Life's New Ingredient: Someone's in the Kitchen with Methane

Zircon Crystal

Early Earth may not have been the methane-rich reducing soup the scientific community previously believed it to be. Researchers at the Rensselaer Polytechnic Institute uncovered evidence that will force scientists to write a new recipe for the atmospheric conditions of early earth that gave rise to the building blocks of life.

Prior to this study, scientists believed that early Earth consisted of an oxygen deficient atmosphere filled with methane, carbon monoxide, hydrogen sulfide and ammonia. To date, theories of how life began on earth were concocted from these toxic ingredients.

In the paper titled The Oxidation State of Hadean Magmas and Implications for Early Earth’s Atmosphere that was published in the December 1st issue of Nature, researchers reveal that the atmosphere of early Earth may be closer to our current oxygen-rich conditions than previously thought.

The theory that the outgassing of magma released by volcanic activity was responsible for forming early Earth’s atmosphere is widely accepted by most scientists. To determine what gasses the magma was supplying researchers at Rensselaer looked at zircons, minerals contained in the magma that had crystalized into solid rock on Earth’s surface, to provide a glimpse into the past. Zircons, being that they are not destroyed over time like most other minerals, are commonly looked to for clues regarding the history of Earth. In this experiment, researchers used zircons to provide them with a sneak peak into the oxidation states of atmospheric gases by determining the oxidation state of the magmas that created the zircons.

Understanding the conditions that gave rise to life on earth is not only crucial to further our quest for knowledge of our own origin but alters the way we look for potential life on other planets in our universe.

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Quazicrystals – They’re Here, They’re Queer, Get Used to It!

Atomic Model of a Quazicrystal Surface

Dr. Dan Shechtman, similar to the quazicrystals he discovered, isn’t afraid to be different. Despite years of ridicule and harsh skepticism from his peers, Dr. Shechtman received the Nobel Prize in Chemistry in 2011 for the discovery of quaziperiodic crystals or quazicrystals.

Quazicrystals, unlike conventional crystals, lack symmetry in their ordered atomic structure. Prior to Shechtman’s discovery, it was widely accepted in the scientific community that repetition in atom packing inside crystals was necessary for their very existence. It wasn’t until the morning of April 8th, 1982 that Shechtman would unearth an image that would prompt him to ask the scientific community to follow him down the quazicrystal rabbit hole.

Dan Shechtman Ph.D.

The seemingly impossible image Shechtman exposed was that of a crystal with an arrangement of atoms that were not in repetition, similar to that of aperiodic mosaics. The discovery triggered oodles of uproar causing Shechtman’s own research team to ask him to ask him to leave the group.

Ultimately the scientific community had to re-evaluate their understanding of solid matter as other scientists obtained quazicrystals in the lab as well as discovered them naturally. Quazicrystals may have applications in diesel engines and frying pans but more importantly for use as a reminder that with an inquiring mind questioning the impossible might win you a Nobel Prize.

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The Science of Fun

Yelena Lacey and daughter Alexie explore the
peculiar effects of liquid nitrogen

Over 1000 kids and parents flooded the field at the University Charter Middle School on October 21st for the third annual CI Science Carnival. Eager to learn about science and math in this hands-on Halloween themed event, kids were able to experience the effects of liquid nitrogen while enjoying cotton candy and the bending of light while they munched popcorn. 

Ashley Reyes learns about how fossils are made 

at the “Prints from the Past” demonstration

“Events like the Science Carnival show kids that science and math can be fun,” said Dr. Philip Hampton, coordinator of the Carnival for the past three years. He went on to say that “too often kids are told that these subjects are hard and, as a result, they can get discouraged from viewing themselves as being able to succeed at them.” I’m happy to report that the kids at the carnival were anything but discouraged.

Tori Hoge prepares to launch a marshmallow
using a compressed air gun

Currently, a five-year Department of Education Hispanic Serving Institutions grant funds the Science Carnival. With attendance for the event skyrocketing year after year it is Dr. Hamptons hope that the event will continue to grow and eventually become sustainable though building partnerships within the community.

Theodore Parra stares in awe at the splitting of 

light through his diffraction grating glasses

While some of the science behind the demonstrations and experiments might be difficult for the kids to understand, Dr. Hampton assures that “by being exposed to these subjects in a fun setting, they can also see that while the subjects might be challenging, they can also be incredibly rewarding.” It doesn’t take a mad scientist to know that’s a lesson worth learning.

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Beating Cancer to the Punch

Ahmed Awad, Ph.D.

Photo Compliments of the 

CI Chemistry Department

Ever wonder what would have happened if Marty McFly didn’t reunite his parents in Back to the Future? He wouldn’t exist of course! Dr. Ahmed Awad and 8 students at CI are on the hunt for ways to best cancer before it exists by developing drugs that specialize in inhibiting gene expression without the use of a DeLorean.

