Banff Inflammation Workshop 2017 | By Christina Amat

The Banff Inflammation Workshop (BIW) has been taking place every other year for 20 years now, with the latest one, on January 26-29th 2017 being the 10th biennual conference. The conference is small, with only about 90 people in attendance (~ 20 trainees), but it allows for well-recognized researchers in the field of inflammation to get to know eachother and the trainees, who are ready to learn.

On Thursday night, we began the conference with an intimate reception dinner where we had the great opportunity to hear from keynote speaker Karsten Gronert about autoimmune responses in the eye – a fascinating topic with lots of gruesome eyeball pictures to finish off with dessert! Friday morning we got right to work, hearing speakers from around the world talk about the various areas of inflammation, including in the areas of cancer, microbiology, and in the human airway system. We had a poster session to conclude the day, where us trainees got to show off our stuff – I received lots of fantastic feedback and had a great time learning from the experts! Saturday was back at it again with many more talks, hearing about musculoskeletal inflammation, inflammation and pain, and different mechanisms of inflammation – all very interesting! The second poster session was later that evening, with more trainees presenting their work.

To conclude the event, Saturday evening was another great dinner with an award session – where I was grateful to receive a second-place prize for my poster presentation. We were also able to hear from guest speaker, Jay Ingram, about the importance of science communication (with a couple of Donald Trump jokes thrown in). All in all, it was an absolutely fantastic conference with a ton of information and so much for me to learn. I am grateful for HPI for the opportunity to be able to go to conferences like BIW where I can learn from the experts!


A short and compact conference on Amebiasis in a warm city in India | By Sharmin Begum

The very short AMOEBAC conference 2016 (November 1-2 2016) was held in New Delhi, capital city of India. This was my first conference on the Asian Subcontinent, and I was really happy to have the opportunity to give a 15-minute talk about my research. To attend the meeting I started my journey two days earlier, as India is so far from Calgary. It was really long journey and after a 20-hour flight with two layovers, I reached India early in the morning. The gentle weather in the morning refreshed all my tiredness from the long journey. I took a taxi to the guesthouse (Indian National Science Academy, INSA) where the conference was arranged. In the morning, we had a good traditional Indian breakfast, and as I am from this part of the world I really enjoyed the food. After breakfast, I had a chance to explore New Delhi, and so I took a taxi to visit famous places close to the science academy. The very well known Delhi Gate was very close, and after that I visited Red fort, Raj Ghat, and Firoz Shah Kotla. I was walking through the streets and really enjoying the city. After having lunch with delicious Indian food the conference started. It was a small conference but so intense. Scientist, students working on Entamoeba histolytica from Japan, USA, Mexico, Canada, and host country India were present their research work, published work and new ideas. On that evening we had 6 talks and among them two were related to the newest findings in amoeba. The dinner was nice and I talked to a lot of students from India. They told me about places to visit, shopping and restaurants. The following day, sessions began after breakfast and it was a fully packed day.

The first talk was given by Dr. Nancy Guillen and after her powerful talk my supervisor Dr. Kris Chadee gave his talk with answering some unknown facts about amoeba infection. I was also presenting my research approach and interest and received some good opinions about my project. It was really very interactive conference and because of the small number of people within one day we all became familiar to everyone.

At the end of the day the organizer of such a dense, short and, well-designed conference Dr. Alok Bhattacharya gave his thank you and closing remarks. Then, we had a dinner and after that me and my supervisor left the guest house for the airport to catch our flights back to Calgary.

sharminThe conference was short, but the content was really remarkable. Hospitality from the local people was really warm. The conference was well organized, and allowed us to talk and get familiar with everyone while sharing our research interests, and ideas. Personally, for me it was a great experience, and if anyone ever has a chance to visit India, they should not miss that opportunity. I am looking forward to attend another such conference again. I would like to give my heartiest thanks to HPI NSERC CREATE for providing funding for me to attend such an impressive and knowledgeable conference.

