SFU Undergrad Researcher: Cassidy Jones

Introducing Cassidy Jones of the Department of Molecular Biology and Biochemistry!

CASSIDY JONES

Name: Cassidy Jones
Major: Molecular Biology and Biochemistry
Year: Fourth
Supervisor: Dr. Sharon Gorski (BC Cancer Agency)

Q: What have you been working on in your research so far?
A: I am currently in the Gorski lab at the BC Cancer Agency, studying the relationship between HER2 and the autophagy-related protein (ATG4B) in HER2 overexpressing breast, gastric and lung cancers. HER2 overexpressing cancers are typically associated with a poor prognosis and acquired treatment resistance to HER2 therapeutics is common. The “big goal” is to modulate autophagy in order to better treat these aggressive cancer subtypes. I have approximately 15 different cell lines on the go at the moment, so I’ve been spending a lot of time in tissue culture! A number of the cell lines are new to the BC Cancer Agency, so I have put in a lot of work optimizing growth conditions and researching methods in the primary literature.

Q: If you were a scientific lab instrument, which one would you be?
A: This semester I feel like I’ve spent a lot of time going around in circles on my research, so I think I would say I’m like the PCR machine. I just keep cycling and cycling, producing a mass amount of data, a lot of which looks the same!

Q: What’s the funniest thing in the lab that’s happened to you?
A: Well this one is more funny/sad, than funny. Recently I have been expanding an extremely slow growing gastric cell line that I need to run siRNA knockdown experiments on. After three weeks of waiting, the cells were ready to be passaged and plated. Unfortunately, the water bath was malfunctioning and overheated to 44C (apparently it doesn’t have an alarm). My media bottle was nearly empty so I didn’t realize it until I went to count the cells on the hemocytometer – yep, they all died. At first I didn’t know what happened, but when I went to get my other media bottles, they were almost bursting from the pressure. So now I have to re-expand this line again from frozen stock! It’s the smallest of details that can make all the difference sometimes – you have to triple check everything.

Q: Favorite science joke or meme from your field?
A: We have this quote posted in our lab – it helps on those long days where nothing seems to work:
“Theory is when one knows everything but nothing works.
Practice is when everything works and no one knows why.
Theory and practice are combined here: nothing works and no one knows why.”

Q: What is a typical “day in the life” in the lab for you?
A: I’ve been pushing the limits of my own endurance this semester, trying to get most of my project finished. I get to the lab most days by 6am and there’s many days I don’t leave until 9-10pm. I’ve also worked “overnight” in the lab this semester, and a 6-7 day work week is pretty normal for me right now. I spend a lot of time in tissue culture “babying” my cells and I have run more gels and western blots than I care to count! I just keep telling myself it will be worth it in the end.

Introducing the Cover for Issue 2!

We are very pleased to officially reveal the cover design of SFU SURJ’s Second Issue!

We received many submissions from across the lower mainland this year, and we are blown away by the artistic talent we’ve witnessed! So, without further adieu….

The Winning Design, by Ryan L.8

“For the image i used for the word “SURJ”, it was a microscopic illustration of bacteria which I altered from its original blue/green hue to a more dark red/purple/pink hue to match with the overall colour of the cover. The ‘cut-out’ design is also meant to symbolize a sense of unknown for the nature of science and the need for research. The major image is a close up of weathered and exposed wood which i also altered it to a more red-ish hue, and for the shadows, i gave it slight blue hue to make the grains ‘pop’ more.

The overall cover is designed with the classic/old-school textbook in mind. After completing the cover, I also realized that I was subconsciously inspired by the “Scientific American” magazine. Other details such as the banner at the top was just a simple yet elegant solution to an awkward space which I felt it completed the design in a subtle way. And I used a similar dark red colour taken from the images for the banner since red is also the colour for SFU and to also keep the colour unified across the whole cover.”

