Seizing serendipity during a European internship

Studying abroad is a popular experience for undergraduates and many students try to take advantage of this opportunity. Being an international student at heart, I was also interested in exploring the world; however, my coursework made it practically impossible to go abroad with the study programs that my college offered. I did not just want to go traveling though, I wanted to invest my time while creating new experiences for myself, and so it occurred to me to independently seek an international research internship abroad. I started searching for the opportunities and with some luck involved I discovered the European Molecular Biology Laboratory (EMBL). The institute actually consists of a large number of member states in Europe including Germany, France, UK, and even, somehow, Australia.

We were completely soaked, but we had to get back. Much to our surprise we got a ride back up to the castle.

We were completely soaked, but we had to get back. Much to our surprise we got a ride back up to the castle.

After a series of e-mails and a phone interview I ended up joining the group of Dr. Christian Haering whose lab is studying the condensin protein complex in yeast. Condensin protein complex does pretty much what you would expect; it condenses and organizes chromosomes together but also has other roles, like regulating gene expression. The project seemed exciting to me, and it also meant that I would be able to spend my summer in Heidelberg, Germany, while learning something new. One of my best college friends also applied to the institute and ended up being accepted to a different lab.

The campus was located in a serene location on top of the hill, which required a healthy hike through the forest in the morning. A lot of things about this place were special: there was a building with two floors spiraling upwards in a double helix, a cafeteria chef with a mustache in a style of a Prussian soldier singing and greeting with “Bonjour!” beer Fridays organized by different labs, journal clubs and coffee breaks with a beautiful spectrum of accents discussing science.

In my research, I worked with fission yeast and tried to isolate condensin and other proteins that might interact with it on some level. I learned new techniques of growing yeast, isolating protein with magnetic nanobeads, and performing Western blots to mention a few. Although I did end up working very long hours during the week, Friday nights meant one thing: my friend and I were literally running to catch a train. We would come to work with packed backpacks and a vague idea of where we wanted to go. Very often we were in the hands of serendipity, which provided opportunities that would be difficult to plan out.

IMG_3695_stitch cc sat60 us. Hohenzollern in thunderstormTo give an overview of one weekend, we were able to visit Frankfurt, Cologne, Bonn, and a tiny city St. Goar on the Rhine River. Almost nearly missing a series of trains but always making it with half-a-minute to spare, we finally missed the connecting train in Frankfurt by 20 seconds and got stuck there. As a result, we arrived in Cologne at 6 a.m., with a stunning view of Cologne’s gothic cathedral filling most of the huge window of the train station. By midday we moved on to Bonn because it was a birthplace of Beethoven. If you ask me how we ended up in the tiny city of St. Goar, I do not know. In St. Goar, by chance we learned that they had closed the road along the Rhine to give bicycles free reign, and so we rented bikes to participate in the procession with other bicyclists. On the way, we climbed up to three castles overlooking the Rhine, and arrived back to our town late at night to get some sleep before work. In a similar manner, we traveled to Switzerland, France, Belgium, the Netherlands and various cities in Germany.

The experience in Europe was rich with emotions and stories: from the Foreigner performance in Mannheim to the Vivaldi’s “Four Seasons” in St. Chapelle in Paris, from sleeping at the train station to being soaked under rain in the attempt to climb a mountain with a castle on top.

I advise undergraduates to actively seek such research and travel opportunities because very few things make you feel so alive like learning and traveling.

Alex Komin, a first-year PhD student in Kalina Hristova’s lab in Materials Science and Engineering Department, is working on new methods to deliver drugs to the brain.

Q & A: Nanopaprika, the social network for nanoscience

About the same time that Johns Hopkins Institute for NanoBioTechnology (INBT) came into existence, which was May 2006, a network was established online for people interested in all things nano. The International NanoScience Community, or TINC for short, wasn’t some government agency initiative or research center based website, but a social network, much like Facebook, that specialized in helping connect people across the globe interested in reading about, working in, studying or otherwise investing their time in all things nanoscience-related.

nanopaprika-logoI joined TINC in the fall of 2007, shortly after coming to work at INBT. Since I was new to nanotechnology, I thought it might be a good way for me to find out about things going on in the field in a less structured way than reading the journal articles published by the faculty I was writing about. I wasn’t actively conducting research in nanotechnology, but it was interesting to read about what other people were doing across the globe. It helped gain perspective on where Johns Hopkins was in the global nanotech environment. I also thought it would be a good way to get the word out about some of the work INBT researchers were doing.