Oxford Nanopore Technologies mini… user meeting | By Jenneke Wit

My first response when arriving at the meeting was that I took a wrong turn. The venue was very flashy, polished and professional. So much so, I felt like I ended up at an Apple launch event! But my nametag was there, and listening more closely it transpired I ended up in Little Britain. Not surprising, given Oxford Nanopore Technology (ONT) hails from overseas.

MinION versus Nokia 5110 – an approximation

ONT, the company organising this meeting, is probably best known for their hand-held sequencer, the MinION. This fancy machine, about the size my first mobile, a – yellow – Nokia 5110, can be used in the lab as well as the field to generate long reads, thousands to over a hundred thousand bases in length. A great feat, but also something that still requires a lot of tweaking and troublesooting, which is why this community meeting was so beneficial for both ONT and its users.

When the talks started it quickly became clear there was more to the meeting than an amazing venue. Talks were of a wide diversity and good quality. We were introduced to technological improvements, including an even smaller sequencer (SmidgION), new reagent kits and molecular protocols as well as a wide range of topics where ONT sequencing played an important role. Diagnosing malaria in India, looking for complex genomic rearrangements in Caenorhabditis elegans and sequencing the human genome were but a few of the exciting topics.

Over the two-day meeting, I got most out of the breakout sessions where there was ample opportunity for discussion following a set of flash talks. These were talks of the people that were getting their hands dirty. Be that in the wet lab, in the field, or behind their computers.

Arwyn Edwards, from Aberystwyth University, gave the talk that stood out most to me. He started out introducing us to cryoconite, a dust partially made up of microbes. When this dust builds up on glaciers, its dark appearance accelerates melting. For studying which microbes are present, he uses the MinION. I have a warm, well-equipped lab at my disposal, but was intrigued by what must be the most high-tech lab-in-a-bag ever. Everything from sampling, DNA-extraction, sequencing and analysis fits in this army-style rucksack and allows Arwyn and his team to study the microbe composition on site (dubbed extreme metagenomics). Evidenced by twitter, I was not the only one enthralled by this travelling lab!

Lab-in-a-Rucksack, ready for the “MetaGenomadic” life – by Arwyn Edwards

Having done a lot of optimizing myself, it was interesting to listen to the approaches others took to tackle the same issues, and, often, come to the same conclusions. This was valid for both the molecular work as well as the concerns we were having about the computational analysis. Especially with regards “what is good data?” when sequencing longer fragments. Consensus is: with long read technologies coverage gives way to longer reads when assembling new genomes. Aiming for fewer but longer reads rather than more “short” (few kb) reads is the way forward.

Souvenir: Personalized sleeves!

Finally, a blog on this conference wouldn’t be complete without a mention of the amazing care they took of our nutritional needs. From breakfast to dinner, everything was equally tasty and well prepared. For vegetarians and meat lovers alike, there was plenty for everyone. The eye for detail was amazing, and provided an excellent souvenir for avid tea-drinker James.

I look forward to further collaborations with those I connected with at the meeting, and would like to thank HPI and the Faculty of Veterinary Medicine at the University of Calgary for supporting my attendance.

ArcticNet, Winnipeg, December 2016 | Fabien Mavrot

From the 5th to the 9th December the ArcticNet conference was held in Winnipeg, Manitoba ( Arctic Net is a network that aims at bringing together different stakeholders in order to share information and collaborate on research in the Arctic. A particular focus is put on the impact of climate change and human activity on the environment and its inhabitants.


Thanks to HPI, I was able to attend to the conference and present a part of my work on muskoxen health and diseases. This conference was the largest that I have ever attended and reflected the diversity of the research supported by ArcticNet: there were oral presentations and posters from fields as diverse as physics, social science, medicine or ecology. In addition to researchers, governmental agency and industry, there were also representatives from Inuit communities. For instance, Matilde Tomaselli. my colleague from the Department of Ecosystem and Public Health co-presented the result of her participatory research on muskoxen and its value for Inuits together with Eva Kakolak and James Hanilak, two delegates from the community of Cambridge bay (Victoria Island, Nunavut). In a context of reclamation of their right to self-government and co-management of natural resources with the Canadian government, I found upstanding that Inuit community members were not only spectators but also actors during this conference.


