Category Archives: Uncategorized

Evolution Can Be More Random Than You Think

Charles Darwin’s Origin of Species postulated that evolution takes a directed approach toward increasing fitness. A recent discovery suggests that evolution doesn’t always need to have a direction. Dr. Matthew Pennell’s findings suggest that evolution on a chromosomal level can have a high degree of randomness.

Dr. Matthew Pennell, an evolutionary biologist specializing in Computational Biology at the University of British Columbia, recently wrote a paper that gives more insight on evolution, entitled Y-Fuse? Sex Chromosome Fusions in Fishes and ReptilesIn this paper, Dr. Pennell uses software and algorithms to determine the factors that drive sex chromosome fusions. Unlike traditional biologists, Dr. Pennell does all of his work on his MacBook instead of using pipettes and microscopes.

Source: Wikimedia Commons, Dr.Pennell uses computational approaches, such as Mathematica for his research.

Source: Wikimedia Commons, Dr.Pennell uses computational approaches, such as Mathematica for his research.

This video, courtesy of universityofbc via Youtub, introduces UBC Killam and NSERC postdoctoral fellow, Dr. Matthew Pennell and talks about his research

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“The simple fact that Y autosome fusions are way more common than W or X or Z, suggests it’s probably just random, which is a kind of interesting and cool result that this huge thing in our genome and across all genomes is just random chance, and this random chance explanation is the most consistent with our data.”

 -Dr. Matthew Pennell

During his graduate studies, Dr.Pennel was part of a team that integrated chromosomal information of thousands of species into an electronic database called The Tree of Sex, which we describe in further detail in our podcast below.

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Now that we know randomness is involved in sex chromosome evolution another question arises: Is sex determination an absolute process? 

As we will soon see there are species, such as the Stickleback fish that change their sex determination system from XY, to ZW, to temperature controlled and so on. However, does this mean that we humans might experience such a change in the future?  

Source: Flickr Commons, Huamns have 22 pairs of autosomes and 1 pair of sex chromosome

Source: Flickr Commons, humans have 22 pairs of autosomes and 1 pair of sex chromosome

“They keep reinventing how they make males and females and this is really interesting and crazy because making males and females is the most basic thing animals do….But they keep switching around how they make males and   females, which I think is pretty cool.”

-Dr. Matthew Pennell

In addition, we were fortunate enough to have the opportunity to interview Dr. Pennell:

https://youtu.be/9obgQ7mI5Ac

Before the interview with Dr. Pennell, our group had a lot of difficulty understanding the premise and messages of the paper. Dr. Pennell provided us with simple insights on the different facets of the evolution of sex chromosomes – from the creative variety of ways that nature determines sex in species, to the mechanisms which drive sex chromosome fusions. Although a lot of these concepts were hard to understand at first, the premise of the paper is very simple to understand – computational biologists often work with real world data sets (ie. “The Tree of Sex”, and try to fit their models to them to determine the relationships between the scientists’ predictions and what’s really happening. In this specific paper, Dr. Pennell and his team concluded that the different models did not relate to the given dataset and the explanation for the real data is attributed to randomness.

 

We would like to give a special thanks to Dr. Matthew Pennell for his time and explanation of his paper.
Authors: Justin Yoon, Julia He, Radu Nesiu, and Matt Golf (Group 2)

First Quantum Code Written – Implications for the Future?

quantumcomputing

Source: Flickr Commons, Charles Opper

November 17, 2015 – about 6 hours before the writing of this post – may be an important day for future generations to remember. Just 6 hours ago, University of New South Wales in Australia has released a press release that the first lines of quantum code has been written. What is quantum computing and why should anyone care?

It’s a very different concept from modern computing – which uses the typical binary system consisting 0’s and 1’s to represent data in a single unit called a bit. Quantum computing opens up many more possibilities than just 0’s and 1’s in a single unit. It can hold double the amount of states where 0-1 and 1-0 can also exist at the same time in a single unit.

Basically, the different between normal computing and quantum computing is similar to trying to send an SOS message using morse code versus texting. Using morse code, you’d have to write nine units of information to get the message across: … — … in such fashion. Using text, you would only have to type “SOS”, 3 units of information to call for help.

