On the Horizon in Machine Learning: Identifying Natural Selection At Work in the Human Genome

Written by: Janet Wilson

Machine Learning (ML) is a rapidly evolving branch of artificial intelligence in which a program is developed that can evolve on its own and improve by learning from data and experience. It can be used to make predictions, classify items, estimate probabilities and more. For example, ML is used in Apple’s face recognition method, Google’s search result algorithms and fraud detection methods used by credit card companies.

In most recent news, ML is being trained and has been successfully identifying evolutionary pressures that the human genome is under and how natural selection is shaping it over time.

Due to the fact that the human genome is comprised of more than 20,000 genes and more than 3 million base pairs, ML has the potential to outperform humans by a large margin. The error-prone, tedious data analysis and DNA sequence searching/comparing methods that would have to be employed by humans would take ages and wouldn’t be nearly as accurate as computer-based methods have the potential to be.

Usually ML involves teaching a program how to perform a task using a method called supervised learning. The programmer will provide the machine with the expected output of the program and from this the machine will determine how it should generate the output. This is called the training phase. This challenging in the case of genome analysis, because the expected result of the computation we want the program to perform simply isn’t known.

Currently researchers are trying to train ML systems to identify evolution based on simulated examples of natural selection, allowing the machine to create and internalize a definition of what natural selection looks like from its own statistical, computerized point of view.

The second phase of ML involves testing the program on data other than that which it has encountered in its training phase. ML algorithms have been tested on genome data and have successfully identified the evolution of the lactase gene in caucasian populations. This is a clear, known example of evolution in the human genome which has allowed individuals with the lactase gene to digest cows milk.

Based on massive human genome sequencing, over 20,000 mutations have been identified that researchers want to understand further through ML. Now the task of researchers is to continue to train and perfect their programs to be able to identify and visualize the evolution of this massive number of mutations, that continues to increase.

Hopefully soon, these machines will be able to trace the evolutionary roots and propagation of all mutations found in the human population. Their refined skills will allow us to understand our evolutionary history and perhaps even predict the future evolutionary patterns of the human race. Although it is unfortunate that this is yet another example of computers outperforming humans, the potential applications of ML are vast and exciting. On top of genetic analysis and evolution-modelling, ML methods are being employed in many other fields and have the potential to drastically improve medicine, technology, marketing and much, much more. So we will have to sit back and see where ML leads!

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Observing Molecular Machines using Cryo-EM

In 2017, the Nobel Prize in Chemistry was awarded to Jacques Dubochet, Joachim Frank, and Richard Henderson for their development of cryo-electron microscopy (cryo-EM). In 1986, Ernst Ruska, and Gerd Binning and Heinrich Rohrer won the Nobel Prize in Physics for designing the first electron microscope and for designing the scanning tunneling microscope respectively. In 1982, Aaron Klug won the Nobel Prize in Chemistry for developing crystallographic electron microscopy. With so many Nobel Prizes having been awarded for electron microscopy, what makes this recent development different from the other two?

The keywords for cryo-EM are proteins and resolution. Binning and Rohrer’s scanning tunneling microscope, designed way back in 1981, had a maximal lateral resolution of 0.1 nm and a maximal depth resolution of 0.01 nm—a resolution high enough to resolve individual atoms. They do this by slowly hovering a needle only one atom wide at the tip over an extremely flat surface of a solid that is made of a uniform lattice of atoms and reading the disturbances in the voltage difference between the surface and the microscope tip.

However, proteins (and other macromolecules but we are less excited about them—“another DNA structure, woooooo,” said nobody ever after the double-helix structure was determined in 1953) are these wild things that require atomic-level resolution to determine how the individual amino acids are oriented, but are also absolutely gigantic molecules where the 3-dimensional configurations of said amino acids matter just as much, if not more as their identities. Therefore it is no surprise that just slowly hovering a really thin needle over a uniform layer of proteins doesn’t really get you to this 3D structure. Not to mention that proteins are really delicate flowers and will precipitate and become some amorphous aggregate if you so much as look at them funny (okay I exaggerate, but only slightly). A good resolution of a protein for structural biologists averages at around 2.5 angstroms (Å, 1 Å = 0.1 nm), though there are many that have a higher resolution. For reference, a covalently bonded carbon atom has a diameter of 1.5 Å.

The current gold standard for protein structural determination is with x-ray crystallography, where an x-ray beam is fired into a protein crystal and due to the crystalline nature of the proteins, the single beam diffracts into many different directions which is caught on a screen. The beam’s diffraction angles and intensities can then be measured to produce a 3D electron-density map of the individual atoms can be reconstituted to eventually yield a complete 3D protein structure. However, protein crystallization often requires the use of poisonous salts and precipitants, and extreme pHs that would never be found in living organisms and very large proteins and membrane proteins are often impossible to crystallize. (Also the actual crystallization process is very luck-based and even for regular sized proteins may or may not happen. Trying to grow protein crystals is very good for building character.) This is where cryo-EM, our star, finally comes into the scene.

