Canadian Digestive Disease Week 2017 | By Nicholas Graves

Canadian Digestive Disease Week (CDDW) is the pre-eminent gastrointestinal sciences conference in Canada and as such commands a field of prominent researchers and clinicians as well as a veritable host of trainees; grad students, med students, post-docs nick copyetcetera.
Up to this point in my life, CDDW is the largest conference I have attended and I was excited to hear from the selection of experts giving talks, although admittedly I was unsure about how well my poster would be received by the Canadian GI community.
The conference started off with a Friday morning session on GI pharmacology and drug development, chaired by Dr. Simon Hirota. It was a very interesting session and a great way to start off the weekend! Later that evening was the trainee mixer. It started off slowly with separate cliques from Calgary, McMaster, Toronto, and Sherbrooke. After a little while though, the people from the different schools getting to know each other, and maybe even planting the seeds for some future collaborations!

The following day included a career development panel with some great insight from people who followed drastically different career paths. Jean-Eric Ghia, from the University of Manitoba gave an entertaining talk about giving TV/radio interviews and speaking to the media in general. Kevin McHugh spoke about moving on from his PhD to working for (and travelling the world with!) the drug company, Abbvie. Sara Hamilton then spoke about how she sent out seemingly endless applications before landing a job as part of the editorial tea
m at the scientific journal, Cell Reports. This session was especially interesting because of the divergent experiences presented and how it really highlighted the fact that you may have to keep an open mind as well as work hard in order to succeed in science.

Later that evening, I gave my poster presentation. Surrounded by purely clinical posters, I felt a little out of place. After a little while though, people started asking me about my work and I got some helpful feedback along with some very interesting new ideas! So, in spite of the slow start, it was a very productive time.

Along with other great sessions on Sunday, there were the research award lectures. Dr. Eric Benchimol the Canadian Association of Gastroenterology’s young investigator of the year, presented his fascinating work on the epidemiology of inflammatory bowel disease in Canada. Dr. Dana Philpott, the CAG’s investigator of the year then gave a wonderful basic science talk on some of the important molecular mechanisms that can lead to Crohn’s disease.
The evening closed with the gala celebration, which was another opportunity to meet colleagues from elsewhere in Canada. It was a very fun night and a great way to end the weekend. There was excellent food, bad dancing and a lot of goofy pictures taken; so all in all a great time!

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Genome Informatics 2016

This annual conference alternates between the Wellcome Genome Campus in Hinxton, UK, and Cold Springs Harbour, USA. While the CSHL campus is quite lovely and prestigious, I was thrilled to finally have a chance to visit the vaunted Sanger Institute; they were pioneers of genomics from the very beginning, and are still a leading source of innovation in the field. The campus was a great mix of older original buildings and modern construction, and the conference drew some of the leaders in genomics.

One of the keynote speakers was Richard Durbin, a leader of such projects as 1000 genomes, Pfam, WormBase, and Ensembl. His book on Biological Sequence Analysis is the standard in the field, and his sequence similarity matching software is probably the most widely used after BLAST. Here, he was speaking about a new way to store genome information, one that the field will likely be using in the not-so-distant future. Today, a genome is typically stored as a sequence of characters, which works very well. But if you sequence thousands of individuals from a population, the vast majority of these characters will be repeated. This ends up wasting terabytes of storage, and further, the collection of files tells you nothing about the population itself without extensive processing. A graphical representation of the population of genomes is far more efficient, allows common errors to be easily identified and corrected, inherently contains information about the population, and lends itself to efficient computation and manipulation. This may seem like a minor and overly-technical detail, but it is likely to change the field in the near future.

There were, of course, many other things to be learned. As an example, RNAseq is a widespread technique used to study gene expression in some cell or organism. Unfortunately, analysis of these data can be misleadingly difficult, and mistreatment can easily result in incorrect conclusions. A Venn diagram is a common way to display complex membership data, and research groups have been using these with RNAseq data for years. However, binning the data in this way completely discards all relative information, and often lower-level membership information as well. A group from Melbourne has developed an excellent tool to make these analyses much easier, even for non-specialists, and adoption of this or similar software could make RNAseq studies more reliable and predictive in the future.

