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 Something in the Water: Tracing the Cholera Outbreak in Haiti April 13, 2012

Posted by srstone in Biology, Environment/Conservation, Evolution, Genetics, Health, Medicine, Policy, Science & Culture.
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 Something in the Water

Cholera Under the Microscope

When we go to the sink to get a glass of water from the sink, we trust that what the water is comprised of is safe for us to drink.  Most of us don’t give a thought as to what could be in it.  This is one of the luxuries of living in a first world country.  However, those in third world countries, such as Haiti, are not so fortunate.  Shortly after the earthquake in Haiti in 2010, a cholera outbreak occurred.  When an outbreak like this occurs, the goal is to not only check the spread of the disease among Haitians, but to prevent the bacteria from swapping DNA with other cholera strains in the country to form a more dangerous bug much harder to treat.

Antibiotic-resistant Cholera: Mechanisms explored

Bacteria reproduce asexually by a process called binary fission.  Binary fission causes two genetically identical bacterial cells to be produced.  If this was the only method bacteria had to procreate, treating a disease with antibiotics would be simple.  Antibiotics aim to either kill bacteria directly or hamper their ability to grow and reproduce.  This can be done by crippling the production of the bacterial cell wall and inhibiting protein, DNA, or RNA synthesis. 

However, when we put our bodies on the attack with the use of antibiotics, bacteria respond by playing their side with different defensive mechanisms.  Some of these mechanisms include changing the permeability of their membranes.  For example, bacteria can decrease the number of channels available for the antibiotics to enter the cell.  Another mechanism works by changing the actual physical structure of the antibiotic once it enters the cell so that the drugs can’t bind the way they were designed to in order to have an effect.  Although both of these mechanisms prevent antibiotics from carrying out their job, bacterial recombination is the most common form of developing antibacterial resistance.  When this happens, bacteria gain genetic variation by swapping DNA with other bacteria.  This allows the bacteria to acquire resistance to the drug.  A plasmid, which is a circular piece of DNA, can encode resistance to multiple antibiotics. Thus if one bacterial cell in the environment has evolved resistance to an antibiotic, it can easily share that information with other surrounding bacteria leading to an epidemic of widespread antibacterial resistance.   A transposon, known as a “jumping gene”, can jump ship from DNA to DNA molecule.  The transposon then becomes part of the plasmid.

Where did it come from?

Cholera, which had never been seen before in Haiti prior to the earthquake, had the advantage.  Nations offering their help focused on the earthquake recovery while cholera entered Haiti under the radar.  Reducing the fatality rate from cholera has been a success; however the response was slow to fully develop.  The most likely story is that cholera spawned from a Nepalese volunteer at the Minustah base.  Understandably, no one wanted to take responsibility for bringing an epidemic to a country that already needed all the help they can get. 

To resolve the “blame-game”, Danish and American scientists collaborated to determine where the cholera came from.  Haiti’s cholera strain and Nepal’s cholera strain of the bacteria were examined using the most comprehensive type of analysis: whole-genome sequence typing.  Virtually identical, the Nepalese were forced to accept blame.  Another method, pulse-field gel electrophoresis was also used as evidence.  Scientists found that cholera erupted in Nepal in July 2010, but was under control the following month in August.  Unfortunately, this was the same month that Nepalese soldiers left for a recovery mission in Haiti.        


Through the application of genetics, the cholera strain has been identified.  Unfortunately, this doesn’t solve Haiti’s problems.  Only 12% of the population has access to piped, treated water.  The rest find their water in rivers and wells.  These are the same rivers that contain feces and that Haitians wash their clothes in.  Vaccinations and supportive care will aid in the conquering of cholera, but until safe water is more readily accessible, the country needs to be prepared for round two.

A Typical Haitian Laundry Room

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.

Taking a Radioactive Drag: Polonium 210 and Cigarettes March 3, 2011

Posted by tsublett in Chemistry, Health, Medicine, Physiology, Policy.
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Radioactive Smoke: A Dangerous Isotope Lurks in Cigarettes

The Unknown and Known Dangers of Smoking

Many of us know the dangers of smoking. We see many friends and loved ones diagnosed with cancer and know of many who die from it each year. We have seen the warning labels on cigarette packages, but what is actually in that smoke? Research says, it’s polonium-210, a radioactive isotope found in fertilizers. The problem is, tobacco companies knew about this, a while ago. According to a 2011 article in Scientific American, “The tobacco industry has known about polonium in cigarettes for nearly 50 years.” Facts like these are disconcerting on many levels.