Over time, I have occasionally posted items and connected with people on TINC. Both TINC and I celebrated six years in nano in 2013, so I thought it would be fun to catch up with András Paszternák, creator and editor of The International NanoScience Community. Here is a short Q&A. Since the URL of TINC is Nanopaprika.eu, Paszternák sometimes just refers to it as Nanopaprika. The site’s tag line says it all “the spicy world of NanoScience,”  and paprika is an important Hungarian spice. Read on!

András Paszternák creator and editor of The International NanoScience Community.

András Paszternák
creator and editor of The International NanoScience Community.

When exactly did TINC start?

On 27th of November 2007, it will be six years old in this month.

What is your goal with TINC?

The main idea was to create something more personal than the other nano networks already on the Internet, something open for students as well as for senior researchers. I was asked by my supervisor Prof. Erika Kalman at the Chemical Research Center of Hungarian Academy of Sciences (Budapest, Hungary) to edit an existing Hungarian nanotech site, but I came up with the idea to create a scientific social network, which could be so much bigger, spreading like a tree and connecting nano scientists across the globe. I have been editing the webpage in my free time along with my professional work as a chemist since the beginning.

Over the last six years, how has TINC attained these goals?

We have today 6,641 members coming from more than 80 countries. Thanks to Nanopaprika, several students have found PhD and postdoctoral positions and found information about new nanotech developments. Senior researchers have met talented students; shared news about their results and found new collaboration partners. Nanopaprika is like an open source to connect nano addicted people and share the latest news in our scientific field.

Why do you think this sort of network is important?

As we can see from Facebook, social networking can really bring people, families and friends closer to each other. I think, next to LinkedIN or ResearchGate (big specific networks with millions of users) small professional networks (like Nanopaprika ) can bring the opportunity to create bonds on a personal level between scientist and students. There is a competition between scientific networks – most researchers don’t like to be registered into several social networks– only the most interesting and most scientific will survive this war. Hopefully, Nanopaprika will be among these.

What do you value most about contributors?

Any news, information is welcome. Some members start just forum topics, others share the abstracts of fresh papers, write blog posts about nanosafety, nanotech education and so forth. A scientific social network is like a LEGO game, everybody can bring their bricks. Just some numbers:  we have 5,090 blog posts, 668 discussions topics, 382 shared nanoevents, 2,208 photos and 387 videos – so Nanopaprika is really a spicy world of nanoscience.

Why should someone join this network?

The door is open for everybody, there is no registration fee, just check www.nanopaprika.eu and if you like it, click on sign In.

By Mary Spiro, INBT science writer.

Picture this: alumni meet up at AIChE annual

From left, Denis Wirtz, Christopher Hale and Terrence Dobrowsky

From left, Denis Wirtz, Christopher Hale and Terrence Dobrowsky

Two alumni of Johns Hopkins Institute for NanoBioTechnology. Dr. Chris Hale and Dr. Terrence Dobrowsky, recently met up with INBT co-Director Denis Wirtz at the annual meeting of the AIChE, held Nov. 3-8 in San Francisco. Chris and Terrence are currently work at Amgen and Biogen, respectively.

Chris and Terrence were both PhD students in Wirtz’s laboratory in the Department of Chemical and Biomolecular Engineering.

Nanotech collaboration between Johns Hopkins and Belgium had INBT roots

Johns Hopkins Medicine recently announced exciting news of a joint collaborative agreement with IMEC, a leading nano-electronics research center based in Belgium. The objective of the partnership is to advance applications of silicon nanotechnology in health care, beginning with development of a point-of-care device to enable a broad range of clinical tests to be performed outside the laboratory. This unique venture will combine Johns Hopkins clinical and research expertise with IMEC’s technical and engineering capabilities.

TIMEC clean roomhe two organizations plan to forge strategic ties with additional collaborators across the value chain in the health care and technology sectors. Development of a next generation ”lab-on-a-chip”, making diagnostic testing faster and easier for applications such as disease monitoring and management, disease surveillance, rural health care and clinical trials, will form the initial focus of the partnership. Denis Wirtz, Associate Director of INBT, will serve on the Advisory Board for the collaboration.

The roots of the new Hopkins-IMEC partnership were initiated over five years ago when Johns Hopkins Institute for NanoBioTechnology (INBT) established a collaborative relationship with IMEC. Since its inception in 2009, the INBT-IMEC partnership has blossomed into a number of collaborative projects, which enabled both graduate and undergraduate students from Hopkins to broaden their research experience with internships at IMEC’s state-of-the-art laboratories in Leuven, Belgium (with some students from IMEC also interning at Hopkins).

