Worms and bugs in the mountains

The Banff Conference on Infectious Diseases (BCID) ran this year from Wed-Sun over the first week of June. It has always been organized jointly between the Universities of Calgary and Alberta, and as usual they brought in many top researchers from around the world. I have attended twice in the past, back when I was working in microbiology and infectious diseases, but this time our lab went to represent parasites. This is actually something that I felt was somewhat missing from my previous degree; in classes or seminars or conferences we heard about bacteria, viruses, prions, and malaria, but almost never about parasitic worms. So my supervisor gave a talk, and I presented a poster about our work on worms.

There were a lot of very interesting talks at the conference. One that stuck in my mind is from a group looking to quantify the response of a single bacterial cell under different conditions. Their rather interesting approach was to use nanotechnology to create bacterial traps. They manufactured a chip with a few dozen very small structures on it, where each was in the shape of a “C” that was just large enough to accommodate a single bacteria inside. When the slide was exposed to heat, the material would swell shut, effectively trapping that bacterium in a set location. You could then expose the cells to any treatment you like, measure a response, and repeat; each measurement would be on the exact same cell so you wouldn’t have to measure only population level data.

Another talk that I found very interesting had to do with horizontal gene transfer in bacteria. It is a well known and studied phenomenon, that many bacterial species are able to uptake DNA from their environment, and that many of them integrate it into their own genomes. It is a common mechanism of spreading useful genes (often virulence factors) even between divergent species. But when you think about it, taking up a whole operon from a different bacteria carries with it quite a bit of risk. A bacteria doesn’t want something that is constantly draining resources for no benefit, or worse, some product that would interfere with the standard cellular processes. And for many complex features, such as a type-6 secretion system or a toxin/anti-toxin pair, all of the parts would have to begin working at the same time in order to be at all useful or safe. It is extremely likely that any foreign DNA would have to undergo many specific mutational changes in order to begin to function properly within the cell, which is extremely unlikely to occur in a short time period. All of these traits would be strong selective pressures to kick out foreign DNA, but on the other hand the rapid spread of new genetic material can provide a very beneficial evolutionary response to changing environments.

It turns out that Salmonella uses the histone-like nucleoid structuring (H-NS) system to have their cake and eat it too. The genomes of different species of bacteria often have very different G-C content (can range from 25%-75%); Salmonella has a relatively high level. This means that any foreign DNA it takes up will likely be comparatively A-T rich. The H-NS system exploits this fact, and is able to bind to A-T rich regions of the genome regardless of the specific sequences. These proteins effectively supercoil the genome at these regions, preventing transcription at very low cost to the cell. Salmonella is therefore able to maintain a diverse reservoir of genes that are not actually active, but can collect mutations over time and quickly be turned on when the appropriate infrastructure comes into being. Systems like these have been found in several other bacterial species, and may help to explain how multi-part complex traits sometimes seem to suddenly spring into existence.

So quite an interesting conference, and a good opportunity for me to see new research that is not directly related to what I do. Hopefully some people found our work as interesting as I found theirs.

A trip to California

When students, or any researcher in the life sciences thinks of international academic conferences, usually a grand scale, thousand attendee event with 17 different synchronous talks, on topics ranging from prions to the evolution of flowering plants comes to mind. Attending such conferences is usually coupled with the inevitable anxieties about how to get there, which talks to attend, how to find (let alone speak with) the people whom made your “must network with!” list, and of course, finding where on Earth the bathroom is amongst the football stadium size conference center the organizers were forced to book. Thus, when I found out that the Anthelmintics: From Discovery to Resistance conference I attended this February was as small and intimate as a specifically titled conference such as this would suggest, I was actually relieved!

The conference was indeed very small and very personable. It consisted of a sold out attendance of ~130 members of a small and tight knit community of researchers who work on anthelmintic drug and drug resistance. Although, small may be a bit of an understatement as the conference and time-slots filled very early, suggesting the community is larger than 130 attendees would suggest. Regardless, the pluses of keeping this meeting a smaller affair seemed, at least to me, quite obvious. To start, there wasn’t 17 (exaggerated for dramatic effect..) sessions going on at the same time, but only one.  This worked out great because, given this was such a specific conference, I was actually interested in the large majority of talks that were given! In fact, if the talks would have been scheduled in more than one session at a time I would have definitely missed some that I flagged as must see. This speaks to the inherent appeal of a small and specialized conference. Given its specialization, those in attendance tend to be much more interested in the topics discussed. Further, as it’s so specialized, the size of the conference is usually small enough to allow all attendees to see every talk.  Really it just seems like more bang for your buck!

In terms of the actual talks, organisms ranged from schistosomes to filarial nematodes, and focused on parasites of wildlife to a diverse set of human parasites. They were also delivered by researchers from a diverse array of institutions, from industry members to students. Talks were followed in the evenings by poster presentations, one of which I gave on the second day.  Another advantage of a specific conference such as this is not only that you can easily meet a lot of the people whose research you’ve been following for years, but also that it’s easier to find the time and place to talk with them about your own research! This was no doubt the most rewarding poster presentation I’ve given for this reason.  In larger conferences there tends to be so many posters allocated to the same time-slot that researchers whom you would like to talk with about your research rarely show up! As this conference had only 30 posters per day concentrated in a much smaller area, it was easy for people to have a good read of every poster in the session, and as a result I got to talk with nearly all the people working in my specific field about my project. Most students will tell you that this is not your normal poster presenting experience 😉

Now on to the fun stuff! We all know (but don’t like to admit) that conferences are half academic, and half social affair.  But can you blame us! We’re shipped off to a cool place for an extra-long weekend with our lab friends and get evenings off, with free food to boot! I think most people who attended Anthelmintics: From Discovery to Resistance would agree that this conference delivered on the fun side as well.  To start, San Francisco is probably one of the coolest places in America to be a tourist for a few days. And again, because of the small size of the conference, we were able to fit in to a snug little hall situated right beside one of the many harbours lining the city’s north shore. Thus it was easy to walk around and explore, especially when situated 10 minutes from the famed Fisherman’s Wharf. Socializing with members of other labs that work in your field is definitely one of the hidden values of the conference experience.  Not only can it more easily foster collaborations, but it’s much easier to have discussions about research direction, and the theory and motivations behind ones research when in a relaxed atmosphere.

