An Ongoing War

At first glance, plants seem pretty harmless. I mean, what's this Honey Mesquite tree going to do to you if you try to cut it down? Fall on you I guess...

Image Courtesy of Encinalense

Apart from the obvious tactics like poison berries, plants have some really cool defense mechanisms to repel or 'take care of' predators. For instance, corn releases volatile chemical compounds when it is being eaten by worms. These compounds attract parasitic wasps that then lay eggs inside the worms. It's a win-win for the plant and the wasp. Other examples include essential oils that plants release when getting eaten. These oils can deter insects from the bad taste or smell, or even cause the plant to fortify its cell walls in order to make it more difficult to consume. That smell of freshly cut grass some people adore is actually a compound the plant releases to warn neighboring plants that danger is coming. Looking at it from that perspective, you're smelling the screams of your lawn.

Poor Things..
Image Courtesy of Pixabay.org

To combat all of these defense mechanisms, insects will have their own novel chemical compounds in their saliva. These compounds will suppress the defenses before the plant has the ability to activate them. Doctoral candidate Loren Rivera-Vega is investigating how a particular kind of caterpillar, the cabbage looper, avoids the defense systems of the plants it eats. The cabbage looper is quite unique in that it can eat a remarkable range of plants without triggering their defenses.

Cabbage Looper Caterpillar
Image Courtesy of Brittany Dodson

In order to determine what it is about the saliva that makes it unique, Rivera-Vega is letting the caterpillars eat different kinds of food sources, and then seeing what changed in their spit. After letting the insects feast on the different diets, she harvests the leaves and the caterpillar, and then does an analysis on the leaves to see what defense compounds were released by the plant. Then she slices up the caterpillars and harvests their salivary glands. The plants are then placed in a salt solution in order to extract the compounds for identification. She has found that the saliva does in fact change based on diet, increasing or decreasing the levels of certain proteins in order to better deal with the defenses of that particular plant.

Her next step is to better analyze the defense compounds put out by the different plants, in order to see if the caterpillar is really better dealing with the plants by changing their spit. This research could be very useful for agricultural purposes, as by better understanding the tactics that insects will take to prevent plant defenses, we can produce crops that are better suited to protect against insect damage. As farm land is getting more and more precious, the idea of efficiency in farming keeps getting more important.

A New Fingerprint

Dusting for Fingerprints
Image Courtesy of ABC

Crime TV shows love dusting for fingerprints, and for a good reason. It's one of the more common techniques in forensic science, since fingerprints are supposed to be unique from person to person. In 2015, it was found that a fingerprint test can even identify someone's gender! However, when it comes to forensic science, more tests are always better. With new insights into body flora, a new novel identification technique is being looked into here at Penn State. An international team of researchers, led by Moriah L. Szpara, assistance professor of biochemistry and molecular biology, is researching how different strains of viruses present in the body may reveal a person's history.

The man of the hour. Pretty cute, eh?
Image Courtesy of Penn State

This all started with the identification of the genome of two different and distinct strains of the herpes simplex virus type 1 (HSV-1). This virus is mostly asymptomatic, which means that most people have it even if they don't know they do. It is predominately acquired from the mother early in infancy. And once you have it, you have it. Once gotten from your mother, you carry this same strain of virus with you for the rest of your life. Think of it like your childhood friend you never knew you had. Except a lot more spherical than your friends probably were (I hope). As viruses go through a lot of mutation when they reproduce inside your body, the genome of the viruses present inside you can be used to identify you, as well as trace your lineage. For example, a particular individual they studied turned out to have two separate strains of the HSV-1 virus, one was a North American flavor (TM), and the other was an Asian flavor. This made sense, as the individual was a veteran of the Korean War. The fact that this showed up in the genetic makeup of the viruses present in his body is amazing. From just looking at what brand of viruses call your body home, one can determine where you have been.

Another consequence of this is the idea that you can determine a person's origin from what strain of HSV-1 they have. The viruses comes from your mother, so this makes perfect sense. This idea could prove to be very useful, especially in the instances of trying to identify a disfigured body at a crime scene. From the strains of viruses in the victim's body, one would be able to tell where they are from, as well as potentially who they are related to. This second part comes from the implication that people who have identical or close-to-identical strains of the viruses will be more closely related than those who harbor completely different viruses. This viral fingerprinting could go even further for forensic science, as it could be possibly used to "locate perpetrators at the scene of the crime."

Currently one issue with all of this is sample acquisition. The research team is working on trying to be able to sequence viral genomes from smaller and smaller amounts of starting sample, in order to  sequence more and more from smaller samples. This would have the added benefit of being less invasive to test an individual.