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Below, we would like to also feature the other fantastic submissions we received! **Please note the designs are in no particular order

By: Grace L.4

“The image this cover depicts is a cross section of an eye from a high school science poster from the 1980s. As an element of design, the circle contains many connotations which I want to communicate. Concepts of totality, eternity, and universality are all connoted when a circle is used. These concepts are reflective of science. To puruse studies and careers in science, to research, to analyze data, to share results is to have a desire to find total and undisputable truths of the universe. Thus using imagery of an eye was also a conscious decision. An eye carries connotations of knowledge and wisdom. The cross section image allows the design to be more abstract, but still carry great meaning”

 

By: Clarissa M.2

*no description provided

By: Serge K. 14

“This little project is an exploration of the human skeleton as well as a conceptualized look at what medical interfaces may look like and how medical UI can help identify areas under stress.

A holographic scan and rendering of the skeleton would allow a practitioner to adjust the display, allowing to zoom in on areas of interest and allow for a better and easier inspection of the issue and diagnosis. Such image processing and analysis technology would allow practitioners and scientists to extract important information from analyzed images in real time.”

By: Jennifer L. 5

“For my cover design, I picked a micrograph of uranium in granite from a ~20 year old issue of the journal Scientific American. I felt that the photo contained elements of scientific observations, geology/earth sciences, chemistry, and physics, while showing the blue, green, purple, and pink of the the SURJ logo. Due to colourful background, I kept all the text clean, san-serif, and white.

Uranium in granite is usually concentrated in a few of the less abundant minerals rather than being evenly scattered throughout the major minerals. This transmitted-light micrograph (magnifications about 50 diameters) shows a slice of granite only 0.03 millimetres thick. The colours result from the interference of the transmitted light waves, which are broken into two components travelling at different speeds as they pass through the the crystalline materials of the sample and through a single-crystal glass plate. Most of the uranium in the field of view is contained in a crystal of zircon or zirconium silicate (ZrSiO4), which appears as the small dark blue grain at the centre.”

 

By: Cherlene C.1

Interdisciplinary Interdependence:

“The design was inspired by SFU’s Architectural design which facilitates interdisciplinary work through design incorporated buildings housing several departments. As such, I incorporated images representative of biology (double stranded DNA), chemistry (structures of organic chemicals), and physics (action and reaction). The thematic blend of translucence and blue reflects the interdisciplinary interdependence, as chemical elements are the building blocks for DNA which are the building blocks to life, and where action and reaction force pairs operate across molecular and organism levels as in myosin and actin fibers generating muscle contraction and the oar stroke of a rower propelling the boat forward by displacing the water backwards. In addition, the pun on the word “reaction” refers not only to the action reaction force pairs, but also to chemical reactions!”

 

By: Lucas L.

7

*no description received

 

By: Jasmine W.15

“My design is inspired by the solar system. It contains a vintage vinyl record player with a futuristic twist on it, with the Sun in the centre and the eight planets in order orbiting around the lines of the disk. The tonearm and headshell also represent a telescope hovering above the planets. The pitch adjustment icons are moons and the 45 adapter is a meteoroid.”

By: Emma Y.3

“The imagery I chose is a photograph of a nebulous area of outer space, specifically the Rho Ophiuchi dark cloud which is the birth place of numerous new stars. I found this image from the July 1982 edition of Scientific American. Going into this design process, I was looking for images of the natural world that elicit a sense of wonder and discovery. Instead of automatically being associated with the wilderness or extreme outdoor sport, my goal was to find an image that was easily identified as scientific. To me, the purpose of science is to try to solve the unanswered questions of our world, and what environment is more filled with mystery as complex as that of outer space? I found a few galactic images in old scientific publications, however I was instantly drawn to this picture due to its brilliant colours which agree so well with the colours in the SURJ logo (vivid blues, pinks, and purples, with just a hint of light green in the bottom left corner of the image). I decided that because the picture is so bright and busy, having a solid, clean title element to centre the design would help focus the eye on the most important aspect of the cover (the title and logo). Because light green is featured quite heavily in the logo and is only slightly visible in the picture, I chose to match the text “Science Undergraduate Research Journal” to the green in the logo just to tie back into the original colour palette. Additionally, I think it’s very appropriate that a picture depicting the birth place of stars is on the cover of a publication filled with new research and discovery – the birth place of the innovation of the future if you will.”