All in all, I have to say that this conference truly delivered in both the content of the formal oral and poster presentation sessions, and in the social atmosphere the organizers encouraged with such a small, specific gathering of researchers.  The event really gave an impression that there is so much going on, and so much progress being made in the study of anthelmintic drugs and drug resistance.  As a result, I’ll definitely be ready to jump right back in for the next one in a couple of years! And I’d encourage anyone else in our field to do the same!

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From top left: 1) The window of the Fort Mason conference room overlooking the harbour. 2,3,4) A railcar, Alcatraz, and China town.. Can’t get more San Fran than that! 5) My 6th attempt to get a reasonable picturesque background shot. Photography is hard! 6) Winds, fog, and rain. I still prefer it to -20… 

“Anthelmintics: From Discovery to Resistance” in San Francisco

Having been suffering from cold weather in Calgary for three months, I had a great chance to attend the “Anthelmintics: From Discovery to Resistance” conference held in San Francisco from Feb 5th to Feb 7th. For me, it is more special because it is my first time to present a talk in an international conference. It was a very successful meeting, including a quite broad range of topics which covered most issues in anthelmintic drug discovery and excellent speakers in this field from all over the world, although it was the first conference in anthelmintic drug discovery.

I am a master student in the Wasmuth lab, working on metabolic network modelling in Caenorhabditis elegans and parasitic nematode Ascaris suum to find essential enzymes as novel drug target. There are some metabolic drug targets in the market now, however, none of them for helminths. That is also our question that if we can explore any metabolic targets in nematodes. First, metabolic networks of C. elegans and A. suum were reconstructed from genome sequences. The method I am using is systems biology approach, including chokepoint analysis and flux balance analysis (FBA). The chokepoint analysis assumes that chokepoints are the only route for metabolite formation and, therefore, removal of these chokepoints disrupt metabolism, functioning as drug targets. FBA optimizes the biomass and fluxes of biomass formation are maximized, and reactions which play a crucial role in biomass formation are essential. Chokepoint analysis is easy to perform, because it is only based on the network itself, while FBA integrates other information, such as reaction activity and biomass components fractions, and it requires a more accurate network. The combination of chokepoint and FBA, hopefully, would better predict essential enzymes in nematode metabolic network. This project is the first attempt to use FBA on metabolism of multi-cellular species. It is hard but interesting.

Surprisingly, I was one of the four students who were selected to give a talk in the meeting. My talk was on the first day, which was good, because I could be relax and enjoy the rest of the talks. Although I had practiced for several times, I still felt nervous – my heart raced. Thanks for all my teammates who encouraged me a lot. The first five minutes was bad for me, and I just kept talking to get calm and comfortable. Finally I completed it in time, which was appreciated, but I knew maybe because I spoke a little fast naturally. The two questions I got were exactly the point of my project, making me think more about my approaches. I think the professors all understood it was a young graduate student’s first presentation, and understood I had to go through the learning process too. I learned from this presentation experience. I was excited that my project was known by others, especially when they were interested in the topic and came to talk to me during the break. I was impressed with some posters related with A. suum such as Ciaran McCoy from Queen’s University – “Building a reverse genetics platform for novel drug discovery in nematode parasites”, Gao Xin from The Genome Institute – “Conserved and diversified functions of the different compartments of the nematode intestine”, and Bruce Rosa from The Genome Institute – “functional analysis and phylogenetic conservation of intestinal proteins in Ascaris suum.

It kept raining for four days when we were in the city – almost raining every day. We had a good time on the first day, the only sunny day.  Living closed to the bay, we could walk along the coastline, and enjoy lots of seafood. The famous Golden Gate Bridge was veiled in mist when we were there. Windy and rainy, it was not a good time for tourism. Be sure to check the weather before travel.

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I wish to thank the University of Calgary’s Faculty of Veterinary Medicine for the travel award, which allowed me attend the conference.

Field Work: A Walk in The Park

One of the great things about working with parasites and especially those using wildlife hosts is the chance to leave the lab and do some field work.  For myself, a PhD student working at both the University of Lethbridge and Calgary, this means a trip to the Cypress Hills Interprovincial Park in southeastern Alberta.  This park spans the border between Alberta and Saskatchewan and is somewhat of an anomaly as it is an island of sorts in the middle of the vast prairie landscape of the Canadian west.  Cypress Hills is an area that was not covered and flattened by the glaciers of the last ice age, resulting in hills that rise 1400 meters above the prairies.  This creates an island ecosystem protruding from the seas of wheat and suitable habitat for many species of animals.  The park boasts a large population of elk and deer, which in turn feeds a healthy population of roughly 30 cougars.  It also houses many species of birds and is a welcome stop over in the migratory routes of many  bird species each year.  Arguably the most interesting inhabitant to the park however is the liver fluke (Trematoda) Dicrocoelium dendriticum.

