Author Archives: Kenny Lin

BIOC 302: General Biochemistry

An interesting course where you dive into the biochemical pathways of lipids, proteins, and nucleic acids. BIOC 302 is a biochemistry course where you are assaulted with biochemical facts and information.

FORMAT OF THE COURSE

The lectures were live at 8AM…fortunately they were asynchronous and recorded due to the pandemic. Lectures were every MWF. There were also optional tutorials where the teaching assistants would go over a set of practice problems. The course was broken down into 3 broad sections. Biochemical processes and metabolic pathways of lipids, proteins, and nucleic acids and overview of DNA replication, transcription and translation. This course is super memory-heavy as you had to memorize most of the structures and names that appear in the slides as well as the complex metabolic pathways. What makes it even more difficult is that you also have to apply this memorized knowledge in different scenarios on the exams.

The assessments for this course consisted of one midterm and one final exam of equal weighting. The midterm tested the first half of the course only (lipids and proteins) while the final exam tested the latter half of the course only (nucleic acids, DNA replication, transcription, and translation). Both exams consisted of matching questions, structure recognition, multiple choice, and long answer questions adding up to 100 points.

GPA 🙂 OR 🙁

This course is very hard and you will need to put a lot of work in to be above the class average. It is imperative that you do not fall behind because then you will need to memorize more content, while trying to decipher what you are memorizing. The midterm exam was by far the hardest exam I’ve written this year (my 4th year); however, the final exam was much easier. The instructor is not shy about scaling, and usually scales the exams by 2-4% to reach an average above 70. The class average for my section was 74.

BIOC 302 Grade Distribtution. Credits: ubcgrades.com

verdict? to take or not to take

Despite being a very hard course, I would definitely take a course if you have a strong interest in biochemistry. This course is also a prerequisite for some professional schools in healthcare like dentistry. The assessments can be tough in terms of ambiguous questions in the exams, but if you’re not too worried about that then you’re good to go!

Gold: Precious in a Different Way

Let’s face it, to most people gold is just an over-glorified rock with no real value; however, that’s not the case at all! Just this month, researchers from University College London have created a novel light-activated coating that kills infectious bacteria. The key ingredient? Gold.

upgrading with gold…

The invention of a bacteria-killing coating sounds ingenious; however, Hwang’s team was actually not the first to come up with this idea. Previous studies have already shown that coatings incorporating the chemical crystal violet can adequately kill bacteria. The problem was that the coating had to be light-activated by UV rays, which harm the skin by promoting skin cancer.

This was exactly the problem Hwang’s team looked to solve; to make a coating that did not require harmful wavelengths of light. They overcame this challenge by incorporating small clusters of gold into a polymer containing crystal violet. The result? Now this new coating could effectively eliminate bacteria upon activation with low intensity white light – the level of light found in offices.

Concentration of bacteria (CFU/mL) across three conditions after 6 hours exposure to low-intensity white light. Star indicates bacterial concentration is undetected. Sample size = 6 per treatment, error bars are standard deviation. Adapted from Hwang et al.’s data

The figure above perfectly illustrates their result. Statistical analyses show that bacterial concentration does not significantly differ between the violet crystal and control (no coating) condition. This indicates that low-intensity white light cannot activate the bacterial-killing function in the violet crystal coating. What’s interesting is that addition of gold with the violet crystal, reduces the bacterial concentration significantly to near zero values, indicating successful activation.

More than a novelty…

The results of Hwang’s study are truly impactful. It is well known that hospitals are a hotbed for infectious bacteria. In fact, 27% of surfaces in hospital rooms are contaminated with bacteria even after regular and thorough cleaning. As such, applying the coating on these surfaces will definitely reduce the chances of contracting a hospital-related disease. Who would have thought? Not only is gold more than just a hunk of rock, it can also save lives.

FRST 303: Principles of Forest Science

A refreshing break from your traditional courses in the Faculty of Science. Although FRST 303 is still a science-based course, the focus is on the growth and evolution of trees and forests.

FORMAT OF THE COURSE

Due to the pandemic this was an online asynchronous course. Lectures were live and recorded on Tuesdays and Thursdays. The instructor, Chris Chanway, was also nice enough to schedule a 15 minute break every lecture. The entire course was graded on one midterm and one final exam. Both were of the same format: define a few words and answer a few long response questions. The exams were not invigilated and were closed book.

