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Effect of environmental toxins on GATC methylation in E. coli May 3, 2011

Posted by ljsteele in Biology, Chemistry, Ecology, Environment/Conservation, Evolution, Genetics, Health, Marian University curriculum, Physiology.
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With the end of the semester drawing near it is becoming that time again when the results are piling in from research you have been working on all semester. As we speak, the final data collection and analysis is taking place in biochemistry, a team of student researchers are exploring of environmental toxins of DNA methylation  in the bacterium E. coli. 

The Bacterial Genome

Bacteria exist throughout the world and can survive in almost any climate . Bacteria are unicellular and can consist in a wide range of environments such as a pond all the way to soil.  One unique attribute of the bacterial genome is that it contains adenine methylation , opposed to mammalian organisms which contain cytosine methylation at GpC islands.  Adenine methylation is when a methyl group becomes attached to the adenine nucleotide on the DNA. When a methyl group is donated from SAM to form a covalent attachment, it is made on the adenine which can cause steric hindrance of transcription factors and differential effects of DNA binding proteins, which can contribute to a change in gene expression.  In previous studies  it has been shown when E. coli is exposed to different carbon sources (ie glycerol or glucose).  Some areas of the genome become demethylated.  In the bacteria E. coli almost every adenine (A) in the GATC sequence is methylated.  To block the methyation at the GATC sequence, a protein must be present to inhibit the DAM methyltransferase from depositing a methyl group on the adenine.

What does Methylation do?

Adenine methylation has many roles in bacteria. Methylation can effect gene expression, cell cycle, virulence, and how proteins interact with the DNA. For the research we are performing, we are concerned with what effect the environment has on changing adenine methylation on the GATC repeats. There are about 20,000 GATC repeats in the E. coli genome and under normal log growth conditions almost every single repeat is methylated. It has been found that when bacterial cells are in a log growth phase there are 6-10 sites which are not methylated. These nonmethylated sites lie up and down stream of promoters of different genes. The lack of methylation may allow DNA binding proteins to modulate their function to allow a functional change in gene expression.

Pollutants and the Genome

In the study we are performing we wanted to see how three classes of chemicals pollutants commonly found in the Midwest affect adenine methylation at the GATC site. We choose three pollutants to represent chemicals that fit into the families of common water pollutants, which are heavy metals, chlorinated compounds and nitrogen rich compounds.Gel Electrophoresis

The above families of compounds will be compared to samples collected from different areas around the campus of Marian University, Indianapolis, IN. Supplements will be added to all the samples to generate a rich liquid media that will facilitate bacterial growth.  With 6 different test groups and 2 controls we are going to seek to determine if any of our known compounds or a compound present in our environmental sample has an effect on the methylation.  The determination of methylation can be done by using restriction enzyme digest with endonuclease selecting specifically for the nonmethylated site.  The enzyme we have chosen was MBO and AVI.  When all the genomic DNA from the bacteria is extracted and digested, then it will be ran on a gel to be imaged to determine if the bands of digested DNA differ depending on the chemicals present during growth.  This is a time efficient way to examine if any changes in methylation levels have occurred.

What Does It All Mean?

For conclusion, the relevance of this study includes a few things.  This study will provide evidence to show if environmental toxins have an effect on bacterial DAM methylation. One role bacteria play in an ecosystem is influencing the flow of nutrients which support plant and algae growth. The results of our proposed study may display that toxins have an effect on methylation patterns which could lead to an increase the mutation rate of the bacteria genome itself.   Destructive mutations may decrease bacterial populations leading to a disruption in the ecosystems nutrient flow, hence disruptions in plant and algae growth with effect additional aquatic and terrestrial organisms.

Carbonic Acid: Not Just for Coca-Cola Anymore. April 30, 2011

Posted by tsublett in Chemistry, Climate Change, Ecology, Environment/Conservation, Policy.
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We sit at an critical point in time with the looming threat of global warming. The world is being changed, but the exact extent of that change is now coming to fruition. Ocean Acidification is one facet of global change that is not being addressed at the same level as, say global warming. Nevertheless, oceanic acidification is going to become a global concern in the next twenty years because its effects are very damaging.

How bad is Ocean Acidification?

