Wednesday, July 6, 2016

Juan en España: Mycobacterium leprae, Green Chemistry, and lots of Ryanair

For the past 5 months, I have been living in the beautiful city of Salamanca in Western Spain! Enrolled in courses at the Universidad de Salamanca – the oldest in the country [est. 1218] and the most breathtaking in my opinion – I returned home with a wider cultural and scientific understanding. I really aproveche [took advantage of] being across the pond and got do some amazing things while taking classes and working!

First the work: Mycobacterium leprae. In between the never-ending travel to century old cathedrals and picturesque Spanish towns, I was working on a developing project for the National Hansen’s Disease Program TravelWell Clinic at Emory University Midtown Hospital. As data flowed in from a pilot study the group ran in Minas Gerais, Brazil from July to December 2015, I was diligently analyzing tested factors to identify any associated disability variables indicative of morbidity for the leprosy-causing bacteria. Endemic to this state and many others in the largest South American country, the data we received ranged in both clinical and social variables. A cross-sectional analysis was performed to determine associations with Grade 1 or 2 nerve disability according to World Health Organization (WHO) criteria.  Overall, patients had a high burden of nerve damage consistent with prior studies in endemic areas. Additionally, older age and lower education were associated with disability grades of 1 or 2 in our population, which has also been found in other studies. Off this and planned multivariable analysis and inclusion of patients’ occupation, I submitted the abstract to present an oral presentation at The American Society of Tropical Medicine and Hygiene National meeting on November 13-17, 2016.

Second, more work: From January until June 8th, 2016 I was enrolled in 5 courses through the University. One of the courses was titled, “Scientific Writing.” This course was taken at the U.Sal’s  department of Filology – taught and graded in Spanish, naturally. During our first recitation, the professor covered the grounds of what was to come in throughout the course. Aside from a few very small assignments, the course grade heavily weighed in on a single final thesis to be submitted in June. I naturally thought of doing a topic related to my chemistry interests, not knowing what I was getting myself into. 5 months and countless, countless, tutoring hours later I submitted my comparative analysis paper on the growing green chemistry movement in Spain vs. other nations. I am grateful to have had the support of both Emory University’s program directors and the department of Chemical Engineering and Filology to guide me through this unexpectedly cumbersome but very enlightening experience.

Lastly, the travel: As aforementioned, I really did aproveche of where I was and made the best of my time abroad. Sure, I maybe sacrificed adequate sleep for a siesta here and siesta there but here are some of the unforgettable things I was able to experience while abroad:
-       Purchased a motorcycle and visited small Spanish pueblos on two wheels
-       Climbed up and skied down some Spanish and Portuguese mountains
-       The running of the bulls [in Ciudad Rodrigo]
-       Attended and fanboyed at the 2016 Geneva Motor Show
-       Ran a Half Marathon in Athens, Greece
-       Did a lap on the Nürburgring! Yes, THE ACTUAL NÜRBURGRING
-       Toured Lanzarote on a BMW G650GS
-       Made some amazing friends, saw some amazing countries, and ate some amazing food

Juan D. Cisneros
Tasting hydro-alcoholic solutions in Porto, Portugal

Aqueduct of Segovia, Spain


Wednesday, June 8, 2016

The IMSD community, my safe space

As an undergraduate, I had the opportunity to work with high school students to prepare for their graduation test. One morning the principal shared bad news about a student. On the way to school, the student had become a victim to an unfortunate crime. Instead of reporting the incident to the authorities or choosing to go home for the day, like most of us would have, the student continued on to school. When asked why they’d chosen to come to school, the student replied ‘I didn’t know anywhere else better to go’. I could never understand why the student chose to come to school of all places until now. The student had found their safe space.
The Advocates of Youth (hyperlink: describe safe spaces as places where individuals can feel relaxed, fully expressive, and without fear. The idea of safe spaces originated with the Women’s Movement. The spaces gave women the ability to speak freely and come together to form a community of collective strength (Kenney 2001). Safe spaces gained popularity and now can be seen as staples in mainly marginalized communities. But the question that remains is if safe spaces are essential to the graduate (and potentially undergraduate) experience.
I’ll start by saying being in graduate school is not comparable to the atrocities of being victim to a crime or experiencing systematic oppression as a result of gender, race, or religious identity. However, I do believe there are difficulties students face in their tenures that call for safe spaces. Whether it be having difficult conversations with your PI (principal investigator), dealing with feelings of being inadequate or an imposter, or balancing the stress of day to day life, there are circumstances best addressed in an environment of comfort, support, and community. 
The IMSD community at Emory University provides that environment for many students. Each week, despite having long tiresome days, undergraduates and graduates pursuing degrees in STEM (Science, Technology, Engineering, and Mathematics) make journeys from various corners of campus to discuss professional development topics. Each Thursday, the Center for Ethics erupts with joyous chatter as students and faculty share their experiences and support to one another. Some can be observed quietly sitting in their seats preparing for the topic at hand for the day. The lecture will begin shortly but it won’t be long before someone raises a hand to mention a difficulty they’ve faced and others rush to respond with support and suggestions. The time flies, as it frequently does when you’re having fun, and everyone will file out or linger around with feelings of assuredness for the days to come.

