Dr. Joseph Bondy-Denomy


Dr. Joseph Bondy-Denomy, Faculty Fellow at UCSF, shares his experiences starting as an accounting major to finding out that working in the lab is his true calling to discovering a whole new component of the CRISPR-Cas system, which he named “anti-CRISPRs”, through his work in Alan Davidson’s lab. As a more recent graduate, Joe offers insight and advice to those that are hoping to pursue a career in academia. Instead of dwelling on the competitiveness and lack of funding, Joe emphasizes the importance of having a polished story and figuring out your own niche in order to obtain a faculty position.

Can you describe your current research to us?

I study bacteriophages, which are viruses that infect bacteria. The recently discovered CRISPR-Cas system was something that came into existence when I started graduate school. I started out studying phage-bacterium interactions in a bacteria called Pseudomonas aeruginosa and I stumbled onto these proteins that turn off CRISPR, which we named “anti-CRISPRs”. This opened up a whole new window of questions and possibilities for how phages interact with bacteria and how the CRISPR system combats them. In the latter part of my studies, I figured out the mechanisms and interaction partners for some of these anti-CRISPR proteins. That opened up even more questions because they all worked through different mechanisms. For example, one that we are currently working on seems to turn the CRISPR system from a DNA cleavage to a DNA binding system simply by inhibiting the nuclease component.

Another aspect of something we’re working on is how the anti-CRISPR is interacting with this nuclease component. The nuclease, Cas3, is particularly interesting because it is common to all Type I CRISPR systems and is present in nearly half of all bacteria, so we think this anti-CRISPR is an interesting protein to use to study this widely conserved nuclease. We’re following up on how that works during phage infection along with some in vitro mechanistic work.

We are also doing a lot of work not focused on anti-CRISPRs, such as looking at non-canonical functions for CRISPRs. For example, we are wondering if bacteria with CRISPR systems can use CRISPR to regulate their own genes. This would be analogous to what small RNAs do in eukaryotic systems in how they can both regulate the genome and protect from parasites. We are wondering if that kind of dual-function is happening in prokaryotes as well.

Lastly, we are branching out into some new organisms of interest, specifically bacteria with CRISPR-Cas systems with functions that have not yet been characterized. Along the way, we are keeping our eyes open for the potential to add more technologies to the CRISPR-Cas toolkit.

Those are some of the questions we are working on, with mostly a focus on CRISPR-Cas biology, with some people working on the phage side and some working on non-canonical roles.

When did you first realize that you wanted to become a scientist?

It was mostly during undergraduate microbiology classes. While I was an inquisitive kid, I don’t have the story of some scientists where they were looking for frogs or something when they were two and knew they were going to be a scientist. I “knew” I was going to play for the Blue Jays. It really was during undergrad in Waterloo and during my first lab job as a co-op student at Western University where I realized that I really enjoy being in the lab. That was a slam dunk for me.

I actually started undergrad in an accounting program. I was at Waterloo, so I did many co-op terms. At first, I was in an accounting firm where I sat in a cubicle all day and had to wear nice clothes. I didn’t really mind that, but then I got to work in a lab. Everyone was around my age and I got to hang out with everyone. No nice clothes required. Everyone was very sociable and active. Even though progress is difficult, you’re doing things that really felt cutting-edge and I found that much more enticing than filling out tax returns. Although that’s important, and I probably would have turned out wealthier had I stuck to accounting, I don’t regret that decision for a second.

So for me, it was the microbiology classes that got me excited about microbes and thinking of the world in that scale. This was solidified when I got to work on virology in a lab at Western and two more co-ops in labs at McGill studying host resistance to bacterial and parasitic infections. I loved being in the lab in all those places. Even when I started graduate school, I didn’t know that I wanted to be a PI. I just wanted to study bacteria more.

Why did you choose the Department of Molecular Genetics at University of Toronto for your graduate studies?

So the dirty little secret is that I actually applied to LMP and got in there. I didn’t even apply to MoGen. But when I was looking through the LMP lists of labs that were accepting students, I was very disappointed because, while there were lots of great labs, most of the ones that I was interested in were not accepting new students. I interviewed with some people that were available, but none of them got me too excited. At the last minute, while I was freaking out, I applied to MoGen. I don’t know why I didn’t apply earlier because there were lots of great labs there too. The graduate coordinator at the time, the person that I was e-mailing, was Alan Davidson. He offered to meet with me and discuss options in the department and his research. It was then that I found out that MoGen had rotations, which really appealed to me also. Alan and I also got along really well, and I was really excited about the work in the Davidson lab, so I ended up joining his lab.

What are some of your favourite memories from graduate school?

Certainly one of my best memories is meeting my wife on the very first day of graduate school. On orientation day, we recognized each other because we both went to Waterloo and about a month later, we started dating and now we’ve been married for two years!

But from the stand point of the lab, I think some of the more memorable moments were the exciting results. When working on bacteria and phages, you do your experiments during the day and the next morning, you come into work and look at your results. It was very instantaneous and while walking/biking to the lab, I would get very excited at the thought of opening the incubator and getting to see something unexpected. When I thought I had found these anti-CRISPRs, it was the most exciting time in my scientific life. Even Alan told me, “you better be excited because this is really as good as it gets”. So coming in and getting exciting results, I don’t think anything can get better than that in the realm of science. Usually, everything is quite a slog, so when you get a cool result, it makes everything worth it.