Electron microscopy usually uses some form of electron interactions between a source and the object to be imaged. In order to not disturb these delicate interactions, the imaging has to take place in an absolute vacuum, which falls under the “will aggregate protein” condition category. Instead, a pure sample of a protein of interest is frozen down and an electron beam is fired onto the frozen protein to produce an image—a “trace”—on a detector. Other than the freezing instead of vacuum, this sounds like pretty standard electron microscopy, no? The key advancements were figuring out how to flash freeze water-soluble proteins (because normal freezing could also fall in the “will aggregate protein” category, and may produce ice crystals which are NOT protein) and how to get the detectors good enough to achieve the really high resolution but also really large width required to image proteins.

The protein in the frozen sample is found in various orientations and from taking an image of hundreds of different orientations of the same protein using the new, high-tech detector that was recently developed, a computer can be used to generate a complex electron density map comparable to those obtained through x-ray crystallography, which can then be used to generate the true structure of the protein in high resolution and accuracy.

An example of cryo-EM images of a protein that together can be used to generate a 3D structure. Image: Maofu Liao, Harvard Medical School.

The beauty of cryo-EM is that it can do everything that x-ray crystallography cannot: image proteins in a non-poisonous environment and image very large proteins. It also doesn’t require painstakingly screening every possible combination of precipitant, salt, and pH possible and hoping and praying that out of one of those potentially thousands of combinations a crystal will grow within your tenure in that lab.

But you may be wondering, “who cares about protein structures anyways?”. Protein structures are very important in drug development, and are also important in understanding the molecular mechanisms of both healthy and disease states. Viruses are also basically protein assemblies, and determining their structures are very important in understanding their pathology and behaviour on a molecular scale. Also, they look cool! (Protein aesthetics is usually how people get suckered into structural biology). Appreciate this nice picture of the Zika virus obtained through cryo-EM. 

Cryo-EM structure of the Zika Virus. PDB: 5IRE Sirohi et al. (2016) The 3.8 angstrom resolution cryo-EM structure of Zika virus. Science. 352, 467-470

Happy lurking the cryo-EMs!

MSURJ Launch 2017

The 12th annual launch of the McGill Science Undergraduate Research Journal took place in the Bellini Atrium, where students from science, engineering, and other faculties joined to celebrate the achievements of undergraduate researchers at McGill. The authors, editors, and peer reviewers were also in attendance. Attendees grabbed some food and drinks, and then gathered to listen to the guest speakers. Three McGill leaders in scientific research generously shared their experiences in research and academia with the next generation of scientists.

First to speak was Dr. Tomoko Ohyama, the newest faculty member in the Biology Department. She talked about her research experiences in Japan, the United States, and Canada. Her research focuses on studying Drosophila larvae and their nervous system. She specifically studies the process of decision making in these larvae. When faced with a decision to make, “you think you are deciding, but I don’t think you are,” she hypothesizes. She hopes to be able to further elucidate the decision making process in humans by studying this process in Drosophila larvae.

Dr. Durcan, an assistant professor researching at the Montreal Neurological Institute, gave a short presentation on his experience in research over his lifetime. Currently, Dr. Durcan uses mouse models and stem cells to study the molecular basis behind neurodegenerative diseases such as Alzheimer’s Disease. He obtains stem cells from blood, which can become pluripotent, or stem cell like. He can then develop the cells into dopaminergic neurons. Before this technique was developed, it was exceedingly difficult for researchers to study neurons. In Dr. Durcan’s lab, he hopes to understand the cellular biology causes behind Alzheimer’s. Since the population of Canada is aging, he described neurodegenerative disorders as epidemics that are sweeping the nation. These disorders have become one of the leading causes of death, particularly for the older generation. Dr. Durcan said that without further research, these diseases will begin to overwhelm the healthcare system. His lab hopes to develop therapies for Alzheimer’s that will repudiate this dire future.

The final professor to speak was Dr. Kenneth Ragan. He is one of the faces that most new science and engineering students at McGill will become well acquainted with. He has been teaching first year physics classes for over 10 years and runs an astrophysics lab that specializes in studying the wave behaviour of particles at very high energies. After the casual mingling, he gave an equally casual speech on more than just what he researched, but rather on how he got to where he was. He talked about the fun and the spontaneity of life. He talked about how a scientist’s dream is to have their research appear on the Big Bang Theory. He talked about how it is okay not to know what one wants to do immediately, because in the end, everything will turn out fine. For a man of few words, he is one of many memorable speeches.

After the professors spoke, the author of the paper featured on the cover of this year’s edition of MSURJ gave a brief talk. She highlighted the importance of interdisciplinary research, as well as creating interdisciplinary teams for policy making. She emphasized that problems can be tackled from many different angles, and that we are more likely to create better solutions by combining the varied skills of different professionals.

This year’s event highlighted some of the exceptional research being done at McGill University by students and professors alike.

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 20^th 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!

(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 things 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.” 

The 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 speaker 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.

The 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!

MSURJ Vol. 11, Issue 1 (March 2016)

(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.