 I cannot speak for the entire IMSD community but I would personally advocate that the safe space provided by the IMSD community is essential for all students and likely advantageous in their success as students. Many of us have moments of feeling down trodden and contemplation of whether or not graduate school is the right place for us. In those moments, it is necessary for students to have somewhere to turn to for support. IMSD provides that exact place. As I am leaving the grant, I can only hope students from across many more departments and many more walks of life will gravitate to such a wonderful community.
Jessica Coates, IMSD Fellow 2013-2015

2015 International Genetically Engineered Machine (iGEM) flashback! by Jasmine Carrothers

My fellow IMSDer, Josh Davila, and I attended the 2015 International Genetically Engineered Machine (iGEM) competition in September. The iGEM competition is an international synthetic biology competition that prompts students to solve real world problems and contribute positively to their community and the world. It was located in Boston, MA and with the help of Georgia State University iGEM, who graciously let us partner with them, the Center for Science Education, who gave us funding for our registration, and mentors Maruf and Dr. Ichiro Matsumura, we were able to attend.
GSU - Emory Team


   Josh and I focused on a mini project called: Project J- Broth (for Josh and Jasmine) where we created media for E. coli cells using materials found on Amazon. The GSU team worked on a project called P4: Protein Products in Pichia and Plants, where they produced mambalgin-1 (compound found in black mamba venom) in yeast and CBDA (compound found in cannabis) in transgenic tobacco roots.

The Hynes Convention Center - Where the magic happened

We medaled silver in the competition and even had time left over to explore the city. Overall, it was a great trip and I hope to return next fall.

The group at Harvard Square!

Friday, May 20, 2016

The Perils of “Publish or Perish” by Luis Munoz

The scientific community witnessed one of the most prominent cases of research misconduct in recent times during the rise and fall of Haruko Obokata in 2014. A rising star in the world of stem cell research, Dr. Obokata took the world by storm when she published two articles in Nature, one of the leading research journals. The articles outlined how her group and collaborators had developed a surprisingly simple way of inducing pluripotency in somatic mammalian cells.  What does this mean? The paper claimed that they could turn ordinary cells into cells that could differentiate into any other kind of tissue cells. How? Just with a bath of citric acid for half an hour and that’s it! You no longer have terminally differentiated cells, but cells with potential (like Obokata) to become any kind of cell type. This was a much faster and easier way to reprogram cells than the one pioneered, back in 2006, by another Japanese scientist, Shinya Yamanaka. Obokata’s method seemed much less likely to damage the cells or, worse still, make them cancerous.

Yamanaka won a Nobel Prize for his work, so this begged the question, when would Obokata get one herself? Especially since she was a rising female scientist in a male dominated field.

But, as it turns out, her success was short lived. Just a couple of days after publication, allegations emerged that her images looked doctored and that whole chunks of text were lifted from other papers. The Center for Developmental Biology at Riken in Japan soon started an official investigation and announced that Obokata was guilty of scientific misconduct. That is when things turned sour.

The media built her up, so after the announcement, they did not hold back in tearing her down. She faced a grueling televised press conference and apologized profusely for errors in methods and sloppiness. Interestingly enough, she never admitted to fabricating data. Obokata claimed she was a victim of benevolent mistakes due to her youth and inexperience. Above all, she stood by her claims that stimulus-triggered acquisition of pluripotency (STAP) cells existed.

So, what happened? Her collaborators supported her claims initially, but eventually detracted. No other group could replicate the results, despite the simplicity of her methods. In the end, the most incriminating piece of evidence surfaced and so did her retraction. It was found that the STAP cells did not match the DNA of the mice they supposedly came from. Yoshiki Sasai, the deputy director of Riken and Obokata’s own supervisor, was hospitalized for depression for over a month and eventually committed suicide leaving behind a note to Obokata. His last plea? “Reproduce STAP cells.”

In theory, reproducibility is the golden standard of modern science, or at least in theory. Researchers don’t often have interest in replicating the work of others, and grants are not awarded to do so, so confirming (or failing to confirm) is unlikely to get you far (or even into publication). The pharmaceutical company Amgen set out to repeat 53 landmark experiments that had been published in top science journals. Only six were reproduced successfully. Bayer set out to do the same with 67 published articles and found that less than 16 were successfully reproduced. If Obokata’s claims weren’t so revolutionary, it is likely that her manipulation would have gone unnoticed. Everybody wanted to know how she had done it, inside and outside the field, and the scrutiny was greater than her sleight of hand.

Misconduct is more of a downward spiral than an all or nothing decision. Imagine sinking days or weeks into a single experiment and months to years developing a story that fits (or doesn’t fit) your hypothesis. You want to prove that what you do is valuable and you are not just wasting your life away under fluorescent lights in a white coat. Competition is high and funding is historically low due to budgetary restrictions. Funding is not only what fuels your professional life, but also your livelihood. What do you do when your results do not make sense or are disappointing? All it takes is a shift in a point on a graph, enhancing an image, editing the raw data, nobody will notice, nobody will suspect. However, once you start messing with the facts, it’s hard to stop. Things get complicated as time goes by, progress is expected and that’s when there is a build up of lies that culminate in research misconduct. Did Obokata begin manipulating data to please her supervisors? Did her colleagues suspect that her results were too good to be true? We will probably never know.

- Luis Munoz