A Tobacco Plant

Ways We Are Exposed to Polonium 210

How exactly this isotope gets into the tobacco leaf is not entirely known, but it is thought to be a “daughter isotope of uranium 238 found in fertilizers. When the fertilizer is spread on the soil, it begins to decay into either an airborne isotope, such as radon 222, or into lead 210 in the soil. Both of these products enter through the roots or into the leaves and eventually decay into polonium 210. The leaves are then processed normally and eventually end up in cigarettes.

The History of Polonium 210 Detection

Now, then, there seems to be a problem. See, polonium 210 was detected first in the 1960s. This should be a BIG problem, because we are now considering its dangers even though it has been known about  for 50+ years! Through a series of papers published during the 1960s, namely a paper published in 1964 by Radford and Hunt, scientists demonstrated how polonium 210 can enter the soil.  Subsequently in a paper published in 1974, by John B. Little and William O’Toole, proved that smokers can develop “hot-spots” on their lungs where polonium 210 accumulates. The hot spots can cause mutations due to alpha decay . The problem is, tobacco farmers and cigarette manufacturers are not removing this isotope. The good news is… they may start doing so soon.

How much polonium do we get when we smoke?

Here is an excerpt from a New York Times article:

A fraction of a trillionth of a curie (a unit of radiation named for polonium’s discoverers, Marie and Pierre Curie) may not sound like much, but remember that we’re talking about a powerful radionuclide disgorging alpha particles — the most dangerous kind when it comes to lung cancer — at a much higher rate even than the plutonium used in the bomb dropped on Nagasaki. Polonium 210 has a half life of about 138 days, making it thousands of times more radioactive than the nuclear fuels used in early atomic bombs.

We should also recall that people smoke a lot of cigarettes — about 5.7 trillion worldwide every year, enough to make a continuous chain from the earth to the sun and back, with enough left over for a few side-trips to Mars. If .04 picocuries of polonium are inhaled with every cigarette, about a quarter of a curie of one of the world’s most radioactive poisons is inhaled along with the tar, nicotine and cyanide of all the world’s cigarettes smoked each year. Pack-and-a-half smokers are dosed to the tune of about 300 chest X-rays.


Is there any relief?

Maybe we should stop smoking, it’s likely the best approach. If you can’t quite kick the habit, the FDA may help. Recently the FDA has taken over the regulation of cigarettes in the wake of the Family Smoking and Tobacco Control Act passed in 2009. With the FDA’s help, the exact content of polonium 210 in cigarettes may soon be published. On a side note, one quick fix may come in tobacco leaf preparation. Simply washing the leaves after harvest may eliminate a large portion of the polonium 210 found in the air.


The Largest Preventable Cause of Death in the World.

It seems like a radioactive isotope found in smoke is just one of many carcinogens that continue to contribute to tobacco being the largest preventable cause of death in the world. According to Scientific American:

The World Heath Organization has made clear that smoking is the most avoidable cause of death. It estimates that 1.3 million people die of lung cancer worldwide every year, 90 percent because of smoking. If polonium has been reduced through methods known to the industry, many thousands of those deaths could have been avoided. The industry, many thousands of those deaths could have been avoided. The industry’s lawyers made the conscious choice not to act on the results of their own scientists’ investigations. But it is the customers who have had to live with-and die from- that decision.

So, cigarettes are bad, but how bad they may be for us is still up in the air. Perhaps we can make them a little less dangerous in the future by removing these dangerous isotopes. Hopefully, with the FDA regulating cigarettes, this dangerous vice will soon be put to rest.

Medical use of marijuana doesn’t actually work? May 5, 2010

Posted by Jill in Health, Medicine, Policy, Science & Culture.
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Could this soon become a reality?

According to the Washington Post, the Washington D.C. Council has proposed a bill allowing doctors to legally recommend marijuana as a potential medicine for treating cognitive diseases like Alzheimer’s disease, or coping with diseases such as cancer or HIV/AIDS. According to this law, doctors are not allowed to prescribe the use of marijuana because the substance is illegal, requiring their patients to acquire their marijuana from illegal sources or though one of the five to eight government-regulated dispensaries. Although doctors cannot prescribe marijuana, the dosage allowed for their patients, according to this law, states that patients can use the marijuana “until they decide they are, well, high enough. The exact dosage and means of delivery — as well as the sometimes perplexing process of obtaining a drug that remains illegal under federal law — will be left largely up to the patient. And that, Chopra said, upends the way doctors are used to dispensing medication, giving the strait-laced medical establishment a whiff of the freewheeling world of weed.”