Some drugs target the protein after it has already formed; however, Awad and his team have a very different approach. “Our target is the messenger RNA,” Awad explained. The drugs consist of small segments of nucleic acids called oligonucleotides, which target the messenger RNA in carcinomic cells. The oligonucleotides react with the RNA by Watson-Crick base pairing via two mechanisms. The first mechanism blocks the translation into the protein. The second mechanism activates an enzyme called RNase H, which degrades the RNA/DNA complex.

“Chemical modifications are important to stabilize these drugs,” Awad noted. Reagents must be stabilized against nucleases, enzymes that cause nucleic acids to degrade. Nucleases are capable of degrading injected oligonucleotides within 5 minutes of injection, before the drug can reach its destination.

With any luck the next generation of these gene-inhibiting drugs will succeed in telling cancer to make like a tree, and get outta here.

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Achievement Unlocked

Solved structure for the M-PMV retroviral protease
University of Washington

From battling asteroids to battling AIDS, video games have come a long way. Using an internet based cooperative game called Fold It, online gamers have managed to solve the structure of an enzyme that has baffled scientists for more than ten years.

Like HIV, Mason-Pfizer monkey virus (M-PMV) causes AIDS in monkeys and apes. A M-PMV retroviral protease, a protein-cutting enzyme, is a key element for the spread of the virus in rhesus monkeys. After numerous attempts with molecular replacement techniques and years of frustration, scientists asked for the help from the Fold It gaming community.

Fold it is designed to utilize the special reasoning skills of warm blooded human beings to find the lowest energy state for a given molecule. It works by assigning points to players as they discover lower energy states for structures within a specified framework that reflects the laws of nature and chemistry. In this case a team of Fold It players solved the structure in less than 10 days time. According to a paper titled Crystal Structure of a Monomeric Retroviral Protease Solved by Protein Folding Game Players that was published in the September 18th, 2011 edition of Nature Structural & Molecular Biology, the structure discovered was “of sufficient quality for successful molecular replacement and subsequent structure determination.”

As a former Tetris addict, I am excited at the prospect that the worlds of video games and science are becoming complimentary. As long as there are tasks and puzzles that human brains can tackle and computer processors cannot there will be a place for citizen science. Who knew that solving proteins could be as fun as saving Princess Peach?

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How to Look “Smart” in Camo

US soldiers conduct an exercise of cold weather exposure training

Through wind, rain, sleet, snow, sweltering deserts and tropical humidity soldiers must be fashion chameleons when deciding what to wear in these sometimes-unpredictable conditions. In the present, soldiers meet these challenges by wearing layered clothing and subtracting layers as the temperature allows.

Though effective against the vast variety of conditions soldiers face this method poses a problem. Layered clothing is heavy and difficult to carry with limited space. Additionally, when soldiers move though different altitudes in mountainous regions the amount of thermal insulation needed can vary greatly. Frostbite and hypothermia may be the result of improper insulation though such conditions. On the other hand if there is too much insulation present the result could be unnecessary sweating, dehydration or even heatstroke.

The United States Army is now on the hunt for a better way to combat Mother Nature. In a paper titled Temperature Adaptive “Smart” Thermal Insulation published by the U. S. Army Research, Development and Engineering Command, a environmentally responsive “smart” material is introduced that can self-adapt to the appropriate thermal balance.

The concept behind the “smart” material is the same as a bimetallic thermostat. The idea is to utilize a bimetallic spring inside fibers. The fibers have two bonded metals that have different coefficients of thermal expansion. With changes in temperature one of the metals changes in length more than the other which bends the spring in the fiber in a way that results in a curl. When applied on a grand scale, materials made from these fibers would thicken in colder temperatures thus providing more insulation.

If this technology is further developed it may have a variety of commercial applications. Perhaps hikers, mountain climbers and emergency response team members alike will soon be lining up for this miracle garb.

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Flawed Diamonds are a Quantum Computer's Best Friend

Though they may not cut the mustard for a marriage proposal, flawed diamonds are ideal for maintaining quantum states. For the past few years scientists have found ways to influence and manipulate atoms near nitrogen-vacancy (NV) centers in flawed diamonds. These capabilities may someday make complex quantum computers or even a quantum internet a reality. 

So what exactly is quantum computing and how are quantum computers different than the run of the mill computers we already have? In a nutshell the difference lies in something called a quantum bit, or a qubit. A qubit is capable of maintaining a superposition of two states whereas classical bits are one state or the other, otherwise known as little ones and zeros. 

The key to understanding these processes lies in understanding the function of the NV center, one of the most common defects in diamond. As everyone knows a perfect diamond is made entirely of carbon; however, if nitrogen is introduced during formation it can become included as a defect.

Model of a Nitrogen Vacancy Center

Carbon alone would attach itself to 4 other carbon atoms; nitrogen however, bonds to only 3 carbon atoms creating the vacancy in the lattice structure where the 4th carbon atom would normally reside. This formation provides an electron free to move around the vacant space and around the neighboring atoms. The electron can then be coupled to the nuclear states of the surrounding carbon atoms and for the purpose of quantum computing they become entangled qubits. 

