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May 8, 2012

Posted by srstone in Biology, Evolution, Genetics, Health, Medicine, Science Education.
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Viruses: Friend or Foe?

What is invisible to the naked eye, can affect the Earth’s climate, has a tiny shell, and can causes cancer?  Viruses are considered non-living, but play a major role in our bodies and environment.  In fact, viruses kill half of the bacteria in the ocean every day.  To get an idea of how much bacteria that is, a teaspoon of water contains approximately a billion bacteria.  Recent estimates show there are 1031 viruses on this earth.  That reads, 10 billion trillion, trillion.  Although viruses are smaller than what the unaided eye is capable of viewing, if all viruses were stacked end to end, they would be lined up for about 100 million light years.

How Viruses Work

 

Viruses are constantly on the attack from the outside of our body desperately trying to get in, but 4 trillion viruses also reside inside our body.  While some viruses are trying to find a host cell and cause harm, many viruses are necessary for a healthy life.  Some of the viruses inside of us can protect us from detrimental bacteria, but can also help balance the population of bacteria vital to our health.  A similar phenomenon occurs in the ocean.  Without viruses consuming half of the bacteria day in and day out, the levels of bacteria in the ecosystem could hamper the living of certain species.  Also, bacteria contain carbon and lots of nutrients.  With the viruses consuming the bacteria, there is a constant recycling throughout the ocean.  There is a hypothesis that because of all the carbon that’s coming out, it could be affecting the Earth’s climate.  Any of the carbon that is sent back to the atmosphere is going to trap heat (greenhouse effect).  It may be an extreme thought, but these tiny, non-living viruses are partially responsible for the weather.

Bacteriophages: the lifeless killers

Viruses that attack and dispose of bacteria are known as bacteriophagesFelix d’Herelle discovered the extraordinary conclusion that viruses can kill bacteria through treating a dish of bacteria with fluid from patients with dysentery!  He actually began a business selling viruses that could cure bacterial infections.  Hypothetically, there are viruses that exist in nature that can kill the most severe bacterial infections, but it’s a matter of discovering the right viruses.  Each species of bacteria has a series of bacteriophages that can eliminate it.

Antibiotics and Viruses: An evolutionary arms race

Before antibiotics were discovered in the 1930s, a method called phage therapywas used to combat infections.  However, once these antibiotic “magic pills” were discovered, phage therapy stood in the distance.  The chemicals were reliable and scientists knew how to make them.  However, with the current widening spread of antibiotic resistance caused by bacteria developing resistance to modern medicine’s most well-used antibiotics, it’s beginning to look like phage therapy wouldn’t be a terrible idea.  One main argument phage therapy new found interest: antibiotics can’t evolve, while viruses can.  Scientists have reached the point where viruses can be engineered and genes can be strategically placed to enhance their effectiveness.  This genetic and evolutionary tinkering could allow scientists to develop viruses to strategically kill various bacteria that might be antibiotic resistant.

Genetic Engineering of Viruses

 

Viruses: Directors of Their Own Fate?

In the wake of the recent deadly avian flu virus, critics have questioned whether the spreading from mammal to mammal could have occurred on its own.  A study completed at MSU by Justin Meyer was started with the thought that it would be a wild goose chase.  Meyer wondered if lambda phages could evolve another way a new way to enter its host.

lambda was used to infect the gut bacterium E. coli.  It is harmless to humans.  The most common means for lambda to get into a cell is by attaching to its outer membrane.  The genes and proteins contained by the lambda are then injected into the microbe.  Meyer used E. coli that didn’t make the molecules necessary for the virus to grab onto.  This meant that the only viruses that would survive were ones that mutated to use a different surface molecule.  Shockingly, within 15 days, Meyer’s experiment showed that viruses were using a new channel in E. coli known as OmpF.

Meyer re-conducted the experiment with 96 lines of the virus and E. coli.  Of those 96, 24 of the lines began to use OmpF as the pathway into the host.  Because of the repeating phenomenon, the genomes of the evolved viruses were sequenced, finding that four mutations were required for the viruses to thrive.  All four were required, not a single one, or even three out of the four.  Meyer estimated the chance of all four mutations arising at once was nearly impossible: one in a thousand, trillion, trillion. However, the lambda viruses evolved to contain all four mutations in a couple weeks on a regular basis.

As incredible as this experiment is, it is somewhat frightening.  Meyer showed how easily viruses can evolve completely new traits, which can lead to new diseases.  This is exactly the reason why when treating a sickness with antibiotics, the patient MUST finish taking the dosage until it is gone, otherwise the virus can come back even stronger.

