Following the people and events that make up the research community at Duke

Author: Thabit Pulak

Growing “Mini Brains” To Understand Zika’s Effects

You probably remember what the Zika virus is because of the outbreak in 2015 that made global headlines.

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An infant with microcephaly (left) with a reduced head circumference, as compared to an infant born with a regular head circumference (right) Picture credit: https://commons.wikimedia.org/w/index.php?curid=63278345

The serious nature of the virus was apparent when hundreds of infants across South America were born with microcephaly – a condition characterized by a very small head circumference as a result of abnormally slow brain growth.

The sudden outbreak of Zika in South America led to a panic of the possibility of spread into the United States as well as beyond – and thus, research into learning more about the disease mechanisms of Zika expanded. However, one of the problems in studying a disease like Zika is the difficulty of modeling a complex organ like the developing brain.

Until now, the current way to model the brain was with a brain organoid – a brain grown in a lab. Organoid structures attempt to mimic whole developing organs – however, current brain organoid technology required the use of a large spinning bioreactor to facilitate nutrient and oxygen absorption to mimic the function of the vascular system in our brains. Large spinning bioreactors are expensive to run and bulky—they require large volumes of expensive media that mimic brain fluid. The size and cost has meant that only a few organoids can be grown and studied at once.

Guo-li Ming, University of Pennsylvania

Dr. Guo-li Ming, a professor of neuroscience from the Perelman School of Medicine at the University of Pennsylvania, set out to work on finding a way to solve this problem. She came down to Duke University last week to give a talk on her findings.  As she spoke, I could feel the minds of the audience firmly captivated by her words. It was truly fascinating stuff – Ming was actually growing brains in the lab!

The work began by finding a way to take the large spinning reactor that the existing brain organoid required and make it smaller. Three clever high school students working in her lab used a 3D printer and a small motor that involved spinning 12 tiny interconnected paddles within 12 small cell culture wells. Each of the wells contain a paddle that is spun by one gear.  All of the individual gears connect to a continually rotating central gear driven by a motor.

Bioreactor schematic

The Spin bioreactor. Source: http://www.cell.com/cell/abstract/S0092-8674(16)30467-6

After many optimizations, the final design was called SpinW,  which ultimately required a mere 2 ml of media per well, resulting in a net 50-fold reduction in media consumption, as well as dramatically reduced incubator space. The large number of wells, combined with dramatically reduced cost of the apparatus and media consumption, allowed for optimal conditions to run multiple test scenarios with ease – essentially meaning that 12 “mini brains” could be tested at the same time.

The design of SpinW costed a mere $400, while the commercial design costs over $2,000, with the added burden of consuming 50 times more media. The success of the design only serves to prove that age doesn’t matter when it comes to great ideas!

A brain organoid infected with Zika virus. ZIKV envelope protein is shown in green; neural progenitor cells marked by SOX2 are shown in red; neurons marked by CTIP2 are shown in blue.
CREDIT: Xuyu Qian/Johns Hopkins University

Dr. Ming and her team used the apparatus to model the Zika virus’s impact on the brain.

The findings indicate that Zika works by killing off neural stem cells, as well as causing a thinning of key brain structures. One of the observations was that, by day 18 of Zika infection of a brain organoid, there was an overall decrease in size, which points to the link of Zika causing microcephaly. The Zika infection of early-stage organoids corresponded to the first trimester of human fetal development.

The brain is the most complex organ in the body, and one of the least understood. The work Dr. Ming and her team has done goes a long way towards helping us understand the way the human brain develops and works, as well modeling its reaction to things like viruses. It was a pleasure and honor to hear Dr. Ming talk to us about her work –I am eager to hear about further developments in this field!

Post by Thabit Pulak

The dangerous persistence of smoking into the 21st century

The "smoking ring" cigarette billboard advertisement in New York City. Picture Credit: theoldmotor.com

The “smoking ring” cigarette billboard advertisement in New York City. Picture Credit: theoldmotor.com

When Harvard historian of science Allan Brandt was a child, he couldn’t help but notice one thing in particular when in the car with his family — the cigarette advertising billboards. At the time, there was a very unique billboard that advertised Camel cigarettes, which actually smoked “rings” from the board. His young mind was captivated by how cool the board looked — and presumably, unaware of the dangers of the product the board was advertising.