As a veterinarian working with wildlife I was of course very interested in presentation related with my line of work, and I was impressed not only by the quality of the research presented at the conference but also by its originality. For example, Molly Ingemney and Sean Perry sought to assess ecological stress in young polar bears by measuring facial asymmetry on close-up pictures. In another talk, Jacqueline Verstege explained why lemmings build their nests directly on top of fox dens (and it is not because they are suicidal…)

Finally, the last evening of the conference the annual Arctic Inspiration Prizes were awarded ( Those prizes are granted to projects proposing concrete solutions to challenges arising in a changing Arctic. The first prize was awarded to “Qarmaapik House”, which provides a safe house for children and help and support for parents during family crises. The joy of the team developing the project when they received the prize was contagious and really touching.

Altogether, what I took back from this conference is a feeling of positive energy, innovative thinking, and a strong commitment to better understand and preserve the Arctic and improve the life of people living up there. It was a very positive experience and I hope I’ll be able to attend to the International Arctic Change conference that will be held in Quebec in December 2017 and will mark the 10th anniversary of ArcticNet.

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.

ASTMH 2016 in Atlanta | Ken Gavina

I recently had the pleasure of attending my first international conference, the 65th Annual General Meeting for the American Society of Tropical Medicine and Hygiene (ASTMH) in Atlanta, Georgia. The conference was held at the Marriott hotel in the heart of downtown Atlanta. This being my first trip to Georgia, I was absolutely spoiled by the warm weather (+20ºC in the middle of November), the delicious food, and the southern hospitality I received when visiting different venues and walking around the neighborhood. A definite highlight of the trip was visiting the Centers for Disease Control and Prevention and the David J. Sencer Museum.

The conference itself spanned over five days and was easily the largest one I’ve ever attended. The conference started with a pre-meeting course I registered for titled, “The Science of Disease Elimination”, which I found to be quite enlightening. The course featured several different speakers and covered a wide range of topics from statistical modelling to political and financial support. The day only got better as the opening reception and keynote address was given by Dr. Carissa Etienne, director of the Pan American Health Organization (PAHO), who spoke about Zika.

I had the pleasure of presenting my research via a poster presentation. The poster I presented focused on work I am doing as part of my PhD, using molecular diagnostics to survey the burden and clinical impact of submicroscopic malaria in pregnancy in Colombia. I developed an RT-qPCR based method to distinguish submicroscopic malaria infections at the species level (Plasmodium falciparum or P. vivax) and we used this assay to assess the disease burden in pregnant women. We found that submicroscopic malaria occurs frequently in pregnancy but despite this, is not associated with negative birth outcome20161117_145949.jpgs. My poster was well received and generated a lot of interest from other researchers working in a similar field.

What I got most out of the conference was the opportunity to engage with my peers, as well as meeting and discussing my work with some very well respected researchers in the field. Memorable moments included talking about career paths with Dr. Peter Crompton from NIH, listening to a talk by Dr. Kayvan Zainabadi from the University of Maryland about a new highly-sensitive diagnostic method for malaria using dried blood spots, meeting trainees from Dr. Kevin Kane’s lab (one of our lab group’s collaborators) at the University of Toronto, and discussing my research with Dr. Stephen Rogerson from the University of Melbourne. It was a great overall experience and it would not have been possible without the support from HPI which allowed to attend the conference.

The Innate Lymphoid Cell conference in the heart of Berlin | Edina Szabo

The 2nd EMBO Conference on Innate Lymphoid Cells was held in Berlin, Germany at the end of November, 2016. To support the European scientific communities the European Molecular Biology Organisation (EMBO) holds conferences and conference series that cover different and evolving aspects of important subject areas. The conference was held in a historic building in the heart of the city, called Kalkscheune (Limestone barn). The place was already set for Christmas, and had a great feeling about it.

The first day of the conference started with registration in the afternoon, followed by two intensive full days, and closing with the Gala dinner. Dan Littman from the NYU School of Medicine, New York, gave the keynote lecture, and well introduced the topic with his talk entitled “Role of ILCs in integrating host responses to microbiota”. The keynote lecture was followed by a session on “ILC development and activation” with speakers from the US, Netherlands, from the Institut Pasteur in Paris, and McGill University in Montreal.