This small fluke is believed to have been introduced to North America and subsequently Cypress Hills from Europe where it is reported to be endemic.  The incredible thing about this parasite though is the life cycle. Dicrocoelium has a complex life cycle involving three hosts.  Adults living in the livers of final hosts produce eggs that end up in the hosts feces where they are ingested by a terrestrial snail.  In the snail the parasite develops, grows and divides into many individual cercaria (tiny, fork-tailed trematode life cycle stage produced through asexual division) and are coughed out of the snail in a mucous encased “slime ball” (it is actually referred to as a slim ball in some of the literature).  Now this is where it gets truly interesting.  Ants will come along and presumably bring this slime ball back to the nest where they all chow down on it.  Once inside the ant the majority of the parasites move to the abdomen and encyst there as meteceracia (the stage infective to the final hosts) where they wait to get passed on to the final host.  The final host in this case is any number of grazing ruminants and in the park specifically it can be deer, elk or domestic cattle that are grazed there.   So how do trematodes in ants get into the livers elk?  Remember how I just said that the majority of parasites in an ant go to the abdomen? The  minority, in this case one, makes its way to the bundle of nerves in the ants head that constitutes the ant brain.  Here it sets up shop by wrapping around the nerve bundle.  Ants infected with Dicrocoelium all have a parasite in the brain and all begin to act shall we say, clingy but not towards other ants they may have a crush on but rather towards plants.  During parts of the day that are cool and won’t dry out an ant sitting in the open the infected ants climb up plants and lock onto leaves and flowers with their jaws.  Here they remain waiting to be accidentally ingested by a grazing animal so they can get to the oh so tasty liver.  This is an amazing example of host manipulation by a parasite  and yes, this guy exists in Alberta less than an hour south of Medicine Hat.

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Infected ants clinging to dandelions in Cypress Hills (Brad van Paridon)

Naturally someone needs to be investigating this oddball and that means someone has to get out there and collect samples of this thing from the park.   Naturally that sounds like a pretty sweet time so I took up the cause and have been working on this system since 2011.  Which gets me back to the joys of field work.  My latest trip to the park was November 2013 and the goal was to collect fresh livers and adult parasites from elk that are killed in the annual elk management hunt.  We do so with lots of help from the Alberta Parks Staff, Conservation Officers and of course the hunters themselves.  Basically any time an animal is shot in the park it needs to be called in to the CO’s who come out an verify the tag.  We just tag along, show up at the kill and get a fresh liver.

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Myself next to the gut pile from a recently deceased elk, and you thought they smelt bad on the outside. (Brad van Paridon)

I have been touting the joys of field work this whole post and we always have a great time.  How could we not with scenery such as this to enjoy.

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However, during one foray out into the park to find some hunters that had just called in a kill things became slightly less pleasant.  As is normal in the park a thick fog descended onto the flat prairie likeplateau of the hills.  The three photos above that look as though they could have been snapped on the prairies are actually theplateau of the hills and are at an elevation of 1400 m where fog and clouds come and go quickly. Blanketed in fog it looks something like this.

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Aside from the obvious driving hazards associated with travelling in thick fog, we must remember that hunting is also going on in these areas and although it is technically illegal to shoot into fog, poor decisions are made on a daily basis.  So this is where we found ourselves.  Outside the truck, standing in the middle of a field, surrounded by fog so thick we can’t see more than a few meters in any direction and trying in vain to locate the hunting party that has just taken down an elk.  Just then we got in touch with the hunters via cell phone and things were looking up.  We concluded we were in the right area but then the man on the other end of the phone stops and says” I gotta go they’re (meaning the elk herd) are coming back around and we are going to take another shot” and then he hangs up.  Well, we quickly put it together that this was for sure time to leave the area as we might get caught in the middle of a live fire exercise.  Needless to say we made a quick exit and upon returning to the area in an hour so found three kills about 100 m apart and no more than 200 m from where we were originally standing.  One of these kills too had not been claimed and was being investigated by the officers present, a situation that might occur if someone did not know they had killed multiple animals until the fog lifted. Hmmmm, makes you think.

Now, I don’t think we ever really came close to being shot, I never heard gunfire while out in that field, but it did make me think that field work really  isn’t just a walk in the park.  It also made me reflect on other situations I got myself into  in the name of field work.  One time while searching for infected ants I disturbed a wasp nest and was stung more than seven times on may face, chest and neck while running away.  I have exposed myself to swimmers itch while collecting aquatic snails, thankfully never got it though.  There was the time I  stumbled across what appeared to be an ideal cougar den complete with bones from the last meal.  This time I was thankful that no one was home.  But these things could happen to anyone who frequents the outdoors right?  That is what I told myself as walked through the pitch black of the Cypress Hills night, alone, carrying bags of liver sections, that would surely entice one of the many cougars in the park, over to the cougar garbage bins.  On second thought maybe I am bringing some of this on myself.

Bradley van Paridon

We’re recruiting the next generation of parasitologists

Question: Are you interested in joining a graduate training program in host-parasite interactions (HPI)?
If the answer is yes, maybe, or simply not no, then the University of Calgary may be able to help you.

We are home to the NSERC CREATE HPI program. Seven PIs whose research falls under the umbrella of host-parasite interactions. Follow us on twitter @HPI_UofC.

Andre Buret – Cell biologist studying Giardia.HPI-newLogo
Kris ChadeeEntamoeba histolytica infection in the gut.
Lashitew Gedamu – Molecular biology of Leishmania.
John Gilleard (@johngilleard) – Drug resistance in parasites.
Susan Kutz – Wildlife parasitology.
Derek McKay – Immunity and parasites.
James Wasmuth (@jdwasmuth) – Parasite genomics and evolution.

In addition to their own research activities, the graduate students and postdocs have many opportunities to enrich their studies. In a regular journal club, they learn about each other’s research, which has led to collaborations. There is an annual bootcamp in the Canadian Rocky Mountains, where trainees get workshops in entrepreneurship, social media and working outside the comfort of the lab. Another area of emphasis is engagement with the public. Our biggest success was a Halloween event at the Spark Science Centre, where HPI trainees put on an amazing display of parasites for thousands of children and their parents.

HPI trainees at the Telus Spark Science Centre

HPI trainees at the Telus Spark Science Centre

If you’re interested in joining the team, please visit the HPI website and contact the PI directly.

The course in review: the coordinator’s perspective

This post originally appeared on my personal blog: wasmuthlab.org.