This project is a collaboration between scientists from the Universities of Penn State, Lancaster, Pittsburgh, Georgia State, Emory, and Princeton. If you'd like to read more about the project, inducing the paper on this subject published in the May 2016 issue of Virology, you can find it here.

Alternate to Antibiotics

I talked in a previous post about research that was being done to determine how to best administer antibiotics in order to mitigate antibiotic resistance. But what about bacteria that are just too virulent to be combatted with typical antibiotics? Kenneth Keiler, professor of biochemistry and molecular biology is working on using something new to stop these virulent strains of bacteria from spreading. In particular, they are currently working with Franscisella tularensis, a pathogenic species of bacteria that can be fatal. It is particularly dangerous as it doesn't take much of the bacteria to infect someone and it can be spread through the air. 

Franscissella tularensis infecting a Macrophage (A type of white blood cell)
Image Courtesy of NIAID

Keiler's group is using two different inhibitors (KKL-10 and KKL-40) to try to stop the bacteria in its tracks. These inhibitors prevent the release of ribosome rescue factors to ribosomes that are stuck translating the same mRNA strand. To help understand what this actually means, we'll go over some basics. Ribosomes are our little protein factories in our cells. They can be found free-floating in our cytoplasm (that gooey stuff that our cell is filled with), or attached to the endoplasmic reticulum. We send a message (mRNA) from our nucleus (where our genetic material is stored) to our ribosomes which then 'translate' that message in to a protein using amino acids as building blocks. The bacteria need constant supplies of proteins in order to stay alive. They need even more to reproduce and infect the body.

Protein Synthesis (big red blob is the ribosome)
Image Courtesy of Biology Discussion Forums

Sometimes ribosomes can get 'stuck' on the same piece of mRNA, and require the release of certain compounds to get 'unstuck'. These compounds, called ribosome rescue factors (which include things like tmRNA, ArfA and ArfB) are able to be blocked by the inhibitors that Keiler's group is utilizing. Stuck ribosomes mean no proteins which means the bacteria eventually will die without reproducing. No bacteria, no infection. Yay you've done it, he's cured!

Being able to cure these difficult infections is becoming ever more crucial, both because of increasing antibiotic resistance and because of the risk of bioterrorism. This risk might been sci-fi, but it is absolutely reality. In fact, the very bacteria that is being tested on in this study was stockpiled during the Cold War to use as a weapon.

When bacteria get too resistant to our current antibiotics, we're shoved right back to ancient medicine (okay, not bloodletting, but still). All we can do it sit and watch and hope the patient's immune system is strong enough to fight it. New, novel methods to cure infections are needed more now than ever.

Keiler's study is going well, and is going into the stages of delivery designs and animal testing.

If you'd like to find out more about his work, you can find his group website here.

That Other Clean Energy

In 2014, nuclear power accounted for 19.47% of the total electrical energy generation of the United States. This 19.47% (or 797 Terawatt-hours) was produced by just 99 commercial reactors. In 2015, there were five new reactors being built. However, even considering those five currently being built, 33 reactors have been permanently shut down since the 1970s. Due to disasters like the Three Mile Island accident in 1979 or the Fukushima Accident more recently in 2011 after the earthquake, nuclear power hasn't exactly been a fan favorite for electricity generation.

Regions and Locations for Nuclear Reactors
Image Courtesy of US Regulatory Commission

Nevertheless, nuclear power remains an important power production method. Lifecycle analysis' of nuclear power plants shows that they produce some of the lowest levels of greenhouse gases when compared to all other power generation methods. So in order to ensure that the benefits of nuclear power generation outweighs the potential dangers, research is being done to find how to lessen the risks associated with nuclear energy.

Michael Tonks, an assistant professor of mechanical and nuclear engineering at Penn State, is exploring new materials to use for nuclear fuel in order to make current light water commercial reactors safer. To put this into a little bit of context, light water reactors use your typical water as coolant. This is in contrast to heavy water reactors, which use deuterium oxide (D2O, or heavy water) as a coolant.

Tonks is looking into altering two different aspects of the fuel: the fuel (pellet) itself as well as the cladding that surrounds the fuel.

Nuclear Fuel Pin
Image Courtesy of whatisnuclear.com

The fuel pellet is pretty self explanatory; it is traditionally uranium dioxide (UO2). The cladding around the pellet is a metal sheath that surrounds the fuel pellet, separating the fuel from the coolant in the reactor. Tonks believes that altering the fuel and the cladding is the "most cost-effective and near-term solution" that could change the course of nuclear energy.

Going back to the fuel pellet; even though uranium dioxide is what is typically used today, it may not be the best option, especially when looking at the safety of the reactors. Uranium dioxide tends to trap heat inside itself (due to its low thermal conductivity), which may lead it to overheat when coolant is lost (which isn't so good, to say the least). Zirconium alloy, which is traditionally used as the cladding, tends to react with water and release hydrogen gas (think big flames at this point).