Oceanic acidification is not a new phenomenon. According to a February 2009 article in Scientific American:

Oceans naturally absorb the greenhouse gas; in fact, they take in roughly one third of the carbon dioxide released into the atmosphere by human activities. When CO2 dissolves in water, it forms carbonic acid, the same substance found in carbonated beverages. New research now suggests that seawater might be growing acidic more quickly than climate change models have predicted.

"Present day" (1990s) sea surface pH

This article explains that the ocean is responsible for the bulk of the work in recycling atmospheric gases. The problem, though, occurs in the rate of carbonic acid formation. “Research at the University of South Florida has shown that in the 15-year period 1995-2010 alone, acidity has increased 6 percent in the upper 100 meters of the Pacific Ocean from Hawaii to Alaska,” according to an article on Ocean Acidification from Plumbot.com

The carbon cycle is a popular topic today. We talk about emissions and about the amount of CO2 given off by an SUV versus a Prius, but what we do not talk about is how detrimental CO2 can be to oceanic processes. The ocean recycles CO2 by converting it into carbonic acid via the reaction:

CO2 + H2is in equilibrium with H2CO3

Is There a Consensus?

Representation of the carbon cycle.

Carbonic acid is not necessarily a bad thing, but concentration influences its danger. I can drink a can of soda and I won’t see any detrimental effects. The sugar may cause problems, but not to a level of lethality. In the ocean, though, the stakes are higher. According to Jason Hall-Spencer, a researcher at the University of Plymouth, “Many of the marine species having calcium carbonate based external skeletons, including corals and mollusks, are affected because, as water becomes ever more acidic, calcium carbonate concentrations in the water decrease, leaving them with little resources to build their skeletons on.” Also, “Marine ecologist J. Timothy Wootton of the University of Chicago…and his team discovered that the balance of ecosystems shifted: populations of large-shelled animals such as mussels and stalked barnacles dropped, whereas smaller-shelled species and noncalcareous algae (species that lack calcium-based skeletons) became more abundant.” This trend is also true of herring populations. According to an articlein the Seattle Times, “For example, computer models suggest that, if acidification reduces one type of plankton eaten by herring, herring populations may go down. But if acidification hits a different plankton species, the number of the fish could in fact increase. In another hypothetical scenario, potential declines in invertebrates such as urchins and sea cucumbers might be less than first expected because their predators — sea stars — decline, too.” Dr. Busch is saying here that the effects of Ocean Acidification are so complex, that it will be difficult to really predict what will be affected.

How Does this Affect Me?

It is clear that, though we would not necessarily be directly affected by ocean acidification, the organisms that feed fish we use commercially could decline, resulting in a detrimental effect on the fishing industry in general. That alone may spark much interest into determining the root cause of oceanic acidification and move individuals into steps geared at remedying this problem. According to Cheryl Logan, in an article from BioScience: “Changes in ocean chemistry will probably affect marine life in three different ways: (1) decreased carbonate ion concentration could affect the calcification process for calcifying organisms (e.g., corals); (2) lowered pH could affect acid-base regulation, as well as a variety of other physiological processes; and (3) increased dissolved COcould alter the ability of primary producers to photosynthesize.”

But I Live in Indiana!

The research that was done here, though it has many implications for the future, does not necessarily focus on the problem of fresh water resources. The ocean, by far, is the largest CO2 sink due to its size, but not much research has really been put into freshwater testing of acidification, other than the testing of acidification by direct dumping. The research that Maria Solis and I performed this year at Marian University attempted to test this theory, that freshwater resources would experience the same process of acidification.

Though we did not definitively prove any new groundbreaking theories about acidification, we think that we are on the right track. For us, the ideas about ocean acidification do not hit very close to home in land-locked Indiana, but we know that lakes are commonplace. We wanted to do something that not many have done before, look at natural acidification based on dissolved CO2 compared with chemical dumping.

For our experiment, we wanted to observe the effects of high and low CO2 concentrations on plant growth rate and snail shell formation. When looking at plant growth rate, we hypothesized that the increasing levels of CO2 would increase the growth rate in plants at lower CO2 levels. The rate would increase to a point, until acidification would lead to a decrease in plant metabolic functions. Testing photosynthetic rate, or in our case growth rate, is a good measure of CO2 metabolism. Photosynthesis depends on sunlight and CO2, so increasing the level of substrates would definitely increase the level of metabolism in the plants that we chose to use. We chose to use three types of plants to get a range of growth rates. We used a common aquarium plant, Egeria densa. For a secondary plant species, we chose Elodea densa.  Finally, for use as a invasive species control, we chose to use Vallisneria, a freshwater species of eelgrass. Eelgrass is an invasive species, that according to Gabriel Garche in his article entitled “Water Acidification Process Reveled by Marine Life,” “seagrass exploiting the excess of carbon dioxide seems to be thriving.” Also, to test the effects of carbonic acid on benthic organisms, we also included mystery snails (a species of Pomacea bridgesii).

