our Our World World 15 Resources Dear Students:

Sail The Seas his issue on marine biotechnology allows us to dip beneath the surface of our planet’s oceans The 1998 World’s Fair in Lisbon, Portugal is devoted to the ocean. If you can’t make it to the fair, you can take a virtual trip and learn T and discover amazing worlds populated by a about the marine world along the way. Pick your travel plan to this tremendous variety of fish, mammals, and microorgan- permanent learning and entertainment center: isms. We hope you enjoy exploring this world and 1) Fly by space shuttle and use remote sensing technology to study learning about marine biotechnology research. whale migration and the ecological system that supports this largest We hope that having a better understanding of the re- mammal on earth. You can also study the ocean’s weather: www.seawifs.gsfc.nasa/gov/OCEAN_PLANET/HTML/oceanogra- search taking place in this and other rapidly developing phy/ fields of biotechnology will encourage you to study science 2) Sail across the ocean on the research vessel Eagle. Use naviga- and mathematics. Perhaps you will select biotechnology as tional tools and research instruments to study whales. For terrific a career and help discover tomorrow’s science. National Geographic images, visit: chili.rt66.com/hrbmoore/ NGSImages/NGS.html 3) Submerge yourself in the Jason, an underwater exploration vessel Sincerely, that explores the deepest parts of our oceans. Visit hyperthermal vents, climb mountains and canyons, and see marine shows: www.jasonproject.org 4) For video clips of thermal action, see www.pmel.noaa.gov/vents/ Jeff Davidson geology/video.html Executive Director, Pennsylvania Biotechnology Association 5) Lisbon at last! Once at the permanent virtual World’s Fair, follow a student guide to the Ocean Supermarket display of all the everyday products derived from the sea. Visit the world’s largest and most modern aquarium: expo98.pt.pt.default.html PBA would like to acknowledge University of Maryland Go Surfin’! Biotechnology Institute’s Center of Marine Biotechnology for their assistance and support in preparing this issue of Your • Thermophiles: whyfiles.news.wisc.edu/022critters/hot_bact.html World/Our World. • Extremophiles: www.sciam.com/0497issue/497marrsbox1.html • Deep-sea vents: www-step.uscd.edu~personal/bartram/html.96/ We are able to publish Your World/Our World only because of index.html the support of the companies and organizations listed below. Please join us in thanking them for their support: • Marine pharmacology: www-csgc.uscd.edu/communication/MP.html • National Cancer Institute’s Division of Natural Products “Cancer Sponsors Web:” www.graylab.ac.uk/cancernet/600733.html The Alliance for Science Education Biotechnology Industry Organization • Columbus Center for Marine Biotechnology: Centocor, Inc. www.columbuscenter.org Fisher Scientific, Inc. • Marine Biological Laboratory: www.mbl.edu Merck Institute for Science Education • Woods Hole Oceanographic Institute: www.whoi.edu Pasteur Mérieux Connaught Rhône-Poulenc Rorer Gencell • National Ocean Science Bowl: core.cast.msstate.edu/nosb.html TosoHaas Beach Reading PECO Energy Company Planet Ocean: Making Sense of Science Series, by Brian Bett Supporting Organizations Utah State University Biotechnology Center Start Exploring Oceans: Discover the Wonders of Life Underwater, by Massachusetts Biotechnology Council D.M. Tyler and J.C. Tyler Maryland Bioscience Alliance

Underwater Wilderness: Life in America’s National Marine Sanctuar- ies and Reserves, by Charles Seaborn Young Scientists Undersea, by C. Pick SUBSCRIPTION INFO G Your World/Our World is designed to bring biotechnology to life by featuring scientific discoveries and applications in a clear and informative way. Issues on different topics in biotechnology are published each Fall and Spring. If you would like information on subscribing (individual, teacher, and library sets are available) or on sponsoring distribution to teachers in your area please call the Alliance for Science Education/Pennsylvania Biotechnlogy Association at 800.796.5806. Twelve previous issues have been published and some back issues are available.

Photo courtesy of Marine Biology Laboratory 16 Marine Biotechnology