The next 5 designs are photos taken from the Trottier Observatory here are SFU! These images are phenomenal and provide us with a first hand flimpse into outer space.

The following 5 image designs were submitted by Sarah K.12

NGC 869 Star Cluster:

Before you lies a collection of 7,600 year-old starlight. This particular sample of stellar photons have traveled for longer than mankind’s written history. Take a moment to breathe that in – you are looking at the purest mediums of history. You are looking at an astro-photograph, an image depicting the visual light spectrum of astral objects.

This is a close up of the 12.5 million year old star cluster, NGC 869. Together with its partner, NGC 884 (just out of this field of vision), they make the aptly-named “Double Cluster”, which resides in the northern sky constellation, Perseus, 7,600 light years away from Earth. The Double Cluster cannot be seen by the naked eye, though it is a spectacular binocular object in dark rural skies, and its beauty can be uncovered in suburban skies using a telescope.

The image was taken at the Simon Fraser University Trottier Observatory on November 29, 2015. Its exposure time was not very long compared to other deep sky images, a mere 8 minutes in total! This image was meant to be a test shot for training, but with some post-imaging work it turned out to be better than I had expected and is my first posted astro-photograph. Four filters were used (luminance, red, green, and blue), each at an exposure of just 120 seconds, with 2×2 binning.

 

11

The Bubble Nebula:

This is an image of the Bubble Nebula and it happens to be the birthplace of a future star. The Bubble Nebula is an emission nebula, meaning this beautiful gaseous structure emits its own light due to the ionized nature of the gas. The predominantly red colour of this interstellar cloud is due to the ionization and light emission of hydrogen gas, the most common element in the universe. Emission nebula, like the Bubble Nebula, are areas of star formation and can even be found in the spiral arms of some galaxies, like the Whirlpool Galaxy (M51). The Bubble nebula is located in the constellation, Cassiopeia, about 7,000 light years away from Earth. It’s estimated that the Bubble is about 300,000 years old. The most amazing aspect of this image is the spherical, bubble-like structure; the diameter of that bubble is 7 light years, meaning it would take 7 years for a light-speed object to travel from one end of the Bubble to the other! That’s almost two times the distance from our Solar System to the nearest star, Alpha Centauri!

This photo was captured and processed by Sarah Savić Kallesøe, a science undergraduate student at Simon Fraser University in Burnaby, Canada on September 29, 2016. The total exposure for this image is roughly 3.5 hours, using Red, Green, Blue, Luminance filters. Each frame had an exposure of 120 seconds. The L frames were captured with 2×2 binning and the colours were taken with 4×4 binning. In the future, I plan to incorporate the Hydrogen Alpha narrowband frames into the image to produce a more vibrantly red image and portray the presence of hydrogen gas in the nebula.

 

10

The Dumbbell Nebula:

This curious celestial structure is called the “Dumbbell Nebula”, named after its visible light resemblance to a dumbbell weight. The Dumbbell Nebula is a planetary nebula, which forms as a layer of gas expands from an aging star. This particular planetary nebula is predicted to be about 1,200 light years away, spans about 4.5 light years across, and is located in the Vulpecula (“Little Fox”) constellation. The Dumbbell nebula is second brightest nebula in our sky (the brightest being the Helix Nebula, located in the Aquarius constellation). Take a moment to think about this: the light captured for this image has travelled for over a thousand years, which means Europe was still in the Dark Ages when this light left the Dumbbell Nebula.

This image is a representation of the visible light emitted by the Dumbbell Nebula and was taken by SFU students Sarah Savić Kallesøe, Zeena Aburgeba, Ryne Watterson, and Rohit Grover. The processing of the captured image was done by Dr. Howard Trottier. This shot was taken between the late hours July 28 2016 at the Simon Fraser University Trottier Observatory. The exposure time per frame was 120 seconds and the total exposure time was 2.5 hours. The luminance frames were taken in 2X2 binning, whereas the red, green, and blue frames were taken in 4X4 binning.