These projects were built around Hopkins/INBT research interests in nanobiotechnology such as controlled drug delivery, microfluidics, stem cell platforms and neural networks to mention a few. IMEC’s massive expertise in nanofabrication, darkfield and lens-free microscopy, neuro-electronics and lithography provides a huge opportunity for JHU researchers to evaluate translational pathways for basic discoveries.

Initial discussions about a broader relationship between the two institutions originated with an INBT-IMEC team exploring possible additional opportunities building on our existing partnership. A visit to Hopkins by senior IMEC management in August 2012 was organized by INBT, and laid the groundwork for subsequent next steps which included a University-wide team. We are delighted to have identified an opportunity for Hopkins to create a collaborative model to develop potentially revolutionary new techniques combining the unique advantages of silicon technology to a new generation of diagnostics and cures.

Separate from this recent collaboration, INBT has hosted students to conduct research at IMEC since 2009. Funding to support students abroad has come from INBT and the National Science Foundation International Research Experience for Students (IRES) program.

Read the official announcement from Johns Hopkins School of Medicine here.

Check out the INBT/IMEC blog.

Read about the INBT/IMEC IRES program here.

By Tom Fekete, INBT director of corporate partnerships.

 

Learning How to Take a Product from Lab to Market

One of the most helpful courses that I’d ever taken as an undergraduate student was a course called, “Engineering Entrepreneurship”. This was an intense course designed to simulate the actual process of developing a startup company based on an original technology. I spent long hours with a team of students working to draw up financial reports for our pseudo company, outlining an operations plan for development and putting together a business proposal at the end. A course like this is so important because many groups in biotechnology, energy, and other industries feel that nanotechnology is on the cusp of being an industry in and of itself if not for a few very impactful ideas.

Ttech-transfer-illohere are many ways for nanotech applications to make it to the marketplace. Indeed, there are various drugs such as Doxil which have been around for years and were “nano” before it became a buzzword.(1)  Nanotechnology has become a part of other industrial processes, giving antimicrobial properties to surfaces or improving microfab processes.  We should look, however, not only to how nanotechnology can be used to supplement existing products or how to reliable existing products as nanotechnology but also how to cultivate a new industry based on nanotechnology.

How exactly can a nanotech industry be created?  I think that is something much too involved to discuss in a single blog post.  What I can suggest is that all engineering students look into taking business courses along with their other requirements.  I believe that if engineers with a background in nanotechnology can become involved in the process of developing startups that then nanotechnology will be as recognized of an industry as biotechnology has become.

1. Doxil Home Page. Accessed 10/24/2013 <http://www.doxil.com>.

By Gregory Wiedman, a graduate student from the Materials Science Department who is altering natural peptides from Bee Honey venom to improve drug delivery.

 

 

What does this do? Atomic force microscropy

Several high resolution imaging techniques have been used over vastly diverse disciplines in science and engineering—from microscale with our light microscope to nanoscale with electron- or X-ray beam-mediated imaging techniques. These have been considered as routine laboratory techniques in order to visualize the micro- to nano-scale features of a certain material. How about seeing an actual bond?

AFM, or atomic force microscopy, have been recently been making news in the scientific community as it was used by two different groups to image actual bonds. This microscopic technique is based on a scanning probe, a cantilever with a tip. The tip is lowered closer to the surface of the sample until the forces between the tip to the surface are enough to cause a deflection in the cantilever, which is then correlated to a ‘signal’ that is processed to construct the image of the surface. It runs in either contact or non-contact mode, depending on the characteristics of the sample to be analyzed.

Just a month ago, researchers from China’s National Center for Nanoscience and Technology have published AFM images showing the first image of hydrogen bonds. The image was for 8-hydroxyquinoline, deposited on a copper surface. This is definitely groundbreaking, as this is showing that these bonds with weaker interactions than covalent bonds can also be visualized using this technique. This proves that AFM can be used as a tool to characterize submolecular features.

H-BOND

http://goo.gl/g66C1A

Earlier this year, another group at the University of California Berkeley have also used AFM in order to monitor a reaction. The group used oligo-(phenylene-1,2-ethynylene), immobilized the molecule on a silver substrate, and monitored the products upon heating. As a routine, organic chemists typically monitor a reaction just by thin layer chromatography (TLC), looking at how the spots develop in the plates over time. Imagine if this technique becomes a routine tool for synthetic chemists, just like NMR or MS— without a doubt, it would definitely revolutionize the way we confirm products by seeing actual bond forming and breaking.

