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.

 

Highlights from the BMES meeting

I recently returned from the Biomedical Engineering Society (BMES) Annual Meeting in Seattle, WA. Many of us from INBT attended the four-day conference, gave podium and poster presentations, networked with professors and grad students from our respective fields. The conference placed heavy emphasis on topics of biomaterials for drug and gene delivery, but also had a strong showing of topics that are relevant to my research — cardiovascular and tissue engineering.

I gave a talk on microfluidics-based microencapsulation of stem cells for cardiac regenerative therapy, and attended as many talks as my mind could handle. From protein/peptide enhancement of angiogenesis (regrowth of blood vessels), to designs in microfluidic devices, to imaging techniques to show tissue functional recovery, I feel enriched and very much inspired.

We also had opportunities to visit parts of Seattle in our down times. Among other exciting things, there was a conference “bash” that was held at the EMP Museum at the Seattle Center which had very unique exhibits. The “underground tour” showed me the history of Seattle that I never thought existed. I’m truly grateful to have had the opportunity to experience this year’s BMES.

Charles Hu is a third year PhD student in the laboratory of Dr. Hai-Quan Mao in the Department of Materials Science and Engineering. Check out a gallery of shots from the trip to Seattle below.

Getting my hands dirty in NanoBio lab

As a second year graduate student, classes take up a non-insignificant part of my day. One of the classes that I had the opportunity to take last spring was NanoBio Laboratory. NanoBio lab is clearly a laboratory class, which is always very exciting for an engineer. I enjoy any opportunity to get my hands dirty and really learn some techniques. And that was exactly what we had the opportunity to do.

NanoBio Lab was our chance to go into many of the labs in The Institute for NanoBioTechnology (INBT) and get an idea of some of the techniques that they use and the general area of research of the lab. Some of the techniques that were demonstrated in this course included gold nanoparticles synthesis, transfecting cells with luciferase (the chemical that makes fireflies glow), and a novel method of analyzing images. While not all of the labs necessarily apply to the work that I am doing, many of them have some relevance and could come in handy in the future.

Through this lab, I have learned techniques that could be useful in my research in the future. Not only have I learned useful techniques, it was also an excellent chance to network within other labs. In this course, we had one or two representatives from many of the labs associated with the INBT instruct us and assist us in learning the techniques. This allowed us to form a relationship with at least one member in the represented labs, which will make it easier to reach out to other labs for help learning new procedures and protocols.

I just found out that I’m going to have to attempt to transfect a cell line, which I have never done outside of the NanoBio lab. Just as all laboratory work I know that it will be difficult, and that I’m likely to fail a number of times before I have any success. Through this class, however, I know someone who I can talk to for advice and assistance as I go through this process.

Moriah Knight is a second year PhD student in Peter Searson’s lab studying Materials Science and Engineering.

Advanced Cell Biology and the engineer

As part of the INBT’s Nano-Bio Graduate Training Program, we are required to take a few courses, on top of our departmental course requirements. To fulfill these requirements, I am currently taking AS.020.686 Advanced Cell Biology.

I expected the course to be just another required course – interesting, but not as exciting as the courses I elect to take. While the 8:30 a.m. time slot is earlier than I would like, the material has been very enjoyable so far.

I have a background in biomedical engineering, but I haven’t actually taken a biology class since high school. As a result, I have an engineer’s perspective on biology, which, as it turns out, is very different than that of a biologist. Even though we are all thinking about the same problems, the things that we emphasize as important are quite different. In Advanced Cell Biology, I have the opportunity to look at biology as a biologist, which has been both refreshing and informative.

My research project is heavily based in biology, but I approach it as an engineer. The course is helping me to see my project in another light. So far, this shift in perspective has proven useful, and I think it will be valuable in my future endeavors, too.

Right now, there are people with many different backgrounds doing biomedical research – biologists, chemists, physicists, mathematicians, engineers, and medical doctors, to name a few – and they present a diverse set of views regarding the best way to approach a given problem. In my experience, they all make important contributions to the larger picture, but no single perspective seems like it will be able to answer the big questions.

I think it will be the combination of these perspectives that will ultimately be able to solve the really big biomedical problems. Taking Advanced Cell Biology this semester is giving me a small taste of how combining two viewpoints – that of an engineer with that of a biologist – can provide new ideas and insights.

Nuala Del Piccolo is a PhD candidate in the department of materials science and engineering. She conducts research on the thermodynamics of receptor tyrosine kinases.

Data visualization helps engineers “see” more

As single-cell technologies continue to improve, it has become possible to measure multiple parameters simultaneously at the cellular- and even subcellular- level. Flow cytometry, for example, allows for the measurement of hundreds of properties for each cell, including features related to its shape, size, and protein expression levels. This new information has allowed for the discovery of behaviors that were previously unseen using population measures, such as Western blotting.