 

13

Lunar surface:

This is the view of the Moon from the telescope at the Trottier Observatory! Unlike most astro-images display here, this image was actually taken by a cell phone camera. This image was taken on February 2, 2017 by Sarah Savić Kallesøe, during a rare moment of steady sky conditions between snow storms. Should you visit the observatory and observe the moon through the telescope, this is similar to what you would see. Mind you, it is not advisable to view the moon without appropriate lunar filters if the moon is more than half illuminated. For your reference, the Moon is about 1.3 light seconds away from Earth.

It turns out that this image captured a number of Apollo landing sites! The markings on the image indicate the following sites: Apollo 11 (the first moon landing with Buzz Aldrin and Neil Armstrong in 1969), Apollo 15 (1971), and Apollo 17 (the last and longest Moon stay, 1972). It is a humbling moment to gaze upon an astronomical body from which a handful of humans gazed right back at our tiny planet

 

9

The Whirlpool Galaxy:

Welcome to the Whirlpool Galaxy, home to more than 100 billion stars! Much like Andromeda Galaxy and the Milky Way, the Whirlpool Galaxy is a spiral galaxy. The distinct blue spiral arms of the galaxy are the sites of star formation and the distance across the Whirlpool Galaxy is estimated to be roughly 60 thousand light years. The Whirlpool Galaxy is a mere 30 million light year trip away and is located in the constellation Canes Venatici of the Northern hemisphere sky. The Whirlpool Galaxy is one of the most iconic spiral and brightest galaxies and one can discover the beauty of the it with just a pair of binoculars under dark sky conditions.

The Whirlpool is also a prime example of galactic cannibalism! Notice there are actually two galaxies in this image, the smaller circular structure below the larger spiral galaxy. The gravitational pull of the larger galaxy is actually pulling the smaller one towards it. Over time, they will eventually become one unit. A similar galactic collision is predicted to be in the fates of our home galaxy, the Milky Way, and our nearest spiral galaxy neighbour, the Andromeda Galaxy. Not to worry, this will happen far after our lifetimes.

This image was captured on the night of May 6, 2016 at the Simon Fraser University Trottier Observatory in Burnaby, Canada. The total exposure of the image is about 3 hours with 120 seconds per frame. The Red, Green, and Blue frames were captured with 4X4 binning and the Luminance frames with 2X2 binning

SFU Undergrad Researcher: William Shen

Introducing William Shen of the Departments of Chemistry and Molecular Biology and Biochemistry!

WILLIAM SHEN.jpg

Name: William Shen
Faculty: Chemistry and Molecular Biology and Biochemistry
Year: Fourth
Supervisor: Dr. Hogan Yu

Q: What have you been working on in your research so far?
A: My research is focused on modifying surfaces to create superhydrophobic and cytotoxic materials with silanes and nanoparticles. My original project was meant to impart hydrophobic properties onto materials but I wanted to direct the applications towards the biology side of things so I implemented antimicrobial properties in addition. Having volunteered in health care for a few years, one of the main things that I noticed is that outbreaks are pretty common and when they do happen, quality of life takes a major nosedive. If I can develop a simple flexible process to modify materials that can limit bacteria derived nosocomial infections through contact transfers, then it would be beneficial to everyone. Another application that I have also spent a lot of time developing are durable superhydrophobic and antimicrobial textiles.

Q: What is a typical “day in the life” in the lab for you?
A: I could potentially be doing anything from creating thin films of polymers on surfaces, synthesizing nanoparticles, performing Kirby-Bauer and other susceptibility tests, or characterizing and interpreting data from instruments like contact angle goniometers and scanning electron microscopy. I don’t have much of a normal everyday routine in the lab in terms of the experiments I plan.

