11.5.15

Data Nugget Workshop at NABT 2015: A Tail of Two Scorpions

You can get the slides from our NABT talk here: A Tail of Two Scorpions

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6.29.15

Salmon in hot water

Chinook salmon in Alaska.

The activities are as follows:

Pacific salmon are important members of freshwater and ocean food webs. Salmon transport nutrients from the ocean to freshwater habitats, and traces of these nutrients can be found in everything from trees to bears! Salmon also support sport and commercial fisheries, and are used for ceremonial purposes by Native Americans. Climate change poses a threat to salmon populations by warming the waters of streams and rivers where they reproduce. To maintain healthy populations, salmon rely on cold, freshwater habitats and may go extinct as temperatures rise in coming decades. Warm temperatures can cause large salmon die-offs. However, some salmon individuals have higher thermal tolerance and are better able to survive when water temperatures rise.

Eggs used in QTL experiment

Eggs used in QTL experiment

Salmon individuals and populations may be better able to survive in warmer waters because they have certain gene variants that help them survive under these conditions. Scientists want to know whether there is a genetic basis for the variation observed in salmon’s thermal tolerance. If differences in certain genes control variation in thermal tolerance, scientists can identify the location on the genome responsible for this very important adaptation. Once identified, management agencies could then screen for these genes in populations of salmon in order to identify individuals that could better survive in a future warmer environment. Hatchery programs could also breed thermally tolerant fish in an attempt to preserve this important fish species.

Scientists working in the lab

Scientists working in the lab

To identify the genes responsible for a particular trait, scientists look for Quantitative Trait Loci (QTL). A QTL is a genetic variant that influences the phenotype of a polygenic trait, such as human height or skin color, and perhaps thermal tolerance in salmon. Scientists can find QTL by conducting experimental mattings then examining the phenotypic and genetic characteristics of the offspring. In this study, parent fish from one population of salmon, some that are tolerant to warm water and some that are not, mated and produced offspring. These offspring now had a mix of genetic backgrounds from their parents, meaning that some offspring inherited genetic variants that made them more tolerant to high temperatures and some did not. Each offspring was tested for their thermal tolerances, and had their genomes sequenced. Differences in the genome between offspring that are tolerant and those that are not reveal areas of the genome that are correlated with thermal tolerance and survival in warm water. If differences in certain genes control variation in thermal tolerance, the scientists predicted they could find regions in the salmon genome that are correlated with survival in warm water.

Featured scientists: Wesley Larson, Meredith Everett, and Jim Seeb from the University of Washington

Flesch–Kincaid Reading Grade Level = 10.9

There are two scientific papers associated with the data in this Data Nugget. The citations and PDFs of the papers are below. The lab webpage can be found here.

Check out these Stated Clearly videos to explore DNA and genes with students!

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6.22.15

How the cricket lost its song, Part I

Screen Shot 2015-06-22 at 12.41.05 PMThe activities are as follows:

Some of the most vibrant and elaborate traits in the animal kingdom are signals used to attract mates. These mating signals include the bright feathers and loud calls of birds or the swimming dances performed by fish. Most of the time the males of the species perform the mating signals, and females use those signals to choose a mate. While mating signals help attract females, they may also attract unwanted attention from other species, like predators.
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Robin is a scientist who studies the mating signals of Pacific field crickets. These crickets live on several of the Hawaiian Islands. Male field crickets make a loud, long-distance song to help females find them and then switch to a quiet courtship song once a female comes in close. Males use specialized structures on the wings to produce songs.

One summer, Robin noticed that the crickets on one of the islands, Kauai, were unusually quiet. Only a couple of years before, Kauai had been a very loud place to work; however, that year Robin heard no males singing! After taking the crickets back to the lab, she noticed that there was something different about the males’ wings on Kauai. Most (95%) of males were missing all of the structures that are used to produce the calling and courtship songs—they had completely lost the ability to produce song! She decided to call this new type of male a flatwing male. But why did these males have flat wings?

Screen Shot 2015-06-22 at 12.29.38 PMOn Kauai, songs of the male crickets attract female crickets, but they are also overheard by a deadly parasitoid fly. The fly sprays its larvae on the backs of the crickets. The larvae then burrow into the crickets’ body cavity and eat them from the inside out! Because flatwing males cannot produce songs, flat wings may help male crickets remain unnoticed by the parasitoid flies. To test this idea, Robin dissected the males to look for fly larvae. She compared infection levels for 67 normal males—collected before the flatwing mutation appeared in the population—to 122 flatwing males that she collected after the flatwing mutation appeared. She expected fewer males to be infected by the parasitoid fly after the appearance of the flatwing mutation in the cricket population.