We don't really want this in our nuclear reactors...
gif courtesy of /r/gifs

Tonks is trying to find better materials to use for both of these tasks. Utilizing computational models, he is able to model a material's behavior under the conditions it may undergo in a reactor. For example, in the cladding, his team has found a simple solution in layering other materials over the zirconium alloy in order to mix the strengths and weaknesses of the different materials. This layering would prevent the evolution of hydrogen gas in the reactor, thus no possibility for boom. Other alternatives they're looking into include completely scrapping the zirconium cladding and switching to a silicon carbide (a simple compound of one atom of Silicon and one of Carbon) composite.

As for the fuel itself (and the not heating up and melting issues), Tonk's team is trying to find various fuel additives for the uranium dioxide, and utilizing modeling, find out what may happen when the fuel with the additives are exposed to the extreme reactor conditions.

Model of Uranium Dioxide using the MOOSE Modeling Framework
Image Courtesy of Microstructure Science and Engineering Lab

Tonks is using a research structure that many groups are also using: mixing both computational and experimental experiments. Computational research can go through and shrink the pool of possibilities  that experimentalists have to try, leading to much more efficient research. While there are many individuals who view one method of research (computational vs. experimental) superior, the fact is that a mixture of both produces the best results.

If you'd like to look deeper into Tonk's research, as well as the research of the people he's collaborating with, you can look at his website.

The Early Education Gap

Affirmative action is a decisive topic, a topic that one of us is even doing for their civic issues blog. Affirmative action, as per the National Conference of State Legislatures, is a collection of policies in which an "organization actively engages in efforts to improve opportunities for historical excluded groups in American society." But why do we even need these policies in the first place? One part of the answer lies in the existence of 'achievement gaps'. These gaps are the continuous discrepancy in education performance between groups of people, groups that may be defined by socioeconomic status, race, and gender. For example, take this graph, which shows the achievement gap (in mathematics performance) between 13 year old caucasians and 13 year old african americans.

Achievement Gap between Caucasians and African-Americans in Mathematics at age 13.
Image Courtesy of US Dept. of Education

The gaps can be seen with all minorities, as well as between high and low income groups in all areas of learning (mathematics, reading, science, etc.). In order to best address the crisis and fill the gap, we have to address the root cause of the problem. To fix a leaky roof you patch the hole, you don't put a bucket under it and pat yourself on the back. That is, on some level, what affirmative action is doing. However, there is still much debate on what exactly the root cause of the problem is. And before we can address what it is, first one must find when it happens. Paul Morgan, associate professor of education, has analyzed data from the first large-scale, nationally representative study of children going through kindergarten and middle school, in order to try to find when the gap begins, as well as identify what may contribute to it.

Morgan's study found that the achievement gap in science begins before children even enter kindergarten, which was earlier than was previously supposed. Further, he found that these gaps can lead to increasing gaps by the end of the first grade. These gaps ended up being good predictors of science performance and the science achievement gaps from third to eighth grade. Which means that the discrepancies in knowledge that children came into kindergarten with are affecting them through the rest of their education.

Morgan then identified some of the factors that influenced the appearance of this information disparity, including information opportunities to learn about science and the natural world. Luckily, most of these factors are modifiable, and with enough effort we can reduce this achievement gap can be reduced. And reducing this gap should be something policy makers should be incredibly concerned about in order to keep America competitive scientifically.

If you'd like to read more about their study, you can read the full publication here.

Balancing the Carbon Cycle

Human processes contribute over 29 gigatons of carbon dioxide to the atmosphere every year. Seeing as how carbon dioxide has a density of 1.98 grams per liter, that's a whole lot (thats the scientific term) of carbon dioxide. In fact, carbon dioxide is the primary greenhouse gas released by humans, and makes a significant contribution to the largest problem facing humanity as a whole: global warming. In global warming, our emissions of Carbon Dioxide upset the global carbon cycle (the global exchange of CO2 between the different areas of the earth, like plant biomass, the ocean, and the atmosphere), leading to an increase of CO2 in the atmosphere overall. This leads to the greenhouse effect, where more heat is trapped in the atmosphere from the sun than is irradiated out, causing an overall increase in the temperature of the earth. 

Image Courtesy of livescience.com

Another disastrous effect of these increased CO2  emissions is ocean acidification. CO2 can be taken in by the oceans, reacting with the water to form carbonic acid. This leads to an overall decrease in the pH of the oceans, in some places to a significant degree. The figure below shows just how acidic the oceans are becoming. It is important to note that pH is a logarithmic scale, meaning that an increase in pH of 1 means that there is ten times the concentration of hydrogen ions in the water. 