Q: What’s your favourite course that you have taken so far in your degree?
A: I have quite a few favourite courses but I would say CHEM 459 – Special Topics in Organic Chemistry is my favourite. The course was taught by David Vocadlo and the topic that he chose was chemical biology. When I started university, I chose MBB as my major because I loved biology and chemistry. I was disappointed that MBB never quite went into the chemistry of anything in any sort of detail…it was sort of just glossed over for the most part. Fast forward to the end of second year and I found out about the Chemistry and MBB joint program and decided to switch into it. It wasn’t until I took chemical biology that I felt like there was a course that satisfied what I wanted originally. It took everything great about chemistry, everything great about molecular biology and biochemistry, and blended it into a different field that I loved. I would definitely recommend the course with Dr. Vocadlo to anyone if you get the chance.

Q: If you were a scientific lab instrument, which one would you be?
A: A scanning electron microscope because it’s my favourite characterization technique by far for materials and who wouldn’t want to be part electron gun???

Q: Who is your biggest science crush?
A: Elon Musk because I always admire someone who has the guts to take on high-risk high reward scenarios where you could potentially lose everything. Plus, he called his tunnel boring company “The Boring Company.” A+

Q: What scares you the most in the lab or the field?
A: Breaking very expensive equipment.

SFU Undergrad Researcher: Cherlene Emma Chang

Introducing Cherlene Emma Chang of the Department of Biomedical Physiology and Kinesiology!

cherlene

Name: Cherlene Emma Chang
Department: Biomedical Physiology and Kinesiology
Year: Third
Supervisor: Dr. Tom Claydon

Q: What do you want to be when you grow up?
A: A bioinformatical and clinical researcher. Computation is an increasingly invaluable skillset in the life sciences to quantify
scientific observations, while clinical relevance engages research with the treatment and management of patients to improve their
quality of life.

Q: How did you get involved in research?
A: I got involved in research through the BPK Co-op Program. Co-op is great for students to explore their career options and gain
valuable experience in their respective fields.

Q: What have you been working on in your research so far?
A: I have modelled the effects on the cardiac action potential as a result of the action of low pH on hERG potassium channels.
Myocardial ischemia occurs when blockage of coronary arteries reduces blood flow, preventing adequate oxygen perfusion. One
major consequence is acidosis, a reduction in local pH, contributing to cardiac arrhythmia. Acidosis profoundly affects hERG
potassium channels which provide a major repolarizing drive in the heart, and may suppress the protective mechanism of hERG
channels in preventing premature heartbeats.

Q: What will you be working on this summer?
A: This summer, my project is on zebrafish (Danio rerio) hearts as an excellent model of human cardiac electrophysiology. I will
use zebrafish hearts to study the action potential duration and cytoplasmic calcium handling using optical mapping techniques. I
aim to assess the effects of acidosis on irregular heartbeats using computer simulations.

Q: What is a typical “day in the life” in the lab for you?
A: I strike a balance between computational analysis and running experiments, where I write code in MATLAB and record ionic
currents in frog eggs (Xenopus laevis oocytes). I find that analyzing the data I collected firsthand enriches my research experience
through offering a well-rounded perspective on how each task fits in the bigger picture.

Q: What’s your favourite course that you have taken so far in your degree?
A: Introduction to Biological Physics (PHYS 347). Specifically, the electric circuit model of action potential propagation along a
neuron offered a fresh quantitative perspective on physiology.

Q: If you were a scientific lab instrument, which one would you be?
A: If I were a scientific lab instrument, I would be a computer. I enjoy modeling experimental data to equations, generating figures
for publications, and preparing powerpoint slides for presentations.

Q: What’s the funniest thing in research that’s happened to you?
A: During the 2017 BPK Research Day, I tripped down the stairs in the auditorium in my three-inch platform boots and spilled water
on myself. I laughed it off. Surprisingly, this incident calmed me down for my upcoming three-minute thesis and poster
presentations.

Q: What scares you the most in research?
A: The uncertainty of the future. Researchers apply for grants to get funded. Oftentimes there are more up-and-coming researchers
than grants available. Nonetheless, I will put my best foot forward in securing future grants.