GPA 🙂 OR 🙁

This course might be the easiest course you could ever take at UBC, especially for science students. Half of the course content is going over basic biological concepts such as what is a cell. Having two assessments make up your entire grade may seem daunting; however, the entire question bank for both exams are provided to you a month in advance. Sadly, only 20/200 students enrolled would show up for live classes because of this. You basically don’t have to study and you can rest easy as long as you just answer all the test bank questions beforehand. I know of some people who didn’t study at all and still got an A+. In fact, the course average for my section was 94.

FRST 303 grade distribution. Credits: ubcgrades.com

verdict? to take or not to take

If you have no interest in trees or forestry I wouldn’t take this course, because the material will seem very dry. If you’re looking to bump up your GPA, need upper year credits, or just looking for a small break in a heavy workload this course is definitely for you!

Embarrassed of Asian Glow? Don’t Worry, The Future is Promising

Ever find yourself beet red after one small drink? You’re not alone! Over one-third of East Asians and eight percent of the world population experience this awkward phenomenon; however, a solution is in the works. Just last month, researchers from Weill Cornell Medical College have solved this problem by experimenting with targeted gene therapy on mice.

What does asian glow look like? A before and after comparison. (Credits: Wikimedia Commons)

The Dangers of Asian Glow

Apart from causing embarrassment, asian glow comes with more serious consequences than just flushing red. The red glow is caused by a deficiency in the ALDH2 enzyme, a key component in detoxifying alcohol. When you drink alcohol, your body converts the alcohol into acetaldehyde. Normally, acetaldehyde is further converted to a safer compound by ALDH2; however in individuals with asian glow, ALDH2 does not function, causing acetaldehyde to build up. Since acetaldehyde is a cancer-causing agent, its accumulation drastically increases the risk of developing esophageal cancer by six to ten folds.

Conversion of alcohol to acetate is stopped in people with asian glow. This leads to toxic buildup of acetaldehyde. (Credits: Me – created with Notability)

A Glowing Solution…

Matsumura’s team reasoned if a lack of ALDH2 enzyme was the problem, maybe they could simply add it back in.

“We hypothesized that a one-time administration of a […] virus […] expressing the human ALDH2 coding sequence […] would correct the deficiency”

They tested their idea on three strains of mice: mice with functional ALDH2, mice lacking ALDH2, and mice with a non-functional version of ALDH2. The latter two simulated the asian flush syndrome seen in humans. After introducing all the mice with the ALDH2 gene and feeding them alcohol, the researchers carefully monitored acetaldehyde levels in the blood.

Their hard-work paid off! In the two strains deficient for ALDH2 function, acetaldehyde levels and abnormal behavior associated with alcohol consumption were back to near-normal levels. Furthermore, they found that one dose was enough to confer persistent and long-term protection.

From Mice to Humans: A Complicated Decision

Matsumura’s team emphasize that a long-lasting treatment for ALDH2 deficiency currently does not exist. Although making the jump from mice to humans will be challenging, they assure that virus-mediated gene therapy shows the most promise in becoming an effective therapy. The million-dollar question is whether the risks of the glow outweigh the benefits of reduced alcohol consumption seen in affected individuals. To this Matsumura’s team say:

“the overall burden […] on human health, particularly […] cancer, supports […] gene therapy.”

What do you think?

The COSMIC Bubble Helmet: A Revolutionary Ventilation System

As the COVID-19 virus evolves into different strains so to has the methods of dealing with the consequences of this virus. In patients with severe COVID-19, they are plagued with acute respiratory distress disorder (ARDS). This is a condition where fluid fills the lungs and prevents air from reaching the necessary gas exchange compartments, similar to what occurs in drowning. These patients are subjected to invasive mechanical ventilation, where a tube is uncomfortably shoved down the patients throat to facilitate breathing.

a potential alternative?

To avoid ventilator-induced lung injury, non-invasive ventilation methods have shown to be well tolerated by patients. Instead of a tube, a tight-fitting nasal or facial mask is used and uses positive pressure to facilitate ventilation. In the context of COVID-19, the use of current non-invasive ventilation methods is not recommended due to virus aerosolization risks which puts healthcare staff in danger of contracting the virus.

Example of a non-invasive ventilation face mask.

A cunning solution

COSMIC Medical, a Vancouver-based organization has designed a “Bubble Helmet” that remains noninvasive but also reduces the aerosolization risks mentioned previously! Additionally, the materials needed to make the helmet are low cost and can be easily be retooled or adjusted by manufacturers due to its simplistic design.

