McGill Biochemistry Research Awareness Day (RAD) 2016

Research Awareness Day (RAD) is an annual event run by the Biochemistry Undergraduate Society (BUGS), which seeks to inform and inspire students about research being done by some of the foremost professors in McGill’s Biochemistry department.

Professors at this event first gave short presentations about the research being conducted in their labs, and then spent lunchtime answering questions from students. Students attending RAD were then given the chance to meet with three different professors in small groups, affording students the opportunity to ask professors more questions about their research and career path. After lunch, Dr. Young gave a presentation detailing ways for students to get involved in research as an undergraduate. The event ended by transitioning into an intimate cocktail hour, during which there were poster presentations by graduate students in these professors’ labs.

Overall, RAD was a well-structured, successful event that gave insight into the groundbreaking research being done by professors in the Biochemistry department. It provided students the opportunity to learn more about a career in research, and how to get involved as an undergraduate.

Listed below are some of the professors at this event, along with a brief overview of the research that they discussed.

 

Professor Albert Berghuis:

With the rapid development of antibiotic resistance, the need for new antibiotics has become increasingly urgent. This is the focus of Dr. Albert Berghuis’ research. The Berghuis lab uses structural biological approaches to examine various biochemical interactions. The goal is to use techniques such as X-ray crystallography, electron microscopy, and NMR spectroscopy to examine the enzymes with which bacteria destroy antibiotic molecules, and use that knowledge to create next generation antibiotics that can bypass the enzymes but remain biologically active. With pharmaceutical companies stopping antibiotic development due to a decreased profitability, it’s up to independent laboratories such as that of Dr. Berghuis to continue the research in this field. His lab also studies the development of anticancer drugs.

Dr. Kalle Gehring:

The prime focus of Dr. Gehring’s lab is to decipher the structure of various proteins, particularly those involved in neurodegenerative diseases and the ubiquitin system, protein folding in the endoplasmic reticulum, and bacterial virulence factors. A typical project at the Gehring lab consists of growing bacteria to extract and purify a certain protein, crystallizing the protein, and the analyzing its structure using X-ray crystallography and NMR spectroscopy. Recently, the lab is pursuing the study of parkin, a protein involved in a link between mitochondria and neurodegenerative diseases such as Parkinson’s disease.

Dr. Sidong Huang:

Dr. Huang’s research is focused on using a functional genomics approach to study cancer-related mechanism, and to create new treatment strategies for cancer using this information. The current approach to cancer treatment primarily involves chemotherapy and drugs that target cancer cell mutations. Current cancer drugs are not very effective as resistant cancer develops in almost all patients. While the main solution to this problem is through the development of new drugs, Dr. Huang uses another approach. Using functional genomic tools such as shRNA, cDNA and CRISPR libraries, Dr. Huang and his students systematically screen each gene and create custom drug combinations that target those that modulate drug resistance. They also hope to uncover genetic dependencies of cancer pathways which then can be exploited therapeutically. This novel approach hopes to overcome drug resistance in cancer patients and to provide a more effective treatment strategy.

Dr. William J. Muller:

The Muller lab creates and uses murine models of human breast cancer to understand the effects of oncogene activation in normal cells, discover the cooperation between oncogenes and tumour suppressors, and eventually develop preclinical models.

Dr. Bhushan Nagar:

The Nagar lab uses structural techniques to analyse macromolecules, with specific focus on determining innate immunity mechanisms and nucleotide-specific interactions in mRNA silencing.

Dr. Nahum Sonenberg (represented by Argel Valles and Nathaniel Robichaud):

The Sonenberg lab conducts diverse research on two major topics: mRNA translation and translational control of cancer. Through researching how different pathways are affected and alter mRNA translation, the Sonenberg lab hopes to better understand Autism spectrum disorders and psychiatric disorders. Research in translational control of cancer aims to understand how non-cancer cells can promote tumour survival, as well as develop methods of tumour selective killing of cancer cells.

Dr. Jose Teodoro:

The Teodoro lab aims to determine the role that transcription factor p53 plays in tumour angiogenesis. Angiogenesis is a natural process in human development and wound healing, but in tumours, angiogenesis allows the cancer cells to have access to nutrients that otherwise would be inaccessible. The Teodoro lab also hopes to use virus target specificity in cancer treatment.

