Sharing your lab notes

SGC’s Extreme Open Science Unit aims to foster communication among researchers

Sharing your lab notes

The Structural Genomics Consortium (SGC) launched the Extreme Open Science Unit (EOSU) in January to encourage scientific collaboration. The initiative aims to make research transparent by fostering communication through sharing research data and notes online. Since its inception, the database has featured scientists from across the globe.

Dr. Matthieu Schapira, head of the Research Informatics group at the SGC, founder of EOSU and U of T associate professor in the Department of Pharmacology and Toxicology, was inspired by Dr. Rachel Harding’s blog, LabScribbles. Harding, a postdoctoral fellow at the SGC, has been uploading notes to LabScribbles for the past two years, continuously updating fellow scientists on her work in determining the structure of huntingtin, a protein linked to Huntington’s disease.

Currently, 12 scientists have contributed to EOSU, and soon an additional eight will be joining.

“I think it fosters collaborations; you avoid redundancy of experiments that somebody else has probably already tried and I think it just kind of brings the science community together, which is great,” said Mandeep Mann, a master’s student in the Department of Pharmacology and Toxicology.

One of the consequences of research is the amount of time it takes for a study to be accepted, peer-reviewed, and published. Professor Aled Edwards, Director of the SGC, wrote that “the average time between experiment and publication… is one to two years. That’s 67 per cent of the average lifespan of an ALS patient.”

The quick turnaround owed to open access could lead to an increase in research output and accessibility.

bioRxiv, a resource available to scientists for feedback prior to journal submission, has seen an increase in the number of manuscripts uploaded to its database. Recently, bioRxiv published a study by Stanford University researchers, which found that the genome editing tool CRISPR-Cas9 could be ineffective in humans. While the research has yet to be peer-reviewed, it allows fellow scientists from around the world to also investigate the caveats of gene editing technology in light of these results.

Unlike literature published in journals, the quick processing and lack of the traditional peer-review process prior to publication may raise certain concerns over the quality of research and findings that are made available.

Harding, however, clarified that “this isn’t validated peer review data, this is an open notebook… [and it] should be read with a different hat on.”

In 2016, Dr. Dan Longo and Dr. Jeffrey Drazen raised concerns around ‘research parasites’ in an editorial in The New England Journal of Medicine.

“Obviously there’s reservations of ‘will someone see this and use this in their experiments and publish something and not credit me with that,’” said Mann. “I think that’s a risk, definitely, but it’s kind of… an experiment on its own.”

Schapira hopes that the risks associated with an ‘open notebook’ paradigm will be small because published data is still in early experimental stages. Both he and Harding see the open publishing concept as an opportunity to connect with experts in the field. Obtaining direct insight and varied opinions from a larger group of people will progress research and potential medical treatments.

“You can create these… miniature ecosystems — where you’re working with other people in the field and you can share data or resources at earlier stages, then you can move the science forward way more quickly,” said Harding.

Despite the benefits of open science and collaboration, some scientists remain wary about the movement. Schapira believes the feeling is warranted, given that it is not the normal modus operandi in the biomedical field.

“If we keep an open mind and a little bit of critical thinking, it can actually help us realize that, really, [open science] comes with real opportunities in terms of extending our network, connecting with peers, generating new collaborations, and progressing faster,” said Schapira.

Self-fertilizing roundworms have smaller genomes

Caenorhabditis briggsae lack 7,000 of the genes found in mating roundworms

Self-fertilizing roundworms have smaller genomes

Some species of hermaphroditic nematode roundworms, including Caenorhabditis briggsae, are capable of ‘selfing’ — reproducing without a mate.

A recent collaborative study led by researchers at the University of Maryland demonstrated that hermaphroditic C. briggsae roundworms have smaller genomes than worms that do not self-fertilize.

The researchers used genome-sequencing techniques to study C. briggsae and found that its genomic size was one quarter smaller than that of the closely related Caenorhabditis nigoni, a roundworm that does not self-fertilize.

The decrease in size is disadvantageous to non-selfing males because the missing genes were found to provide sperm with competitive benefits during mating.