 

 

 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.        

Resolutions?

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

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.

Mystical “Catnip” May 3, 2011

Posted by mhostetler099 in Behavior, Biology, Chemistry, Health, Physiology.
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So what is it about “catnip” that makes cats crazy, mosquitoes fly away and at the same time has seemingly no effect on human beings?  In actuality, the better question is what are the distinguishing factors allow different organisms to interpret “catnip’s” chemical signal differently or not at all.

The 6th Sense (the vomeronasal organ in cats)

It is well documented that all mammals posses 5 senses (sight, taste, touch, smell, hearing); BUT could mammals have a 6th sense?! Some scientists would say YES and pinpoint this sense to be related to the mysterious vomeronasal organ located above the roof of the mouth.  This sensory organ is attributed to sensing chemical signals from other organisms and the environment known as pheromones.  The vomeronasal organ is present in most mammals and is considered a chemoreceptor organ which exists as a separate entity than the nasal cavity.  Chemoreceptors detect chemical signals from the organism’s environment and transduce a physiological response accordingly. Studies indicate that nepetalactone (the chemical produced by “catnip”) is responsible for eliciting a psychosexual response in cats by mimicking a sex pheromone and interacting with the feline vomeronasal organ.  Although human beings and felines are both mammals, they react to the chemical in “catnip” much differently than one another.  “Catnip” elicits no response in human beings and a rather strong response in felines.  The distinction between these responses can most likely be attributed to a physiological difference in the feline and human sensory system.

The Vomeronasal Organ in Humans

The function of the vomeronasal organ in human beings is actually quite controversial.  Studies on human embryos have indicated that the vomeronasal organ does correspond to the vomeronasal organ in cats and other mammals.  Although the vomeronasal organ is common in both feline and human species, the organ in humans was thought by scientist to be vestigial (or no longer functioning).  The vestigality of the vomeronasal organ in human beings may explain why humans do not react to chemicals in “catnip” however this is an unlikely explanation because studies have shown human beings can react to pheromones.  Another explanation to the differing reactions could potentially be attributed to the physiological differences in the organs themselves (show left). 

 So Why are Mosquitoes Repelled?

So why are mosquitoes seemingly repelled by some essential oils extracted from different plants and herbs (including “catnip”)?  This question is a little more difficult to answer directly because little is known about insect sensory system.  Studies have shown that mosquitoes are more attracted to people with high concentrations of steroids and cholesterol on the surface of the skin.  Mosquitoes are attracted and repelled by certain pheromones.  More than likely, the chemical nepetalactone in “catnip” is able to mimic a pheromone that triggers a chemical signal causing the insect to become repelled (acting as an insecticide).

It is truly amazing that the same chemical can signal different responses in different organisms.  The responses to chemical signals in the organism’s environment are evolutionarily beneficial; whether it be to attract a mate or flee from impending danger.  According to a news report conducted by NPR the CDC is working on natural repellant consisting of extract from cedar tree.  This substance is completely environmentally friendly and actually acts as an insecticide.  It is able to kill the mosquitoes by blocking receptors on their nerve cells (absent in human beings).  Although the chemical found in “catnip” is not known to be an insecticide, the similarity between natural extracts (from “catnip” and cedar tree) may certainly explain insects natural repulsion from them.

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.

An ‘Amazing Race’ of the Senses April 29, 2011

Posted by abueno526 in Biology, Fun, Physiology.
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The last team to check in may be eliminated…

The Amazing Race is a reality tv show in which pairs of contestants race around the world in a challenge of wits, strengths, and abilities to try to ultimately come in first place and win the coveted million dollar prize and of course, bragging rights.  Throughout its 18 seasons in the United States, contestants have been put through a wide array of challenges, including participating in an acrobatic act, carrying furniture and grains across the city, and identifying a correct tune being played in a sea of pianos.

Tea anyone?

In a specific episode this season, the contestants were required to drink a cup of papaya mango tea in a small shop in China. Later on that day, they had to pick out that same flavor of tea from a table of hundreds and hundreds of different cups of tea by recognizing the smell and taste. Although a daunting task, all of the teams successfully completed the challenge by identifying the tea.  But, with so many scents and flavors on the table, how were they able to identify the correct cup?

Olfaction – Odorants

All things considered, humans have the ability to recognize and distinguish 7,000 to 10,000 different smells.  But how is this possible?  The first thing to consider is the human capability to detect odorants, which are typically small organic molecules with some amount of volatility so they can be carried in a vapor from to the nose.  These small odorant molecules are actually detected by their shape, not from any other physical properties that they exhibit.  This means that the different smells come from the way the molecule interacts with the binding site it is associated with.  A common example to better explain this idea can be seen in the molecule carvone (depicted left), which has distinct R and S configurations.  Although the two are mirror images of one another, the R conformation has a scent of spearmint, while the S configuration of caraway, indicating their difference in binding.