Dr. Ian Watson:

The Watson lab aims to translate the genome of melanoma, the deadliest form skin cancer, in hopes of developing new therapeutic strategies.

Dr. Jason Young:

The Young lab focuses on the function of chaperones in protein folding, with emphasis on the roles of misfolded proteins in neurodegenerative diseases such as Parkinson’s disease. The function of the Hsp70 chaperone system and its role in disease states are of particular interest.

McGill’s 2016 Undergraduate Research Conference

The Undergraduate Research Conference that took place during the fall semester of 2016 featured original research projects by students selected across various science majors. The keynote address was given by Dr. Frederic Bertley (B.Sc 1994, Ph.D. 2000; Senior Vice President of Science and Education, The Franklin Institute, Philadelphia, Pennsylvania), entitled “A Note to Our Future Scientists: Pay Attention to the Importance of Science in a Growing Clueless Society”. Some highlights from the many great research projects are given below.

Jason MacKay is a U2 Honours Math and Physics student. He has worked on developing a cost-effective Compton gamma ray imager. This device detects the presence of gamma rays and is currently used around the globe in astrophysics, nuclear medicine, and detection of nuclear threats during security checks. MacKay was able to develop a model that significantly reduces cost, while still maintaining the resolution of current Compton gamma ray imagers by using PMT detectors on either side of a scintillating material.

Michael Chen‘s research centred on organic dust (OD), a pollutant that pig farmers are exposed to. Prolonged exposure to OD can result in inflammation of pulmonary airways. His project focused primarily on examining the role of Nrf2, a protective transcription factor, whose inhibition may be the cause of inflammation caused by exposure to OD.

Carina Fan studied the relationship between memories and decision-making. Memories can be classified into episodic memories, created by personal experiences, and semantic memories, created by the memorization of facts. This research project sought to discover which of the two categories had a greater influence on clinical decision-making. She assessed this through a case study, and concluded that engaging episodic memory processes when learning appears to bias later diagnostic decisions.

Miles Cranmer is a physics student who spent last summer developing “BiFrost.” This software allows one to analyze data much more efficiently in only a line of code. Cranmer’s project has applications in analyzing data from interferometers, such as the powerful Event Horizon Telescope, by deleting useless data and keeping the useful ones.

Marilena Anghelopoulou‘s research project explored the impact of the production, use, and disposal of metal halide lamps compared to their more modern counterparts – solid state lighting. The latter emerged victorious as it was determined to be the safest for the environment and human health during its entire life cycle.

Johnson Ying is a neuroscience student who studied the progress of Alzheimer’s disease in model J20 mice and the effect of the disease on special navigation. He tracked the behaviour of grid, head-direction, and border cells in the mice with the help of microdrives that held moveable tetrodes. Ying’s results showed that the cells begin to disrupt as early as two months, thus affecting the special navigation of the mice.

Ariel Geriner‘s project was on the topic of habitat loss. This research project studied how habitat connectivity impacts an ecosystem’s health. It found that the less connected an ecosystem is, the greater the impacts are, and that these impacts can take effect in a much shorter time.

 

 

 

The 2016 Lorne Trottier Public Science Symposium

The 2016 Lorne Trottier Public Science Symposium took place in Montreal on October 17 and 18. This year’s event, entitled Science and the Media: The challenge of reporting science responsibly, offered public lectures from four prominent science journalists. The talks all focused on one main theme: the role of the media in interpreting science and communicating its ideas to the public. Scientific papers often include technical jargon, making them rather inaccessible to the general public. As such, journalists become the interface between the scientific community and the wider population.

DAY 1

The first guest speaker was Julia Belluz, the senior health correspondent for the news website Vox. She brought the issue to light by highlighting the degree to which misinformation permeates the media, and the responsibility that science journalists carry. To report science responsibly, she outlined a five-step plan that she abbreviates as ISCES (not the terrorist group, she assured).