The conference was excellent, and I would absolutely encourage others to attend future iterations if they are interested in genomics. I sincerely appreciate the support of the Office of Graduate Education and the HPI for allowing me to go.

Mothur Workshop in Detroit | By Camila Queiroz

On 14th to 16th December 2016 I had the opportunity to attend a Mothur workshop, a free software for bioinformatics analysis developed for microbial ecology community.

The workshop is offered twice a year in Detroit, Michigan, US, by his creator, Dr. Patrick Schloss. There was around 100 people from different areas, most of them working with microbiome, but in different areas. I was amazed of seeing so many different applications of microbiome and for sharing knowledge and experiences with people with different backgrounds.

Some important topics were covered by the course, as an overview of methods used in microbial ecology, DNA sequencing technologies, improving sequence quality and population level analyses. It was relevant to me as a PhD Student since my project is studying the nematode population genetics and the molecular epidemiology of the resistance against the anthelmintics used in Canada and those commercially available but not used in Canada yet.

The course mixed theory and hands-on practices using mothur software and we also had opportunity to talk about our research’s challenges and aims. Overall, it was a friendly environment and I strongly recommend this course for those who will work with molecular ecology and population study.

The back home was a real challenge – due to weather conditions my flight was cancelled and then altered twice. Because of it, I had to spent the night on Chicago waiting for the flight back the following day. I was supposed to arrive in Calgary on Saturday 3pm and I got here on Monday 3am. However, it was not so bad since I had some colleagues from the workshop in the same situation – someone to complain with!

NSERC CREATE HPI supported all the expenses associated with the trip. I therefore want to highly thank my supervisors, Dr. John Gilleard Dr. Michel Levy, our program coordinator, Teresa Emmett and HPI executives for providing me this opportunity.

NIPGIT 2016 in Banff | By: Christina Amat

I was fortunate to be able to attend the NeuroImmunoPhysiology of the Gastrointestinal Tract (NIPGIT) conference this year, taking place in the beautiful mountains of Banff, Alberta. The conference took place at the Banff Centre – our meeting room featured the beautiful Rocky Mountains as our backdrop and we enjoyed our meals in the awesome Vistas Dining Room. Such an amazing view to start off the morning and end the day!

The conference was one of the smaller ones I’ve been at, and with only about 100 people in attendance, it was easy to get to know the fellow attendees and spend some time talking with researchers who are amongst the best in their field. Some of my personal highlights included learning how virulent strains of bacteria can switch on or off genomic “hot spots” to hide from the host immune response by Dr. Eugene Chang from the University of Chicago, how the microbiota of human irritable bowel syndrome patients can alter the behaviour of mice by Dr. Permysl Bercik from McMaster University, and also how the microbiome is a key regulator of behaviour in IBS patients from Dr. John Cryan at the University of Cork, how the inflammasome may regulate mucus secretion from Dr. Bruce Vallance at the University of British Columbia, and lastly, how enteropathogens (including parasites!) can induce inflammation by altering microbiota biofilms from the University of Calgary’s very own HPI researcher Dr. Andre Buret. All in all, it was a great conference full of exciting talks and I’m incredibly grateful to HPI for allowing me the opportunity to attend.

Microbiota and Mucosal Immunity |by Aralia León

The Society for Mucosal Immunology held this year’s symposium “Microbiota and Mucosal Immunity: Rules of Engagement in Health and Disease”. Attending this meeting was a unique opportunity since my work is focused in elucidating the role of microbiota and mucus layer in gastrointestinal health, so by participating in this meeting I got amazing feedback about my work, got to talk with experts on the field as well as with trainees from labs all over the world and more importantly share my results to an audience of experts. One of the things I liked the most was the high quality of research that was presented in this meeting, they had clinical work, basic science work, work done in animal models, all kinds of different approaches to microbiota study.