I would also say that I enjoyed all the retreats, the Last Fridays of the Month parties, the Christmas parties, etc.. MoGen is such a big department, so all the social gatherings were really great because there were so many great people and you got to have a lot of fun. 

What was the most important thing you learned in graduate school?

I think the most important thing I learned was to do experiments. Often we try to almost be a bit too smart. We read lots of papers, think too much and sometimes we would almost talk ourselves out of doing experiments. I was lucky because in the bacteria and phage world, we can do a lot of experiments quickly and cheaply, so this doesn’t apply to everybody, but the principle does. You just have to do the experiments. You have to not be afraid to do lab work and be there for many hours and do a lot of different experiments. You can’t just say “should I do A or B?”, but do A and B. And do it with your eyes open, look at unexpected results the hardest. In the words of my friend, colleague, and fellow Canadian here at UCSF, Dr. James Fraser, “it’s not beer or tacos, its beer AND tacos.”

I think that’s really important, but you obviously have to do everything carefully, which brings me to my next thought, which is to talk to as many people as you can. They can point you to a paper or method, give you a new idea or tell you that your idea is crap (with a good reason). I talked to every professor on my floor at one point about one thing or another, whether formally or informally in the hallway. I think talking about your work also shows others that you’re really into it and a good scientist. You can learn a lot by listening to smart people.

Therefore, I think combining the willingness to do experiments and to talk about your work are the best ways to move things along.

Can you elaborate on your position as a Faculty Fellow at UCSF and how you obtained this position?

I obtained it by applying with a research proposal, a CV, referenece letters, etc. I worked really hard on the research proposal, which was a lot of work, and got an interview with four other applicants, and ended up getting the position. I think interviews are really what make and break a lot of things, so that goes back to my last point about being comfortable talking to people about your work. The more you practice it, the better you will be in the stressful situations. It is really essential for many aspects, from getting ideas for experiments to job applications.

The position is fantastic. I’m a faculty fellow, which means I am not a tenure-track faculty member, but I do have principal investigator status at the University. I have independence and I can apply for grants. The Fellows program gives funding to the lab and any extra funding I get is more gravy on top. I can co-supervise graduate students and can hire post-docs. I currently have one graduate student and technician in the lab, with a post-doc starting shortly. I am also currently in the middle of rotations with four different rotation students. We are pretty much like a standard faculty member. The best part is that we don’t have very many formal responsibilities outside of research. I can do as little teaching as I want to and I don’t have to spend a lot of time on committees and all the other things real faculty have to do. It’s meant to be a junior position where you’re ushered into independent research, with a lot of help from those around you. Most importantly, you get to run your own research program and do the work that you are excited about.

Having just started your own lab, without completing a traditional post-doctoral training, what was the most difficult aspect of transitioning from graduate school to becoming a principal investigator?

I think figuring out your style is a challenge. You want to blend together all the best of everyone who has ever mentored or supervised you. To figure out that style, you need to think about how friendly you want to be and when to be more forceful and serious. You have to ask yourself “how do I want to be seen by my other lab members?”. And ultimately, “how do I help my students be the best that they can be?”. People can go about doing that in many different ways, so that’s something that is still a work-in-progress for me. I’m still figuring out how to be a supervisor and an effective mentor.

And personally, I think the hardest thing is figuring out who to take on in the lab. That is something you do not get any experience with as a graduate student. You have to think about how different personalities fit in the lab and who to take versus who not to take, which is based on more than just their CV and how smart they are. It’s based on what they are interested in, what kind of person they are, and who you already have in the lab. Everyone is very different and come from different backgrounds, so you also have to teach them differently based on their different personalities. It’s the “people-stuff” that is really the hardest thing.

The last thing is that with the Fellows position, the lab is intended to be small, so I take on the role of a PI during the day, and a post-doc at night. I’m sort of doing double duty in that respect, so time management is an additional challenge.

If you could only offer one piece of advice to graduate students and post-docs who are hoping to pursue a career in academia, what would it be?

The one answer would be “polish your story”. But that means a hundred different things. To polish your story, you need to talk to people, present your work, and take any opportunity to write about your work. Most of my day is actually spent writing (i.e. editing the work of others, writing abstracts, applications, grants, etc.), so writing becomes really important after graduate school. Then, with a broader scope of polishing your story, you need to figure out what you are going to be known for, what your “thing” is going to be. When you’re thinking about applying for an academic job, you need to think about what people want. Departments want someone who is doing something cool, interesting, new, and carving out their own spot. They have a polished story and a polished plan. That only comes with writing and speaking to people about it.

What do you see as the biggest challenges facing scientists today?

The obvious answer is funding and lack of jobs. But you can’t dwell on that too much. I can’t affect funding in the short-term and I can’t create more faculty jobs. While both are definitely problems, you need to make do with what is there. The challenge is finding your “space” or “niche”. You need to figure out what you’re going to be known for. That will take a lot of work, finding your own thing, and challenging yourself in being a bit different in order to carve out your own spot.