  1. Infiltrate. Ms. Belluz’s first recommendation was to “avoid preaching to the converted,” and to reach out to audiences that normally wouldn’t be reached. She suggested that journalists use YouTube and social media as outlets to reach wider and atypical audiences.
  2. Shame. Her second recommendation was to hold people accountable for poor scientific journalism. In addition to the journalists responsible for misleading articles, the publishers should be penalized for enabling irresponsible reporting.
  3. Contextualize. When reporting on quackery, Ms. Belluz asserted that the context must be taken into account. Pseudoscientific books that aren’t prominent in the public consciousness might not be worth reporting on, when more influential forms of irresponsible science communication can be debunked.
  4. Educate. From a young age, children must be taught critical thinking skills, or, as Ms. Belluz put it, to “detect bullshit when bullshit is presented to them.”
  5. Sympathize. Her final recommendation was to have sympathy when considering peoples’ misinterpretations of science. She discussed the case of an unvaccinated Amish community in Ohio, which was the site of the largest measles outbreak in recent US history. When she contacted them, they explained that it wasn’t vaccine denial or their religion that founded their distrust of vaccination. Instead, it was an alleged instance in which a member of their community had been harmed by a vaccine. This had founded generational fear, which had been difficult to surmount.

The second speaker was Erica Johnson, a Canadian journalist and host of the TV series Marketplace on CBC. Her talk focused on the increasing use of alternative medicine, and the role of the media in scrutinizing claims made about such products. She shared her experience in reporting on homeopathy, a form of medication where substances that normally cause certain symptoms are diluted to minute amounts in order to “treat” illnesses that cause those same symptoms. In her investigations, she found that some of these pills contained only sugar. In some instances, companies that were pressed for the scientific basis of their products presented improperly conducted studies. Ms. Johnson went on to critique Health Canada, which has issued licences for thousands of alternative treatments that have little scientific backing. Such treatments, even if innocuous in themselves, can be highly dangerous due to the false sense of security that they foster. In the belief that an alternative medicine is sufficient treatment, people may neglect proper medical care for life-threatening conditions.

DAY 2

The first speaker on the second day of the conference was Trevor Butterworth, the founding director of the non-profit Sense About Science USA, and the editor of STATS.org. He discussed inadequacies within scientific journalism throughout the 20th century, with poor reporting on prominent scientific advances such as the telegraph, Sputnik, and the atomic bomb. The public was often more interested in the image of the absent-minded professor than in the science itself. A foolish story about Albert Einstein miscounting his change was of more interest to the public than his theories about the universe. Even other types of media propagated this negative view of science, with prominent films such as The Thing and Dr. Frankenstein presenting science as an obsession with knowledge, coupled with amorality. With the popular ideas of the absent-minded professor and the dangers of science, it is unsurprising that in the late 1950s it was thought that only 12% of people understood what science truly entails. Mr. Butterworth then turned towards issues that still permeate modern science today. For example, the use of the term Frankenfoods as a popularized word for genetically modified foods demonstrates that it is still taboo to interfere with nature. On a separate note, Mr. Butterworth also discussed the issue of poorly conducted science. The lack of repeatability in research is an issue, and, as he put it, some researchers are doing “too much trusting and not enough verifying.” To close, Mr. Butterworth showed that the public grasp of science has somewhat improved, with 29% now estimated to understand its conduct. However, he advised both scientists and journalists to carefully frame their facts, lest they become actors in the wrong stories.

The final speaker was Joel Achenback, an author and staff writer for The Washington Post. His talk focused on the role of science in not only debunking quackery, but also in enforcing more rigour within science itself. Citing examples from his career as a journalist, he illustrated that even good scientists can make mistakes, and that peer-review is essential in correcting these mistakes. Mr. Achenback suggested reasons for why the public may sometimes find it challenging to accept scientifically supported ideas. For example, he discussed the way in which our beliefs can often become tied to our identity. When elaborating, he apologetically brought up the 2016 US Election and Donald Trump’s views on science. According to Mr. Achenback, when Trump voices his opinions on climate change, he is not simply making a statement about science, but is identifying as a member of a community of people who don’t believe in climate change. Mr. Achenback argued that people often live within specific spheres of influence, citing his interaction with a Trump supporter at one of Trump’s rallies, in which she claimed to know no supporters of Hillary Clinton. The media we choose to watch and the people we choose to spend time with are usually those that share similar views. This can lead to ideological isolation, which acts as a barrier to the broadening of perspectives and the spread of information. In the final minutes of his talk, Mr. Achenback explained that science does not simply provide a series of absolute truths, but helps us get closer to the truth over time.

