Category Archives: Admin

Amorphous Ice: Its formation and uses in Cryo-Electron Microscopy

Water is a little bit strange relative to the vast majority of chemicals because its solid form is less dense than its liquid form. When ice forms naturally, it assumes a rigid crystal lattice structure which keeps the molecules more spaced out than when they’re in the liquid form. In fact, water expands 9% when it freezes and ice has a density of only 0.917g/ml. but it’s a little more complicated than that. Did you know that there are actually 16 known types of ice? They are categorized based on their physical and structural properties, which are due to their mechanism of formation. In the 1980s, scientists discovered a novel type of ice called amorphous ice or vitrified water, which can have a density higher than liquid water because it does not form as a crystalline structure. But how do you stop water from doing that?

Scientists figured out how to make amorphous ice and have since been able to utilize it for important biological applications. Amorphous ice can be classified as Low Density (LDA) at 0.94g/ml, High Density (HDA) at 1.17g/ml or Very High Density (VHDA) at 1.26g/ml. The form that the amorphous ice assumes depends on its mechanism of formation in which the key factors are temperature and pressure. Water has a Glass Transition Temperature (Tg), which is 136K or -137⁰C, and the water must melt at a temperature lower than this to form amorphous ice. When ice forms at a higher temperature than Tg it will crystallize spontaneously.

LDA can be formed by very slowly depositing water vapor onto a smooth metal surface at a temperature less than 120K. This laboratory method mimics the way LDA water forms in space when it comes in contact with extremely cold solids. HDA can be formed by compressing regular ice under 1.6 GPa which is about 15,790 atmospheres of pressure! This must be done at a temperature lower than 140K. If it’s done at 77K (the temperature of liquid nitrogen) then the pressure can be raised back to one atmosphere and the amorphous ice will remain in that form (with the temperature kept at or below 77K). It was discovered in 1996 that HDA could be further manipulated into a higher density by warming it to 160K under 1 – 2 GPa of pressure and then cooling it back down to 77K and ambient pressure for storage.

Amorphous water (or other solvents such as ethanol or ethane) is used in cryo-electron microscopy as a means of preservation of the delicate sample without it being destroyed by ice crystal formation (which would happen if it was just frozen normally). This type of microscopy is particularly important in the imaging on protein structure. Dehydration of biological samples and bombardment with UV rays can alter the structure of interest, causing the microscope image to be non-representative of the structure in a physiological environment.

This type of research is also Nobel Prize worthy! The 2017 Nobel Prize in Chemistry was awarded jointly to Jacques Dubochet, Joachim Frank and Richard Henderson “for developing cryo-electron microscopy for the high resolution structure determination of biomolecules in solution”. Super cool stuff! (Pardon the pun).

Nicole Rogers

Destroying the Amazon Rainforest

In the last century, we as humans, have solidified our role as the most destructive species to ever live on Earth. Taking a step back and viewing humankind from an outside perspective illuminates our deplorable acts as we continually subdivide the planet that has given us all we need to advance and prosper. We have committed so many acts of planetary treason, yet deforestation of the Amazon may be the most horrible.

The Amazon Rainforest is a huge habitat for a wide array of all types of organisms including highly intelligent primates and dolphins.

Most people, including me, struggle to comprehend the absolute importance of the Amazon rainforest to innumerable aspects of life on Earth. The Amazon rainforest contains over half of the remaining rainforests worldwide. Appropriately nicknamed the ‘Lungs of the Planet‘, the immense size of this forest accounts for 20% of the oxygen produced into our atmosphere. To me, the most astonishing truth about the Amazon is that it is home to half of all of the species of plants and animals that live on Earth. Considering the Amazon is so dense, vast and teeming with untold biodiversity, its clear that unexplored regions far outweigh those where humans have ventured. It is exhilarating, and unimaginable to think how many organisms are still left to discover in this prosperous ecosystem. To this day, tribes people still exist in the Amazon remaining untouched by modern civilization. It is speculated that roughly 25% of the ingredients in modern medicine and up to 80% of the developed-world’s diet originated from the Amazon rainforest.

The Amazon Rainforest is vital to the health of the planet but is being destroyed at an alarming rate.

In the last 50 years, we have decimated nearly 20% of the Amazon for urbanization and agriculture. Now, 20% might not seem too substantial, but that is 300 million aces of land (1.1 million km2) destroyed, while we continue to chop down another 150 acres every minute! At this rate, it is projected that the amazon rainforest could completely vanish within the next 1-2 centuries. This destruction timeline is not a prophecy but a warning. The uncertainty in this projection is reliant on the decisions we make now.

Deforestation is a major contributor to the extinction of up to an astonishing 35 species every day in the Amazon. Obviously, forest loss destroys important habitats and destabilizes the ecosystem. But, what is often overlooked is the negative affect on an expansive number of organisms as the pesticides and fertilizers, along with urban sewage and runoff, pollute the rivers and soil that is vital to the prosperity of the Amazon. We are destroying the Amazon rainforest and it appears we will only realize our crucial oversight when it is too late.