Owing to its flexible design, patients freedom of mobility will not be hindered as they can lie face up or down comfortably. Furthermore, the helmet is made of transparent material, thus a patient’s vision will be unobstructed, further enhancing comfortability.

the next steps

There are still many hoops to jump through before this helmet can be offered to patients. These steps include obtaining regulatory approval and completing clinical trials. So far results have been obtained in an experimental setting, thus the effectiveness of the helmet must be measured in clinical settings as well. Currently the Bubble Helmet design is open source and available to all to peruse. Check out the open source paper!

BIOL 371: Principles of Neurobiology I

This course will have you rethinking about what you know about the nervous system! BIOL 371 is a neurobiology course that focuses on neurons, their corresponding action potentials, and neurohormones.

FORMAT OF THE COURSE

Arghh…. it’s an 8AM class but it is definitely worth waking up for (an early start to the day is always nice). There live lectures are all recorded so one could always sleep in. The non-exam marks are broken down into pre-reading quizzes and literature worksheets all submitted on Canvas. The quizzes are pretty straightforward and all the answers are found in the readings. They usually include a “Have a Guess Question” which is more of a thought exercise and is marked for completion rather than correctness. There were 5 neurobiology papers we had to read and 5 classes dedicated to helping us decipher these papers. The paper lectures were really guided and helpful and the subsequent literature worksheets were only marked for completion!

In terms of exams, there were 2 midterms (20% each) and one final (40%). However, there was a reweighting policy implemented in the middle of the term that reduced the weight of the midterms if we did better on the final. Exam format is a mixture of true/false and open-ended responses. What I really love about this course is that they adjust the marking scheme to accommodate students who come up with a reasonable answer that wasn’t considered in the scheme before. The teaching team was really careful about the exam design and were not shy about taking out unfair questions or allowing more flexibility for ambiguously worded ones.

GPA 🙂 OR 🙁

I really liked this course so I did really well; however this course is not a GPA booster. However, this course isn’t a GPA killer either even though the content is quite difficult. The content is difficult because the course takes an approach such that we’re looking from the lens of a researcher. We’re tasked to try to prove why a certain fact in the textbook is true by looking at the experiments that were done (eg. how did we know that ion channels were involved in the action potential rather than just simply being told they are involved). The course average was 76 when I took it.

verdict? to take or not to take

A lot of the course is interpreting data from the primary literature, so if you really enjoy reading about research I would definitely take this course! Even, if you struggle with interpreting data-heavy slides, the professor, Dr. Irene Ballagh, is super approachable and always willing to help (one of the best professors I’ve had at UBC).

Stress and Grey Hair: An Answer to a Biological Mystery

Everyone has heard that too much stress will cause grey hair. This is easily seen in former president of the United States, Barack Obama, whose hair could not escape the stress of the Oval Office! But what exactly links grey hair and stress? This year, researchers at Harvard University found that the nervous system eliminates pigment-regenerating stem cells responsible for coloring our hair!

Barack Obama’s hair color at the start of his presidency versus seven years after. Credits: DailyMail.com

THE ROOT OF THE PROBLEM

When you are stressed, your body responds in three distinct ways: the activation of your immune system, the activation of your sympathetic nervous system (SNS), and the release of cortisol, an energy-stimulating hormone. All these responses put your body into a “fight or flight” mode; increasing heart rate and blood pressure. The challenge for Zhang’s team was to sort through these three responses and determine which caused grey hair.

Zhang’s team tackled this problem by performing a series of experiments on black-furred mice. They first tested if immune system activation was the cause by seeing if the fur greyed under stress, even when the immune system was deactivated. They indeed found that stressed immune-deficient mice still greyed, indicating that stress causes greying, independent of an immune response.

They also ran similar experiments using mice mutated to not respond to cortisol or noradrenaline, a molecule involved in SNS activation. The idea being that if  a response was involved, stress should not cause the fur to grey if it was removed. In mice lacking response to cortisol, the fur still greyed; however, in mice lacking the response to noradrenaline, their fur remained black! This indicated that the SNS was the main driver in hair greying.

Figure 1. The results of the experiments described above are shown. Note that mice unable to respond to SNS activation do not grey under stress. “Control” refers to unmutated mice. Also note that a different type of control (non-stressed vs stressed) was ran in the immune-deficient case. (Sample size = 6 for each condition, standard error bars). Credits: Adapted from Zhang et al.’s data.