The problem with using the vacancy as a means for quantum computation is that it’s impractical to implant single nitrogen atoms one by one through a thin layer of diamond when you’d need several thousands in a single layer. In a study titled Chip-Scale Nanofabrication of Single Spins and Spin Arrays in Diamond, published in the July 23rd issue of Nano Letters, researchers described a method for mass-producing these NV centers, which may be fundamental in creating quantum networks. 

In the process researchers employed a thin layer of resist to cover the diamond. Through the resist they blast away using electron beam lithography. Next they shower the resist with nitrogen ions that end up going through the holes that were created in the top film layer. Once the nitrogen ions pass through the holes in the resist they embed themselves in the actual diamond creating the desired vacancies. Since the researchers were able to control the array of holes, they were able to control the array of vacancies. 

Thanks to these advancements it may now be possible to create vast networks of qubits, which someday may be lead to scalable quantum computers capable of complex problem solving. The next step to move forward in the quantum-computing race is for scientists to develop qubits that are able to hold their states for longer. This would provide processors with the means to run complex algorithms and perform practical problem solving. While diamonds are forever, unfortunately quantum states are not.

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Recipe Fit for a Queen

Honeybees and Queen in Honeycomb

All female honeybees are created equal, until they’re 72 hours old that is. While still in the larvae state, the female honeybee (Apis melifera) has an uncertain fate. Though it is highly likely that she will become a worker bee, there is a slight chance that she will be destined for royalty. There are two female castes amongst honeybees: the worker (a sterile female), and the queen (a fertile female). It is impossible to differentiate genetically between worker bees and queen bees. So what makes a queen, a queen? 

Royal jelly, a substance secreted from the heads of worker bees, is fed to all bee larvae up to 72 hours. At that time larvae meant to be workers are switched to a diet of honey and pollen whilst the larvae fated for queendom continue on a strict royal jelly diet. It has been known for some time that royal jelly is the cause of the transformation from a normal female honeybee in the larvae state into a queen bee with increased size, reduced developmental time and enhanced ovary development; however, the specific mechanism has remained unknown. 

In a paper published by Japanese researchers in the April edition of Nature, evidence was presented that suggests Royalactin, a 57-kDa protein found in royal jelly, to be the cause of the queen bee’s superior development. Royalactin not only enhanced growth in the female honeybee but in fruit flies (Drosophila melanogaster) as well. Mechanistically the protein was found to promote queen development via an epidermal growth factor receptor (EGFR) mediated signaling pathway by activating and increasing the activity of mitogen-activated protein kinase, which was found responsible for promoting many queen like qualities. In the study researchers found the knocking down of EGFR expression in the bees and the fruit flies stifled the queen like superior development, showing that EGFR facilitates these processes. 

For years the royal jelly effect has fascinated humans. Though there hasn’t been much conclusive evidence regarding it's benefits for human application or consumption, royal jelly has found it’s place in several herbal remedies and beauty products. Perhaps royalactin will be the next big thing at health spas and beauty salons where human workers will be the ones providing the royal treatment.

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Where in the World is Simone Aloisio?

Power Plants on the Japanese island of Shikoku

Photo compliments of Dr. Simone Aloisio

While some might choose to take a Caribbean Cruise or ski the Alps if granted a sabbatical, you can’t say the same for Dr. Simone Aloisio, associate professor in the Chemistry department at CI. Aloisio has been hard at work this semester performing data analysis for a research project being done on the Japanese island of Shikoku aimed to develop a new cheap, effective way of measuring column carbon dioxide (CO2).

Dr. Aloisio and his colleagues Prof. Gen Inoue and Prof. Masahiro Kawasaki are hoping to determine the CO2 emissions from two power plants (no, not Fukushima) using an instrument meant to measure CO2 emissions from a specific point source. “The reason for doing this particular project,” Aloisio stated, “is to be able to measure the amount of CO2 emitted directly from a regional source, such as a power plant or a fire.” In the past this task has been a difficult feat for scientists to achieve.

The newly developed instrument used in the project measures overhead atmospheric carbon dioxide. Aloisio explained “the instrument collects infrared light from the sun in a region of the spectrum where CO2 absorbs light.” A distinctive feature of this particular machine Aloisio stated in his progress report, “is how the absorbing and non-absorbing wavelengths are obtained.” He said the “instrument uses a series of filters including an etalon filter to restrict the wavelengths of light detected.” The concentration of CO2 is determined by fitting the transmittance to a simulated spectrum. Aloisio’s contribution to the experiment involved adjusting the simulation routines to reflect only CO2 emissions and eliminate interference from water in the atmosphere. 

CO2, one of the primary greenhouse gases, is the main cause of global warming on our planet. Human actions such as the burning of fossil fuels are considerably increasing the CO2 concentration in the atmosphere. When Aloisio returns to the United States on April 25th he and his colleagues will have taken us one step closer to understanding the climate change that the planet earth is currently undergoing and what we can do to stop it.

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