The second day started early at 8.30 am with talks on “Regulation of ILC fate and functions”, and continued with “ILCs homeostasis” in the afternoon. I have particularly enjoyed the talk by David Withers from the University of Birmingham. His group is looking at the importance of a particular receptor for cytokine production by ILC3 cells in the small intestine. Another talk that caught my attention during the afternoon session was the “ILCs and immune regulation at barrier surfaces” presented by David Artis from Cornell University, New York. His findings showed that commensal microbes have a significant regulatory influence on lymphocyte, innate lymphoid cell, and granulocyte function. After the talks we had a chance to explore the city a little bit in the evening, and try the local cuisine.

The final day started early as well, and by then most of us were pretty exhausted, but we had great talks and the gala dinner to look forward to. Emily Thornton’s talk from University of Oxford, was very interesting, which was exploring how ILC3s are involved in the initiation of acute intestinal inflammation. In the afternoon also several talks were on intestinal ILCs, including speaker such as Henrique Veiga-Fernandes from Lisboa, Arthur Mortha from New York, and David Voehringer from Germany. My favourite talk of the day and the whole conference was the “Innate lymphoid cells and IL-22: functional analysis in zebrafish” by Pedro Pablo Hernandez, whose project is to investigate the existence of ILCs and the conservation of the function of IL-22, which is produced by ILC3 cells.

The highlight of the day was the Gala dinner in the Natural History Museum, right by the dinosaur exhibition.

I would like to take the opportunity to thank NSERC CREATE HPI for funding to attend this conference. I had a great time at the conference, and learnt a lot about ILCs, as well as I had a chance to visit some of my family in Berlin.


NALMS | By Michelle Gordy

Two men walk into a bar. The first man tells the bartender “I’d like some good ‘ol H2O”. The second man says “I’ll have some H2O too”. The second man died.

Despite this horribly punny joke, I think it’s safe to say, we can all agree that water quality is important, whether it is your drinking water, or the water used for recreational purposes, like lakes. In consideration of our changing climate, our increasing demand and use of freshwater sources, and our ever-expanding anthropogenic impact on the environment around us, it is pertinent that we work to protect the fresh water we have and make sure it is sustainable for generations to come. Such a task cannot be done in isolation, but requires the collaborative efforts of everyone. Hence, this year’s theme of the North American Lake Management Society’s (NALMS) International Symposium was “Science to Stewardship: Balancing Economic Growth with Lake Sustainability”.

I recently had the pleasure to attend the annual NALMS meeting in Banff, Alberta. Held at the Banff Springs Hotel, the conference literally took place in a castle in the mountains, and the views were outstanding! (Insert pics here)

The conference started out on a high note—literally—as the pub crawl on the first night ended at a karaoke bar with a mechanical bull, and yes, I rode it. Let me just give big props to all the cowboys out there and to NALMS for really knowing how to get a conference off to a good start!

Of all the conferences I’ve attended, this one was quite unique, in that the attendees were a conglomerate of scientists, government representatives, lake managers, members of watershed associations and stewardships, and environmental consultants. Topics spanned all areas of lake health and management, from the molecular level to the involvement of stakeholders and citizen scientists. The conference provided a unique perspective into applied research and all levels of opportunity to be involved in protecting our lakes. It was particularly interesting and encouraging to see the level of community involvement in accomplishing much of the data collection for many studies.

What I found most appealing about many of the talks was the practicality around them. I learned some useful things about how to best use maps to communicate data to the public, as well as how not to use maps…probably a much more important skill. I learned about the importance of involving the community in lake-based monitoring projects early on, to attain a common ground and understanding about the importance of the data collection on top of maintaining a healthy lake ecosystem.

While this conference was not parasite-focused, and perhaps the only talk about parasites was the one I gave, it was such a great opportunity to gain a new perspective outside of the little box that is my research. I am incredibly thankful to HPI for funding my attendance to this conference.


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.