This year, the symposium was held in the city of Toronto, at the Westin Harbour Castle Hotel with a magnificent view to the Marina and Lake Ontario.  It was my first time in Toronto, so I took advantage of the hotel location and went from knowing a bit about this city to finally falling in love with Toronto´s vibe, markets and multiculturalism!

The first day we had a keynote lecture at the University of Toronto where Dr. Relman from Stanford talked about stability and resilience in the human microbiome.

The second day started early with sessions about I) Influence of microbiota in asthma and allergies, II) Secretory IgA and regulation of mucosal microbiota and III) Microbiota and gut immune system development, all these plenary sessions were given by experts on the field, in between plenary sessions we had concurrent sessions where I had the chance to present my work. The day ended with a poster session where I presented my poster and received very valuable feedback about my experiments.

On the third day the plenary sessions included: I) Intestinal microbiota and IBD and II) Mucosal immunity of the urogenital tract microbiota, with an afternoon trainee networking reception and the last poster session.

The last day was only half day where we had a session about therapeutic modulation of the human gut microbiota and ended with a Rising Star session where the organizers chose the top 4 work done by trainees, giving them the chance to present at the plenary session. It was a nice opportunity for listening to peers who are working on my same field and are having amazing results and using the most advanced technology.

This symposium was one of a kind in terms of relevance for my work, the knowledge I got from it will help to move forward my work and gave me a personal perspective of where is the microbiota field moving to.

I want to thanks NSERC-CREATE HPI program and the Society for Mucosal Immunology for providing with the funds for this trip.

Bioinformatics in Toronto

139322084-lysanyqu-_dsc21070001In May of this year the University of Toronto hosted the first Canadian Computational Biology Conference, and bioinformatics geeks like myself flocked to their beautiful campus from all over the continent and across the pond. There was a lot of cool new work being presented, and it’s always interesting to get an update on the current state of our art. It was especially striking as the conference took place at Victoria College, which is essentially a castle sitting on on the U of T campus. I’ve never before heard about new applications of set cover machines or the pitfalls of failing to treat metagenomics data as compositional, while the speaker is being framed by beautiful 180 year old stained glass windows.

me_presenting_2I was fortunate enough to be able to present my work in a talk, which was somewhat nerve-wracking as my session was chaired by Dannie Durand, the very researcher whose work I have adapted and modified for my own purposes. She spoke about their recent work analyzing gene families by considering the evolution of each domain separately. We also heard about the staggering complexity involved in trying to predict transcription factor binding behavior, about how representing bacterial genomes as profiles of k-mers yields better phenotypic information than standard phylogenetic analyses, and how disordered regions on eukaryotic proteins are vital to their functions (especially transcription factors).

In addition, we heard about several projects out of Greg Gloor’s group, with his talk titled “We’ve been analyzing high throughput sequence data in the wrong geometric space”. It raised a fundamental problem with how abundance sequencing data is commonly handled, essentially suggesting that most of the metagenomics field have been analyzing their data incorrectly. It boils down to the fact that 10% of one sample can’t be assumed to be the same as 10% of an independent sample, when you have no idea about how many total data you have in each sample. If your data are ratios, you can’t treat them the same as if they were actual counts. Spurious correlations will absolutely appear simply due to the structure of the data, and even simple operations like addition and subtraction no longer really work. Researchers have not really properly respected this fundamental issue, but there is now a tool available called CoDaSeq to help them handle it in the future.

Overall I found the conference very valuable, and I am very grateful to the HPI for the funding and support that sent me there. Hopefully this conference will continue in the future!

 

American Society of Parasitologists 2016 | Sydney Rudko

This July I had the privilege of attending the American Society for Parasitologists meeting, held in my very own backyard at the Westin, in the heart of Edmonton’s downtown. This was my first ASP, and I had high expectations, as my lab mate Michelle, ASP’s biggest fan, has been boasting about its greatness it for years.

Beyond the Eminent Parasitologist Lecture delivered by Nobel Laureate Bill Campbell, the wonderful and ornate appetizers at the Muttart, and beyond even presenting my own work, what really stood out to me about ASP was the focus on students.