Example of data visualization (Source: http://www.flickr.com/photos/luc/5418037955/)

Example of data visualization (Source: http://www.flickr.com/photos/luc/5418037955/)

Along with this new information, however, comes a challenge. With multiple dimensions of data, it is difficult to perceive and properly interpret the message presented. Because of this, much of the information gained from single-cell resolution can be obscured or completely lost depending on the way the data are presented.

This perception problem leads to the need for dimension reduction, or a method that can transform the multi-dimensional data into a dataset with only two or three dimensions. To do this, a technique, “t-SNE”  was developed to visualize multi-dimensional data through the identifications of similar clusters within the dataset. t-SNE works by minimizing the differences between data points in order to identify the regions where data are most similar. Once these similarities are identified, t-SNE remaps the multi-dimensional data into three dimensions for visualization – two arbitrary axes and color, for visual separation of clusters. This remapping of the data allows for visual identification of the difference in data points that would be nearly impossible to show with the data in its original form.

One current application of t-SNE, a joint effort from groups in Stanford and Columbia University, uses this data visualization technique to show the heterogeneity in leukemia, and even the tumor subtypes they believe are responsible for relapse. This group took bone marrow samples from individuals who were considered healthy and those with leukemia, and compared these samples using flow cytometry.

With flow cytometry, they were able to study the expression of 29 different proteins, as well as the morphologic features of each cell. After processing the data using t-SNE, the group was able to not only distinguish the healthy cells from the cancerous cells, but also identify the protein expression profiles that were associated with relapse in these patients.

Data visualization is an increasingly important area of research as the amount of information gained from each experiment continues to increase. t-SNE is only one example of many that aims to allow for better perception of high dimension data to maximize its impact. This highlights the need for a researcher to not only design well-planned experiments, but also be creative with the presentation of their data. Creativity, combined with interesting data, will allow for a more thorough presentation of information and ultimately foster a better understanding of many areas in biologic research today, from genomic data to single-cell technologies.

Jacob Sarneki is a second year PhD student in Dr. Wirtz’s lab working on quantification of signal transduction at single cell resolution.

Why biomedical engineers should consider microgravity

The Biomedical Engineering Society (BMES) annual meeting was held last week, and as would be expected, there were a number of highly enlightening talks from researchers preeminent in the field. However, there was one talk that stood out if for nothing else than its uniqueness – a session from Dr. Donald Pettit, Ph.D. and NASA astronaut. In his talk, he described some of the questions and discoveries that arise from one of the greatest frontiers.

Free fall produces the effects of microgravity. Photo by http://www.photoree.com/photos/permalink/15089034-54636546@N02

Free fall produces the effects of microgravity. Photo by http://www.photoree.com/photos/permalink/15089034-54636546@N02

Microgravity (a.k.a free fall) produces a number of interesting and downright quirky effects in some things we take for granted on Earth; lighting a match literally produces a floating fireball and boiling water decides to ooze out in every direction. While these may seem trivial, Dr. Pettit’s playing around with salt in a bag may have solved a standing question in astronomy of how planetary bodies begin to take form from extremely small particles.

All of which is very interesting, but it doesn’t really have to do with medicine or biology. Still, it got my interest piqued so I killed some time looking at other discoveries made in space, that final frontier. Many people are familiar, for example, with possible problems in bone mass and density after long expeditions in space. However, there are problems even deeper than that. Microgravity can weaken the immune system, while conversely strengthening some bacteria. This could pose a major problem if the native fauna within our bodies, necessary to our survival, start acting up. If this seems unfair to you, it’s not all bad news – some scientists think these effects could have applications in vaccine development.

Here is a NASA link with a more detailed explanation of microgravity.

Jason Lee is a second year Ph.D. student in the Hai-Quan Mao laboratory in the Department of Biomedical Engineering.

 

 

Global Engineering Innovations teams seeking new members

Johns Hopkins Institute for NanoBioTechnology is seeking new participants for its Global Engineering Innovations program and will host a presentation by the leader of the team in Brazil on Monday, October 28 at 5 p.m. in Schaffer 304 on the Homewood campus. Global Engineering Innovations (GEI) involves interdisciplinary student teams collaborating with international hosts to develop solutions to problems around the world.

Image courtesy of Master isolated images

Image courtesy of Master isolated images

Nathan Nicholes, pre-doctoral student in the chemical and biomolecualr engineering lab of Marc Ostermeier, will discuss the work his team has accomplished so far in Amazonas, Brazil developing an improved cassava mill. GEI is actively recruiting team members to join the group in Brazil. The team from Ocurex, which manufactures a portable retinograph machine, will also present their work for consideration for a future project.

Come learn how you can be involved in this program that combines engineering skills with international outreach. Pizza and soda will be provided.  For more information, visit INBT’s Global Engineering Innovations website here.

Download the event flyer here.

RSVP to attend to Ashanti Edwards at ashanti@jhu.edu.