My Kingdom for a Mitochondrial DNA Test!

Richard III really did not have a good life.

Or, at least, that's the way historians have painted it. Vilified as the last king of the House of York, as the object of satire in Shakespeare's play Richard III, and as the man who plead, "My kingdom for a horse!", King Richard III proves that history is not kind to those on the losing side of war. The possible discovery of his remains in a parking lot only goes to further desecrate his memory (the poor man).

Killed at the Battle of Bosworth, the final, monumental battle between the Houses York and Lancaster in the War of the Roses, Richard III is famously remembered as the deformed, villainous king who seized the throne after his brother's death and killed the remaining heirs, his young nephews, to ensure his reign. Only lasting two years, his reign marked the end of the House of York, proving once again that you should never kill your family relations if you want your lineage to remain on the throne. (Come on, Richard). Although his remains were buried at a Greyfriar's friary, time had since destroyed the church, and the known location of Richard III's unmarked grave had been lost to history.

Until a group of people decided that it was a brilliant idea to look underneath a Leicester parking lot. No, really. Recently, archeologists had discovered the remains of an individual who was theorized to the infamous king of the 15th century. Although the skeleton showed signs of scoliosis (which Richard III was afflicted with) and battle injuries to the skull and spine (injuries that were also reportedly what killed the king), researchers needed more concrete evidence to ensure that the body really was the infamous king. Which is why they turned to radiocarbon dating and mitochondrial DNA testing to prove that the remains were truly those of Richard III.

Radiocarbon dating is specifically geared towards determining the how much time has passed since an organic organism died. Radiocarbon dating measures the ratio of carbon-14 to carbon-12. While an organism is living, it absorbs the carbon-14 and carbon-12 in the atmosphere into their system. When the organism dies, however, it retains the carbon-12 in its system, as carbon-12 is a stable isotope, but gradually begins to lose the carbon-14, as it is a radioactive isotope and degrades over time. Because the half-life of carbon-14 is known, the amount of carbon-14 lost in a dead organism (found by comparing the ratio of carbon-12 to carbon-14) can tell the researcher how long the organism has been dead. Radiocarbon dating of the skeletal remains found in the parking lot show that they were from an individual who died between 1455 and 1540, a range that encompasses the time of death of Richard III.

A time range, however, is hardly enough to conclusively determine if the skeleton was the real deal.  To be able to determine whether the poor guy was the notorious 15th century king, the researchers at Leicester used mitochondrial DNA to test for a DNA match to the later relations of the king. (And this is where archaeological research begins to sound more and more like a paternity test.) Mitochondrial DNA analysis is basically the same as any other DNA analysis, except the researcher sequences the genome of the mitochondrial DNA instead of the traditional, nucleus DNA. The primary reason for sequencing mitochondrial DNA is simply because of the amount of DNA available to sequence. In a cell there are hundreds of mitochondria to one nucleus. Not only is it easier to find mitochondrial DNA than it is to find nuclear DNA, the degradation of the skeletal specimen Leicester researchers found makes it even more necessary to find enough DNA that had not degraded over time to be used in the analysis.

With the sequencing of the mitochondrial DNA (which basically means they mapped out all of the DNA nucleotides and determined the specific order each of them) they then compared them to the mitochondrial DNA sequences of known relatives to the lost king. The relatives, which include Canadian carpenter Michael Ibsen and a confirmed anonymous descendant, prove "beyond reasonable doubt" that the genomic sequences match and that the skeletal remains are those of a relative to the two Richard III decedents. By simple deduction and process of elimination, the conclusion is obvious.

Yeah! The mystery is solved! We can go home!

But who really wants to go home? As Dr. Turi King, from University of Leicester, said, "It is an extremely rare occurrence that archaeologists are involved in the excavation of a known individual, let alone a king of England...Sequencing the genome of Richard III is a hugely important project that will help to teach us not only about him, but ferment discussion about how our DNA informs our sense of identity, our past and our future." In other words, the genomic details of Richard III's DNA will allow us to know several key aspects to his genetic make-up, such as his hair color, his eye color, and how easily he contracted diseases. His DNA will allow researchers (and avid readers like us) to take a quick glimpse into the past and see how his genetic ancestry could have possibly affected the modern population, and if any other organisms, such as pathogens, decided to snuggle in with Richard III's DNA and make a new home.