A new study questions these findings

The use of medicinal marijuana is prescribed for Alzheimer’s patients because previous studies have shown that HU210, which is a synthetic form of the cannabinoids found in marijuana, reduces the toxicity of plaques in the brain as well as promotes the growth of new neurons. A new study conducted by Dr. Weihong Song, Canada Research Chair in Alzheimer’s Disease and a professor of psychiatry in the UBC Faculty of Medicine, was the first to test those findings using mice carrying human genetic mutations that cause Alzheimer’s disease — widely considered to be a more accurate model for the disease in humans, rather than the previous study which exposed the HU210 compound to rats carrying amyloid protein, the toxin that forms plaques in the brains of Alzheimer’s victims. The new study found that the mice treated with the HU210 compound still had formation of amyloid plaques as well as the mice that were not treated with the synthetic compound, which brings up questions as to the validity of the use marijuana having medicinal value.

Questions of policy addressed

Clearly, the medical benefits of using marijuana are still highly debated. So is it right that laws are being passed to use marijuana medicinally even though it is unclear what the effects of using marijuana are? Not to mention, if this law is passed, there will not be a restriction on how much marijuana that can be smoked, eaten, or vaporized for it is left up to the discretion of the patient. This idea goes against all logic and modern practices and policies regarding modern medicine. Doctors do not prescribe Vicodin for patients and let the patients determine how much they should take nor do they supply it at the patients demand. Doctors prescribe recommended amounts and only in small quantities for controlled, addictive substances because they are simply that, addictive, and the ability to obtain these prescriptions is still highly abused. If the use of medical marijuana is legalized in Washington D.C. according to the stipulations of the law currently, what will prevent the abuse of another addictive and misused drug ?

The full article covered by the Washington Post can be found here.

The HU210 studies can be found in the journal Current Alzheimer Research

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.

Bees could be in trouble May 2, 2010

Posted by Kyle in Biology, Environment/Conservation, Policy.
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honey bee pollination

To many people bees of the family Apidae (including honey bees, Apis mellifera and bumblebees, genus Bombus) may seem like an annoying insect, but to flowers and other plants they are vital. Bees pollinate many crops that we rely on as a food source.  For this reason, bees are essential. Bees are obviously important in the wild, but they are also used commercially in greenhouses.  Scientists have noticed, however, that these important creatures have been on the decline. This could potentially be devastating to the crops that rely on bees for pollination as well as populations that rely on those crops for food.

Researchers Michael Otterstatter and James Thomson of the University of Toronto believe that the decline in bee populations could be a result of a pathogen spreading from commercial populations to wild ones. Commercial bees are often infected with the pathogen Crithidia bombi. To test this hypothesis, researchers tested populations near greenhouses as well as populations not near greenhouses to determine the percentage of infected individuals. As was expected, wild populations of bees closer to greenhouses had higher infection rates than those that were not near greenhouses. This points to commercial populations of bees as the source of the infection. As the commercial bees escape and mingle with wild bees, they are spreading the pathogen that is causing declining bee numbers.

While this problem may not be so bad now, over time there could be serious consequences. The declining bee numbers could have a negative impact on crops, potentially leading to a shortage in the food supply. As researchers in Europe have discovered, a decline in bee diversity is also making it harder for wild bee populations to survive. As a result, bees have not only started to disappear, but plants have as well. A study found that in 80 percent of bee populations biodiversity had declined.  As biodiversity declines, so do the chances that populations would survive widespread infection. At least in this study, it is unclear what is causing the declines in both bees and plants, or if they are related. These two studies highlight the importance of regulating commercial operations where biodiversity can be influenced. By better managing the diseases found in commercial bees as well as species overlap with wild populations, the issue could be curtailed.

Gattaca… is it now a reality? April 30, 2010

Posted by Jill in Biology, Genetics, Health, Medicine, Policy.
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Lego DNA helix

For anyone who has seen the movie Gattaca, the concept is mind-boggling. Could molecular genetics really go as far as artificially selecting for so traits as specific as having an innate ability to speak or play the piano or be a world-class swimmer, not just choosing for a tall blond-blue eyed baby? In the movie Gattaca, Vincent is one of the last “natural” babies born into this genetically-enhanced world, where life expectancy and disease likelihood are determined at birth. Myopic and scheduled to die at 30, he has no chance of pursuing a career in a society that now discriminates against your genes, rather gender, race or religion. He assumes the identity of Jerome, a world-class swimmer who was crippled in an accident, in order to achieve prominence in the Gattaca Corporation, a spaceflight company, where he is chosen for his lifelong dream of being on a manned mission to Saturn.