All hermaphroditic C. briggsae worms lack male secreted short (mss) genes, which are active only in male roundworms that do not self-fertilize, such as males of the C. nigoni and Caenorhabditis remanei species.

Upon using gene-editing tool CRISPR to remove four mss genes from the sperm of male C. remanei, the researchers discovered that these roundworms could not compete effectively against the sperm of males with all genes present.

When they inserted these four mss genes into C. briggsae males, they found that the competitiveness of the sperm now exceeded that of the hermaphroditic C. briggsae roundworms and the C. briggsae males without inserted mss genes.

After analyzing both roundworm species, they found the genome of C. briggsae contained 7,000 fewer genes than that of C. nigoni.

To confirm this finding was due to the evolution of selfing in C. briggsae, the researchers also determined that the missing genes in C. briggsae were more active in C. nigoni males, which undergo selfing, than C. nigoni females, which do not.

“Our analysis showed that genes with functional activity biased toward males were more likely to be lost in species that have [hermaphrodites], but were retained in species with males,” said co-author Dr. Asher Cutter, a U of T Professor of Ecology and Evolutionary Biology.

According to Cutter, “males are vanishingly rare in natural populations of nematode roundworms that have evolved hermaphroditic self-fertilization. So… the evolution of hermaphrodites disproportionately involved the loss of genes that would be primarily functional in males.”

“This is consistent with the idea that functional copies of genes that promote male function exact a cost to hermaphrodites, and so natural selection likely favored their elimination from the genome,” said Cutter.

These findings demonstrate the varying evolutionary transitions that organisms undergo in their reproductive behaviours.

“In fact, the activity of genes that promote male reproduction in those species with hermaphrodites might even impose a cost,” said Cutter.

Future experiments will be designed to elucidate the roles of all 7,000 genes missing in C. briggsae, including determining how mss genes help sperm compete.

U of T prof’s startup takes cancer therapy to clinical trials

Pionyr Immunotherapeutics raises $62 million in series B investment round

U of T prof’s startup takes cancer therapy to clinical trials

A biotech startup co-founded by Sachdev Sidhu, a professor in U of T’s Department of Molecular Genetics, has drawn in $62 million USD following a second round of funding, bringing its total investments to $72 million USD.

Pionyr Immunotherapeutics, which is now planning to take its anti-cancer therapy to clinical trials, initially began as a research collaboration between Sidhu and Max Krummel, a professor at the University of California, San Francisco School of Medicine. Founded in 2015, the California-based startup combined Sidhu’s expertise in antibody phage-display technology with Krummel’s immune system biology research.

This project is a collaborative effort with Toronto Recombinant Antibody Centre (TRAC), which was founded by Sidhu and Dr. Jason Moffat, who is also a Molecular Genetics professor at U of T. Housed in the Donnelly Centre for Cellular and Biomolecular Research, TRAC researchers are working to harness the therapeutic potential of synthetic antibodies.

Synthetic antibodies can be engineered to target a variety of molecules implicated in disease and they are key for drug development. Pionyr’s anti-cancer therapy, known as Myeloid Tuning, uses the high specificity afforded by synthetic antibodies to bolster the immune system’s defence against cancer by manipulating a tumour’s microenvironment.

The immune system uses T cells to detect foreign molecules to evoke a defensive response. Because tumours are created from existing cells in the body, they evade recognition by T cells, dampen the immune response, and proliferate uncontrollably. The key is to restore the body’s immune capacity to fight cancer — this is the premise of immunotherapy in oncology, better known as immuno-oncology.

“So the idea there is simple: you want to turn on a T cell, you simply find proteins that are inhibiting that T cell,” said Sidhu.

Myeloid Tuning achieves this by “alter the tumour microenvironment to favour immune-activating cells over immune-suppressing cells” and enhances anti-tumour defenses. “T cells are activated not by targeting them but by eliminating the inhibitory cell population,” said Sidhu.

Pionyr’s technology could also complement existing anti-tumour therapies like T cell checkpoint inhibitors. Checkpoints are regulators that mediate communication between T cells and the immune system. They are responsible for fine-tuning the body’s immunity and downregulating it when it detects native cells, which would otherwise lead to an autoimmune response. By incorporating checkpoint inhibitors, therapies can be developed to block a tumour’s ability to evade T cell detection.

