Tuesday, July 18, 2017

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!

Sunday, July 2, 2017

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

Tuesday, June 27, 2017

Our First Sample Collection Experience

Today marks our three week anniversary of landing in Sibu, and Iooking back, I am in awe of all we have accomplished and experienced. This past week, members of the Swine Study (Laura, Kerry and I) started collection of bioaersol samples after facing some unexpected hurdles. 

For those of you who don’t know what I’m doing this summer, I’ll give you a bit of a cliffnotes. Laura, Kerry and I will be working closely to find out if a host of viruses are present in the air. Kerry and I will be focusing on the collection of bioaerosol samples using a pump in a backpack, and Laura will be focussing on the collection of nasal washes as well as bioaersol samples using a pump on a tripod. 
(Photo of chickens in newspapers being sold. Photo, Kerry Mallinson.) 

(Photo of the Swine Study Members at Sibu Jaya. Photo, Greg Gray.)
So, this Wednesday, our small team visited Sibu Central Market, one our collection sites. This open air market is often boasted as the largest in Malaysia; however, I’m sure most of the Sibu Six would rather attach the superlative “best bagels” to the market instead. In fact, our very own native New Yorker, Kerry Mallinson, seems to be more excited about this find than the Rainbow Bagel trend that has been making its way onto every Instagram feed. This infatuation has set Mallinson on a wild goose chase in search of cream cheese as a pair to her newfound love.

(Photo of Sibu Central. Photo, Rick Tsao.)

(Back to business…) To use the samplers that we had brought to the field, it is necessary to calibrate pump and do some other setup work at the site. This meant that we had to pull out our pump, adorned with a huge timer display and some flashing green and red lights, to mess around for a few minutes. Surely, you readers know how this would look. Well, so did we. Thankfully, we were able to discretely run through the set up with no conflicts, and we’re still allowed back to the place with the nice bagels. 

(Photo of me at Sibu Jaya. Photo, Kerry Mallinson.)
In the market, we had a set amount of time that we intended to walk around and collect air. And while the suspicious looking pump with the lights was discreetly placed in a sound muffling briefcase and then stuffed into a normal-looking backpack, there was still a plastic tube that popped out of the bag and connected to a metal device on one of the shoulder straps. In other words, I still looked incredibly suspicious (see below). However, we were only approached once, and that situation resolved itself pretty fast when we explained that we were conducting research. We did notice that some were some side-eyed glances, but it was, overall, a successful trip.

We had arrived at the market around 11:30, in the middle of the day. Nearly every stand was open, and the market was simply bustling. The market serves the local population, selling seafood, produce and other household essentials everyday of the week. In addition, butchers come every Thursday through Sunday. During the sampling, we got the opportunity to browse the oddities offered by the market. We saw everything from sharks to snake-skinned fruits, called Salak. Exotic fruits such as waxed apples and guavas are also sold here. This is certainly a must for any travelers passing by and wishing to sample Sarawakian culture. 

Monday, June 19, 2017

First Trip to Kapit

On Thursday morning at 5:45, our little group gathered at the Sibu ferry. Five of the Sibu-Six and two of our Malaysian colleagues had met together that morning to travel to Kapit, a little town about three-hours boat ride from Sibu City. Our mission was two-fold. First, we wanted to meet Dr. Hii and the medical officers working under her guidance at Kapit hospital, and train them on how to enroll patients and collect samples for the pneumonia-based portion of our study. Secondly, we wanted to visit local wet-market to see what kinds of meat are sold there, and begin drafting plans for how to collect samples during future trips.

To our pleasant surprise, we discovered that the boat to Kapit was comfortable and fast. In fact, the air conditioner in our cabin area was so powerful that it created artic-like conditions which forced the team to don jackets and long sleeves...in 100% humidity! It seems we hardly noticed, as we were all soon fast asleep, and shortly there after had safely arrived at the wharf in Kapit.
(The boat we took from Sibu to Kapit. Photo, Hudson Berkhouse.)

(Walking up to landing in Kapit. Photo, Hudson Berkhouse.)