The student talks were easily some of the best talks I’ve ever seen at any conference. They covered a wide variety of topics including Host-Parasite Interactions, Life Cycles and Epidemiology; Taxonomy, Systematics and Phylogeny; Evolutionary Ecology; Biochemistry, Physiology and Immunology; Chemotherapeutic and Drug/Vector; and Genomics and Molecular Biology. Truly, there was a session for everyone, and most of the talks were highly interdisciplinary. I even saw a number of excellent diagnostic parasitology talks in my own session, Genomics and Molecular Biology. I was so impressed by the breadth and knowledge of the students, but moreover, the willingness of the Professors to engage with students was remarkable and truly demonstrates the best parts of science, mentorship and learning from others.

There was also an incredibly exciting student auction, which raised money for student travel awards to the meeting, and four of Noble Laureate Bill Campbell’s raised a pretty penny to support student travel awards to the meeting. Once again, this event showcased ASP’s focus on students, and the Society’s desire to engage up and coming scientists, and mentor them in the broad and diverse field of parasitology.

In short, it was a pleasure to be treated as an equal amongst so many successful scientists. I felt genuinely encouraged in my pursuits by nearly everyone I spoke to at the conference. Furthermore, it was remarkable to see the breadth, diversity, and adaptability of the scientists present. ASP is an absolutely essential conference for any student who is interested in parasitological research to attend. Thank you to HPI for covering the cost of registration for this excellent event.

Great Lakes Bioinformatics Conference by Sonja Dunemann

Blue sky; the Toronto skyline on the close horizon. A church tower to my right – I think it is my right. There is a delightful hubbub in my head – I am in Canada! I am in Toronto! I am lying on a rooftop patio of the most recommended hostel by The Lonely Planet, my favorite travel adviser. I am thinking that I want to implement all the terrific things I have learned at the conference, and about where I am going to go next.

Okay, this is a challenge: which Great Lakes Bioinformatics

(GLBIO)/Canadian Computational Biology (CCBC) workshop should I sign up for? There are several workshops that are of major interest to me and could potentially be helpful for my current research project: proteomics of the zombie ant parasite. Before I can decide, the machine learning (ML) workshop is full, so I sign up for the Cytoscape Networks workshop (Networks, proteins! This might be helpful!).

In the end, I shouldn’t have worried too much. There was space left in both workshops that I did not sign up for, namely software engineering and machine learning, so I could go to all the workshops I was interested in. The software engineering workshop was as basic as expected (thanks to well informing websites of the organizer), but I figured I could learn a couple of helpful tricks to improve upon my coding. The Cytoscape Network workshop was more directed to Biologists than to Bioinformaticians. It presented the Cytoscape software and how to use it. But luckily, I could finally learn something about algorithms such as random forests in the ML workshop (thankfully it was in the evening so I could – miraculously – find a spot for myself). Material for the ML workshop can be found on GitHub (https://github.com/morrislab/mlworkshop).

Before going to the CCBC conference, I became familiar with the field of proteomics. I read a lot of papers and tutorials by authors not yet known to me. It has always been a highlight for me to meet the authors of papers I studied, especially if these papers were of high relevance to my own research. At the CCBC conference, I had the privilege to talk to the leader of the proteomics field, Alexey Nesvizhskii, in person.

My own contribution to the conference was a poster about my proteomics project. Although the project was not yet complete, I presented some preliminary results. Due to numerous questions of people that were not familiar with the project, I could remind myself of the big picture behind it, and its necessity. A fellow German student presented her poster next to mine, and we exchanged our thoughts and challenges.

Going to many talks a day, our attention might wander off from time to time. The keynote speaker Jennifer Gardy however told us a captivating crime story about a tuberculosis outbreak, and how genomics can come to the rescue. Yes, that is what we like! More of that!

In conclusion, I gained a lot from the conference: networking, making friends, and learning new things about my own field. I would like to thank the NSERC-CREATE HPI program for providing travel funds that helped me attend this conference.