Ipilimumab, commercially known as Yervoy, set the precedent by becoming the first United States Food and Drug Administration-approved therapeutic antibody against skin cancers and for ushering in a new wave of immuno-oncology. The drug, co-invented by Krummel, inhibits cytotoxic T-lymphocyte-associated protein-4, one of many checkpoints found on T cells. Similarly, pembrolizumab, or Keytruda, inhibits the checkpoint called programmed cell death protein 1 (PD-1).

“Anti-PD-1 binds the T cell and… activates it that way, and then we add another antibody that eliminates inhibitory myeloid cells, so you get double [the effect],” said Sidhu.

Sidhu says there is a critical question in field: does the rest of the tumour simply not have T cells that can attack them or are there additional yet unidentified breaks? These possibilities are not mutually exclusive and are already being investigated. According to Sidhu, the future of immuno-oncology is already here.

Myeloid Tuning is a very promising method, but it is not the only immuno-oncology treatment in the works. Currently, therapeutic agents being researched involve other immune cells like macrophages and natural killer cells that can be exploited for anti-tumour therapies.

“[There is] very little that is not being explored as far as immune cell activation,” said Sidhu. “It’s exciting in that, while only a subset of cancers responds to immunotherapy, the ones that do respond often respond tremendously.”

Op-ed: Undergraduate research — it exists!

The ASSU President writes on the need to support undergraduate student work beyond the classroom

Op-ed: Undergraduate research — it exists!

The University of Toronto is often ranked among the best universities globally, and it is consistently ranked as one of the best research universities in Canada. We undergraduate students know these rankings are not in reference to research produced in U of T’s graduate programs. What few of us realize, however, is that U of T has many resources to support undergraduate student research, giving students a chance to apply and test their knowledge as well as prepare for further studies in graduate school.

For instance, the Undergraduate Research Fund, co-funded by the Arts & Science Students’ Union (ASSU) and the Faculty of Arts & Science (FAS), finances self-started student research that is not part of regular coursework. There are a wide variety of research opportunities for second-, third-, and fourth-year students, including research opportunity programs and upper-year independent study options. Some other funding programs include the University of Toronto Excellence Awards, the Munk School of Global Affairs’ Richard Charles Lee Insights Through Asia Challenge, and the Jackman Humanities Institute’s Scholars-In-Residence program.

It is unfortunate that students may not have not heard about such opportunities. The FAS is unique in that it organizes its students through two main structures: the program departments and the colleges. Given this, all students registered as Arts & Science students have differential access to opportunities on campus. Hence, one of the major issues is a communication gap, wherein the faculty is unable to directly and effectively reach its students — approximately 25,000 of them.

The burden to remedy this communication gap should be shared between the university and ASSU. The Arts & Science Undergraduate Research Conference (ASURC), taking place on Friday, January 19 in Sidney Smith Hall at UTSG, is the first conference at the faculty level to showcase the interdisciplinary work of undergraduate students from arts, science, and social science disciplines. I decided to take on this event as a way to test for interest in such opportunities and to gauge how much undergraduate research work is actually out there — a mini research project of my own, you could say.

What I have found is that there is a lot of undergraduate research being conducted at U of T. However, if the current opportunities are better communicated to students, then more students would take advantage of them, resulting in more undergraduate research being produced. Since we began planning ASURC in the summer of 2017, we have had hundreds of students express interest in participating in the conference in difference capacities. In total, we received over 120 research abstracts from arts, science, and social science disciplines. Given the sheer volume of interest we have received, we know that there is a need for opportunities showcasing academic student work.

The university recognizes this and has been very supportive in the production of ASURC. The FAS has served as a main co-sponsor, and President Meric Gertler and Dean of the FAS David Cameron are both delivering welcome notes to the conference’s presenters. At the same time, while the university administration has provided great symbolic and financial support, it often falls on students to self-start and dedicate time to the actual organization of projects. A variety of student-produced academic journals, colloquiums, and conferences inspired us when we were organizing ASURC, many of which were produced by ASSU course unions.