REACTION

http://www.sciencemag.org/content/340/6139/1434

 

 

 

 

 

 

The field seems to be more and more exciting, and maybe we just have to wait for another groundbreaking AFM news before the year ends. Given how direct and informative the images are that we can take from this technique, hopefully, researchers will be able to find a way to make it as a routine synthetic characterization tool someday. This will not only help synthetic chemists, but also materials scientists and other researchers that delve on nanotechnology.

Here’s the link to the papers, for reference:

http://www.sciencemag.org/content/early/2013/09/25/science.1242603.abstract

http://www.sciencemag.org/content/340/6139/1434

Herdeline Ann Ardoña is a second year graduate student in the Department of Chemistry under Professor J.D. Tovar, co-advised by Professor Hai-Quan Mao.

My summer internship at Novozymes

Over this past summer, I had the opportunity to complete a 3-month internship with a biotechnology company near Raleigh, North Carolina. Novozymes, headquartered in Denmark, produces some microorganisms and biopharmaceutical ingredients, but their main focus is the production of enzymes for industrial use. These enzymes go to customers in the household care, food and beverage, and bioenergy industries, to name a few. Some of Novozymes’ customers you may be familiar with include Procter & Gamble (Tide laundry detergent), Nabisco (Ritz crackers), and Anheuser Busch. My summer was spent in the Research & Development department working with enzymes for biofuel production.

The corn-to-ethanol process consists of two main stages. Briefly, corn is ground, and an alpha-amylase enzyme is added to solubilize and start to break down the starch. This stage, called liquefaction, takes approximately two hours. Next, in the fermentation stage, starch is broken down further with a glucoamylase enzyme and is fermented into ethanol using yeast over the course of two to three days. Ethanol is then used as a gasoline supplement; it can increase octane rating and improve vehicle emissions.

My first task as a Novozymes intern consisted of an internal assay development project seeking to increase the throughput of corn fermentation enzyme screenings. Novozymes is planning to purchase a new liquid-handler robot to automate and quicken the lab-scale fermentation process as they test which enzyme blends can obtain the best ethanol yields. It was my job to optimize parameters such as mixing and venting within the new system and test if it could match results from conventional screening methods.

A separate project that I focused on during the second half of the summer involved a joint effort between the Research & Development and Technical Solutions departments to formulate new product blends for liquefaction and fermentation of milo, or sorghum, a grain similar to corn. Milo may provide an advantage over corn because it is not a main ingredient in food manufacturing and may help keep grocery prices down. Milo may provide an environmental advantage as well, as it is more tolerant of drought than corn crops and requires less water. This project was especially interesting in that I was able to experience some of the business applications side of research and development. In formulating new product blends, our team had to keep in mind what process conditions and enzyme prices potential customers would be willing to agree with.

Everyone at Novozymes was extremely friendly and willing to help. The internship program at the Franklinton, North Carolina location, which houses the company’s North American headquarters, is fairly large, so I was able to meet about 20 other interns at both the undergraduate and graduate school levels. The People & Organization department (a.k.a Human Resources) organized a networking lunch with site managers as well as a career prep workshop and resume review. We also attended a Carolina Mudcats baseball game, and an ice cream truck came around the work site to give out free ice cream every few weeks! Of course, there was always enough Carolina barbeque and sweet tea to go around.

Overall, my Novozymes internship was a well-rounded, enjoyable, and valuable experience. In addition to the Franklinton site, Novozymes operates in Virginia, California, Nebraska, and all over the world. The company offers internship and co-op positions at many of these locations. If you are interested, I highly recommended checking out their career site for available opportunities!

Story by Allison Chambliss, who is entering her fifth year as a PhD student in the laboratory of Denis Wirtz in the Department of Chemical and Biomolecular Engineering.

What’s mechanics got to do with tissue development?

A recent study at Harvard, published in the journal Science, found that mechanical factors play a significant role in tissue development. Learning these factors that contribute to the natural formation of tissues will not only improve our understanding of tissues, it will also improve our ability to engineer tissues in the future and improve our ability to discern developmental problems.

Intestinal villi small http://goo.gl/DlKA7p

Intestinal villi small http://goo.gl/DlKA7p

The walls lining the intestines are not smooth. They are covered with many tiny, finger-like protrusions, or villi, yielding a high surface area for high nutrient absorption. These villi are present in many different animals including humans, chickens, and mice. This study follows the chick’s gut from earlier embryonic stages through the gut formation.