MSURJ Volume 11 Launch!

CVE-7574 CVE-7608 CVE-7649 CVE-7668

(Photography credits: Carter van Eitreim)

On March 31, students, authors and guest presenters gathered in the Bellini atrium for the launch of MSURJ Volume 11. Armed with champagne, cheese and freshly printed copies of the journal, guests mingled, discussing the featured research (and drinks). Presentations by four guest speakers followed, covering topics from industrial success in the scientific field to advice for future researchers. With no pedestals or microphones, the presentations had an air of genial informality, as if the speakers were having an intimate conversation with all attending guests.

 

The Speakers

“One of the main thiScreen Shot 2016-04-15 at 8.57.12 pm.pngngs in my mind when I started my undergrad was that I really wanted to do research,” Kevin Chen, the CEO and co-founder of Hyasynth Bio, conveyed to the guests. With an audience composed mostly of undergraduate science students, he was speaking to people who could likely relate to this aspiration. However, after this, Kevin’s pre
sentation took a twist as he narrated his departure from the typical path of academia. Running with a chance, he opted to try research in a different form, and now, at 24 years old, he is the co-founder of Hyasynth Bio, a biotechnology company that engineers microbes to make natural molecules. Specifically, medical cannabis— in an attempt to replace the acres usually required to produce the plant with tanks of yeast. In closing, he reiterated to the students, “Ignore the idea of academia versus industry and science versus applied science. Science is science.” 


Screen Shot 2016-04-15 at 8.58.53 pm.pngThe next speaker, Dr. Shireen Hossein, related the story of her career in academia, from her PhD that focused on the cell biology of myelination and nerve development to her position with Dr. Gerhard Multhaup here at McGill. With Dr. Multhaup, she has been provided with many diverse opportunities, from learning new techniques like protein mass spectrometry, to supervising students, to designing projects for herself. These experiences have allowed her to grow not only as a scientist, but also as a person. To close, she reiterated the importance of “finding an area of research that fuels your passion.” She also highlighted that research areas can be changed throughout a scientific career, and that a chosen research line now will not necessarily be a lifetime contract.

Our third speakCVE-7610er was Dr. Jesper Sjӧstrӧm, a neuroscientist researching the mysteries of synaptic plasticity and the organization of neuronal connections. However,  rather than speaking about his research, he instead provided the audience with a failsafe, three-step “recipe for success”:

  1. Work hard.
  2. Have the flexibility to say “yes”.
  3. Learn one new thing at each stage of your education.

Through stories of his past experiences, he related to the audience the importance of these steps. He spoke of the times he would stay up until 2 or even 3 in the morning working on his projects, stating that these wee hours are the times “you bump into new discoveries”. He advised the audience to always say “yes” to new and cool experiments, not new and cool cities. Lastly, he highlighted the importance of learning one new technique, and learning it to perfection, at each stage in education. With this simple recipe, Dr. Sjӧstrӧm shared some valuable life lessons and honed in on what it takes to become a successful researcher.

CVE-7617The evening’s final speaker was Dr. David Harpp, an incredible scientist, professor, and mentor to all those interested in research. Much like the previous speaker, Dr. Harpp recounted his personal experiences with research and academia, all the while emphasizing several important lessons. Ranging from his post-doctorate days to his experiences as a professor at McGill University, Dr. Harpp was able to inspire the entire audience with his stories. One memorable moment was when he narrated how one of his potential graduate students saved Matt Damon’s father (Matt Damon’s!) through the inception of Velcade, a drug for bone marrow cancer. Quirky, inspiring, thoughtful, and anecdotal, Dr. Harpp’s words gave the audience a look into the exciting and serendipitous aspects of scientific research.