After disembarking, Mr. Chong, one of our Malaysian colleagues from the Sibu divisional health office, quickly guided us to a small café for our choice of iced tea or coffee with condensed milk and batter-fried plantains. As we enjoyed our breakfast we looked around and familiarized ourselves with Kapit. This was made easier by the fact that Kapit constitutes one main road leading to the town-square and wet-market, intersected by only a few smaller streets. Across from our café we could see our hotel. Ironically named Greenland Inn, the hotel we stayed at sits squarely atop Sugar Bun, one of only two fast-food restaurants in town. I can personally confirm that their fried chicken is "finger-lickin good", but cannot as of yet attest to the local quality of their internationally famous competitors just down the road. I can only say that it was a little surreal to see The Colonial grinning down at me with the Sarawak jungle as a backdrop.

(Breakfast right after we arrived. Photo, Hudson Berkhouse.)

(The Sugar Bun below our hotel. Photo, Hudson Berkhouse.)

After breakfast, Mr. Chong arranged a truck to drive us to Kapit hospital, only five-minutes walk away from our hotel. The staff had readied a conference room, complete with bottled water and assorted buns and Korean-style-rolls, for which Kapit is famous. Dr. Hii along with the medical officers and lab technicians in attendance listened attentively to our presentations and asked insightful questions. We were so encouraged to see how invested they all were in collaborating on our projects.

After the initial presentations, the pneumonia group stayed behind to go through an enrollment with the medical officers while the bio-aerosol group went with Mr. Chong to see the local-wet market. One medical officer took the lead during the enrollment process and demonstrated for her co-workers how to take a nasal swab. The only difficulty we encountered was that the formal-style Malay language used in our enrollment forms is not widely used in Kapit. However, the medical officers again showed their professionalism by adapting our questions into the locally spoken language.

(Antoinette, a lab technicians at Kapit hospital, working with us to process a blood sample. Photo, Hudson Berkhouse.)

That afternoon, we explored Kapit with our other Malaysian colleague, Kamila from Sibu hospital. She introduced us to some local snacks, including ABC, a smoothie like drink, and half-moon cake, a thick, fluffy pastry with peanut butter in the middle. Exhausted from an early morning and full of local snacks, we returned to the hotel for some well-needed rest.

In Kapit, almost everything closes when the sun sets around 5:00 or 6:00pm. However, just across from town square there is an elevated alley of sorts on which are two rows of food vendors, with tables and chairs arranged under tarps. The sunset is just the start of the relaxed night-life in this area. To us it seemed like the entire town closed shop and walked to this area to enjoy a leisurely dinner with their families and friends. There we were able to sample food from different vendors, pointing out to them where we were seated. We chatted there for quite a while, between bites of roti-chani and sips of milk tea.

(The evening food court in Kapit. Photo, Hudson Berkhouse.)

The next morning was rushed as half of us went back to the market while the other half returned to Kapit hospital to work with the lab technicians to process a blood sample collected in the early hours. We met back for an early lunch with Dr. Cheesan Lee who had just arrived from Sibu with two of his colleagues. He treated us to a delicious meal of wild boar and local-style noodles before we had to had to leave for the ferry.

(Lunch with Dr. Lee, middle right. Photo, Waitress at the restaurant.)

On the boat ride home we all remarked how much we enjoyed the relaxed pace of live in Kapit. Our experience there was wonderful, and we all very much look forward to the next time our schedules give us occasion to return. To all our new friends there, we look forward to seeing y'all again soon.

(The Sibu Six, minus Sara and plus Kamila, on the boat back to Sibu. Photo, Hudson Berkhouse.)

Thursday, June 8, 2017

First 100 Hours: A Sibu Welcome

Its been a whirlwind first few days here in Sibu, the rest of the team arrived late Monday night and I landed early Tuesday morning. Since then, we have been shown where we'll be working this summer and introduced to the people with whom we'll be working.

I left from the airport Tuesday in a cab arranged by our on-site collaborator, Dr. Toh, and was taken to the hospital to start our long orientation day. We were briefed on the hospital guidelines for being in the wards and working here and introduced to various hospital officials. Importantly, we were shown the temporary lab spaces at the hospital we can use while the Clinical Research Center's (CRC's) more permanent space is finished. On Wednesday and Thursday we met with collaborators to discuss the logistics of executing our various summer projects. Needless to say, we are all very excited about getting started on sample collection and analysis!