ZOOMING IN FURTHER…

With the culprit in hand, Zhang’s team didn’t just stop there! Through further experimentation, they illustrated that the SNS over-stimulates MeSC, the stem cells involved with hair pigmentation. During hair growth, these MeSC cells transform into pigment-producing cells and color the hair. Under stress, the SNS causes these MeSC cells to transform at an abnormally high rate, quickly depleting these cells and leading to grey hair.

THE REASON BEHIND THIS LINK?

In truth, the reason why this MeSC and SNS interaction exists is unclear. Zhang’s team suggests an evolutionary perspective. Since octopuses, a distant relative to mice and humans, can modify pigmentation of their skin using the SNS, they hypothesize that this interaction was simply conserved. Whatever the reasons may be, this just further shows that the mystery has yet to be completely solved!

Sugar Chemistry: A Pathway to Antibiotics

We’ve all heard it endlessly as kids. Don’t eat too much sugar, it’s bad for you. However, what if I told you that sugars aren’t all that bad and in fact, careful changes to its chemistry can lead to life-saving drugs, such as antibiotics! Just last year, researchers at the University of British Columbia, led by Stephen Withers, found a unique way to tinker with sugars’ chemical structures by using molecules in bacteria. The same bacteria found in our poop!

A view of E. Coli, the bacteria that was used by Wither’s and his team. Credits: The Philadelphia Inquirer

SWEET…BUT WHAT ARE THEY?

Before we go further, let’s start with a simple question: What exactly are sugars? Sugars are molecules shaped like hexagons which are often joined to other molecules known as “acceptors”. In a way we are kind of like sugars; we find someone we like, confess how we feel, and they accept our love! Right? Wrong. As we all know the last part rarely happens and this is the same in sugars, as chemists have yet to find easy ways to join the sugar and acceptors. Luckily for sugars (and unluckily for us), Mother Nature has come up with some solutions, using helper molecules known as enzymes.

Curious as to what type of sugars chemists work with? There’s no ambiguity here, chemists use the same molecules found in sugar cubes. Yes! The ones you put in your coffee. Credits: The Verge

A SOLUTION UNDER OUR NOSES…

Instead of struggling to find ways of joining sugars and acceptors, Wither’s team thought: Why not just use these enzymes? In other words, hijack Mother Nature. To make their idea a reality, they extracted sugar-specific enzymes from E. Coli, a bacterium that lives inside the human digestive tract. Their efforts gave them 175 sugar-specific enzymes, and from this they chose 8 enzymes that were most specific to the type of sugars and acceptors they were interested in.

“With the 8 enzymes in hand, Withers and his team could now easily make these sugar-acceptor linkages” is what I would like to report; however, things are never so simple. It turns out that the sugar-specific enzymes they got from E. Coli did the exact opposite of what they wanted. Instead of forming sugar-acceptor linkages, they were specialized in breaking them.

Unsurprisingly the savvy researchers expected this and already had a reliable strategy to reverse-engineer these enzymes from linkage breakers to linkage makers. You may be wondering how they re-purposed something to work completely opposite of what it was intended for. To reconcile this, think of this example: hammers. If you’re feeling angry one day you would likely use the hammer to smash things. However, if you’re feeling innovative one day, the hammer would help you build things by hammering in nails. These enzymes are similar; an enzyme that breaks sugar bonds differs very little from one that builds sugar bonds.

MORE THAN JUST A BOND…

Sugars go way beyond than just satisfying your sugar fix. They are molecules essential to the maintenance and regulation of not only your body, but in most living things! Because they are found everywhere, including infectious bacteria, sugar-based molecules serve as effective antibiotics, however making these drugs are difficult. Why? Well as mentioned before, chemists have trouble making these sugar-acceptor bonds; however, the research done by Wither’s team show that this will not remain the case. On a lighter note, they also created a sugar-based molecule that had nothing to do with health; detergent. This just further shows that these bonds are far-reaching and relevant in many contexts.

Story source

Armstrong, Z.; Liu, F.; Chen, H.-M.; Hallam, S. J.; Withers, S. G. Systematic Screening of Synthetic Gene-Encoded Enzymes for Synthesis of Modified Glycosides. ACS Catalysis 20199 (4), 3219–3227.

Adapting to Virtual Learning

With attendance at Zoom university being at an all time high, the team at The Undergraduate Scientist would like to share some tips of how they’ve been adapting to the online term. These tips range from study advice to self-care.

1. structure your day

Many students have complained about the lack of structure to their day due to most courses being asynchronous and recorded. This leads to a loss of motivation and a sense of aimlessness. We encourage students to attend live lectures, or to schedule set times where the students plan on watching the recordings. The goal is to simulate what it would be like if classes were in person, and hopefully having allocated times as to when you’re going to engage with classroom material will give you a sense of direction for the day.