This means that once this technology is better understood and as more complex code for this system can be written and computed, it will be possible to store information in exponentially smaller files and compute faster. Check out the video below about quantum computing by user Veritasium on Youtube if you want to find out more about it.

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Researchers at the Google funded artificial intelligence lab at NASA believe that quantum computing could be the key to having enough processing power and efficiency, along with data efficiency to achieve artificial intelligence. I am not so sure if that is something that I would want in my life time. Call me paranoid but it would seem wise to assume that an intelligent entity would learn to put its own needs before any other being’s.

AI

Source: Flickr commons, Magdalena Ladrón de Guevara

Having said that, I think the benefits of quantum computing and coding, once masterd by engineers and scientists, will be a leap forward in technology. With the potential of exponentially faster processing power, we could expect next-generation iPads to outperform today’s supercomputers. Think of the possibilities!

By Justin Yoon

Brains and games in 21st century – How do video games affect us?

There is a lot of debate regarding how video games influence our brains development and whether or not games are beneficial or damaging. Scientists have examined both sides and the question that needs to be answered is whether games are beneficial or they are transforming us into machines.

digital mindcredits: http://guardianlv.com/2013/08/researchers-develop-mind-control-using-the-internet-video/

Some studies show that prolonged exposure to video games has negative effect both on the body and the brain. Games decreases attention span, increase the risk of obesity and violent games decrease sensitivity towards aggression. The implications are troubling since decreased attention implies lower academic performance and obesity is a health risk factor. Furthermore it is shown that decreased sensitivity towards aggression not only makes us consider aggressive behavior acceptable but it also increases the chance that we will become aggressive.

aggressive gamers

credit to: http://yoursinglesourcefornews.com/ academics-debunk-theory-linking-violent-video-games-with-aggression/1379/

Another fact that must be considered is repetitive tasks in games. Because there are lots of games that become repetitive and have reward systems that encourage that behavior gamers are exposed to lose of creativity. Since repetitive tasks are better suited for a computer we could ask ourselves if our mind is encourage to become a basic processing unit.

However, there is another side of games which was investigated by researchers and the findings encourage people to become casual gamers. The benefits from games are as follow: better cooperation skills, adaptation to new challenges, fast reaction time and better attention to details.

brain-skills-games

credits: http://www.jklmgames.co.uk/how-games-can-train-the-brain

Besides the standard types of games we should also consider games that involve movement (e.g. some Nintendo Wii games) which are shown to motivate exercise. Those type of games should become encouraged in populations with increased risk of obesity, where the reward system should be tailor for the customers.

The tricky part of the games is the reward system which acts as a drug since it releases dopamine which is the hormone for excitement. Using this we can develop games that can stimulate people to learn and train. A study done on surgeons  showed it is possible to increase job performance via gaming. Here is a TED talk about games and how we can use them to construct a better world.

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Based on what we seen so far casual consumption of non-violent games have beneficial effects, however one must take extra care since crossing the line and becoming an addict can severely impact us.

Radu Nesiu

Jelly-like Features of Disease-causing Proteins

I remember when I was a kid (or even now), one of my all time favourite snack is strawberry flavoured Jell-O (or jelly). Not to mention, making it was so easy and so much fun, as the strawberry aroma would fill the kitchen.

C. elegans worm used in the study. Source: Wiki Commons

C. elegans worm used in the study. Source: Wiki Commons

Scientists at the University of Cambridge, led by Peter St George-Hyslop used nematode worm C. elegans as a model for amyloid lateral sclerosis (ALS) and frontotemporal dementia to study the physical properties of FUS, an essential RNA-binding protein in the body. The behaviour and physical properties of FUS can be closely compared to that of jelly. All RNA-binding proteins have two common domains: one for binding RNA and the other where the protein appears to be unfolded. It is at this unfolded region that the FUS undergo a process of reversible ‘phase transition’, which closely resembles the formation of jelly.

Comparison of ALS-affected and normal nerve cell. Source: Sarah Scoles

Comparison of ALS-affected and normal nerve cell. Source: Sarah Scoles

One common characteristic of all neurodegenerative disease is the irreversible accumulation of misfolded or mutated proteins aggregates in the brain, which as a result causes damage to the brain and disrupts communication between brain cells.  FUS is one of many types of RNA-binding proteins that is essential to the brain. It is essential in the regulation of protein synthesis, with functions in the nucleus and cytoplasm of a cell. However, the accumulation of mutated FUS and other associated proteins is also the underlying cause of the neurodegenerative diseases such as ALS and frontotemporal  dementia. Until recently, the significance and how FUS proteins affects the development of these neurodegenerative disease has been unclear.