All of a sudden California – EB 2016

“All of a sudden California” is the name (translating from Portuguese) of a popular song in Brazil, my home country (you can listen to the song in this link https://youtu.be/cx7U3_u12EU). In this song, the singer (Lulu Santos) says that he is going to California to be a movie star. I grew up listening this song, imaging the paradise described in the words and dreaming to visit California. The diference is that I never wanted to be a movie star. My dream was to be a scientist.

This year, science and NSERC CREATE HPI brought me to California. It was to attend the Experimental Biology (EB) 2016, held in San Diego. EB is an annual meeting comprised of over 14,000 scientists and exhibitors representing six sponsoring societies and multiple guest societies. It’s just huge!

The trip started a little stressful. It’s because, in Brazil we use two family names. One from mother family and other from father name. When I booked my fly, I filled the field “last name” with my last name (Lopes, which is my father’s family). But in my passport the reference is not last name, but family name (Carvalho Lopes). At check in, the airline said I wasn’t the guy in the booking. In the end, after much stress, I got to board, and everything after this was smooth. I wanted to drop this line mainly to Brazilians and other Latin people who have two or more family names. For somes, last name does not means the name that comes last, but the hole family name. Anyway!

I presented my research in the first day of the conference. A project which I develop with my principal collaborator since I arrived in Dr. Derek McKay’s lab, Dr. Jose Reyes, a former HPI trainee. In this project we have identified a cellular population that is recruited by extracts from worm parasite. Moreover, this cell population have the ability to inhibit a model of Crohn’s disease, identifying mechanisms to treat patients with Crohn’s disease.

Having done my main task in the conference in the first day, I had four more days to have fun. Nothing is more fun than appreciate the cutting edge science that is being doing around the world. And where would it be better than a conference with 14,000 attendees? The talks and posters blew my mind. I got many new ideas to improve ongoing projects and to new projects. I also could narrow laces with scientists who I already knew, and to know others for the first time. This was formidable to my network.

And sure, I also had fun out the conference. San Diego is beautiful. At least the downtown, where I was hosted, and had the chance to look around. Amazing restaurants and pub, car that you can just see in south of California and a beautiful marina, where I ran in the mornings before the conference. One night, I attended a traditional event in EBs. The concert of the band GI Distress. It’s a band formed with professors in the gastrointestinal field from different parts of the globe who meet every year to do science in EB and make rock’n’roll. And believe me, they rock!

All of a sudden California, science and rock’n’roll. It’s a dream accomplished.

Fernando Lopes – Post doc Fellow – Dr. Derek McKay lab – HPI

Bonjour Montreal – CDDW 2016

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Thank NSERC CREATE HPI I had the opportunity to attend, for the third time, the Canadian Digestive Disease Week (CDDW) 2016. This year, the Annual Scientific meeting organized by the Canadian Association of Gastroenterology (CAG) and the Canadian Association for the Study of the Liver (CASL) was held in Montreal. The conference joins clinical and basic science research in the same venue, being a unique opportunity to translate bench to bedside to bench.

As I am a regular attendee of CDDW, every year I look forward the conference. This because I can meet other regular attendees and appreciate their evolution on their projects and discuss with them the advances in my projects. Parasite in a hot subject in the conference, as new experimental treatments have emerged. To treat malign parasite infections that affects the gastrointestinal tract, but also and more interesting to me, the understanding of the mechanisms whereby parasite infections regulate the immune system and how to use those mechanisms to treat immune/inflammation driven diseases.

I presented data from a project that I have been developing with a former HPI trainee, Dr. Jose Reyes (who is a freshly recruited professor in the Universidad Nacional Autonoma de Mexico (UNAM)) in the laboratory of Dr. Derek McKay. In this project we show how immune mediators can regulate other immune mediators and the such relevance on worm therapy to treat a model of Crohn’s Disease. The input that I received from attendees in the conference were fundamental to the progress in the project, which we hope to publish the manuscript this year.

Au revoir et je l’espère vous voir à la prochaine CDDW!

Fernando Lopes – Postdoc Fellow – Dr. McKay Lab – HPI