The issue with student-run initiatives is that, with changes in the executive committees of each group happening each year, the possibility of an initiative being discontinued is always a concern. Many of my fellow student leaders on campus share this fear. Despite the precedent set by all our work organizing the first ASURC, I have no formal assurance that next year’s ASSU executives will continue such a long and logistically challenging process.

On the other hand, colleges and faculties have a more continuous presence on campus, creating the potential for long-term improvement of research initiatives. Therefore, I believe the solution lies in campus administrations playing a more active role in filling the communication gap and providing more formal opportunities to showcase student work. While administrations like those of Trinity College, St. Michael’s College, and Victoria College do hold their own undergraduate conferences, they limit participation to their own students, rendering other Arts & Science students at a disadvantage simply due to their college affiliation. In comparison, the University of British Columbia and McGill University both have conferences dedicated to undergraduate research at a far broader level.

From organizing ASURC, I have come to realize the key to undergraduate research. Many times, all it takes is incentive for students to build on and rework their research from their regular FAS courses. Because our academic work is primarily submitted for grading purposes, repurposing it to contribute to research is something we do not usually consider. Funding incentives and showcasing opportunities such as the ones outlined above are incentives to getting students to work out their ideas and engage with their immediate academic communities.

This was the goal of ASURC. In processing over 120 applications, our selection committees prioritized student presenters who had not been published nor had had a chance to present at a conference before. We prioritized topics of study that were interdisciplinary and unique. Research opportunities should not be restricted to graduate students or to the few elite undergraduate students who have been fortunate to have access to them. They should be made available to students interested in developing their ideas beyond the classroom.

 

Priyanka Sharma is a fourth-year student at Trinity College studying Criminology and English. She is the President of the Arts & Science Students’ Union.

The truths and myths of Blue Monday

Although recognized as pseudoscience, the phenomenon sheds light on SAD

The truths and myths of Blue Monday

The holiday cheer has finally worn off and we find ourselves in the most bleak time of the winter season. According to former Cardiff University lecturer Dr. Cliff Arnall, there are certain factors that make the third Monday in January the most depressing day of the year.

Arnall determined this date, dubbed ‘Blue Monday,’ through a series of mathematical calculations that take into account other potential causes of a dismal day. These include the arrival of post-holiday credit card statements, broken new year’s resolutions, and the age-old distaste for Mondays. But the calculations behind Blue Monday have been criticized for being pseudoscientific.

Arnall was commissioned to develop his equation by a British travel agency in 2005 and was tasked with determining when people were most likely to book a summer holiday — the rationale behind this being that people are more likely to book a summer vacation when sad.

While the factors that Arnall used in his equation are depressing truths, there is hardly scientific legitimacy to one day of the year being more depressing than all others. As useful as it would be to see depression coming from a mile away, the illness is too complex to be predicted in such a way, and Arnall’s mathematical jargon is useful only as a marketing gimmick. Still, the entire concept is not a complete myth, as there is one component with some merit that deserves attention: winter weather can cause mood fluctuations — and this can be serious.

Seasonal affective disorder (SAD) — colloquially dubbed ‘winter depression’ — is a mood disorder subtype that many understand to be a result of the colder weather. “There are [biological] theories as to why that is… which have to do with some people having a brain that is more wired to be sensitive to changes in light,” said U of T psychiatry professor Ari Zaretsky.

It has been hypothesized that serotonin levels are affected by light and that during the wintertime, the system is insufficiently activated due to decreased sunlight hours. The consequently lowered serotonin levels can lead to unregulated moods and depressive episodes.

Zaretsky explained that the occurrence of SAD can vary based on geography: approximately one per cent of Florida’s population develops SAD in the fall and winter, whereas almost nine per cent of the population in areas such as Yukon or Alaska experience it. For Toronto, the number lies at three per cent.

Light therapy is a common treatment method for SAD, which involves exposure to a light that gives off the same wavelength as sunlight for a minimum of 20–60 minutes each day, preferably in the morning.

Treatments for this disorder, unlike its causes, are not strictly biological.