A month has now passed since the close of the Fall Semester or Michaelmas Term, depending upon your vernacular. Over the last four months I coordinated three courses:

  1. Genetics & Molecular Biology, part of the DMV undergraduate programme.
  2. Advanced Topics in Microbiomes, a graduate course in the Veterinary Medical Sciences (VMS) programme.
  3. Helminthology, another graduate course in VMS.

With the new semester well underway, I thought that a little introspection would be worthwhile. How well did I think each course went? What did I do right? What could be improved upon? And what completely failed? I am able to include informal feedback from students, but the official feedback is withheld until the end of the academic year. Despite, this being an exercise in self-reflection (brooding?), I am at heart, mouth and deed an extravert. Hence, I thought I’d share…
I’m going to start with the Helminthology course, because we tried to go beyond what seems to be the standard for a graduate course.

Motivation
The University of Calgary’s Faculty of Veterinary Medicine (UCVM) has (unwittingly?) built up research strength in helminthology (parasitic worms) covering Wildlife Ecology ( Susan KutzAle Massolo), Pathology (Padraig Duignan), Molecular Biology (John Gilleard) and Genomics (my goodself). Further, Biological Sciences has Constance Finney and Medicine has Derek McKay, both immunologists working with helminths. Graduate students training in our labs leave knowing (hopefully) a lot about the specific field of study and on the specific species upon which they focused. However, what has been absent is a wider view on field. Is it not important that my students understand the ecosystems which interact with the genomes they’re sequencing? Shouldn’t ecologists know more about how the host tries to expel the helminth and how the helminth fights back? We thought so.

A total of nine graduate students and three postdocs took this course, making it the most populous elective graduate course in the Veterinary Medical Sciences programme.

Course Structure
Each week a different topic was covered, see below. A instructor-led lecture on the Monday was followed by a student-led workshop on Friday.

TOPIC INSTRUCTOR
Ecosystems & helminths Andrew Dobson (Princeton) with Susan Kutz
The impact of climate change and helminths of wildlife Peter Molnar (Princeton) with Susan Kutz
Helminth morphology Mani Lejeune
Helminths of livestock John Gilleard
Drug resistance John Gilleard
Helminths of humans James Wasmuth
Genomics James Wasmuth
Host immune response Constance Finney
Immunoregulation by helminths Constance Finney

The lecture component was left up to each instructor; I’ll comment on my two lectures in another post. The student-led workshop were given a basic structure. It was important that students read the primary literature around each topic. However, we wanted to go beyond the traditional journal club presentations, in which one person presents a paper with powerpoint and the others may (or may not) ask questions. The structure we adopted was based on a recommendation by Mani Lejeune. Briefly, each week:

  • All students were expected to read both papers
  • Two students were assigned as moderators

A moderator’s job was to summarise the papers and then promote discussion among all those in attendance. Each student was assigned two sessions and when possible, the topics were outside his/her research focus. The PI for each topic was present during the discussion. My briefly guidelines were that PIs remain in the background and participate when asked a question or when prudent to do so.
After the discussion sessions, the moderators were then charged with writing a blog post each: https://ucvmhelminthology.wordpress.com/. They could decide between themselves how they wanted to split it up. They were also encouraged to go beyond a description of the paper and incorporate discussion points from the class. The students were also to set-up and administer the blog.
As it’s a course, the students needed to be awarded a grade. Each instructor scored the students’ participation in class, which was 50% of the grade and I reviewed the blog posts which accounted for the other 50%.

So… how did it go?
From a PI point-of-view, the course seems a success and we hope to run it again in 2015. I know, I know, you want to know that the students thought. Once I get the official anonymous feedback, I’ll share the love. As this may not be until the summer, I ran a one hour feedback session with the attendees.

What they liked:

  • The breadth of topics
  • Discussing the papers
  • The idea of writing the blog posts

What they didn’t like:

  • Not enough genomics
  • Writing a blog post outside their comfort-zone
  • The time spent writing the blog posts

I’m happy that the students enjoyed the structure of the course. I has been apprehensive of how the discussion sessions would pan out. After a slow start, all of the students got involved, some excellently so.

I’ve spent some time dwelling on their reservations towards writing blog posts. Among the PIs, we felt it important that they write more and embrace a form of communication that’s increasingly popular, if not commonplace in science literacy. Also, I thought that the blog posts were great. Check ’em out: https://ucvmhelminthology.wordpress.com/. Therefore, I was initially disappointed by the feedback. Now, I feel that there were two core problems: 1) Blogging is new to them, 2) they were being graded. While, I do not believe the tail should wag the dog, I will probably make some changes for the next running of the course:

  • Award a pass/fail for the blog – if they write something, they pass.
  • Allow the students to write one a topic of their choosing, rather than assigning all of the topics.

I asked the students and postdocs if they wanted to carry on contributing to the blog and there was nodding of heads. I asked if they would try and spend 90mins each month, writing about an aspect of helminthology they found interesting. That’s not much time and I hope that some of the students can embrace the opportunity. I look forward to reading and learning…

Worms in a Pill? Hurdles the Pharmaceutical Industry must face in order to develop Helminth Therapy.