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[Video courtesy of C.D. Net]

FUS starts out as soluble monomers (like the initial powered-form of jelly), and forms distinct localized accumulations. As it further condenses, a thick gel-like hydrogel structure is formed (like the formation of jelly after it cools in the fridge). This process can be reversible (like warming and cooling jelly repeatedly). Furthermore, during these transitions, RNA and proteins are continuously released from protein assemblies (like suspended fruits in the jelly as it is re-warmed and re-cooled).

The above processes are beneficial because it allows the cells to accumulate cellular machinery in a confined three-dimensional space (with no cell membrane required)  when needed to perform key tasks, but also disassemble when not needed. In addition, it is also faster and less-energy costly compared to the formation of a membrane-bound vesicle.

Although FUS is able to carry out vital cell processes by interchanging between different states, “this essential property also makes them vulnerable to forming more fixed structures if mutated, disrupting their normal function and causing disease” says Professor St George Hyslop. Mutation of FUS causes it to over-condense and become a thick fibrous gel, irreversibly trapping the essential RNA and proteins required for protein synthesis. It is the accumulation of misshaped FUS and other RNA-binding proteins that causes serious neurodegenerative diseases. However, further research and understanding of what are in these assemblies can bring us one step closer to curing ALS and other neurodegenerative diseases.

 

 

Effects of Sleep Deprivation

It doesn’t come as a surprise that a night without enough sleep can lead to a dazed morning. However there are more serious side effects to sleep deprivation than just drooping eyelids and yawns. There is no clear definition of exactly how little sleep is considered as sleep deprivation since each person needs different amounts of sleep. Rather, a person is considered sleep-deprived if they do not get enough sleep to feel awake and alert.

Still, research has shown that people can be both physically and psychologically damaged from sleep deprivation. In fact, it is unethical to purposefully deprive someone of sleep because the damage can be severe. The problems start on a minor scale, since the brain does not work very well when sleep-deprived. Some of the first impacts involve the ability to experience positive emotions. A sleep-deprived person may say they’re happy, but will have a neutral face, and they won’t recognize other people as happy either. The sleep-deprived brain may not be as capable of detecting positive emotions as well as a well-rested brain.

As well, as little as a single night of sleep deprivation can result in a phenomenon called “microsleeps”. During microsleeps, a person begins to fall into mini-snooze sessions which last about 30 seconds. The brain will go into a sleep state uncontrollably, and although people can force themselves awake, they will soon fall into another microsleep.

On a more major scale, losing sleep may cause delirium and even death. True delirium occurs when a person becomes completely disoriented. This often happens in patients who are hospitalized in intensive care units where lights and sounds continue all day and night, and doctors think loss of sleep is a major reason they develop bizarre behavior. Most seriously, researchers have found that no sleep can kill lab rats. In 2012, a Chinese man reportedly died from 11 days of sleep deprivation. Of course, it is not an easy venture since a person will most likely fall asleep before they die of sleep deprivation. Everything we know about sleep deprivation is harmful, but on a more positive note, most of these detrimental effects dissipate with enough sleep.

Here is a TED talk on why we sleep:

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post by Katherine

The Promising Near Future of Blood Transfusions

rbc

Rendering of red blood cells. Source: Flickr Creative Commons – Nocturnal lust

Have you ever donated blood? Canadian Blood Services is always looking for more blood, because they need lots of it. For example, here’s a table of the required donations per single procedure.

Required amount of blood donors per case. Source: Canadian Blood Services – Who does my donation help?

As you can see, a single car crash can require blood from up to 50 donors. Such events can cause a shortage of blood. In fact, just last year, Canadian Blood Services issued an appeal for more blood donations, as blood supplies hit an all-time low, especially for type O universal donors.

What are universal donors? Donors of blood type O can donate to every other blood type, because they have no antigens (molecules that can cause severe and harmful responses by immune system on the recipient of the transfusion). The video below explains the concept of blood types and why some people can flexibly donate to all others blood types. Credit for this video goes to user nafis A on Youtube.