Olfaction – Odorant Receptors

Scents are detected in the main olfactory epithelium  of the nose, and are are identified by one of the million sensory neurons that dwell there, which all contain cilia with receptors.  Although we are able to recognize upward of 7,000 distinct scents, humans only have 350 odorant receptors  As seen in the picture to the right,molecules bind to the receptors that are on the cilia, nerve impulses are generated from the binding and travel through the neurons, and finally move to the olfactory bulb.  Throughout this process (binding to olfactory bulb response), cAMP and GTP levels in the body increase, meaning that the process uses 7TM receptors.  These compounds are released in a cascade process, depicted to the left.  When the odorant binds to the receptor, a G protein is activated and binds to

GTP.  This complex then moves to activate an adenylate cyclase, which increases cAMP levels.  High cAMP levels activate and open ion channels, which creates an action potential and allows the smell of an odor to come through.

Olfaction – Scent Recognition

But with only 350 distinct receptors, how are we able to detect thousands of smells?  The answer lies in the fact that most smells are composed of several odorant receptors, which can be activated at different levels of odorant.  In other words, there is not a one to one relationship for odorant to receptor, but instead odorants can activate multiple receptors and receptors can be activated by multiple odorants.  As an example, the odorant C6COOH activates six different receptors, while C5OH, C6OH, and C7OH all activate the same receptor.

Olfaction gone awry 

Sometimes, we are unable to detect some scents, called a specific anosmia.  although everything seems to be functioning normally, certain compounds are not detected by these individuals, indicating that it it a genetic inheritance of a mutation.  Although over 80 have been identified, some examples of molecules that are unable to be smelled include isobutyric acid, which is responsible for the  smell of sweat, and n-Butyl mercaptan, the smell that skunks give off.

Gustation – An Overview

The tongue has the ability to recognize 5 major tastes in the mouth: bitter, sweet, salty,sour, and umami (savory).  A diagram of where these individual taste buds are located can be found to the right, excluding the umami taste.  “Umami” is a word derived from the Japanese language, and includes the tastes of glutamate and aspartate.  Much less is known about this taste than the others because this “savory” flavor has only been distinguished from the others within

the past five to seven years.  Receptors for tastants are more commonly referred to as taste buds, which are made up of about 150 cells.  Microvilli on the surface of the tongue bind to tastants and send an impulse through the sensory neurons to the brain to identify the specific taste.  The tastes use different methods to detect the taste, all of which are outlined below.

Gustation – Salty and Sour

Salty and sour tastes opperate in a similar manner in the fact that they both utilize ion channel interactions.  In the case of salty flavors, this is done through sodium ion and their corresponding amiloride sensitive Na+ channels.  Sodium ions pass through the channels on the front of the tongue creating a current, amiloride attempts to block this current, and a salty flavor can be tasted.  Similarly, the sour taste acts through a hydrogen ion channel .  Hydrogen ions flow through the pores on the sides of the tongue, and a sour taste is observed.

Gustation – Sweet and Bitter 

Unlike the salty and sour tastes, both the sweet and bitter receptors utilize a 7TM receptor complex, as mentioned above in the olfaction discussion.  Because of this, they respond to a larger range of stimulants.  Sweet receptors typically respond to glucose, sucrose, aspartame, saccharine, and even some proteins.  While being researched, scientists discovered that these compounds interact with the T1R1, T1R2, and T1R3 receptors in different combinations with one another.  They all pick of variations of sweetness, with the T1R2 and T1R3 receptor being the most sensitive to the sugary taste and the T1R1 receptor by itself being the least sensitive to the taste.  The bitter receptor acts in a similar manner, however, its receptors respond to toxic alkaloids.  TR2 receptors are responsible for this taste, which is typically recognized at the back of the tongue.  In this regard, it should be noted that taste receptors are much less selective than the scent receptors due to sheer number (350 vs. 5).  For example, in the case of the bitter taste, we usually recognize just bitter in general and are unable to distinguish one bitter compound from another.

Gustation – Umami 

The final taste is umami, which is recognized as the savory flavoring and utilizes 7TM receptors as well.  These receptors respond to glutamete, aspartate, and even MSG.  It is similar to the sweet receptor in the fact that it utilizes the T1R3 receptor, but it is also paired with the T1R1 receptor.  Unlike the sweet receptor that may utilize different combinations of the receptor, the savory flavor can only be obtained with activation of both the T1R3 and T1R1 receptors simultaneously.