As time passed, it became increasingly clear to Brandt and to the American public that smoking cigarettes was bad for you. Brandt’s most recent book – The Cigarette Century, was awarded the Bancroft Prize in 2008. In Brandt’s words, cigarettes are the “most dangerous product ever produced in such large quantities.” And indeed, the numbers are shocking — over 480,000 Americans die annually of tobacco-related diseases.

Given such obvious problems associated with cigarettes, Brandt started wondering, “How could something so bad for you be so advertised in such bold ways?”

2015BoyarskyflierREVThe answer, Brandt explained to a Duke audience gathered on Nov. 11 for the 2015 Boyarsky Lecture in Law, Medicine and Ethics, was manipulation — the American public was being grossly manipulated by the bold advertising of cigarettes. Brandt talked about Mr. Edward Bernays, who, according to Brandt, is one of the main founders of the concept of modern public relations, made extensive efforts to put smoking into the mainstream media. One of Bernays’ biggest achievements was the widespread introduction of smoking to Hollywood. The efforts to introduce smoking to mainstream media worked amazingly well. By the mid-1950s, nearly half of all Americans were smoking. To put this into perspective, at the turn of the 20th century, nearly no Americans were smoking!

However, as more and more research proved that cigarettes were actually harmful to Americans’ health, another curious phenomenon happened, where cigarette companies were actually funding their own research.

Brandt pointed out how this was a thinly disguised attempt to publish misleading conclusions about cigarettes to the public by establishing it as “science.” Such biased research funding occurs today in other industries as well, such as for oil companies, for research concerning climate change.

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Children smoking in various developing countries is not uncommon, and poses a huge health risk to them. Picture Credit: CBSNews

However, public health campaigns still showed measurable positive impact — today it is evident that there is a declining trend in the number of smokers in America. However, wouldn’t that mean that the cigarette industry would die down? According to Brandt, it couldn’t be farther from the truth. The cigarette industries have now moved to exporting cigarettes to the developing world, where populations are less educated, and there are fewer regulations concerning such sales.

According to Brandt, in 2000, four million people died — two million died in the developed world, and two million in the developing world. By the year 2030, over 10 million people total will be killed by cigarette use — three million in developed nations, and seven million in developing nations. The rapid proliferation in such developing countries due to lack of education and awareness is heavily evident, especially with the much higher rate of childhood smoking. It is heavily evident that most of the disease fatalities will be borne by developing nations in the coming years, and will ensure copious profits for cigarette companies for years to come.

While Brandt did acknowledge the very persistent growth of the cigarette companies in the near future, he did not rule out that it was still possible to fight against this. By working together, we can all help bring awareness to the parts of the world where cigarettes are being advertised to uneducated people.

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Thabit_Pulak_100Post by Thabit Pulak, Duke 2018

 

The Realities of Dealing with Ebola and Field Research

(EDITOR’S NOTE — The original version of this post rendered Dr. James Russell’s name incorrectly throughout as Dr. Hill. Duke Research Blog apologizes for the error, which has been corrected.)

We’ve all heard about the recent outbreak of Ebola affecting various countries in West Africa. Being in the United States, problems like these often seem “too far away.” And after the initial media craze, Ebola has largely been absent from headlines recently.

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Dr. Nathan Thielman (on right), the director of the Global Health Residency/Fellowship pathway program, gives Dr. James Russell a token of appreciation after his talk, on behalf of the Duke Global Health Institute.

However, there is still a large amount of work going on behind the scenes by doctors and scientists in Africa, where there is a massive effort not only to help improve public health facilities, but also a push in research to help with treating Ebola and other diseases affecting the region. The Duke Global Health Institute recently brought in Dr. James Russell from Sierra Leone to tell us about the Ebola crisis affecting West Africa.