The Research 

Finally, here are a few brief descriptions of the papers included in this year’s MSURJ—Find Vol. 11 on stands, or click the cover (designed by Samer Richani) below to read the full articles!

(Page 11) Vanessa Caron et. al.

Coral reefs in the Caribbean Sea have been degrading at an alarming rate since the 1970s. In an effort to gain insight into coral reef protection, this research team investigated how algal cover on coral reefs is affected by the herbivore abundance. With research conducted in Western Barbados, the research team deduced a number of contributing factors, such as groundwater input levels.

(Page 16) Zhubo Zhang et al.

This research team investigated the ambiguity inherent to sensory adaptation—the phenomenon where a neuron’s “coding rule” changes in response to a stimulus. However, ambiguity arises from the fact that different stimuli are able to produce the same neural response. Working with in vivo extracellular recordings, the team was able to conclude that less sensory adaptation leads to a stronger ability to disambiguate different stimuli.

(Page 22) Jesse Mendoza et al.

This research project was focused on determining if the knockout of a nicotinic cholinergic receptor would have similar effects on vestibular and auditory systems. The receptor, 𝛂-9, is important in the regulation of auditory and vestibular peripheral hair cells, and deficits also leads to abnormalities in cochlear hair cell development. Through a knockout study on mice, the team reported that the absence of the  𝛂-9 receptor does not lead to vestibular function deficits.

(Page 28) Moushumi Nath et al.

Noise correlation is defined as the correlation in non-stimulus evoked activity between neurons. This research team focused on investigating visual perception and whether changes in noise correlation could predict behavioural performance in a motion detection task. Their findings support this notion, and suggest that noise correlation may be an important parameter in understanding the mysteries of visual perception.

(Page 32) Mariya Stavnichuk et al.

Osteoclasts are cells responsible for bone degradation, and their malfunction is at the root of many bone-related diseases. This study investigated changes in Ca2+ concentration in osteoclast precursors upon application of RANKL, a key osteoclastogenic cytokine. The findings indicated that RANKL induces oscillations in Ca2+ concentration as well as modulations in cellular responses to ATP.

(Page 36) Liang Chen et al.

Gene expression can be controlled on multiple levels, and one of the key proteins involved in translational control is eIF4E. The researchers investigated the role of several testis-specific isoforms in Drosophila spermatogenesis, and found that the loss of function of individual proteins had no significant effects, but defects in spermatogenesis were observed when paired knockdowns were conducted. This indicates overlapping functions that can compensate for one another. From the results, the team were also able to conclude specific functions of each isoform.

(Page 40) Ling Lin et al.

Investigating cosmic strings, the research featured on the cover of the journal focused on globular clusters and their origins. Globular clusters are galactic structures that are poorly understood. The authors proposed that cosmic strings are at the root of globular cluster formation, and their results largely agree with this hypothesis. Their evidence suggests that globular clusters form around slowly moving cosmic string loops with a speed of less than 3% the speed of light.

 

 

Meet MSURJ: Sebastian

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Hello MSURJ enthusiasts! My name is Sebastian Andric and I am a Junior Editor on

the MSURJ team. I am currently a first year undergraduate student hoping to get

involved with the research community here at McGill. Although I’m only starting out

my post-secondary academic career, I am interested in pursuing research in either

neuroscience or genetic engineering. Aside from reading and editing research papers,

my interests include traveling, playing piano, listening to music, especially jazz and

hip-hop, and gaming.  I’m looking forward to working with MSURJ and I hope you

all pick up a copy!

Infinity Series II: Zero Volume With Infinite Surface Area

Ascending and Descending (M. C. Escher, Lithograph, 1960).
This is the second entry of the “Infinity Series”, which will introduce you to the peculiar world of infinity. Last time we discussed the Koch Snowflake, which has finite area but infinite perimeter. We did not specify the size of the circle into which we fitted the triangles, so the circle could have been as small as you wanted and still have an object that sits inside with infinite perimeter. But that raises the question, “can you make it to be 0?”
In fact, you can – but you have to add a dimension. This is basically an extension of the last entry.

Initially start with a cube which is constructed by putting 6 square faces perpendicular to each other.