Picture1 needle
Our wonderfully complex immune system consists of cells, molecules and tissues which work together to protect the body from “foreign invaders”. When it encounters one, the immune system releases an arsenal of chemicals and antibodies to find and wipe out these invaders, and then has the capacity to remember literally millions of these pathogens for a rapid response if ever encountered again.
There are several arms of the immune system to deal with invaders depending upon whether they are bacteria or virus or other intercellular pathogens (by up-regulation of the Th1 response and damping of the Th2 response) or whether they are large extracellular pathogens such as helminthes (resulting in an up-regulation of the Th2 response and a damping of the Th1). When communication breaks down between the different arms of the immune system, auto-immunity (attacking one’s own tissue) may occur.
Picture: Picture2 immune system
As humans, and their immune systems, have evolved one foreign invader: helminth parasites, have also evolved and formulated several clever mechanisms to manipulate and evade the immune system. One of which is a dampening of the immune response (activating a Treg response).
One hypothesis (the hygiene hypothesis) given for the rise in auto-immunity in developed countries, may be that, due to impaired development of the immune regulatory system, at an early age, from the lack of intestinal flora and fauna has caused a shift of the immune system to a hyper-Th1 response.
Helminth Therapy to treat autoimmunity has been investigated with growing interest in the last 10 years. Several groups have demonstrated that helminthes can both protect and stop ongoing auto immune disease (see: http://dx.doi.org/10.1016/j.ijpara.2012.10.016).
Picture: Picture3 helminth therapy
In order for helminth therapy to be effectively developed the support of pharmaceutical companies is required. The paper reviewed in our Helminth 690 course: Tilp et al, International Journal for Parasitilogy 43 (2013) 319-325 (http://dx.doi.org/10.1016/j.ijpara.2012.12.003) suggested a number of reasons why this support may be stymied.
There is currently a very complicated picture immerging about Helminth Therapy: 1) not all helminth infections result in reduced autoimmunity’ 2) cohort studies performed in different labs have given different results’ 3) in many cases where there is reduced auto-immunity after helminth therapy auto-immunity still develops to some extent.
Several factors for why pharmaceutical companies are not investing in Helminth Therapy are the lack of reproducibility in current data; and the need for quality controlled clean helminth products; and the requirement to test Helminth Therapy for the relevant auto-immune disease with the correct timing; and marketing issue – making ingestion of parasites palatable to the public.
The Tilp et al., paper suggested several ways in which pharmaceutical participation could be enhanced. One of which was making helminth therapies for “orphan diseases” (diseases which are devastating but occur at low rates), for these diseases the extensive clinical trials and regulations are fast-tracked, thereby making it worth the time and money in developing them. Also, support could be enhanced by ensuring that the therapy is or can be patent protected. Other ways in which interest from the pharmaceutical companies could be enhanced would be for researcher to specifically address many of the outstanding questions such as the safety and side effects of Helminth Therapy.
Picture: Picture4 Tilp etal

What can the genomes of 4 tapeworms tell us about their history?

Last week in Helminthology we discussed two selected papers from the emerging field of parasite genomics. As with researchers in most areas of study in the Life Sciences, researchers who study helminths (or in the case of these papers, parasitic helminths) are embracing recently developed advances in sequencing technology as a means to sequence and assemble the genomes of their study subjects. This universal embrace of the emerging field of genomics is occurring primarily due to the promise genomics offers in informing us about an organisms ecology, evolutionary history, and in the case of parasites, epidemiology and pathology. Next generations sequencing (NGS) technology, although being only seven years young, has completely changed how researchers across the world approach the study of pathogens. These two papers offer glimpses of how researchers are using these technologies to understand these pathogens, and shed light on how they have evolved into their very specific, and often amazing, life histories.

The first of these papers looked specifically at inferred metabolic pathways from ten different nematode species (Taylor et al. 2013, doi:10.1371/journal.ppat.1003505) including five Caenorhabditis species including C. elegans, and five parasitic nematodes. The purpose of this study was to identify chokepoint reactions in the metabolomes of each of these species. Chokepoint reactions were defined by the authors as any metabolic reaction that either creates a unique product, or consumes a unique substrate (see below).

In this figure the red arrows represents chokepoint reactions with a unique substrate (A), and a unique product (B).

In this figure the red arrows represent chokepoint reactions with a unique substrate (A), and a unique product (B).

Through their analysis they gained a list of inferred chokepoints for each species under study. They then conducted a comparison between the different chokepoints of each of the worms. In the end they identified a list of enzymes that may act as potential drug targets in future drug development. The details and an in-depth discussion of these results can be found below in Keyu Li’s post “From Genome to Drug”.

The other paper that was discussed at length last week was an ambitious project that sequenced and assembled the genomes (and characterized the transcriptomes) of four different platyhelminth tapeworms (Tsai et al. 2013, doi:10.1038/nature12031). Specifically this paper focused on two human infective Echinococcus species (multilocularis, and granulosus), one human infective Taenia species (solium), and one rodent tapeworm (Hymenolepis nana) that has been used as a model for studying this group of parasites. The three human infective tapeworms represent a major health concern across much of the world, including the first world, and are the first forays into creating fully assembled and annotated genomes of tapeworms.

Tapeworms don’t normally come to mind when the public is asked to think about the most severe human diseases. The consensus as to why these parasites aren’t generally perceived as a top priority in the public (as well as the research community) consciousness generally comes down to two factors. 1) The negative effects of chronic tapeworm infection are usually very subtle, and 2) Tapeworm infection is primarily a problem of the developing and third world. These two realities have led diseases caused by tapeworm to be classified as two of the seventeen neglected tropical diseases by the World Health Organization (WHO). The WHOs calculation of the negative impact of a disease uses disability adjusted life years, as opposed to the more conventional measurements of a diseases severity (such as death rates), and therefore the severity of disease caused by tapeworm (as well as numerous other parasitic helminths) are estimated as some of the greatest of all human diseases. This reality is stressed by the papers authors as justification for the large amount of technical and human resources that were required in the creation and analysis of these four tapeworm genomes.

In addition to the creation of these genomes and transcriptomes, the study also conducted a comparative study of gene family expansions and reductions which yielded some interesting findings. The gene sets involved in metabolic capacity and the absorption of nutrients were extremely skewed towards a parasitic lifestyle. Particularly the tapeworms showed marked expansions of detoxification pathways, and marked reductions in gene families involved in the metabolism of certain compounds, such as fatty acids, which are instead uptaken from the surrounding intestinal environment. Another noteworthy expansion was that of the heat shock proteins, suggesting adaptation to the extreme temperature fluctuations that helminths are forced to endure inside their hosts. Lastly, the study (similar to the metabolomic chokepoint paper (Taylor et al 2013)) assesses the transcriptomes of these worms for potential drug targets. The authors identified ~500 potential kinases, proteases, G-protien coupled receptors, and ion-channels that may potentially be utilized in the development of new anthelmintic drugs.