Although Shakespeare described Richard III as a man who "clothe [his] naked villainy /  With odd old ends, stol’n out of holy writ / And seem a saint, when most [he] play the devil," the physical man leaves remarkable DNA and materials that prove to be a godsend to both historians and archaeologists alike. Whether the man truly uttered the words "My kingdom for a horse!" we know now that the man lived and ate and breathed just like us all (aside from the fact that he was the ruler of England and we all, presumably, are not), and the discovery of his remains truly breathes new insight and information into the history that we all know and love.
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My name is Diana. I’m a pianist, a snail lover, and a lock-pick smith in training. 

What the "Frack"?

Few topics in modern chemistry and environmental science have been as polemical as fracking. Ask anyone well versed in drilling, environmental activism, or alternative energy, and you are sure to hear his or her passionate (read: loud) opinion. The rest of us, who are perhaps less literate in these topics, have certainly heard the buzzword before, and are familiar with the heated debate it prompts.

Whether you know what fracking is or not, you definitely know that people either love it or hate it. However, before newcomers can fully form their opinion, they often get lost in the chemical jargon.

So, what the “frack” is fracking anyway?

“Fracking” refers to hydraulic fracturing, a process of removing natural gas and oil from the ground. Fracking is often proposed as an alternative to traditional extraction methods, such as oilrigs. The process is as follows:

First, “fracturing fluids”, made of water and sand, are pushed into the ground at high pressures. The force fissures the ground, and frees the natural resources from the rocks below. This process takes place deep in the earth’s crust, no less than 7,000 feet below.

Once free, the resources travel horizontally, meet a deep vertical well, and move upwards to the surface casing, a large steel pipe. The surface casing preserves the groundwater from natural gas related contamination, and move the resources towards the purification center. At the purification center they are processed and prepared for distribution and consumption.

 Sounds great, right?

Well, not everyone thinks so. Much of the scrutiny of fracking, particularly from an environmental lens, points towards the possibility of contamination and the potentially dangerous repercussions on surrounding land.

For example, fracking plants have a tendency to increase downstream pollution, sometimes up to 200 times more radioactivity due to fracking by-products. Looking beyond surface water, contamination due to “fracturing liquids” exposure is a serious issue as well. The chemicals that make up “0.5-2.0 percent” of the solution used to fissure the ground can be very dangerous. If this mixture is not pressurized out of the ground properly, it can lead to serious ground water contamination and may alter crop growth.

However, do these issues nail the coffin for fracking completely?

No, and here’s why: Fracking is a great way to utilize otherwise inaccessible natural gas and resources to stabilize our energy consumption needs. For one, the streamlining of the gas flow from the rig to the well is highly economical. Instead of having to construct several heavy duty, expensive rigs in many places, fracking allows for a greater field of resources to be plucked from the ground, without superfluous construction.

Further, in terms of global energy issues, fracking may be the answer that the United States, and other severely petroleum dependent countries, needs to wean itself off of Middle-Eastern resource reliance. The increase in job availability and promotion of local fuel development might just be the economic push the US needs in these trying times, with a potential 1.6 million new jobs in the next 20 years.

Nor does fracking mean environmental ignorance in favor of economic stability. A recent study from the City Journal suggests that fracking may reap environmental benefits as well. For example, shale is significantly cleaner than coal, and emits fewer green house gases. In fact, the greater prevalence of natural gas use is most likely the source of the drop in America’s greenhouse gas emissions by “5.3 percent” from 2011 to 2012.

Sure, fracking is not perfect and should not be treated as such. However, through the current reality of quickly depleting energy sources and overt foreign dependency, fracking may be the only viable, consistent, and environmentally friendly alternative to oil at this time.

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Hi! I’m Sonia, a DCDS grad who will be attending UMich in the Fall.( Go Blue!) I love to travel, play soccer, and read at least 3 books simultaneously. Excited for the future, I hope to study biology and/or environmental science. 

Keep Calm and Curry On.

Sophomore year, whenever the school cafeteria would serve chicken curry, I would run towards the lunch lines (the only running I ever did) while screaming like a toddler. My Indian friends would grin at each other as I engulfed my fourth helping of "buttered chicken."

“Patrick” they would say, “stop eating that trash”. Later I would learn that the school’s buttered chicken was an inferior imitation of authentic Indian buttered chicken, which is orange to yellow in color, compared to the sickly pale color of my school’s buttered chicken. Buttered chicken takes its color from turmeric, a spice native to Indian. Because of its vibrant color and tendency to stain, turmeric has been used historically as a dye. The compound Curcumin, shown below is responsible for its color.