A direct image of tanks used during our experiment

To establish an effective experiment, we obtained six, ten gallon tanks, into which we placed plants into the first three. We placed around 4-5 snails into each of the six tanks. We wanted to simulate the effects of dissolved CO2, so we placed stone bubblers into four of the tanks, into which we bubbled varying amounts of CO2. For two of the four tanks, we used stone bubblers that had room air bubbled into them. So, in total, we had three tanks with plants, all six with snails, four with CO2, and two with room air bubblers. See Photos below:

We were unable to measure dissolved CO2, so we used Vernier dissolved O2 sensors to measure the change in dissolved oxygen as a function of time. Also, we used pH probes to measure the change in acidity as a function of time. To measure photosynthetic rate, or rather metabolic rate, we measured all plants prior to experiment starting time, to develop a before-and-after measurement that would confirm growth rate. Also, we weighed all snails as a function of tank, measuring all by mass and volume to determine shell growth  rate. These measurements gave us a benchmark from which we would determine the level of growth as a function of tank. The experiment was carried out for several days.

Low CO2 (Snails and Plants)

Unfortunately, due to time constraints. We were unable to conclude much from the experiment itself.

Due to the fact that the water we used was fresh water, the pH sensors, based on their configuration for measuring ions, did not register much of a pH change. We will need to find a better method for measuring pH in non-alkaline solutions. An interesting effect we observed was in the snail populations. We observed that all snails in the high CO2 environments died, most likely due to the lack of oxygen. This result was not in keeping with our hypothesis of reduced shell growth, but does speak to the effects of a high CO2 environment on snails. The snails in the tank with low CO2 and no plants died as well. We saw some die in the tank with low CO2 that included plants, but not all died. This seems to indicate that the plants in the tank were able to utilize enough of the CO2 as to provide the snails with oxygen. The tanks with air bubbled in showed all living snails. 

The dissolved O2 sensors were sporadic at best. They needed water movement to best determine the dissolved O2. We ran out of CO2 early in the experiment, so without movement, our sensors were unable to register consistent measurements of dissolved O2. We will, in the future use bigger CO2 tanks to get a more prolonged test, so that our O2 sensors may become more effective in giving us detailed results. We also observed plant growth in all tanks. So, we were not successfully able to quantitatively determine what we set out to determine, i.e. pH and dissolved O2, the death of our snails and the growth of our plants gave us a qualitative result that demonstrated that the plants grew in this environment, but that the snails were unable to thrive.

The experiment, if it could be carried out for a longer period of time, would likely demonstrate a trend. This trend would show that the tanks that had high CO2 bubbled into it with plants would show a slower trend of dissolved O2 trending toward a higher CO2 rate. The plants would show growth at a rate higher than the control tank that had room air bubbled into it. The snails would probably not show much change in size, but would most likely thrive better in the tanks that contained the plants that had room air bubbled into. The rate of CO2 bubbling would need to be scaled back, so that our snails would have a chance to thrive in the high CO2 tanks. That way we would be able to measure relative growth rates based on mass and volumetric displacement. The high CO2 tank that contained snails that had no plants would most likely show death of snails, if no growth rate at all.

With these results, we would prove that acidification of freshwater can occur, but most likely not to the level observed in the ocean. This is due to a lack of calcium carbonate in the water itself, a molecule that interacts with CO2 to form carbonic acid.

With an understanding of the crisis that awaits us if CO2 is continually added to the water supply, we must begin to take steps to mediate acidification. One way to do this is to stop adding more CO2, allowing the algae and other CO2 metabolizing organisms to work to reduce the oceanic concentration. Hopefully, with the boom in growth rate that would be observed, the rate of acidification can be slowed to a degree that would diminish detrimental effects. Only time will tell if acidification of both the ocean and freshwater resources will be as detrimental as projected, or if mankind can do something about it. This crisis will affect all of us, if not directly. We need to think and act now.