Featured scientist: Robin Tinghitella from the University of Denver

Flesch–Kincaid Reading Grade Level = 9.1

Additional teacher resources related to this Data Nugget include:

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8.13.14

Dangerous Aquatic Prey: Can Predators Adapt to Toxic Algae?

Figure 1: Scientist Finiguerra collecting copepods at the New Jersey experimental site.

Figure 1: Scientist Finiguerra collecting copepods at the New Jersey experimental site.

The activities are as follows:

Phytoplankton are microscopic algae that form the base of all aquatic food chains. While organisms can safely eat most phytoplankton, some produce toxins. When these toxic algae reach high population levels it is known as a toxic algal bloom. These blooms are occurring more and more often across the globe – a worrisome trend! Toxic algae poison animals that eat them, and in turn, humans that eat these animals. For example, clams and other shellfish filter out large quantities of the toxic algae, and the toxic cells accumulate in their tissues. If humans then eat these contaminated shellfish they can become very sick, and even die.

One reason the algae produce toxins is to reduce predation. However, if predators feed on toxic prey for many generations, the predator population may evolve resistance, by natural selection, to the toxic prey. In other words, the predators may adapt and would be able to eat lots of toxic prey without being poisoned. Copepods, small crustaceans and the most abundant animals in the world, are main consumers of toxic algae. Along the northeast coast of the US, there is a toxic phytoplankton species, Alexandrium fundyense, which produces very toxic blooms. Blooms of Alexandrium occur often in Maine, but are never found in New Jersey. Scientists wondered if populations of copepods that live Maine were better at coping with this toxic prey compared to copepods from New Jersey.

Figure 2: A photograph of a copepod (left) and the toxic alga Alexandrium sp. (right).

Figure 2: A photograph of a copepod (left) and the toxic alga Alexandrium sp. (right).

Scientists tested whether copepod populations that have a long history of exposure to toxic Alexandrium are adapted to this toxic prey. To do this, they raised copepods from Maine (long history of exposure to toxic Alexandrium) and New Jersey (no exposure to toxic Alexandrium) in the laboratory. They raised all the copepods under the same conditions. The copepods reproduced and several generations were born in the lab (a copepod generation is only about a month). This experimental design eliminated differences in environmental influences (temperature, salinity, etc.) from where the populations were originally from.

The scientists then measured how fast the copepods were able to produce eggs, also called their egg production rate. Egg production rate is an estimate of growth and indicates how well the copepods can perform in their environment. The copepods were given either a diet of toxic Alexandrium or another diet that was non-toxic. If the copepods from Maine produced more eggs while eating Alexandrium, this would be evidence that copepods have adapted to eating the toxic algae. The non-toxic diet was a control to make sure the copepods from Maine and New Jersey produced similar amounts of eggs while eating a good food source. For example, if the copepods from New Jersey always lay fewer eggs, regardless of good or bad food, then the control would show that. Without the control, it would be impossible to tell if a difference in egg production between copepod populations was due to the toxic food or something else.

Featured scientists: Michael Finiguerra and Hans Dam from University of Connecticut-Avery Point, and David Avery from the Maine Maritime Academy

Flesch–Kincaid Reading Grade Level = 10.6

There are three scientific papers associated with the data in this Data Nugget. The citations and PDFs of the papers are below. 

Colin, SP and HG Dam (2002) Latitudinal differentiation in the effects of the toxic dinoflagellate Alexandrium spp. on the feeding and reproduction of populations of the copepod Acartia hudsonica. Harmful Algae 1:113-125

Colin, SP and HG Dam (2004) Testing for resistance of pelagic marine copepods to a toxic dinoflagellate. Evolutionary Ecology 18:355-377

Colin, SP and HG Dam (2007) Comparison of the functional and numerical responses of resistant versus non-resistant populations of the copepod Acartia hudsonica fed the toxic dinoflagellate Alexandrium tamarense. Harmful Algae 6:875-882

3.25.14

Coral bleaching and climate change

A Pacific coral reef with many corals

A Pacific coral reef with many corals

The activities are as follows:

Éste Data Nugget también está disponible en Español:

Corals are animals that build coral reefs. Coral reefs are home to many species of animals – fish, sharks, sea turtles, and anemones all use corals for habitat! Corals are white, but they look brown and green because certain types of algae live inside them. Algae, like plants, use the sun’s energy to make food. The algae that live inside the corals’ cells are tiny and produce more sugars than they themselves need. The extra sugars become food for the corals. At the same time, the corals provide the algae a safe home. The algae and corals coexist in a relationship where each partner benefits the other, called a mutualism: these species do better together than they would alone.