Then divide every face of the cube into nine equal smaller squares. This can be done nicely by dividing every edge into thirds. This will create 27 smaller cubes. Then, extract the smaller cube in the middle of each face as well as the cube in the very center; this leaves us with 20 cubes. The surface area has increased, since every removed cube on the faces actually created three more faces of the same size (i.e. removing a cube on the face deletes one of the nine divided squares of the face but creates four more of those squares).

Similarly, divide each remaining cubes into nine smaller cubes and extract the middle cube of each face as well as the central one. Since you’re essentially performing the same operation on the smaller cubes, the volume has again decreased and the surface area increased.

Performing this one more time will leave you something like this.

As you can imagine, this operation can be done an infinite number of times. After an infinite time of iteration, you are left with something that has an infinite surface area but 0 volume.

How can I be sure that I have 0 volume?

I challenge you to give me any positive number, say epsilon, and this number can be as small as you want it to be (but not zero  – positive numbers don’t include 0). I will win the challenge if I can perform the operation enough (finite) times to get a volume to be smaller than that epsilon. The truth is, I will always win and this can be seen from the fact that the volume decreases by 20/27 per iteration.

How can I be sure that I have infinite surface area?

Let’s play a similar challenge. Give me any number, say delta, and this can be the biggest number that you can possibly think of. But I have the power on mathematics to my side and I can assure you that by performing the above operations enough (finite) times, I will have a surface area larger than your delta (by a similar argument as above, but this time increasing the area at every iteration).

This particular object with infinite surface area but 0 volume is called the Menger Sponge.

If you had built a house of Menger sponge, it would have taken you an infinite amount of time to paint the walls but you would have just built yourself a house that no one (including yourself) can fit inside.

If you were to make a swimming pool of Menger sponge, then you would need an infinite amount of tiles but even a single drop of water would overflow the pool. Perhaps not so much fun.

By creating the Menger sponge, you are essentially creating something (as a matter of fact, something infinite) out of nothing.

NOTES: Images of Menger Sponges from Wikimedia Commons (Saperaud / Wikimedia Commons)

Infinity Series I: Finite Area with Infinite Perimeter

Original lithograph (M. C. Escher, 1961)

This is the first entry of the “Infinity Series”, which will introduce you to the peculiar world of infinity. Today, we will be talking about something with finite area but with infinite perimeter. That sounds odd and impossible but I’ll show you how it can be done.

Draw a circle and an equilateral triangle inside it, with the three vertices of the triangle touching the circle.

Since we know that the circle has a finite area, the triangle inside must have finite area as well. At this point, we still have finite perimeter on the triangle as well.

Now, divide each edge of the triangle into thirds; draw an equilateral triangle using the middle piece of the divided edges as the base, as follows:

With careful observation, you can see that the perimeter has increased. Specifically, the perimeter increased by a third: instead of one edge, now two edges of each newly-drawn equilateral are part of the shape . The area inside the shape increased too – but notice that it is still within the circle, so the area is finite.

Now, perform a similar operation by dividing each edge into thirds and draw an equilateral triangle using the middle piece as the base. It now looks like this:

Although a small change, the perimeter has increased and so has the area. But since the shape is still within the circle, the area is still finite.

As you can imagine, this operation can be performed an infinite number of times and the perimeter will keep getting bigger and bigger onto infinity. On the other hand, the area keeps getting bigger and bigger as well but will always remain smaller than the circle, hence finite. For a more mathematically-mature audience, the area converges while the perimeter diverges.

(Wikimedia Commons user António Miguel de Campos / Wikimedia Commons)

Hence if you were to make a football field in this shape, you will only need a finite amount of grass but infinite amount of white paint to draw the sidelines.

On a soccer field of this shape, the assistant referees in charge of calling the offsides will have to run an infinite distance to get from the goal to the half line (whatever that may be).

If a castle with such walls had guards monitoring on top of the walls, only an infinite amount of time will suffice the guard to make one circle and the kingdom would’ve needed an infinite amount of rocks or bricks to build the walls to begin with.

Odd?

Welcome to the world of infinity.

NOTES: This shape is called the “Koch snowflake” and is a good introduction to the world of fractal geometry.