Category Archives: Outreach Project

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)

Looking deep within a cell, super resolution microscopy technique improved by researcher at UBC

What do you think is the smallest scale visible through a light microscope? Bacteria in micrometers? Guess again. The answer is thousands of times smaller. Last year, a Nobel Prize in Chemistry was awarded for the development of super-resolved fluorescence microscopy, which brought the imaging scale down to nanometers (billions of times smaller than a meter). Recently, Reza Tafteh, a PhD candidate from the University of British Columbia further improved on this technique. The specific version of super resolved microscopy Reza improved on is called single-molecule localization microscopy (SMLM), and it allows scientists to image deeper into a target cell with greater accuracy. An interview with Reza is available in this podcast: 

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The computer system used to operate Reza’s microscope, photo credits: Ivan Lan, Reza Tafteh

As Reza explained in the podcast, SMLM achieves high resolution through image reconstruction. Imagine looking into a traditional microscope like looking down on the city of Vancouver at night from an airplane above. It is hard to tell the contour of the city with the limited lighting. Using fluorescence on the target sample is like turning on the building lights in the city, allowing us to observe things that aren’t normally visible under the moonlight. Now imagine that these lights are constantly on and extremely bright. If the location of the lights are too close together, many of them may seem blended with each other. This makes it harder to tell apart (or resolve) smaller structures such as narrow streets from one another; which in this case is like trying to resolve narrow structures within cells. SMLM reduces this effect by turning the lights on and off at different times for different parts of the city, which you can find more details in the podcast and the video.

However, the traditional SMLM technique isn’t perfect. Alongside major limitations in stability mentioned in the podcast, another major limitation is the distortion of an image caused by changing refractive indices through several different media, just like a pen appearing bent when inserted into a cup of water. Refractive indices varies from the cover-slip to the media (the substance the cell is placed in for imaging), and from the media to the cell.

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Refractive Index difference causing image refraction. Source:Flicker Commons, Author: Mohammad Tajer

Reza Tafteh has improved on both of these limitations. His approach can produce stabilized images with reduced distortion when imaging deep into samples. Here is a video of him demonstrating his stabilization technique.
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Reza is now trying to push the limits of SMLM even further, he sets his eyes on improving the technique’s inability to image live cells, while continuing to increase the resolution and clarity of microscopy images. It is exciting to think that specific cellular structures such as heart cell calcium receptors can be observed in unprecedented detail. It is not hard to imagine the many biological fields that can benefit from this microscopy technique. Reza’s improvement on SMLM  can potentially lead to better understanding of molecular biology, which may one day lead to new treatments for diseases such as central core disease.

Music and sound material used in podcast:

A sincere thank you to Reza Tafteh for participating in this project.

By: Group 3, Brian Cheng, Esther Lo, Ivan Lan, Sainan (Stephanie) Liu