April 5, 2011

Posted by Dr. O in Biology, Ecology, Environment/Conservation, Institute for Green & Sustainable Science (IGSS), Marian University curriculum, Physiology, Science Education.
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Congrats to Marian University’s very own, Cassie Freestone! Check out her spread (click on picture to expand) in the Spring 2011 issue of Marian University’s magazine, The Magnet.


Cassie Freestone has participated in numerous independent research endeavors at Marian University from a rigorous summer research course at the Institute for Green & Sustainable Science, to taking independent research credits. Her research experience has given her the toolkit to attract and succeed in internship opportunities like this international marine research study.



Stress and the GI Tract December 17, 2010

Posted by ljsteele in Behavior, Biology, Chemistry, Ecology, Environment/Conservation, Health, Neuroscience.
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The mechanics of stress and the gut.

Stress is shown to have a huge effect on the body, whether or not it is experienced as an acute or chronic stress.  A major topic of interest is what effects stress has on the gastrointestinal tract in organisms.  According to a multi-part scientific paper entitled “Stress and the Gastrointestinal Tract”, there are many different stressors that can be examined within a variety of organisms.  Examples of the stressors explored include food deprivation, fearful sounds, weather changes, and water avoidance ( an acute stressors explored in lab organisms such as mice, rats, and guinea pigs).  It has also been shown that acute stressors in humans, such as pain exposure, anger, fear, and intense exercise can cause gastrointestinal shut down.

From the stressors listed above, research has explored how stress influences gastro muscles to slow contraction,  thus inhibiting the processing of food.  An interesting reaction to this slowing of peristaltic movement is the fact that many organisms lose control of their colon, showing defecation in response to certain stimuli such as fear and water avoidance.  Corticotropin releasing hormone, also known as CRH  (or CRF, as identified in the aforementioned paper), is released from the hypothalamus, and blocks the effects of the vagas nerve, while also traveling through the solar plexus, and attaching to receptors in the stomach.

Stomach ulcer

Once bound, this hormone has been shown to inhibit gastro movement, and thus preventing emptying of the stomach. The difference between the stomach and the colon is that the stomach requires contraction of the muscles to push food through, whereas the colon requires contraction to keep bowel movements inside the body.  With the effect of CRH binding to the receptors, relaxation in gastrointestinal muscles occur, which is why the release of the colon sphincter results.  However, the results explored here were in response  to short term stressors.  The effects of long-term stressors have yet to be studied.

Stress and Ulcers

What does this research mean to you?  Well, the results we glean from research like this offer powerful implications for human medicine and today’s society.  Many people not only experience acute stress, but chronic stress as well.   Short term affects of acute stress include accelerated of heartbeat and an increase in metabolism, but it is only natural to ponder the long term effects of chronic stress.    We can extrapolate from the results of  acute stress that it would make sense that we, as humans, would not want these effects to be long lasting.  Major problems would arise with the decrease of gastro movement.  Problems manifest from a build up of bile and stomach acids in the stomach.  Since gut motility is decreased when stressed, less movement would mean that more bile, which is highly acidic, would sit in the stomach longer and could lead to stomach or intestinal ulcers.

Sympathetic Nervous System

Chronic stress can also lead to a decrease in the immune system of the organism as well as a decrease in the second messenger systems within the body.  An example of this effect on a second messenger system is the attachment of CRH to CRH-receptors in the solar plexus.  The binding of these receptors causes the effect of the decrease in gastro movement.

How much stress is too much stress?

Lastly, with chronic stress and chronic stimulation of the CRH/CRF system, we might see a scenario in that the more that these receptors are activated, the more desensatized they can become. This could cause problems for people and their response to stress.  If the are “desensitized” this may mean that these people have a problem when trying to   properly responding to an acute stressors when needed.

Frogger, More Than just a Game December 12, 2010

Posted by zach in Biology, Chemistry, Ecology, Environment/Conservation, Health.
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As a child you learned that a frog isn’t born as a litGraphic depicting life stages of a tadpole to a frogtle frog, but rather its life begins as an egg and develops into a frog through metamorphosis. This poses a lot of interesting questions for molecular biology because appendages have to grow at the same time the tadpoles tail is lost. The frog is an ideal model organism for how morphological changes can take place, since frogs are so easily kept in captivity it’s easy to manipulate their environment. When you are able to change their environment it makes it easier to identify what hormones, enzymes, or other environmental cues influence how the tadpole develops into a frog.