When the water gets too warm, the algae can no longer live inside corals, so they leave. The corals then turn from green to white, called coral bleaching. Climate change has been causing the Earth’s air and oceans to get warmer. With warmer oceans, coral bleaching is becoming more widespread. If the water stays too warm, bleached corals will die without their algae mutualists.

Scientist Carly working on a coral reef

Scientist Carly working on a coral reef

Carly is a scientist who wanted to study coral bleaching so she could help protect corals and coral reefs. One day, Carly observed an interesting pattern. Corals on one part of a reef were bleaching while corals on another part of the reef stayed healthy. She wondered, why some corals and their algae can still work together when the water is warm, while others cannot?

Ocean water that is closer to the shore (inshore) gets warmer than water that is further away (offshore). Perhaps corals and algae from inshore reefs have adapted to warm water. Carly wondered whether inshore corals are better able to work with their algae in warm water because they have adapted to these temperatures. If so, inshore corals and algae should bleach less often than offshore corals and algae. Carly designed an experiment to test this. She collected 15 corals from inshore and 15 from offshore reefs in the Florida Keys. She brought them into an aquarium lab for research. She cut each coral in half and put half of each coral into tanks with normal water and the other half into tanks with heaters. The normal water temperature was 27°C, which is a temperature that both inshore and offshore corals experience during the year. The warm water tanks were at 31°C, which is a temperature that inshore corals experience, but offshore corals have never previously experienced. Because of climate change, offshore corals may experience this warmer temperature in the future. After six weeks, she recorded the number of corals that bleached in each tank.

 Featured scientist: Carly Kenkel from The University of Texas at Austin

Flesch–Kincaid Reading Grade Level = 8.0

There are two scientific papers associated with the data in this Data Nugget. The citations and PDFs of the papers are below. 

If your students are looking for more data on coral bleaching, check out HHMI BioInteractive’s classroom activity in which students use authentic data to assess the threat of coral bleaching around the world. Also, check out the two videos below!

  • Another BioInteractive video, appropriate for upper level high school classrooms. Visualizes the process of coral bleaching at different scales. Video includes lots of complex vocabulary about cells and the process of photosynthesis.

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1.8.14

Fair traders or freeloaders?

Measuring chlorophyll content in the greenhouse

Measuring chlorophyll content in the greenhouse

The activities are as follows:

When two species do better when they cooperate than they would on their own, the relationship is called a mutualism. One example of a mutualism is the relationship between a type of bacteria, rhizobia, and legume plants. Legumes include plants like peas, beans, soybeans, and clover. Rhizobia live in bumps on the legume roots, where they trade their nitrogen for sugar from the plants. Rhizobia fix nitrogen from the air into a form that plants can use. This means that legumes that have rhizobia living in their roots can get more nitrogen than those that don’t.

Under some conditions, this mutualism can break down. For example, if one of the traded resources is very abundant in the environment. When the plant doesn’t need the nitrogen traded by rhizobia, it doesn’t trade as many sugars to the rhizobia. This could cause the rhizobia to evolve to be less cooperative as well. Less-cooperative rhizobia may be found where the soil already has lots of nitrogen. These less-cooperative bacteria are freeloaders: they fix less nitrogen, but still get sugars from the plant and other benefits of living in nodules on their roots.

Photo by Tomomi Suwa, 2013

Rhizobia nodules on plant roots. In exchange for carbon and protection in the nodules from plants, rhizobia provide fixed nitrogen for plants.

One very important legume crop species is the soybean. Soybeans are used to produce vegetable oil, tofu, soymilk, and many other food products. Soybeans trade with rhizobia for nitrogen, but often farmers add more nitrogen into the field as fertilizer. Since farms use a lot of nitrogen fertilizer, researchers at KBS were interested in how different types of farming affected the plant-rhizobia mutualism.

They grew soybean plants in a greenhouse and added rhizobia from three different farms: a high N farm, low N farm, and organic farm that used no N fertilizer. After four weeks, the researchers measured chlorophyll content of the soybean plants. Healthy plants that have lots of nitrogen will have high chlorophyll content, and plants with not enough nitrogen will have low chlorophyll content. Because high nitrogen could lead to the evolution of less-cooperative rhizobia, they expected that rhizobia from organic plots would be most cooperative. They predicted rhizobia from high N plots would be the least cooperative, and rhizobia from low N plots would fall somewhere in the middle. More-cooperative rhizobia provide more nitrogen, so the researchers expected plants grown with cooperative rhizobia to have higher chlorophyll content than plants receiving less-cooperative rhizobia.

