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.