Russell has been involved with the Ebola crisis in Sierra Leone since its start and has worked on helping patients affected by the virus, and spearheading research efforts in the region to trace sources of Ebola and identify potentially new treatments.

He said the fundamental tool, alongside infrastructure improvement, was improved clinical research. Clinical trials for treatment of Ebola have begun. Russell is also trying to answer certain questions concerning the circumstances of Ebola emergence, such as where another possible outbreak could happen so the response would be quicker and streamlined. “We know it will happen (Ebola)…but when and where?” Russell said. However, doing clinical research in the field is much more different than doing it in a controlled setting like a university laboratory. Russell talked to us about the difficulties of conducting clinical research in Sierra Leone.

Sierra Leone is a small coastal country located in Western Africa.

Sierra Leone is a small coastal country located in Western Africa.

Such problems include community dependency, which was the tendency for communities to rely on the research institute for their health care needs. The members of a community eventually see the research institute as another donor agency.

Another somewhat indirect problem is that of brain drain: Private research institutes come into communities and offer research assistant jobs to carry out trials which are often higher paying that comparable government-sponsored agencies in Africa. This ultimately takes away workers from those government agencies.

Even something as simple as a consent form turns out to be a problem when conducting field research in an impoverished region, Russell said. Illiteracy is a significant challenge, making it more difficult to get across the message typically contained in very long consent forms.

And finally, dealing with a community also means striking a careful balance between respecting the cultural beliefs of the regions, and executing the goals of the research. Russell said that in certain communities he worked with in Sierra Leone, blood was considered “sacred,” and thus people within those communities were very resistant to the idea of having blood samples taken from them.

As an undergraduate student at Duke, I’ve been exposed to research in the confines of labs within campus. Now I’ve learned from Dr. Russell’s talk that this is nowhere like working in the field, where one can’t control for all the potential factors that can affect results. Fortunately, Duke offers ample opportunity for students to have a chance to get field exposure in addition to their “in-campus” exposure to research problems, through initiatives like the Student Research Training Program, sponsored by the Duke Global Health Institute (who also hosted this talk).

At the time Russell gave this talk (October 29th), Sierra Leone wasn’t considered Ebola-free. Thanks to the efforts of people like Russell, as of November 7th, the World Health Organization declares Sierra Leone as being officially Ebola-free.

Thabit_Pulak_100Post by Thabit Pulak

 

A fireside chat with Marc Jeuland

Living in Few dorm has its perks, aside from being right beside the bus stop. My faculty-in-residence, Dr. Hwansoo Kim had kindly hosted a reception in his residence, where he invited Dr. Marc Jeuland for a talk about the development of water infrastructure to help improve health. A Chat with Dr. Jeuland
I was immediately captivated when I saw the email invite – as I personally had worked with affordable water filtration, in the developing world, so this was right in my field of interest.

Jeuland is an assistant professor in the Sanford School of Public Policy and the Duke Global Health Institute. He shared his experience working on one of his most recent, major projects, which was of his water infrastructure improvements in Zarqa, Jordan. For a long time, Jordan has been experiencing a water crisis. For the residents of Zarqa, water often has to be purchased from other areas, and then carefully preserved for days, or weeks, and even up to a month. The piped water infrastructure that currently existed in Zarqa was very inefficient, and was a major source of the shortages.

Jeuland, who is an environmental engineer, said that as much as 70 percent of this water can be lost from pipelines as the water reaches the citizens of Zarqa. Jeuland worked to assess inefficiencies within the current water supply systems and tried to design and implement improvements to remedy the faults.

marc-jeuland-headshot

Marc Jeuland is an assisstant professor of global health and public policy

Aside from his work in Zarqa, Jeuland has been involved with countless other projects and studies that have ultimately benefited underserved communities around the world. He has characterized the effects of contaminated groundwater on inhabitants in Rift Valley, Ethiopia and done a detailed analysis of the correlation between water quality and kidney disease in Sri Lanka.