Psychological and behavioural interventions are just as effective — Zaretsky pointed out that patients participating in cognitive behavioural therapy developed specifically for SAD have demonstrated significant improvements. “It’s important to recognize that just because something has a biological basis doesn’t mean that psychological interventions or behavioural interventions can’t make a difference — they can.”

There is a misconception that SAD is not as distressing as classical clinical depression, and myths like Blue Monday can perpetuate these flawed assumptions. Critics of the Blue Monday phenomenon have become more vocal about their concerns, fearing that it is skewing public knowledge of mental health and discounting the gravity of depression.

“I think [Blue Monday] develops a life of its own because there is a kind of fundamental truth to the fact that people find it difficult to face day upon day of darkened lighting circumstances,” said Zaretsky. “It’s almost like something that becomes part of the culture through media [and] advertising.”

Being faced with yet another year of companies capitalizing on bad science, there is hope that Blue Monday might at least generate conversations about and bring awareness to mental health.

Love makes scents

UTSC professor’s study finds ring-tail lemurs use ‘stink-flirting’ to attract mates

Love makes scents

If you think the smell of Axe is bad, be glad you’re not a lemur. In a study led by Amber D. Walker-Bolton, a UTSC professor in the Department of Anthropology, researchers found that male ring-tailed lemurs use their ‘stink’ to impress potential mates.

This unique behaviour allows lemurs to display their rank among other males and attract suitable mates, albeit at a cost.

Lemurs belong to the Strepsirrhine sub order and live in male groups that have a core female lineage. Each of these groups have dominant central males and periphery males, where rank is correlated with age.

‘Stink-flirting’ refers to male display of tail anointing and wafting, which is considered “a submissive display prior to a close approach.” The study found these displays are associated with male dominance and that they are reciprocated by females. Females preferred the exaggerated displays and are said to set the male apart from the rest of the population.

Additionally, the study found females showed a preference for dominant resident males as opposed to lower-ranking immigrant males. Immigrants are rarely found mating with females of the group.

Surprisingly, male lemurs are more frequently faced with aggression from both females and other males when they perform stink-flirting displays compared to other mating rituals. Only when females in estrus were receiving the olfactory display would they then mate.

Some of the females are also mate-guarded by a male. These guarded females were found to receive a higher rate of displays than non-guarded females. Although mate-guarding doesn’t completely eliminate displays from other males, it hinders approach to guarded females.

While the majority of females chose the most dominant mate, the opposite was not the case. According to the study, male ring-tailed lemurs did not “preferentially target high-ranked females for olfactory displays.”

In the future, Walker-Bolton’s team hopes to study the correlation between ‘stink-flirting’ and reproductive success.

A million deaths and counting

U of T global death study receives funding from the Connaught Global Challenge Award

A million deaths and counting

“If you want to help the living, count the dead,” said Dr. Prabhat Jha, a recent winner of the Connaught Global Challenge Award for his Million Death Study.

Jha, a Professor of Epidemiology at the Dalla Lana School of Public Health, has been counting deaths in India since 2002. After almost two decades of research he is finally nearing his million-death goal.

More than 80 per cent of deaths in low- and middle-income countries occur at home and without proper medical diagnoses. As a result, many of the world’s deaths are not properly documented.

The Million Death Study attempts to alleviate these discrepancies between global death data and the actual number of deaths that occur annually. The project is led by Jha who is also the founding director of the Centre for Global Health Research, a non-profit organization co-sponsored St. Michael’s Hospital and U of T.

The project has recently received $250,000 of funding from the Connaught Global Challenge Award to expand their study. The award, supported by the Connaught Fund, strives to support interdisciplinary research that helps heighten U of T’s global impact.

Data on deaths are collected through what Jha calls “verbal autopsies” — personal accounts of death gathered through interviews with those close to the deceased. Those death records are then reviewed by local doctors who assign a likely cause of death based on the given information.

The study brings together researchers in demography, epidemiology, computer science, geography, geospatial science, economics, and business to tackle a common problem. “The Connaught helps us… bring together people who don’t normally think about [these] problems… in medicine and public health,” explained Jha.