Keto form of Curcumin

My good friend, Vivek Nair, further said that turmeric had disinfecting properties and has been used as a folk medicine in India for quite a while now. He gave an anecdote about how his grandmother would boil water, then sprinkle a dash of turmeric in it further help disinfect it. How does turmeric kill bacterial and viral infections? This remains unknown. Researchers are not certain if turmeric is even capable of disinfecting wounds. Perhaps Vivek is just a big, fat liar. Perhaps this is something worth investigating myself. It’s a shame that I’ll have to resort to self-testing as no one seems keen to me sprinkling orange power into their open wounds.

I did not discover until later while writing this blog that while turmeric may be incapable of disinfecting wounds, it has been found to inhibit the growth of V. parahaemolyticus, a bacterium found to cause gastrointestinal illness when ingested. Turmeric is also the most effective at inhibiting the growth of Helicobacter pylori, a similar bacterium that causes stomach illnesses.

While its disinfectant properties are uncertain, turmeric boasts a myriad of other medicinal properties. With its ability to reduce inflammation, treat digestive problems and hinder some cancers, I am tempted to label it as a wonder spice. However, the University of Maryland Medical center warns that some of these effects have not been tested in humans and that only cucurmin extracted from turmeric, not turmeric as a whole, has been used in these tests.  

In 2007, a group of researchers demonstrated that turmeric inhibits the growth of Vibrio parahaemolyticus, Bacillus cereus, Pseudomonas aeruginosa, and Proteus mirabilis all of which are histamine-producing bacteria. (Histamine is responsible for inflammation). However, I was disappointed to find out that cinnamon and clover are more effective at inhibiting the growth of such bacteria.

What about turmeric’s ability to combat cancer? Turmeric has been shown to decrease uncontrolled cell reproduction and to induce apoptosis (programmed cell death) in tumor cells. Mice injected with cancer cells were then treated with turmeric (10-40 grams). Researchers found that mice treated with turmeric experienced up to 80% less tumor formation than untreated mice.

 Cinnamon Turmeric Challenge

Hold on, hold on, you may say to yourself. “Self, is this turmeric substance really as good as this Patrick fellow says it is? If it’s so good, how comes it isn’t more popular?” The University of Maryland Medical Center suggests that long-termed consumption of turmeric may cause stomach upset. Turmeric also acts as a blood thinner and may lower blood sugar count. Before rushing off to the nearest supermarket to hoard turmeric, you should be advised that the turmeric from the store may contain some impurities.

Remember, when you’re eating butter chicken, you’re not getting fatter, you’re building immunity to cancer. 

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I'm Patrick. I'm young, and I have dreams and passions.

Shoo Mosquito, You Can’t Bother Me

The newest scientific breakthrough: invisibility…well, invisibility to mosquitos at least. This new discovery in the chemistry sphere could eliminate a problem that has been, pardon the pun, bugging innocent kumbaya-singers and twilight pontoon cruisers around the globe for ages. We’ve all been there: sitting around the campfire at a summer powwow, enjoying a friendly conversation, when you are interrupted by a tingling…no…gradual itching sensation on your ankle. The worst part is that as much as you try to swat that little blood-sucker away, it always manages to find its way back. Talk about persistence.

Making humans invisible to mosquitos may seem like a daunting idea. To understand it better, it helps to be familiar with how the critters find their way to our elbows and ankles in the first place. Mosquitos follow carbon dioxide trails that waft away from all living organisms and can use these gaseous paths to sense a host up to 100 feet away. At a closer range, mosquitos use body heat to find and latch onto humans. This description might have you thinking that all they want is a warm hug, but don’t be fooled. Researchers have determined that hungry mosquitos use cpA neurons, olfactory cells located near their antennae, to track down hosts from distances exponentially larger than the little buggers themselves. Aside from the mosquito’s biology, secretion from your skin also helps the blood-feeders find their next meal. To determine which secreted chemicals mosquitos use to pinpoint hosts, scientists conducted an experiment where they sprayed different bodily substances in a cage chock full of the insects and inserted their own hands as bug bait. However unpleasant the process sounds, the results were worthwhile. In addition to other enticing chemicals, experts found that human sweat, mainly comprised of lactic acid, attracted almost 90% of the mosquitos. Sounds appetizing, right?