One hormone that has been shown to affect the metamorphosis of tadpoles is thyroid hormone (TH). In the presence of dilute concentrations of thyroid hormone the frog’s metamorphosis is accelerated.   The converse is also true, when TH is blocked by compounds such as goitrogens, tadpoles will not develop into frogs but, stay in the tadpole life stage.  We know that TH acts through nuclear receptors to activate transcription or, the process of DNA going to mRNA then translated into proteins.  With many advances taking place in the field of biochemistry my question is how is the structure of the chromatin affected through metamorphosis?  What chemical present in local ponds affect the structure of the chromatin?  There are many different mechanisms in which the structure of the chromatin can be altered.


Two of the most common ways the structure of the chromatin is altered is by methylation, which is adding a methyl group to a cytosine nucleotide, or acetylation, which is the process of adding an acetyl group on to the lysine residue on histones. Both methylation and acetylation can function to change gene expression. Methylation causes a steric hindrance for the transcriptional machinery and acetylation alters how much the gene is exposed to transcriptional machinery.  Both methylation and acetylation takes place through enzymes that cause a change in how the transcriptional machinery operates.  The enzymes can be influenced by a variety of different means, for example acetylation of histone H4 lysine acetylation can be blocked by Nickel compounds.

The question that I want t0 ask is what effects are on the epigenome, when frogs are exposed to pollutants at different life stages? When tadpoles are exposed to high levels of Ni2+ compounds they all die. Is the death of the tadpoles a result of an absence of H4 lysine acetylation or through a different molecular mechanism?  Since epigenetic mechanisms are critical to regulating gene expression it is plausible that the epigenome is tightly correlated with tadpole metamorphosis. Since the habitats of amphibians are becoming more and more polluted, it is urgent to discover the mechanisms in which their metamorphosis acts though in order to reduce a certain group of pollutants.

Using Fish to Detect Estrogen-like Endocrine Disruptors October 15, 2010

Posted by Grace Dible in Biology, Chemistry, Ecology, Environment/Conservation, Genetics, Health, Medicine, Physiology.
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Endocrine disruptors, according to the EPA, are substances which mimic a hormone, stimulate a body to over respond to a stimulus, cause hormones to respond at inappropriate times, or cause an under/over production of a hormone.  The EPA is most concerned with endocrine disrupting chemicals that end up in the environment and affect the environment and wildlife.  Chemicals of more recent concern are synthetic, natural, and mimic estrogens.  These chemicals include 17α-estradiol (found in birth controls) and herbicides like atrazine.  Much of the recent research is trying to determine whether or not these endocrine disruptors are causing intersex fish, which could possibly lead to population declines.

This flow chart shows how endocrine disruptors may lead to sex changes in a fish population.

One way to determine the estrogenic endocrine disruptors in an aquatic environment is to use different transgenic fish as biomarkers, specifically zebrafish (Danio rerio) and medaka (Oryzia latipes).  Current research is underway in order to determine the affects of these different endocrine chemicals on bioactivity.  Both Medaka and Zebrafish can be transgenic with different fluorescent proteins, which were originally found in bioluminescent jelly fish.    At Marian University in Indianapolis, I am currently trying to determine the best methods for determining the affects of estrogen-like endocrine disruptors in transgenic medaka with green fluorescent protein (GFP).  This GFP is expressed in the liver of the fish when a large amount of vitellogenin, an estrogen inducible promoter, is in its system.  Ordinarily, vitellogenin is found in the female medaka liver, but if an endocrine disruptor is in the environment, then a male medaka may be able to express the GFP as well; the GFP is these medaka have a 100% binding affinity to 17α-estradiol.

Medaka fish expressing GFP in the liver

According to recent review on the effects of a supposed endocrine disruptor like atrazine (A Qualitative Meta-Analysis Reveals Consistent Effects of Atrazine on Freshwater Fish and Amphibians – Jason R Rohr and Krista A McCoy – January 2010  Environmental Health Perspectives), they “found little evidence that atrazine consistently caused direct mortality of fish or amphibians, but we found evidence that it can have an indirect and sublethal effects.”  These sublethal effects in fish may include a decrease in motor skills, perceiving predator risk, olfactory sensitivity, and gonadal morphology.  Atrazine may also lead to the body’s production of aromatase, an enzyme that converts testosterone into estrogen.   Studies still need to be done to see if this supposed endocrine disruptor is causing the fish population sex ratios to change or the production of aromatase.