The interdisciplinary nature of the project helps the team make their methods cheaper, faster, and more accessible to a larger demographic. “We want to make it simpler so more countries can adopt this approach,” said Jha.

While the project is expected to reach its million-death goal in the near future, India is just the beginning. There are initiatives in place to expand the project to Mozambique, Ethiopia, and Sierra Leone.

Jha intends to build and expand this method of recording death throughout the next few decades. “Hopefully it will become routine [and] every country will have these kinds of systems,” he said.

However, the study is not limited to just low- and middle-income countries where death records are inadequate. Although deaths in Canada are documented with medical certificates that include important information like cause of death and contributory risk factors, that data is not used systematically, according to Jha.

“The second part of [this study] is not creating new data, but using existing data in high-income countries to better understand the causes of death, the patterns, the risk factors, [and] the importance of key drivers of the epidemic.” Jha hopes that the project will help change our global understanding of death and how we can use it to help the living.

Jha and his team are also working towards making the data from the study accessible to all U of T students. He believes that allowing students to play with this type of data in an unrestricted manner will result in more innovations and insights.

Moving beyond the Million Death Study, Jha hopes to eventually build a what he calls a “death institute” in Canada. The multidisciplinary institute will focus on using mortality statistics to create new systems to help the living.

“A lot more countries are sending people to train [in Canada and] learn about how to set up these systems” said Jha. “So that’s the idea — do a death institute.”

A game of fire and ice

New freeze-drying method preserves tiny electronic structures assembled using light

A game of fire and ice

Imagine moving an object simply by shining a laser or projecting a light pattern. It sounds like a page ripped out of a science fiction novel, yet optical micromanipulation has led to the development of tools for handling objects with light.

Though this concept was first demonstrated over three decades ago, an international group involving researchers from Scotland, Belgium, China, and France recently reported an advancement that may facilitate bringing this technology to microassembly facilities to create nanowires, bio-lasers, and tiny electronics.

The team used optoelectronic tweezers (OET), an optical micromanipulation technique involving light patterns projected on a conductive surface, to trap and move particles. The conductive surface must be photosensitive, allowing the light to create a mismatch in conductivity between the area exposed to light, and the area left in shadow.

The team showed that OET could move solder beads — particles of tin, lead, and silver commonly used in electronics production — and place them in precise positions. They handled multiple beads simultaneously and could, in theory, move 10,000 beads in parallel.

These findings proved OET’s promise in manufacturing tiny electronic components. However, the technique required a liquid environment, and the researchers lacked an effective method for removing liquid from the beads after assembly.

The most obvious answer, evaporation, produced an undesirable side effect: as the liquid droplet shrank, it pulled the beads with it, disrupting the orderly line that had just been assembled.

This problem perplexed Shuailong Zhang, a postdoctoral fellow at U of T, formerly of the Micromanipulation Research Group at the University of Glasgow. The solution came to him on a snowy day. To avoid a liquid-to-gas transition, he could freeze the liquid to make it solid.

Unlike the snow he saw melting that day, Zhang didn’t need to return to the liquid phase to get rid of the solid. Instead, he used a technique called freeze-drying. After freezing, he would place the solid, with its embedded bead assemblies, in a low-pressure chamber. At low pressure — the exact pressure depending on the substance — solids can turn directly into gas.

The method worked. The beads stayed in place as the surrounding medium was removed.

In the last step of what Zhang called a “fire and ice game,” he heated the solder beads to fuse them together, and showed that the fused line of beads conducted electricity.

In other words, the research team used OET to form an electrical component, albeit simple, which could be reliably removed from its formative liquid medium.

Zhang envisions the technique being used to manufacture more complex devices, such as nanowires and nano-photonic devices. However, he thinks “the biggest potential application is in biology and medical science.”

Optical micromanipulation is not limited to moving metal particles; it has also been used to trap atoms, viruses, and cells. With its ability to precisely position individual cells, it presents a new way of probing biological questions. “It can be used for cell patterning, it can be used for cell sorting, and also it can be used to study cell competition and communication,” said Zhang.

The team is now developing a phone and tablet app to make light-based particle handling easier for future users.