Among the many impressions that I've had since arriving, the one that stands out to me most is the absolute hospitality we've been shown by everyone here. Our direct supervisor, Dr. Lim, has been incredibly helpful with introducing us to local foods at the hospital canteen. Our favorite was a dish called Laksa which is a spicy soup with rice noodles and protein. He's also taught us the Malay words for common foods. Most importantly, I've already learned how to order black iced coffee in Malay (those of you that know me understand how necessary this is). Dr. Lim has also answered any and all of our questions about local customs and ways we should interact with people in the hospital.

Tea drink (Tae ci beng) served at the hospital canteen, photo credit: Hudson Berkhouse

Tuesday night, Dr. Toh graciously invited us to his home for dinner where we were treated to delicious food and a dish found only in Sarawak: Midin. Midin is stir-fried ferns and is absolutely delicious. Thursday night, we were introduced to local Chinese cuisine and the night market in Sibu by our Airbnb hosts and their family. They have also offered to show us around Sibu and to answer any of our questions about local culture and things to do. Hudson also got the chance to practice his Chinese with their two young daughters!

Dinner on Tuesday, June 6 at Dr. Teck-Hock Toh's home; left to right: Hudson, Laura, Jane, Kerry, Rick, Dr. Lim, Sarah, Dr. Toh; photo credit: Hudson Berkhouse

It is apparent to me that everyone here wants us to feel at home, and it is definitely working. Everyone has been so kind and helpful. Words cannot express how thankful we all are to be in a place with people who are so gracious and welcoming. It seems that the people we have interacted with are just as excited as we are for us to spend our summer in Sibu. I can't wait to get to know them all better and work with them on our projects. 

Saturday, June 3, 2017

Sibu Six: The Journey Begins

It’s been a long time coming with our preparation for fieldwork in Sibu.  You could say we’ve generally been getting ready since August, and more directly since December.  From then, our questions and concerns have steadily shifted from research to travel and back.  First it was a general question: What are we going to study?  We’ve all identified some interesting One Health oriented viral surveillance projects, and spent months creating study documents, seeking ethical approval, verifying laboratory assays, creating supply lists, and much much more, with lots of help from the Duke Global Health Institute and Duke One Health teams (thanks guys!).  

As we’ve crossed those items off of the list, we bought our plane tickets and started getting ready for travel.  So many questions and discussions have happened in that time.  Where will we stay?  How will we get around?  What clothing should we wear?  What vaccinations do we need?

With 2 weeks to go, all six of us (Hudson, Jane, Kerry, Laura, Rick, and Sarah) met in person for the first time; we've even dubbed ourselves the Sibu Six (t-shirts pending 😉).  Just to briefly introduce the team:

  • Hudson is from Midland, TX.  He's a MScGH candidate at Duke Kunshan University.  He did his undergraduate at Texas A&M, and studied wildlife and fishery sciences (as he calls it, WiFiSci... it'll catch on eventually).
  • Jane is from Washington D.C.  She's a MScGH candidate at Duke.  Prior to to her time at Duke she studied cultural anthropology and French at Hamilton College, and was a Peace Corps volunteer in Benin.
  • Kerry is from Pelham, NY.  She's joining us through Bass Connections.  She's a rising junior at Duke studying biology and global health. 
  • Laura is from Truman, MN.  She's a MScGH candidate at Duke.  She studied biology and anthropology at the University of Minnesota, Morris.
  • Rick is from Milpitas, CA.  He's also joining us through Bass Connections.  He's a rising sophomore at Duke studying chemistry and global health (provided we can convince him to join the ranks).
  • Sarah is from Northville, MI.  She's also a MScGH candidate at Duke.  She studied biology with a minor in theology at Notre Dame.

Photo Credit: Ben Anderson (aka the team dad)
Sibu Six, left-to-right: Rick, Kerry, Sarah, Hudson, Laura, and Jane
As you can see, we’ve packed up 5 HUGE duffel bags full of laboratory supplies (along with our own personal effects), and today we're setting off for Sibu!

We're all very excited to have made it through baggage check and security.  Soon we'll reach our first stop: London!  We've got a long layover during the day, so we're anxious to explore the city for a bit before we get back on that flying Pringle's can to Malaysia.

That's all for now.  Stay tuned for an abundance of adventures to come!