An advantage of online classes is the flexibility, however this does not mean you should only be watching lectures when you feel like it. Often times, one ends up playing catchup on lectures a few days out from an examination, which is not only very stressful but also ineffective.

2. Find a hobby that doesn’t use a screen

I remember at the end of the term, my eyes became so tired and I couldn’t focus on the words displayed on my computer. Remember to take breaks and rest your eyes. Try to schedule 2-3 hours away from the screen each day. Find a social-distancing friendly hobby so you won’t be tempted to check social media on these breaks. For me this is golf, but some suggestions for other hobbies can be jogging, skateboarding, cycling, walking your dog, etc.

3. invest in a secondary monitor

You can get these for as low as $40 dollars for used models or $300 for high-quality ones. This makes computer work much easier as there is more space to work, as opposed to squinting at my laptop all day. You can also put reference material on this screen, which minimizes clicking through tabs to find things, only to be lost as to where your original tab was located.

4. don’t overload yourself

It’s tempting to take on more jobs or extracurriculars, because there is now more available time. This is especially true for commuter students who might gain 10 more hours a week, since now they don’t need to travel back and forth from UBC. This being the case for me, I decided to take on more than usual this school term, resulting in burnout in the middle of the term. You can definitely add one more commitment than usual, but I recommend allocating most of the extra time as breaks. Trust me, your eyes and your back will thank you.

5. Stay in touch with family and friends

A big drawback of virtual learning is that people feel out of touch with their peers, leading to a dwindling sense of community. Quarantine and social distancing accentuates loneliness, even when we don’t actively realize this. Make sure to call or contact your family members and friends regularly not only to check up on them, but to alleviate loneliness. Always make time to attend to the relationships in your life, because these relationships are much more valuable than school.

Hope this was helpful!

CHEM 203: Introduction to Organic Chemistry

Most Science students have heard about the dreaded CHEM 233, but did you know that Chemistry/Biochemistry majors actually aren’t allowed to take that course? Meet CHEM 203, the introductory organic chemistry course that is much more difficult and intensive compared to CHEM 233. However, if you’re really interested in organic chemistry, this course will build solid fundamentals for you to utilize in advanced courses.

FORMAT OF THE COURSE

The format of the course is fairly standard for a typical organic chemistry class. There are live lectures where the professor goes over the details of a reaction and its mechanisms. One really needs to brush up on CHEM 123 knowledge as you’ll be swamped with numerous reactions that need to be memorized on as early as the second week. There are also no slides, as this would be hard to do with a drawing-intensive course such as organic chemistry. The professor writes real-time notes as he talks over reactions, which makes for very organized and structured note-taking.

Along with a lecture portion, there is also a lab portion worth 25% of your entire grade. Surprisingly, these labs had less of a workload than the first year labs. However, instead of labs once every two weeks, you have labs once a week. Unlike the first year labs, there are no unreasonable 10 minute quizzes! In fact, you won’t even have to write any lab reports! The workload consists of pre-lab work, the lab, and post-lab work (which is just filling in a report sheet). Pre-lab and post-lab work usually took me 2 hours a week to accomplish, mostly because I get distracted easily. Unfortunately, your technique mark is largely dependent on your TA. Personally, I had a really bad experience with my TA where it got to the point that I would dread every lab and be too afraid to ask questions (as he would take off marks for any questions he deemed “dumb”). This being said, the lab instructor for this course is very considerate, and would give back marks that were not supposed to be lost (interestingly everyone who had my TA was scaled up in the end…).

GPA 🙂 OR 🙁

This course will tank your GPA unless you have a strong interest in the subject material. There were basically no “free marks” in the course (eg. clickers, participation) as the marks were distributed between two midterms, the lab, and the final exam. All of the examinations were difficult, with averages hovering at mid to high 60s. The final exam average is unknown, but I remember not being able to finish the exam because of length and difficulty. The course was definitely scaled up in the end as I ended up with an A+, despite not being able to finish. The course average for my year ended up being 68.

Credits: ubcgrades.com

verdict? to take or not to take

If you’re not passionate about organic chemistry and you’re not planning on taking any organic chemistry classes in the future I would opt to take the easier CHEM 233 course. If you’re planning on taking more organic chemistry in the future, I 100% recommend taking this course. Even though it is much harder than CHEM 233, you will gain much more solid fundamentals and this will benefit you as your academic career progresses.