Featured scientist: REU Jennifer Schmidt from the Kellogg Biological Station

Flesch–Kincaid Reading Grade Level = 10.1

For more information on the evolution of cheating rhizobia, check out these popular science articles:

If you are interested in performing your own classroom experiment using the plant-rhizobium mutualism, check out this paper published in the American Biology Teacher describing methods and a proposed experimental design: Suwa and Williamson 2014

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1.7.14

Cheaters in nature – when is a mutualism not a mutualism?

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The activities are as follows:

Mutualisms are a special type of relationship in nature where two species work together and both benefit. Each partner trades with the other species, giving a resource and getting one in return. This cooperation leads to partner species doing better when the other is around, and without their partner, each species would have a harder time getting resources.

One important mutualism is between clover, a type of plant, and rhizobia, a type of bacteria. Rhizobia live in small bumps on the clovers’ roots, called nodules, and receive protection and sugar food from the plant. In return, the rhizobia trade nitrogen to the plant, which plants need to photosynthesize and make new DNA. This mutualism works well when soil nitrogen is rare, because it is hard for the plant to collect enough nitrogen on its own, and the plant must rely on rhizobia to get all the nitrogen it needs. But what happens when humans change the game by fertilizing the soil? When nitrogen is no longer rare, will one partner begin to cheat and no longer act as a mutualist?

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Worldwide, the nitrogen cycle is off. Not that long ago, before farmers used industrial fertilizers and people burned fossil fuels, nitrogen was rare in the soil. Today, humans are adding large amounts of nitrogen to soils. The nitrogen that we apply to agricultural fields doesn’t stay on those fields, and nitrogen added to the atmosphere when we burn fossil fuels doesn’t stay by the power plant that generates it. The result is that today, more and more plants have all the nitrogen they need. With high nitrogen, plants may no longer depend on rhizobia to help them get nitrogen. This may cause the plant to trade less with the rhizobia in high nitrogen areas. In response, rhizobia from high nitrogen areas may evolve to try harder to get food from the plant, and may even cheat and become parasitic to plants. If this happens, both species will no longer be acting as mutualists.

When Iniyan was a college student, he wanted to study human impacts on the clover-rhizobia mutualism. To find out more, he contacted Jen Lau’s lab at the Kellogg Biological Station one summer, and joined a team of scientists asking these questions. For his own experiment, Iniyan chose two common species of clover: hybrid clover (Trifolium hybridum) and white clover (Trifolium pretense). He chose these two species because they are often planted by farmers. Iniyan then went out and collected rhizobia from farms where nitrogen had been added in large amounts for many years, and other farms where no nitrogen had been added.

Iniyan completed this research as an REU at KBS.

Iniyan completed this research as an REU at KBS.

To make sure that there were no rhizobia already in the soil, Iniyan set up his experiment in a field where no clover had grown before. He then planted 45 individuals of each species in the field. He randomly assigned each plant to one of three treatments. For each species, he grew 15 individuals with rhizobia from high nitrogen farms, and 15 with rhizobia from low nitrogen farms. To serve as a control, he grew the remaining 15 individuals without any rhizobia. To add rhizobia to the plants he made two different mixtures. The first was a mix of rhizobia from high nitrogen farms and water, and the second was a mix of rhizobia from low nitrogen farms and water. He then poured one of these mixtures over each of the plants, depending on which rhizobia treatment they were in. The control plants just got water. No nitrogen was added to the plants.

After the plants grew all summer, Iniyan counted the number of leaves and measured the shoot height (cm) for each individual plant. He did not collect biomass because he wanted to let the plants continue to grow. He then averaged the data from each set of 15 individuals. Plants with fewer leaves and shorter shoots are considered less healthy. He predicted rhizobia that evolved in high nitrogen soils would be worse mutualists to plants, while rhizobia that evolved in low nitrogen soils would be good mutualists.

Featured scientist: REU (NSF Research Experience for Undergraduates) Iniyan Ganesan from the Kellogg Biological Station

Flesch–Kincaid Reading Grade Level = 9.5

For more information on the evolution of cheating rhizobia, check out these popular science articles:

If you are interested in performing your own classroom experiment using the plant-rhizobium mutualism, check out this paper published in the American Biology Teacher describing methods and a proposed experimental design: Suwa and Williamson 2014

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