Fun on the Farm: a day in the life of a farmer-turned scientist

We’re about half-way through week seven (yikes!) and the pressure is about to set in for the Sibu Six.  There’s been talk of wrapping up sample collection soon, and it’s crazy to think things are moving this fast!  So, what have we been doing these past 6+ weeks you ask?  Jane, Hudson, and Sarah have been working with medical officers in the hospital to enroll patients.  Kerry and Rick have become regulars at the local markets on their daily strolls with the bioaersol samplers.  And of course, we’ve all been putting in lots of lab time doing DNA/RNA extractions and RT-PCR.  On top of all of that, we’ve been hitting the field, and by that I mean the pig farm! 

Sarah and I collecting samples from the pigs.  Photo credit: Jim Rogalski

Two of our three major studies are using samples collected from pigs.  The study Kerry, Rick, and I are working on involves collecting oral secretions and fecal samples from the pigs, bioaersol samples, and nasal wash samples from the workers (explanations to come, don’t worry!).  Our main objective is to see if viruses infecting the pigs are being aerosolized and hanging out in the noses of the workers.  Sarah is also using the pig fecal samples to see if the same diarrheal virus she’s looking for in humans (norovirus) is infecting pigs as well.  Isn’t research glamorous!

To describe a typical farm visit would be nearly impossible (though I’m going to try) as every farm has many quirks and kinks of their own.  We’ve seen your standard farms with pens of big pink sows munching on corn meal, and we’ve also seen your glorified mud pits with “local pigs,” or as they’re known in Malaysia, babi kampung. 

Mix of babi kampung and traditional domestic pigs enjoying what can only be described as pig heaven.

Our first farm visit was a mild train wreck.  We were overly prepared in some respects, but essentially unaware of what to expect in others.  After nine visits (and counting), we’ve got somewhat of a routine down.  After we’ve confirmed consent with the farm owner, Sarah and I head off to collect the pig samples while our local collaborators start enrolling workers, and Kerry and Rick find the perfect spot to setup the bioaerosol sampler. 

Piggo enjoying rope.  10/10 would recommend

The oral secretion collection is dependent on pigs chewing on a piece of cotton rope, and while some pigs LOVE the new toy, others just won’t bite (mainly the babi kampung, we’ve noticed.)  The fecal specimens are collected by “convenience sampling,” but it’s not always convenient for us to reach and sometimes the pigs get a bit too nosey when we’re swabbing.  After we’ve collected five of each sample type, we rejoin the rest of the group and help with human nasal washes.

To answer what I’m sure is just one of many questions at this point, a nasal wash is a simple application of water into one nostril that the participant then expresses into a sample collection cup.  A wash, in this scenario, provides a more comprehensive sample than a simple swab by getting into more of the nose’s nooks and crannies- again, glamourous stuff.  Once we’re done, we bleach down and head back to the lab to process samples.  The viruses we’re looking for are currently only known to infect pigs, but we’re looking to see if humans are at any risk of inhaling aerosolized virus.  This study alone won’t prove infection, but it’s a pilot for future, more comprehensive studies.

Needless to say, it’s been a spectacular, albeit smelly summer.  We’re still loving Sarawak and all the adventures (and food) it has to offer.  

Now, it’s time to hit the lab, and soak up what we can from our last three and a half weeks in Sarawak (the Borneo Cultural Festival begins in a few days and we’re very excited!).  The Sibu Six are sure to make some exciting findings, so stay tuned for crunch-time updates!

Barriers, Boxes, and Borneo Adventures

We’ve been here in Malaysia for almost a month, and time is flying. Research was slow to start as we were developing protocols and reaching out to our field collaborators about sample collection. But now, it seems I blink and 6 new things have happened. Sometimes these are good, other times they are pretty big road blocks we have to find a way around. More times than not, I feel we take 2 steps forward and one step back.

One of our biggest challenges starting here was our lab space. Over the summer we have plans to collect hundreds of samples from local markets, hospitals, and pig farms. Then, we have to extract the genetic material from any viruses present in the samples and run PCR to see if one of our 19 target viruses are present. Needless to say, there is a lot of lab work to do, but we didn't get our own lab space until our 3rd week here. Drs. Toh and Lim were tirelessly working with contractors to get the lab finished, but our short timeline this summer made any delays that much more stressful. Thankfully we're now fully moved into a wonderful lab space (I think we have more room than at Duke!). It's really exciting to get a lab up and running not only for our summer research, but also for (hopefully) future international research collaborations.

Before and after pictures of the Clinical Research Center lab at SEGi University where we are working for the summer.

One barrier we've started to face recently isn't necessarily bad, but can lead to some logistical nightmares without careful planning: we all need access to a biosafety cabinet before we can do any analysis on our samples. Sometimes, we realize too late that we have all planned on using the cabinet at the same time. We learned pretty quickly that we needed to spend more time talking about our daily lab plans to avoid any unnecessary stress during the day. Unfortunately, some of our barriers have posed a greater problem than too many people trying to work at once. I'm going to start by quoting well known fictional character Neville Longbottom:

"The only problem is I can't remember what I've forgotten"

Sometimes, you don't even remember you've forgotten something. Despite all of our careful planning, a few key supplies fell through the cracks and we left them at Duke. Just like Neville, we couldn't remember what we've forgotten until its too late and we needed to use whatever it is we forgot. Luckily, because we have an incredible support system with our collaborators here in Malaysia and the rest of the lab group back at Duke, the supply issues were quickly solved and we've been able to push forward on sample collection.

One of the more surprising obstacles we've faced happened on our first visit to a pig farm. Before entering the barn to start sample collection, Laura, Rick, Kerry, and I were asked in what year we were born. The farm owner was interested in learning our Chinese Zodiac sign to make sure they weren't threatening to the pregnant sows and the piglets. Rick, born in the year of the tiger, was seen to be too threatening and wasn't allowed in the barn. Fortunately, this gave him the chance to collect nasal washes from the farm owners while Laura and I walked ankle deep in mud to collect samples from the pigs.

Left: Laura "suiting up" before entering the pig enclosure

Right: Me (Sarah) collecting pig stool sample

Despite all of these potential issues, our team has found ways to enjoy ourselves and destress after long days in the hospital. We had the chance to celebrate Hari Raya with Dr. Toh and his family by visiting the homes of Muslims throughout Sibu. We had so much great food, and one thing we really loved were the many varieties of layer cakes found only in Sarawak that are served for holidays and special events.

Left: Us in the home of one of the hospital nurses celebrating Hari Raya at her family's open house

Right: Image of typical Sarawak layer cakes, kek lapis, served for holidays and special occasions

We also managed to find an "escape room" here in Sibu. For those of you who don't know, you pay a company to get locked in a room and then have to solve puzzles in under an hour to find your way out. Unfortunately, we didn't make the time cut (we got out in 61 minutes), and I still think the language barrier had something to do with our ultimate demise. They have 3 other rooms and we definitely plan on going back to redeem ourselves!

Jane, Rick, and Sarah with Jane's friend from home, Gabe (the pirate), and her boyfriend, Bubby (clown wig).

Needless to say, we're really enjoying both our research and our free time here. We've been able to overcome hurdles through teamwork and creative thinking. I'm thankful for the research team, both here in Malaysia and at Duke. Together I know we're going to accomplish some really cool stuff this summer.