Although this movie is fiction and was produced in 1997, how far away from this society are we really? The Stanford University School of Medicine analyzed a healthy person’s DNA in an attempt to predict the long-term diseases or medical conditions he would face in the years to come. The genome was of Stephen Quake, who is the Lee Otterson Professor of Bioengineering. The thought is that along with a family medical history, patients could potentially have a genetic component to their medical history that would help physicians in determining whether or not certain medications will work or have adverse side effects for that patient based on their genetic makeup. Patients that are at a potentially higher risk for a certain condition or disease will be able to have closer monitoring of that condition through testing or observation even if not present in the patient. Another benefit to this form of “pre-screening” of genetic disorders is that it will be more cost effective and be more economically sound because it will reduce the prevalence of unnecessary tests, making medicine more efficient.

In conjunction with bioinformaticians, Atul Butte, MD, PhD, assistant professor in bioinformatics, and his lab members have already done a lot of the necessary leg work for interpreting the genetic code into something meaningful, like what individual codons or even base pairs mean in a particular part of the genome. They spent 18 months cataloguing publications that associated particular genetic changes called SNPs (single nucleotide polymorphisms) with effects on specific diseases. It was the first time anyone had compiled all the information in one database.

Upon receiving the genome of Steve Quake, researchers were able to create an algorithm that analyzed all of the data they had compiled from previous studies against Quake’s genome to determine his risk factors for certain conditions such as obesity, Alzheimer’s, type-2 diabetes, and prostate cancer. They determined Quake’s risk of prostate cancer is about 23 percent, risk for Alzheimer’s diesease is 1.4 percent due to protection, and type-2 diabetes, coronnary artery disease, and obesity all at 50 percent. This information raises questions of patients actually knowing these alarming statistics because they are afraid of living their everyday lives. I’m sure this is similar to the idea of life insurance companies providing you the statistics for the likelihood that you will die if you walk across the street to your daily job. Most people do not want to know these things and if the problem arises, they will deal with it then instead of relying on knowing odds to predict what could potentially happen to them.

This new scientific research raises many ethical questions like should this be implemented to aid patients or should it be optional or is this an exploitation of personal information? As more of these findings are published, there will certainly be more controversial discussion in terms of what is right and wrong in exploring the meaning of our genomic fate.

The whole article can be found here.

Pollution is Good? April 28, 2010

Posted by Colleen in Climate Change, Environment/Conservation, Health, Policy.

Marian University celebrated Earth Week  last week (April 19th-22nd). We even hosted an outdoor movie and taught everyone the importance of recycling!  That same week the EPA put out a report saying that air pollution has dramatically reduced over the past twenty years. To me, that seems like a really good thing, but according to a recent NPR story, clean air could actually be intensifying global warming.

Shocked?  Me too.

But, according to science writer Eli Kintisch, this could be the case.

Why is this so?

Well, there are two kinds of air pollutants: aerosols and greenhouse gases. Greenhouse gases warm the planet, which we are well aware of, but recently scientists have discovered that aerosols actually have a temperature maintaining effect for the earth. Apparently if all man-made air pollution was stopped, global warming could be sped up by as much as a degree Fahrenheit. While greenhouse gases absorb heat, adding to global warming, aerosols actually reflect sunlight away from the earth causing the earth to cool down rather than heat up. By cleaning the air, we’re taking away this stuff away, perhaps adding to the increase in the global temperature. These pollutants still cause health problems, like asthma and respiratory disease, so letting them stay in the atmosphere isn’t necessarily the answer. The scary thing is that we don’t know how much these cooling effects have slowed down global warming. If it’s a lot, then taking the aerosols away could cause a huge problem. This would mean that we’ve been causing a larger warming effect than we originally thought. If not, then it may not be as much of a concern.

One idea that has come about from this knowledge is to use geothermal engineering to fix the problem caused by removing these cooling pollutants. What we would do is inject new pollutants into the clouds, allowing for the cooling to occur. Theses sulfur aerosols are distributed naturally during volcanic eruptions, such as the one we’ve been seeing in Iceland. Volcanoes, when they erupt, put out a lot of sulfur aerosols  into the stratosphere and can cause cooling to happen. The idea is that if there is a natural emergency in the future caused by the warming, it might be possible to slow or stop the warming by mimicking the volcanoes and injecting these aerosols into the stratosphere.

Crazy huh?

To hear the whole story, click here.

