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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

Cramming: A Student’s Best Friend? March 4, 2011

Posted by ljsteele in Behavior, Biology, Chemistry, Health, Medicine, Science & Culture, Uncategorized.

The night flies by…

As a senior undergraduate student, slowly over the past four years I have realized the importance of cramming before a test. Simply put, by this stage in my academic career, it has become routine to stay up all night before a test to study.  In classes where there are multiple choice tests, it appears to be easier to stay up all night cramming, as is the belief that if you at least can recognize the question, ruling out the different choices for the answer becomes quite simple.  It has been shown that over a third of students cram the night before a test.

Equal Justice?

However, although many students utilize the practice of cramming, whether or not it helps students is up for debate. There are different levels of cramming, and each appear to cause different results when it comes to grades and GPA.  The issue that is starting to be seen is that although cramming may help in terms of short term memory, the retention of that information weeks after the course ends seems to be up in the air.  Of course, when cramming is being utilized, it only makes sense that the information storage would be contained in the frontal lobe of the brain, while long term memory, which would be associated with studying that has taken place over numerous days or weeks, would be stored over multiple parts of the brain.

Green highlighted area represents the frontal lobe of the brain

Many different universities have brought to light the health implications that one may bring upon him or herself when cramming. But, it is also shown that certain periods of acute stress are positive for the human body, which cramming would appear to fall under the category of acute stress. During acute stress, the body increases its fight or flight response (epinephrine and norepinephrine), shuts down digestion, reproductive systems, and boosts metabolism. Vasoconstriction and vasodilation also take place, therefore pumping blood into certain areas of the body and brain that during a normal day’s activities may not get stimulated very often.  Especially during the fight or flight response, one becomes more attentive, which would seem to help with say, studying for a huge test.

Are there more effects than just retaining information?

Although cramming may not be ideal for certain people, research needs to continue in terms of stress and cramming, and even learning styles.  Certain people are exposed to more stress than others, so possibly stress levels are compromised, leading to a decreased ability to study and cram the night before a test.  Students continue to cram because results are obtained on tests and finals.  Quite possibly cramming could do more than just get a student a good grade on a test-it could also help to train the body for different stress activities that otherwise may not be achieved.

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.

The “CSI-effect” May 3, 2010

Posted by Kyle in Genetics, Science & Culture.
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I recently found an interesting news article addressing an issue stemming from some popular television shows. As you have probably noticed, it is almost impossible to flip through the channels and not find at least one cop drama. While these shows may be interesting, some people are apparently having trouble separating reality from television.  According to the Marion County Crime Lab, there has been a dramatic increase in the demand for DNA evidence in criminal cases. This has been referred to as the “CSI-effect.” While this is not necessarily a bad thing, it has created an increased work load for the crime lab technicians, by roughly fifty percent.

"CSI-effect" based on the popularized TV series

Unlike the shows on T.V., there isn’t always DNA found at a crime scene. Also, it just simply isn’t possible to test every square inch of every crime scene. This has created issues in criminal cases when jurors want DNA evidence, but there isn’t any. When jurors confuse reality and television, they can begin to have unrealistic expectations of investigators. However, the positive side is the increased work load for the crime lab has led to the identification of many suspects, who may have never been identified otherwise.

DNA testing of firearm

A more recent article reported that prisons will begin to use DNA testing to determine the owners of items such as weapons and cell phones confiscated. Officials hope that this new tool will help cut down on the amount of contraband in Indiana prisons. An Indianapolis based company, Forensic ID,  has been contracted to run the program. With the advancement of science and technology many things are now possible that sound like they are from a science fiction movie. It is hard to imagine what will be possible in a few hundred years from now.

Avatar offers more than just a great story line and cool special effects May 3, 2010

Posted by Jill in Fun, Science & Culture.

Cameron now working with NASA

Although Avatar provided a great turnout for the Marian University Science Club showing of the Earth Day outdoor movie, it appears that the film might have scientific benefits as well. Because of the 3-D camcorders used in the

blockbuster, James Cameron’s Avatar, NASA is partnering with James Cameron to help build 3-D cameras for the next Mars rover, appropriately named Curiosity. Attempts to build such a type of camera were abandoned in 2007 due to the mere cost of production of such a camera. Cameron petitioned to NASA to help build the 3-D cameras for the new rover even though all four cameras, called Mastcams, for the rover have been built.

The last two cameras built will be replaced by the new 3-D camera if construction and testing can be finished in time for final rover testing happening in the early portion of next year. The 3-D zoom Mastcams that NASA plans on building with Cameron’s state-of-the-art equipment will be used to capture better, more detailed images than previously able to capture with the original Mastcams. Another benefit of these cameras is that the rover will be able to shoot 3-D cinematic video while on Mars.