As a whole, these studies are a great example of how genomics can be used to inform us on the big picture of an organisms genome, which subsequently can inform us on the factors that make that organism unique. In particular, the Tsai et al. (2013) paper shows us how one can take a mass of genomic data and use it to elucidate how an organism adapts and evolves to their changing environments over time. This is certainly exciting given that none of this would have been possible just a few years ago. And it will certainly be exciting to see how the field of comparative genomics progresses into the future!

Andrew Rezansoff

Helminths for health

Isn’t it fascinating to know that worms which we fear of having in our body are protecting the body from several auto-immune diseases? Wow! This was truly sensational to me to know how parasitic helminth modulate the immune system of the host to render it immune against autoimmune diseases like irritable bowel disease (IBD), asthma and allergic conditions.

So how important are worms to human body? Taking the message from the helminthology course, my perception regarding the parasitic helminth has changed drastically. What I feel now is, “the balance” if there’s balance between the diverse fauna inside you, nature has made all the arrangements to protect you from anything. The immune reactions and disorders are the result of imbalance between natural and acquired forces. Worm therapy (helminth therapy) uses the helminth as treatment of some immunological diseases by infecting deliberately with a helminth or ova of the helminth.

Parasites and hygiene hypothesis

Parasites have as long history as do Homo sapiens, history of human parasitology clearly explains that Human evolution and parasitic infections have run hand in hand (Nature Publishing Co. 2001. The human genome. Nature 409 (Suppl.):813-958). Parasites have been a part of people’s life since eternity. They were made to coexist in human body along with other organisms. With the advancements in knowledge and societies being more affluent, people have made significant achievements in being “worm-free” in developed world but no-one can refute the bitter truth that, they have also encouraged the auto-immune diseases like Ulcerative colitis, Crohn’s disease (CD), asthma, rheumatic arthritis etc. over the years. Looking at the CD incidence and prevalence, it appears to be higher in urban areas among people experiencing higher socio-economic class. In several studies it was found that, CD incidence was <1 per 100,000 in Asia and South America. 1-3 per 100,000 in southern Europe, South Africa. 16 per 100,000 in New Zealand and Australia, 14 per 100,000 in Canada and 7 per 100,000 in USA. The data above clearly speaks the truth. Asia, which comprises most of underdeveloped and developing countries have lower CD prevalence. The increasing rate in Asia is mostly contributed by developed countries of Asia, especially East Asia like Japan, a socio-economically advanced country. These developed countries have eradicated several parasites due to the availability of efficacious drugs and proper hygiene standards. In developing countries, however, helminth infection is still a major problem. (Weinstock et. al., 2005). These epidemiological studies at the end of the day convey the same message – “the frequency of worm colonization and prevalence of IBD is inversely related”. This is a basis of now world-famous “hygiene hypothesis”, which was first used by David P Strachan in the British Medical Journal after he studied hay fever in British children (D. Strachan 1989) .Elliott et al. in 2000 described it again putting forward the hypothesis that the loss of exposure to parasitic worms increases the risk of IBD. (Elliott et al., 2000). The Hygiene Hypothesis was further refined into the “Old Friends” hypothesis, which suggests that the human immune system had evolved with certain organisms for so long that they had become mutualistically symbiotic. In other words, we had evolved around the presence of certain parasites and that their absence could result in “abnormal” conditions. This positive relationship has been referred to as the “Old Friends” theory by Dr. Graham Rook, MD, Emeritus Professor of Medical Microbiology at University College London.

Researches in worm therapy

This underlying idea gave scientists a unique opportunity to try and experiment the concept of “worm therapy” which in the beginning looked weird as there were several ethical and practical difficulties. One of the early studies in 1980s by Neil Lynch et. al., suggested the inverse relation between the worms and the emergence of asthma and allergy in varying economic background. His overall findings reflects that worm burden was less and allergies was high in affluent Venezuelan society. After that a series of studies are published most of which tell the same story. Joel Weinstock and his colleagues at the University of Iowa are considered as the integral developers of this epidemiology. He has been involved in several studies which mainly aims at identifying worms as treatment of autoimmune diseases. In an attempt to test the hypothesis, he has yielded promising results. Presently he has been trying to explore more on helminth therapy and its relation to inflammation and IBD. (http://sackler.tufts.edu/Faculty-and-Research/Faculty-Research-Pages/Joel-Weinstock). Success stories over the years have made this approach more interesting and intriguing. The 2005 experiment by Weinstock involving 29 participants with Crohn’s disease, 23 patients given with whipworm eggs every 3 weeks for 6 months improved significantly and 21 experienced remission. Another success story involved 52 patients with colitis given with 2500 whipworm eggs or placebo. 13 of 29 who received eggs improved compared to 4 of 23 who received placebo. These trails and success stories are often considered as experimental evidence of global pattern. It is really interesting to read how this worm therapy have been accepted by so many people across the global and actually doing good for them.(Eg. http://www.hookworm4crohns.blogspot.ca/, http://www.hookwormdiary.com/, http://parasites-film.com/main/helminthic-therapy/ ). Even more fascinating to read is this piece reporting how actually helminth therapy is changing lives of so many people (http://www.foodsmatter.com/natural_medicine_comp_therapies/helminthic_therapy/articles/ht_success_stories.pdf )

How does it work?