But, in all seriousness, the question still remains: how does one go about making themselves invisible to this seemingly inescapable summer pest? Dr. Ulrich Bernier, a chemist in the Mosquito and Fly Research Unit of the U.S. Department of Agriculture, is close to an answer. He has identified over 200 naturally occurring chemicals called attraction inhibitors on human skin that actually, if in a large enough concentration, prevent mosquitos from successfully locating a host. If they could be harnessed in substantial amounts, Dr. Bernier would have an amazingly effective bug spray on his hands, giving OFF!® a run for their money.

As close as research appears to improving the lives of campers, boaters and outdoorspeople everywhere, as of now solutions are still in the laboratory experimentation phase. With any luck, we can expect to be superheroes, invisible to those irksome mosquitos, in the near future. Until then, we’ll be itching with anticipation.

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My name is Leanna. I’m a horse rider, volleyball player and chemistry student!

Colors and Critters

Like many of my classmates, I feel the pressure of a second-generation teenager trying to fulfill my parents’ aspirations. I have to admit I’m pretty “white-washed,” but my Indian culture—from the spicy satisfaction of a crispy, golden samosa to seeing my groom ride in on a horse—holds a place dear to my heart. As a dancer, I love the colorful outfits most of all. 

I know that my grandmother’s neighbor’s sister’s gardener set us up with these silk dresses, but where did they really come from? To put it bluntly, they came from bugs. Silkworms. I refuse to share a room with a spider, but thank goodness for these little guys. Silkworms are just about three inches long and—fun fact—shed their skin five times as larvae. For over 5,000 years, they have been spinning cocoons for silk production. But these fibers are creamy white, and most of us want something more interesting. The energy consuming practice of dying silk externally creates so much toxin-filled wastewater that scientists have turned to a new method: feeding caterpillars dyed leaves. The silkworms are fed just before they start spinning and can then spin colored, rather than white cocoons. Pretty cool, right? Researchers in Pune and Mysore dipped mulberry leaves (their food) in azo dyes and found that three out of seven types of dyes transferred into the caterpillars’ silk and fortunately did not affect their growth.

Why did some dyes work, and others not? Basically, certain dyes dissolve better in water than others. If you want to get technical, it has to do with the hydrophobicity of the dye as it goes from the feed to silk fiber. Scientists look at how the coloring dissolves in a hydrophobic solvent like octanol (it has a phobia of water) to how well it dissolves in water itself. The more hydrophobic, oily molecules tend to show up in the silk because they aren’t easily cleared from the silkworm’s body. Hydrophilic (water loving) coloring molecules, on the other hand, are often dissolved out when the cocoons are dipped in water. Using the right dye can produce vibrant yellows, pinks, and greens without the dangers of external dying.

The bottom line here is that these ideas are pretty great—a greener way to make beautiful clothing. If research goes well, there will definitely be perks. When I get dolled up for an Indian wedding or shindig, I won’t have to feel guilty for killing some innocent fish. (Three dead pet goldfish are all a girl can take).

But wait, it gets even better. The super silk has healing powers too. Researchers in Singapore found that the feeding process may be used to create thread with antibacterial properties. Antimicrobial drugs can be transferred into the silk just like the dye, and slowly released through an implant. To be honest, I’m up for any way to avoid choking on another white pill during flu season. The possibilities are endless, really. The same researchers are now monitoring cancer cells by feeding silkworms cancer-fighting drugs.

New methods for cultivating colored silk certainly look promising. I have a new found appreciation for the stranger who makes my grandmother’s outfits—who will help make my dream wedding dress a reality. If you’re curious, look here.
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N^2: DCDS, 2014.  I will be attending the University of Pennsylvania in the fall. I like music, travelling, and chemistry.

Barking up the Right Tree

Why don’t Native Americans get headaches? No, this isn’t the opening to a politically incorrect joke, and the answer is actually quite simple: willow bark! Native Americans have long chewed the bark of willow trees as a remedy for headache and muscular pain. The same is true about ancient Egyptians and Greeks. Now, while many ancient remedies don’t have great success rates (cough bloodletting cough), willow bark has shown up in multiple cultures and has stood the test of time. This article talks about the role willow bark has played in both ancient civilizations and as well as in the life of plants. So, is there any truth to willow bark’s salutary effects?

There sure is! Willow bark (particularly that from the white willow tree) contains a substance called salacin. The prefix, sali-, even comes from the Latin word salix, meaning willow. When salacin is ingested, the human body converts it into a new compound called salicylic acid. For the full process on how the body converts salicin to salicylic acid, look here. Salicylic acid is one of the main constituents of acetylsalicylic acid, more commonly known as aspirin.