Chief Raoni is a powerful indigenous leader and environmental activist. Since the age of 15 Raoni wears a lip disc to signify he is ready to die for his land.

The Chief of the Kayapo indigenous Amazon people, Raoni Metuktire, is working diligently on a mission to save his home for future generations to respect and replenish. Chief Raoni is a worldwide symbol for the preservation of the natural world and is one of my greatest heroes. Along with the United Nations and environmental activist groups, indigenous people of the Amazon are trying to save one of the most vital environments on the planet. We consider ourselves to be advanced beings yet even when it is blatantly obvious that what we are doing is destructive to us, and all life on Earth, we are unable to stop. Changes need to be made. We must put our greed aside and fix our mistakes before we don’t have the option to.

Joey Krahn

Goodness that’s loud!

Imagine if each time you tried to have a conversation with a loved one, someone came up from behind you and blew an air horn in your ear. Horrible right? Now, try to imagine that that conversation was not just your only form of communication, but is also your directionality and means of obtaining nutrients. I agree, it sounds unbearable and ridiculous. But, this is the kind of struggle that cetaceans, intelligent marine mammals such as dolphins and whales, experience daily from human activities in the oceans.

A basic schematic of how sound travels for echolocation in cetaceans

Have you ever seen a photo of a beached whale bloated and dying? Its hard to admit that theres a good chance that the whale you’re feeling sorry for died because of human ignorance. In the expansive environments of the oceans, sound is vital for survival and is used as the primary source of navigation, long range communication, and food location for cetaceans. When these sounds are interrupted it can have dire effects on the health of the marine environment.

Beaked and pilot whales are common victims of stranding due to noise pollution

Noise pollution is an often misunderstood and under-appreciated form of environmental deterioration. Our activity in the ocean can be so loud that is damages the hearing of cetaceans, even causing organ damage in severe instances. Cetaceans that dive to avoid intense air gun blasts are afflicted with decompression sickness (‘the bends’) and often die from their injuries. Marine mammals are playful, loving, and emotional creatures. We are overlooking our destruction of their habitat for the means of industry and war. Whale populations around the world are decreasing at an alarming rate.

Our influence is destroying parts of the marine environment where cetaceans have thrived for nearly 50 million years. Increased shipping, military sonar, and the seismic search for fossil fuels are sending cetaceans on a rapid path to endangerment and extinction.

Noise pollution has doubled every year since 1950 (plot projected until 2020)

Scientists and environmental activists are working to educate the public on the consequence of noise pollution. Although noise pollution is gaining more international recognition, studies show that minimal action has been taken to restore these delicate marine ecosystems. We must determine the importance of a prosperous ocean and the value of a healthy planet for future generations to advance and replenish. The ocean is indispensable to all life on this planet. The time to act sustainably is now.

Joey Krahn

Did We Forget Fukushima?

The Fukushima Daiichi Nuclear Power Plant. Attribution: Google Maps

You may recall, in March of 2011, the magnitude 9.0 undersea megathrust Tōhoku Earthquake that devastated the coast of Japan by tsunamis and killed tens of thousands. You may also recall the nuclear disaster when the Fukushima Daiichi Nuclear Power Plant’s emergency generators shut down, causing meltdowns, hydrogen gas explosions, and radioactive release into the ocean. While, like me, you may remember the constant focus by the news on the disaster and the failure of the Tokyo Electric Power Company in adequate preventative measures leading to the plant’s inability to manage during a tsunami.

That being said, you, also like me, may have put your focus on other, more recent topics, and forgotten about the entire situation. News is constantly updating and to think of what is happening now and what has ever happened is simply too much for the brain. So, let me remind you.

The nuclear plant is still leaking. According to the Japanese government, 300 tons of radionuclide-containing water is released to the surrounding ocean daily, particularly, cesium. This radioactivity is being found in fish, contaminating the fisheries market, and will take decades to clean from oceans or decay.

The Tokyo Electrical Power Company aims to have collected and treated the water pooled around the reactors by 2020 ; however,  to collect all would be impossible and the consequences of the event will remain. Without even considering the everyday struggle that Japanese radioactive refugees are still dealing with, ocean pollution is everyone’s problem.

For more information, watch the following video by Microsoft Research, YouTube Preview Image

 

 

-Lori Waugh

 

 

 

Pack Your Things, We are Going to Mars

Who said that we are going?

Around a year ago, the South African-born billionaire, Elon Musk, announced his plan for the colonilization of  Mars in a live video that went viral. Musk planned to land on Mars in the next decade and get it ready to host life by 2030. Since then, many have questioned the feasibility of the plan, including an esteemed astronaut who hypothesized that the project would stop as soon as Musk realizes the investment is not rewarding.

Are we even close?