Helminth therapy is just a means of restoring the natural environment of our body. Like the use of probiotic and natural products like yoghurt which contain the useful micro flora, these therapies attempt to replenish the lost fauna which used to coexist in the gastrointestinal world balancing the system. Our body have evolved along with the parasites so it expects them to be present in symbiosis with it. Reintroduction of parasites, such as hookworm and whipworm, is a step in redressing the natural evolutionary balance of the immune system, giving the immune system an appropriate target to work against, thus halting the destructive actions of the immune system on its own tissues or benign substances such as pollen, cat dander etc.

To understand the theory behind this phenomena the immune response should be understood first. The figure below summarizes all the responses when a body finds a foreign thing including parasitic helminth.

http://livingwellnessblog.wordpress.com/2012/10/12/am-i-th1-or-th2-or-th17/

Immune regulation in host in response to foreign antigens.

The logic behind the helminth therapy has found to be 3 fold

Mode of action of helminth therapy

Mode of action of helminth therapy

 1. Immunomodulation by the parasite. Helminth infection is associated with a special type of immune regulation called Th2 response. This type of response produces antibody-mediated immunity which is protective against extracellular parasites, asthma and allergic conditions. The inflammatory processes, autoimmunity disorders like IBD is the result hyperactive Th1 response in the gut which in natural condition is balanced by counter regulatory mechanism of Th2.
Counter-regulatory mechanism of Th1 and Th2 response

Counter-regulatory mechanism of Th1 and Th2 response

2. Secondly, they have been found to be associated with changes that activate regulatory T cells. These cells dampen immune responses and curb autoimmunity by maintaining the immune homeostasis and preventing the body from over stimulation of immune response.

3. Also studies suggest that they have probiotic like action, which alter the bacterial composition of intestinal flora. Research in mice suggest that, they are advantageous to gut micro-organisms thereby maintaining intestinal health and protecting from inflammatory diseases of the gut (DM McKay 1999).

Challenges

In spite of having promising results in few clinical trials and opinions of experts, many experts are still against it. Dr. Peter Hotez who is working in George Washington University to develop a hookworm vaccine refutes the theory and is in against deliberate infection of helminth. He says this “makes absolutely no sense at all” and says that this is based on false reasoning.  He explains that hygiene hypothesis ignores the fact that high rates of helminthic infection is still prevalent in the US and this has nothing to do with the allergies. He also bolstered his argument saying that whipworm infection is actually the leading global cause of IBD and allergies have been linked to toxicara infestation in American cities. In contrast, Elliot completely supports the hygiene hypothesis giving the example of South Korea, where Crohn’s disease appeared in the scene immediately after the helminth eradication program.( http://scienceline.org/2010/12/hookworms-and-whipworms-our-immune-system%E2%80%99s-attachment-to-parasites/) Popular name in this field Joel Weinstock is dedicating his life in this field and believes that worm therapy has sound logic and carry a huge potential.

In summary, this interesting approach has several challenges before to be unanimously accepted as therapeutic agent. Not all the people are brave enough to eat live worms or products of it in the hope to cure the next. Pharmaceutical companies have a huge challenge in accepting this treatment regime and commercialize it. There are still a lot of biological complication which may perpetuate as a result of immune modulation by worms. Although seems straightforward in paper, modulating one type of immune cell may create serious imbalance in this complex human immune system. The USFDA defined hookworms as investigational new drugs which requires much more clinical trials and regulations to be accepted. No any agency has approved this method of treatment which makes validating worm therapy more challenging.

The process for drug acceptance may be “marching along,” but it needs to move in double time. Millions of people suffer from autoimmune and allergic diseases which cause immense human suffering. This method seems to carry a possibility to relieve people’s suffering so needs greater attention. However, more clinical trials, double blinded trails, safety and efficacy studies should be carried out to convince the public to by worms and treat themselves.

 

References

J. V. Weinstock, R. W. Summers, and D. E. Elliott, “Role of helminths in regulating mucosal inflammation,” Seminars in Immunopathology, vol. 27, no. 2, pp. 249–271, 2005.

Strachan, David. “Hay fever, hygiene, and household size.” British Medical Journal. 1989 Nov; 299 (6710):1259–60

D. E. Elliott, J. F. Urban Jr., C. K. Argo, and J. V. Weinstock, “Does the failure to acquire helminthic parasites predispose to Crohn’s disease?” The FASEB Journal, vol. 14, no. 12, pp. 1848– 1855, 2000.

McKay DM. Intestinal Inflammation and the gut microflora. Can J Gastroenterol 1999; 13: 509–16.)

Posted by: Pratap Kafle

The Dangers of Helminths with Concurrent Malaria

Often when we talk about a particular disease, we get caught up in the idea of that disease in isolation. We think only of just that disease, and not the real world implications of that disease. Unfortunately, the reality is that many people in developing nations are afflicted with many debilitating diseases, not just the disease in question. For example, individuals in Africa have a host of debilitating diseases to contend with, including helminth caused diseases, HIV, malaria, hepatitis, and typhoid fever ­­­­just to name a few. When an individual has concurrent disease (or more than one disease at a time), this can greatly influence the progression of all diseases in question.

In this past weeks’ discussion, we talked about how helminth infections can change or alter the disease progression of malaria. Given the pervasiveness of helminth infections in the developing world (the World Health Organization estimates that 2 billion people are infected with soil-transmitted helminths alone, worldwide), to gain an understanding of the actual disease progression of malaria, we must understand how helminths affect the immune system.

Previous research has shown Helminths play a very important role in modifying the immune system of the infected host. This is a defense mechanism to allow for the survival of the helminth while also prevent the hosts’ immune from going into ‘overdrive’. In a typical infection, the hosts’ immune system will mount a response to get rid of the invading virus, bacteria etc. This usually involves various amounts of localized inflammation, however, given the large size of helminthes, mounting a large immune response towards the helminth would result in a lot of damage to the host as well. As a result, host and helminth have co-evolved to produce an immune response that will keep the helminth in check, without harming the host too much. It is important to remember that helminths do not usually cause severe pathology, and therefore the host can ‘tolerate’ having a few helminths kicking around in its system. It is not worth the damage that would result from attacking the helminth head on.