Jeuland’s work shows the real-world applicability of interdisciplinary fields. His work has encompassed the field of not only environmental science, but also behavioral science, economics, and engineering.

For those of you interested in learning more about the interdisciplinary fields of global health and environmental sciences/policy, it would definitely be a great idea to take a look at the classes Jeuland teaches, which include “ENVIRON 538: Global Environmental Health: Economics and Policy” and “GLHLTH 531: Cost Benefit analysis for Health and Environmental Policy”.

It was an honor to get to meet Professor Jeuland. I could tell he was a very busy man. By the time you read this, he is probably off traveling somewhere else in the world, working to improve more lives.

Thabit_Pulak_100By Thabit Pulak, Class of 2018

 

 

Not Sure What To Do This Summer?

200+ clamor for info about summer research opportunities

By: Thabit Pulak

Dr. Grunwald discussing research opportunities at the Summer Research Programs event

Dr. Grunwald discussing research opportunities at the Summer Research Programs event

“What are you doing this summer?”

Whether it is coming from a concerned parent, or just a friend, this is a question that makes most of us anxious. What can I do this summer? Well, you can kick off your sandals and relax by the seashore. Or you can take a road trip across the country with your friends. Or go backpacking in Europe. Or sleep for 10 hours a day, and watch some extra… Oh, did you have something else in mind? I suppose there’s always some exciting summer research opportunities 🙂

When an info session titled “Summer Research Opportunities” popped up in one of my emails. I thought it would be pretty interesting, so I decided to attend. As I made my way to Perkins 217, I saw a flood of people  trying to enter at the same time as myself. The room had capacity to seat at least 200 people, and not only was it filled, but some people had to sit on the floor. This must have some pretty exclusive stuff, I thought. It was like Black Friday, except it was for people trying to get to a stack of handouts near the entrance of the room, which had a list of the summer opportunities (if you weren’t there never fear, here is a link!)

The event was lead by Dr. Ron Grunwald, who directs the Undergraduate Research Support Office. He started by pointing out Duke’s undergraduate research website, highlighting a few of the countless opportunities available to Duke undergrads for research.

I have listed a handful of them below with a brief description:

These programs are just a few of the opportunities that are available. Good luck in your summer research hunt!

 

 

How To Get Your Foot In The Door At A Research Lab

By: Thabit Pulak

So now you are at Duke — one of the world’s best research universities — but now what? You might be taking cool classes, but how can you take advantage of the world-class research happening here? Roughly 50 percent of Duke undergrads do so at some point. Getting involved in research as a freshman might sound intimidating (I know it did to me!), but a little luck and perseverance can get you off to a strong start.

Alan working in Dr. Eroglu's laboratory.

Alan working in Dr. Eroglu’s laboratory.

I had the opportunity to talk with Duke freshman Alan Kong about his experiences trying to get into research labs, and how he successfully ended up finding one to join. Alan is considering majoring in biology whilst on the premed track.

He initially started to look into labs within a month of  starting classes at Duke. He spent about two months sending out emails to professors who were working on interesting projects.

“It was a very frustrating search, and initially difficult. I emailed five professors, and emailed each many times,” Alan said. “But perseverance ultimately paid off.”

Alan now works in the lab of Dr. Eroglu who is an assistant professor of cell biology, associated with the Duke School of Medicine. According to the Duke Institute of Brain Science website description, Eroglu’s laboratory “is interested in understanding how central nervous system (CNS) synapses are formed.”

Alan was also accepted into two others labs, but ultimately felt Dr. Eroglu was the best fit. “I picked Eroglu because her research was very interesting, and relevant to my interests,” Alan says. “I felt I could learn more interesting techniques in research, such as working with live animals.”

Now, Alan has been working in Dr. Eroglu’s lab for a month. When I asked him how it was going, with a smile he exclaimed, “It’s great!”

“Right now I am learning techniques such as genotyping, western blot. I even took out the retina of a rat!” Alan said. “I am learning the ropes of the lab, and my mentor said that down the road, if I learn properly, I can eventually work on my own independent project!”