According to researchers from the University of Lisbon and the University of Porto, we are. In their paper that was published on 18 October 2017, in the Journal Plasma Sources Science and Technology, Vasco Guerra et al. argue that Mars has nearly ideal conditions for CO2 dissociation to O2 and CO in Plasmas. As a result, production of O2 in Mars from CO2, which constitutes 95.9% of the Martian atmosphere, is possible.

Wait…what?

This is an illustration of a plasma lamp. When current is passed through plasma, amazing colours are observed. Uploaded by Joshua_Willson to Pixabay.com April 26, 2017

Basically, plasma is a state of matter where positive gas ions are surrounded by free negatively charged electrons. It can have interesting applications, such as plasma lamps. This state does not necessarily require high temperaturet. For example, non equilibrium low temperature plasma is a very interesting field of study and it is the type that Guerro describes as “the best media for CO2 dissociation”. There are several studies about how plasma assists the dissociation of pure COin the presence of a catalyst, usually TiO2. First, plasma supplies energy to drive the highly endothermic dissociation of CO2 through electron direct impact, in which an electron from the plasma transfers its energy to the CO2 molecule by collision, which aids the break of the C=O bond. Second, plasma adjusts the particles to the catalyst’s interface. Third, low temperature hinders the reverse reactions.

Why mars?

That is exactly Guerro’s argument. Guerro states that the atmospheric pressure of mars, 4.5 Torr, replaces the use of vacuum pumps that are necessary for the process on earth. Moreover, the average Martian atmospheric temperature, -63 oC, enhances the energy transfer from the plasma to the CO2. Also, Guerra mentions that the operation only requires as low as 20 W, which can be achieved on mars. Finally, the Martian atmosphere consists of 95.9% CO2, so O2 should be produced from this abundant source. Guerro says that the byproduct of this reaction, CO, can be used to fuel the return trip. In this way, the CO2 decomposition provides two benefits. Also, look at how beautiful it is:

An illustration of Mars, which is very beautiful. Uploaded by GooKingSword at pixabay.com

 

Personally, I used to think that if we can fix the atmosphere on Mars, then we should be able to fix it on Earth first. However, it turned out that Mars is helpful, but Earth is not. I started packing already…

By: Maged Hassan

Scientific Innovations in Nature: Yesterday, Today, and Tomorrow

Faced with the challenge of determining where we are and where we are going, humans took advantage of the magnetic field of the earth to provide a consistent orientation, with our invention of the compass, in 11th century China. Over 1.9 billion years prior, magnetotactic bacteria developed that same ability, albeit in a very different form. These bacteria contain chains of magnetic particles which orient themselves in response to the earth’s magnetic field, meaning the bacteria itself behaves like a compass needle, and will always point north (or south, depending on the species). This is one of many examples of how, in parallel to our development of technology through the use of the scientific method, the natural world has been using a different method, namely evolution, to develop its own tools which take advantage of physical phenomena.

Illustrative diagram of magnetotactic bacteria Credit: Wikimedia Commons

A study which highlights the continuing relevance of innovation in the natural world was conducted by a team of researchers at MIT. The team, headed by Kripa K. Varanasi, were looking into how to design surfaces which minimize the contact time of a bouncing drop. In situations where a liquid is dripping onto a hydrophobic (water-repelling) surface, the droplet of water will flatten upon hitting the surface, then reform a droplet and bounce off. The time it takes for the droplet to turn from its flat, pancake- like form into a droplet again is called the contact time. Minimizing contact time can be very important in applications such as the design of plane wings, where a shorter contact time can prevent drops of rain from freezing to the wing and beginning to build up.

Drops of water on a hydrophobic lotus leaf. Were these drops to have fallen onto the leaf, they would have first flattened, then reformed as droplets and     bounced off. Credit:  Flickr User Aotaro

Traditionally, contact time is reduced by decreasing the interaction between the liquid molecules and the molecules of the surface. When this interaction is decreased, it becomes more favourable for the water molecules to interact with each other, which causes them to clump together faster. However, once the liquid-surface interaction had been reduced to zero, no methods were known to further decrease the contact time. To get around this, the research group at MIT developed a new strategy, which has actually been used in nature for millions of years. By creating macroscopic ridges in the surface of the material, the researchers decreased the contact time by 40%. In their paper, the researchers acknowledge that both Morpho butterflies and the Nasturtium plant use macroscopic ridges in the same way: Morpho butterflies to keep their wings dry, and Nasturtium plants to clean their leaves. Lotus leaves are also very hydrophobic, and have often been thought to be the most hydrophobic surface in nature. However, because of these microscopic ridges, Nasturtium actually has a shorter contact time than even lotus leaves.

The wings of the Morpho butterfly have many amazing properties, including iridscence and extreme hydrophobicity. Credit: Wikimedia Commons

The oft-repeated quote by Isaac Newton “If I have seen further, it is by standing on the shoulders of giants,” speaks to the importance of prior work in the progression of science. As demonstrated by these examples, whether observed in bacteria, plants, or insects, the innovations of evolution can provide us with a continuing source of ways to see further.