Is it a good or bad time for students who dream of going to medical school? April 28, 2010

Posted by Jill in Health, Medicine, Policy.
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With the passing of the 2010 healthcare bill, many more Americans will have access to healthcare.  Prior to the bill many people were unable to afford the astronomical costs of seeing a doctor regularly, not to mention paying for surgery or major medical procedures without insurance.

For many aspiring medical students, this is great!

There will be a need for more physicians to accommodate the number of patients that will be receiving this affordable healthcare. The need for primary care physicians is expected to skyrocket based off of the sheer number of physicians needed to meet the demand of a growing number of potential patients.

Where do we get these primary care physicians?

The problem that arises with the growing need of primary care physicians is that so many medical school students want to specialize in a particular field of medicine such as surgery or  cardiology because they have a particular passion for their interest. Also, physicians that specialize have a significantly higher income than those who are primary care physicians. Today, the United States is already shorthanded when it comes to primary care physicians and it will be difficult to meet the needs of the growing number of patients as they receive greater healthcare benefits.

There are some medical schools in the United States such as the University of Colorado School of Medicine and Rocky Vista University College of Osteopathic Medicine that are responding to this call for primary care physicians by encouraging their students to get into primary-care medicine, such as pediatrics, OB-GYN, internal medicine, and family practice. With the annually increasing cost of medical school, it is difficult to steer students away from high-paying specialties. The University of Colorado, along with other medical schools, has started a “pipeline” program which allows promising high school students direct admission to medical school following college and help them with their debt, so as to encourage students to defer the cost of medical school. Also, increasing the size of medical school classes has helped in graduating more physicians per year, which will help in meeting the soon high demands of patient care.

How do we encourage students to be  primary care physicians?

Because the cost of medical school is so high, more programs need to be implemented to help medical students pay for their medical school and not have to rely on specializing in order to repay med school loans. The benefit of going to medical school at this point is that the job market isn’t saturated in the field for primary care physicians, but the question remains, who is willing to take the pay cut and potentially lengthen the amount of time it will take to pay off the debts of medical school?

If our government is willing to provide insurance to those who could not before afford it, should our government also be responsible for helping medical students with their tuition costs in order to provide these new patients with the proper healthcare that our country is known for as well as the manpower to manage the number of new insured patients?

Save the Whales! April 23, 2010

Posted by ecogeeko10 in Biology, Environment/Conservation, Genetics, Policy.
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We are having a great time in our Molecular Genetics class (BIO 415) right now because we are currently underway on a project genetically analyzing different fish products being sold in local markets and restaurants. Apparently there has been a real problem with the mislabeling of these fish products throughout the country, which can lead to the illegal sale of endangered species or the misrepresentation of the demographics of  fish sold making it hard to police sustainable fishery methods.   We wanted to see if this problem is prevalent in our hometown of Indianapolis, IN.  It was for this reason that I was excited to see that the same experiments and techniques are still being used elsewhere.

Just recently, a team of filmmakers, Oregon State University scientists, and environmentalists investigated some sashimi being sold at sushi bars on the west coast and found that there is whale meat illegally circulating in this market. Through genetic analysis, the team was able to find that these sequences were genetically identical to whale products that have been previously purchased in Japanese markets. Unfortunately, these products are most likely coming from what is supposed to be Japanese “scientific whaling” expeditions. This means that whale meat is being traded as a food product even though the commercial hunting of whales was banned by the International Whaling Commission (IWC) in 1986. The restaurants have subsequently been shut down as a result of these findings.

This illegal trading activity isn’t just occurring between the United States and Japan, though. Further studies have revealed there to be a total of 13 whale products being sold in places as far as Seoul, South Korea. However, the samples can’t be conclusively linked to an individual whale unless the genetic identity records of the “scientifically killed” animals are released by the Japanese government. As of now, Japan is conveniently refusing to release this important information. Therefore, one of the major focuses of the researchers, right now, is to obtain these records because it is only with this information that they can provide resource managers with the best possible science.

Though it is very sad to see that such illegal activity is still going on around the world, I think it’s cool to see that certain tools and techniques that we are using in our Molecular Genetics class is up to date and is still being used throughout the scientific community. It also amazes me that science has become so advanced over the years that we are now able to do the unimaginable. Who would ever thought, fifty years ago, that we would be able to narrow down the source of a particular piece of whale meat being sold in Los Angeles to a single whale population off the coast of Japan. Hopefully our newfound abilities in molecular genetics will continue to help scientists in uncovering various illegal activities and will help to better prevent such activities from continuing. Now, however, it seems like our biggest problem is trying to get the necessary information from the appropriate individuals (e.g. the whaling records from the Japanese government). It is with these tools and information that we can achieve our ultimate conservation goals.