How could this research be beneficial to human health?  Waste water treatment plants currently don’t filter out estrogen-like endocrine disruptors. Right now Dr. Paul Winchester, at the Indiana University School of medicine, is trying to determine whether there is a correlation between the supposed endocrine disruptor atrazine and birth defects.  Another focus of the research is whether or not areas with high amounts of atrazine can lead to higher rates of breast, ovarian, and prostate cancer.   Dr. Paul Winchester recently did an interview with Indianapolis based NUVO magazine to help spread information on this endocrine disruptor so that people are more aware of what is in drinking water.

To see his Dr. Winchester’s full interview click here.  To view the EPA statements on endocrine disruptors click here.

Urban ecology…right here on campus! May 28, 2010

Posted by Dr. O in Behavior, Biology, Ecology, Environment/Conservation.
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So this is our resident, young, red-tailed hawk…

(Please click on pictures for better resolution)

Red-tailed hawk (Buteo jamaicensis)

This young red-tailed hawk enjoys a very urban lifestyle on Marian University’s campus. I have watched this bird pick off fat, almost tame, squirrels as they exit a garbage can with the crust of a Subway sandwich. The hawk will narrowly, but deftly, miss flying into people’s heads as it goes in for the kill.

Today I arrived on campus, pulled into my parking spot, opened the door, and heard a ruckus of robins.

When I looked, I saw said hawk and thought, “hmm…guess the robins don’t like it roosting there”, but then when I looked closer, I realized that the hawk was IN THEIR NEST! As my jaw dropped the hawk took off with two fistfuls of nestling robins. The hawk flew to the nearest tree (where it perches above previously mentioned garbage can/squirrel haunt) and picked apart its breakfast. Amazing!

paranoid parent robin (left) and empty nest (right)

Red-tailed hawks don’t eat birds (usually), not small birds.

The hawk must’ve been watching and knew where this nest was. It’s not like it went after a fledgling not able to fly…it went INTO the nest to grab them! And the nest was fairly hidden! I think this is incredible urban behavior in a predator; not afraid of people, and exploring novel food items.

Here are two videos of the hawk eating the nestlings and of the adult robins guarding their, now empty, nest:

Here is a collection of play-by-play photos of the event:

Empty robin nest…the hawk had just taken off while I scrambled for my camera.

The hawk took off with two fistfuls of nestlings and landed on its favorite perch…20 yards away.

Red-tailed hawk eating nestling number one.

And onto nestling number 2…

Sometimes it’s a bird-eat-bird kinda’ world.

At this point, I’m under the branch and don’t have to use my zoom lens. This particular hawk isn’t scared of humans.

Note fluffy downy feathers. This was a nestling taken from the nest, not a fledgling that was on the ground.

Pin feathers are all that’s left.

More pin feathers found under now empty nest.

Pin feather

Now empty nest. As you can see, the nest is quite camouflaged from aerial predators, thus this young hawk must’ve been watching and waiting…knowing there was a nest full of tasty baby birds there.

The nest was a clutch of three. This nestling survived…luckily hawks only have two feet.  I did not return it to the nest, as it wasn’t necessarily a safe place. Parents are taking care of the baby on the ground.

Note large amount of bird poop. This is where the hawk hangs out. I’m sure it will be back to feed again on many urban creatures.

The spill from space May 4, 2010

Posted by Dr. O in Ecology, Environment/Conservation, Policy, Science & Culture.
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You can see the oil slick from space

And that’s not a good thing.  Pictures from NASA’s Earth Observatory website show the every increasing size of the oil spill that has spread across the gulf coast.

The spill from space. It's huge!

Some recent news statements have said that the slick is smaller today, but scientists warn that it means that the oil has only begun to sink to the bottom of the ocean. While it may not coat bird feathers at that point, it will kill oyster beds, kelp forests, and destroy lots of fish and invertebrates.   A major cause of concern for environmentalists and local fishermen.