Salicylic Acid

Salicylic acid and aspirin have similar structures and similar effects on the body. Both help reduce inflammation and mitigate pain. Thus, chewing some willow bark and gulping down an aspirin are going to have comparable results. However, there are notable differences. The effects of willow bark have been reported to be much slower than those of aspirin. The effects of willow bark have also been shown to last longer. Both treatments can cause an upset stomach, but willow bark has been reported to cause this side effect less frequently.

Willow bark is definitely a viable treatment for minor aches and pains. However, the amount of salicylic acid you can get from willow bark is relatively low, and chewing willow bark or drinking willow tea means you have to deal with their bitter taste. If you need quick relief, or you’re just not in the mood for an attack on your taste buds, then aspirin is probably the way to go. But if you’re looking for a natural source of pain relief that has hard science backing it up, then willow bark is a pretty good option.

Just couple of warnings. If you intend to remove bark off a willow tree, try to avoid taking it off the main trunk if you can. I mean, causing permanent damage to a tree is no way to say thank you! Also, remember that taking willow bark is a lot like taking aspirin. If you are allergic to aspirin or are not able to take it, you shouldn’t be taking willow bark either. The University of Maryland Medical Center has info on the dosing and usage of willow bark and is a recommended read to those interested in willow bark as an herbal therapy. Despite the trouble of finding a willow tree, the flavor, and a couple of other issues, I think you’ll agree that when it comes down to it, willow bark is a lot better than its bite.

If you’re interested in making some willow bark tea yourself, check out this site for a nice, simple to follow recipe.

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My name's Vivek. I'm a mountain biker, a card player, and an aspiring scientist. I'm a Michigander and a dog lover. Enjoy the post!

The Un-Bee-Lievable Antibiotic Properties of Honey

We’ve all squeezed the stomach of that golden bear sometime in the last couple of months and watched that gluey, sweet liquid emerge, whether to make a dessert or to sweeten some tea. Yes, I’m talking about honey, the wonderful sweetener that bees make by buzzing from plant to plant collecting nectar. However, we seldom realize the wondrous properties of honey that extend past our taste buds: like medicine!

Honey has been documented in diverse ancient civilizations for its antimicrobial properties and as a treatment for wrapping wounds. Yet, the antibiotic nature of honey had not been fully appreciated until recent years. Reading about the antimicrobial tendencies of honey, here and here, I realized that honey is so much more than a cooking ingredient; it’s a miracle worker for wounds and infections!

As it turns out, honey has some peculiar qualities (although these vary with various types of bees) that specifically aid in its war on bacteria.

•  First, and probably the one that you and I are most thankful for, honey’s high sugar content and low water content lead to honey being hygroscopic (jargon for something’s tendency to absorb moisture). As a result, it hinders the growth of bacteria in open wounds by creating a hostile environment.
• Second, honey has a relatively acidic pH (~4) that inhibits bacterial growth. In other words, honey sends bacteria packing because they can’t handle the harsh (and ironically sweet) climate.
• Third, honey also naturally produces a substance that you would otherwise find in the brown bottle at your local pharmacy: hydrogen peroxide (H₂O₂). Hydrogen peroxide production in honey is initiated by an enzyme called glucose oxidase, put into honey by our good old friend the bee, when the honey becomes diluted (e.g. when you put it on a burn or cut).
• Fourth, honey also seems to have been specially crafted by our Apis friends to have some particular bacteria-fighting agents, such as a protein called bee defensin-1 or HMF (Hydroxymethylfurfural), which both inhibit particular metabolic functions of the bacteria.

So, at the end of the day, the honeybees end up getting the bad rap while we should be thanking them for giving us nature’s antibiotic. I mean, we all know what it feels like to get stung by a bee (personally I’ve been stung by three at the same time – it HURTS), but we should also realize the tradeoff; in recent studies, honey has actually been more effective than some common antibiotics used in hospitals at treated burn and open wounds. So while you may hate or resent that flying, striped coat, it might end up helping you recover from an injury, suppress a cough, or even sweeten your cup of tea.

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Mihir: I am a chemistry student and an avid sports fan and player. I watch several sports, though football (because I play) and baseball have to be my favorites. In football, I play on the offensive line and hope to possibly pursue a college career as well. This is my first time blogging, so I hope you enjoy!