In the beginning of gut formation, the intestine is a smooth, cylindrical tube. As the embryo matures, a outer layer of smooth muscle binds the inner regions. The inner region continues to expand, but the outer region restricts it causing the inner tube to buckle and bend back over on itself. As the embryo continues to grow, the outer layer is enhanced and strengthened, causing the inners layers to make smaller and tighter folds, eventually yielding the villi. This paper shows that without the outer muscle layer, the inner layer will continue to grow, but rather than forming villi, it just ends up with a larger circumference.

This study goes on to show that across different animals (xenopus, chick, and mouse), while the time scales and intermediate steps may vary, the constraints from the outer loop cause the buckling of the inner layer into the villi.

This research establishes that in natural formation of specific tissues—and consequently engineered tissues—mechanical factors must not be ignored.

Villification: How the Gut Gets Its Villi 

Charli Dawidczyk is a PhD candidate in Materials Science and Engineering working in Peter Searson’s research group.

 

Molecular ‘muscles’ flex to external cell forces

If you have ever watched one of those weather people on television being buffeted about while trying to report on a hurricane, you might have some appreciation for what the life of a cell might be like inside a body.  New research from the cell biology laboratory of Doug Robinson, professor at the Johns Hopkins School of Medicine, reveals how the cell uses certain proteins to react and respond to these extreme external forces at the molecular level.

Cytoskeletal proteins move to different areas of a cell in response to the different forces created by suctioning with a thin glass tube. Robinson Lab

Cytoskeletal proteins move to different areas of a cell in response to the different forces created by suctioning with a thin glass tube. Robinson Lab

Graduate student Tianzhi Luo from the Robinson lab studied the cells experimentally by pulling on the cell’s outer membrane (or cytoskeleton) with a tiny glass vacuum tube. Images of fluorescently tagged membrane proteins were captured. Working with Pablo Iglesias, professor of electrical and computer engineering at the Whiting School of Engineering, and his graduate student, Krithika Mohan, the team developed a computer model to predict how cytoskeletal proteins would behave under certain physical forces. The work is summarized in the journal Nature Materials.

“For the first time,” said Robinson, “we are able to explain what a cell can do through the individual workings of different proteins, and because all cells use information about the forces in their environments to direct decisions about migration, division and cell fate, this work has implications for a whole host of cellular disorders including cancer metastasis and neurodegeneration.”

Read the full article paper here.

Read a press release about this research here.

Watch several videos demonstrating the computer model below.

Getting WISE about science and engineering

As a graduate student, outreach is an instrumental part of our educational experience, whether we are presenting our recent work at a conference or mentoring a new student who joins the lab. Here at Hopkins, we are presented with ample opportunities that would fall under each of these categories. One of the rewarding activities in which I have participated is the Women in Science and Engineering (WISE) program in partnership with Garrison Forest Schoo (GFS)l, an all-girls school located in Owings Mills, Maryland.

labwarestockThe WISE program is a partnership between GFS and Johns Hopkins University, and each year, around 14 interested juniors and seniors take part in a four-month research program. Students in the WISE program are matched with a graduate student research mentor who could be from a number of Hopkins programs, including the Schools of Engineering, Medicine, Arts and Sciences, and Public Health. The WISE students come to Hopkins for six hours each week, where they are able to participate in laboratory activities, department seminars, group meetings, classes, and even try their hand at a few experiments.

During my second year, I was able to serve as a mentor to two WISE students, and I greatly enjoyed the opportunity to mentor them. It was a wonderful opportunity for me to be able to explain my project on nanoparticle-based drug delivery systems for cancer treatment so that they could understand the research and also be able to explain it to their fellow students and teachers. I wasn’t sure how much they would be able to do, but throughout the course of the program, they were able to learn how to use pipettes, prepare the nanoparticle solutions and even try to culture cells and view them under a microscope. At the conclusion of the program, they both gave ten-minute presentations on all that they learned. Both said that without this program, they might not have strongly considered a future major in a science field but would certainly do that as a result of their experiences.

Again this year, we have another WISE student working in our lab with a first-year Biomedical Engineering graduate student. Between reading some background information on the project, learning how to use the equipment, and even trying a few simple experiments, it has been a busy, but enjoyable, first few weeks in the program.

If you are interested in more information about the WISE program, please visit http://www.gfs.org/academics/the-wise-program/. I would encourage everyone to strongly think about becoming a mentor for a WISE student in the future. It was a rewarding experience for me, and I hope it will continue to push new students into STEM fields for their future careers.

John-Michael Williford is a PhD candidate in biomedical engineering working in the laboratory of Hai-Quan Mao.