A Complimentary Combination 

So, through a combination of the senses, contestants were able to identify the correct cup of tea.  Using the odorant receptors to bind to the scent molecules and the specific taste buds on the tongue to identify the tastes, it is possible to identify a particular item in a sea of many.  As a tip for the contestants for next time, they may want to rely on their nose more than taste due to the high specificity of the olfaction system!

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.

 

 


Crazy for “Catnip” March 14, 2011

Posted by mhostetler099 in Behavior, Biology, Chemistry, Fun, Health, Uncategorized.
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“Catnip,” a feline favorite, is a perennial herb in the mint family

Nepeta cataria, more commonly known as “Catnip” is a perennial herb that belongs to the mint family.  This herb packs a powerful punch to cats by provoking a state of euphoria usually lasting several minutes (video).   Many times herbs are utilized for medicinal purposes , but “catnip” obviously doesn’t affect human beings in the same way that it does cats.  What is it about “catnip” that provokes a euphoric response in cats but not in human beings?

The chemical component responsible for the effects of catnip

Studies suggests that the chemical nepetalactone found in “catnip” is primarily responsible for triggering the response in cats.  Nepetalactone evokes a psychosexual response in both male and female cats by mimicking a sex pheromone found in cat urine.

Bugs aren’t so crazy for “catnip”

The chemical nepetalactone may attract felines, but does quite the opposite to some insects.  Researchers at Iowa State University found that the chemical nepetalactone is a successful repellent of mosquitoes, flies, and cockroaches.  Particularly, the research team at Iowa State found that a solution of catnip extract is comparable in effectiveness to a ten times more concentrated solution of DEET.  Research in finding alternatives to repellents or pesticides, such as DEET, is very important because chemicals contained in most pesticides pose a serious threat to human health and the environment.  Unfortunately, the essential oils in “catnip” are extremely volatile and have a potent, but short lived repelling effect.  Further research in reducing its volatility is essential before such repellents can be used by the general public.

Catnip’s properties are multifunctional

Interestingly, researchers at the Max-Planck Society found that birds that used different types herbal plants in their nests produced offspring that were less prone to infestation of mites.  This study indicates that other herbs may have the same insect-repelling power as “catnip” and that organisms other than humans are using this characteristic to their benefit.


In the future, the active ingredient, nepetalactone, may be found in the bottle of repellent you spray on yourself or the pesticide you sprinkle on your plants.  You can be sure that the product you are using is much safer than the products of old, but if you have cats you must beware!  Such products will still provoke the same euphoric response caused by “catnip” sold in pet stores.


Survivor? Or Starvation? March 4, 2011

Posted by abueno526 in Biology, Chemistry, Nutrition.
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Outwit. Outplay. Outlast.

Survivor. A show with the motto above,  “Outwit, Outplay, Outlast.” Contestants are put on a deserted island with meager food, shelter, and comforts to compete in a series of challenges as they try to become the ‘Sole Survivor”.  Although the glory of winning the title is great, what is physically happening to contestants’ bodies as they put themselves under these extreme conditions?  Some, like Russell Swan from Survivor:Samoa, get fatigued earlier than others, having to be removed from the game for medical reasons.  When this shut down occurs, what is happening?  How far can they really be pushed until they move into a starvation-like mode?

How does it all start?

Typically, glucose is the major energy provider to the body.  Fats can be a precursor to glucose, and ample amounts of them in the body lead to proper function and metabolism.  When one is in starvation mode, the liver is the first to sense this.  Because the body is unable to convert fats into glucose, it biochemically makes a shift to harness more of its energy from ketone bodies in order to save the muscles from deterioration via protein breakdown.

And the downward spiral begins

This switch to the use of ketone bodies is also vital to supplying energy to the brain cells, which is a top metabolic focus for the body no matter its state. In this protection mode, and use of a new fuel source by the brain, blood glucose levels drop dramatically.  This way of living will continue until all fatty acid energy stores have been used up.  Metabolic function will switch from using ketone bodies to its last

resort of proteins for energy.  Final stages of starvation such as these can result in heart arrhythmia, liver failure , and a discontinuation of muscle functioning, ultimately leading to death.

What would you do for a million dollars?

So, when a Sole Survivor is picked at the end of 39 days, what sort of condition are they in?  Although perhaps a few sizes smaller, the contestants will not have reached a true starvation mode due to the time frame of the show and availability of some food for nourishment.  Although they can do it, it’s definitely not recommended unless you’re playing for the million dollar prize!

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

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