The problem with blood donations is that we can’t simply take many donations and stop worrying about blood reserves. This is because, just like milk, blood is perishable. Blood Centers Organization states that red blood can only be stored for 42 days before going bad. This creates a need for a continuous supply of blood donations to account for any emergencies.

On the bright side, the future of blood supplies look promising due to a recent publication by a research group at the University of British Columbia (UBC) at the Centre for Blood Research. They discovered a method to genetically enhance an enzyme which removes the antigens from blood. To do this, they used a genetic manipulation method called directed evolution.

David Withers’ Research Group at the Centre for Blood Research. Source: UBC Centre for High-Throughput Biology

This process introduces step-wise mutations in the DNA that encodes the enzyme. They use a multi-pronged approach by introducing many random mutations to the gene, and select the best performing mutants and do this for multiple rounds. The researchers at UBC claim that after five rounds of directed evolution, the enzyme which removes antigens from red blood cells is 170 times faster than the original enzyme. The original enzyme, although functional, was never fast enough to be a feasible way of removing antigens from blood. This genetically enhanced enzyme, however, can be used practically in the medical setting.

This discovery could potentially eliminate the shortage of antigen-specific blood by converting all donated blood to donor types! I think this has great potential for saving lives. From what I know about Biology, once the DNA of this hyper-enzyme has been sequenced, it can be easily generated from protein farms – where bacteria produce large quantities of the protein which can be purified and extracted for clinical use. I think it’s amazing to hear that my university is at the frontier of such impactful discoveries!

Blog by Justin Yoon

Commented on the following blogs:

Electronic cigarettes by Brian Cheng

Bioethics dilemma by Paul Yi

Imposter syndrome by Luxi Xu

Trash to Treasure

Wouldn’t it be great to convert something that is harmful, yet naturally occurring in the environment to something that is useful to the human kind? That is exactly what a few researchers led by Dr. Da Deng at Wayne State University in Detriot did.

Multi-colored algae blooms may sound like one of nature’s many beauty wonders, however it is far from wonderful. Typically, these harmful algal blooms (HAB) consists of massive growth of one or more phytoplankton species, blooming up to a concentration of hundreds to thousands of cells per millilitre. These blooms of varying size can cover the surface of water for weeks. Some blooms are large enough, they can even be seen from space!

This satellite image capture algal bloom in Lake Erie Basin, taken on July 28, 2015. source: Nasa Earth Observatory

This satellite image captures the algal bloom in Lake Erie Basin, taken on July 28, 2015. source: Nasa Earth Observatory

In 2011, the algal bloom that occured in Lake Erie broke the record of worst algal bloom ever observed, topping the chart at 10 of the 10-point severity index. In August, 2014, the Toledo water crisis in Lake Erie left nearly half a million people without safe drinking water. Although the exact cause of algal bloom is yet to be determined, scientists believes that are many contributing factors including: water temperature, sunlight, current and presence of essential nutrients like nitrogen, carbon and oxygen. Although only a few algae species produce toxins, the effects they have on humans and aquatic life are detrimental as the toxins make their way up the food chain into animals we eat.

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[Video Courtesy to: Ohio Sea Grant]

Dr. Da Deng and his team of researchers aimed to reduced HAB in freshwater lakes by converting it to something useful. The team collected samples of  toxic HABs from Lake Erie, and converted it to hard carbon by heating it in argon gas at high temperatures of  700-1000 °C. Hard carbon, often derived from petroleum made from biomass, is an ideal electrode (electric conductor used to connect non-metallic part of the circuit), used for sodium-ion batteries. The final electrodes created by the researchers consists of 80% hard carbon (derived from algae), 10% black carbon and 10% binder. The scientists found that overall, the sodium electrode had a high capacity of up to 440 mAh/g in the first cycle. However, there were some issues of irreversible capacity loss after the first cycle, resulting in a lower capacity of 230 mAh/g.

Although, Lithium-ion batteries are more dominant in use right now compared to Sodium-ion batteries, sodium is more abundant and could potentially replace the more-expensive Li-ion batteries in the future. However, more extensive research still needs to be conducted to increase the stability and capacity issues with these algae-derived sodium electrodes to improve their performance in the future. The researchers also noticed that the temperature of which the algae was heated also affected its stability and capacity performance. This is something scientists can take in account as they aim to improve this discovery.