The rover was originally set to launch in 2009, but due to funding restraints, the launch was postponed until further funding could be gathered. The mission of Curiosity is to determine if life had existed on Mars and also to prep for an eventual manned mission to land on Mars. Critics, like Steven Hawking, warn about the potential dangers associated with contacting or attempting to find life outside of Earth for many reasons including the problems encountered in the film, Avatar, including the fact that invading or even potentially contacting another life form could “be much as when Christopher Columbus first landed in America, which didn’t turn out very well for the Native Americans.” As Uncle Ben says to Peter Parker in Spiderman, “with great power comes great responsibility.” Hawking, as well as others, admonishes researchers to be weary when contacting or exploring life outside of our planet because it is impossible to know what encounters we will find and how other life forms could potentially react to non-natives.

The full news article can be found at NASA: James Cameron to develop 3-D camera for Mars rover.

Marian University encourages the Town of Speedway to Go Green May 1, 2010

Posted by Colleen in Environment/Conservation, Marian University curriculum, Science & Culture.
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This semester, I have been part of a business creation and development class at Marian University called the A-Team. The A-Team is a student consulting group made up of students that come from a number of different backgrounds and disciplines but come together to work on a specific engagement. The team acts as a consulting group for a business or organization that comes forward with a specific problem or question that they would like us to answer. This semester our team chose to work with the Town of Speedway. Speedway has been having a problem over the past 20 years with their population declining causing an increase in housing stock and a decline in the overall upkeep of some of the houses. They came to us to try to figure out how to get young professionals to move to their town as well as how to deal with the blight that has been beginning in their neighborhoods.

modern windspire to generate energy

solar-panels on house

You may be wondering now what exactly that has to do with a science blog. Well, I’ll tell you. We came to the conclusion that

Speedway should work on becoming a green community. There is nowhere else in the Indianapolis area that can make the claim that they are a green community. We all agreed that if Speedway were green we’d move there in a heart-beat. I personally think that the concept of living in a green town would be really cool! What we did as consultants was work on finding some suggestions for things that they could do. Some of the team members found lots of green grants and tax credits that the citizens could potentially use. There are things as extreme as installing solar panels or wind turbines. This would significantly decrease energy costs for the home. Also, there are other, smaller-scale things we suggested they look into.

go green with energy efficient light bulbs

By upgrading appliances to more energy efficient models, the homeowner saves a lot of money over time as well as doing something good for the environment. Houses can be made more green and energy efficient by installing energy-saving windows and insulation, and most simply by putting in compact fluorescent light bulbs.

We hope that Speedway listened to what we had to say (we gave them our presentation yesterday evening) and will work on going green!

Creationism vs. Evolution: How did we get here? April 30, 2010

Posted by Jill in Evolution, Genetics, History of Science, Science & Culture.
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Darwin's finches

I was in the library this week studying for finals and finishing up the rest of the work in my classes when I came across this book called Is God a Creationist, which contained many valid arguments for both scientific theory as well as theological explanations as to how life on this planet began. The age-old question of our existence has long been debated by both scientists and theologians.

Since Charles Darwin published his findings on the Galapagos finches and his theory about evolution, there has been an intense debate between scientists and theologians. Scientific evidence, such as carbon dating, dates the earth at about 4.54 billion years old, long before the existence of mankind. Theologians argue the biblical implications of the origins of the world saying that Earth was created by God and all living things were created by God. Literal interpretations of the Bible are difficult to comprehend for many reasons including the fact that the Bible was written 3,000 years ago so the interpretation and meaning of words could have been different than what they mean today and the fact that the Bible was not written as or intended to be a historical accurate account of the world because it is a book filled with symbolism.

The Bible contains two creation accounts in the book of Genesis. The first creation account can be found in Genesis 1-11. According to Michael D. Coogan, the first account of Genesis describes the “formation of the cosmos, an ordered universe, out of preexisting but chaotic matter—an unformed earth and unruly sea over which a wind from God swoops like a large bird” (Coogan 28)

The majority of evolutionary theorists believe that there was preexisting matter from which our universe has evolved. Besides the concepts of evolution, scientists are also known for having developed the “Big Bang Theory” to explain the origins of matter in a naturalistic framework, from which our universe was theoretically created. The Big Bang Theory is described as a moment 15 billion years ago when the total amount of matter in the universe exploded from a point and moved out to form the expanding universe today. The scientific perspective on the origins of the world can be described by: “the world had a beginning under conditions in which the known laws of physics are not valid, and as a product of forces or circumstances we cannot discover…the scientist’s pursuit of the past ends in the moment of creation” (Is God a Creationist 35)

Evolution and natural selection cannot be ignored even by theologians because there is significant scientific evidence that states that both do and have existed. At the very least, it is evident that at least artificial selection exists because of the domestication of animals such as horses, dogs, and cats. Humans were able to domesticate or breed certain characteristics of an animal, for example wolves that were friendlier to man than those that tried to attack, and cultivated these characteristics over thousands of years to produce the species we know as our four-legged friends, dogs.

