Author Archives: julia

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:

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)

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.

 

 

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.

 

 

My Grandma Can Become Stronger by Eating Apples and Tomatoes

I remember when I was little, my mom and teachers at school would always tell me: “an apple a day will keep the doctor away.” While there may not be concrete scientific evidence that supports the accuracy of this saying, Dr. Christopher Adam and his colleagues from the University of Iowa have found evidence that consuming apples and tomatoes will keep our muscles strong and healthy.

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Video courtesy of CNN NewsByJim’s

Scientists have identified age-related muscle weakness and atrophy as a common trend in both humans and animals. Such phenomenon is often caused by disuse or denervation of muscles. Generally, muscle strength will start to decline between the ages of 30 to 40, and continue to decrease for the next several decades until the age of 70, when it begins to accelerate. Simultaneously, muscle mass is also decreasing, but at a slower rate. This loss of muscle mass and strength will consequently reduce the individual’s quality of life, and increase mortality. Up until now, exercise and healthy eating are the only approved approach to slow muscle atrophy.

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Video courtesy of Mayo Clinic

 

Researchers at the University of Iowa have recently discovered two compounds that reduce muscle mass and quality due to starvation and inactivity in elderly mice: ursolic acid in apple peel and tomatidine in green tomatoes. Both these compounds are believed to turn off genes activated by the harmful ATF4 proteins that is partly responsible for the age-related muscle loss and weakness. When this protein is expressed, it causes changes in gene expression so that protein synthesis is suppressed and protein degradation is elevated for muscle cells.

In their study, the researchers fed elderly mice with age-related muscle weakness and atrophy a diet either containing or lacking 0.27% ursolic acid, or 0.05% tomatidine for two months. The results of this study were significant. When the researchers measured the muscle mass of the elderly mice fed with either ursolic acid or tomatidine, they found that the mice increased their muscle mass by 10%, and their muscle strength by 30%.

These finding are significant as they can potentially increase the lifestyle and mobility of elderly people with muscle weakness and atrophy. The next step for the researchers is to continue their investigation in human clinical trial, and see if ursolic acid and tomatidine have the same effect in elderly humans as they do in mice. Ursolic acid and tomatidine can furthermore be developed into pharmaceutical supplements than can help with muscle strengthening.

Julia He