Change in Sea-Surface pH since the 1700s
Image Courtesy of GLODAP

This acidification is so disastrous due to how sensitive living things are to changes in pH. Organisms like clams and oysters are particularly sensitive, and may be affected first. Thanks to how dependent we, as well as other animals are on these shelled creatures, the entire food web is at risk when these organisms are affected.

So what can we do to fix this? The biggest effort today is all about reducing our emissions of carbon dioxide through clean energy. Chunshan Song, director of the EMS Energy Institute, has something additional to add to this school of thought. What if we looked at CO2  not as a waste product, but instead an ingredient to create fuels and chemicals? Traditionally such products like olefins (which are used to create things like plastic bottles and ziplock bags) are produced using oil, but utilizing novel catalysts, Song is able to use carbon dioxide (along with some hydrogen gas) to create these products. Catalysts are specific substances (commonly metals) that lower the energy needed to be put into a reaction to get it to proceed, enabling new chemical pathways that result in products that you would not originally be able to produce. In the case of the olefins, Song is using a copper and palladium catalyst to produce this very useful chemical.

Song is trying out many different catalysts to see what new products that he may be able to create using carbon dioxide conversion. It is possible that CO2 will be able to be converted into all of the petroleum derived products, reducing and perhaps eliminating our reliance on the unsustainable fuel.  

Catalysts that have been investigated
Image Courtesy of Penn State

 Song hopes that the process will lead to a new "sustainable green energy cycle" that both reduces  CO2  emissions and reduces the global CO2 levels back to a earth-friendly level.

If you'd like to read the paper regarding the Cu-Pd catalyst, you can find it here.

Safety of Vaping

I'm sure you've seen people around campus with e-cigarettes blowing out these big clouds of what looks like smoke (it's not, it's water vapor). It's actually kind of impressive how much vapor some of these things put out.

Image Courtesy of CFCF

A surprising number of people use e-cigarettes. Per the CDC, 21.6% of people age 18-24 have used or have tried using an e-cig, a number that only seems to be rising. They're commonly touted as the safe and healthy way to get your nicotine fix, as instead of burning tobacco (which comes with a whole myriad of health consequences I'm sure you're familiar with), e-cigarettes uses water vapor as a way of delivering nicotine to the body.

Combine this rather new delivery method with almost no regulation from the FDA, and you're left with a lot of unanswered questions. And not a lot of people are there to answer those questions, as not much is known yet about the health affects of using these popular devices.

Researchers at the Penn State College of Medicine are trying to find more about what e-cig vapor actually contains, which would help indicate what the long-term health affects may be. As John P. Richie Jr., professor of public health sciences and pharmacology says, "While e-cigarette vapor does not contain many of the toxic substances that are known to be present in cigarette smoke, it's still important for us to figure out and to minimize the potential dangers that are associated with e-cigarettes."

Many of the toxic substances present in large quantities in cigarette smoke are aldehyde containing chemicals, which can restrict airways. A common chemical often referenced in this category is formaldehyde (you know, that stuff they use to preserve organs and dead animals).

Formaldehyde
Image Courtesy of Wereo

Luckily, studies have found that this particular chemical isn't present in significant quantities in e-cig vapor (yay!). However, thanks to the studies by Penn State College of Medicine, another class of harmful chemicals are: free radicals. Free radicals are atoms or molecules that have unpaired valence electrons (electrons that participate in chemical bonding). They're produced when the nicotine containing liquid is heated within the e-cigarette. You probably learned in chemistry class that valence electrons normally go in pairs. When they're not in pairs, they're kind of sad and lonely... They desperately want to find a buddy. This is leads to them being incredible reactive and unstable.

Poor guy on the end looks so lonely..
Image Courtesy of SmokeyJoe

These free radicals can react with the cells in your body, most notably DNA, causing mutations. And unfortunately, whenever you start talking about mutations, cancer comes into the equation. These free radicals contribute to cancer in cigarette smoke, and it would make sense that the same would prove true for e-cigarettes. Luckily, it was found that e-cig smoke contains 100 to 1,000 times less free-radicals than traditional cigarette smoke. Dr. Richie states that  "the levels of [free] radicals that we're seeing are more than what you might get from a heavily air-polluted area but less than what you might find in cigarette smoke." It is still not known exactly what affect these specific free radicals might have on the body, which is why further research is currently being done to identify what free radicals are being produced and how they might interact with the body. While it's no reason to ditch e-cigs for traditional cigarettes (especially when e-cigs are helping smokers quit their addiction), it shows that this new form of nicotine still needs to be looked at more closely, and potentially regulated more to ensure the safety of those using them.

If you'd like to read the full study, it can be found on PubMed here.