Do chimps think and act like us because they are one of our closest ancestors?

Through molecular genetics, it is possible to find evolutionary pathways through the similarities in homology of DNA between different living species. Also, extracted DNA from fossilization records are the scientific equivalent of “paternity tests” of our earliest ancestors, determining how closely related we are genetically to other species, namely apes. Molecular geneticists as well as evolutionary theorists believe that chimpanzees and humans emerged from a common ancestor 6 million years ago, dating long before the creation of Adam and Eve (according to the Biblical timeline). The genetic evidence for humans being potential “cousins” of chimps is astounding in that approximately 99% of our DNA is identical to that of chimpanzees. The one percent variance between our DNA and that of chimpanzee DNA is what distinguishes us from apes, but in the genetic world one percent could potentially mean that all of the DNA in that one percent is what makes us distinctly different from say starfish. Although theologians refuse to believe that humans evolved from apes, how do we account for species such as the Geico Neanderthals or other upright-walking mammals that shared more behaviors with humans than chimpanzees do. Neanderthals looked more like humans today than modern apes do, so how does religion account for these differences?

An interesting view on the culmination of both the scientific and religious aspects concerning our existence can best be described by John MacArthur: “For the scientist who has lived by his faith in the power of reason, the story ends like a bad dream. He has scaled the mountains of ignorance; he is about to conquer the highest peak; as he pulls himself over the final rock, he is greeted by a band of theologians who have been sitting there for centuries.”

The PCR song April 29, 2010

Posted by Dr. O in Biology, Fun, Genetics, Science & Culture, Science Education.
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To build on the post containing the rap song on photosynthesis, I thought I’d add this little music video montage put out by Bio-Rad. It’s hilarious.  See…scientists DO have a sense of humor.

Here is the original Bio-Rad link.

Bacteriophages have been found to have new uses–making car fuel! April 29, 2010

Posted by Jill in Biology, Chemistry, Environment/Conservation, Fun, Genetics, Science & Culture.
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hydrogen-fueled car

For those molecular geneticists out there, you will appreciate the new discovery of using a genetically modified M13 phage as a source for making hydrogen fuel out of water!

The M13 bacteriophage is often used in molecular genetics work as a cloning vector. The phage contains a single strand circular DNA genome of 6407 nucleotides that is released into a host cell as a result of the phage absorption. When used in a host cell, the, the host cell proteins will form the double-strand replicative form (RF). This new circular RF DNA is required for M13 packaging because the viral proteins are synthesized from mRNA transcribed off the strand of the RF molecule. From here, M13 DNA is packaged at the host cell membrane, and then releases the infectious particles.

Researchers have found a way to harness the M13 virus in such a way to break apart water molecules, producing hydrogen fuel. Researchers have been able to genetically modify the M13 virus, normally infecting bacteria, so that it would instead bind to a catalyst called iridium oxide and a biological pigment, zinc porphyrins. The viruses then will naturally arrange themselves into a wirelike structure while the catalyst and pigments will harvest sunlight to divide the oxygen from the water molecule. The virus works in this mechanism in that the pigment acts as an “antenna” to collect the sunlight and transfer the energy down to the virus, emulating photosynthesis.

Researchers have successfully been able to separate the oxygen from the water molecule, which is the hardest part of the water-splitting process. The hydrogen will then split into its parts (electrons and protons), but researchers are still attempting to harvest the hydrogen parts in order to collect the gas separately and then convert the gas eventually into hydrogen fuel.

The benefits to this are numerous, including finding a green way of obtaining hydrogen fuel without creating carbon emissions as well as making the process self-sustaining. The ability to harness the mechanisms of photosynthesis in order to control the electron transport in a system is one of the biggest problems in creating a system for artificial synthesis, but this approach allows the transfer of electrons to be controlled.

The full article can be found here: GM viruses offer hope of future where energy is unlimited

I have also included an entertaining rap dealing with photosynthesis: Photosynthesis Rap

And before you’re a skeptic and are thinking that no one would make up a rap about photosynthesis, I found another rap about ATP synthesis: ATP Synthesis Rap