When asked for any advice for other students thinking of getting into research, Alan said “Persistence is key — don’t give up! It’s a difficult process; don’t let small things get in the way. Keep trying until you find one.”

Alan

“Persistence is key – don’t give up!” Alan says

Learn more:

More information regarding Dr. Eroglu and her research: http://www.dibs.duke.edu/research/profiles/46-agla-eroglu

List of all Duke Faculty affiliated with Cell Biology with contact details: http://www.cellbio.duke.edu/all-faculty/

Summer research opportunities in math and statistics: http://bigdata.duke.edu/research/?field_project_topics_tid=19

Research opportunities in biology: http://cubr.biology.duke.edu/projects

For other research and summer opportunities visit https://biology.duke.edu/undergraduate/current-students/research-independent-study/summer-opportunities

For a list of research opportunities across the sciences, arts, humanities and social sciences visit: http://undergraduateresearch.duke.edu/uploads/media_items/summer-2015-funding-opps.original.pdf

 

 

Joining the ride – Thabit Pulak

By Thabit Pulak

Howdy everyone! My name is Thabit Pulak, and I am currently a freshman, hailing from the grand nation of Texas! Although I haven’t declared my major yet, I am interested in Public Policy, and Medicine.

My first arsenic filters -- fresh from the factory!

My first batch of custom-made  water filters, fresh from the manufacturing plant in Bangladesh!

I’ve been interested in science ever since I was really young. As I got older, I became more aware of my surroundings. Ethnically, I am from Bangladesh, which is a poverty-stricken nation. Amongst the many problems the country faces, one that personally caught my eye was that of arsenic water poisoning, which affects nearly 70 million people in Bangladesh, and about 300 million people across the world. Continually drinking arsenic-tainted water results in arsenicosis, which is a chronic state of arsenic poisoning that gradually develops into various types of bodily cancers. So I thought, if exposure to arsenic was reduced, then the incidence of cancer would decrease as well.

Studying the issue closer, I noticed that solutions for filtering arsenic from water did exist, but they were very expensive (nearly $70) for the average villager, who makes around $1 a day. This was definitely a problem, as what good use was a solution, which was financially inaccessible to the target audience?

My meeting with the Minister of Bangladesh

I started to delve into this problem, trying to figure out what I could do. I read research articles on how other filters on the market worked. I noticed that the technologies used in other filters were plagued with various problems that brought cost up, such as being patented, or technologies not available natively in Bangladesh. Working in the kitchen of my home in Texas, I slowly developed an arsenic water filter that could also filter bacteria from water at an affordable price. I designed my filter in such a way that the whole filter could theoretically be built using materials in a typical village home.

Throughout the process of working on this project, I had the privilege of meeting many people who supported me along the way. I met with Bob Perciaspe, who at the time, was the head administrator of the EPA. I also met with Senator Ted Cruz of Texas, who lent me his endorsement towards carrying on with my work, with the future focus of expanding into rural areas into Texas, which also include arsenic affected regions. And, to my huge surprise, I was invited to the White House and met with President Obama!

I am now working on implementing my design. I founded iKormi, a non-profit organization, with the goal of alleviating problems faced by the underprivileged, in which my primary focus was arsenic water poisoning. Using some grants and money I raised, I was able to start up a small water filter plant in Bangladesh which manufactures arsenic water filters according to my design, consisting completely of local materials, using local labor. The filters were being built at a tenth of the cost. In addition to the manufacturing process, I also was able to gain support of many influential people in Bangladesh, including the Minister (and former general secretary) of Bangladesh. While there is definitely a lot more work to do, I definitely look forward to expanding this operation to be able to serve a wide variety of people who need access to clean drinking water.

At Duke, I hope to continue with my work in Bangladesh through the wealth of opportunities available to students in terms of research and working abroad. I look forward to writing for the Duke Research Blog!

Thabit and Obama

Me and President Obama in one of the Bangladesh national newspapers!

[youtube http://www.youtube.com/watch?v=9EE5q1F7HY8?rel=0]

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