A failed experiment

Deepwater Horizon exploratory rig in flames

What I think warrants concern here is that this offshore rig was experimental and it was working under guidelines that many in the business thought were unsafe.   Additionally, while there are many supposed fail-safes on all rigs…every single piece of safety redundancy failed on the Deep Horizon rig and BP doesn’t seem to be able to deal with the catastrophic aftermath.  Lastly, you may have heard about special dispersants being sprayed to “break up” the oil, however questions about their role as toxins to the environment remain.  Are we really left with choosing the lesser of two evils here?

What does it all mean?

Regardless of your stance on fossil fuel dependency, big oil’s big business role, and government regulation…this should give us pause to reflect on our current choices and regulations of fossil fuel use.

There was a devoted discussion to the aftermath of this environmental crisis on the Diane Rehm show yesterday.  Click here to listen.

Click here for an earlier post discussing the long-term environmental toll oil spills can have.

Follow the slick on your phone

Here is a list of apps that will allow you to follow the gloomy progression of the slick.

Penguins, endangered? May 3, 2010

Posted by Kyle in Behavior, Biology, Climate Change, Ecology, Environment/Conservation, Evolution, Fun.
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"I believe I can fly!"

Cape penguins (Spheniscus demersusare) are an endangered species of penguins off the coast of South Africa. Between 2001 and 2009 there was a 60% decline in population numbers of Cape penguins. Researchers believe that the decline in Cape penguins is partly due to the lack of food as a result of overfishing.  Without food, the penguins obviously can’t survive.  A study done by researchers in South Africa has shown that by managing commercial fishing, they may be able to restore population numbers in penguins.

After doing a little more research, I discovered an easier solution to the problem. The penguins could just fly away (similar to polar bears rapidly evolving), and using a strategy similar to what was done in the movie Fly Away Home, the penguins could be saved. While it may seem slightly unrealistic, just watch the video below and all doubt will be removed. It seems that penguins learning to fly isn’t that crazy of an idea. (The video is obviously not real, and I am not serious.)

Lazy Birds May 3, 2010

Posted by Kyle in Behavior, Biology, Ecology, Evolution.
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Being a bird can be extremely difficult, especially when it comes to raising offspring.  The best way to pass on your genes, and at the same time spend no energy in doing so, is to let another bird do the work!

Brood Parasites

brood parasite young outcompete their host "siblings"

Brood parasites get around the huge investment of raising offspring by tricking another bird into doing it.  Brood parasitism is not a very common reproductive strategy across species (although rates of brood parasitism are high), but it definitely has its benefits.  The less time a bird is spending incubating eggs, the more time that individual can spend on foraging or mating.  The handful of species that use this strategy to gain an edge are constantly trying to trick the host birds, while the host birds are always on the lookout for parasitic eggs. This has led to an evolutionary arms race, with both sides working hard to win.

The costs of being fooled by brood parasites are huge. Not only does the fooled bird have to spend time raising someone else’s offspring, usually it’s not even the same species of offspring.  There is no genetic benefit in raising someone else’s young.  There is also the possibility that the parasitic chick out-competes the host’s chicks. This is the case with the Cuckoo Finch (Anomalospiza imberbis) and the Tawny-flanked Prinia (Prinia subflava). If the Cuckoo Finch egg is not discovered by the host, the Cuckoo Finch chick will hatch first and grow larger than the host’s chicks, out-competing its “siblings” for food and space until the host’s chicks eventually die. The cost associated with this relationship has led to a complicated defense system used by Prinias.

egg patterns of host and parasite are very similar

In a study done by Dr Claire Spottiswoode and Dr Martin Stevens of the University of Cambridge, the researchers worked on the two tropical African species to determine what strategies are used by both sides to win the battle. The back and forth struggle between the two species has resulted in Cuckoo eggs being almost identical to those of the Prinia. Researchers tested how Prinias detect impostures by taking eggs from Prinia nests and putting them in other Prinia nests. They then observed whether or not the eggs were rejected.  The results showed that the Prinia are extremely talented when it comes to distinguishing between their own eggs and those of another bird. By using color and pattern the host birds are able to distinguish among their eggs and those of the parasite birds. Although this sounds like a great plan, the reason it isn’t so popular is because it doesn’t really work that well. In another study researchers used Zebra Finches (Taeniopygia guttata) to look at brood parasitism, and found that only one-third of the eggs laid by brood parasites are actually reared.