Broadly speaking there are two major branches of the immune system, the innate and the adaptive immune system. The innate immune system can identify foreign pathogens, and usually eradicate the invader by releasing granules (small particles) that can break down the foreign particles. However, due to the size of these pathogens, a great deal of granules would need to be released in order to kill and break down the worm. While this is certainly possible to get rid of the worm, it would most likely kill the host in the process. Because the helminth must survive until it can reproduce (usually a couple weeks depending on the species) it is not in the helminths best interest to let the host die. Therefore it tries to evade and suppress this aspect of the immune system. Various helminths have a plethora of different tools in their arsenal, which inhibit the innate immune response. This leaves the adaptive immune system.

The adaptive immune system (also known as the acquired immune system) is responsible for a more direct attack of pathogens compared to the more generalized action of the innate immune system. There are two main types of immune cells in the adaptive immune system, B-cells which are responsible for the production of antibodies, and T-cells (Effector [CD8+] and helper [CD4+]) which are responsible for carrying out the adapted immune response. The antigens present on the outside of the worm can be recognized by the T-cells (CD4+) after being presented by dendritic cells, which influences the type of immune response that occurs from the adaptive immune system. The CD4+ T-cell will usually differentiate into either a Th1, Th2 or Treg cell. Each of these cells release molecules known as cytokines, which signal other cells to perform certain actions. The Th1 cell releases cytokines (IFNγ) which is usually associated with pathological inflammation. Th2 cells releases cytokines (IL-4, IL-13), which suppresses the inflammation of the Th1 response, but still has some inflammatory processes. In the case of helminths there will be enough localized inflammation and regulation to keep the helminths ‘in check’ and prevent them from causing too much damage damage. The Treg cells are responsible for winding down the immune response and stopping the Th1 and Th2 responses.

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Image courtesy of: http://www.nature.com/nri/journal/v7/n12/pdf/nri2199.pdf

In a typical helminth infection, Th1 immune responses will be down-regulated because this amount of inflammation is not good for either the host or the helminth (as mentioned previously). Helminths will secrete molecules that will drive the immune response towards a Th2 and Treg response to ‘tone down’ the immune system to reduce the amount of inflammation caused by the immune system. The exact mechanism of this has not yet been determined, but it is the focus of much research to identify these molecules and the hope is that they will be discovered soon.

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Image courtesy of: http://www.nature.com/nri/journal/v3/n9/full/nri1183.html

This is generally broad overview of the affect helminths have on the immune system, for a more comprehensive summary of these effects please see the two Nature reviews on this topic (Protective immune mechanisms in helminth infection, Diversity and dialogue in immunity to helminths)

So how does all this nonsense relate to malaria infections?

Researchers have shown the helminths heavily influence the immune system in this manner (skewing it towards a Th2/Treg response compared to a Th1 response), to the extent that it compromises the hosts immune response to other pathogens such as malaria. If we look at the lifecycle of malaria:

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Image courtesy of: http://www.cdc.gov/malaria/about/biology/

We can see that malaria goes through two stages in the host, one in the liver and one in the blood. Given the typical response to malaria (shown below), we can observe that the blood stages of the parasites will typically drive a Th1 mediated immune response in the host. Symptoms of acute malaria often include headache, fever, muscle pains, chills, sweating, nausea, vomiting and spleen enlargement. These are characteristic of an inflammatory Th1 immune response. These responses help control the replication and proliferation of the malaria parasite Plasmodium spp. in the blood. Without these control measures the malaria parasite can quickly replicate and infect numerous red blood cells leading to severe anemia and death.

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Image courtesy of: http://www.nature.com/nri/journal/v4/n3/fig_tab/nri1311_F3.html

We know that in sub-Saharan Africa the prevalence of helminth and malaria infections is very high. It is very likely that numerous individuals will be infected with both helminths and malaria concurrently. These concurrent infections will change the disease progression of both diseases but we will focus on how helminths change malaria infection for the time being.

5

Image courtesy of: http://www.ncbi.nlm.nih.gov/pubmed/16989681

As mentioned, helminths will drive a very strong Th2 and Treg response, and suppress the Th1 response that would be the typical response in a malaria infection. Researchers have noticed as a result that there is an increase of severe malaria cases in individuals who have concurrent helminth infections, most likely due to the inability for the host to properly regulate the malaria parasites through an inflammatory Th1 response.

This is very problematic and questions our current treatment strategies. For example, we may want to tailor malaria control by administering anthelmintics to those at risk for malaria to lessen the severity of the malaria infection.

However, the severity of malaria is not the only issue that needs to be considered, the ability to administer vaccines to control for certain diseases are also affected. While we do not currently have a vaccine for malaria, several are currently in development and undergoing field-testing. Research has shown that the helminths’ ability to skew the immune system to a Th2 mediated response, can alter the host’s response to vaccines by dampening other immunological responses. This may have complex consequences for any future malaria vaccines.

A set of researchers have shown that in mice deworming (removing helminths) prior to the administration of a malaria vaccine significantly increases the effectiveness of the vaccine when the mice are administered malaria. The most likely explanation is that the removal of the helminth, stops pushing a Th2 immune response, and allows to host to react efficiently to the administered vaccine. This has very real implications in how we should approach the management of both malaria and helminths in the field. If we are able to develop an effective malaria vaccine it is likely advisable to clear patients of helminths (even if there are no clinical helminth symptoms), so that they can properly respond to vaccination.

In previous weeks we have discussed the use of helminths as a means to dampen inflammatory responses to assist people with auto-immune diseases. While these applications may seem promising there are very real, and very significant drawbacks to presence of helminths in patients, and any use as possible therapeutics must be carefully evaluated.