REU Profile: making connections in metastasis

Kelcee Everette was part of Johns Hopkins Institute for NanoBioTechnology’s summer research experience for undergraduates. She blogged about her experience below:

My name is Kelcee Everette and I am a rising sophomore at Harvard University. During the summer, I worked in the Denis Wirtz Lab in the Department of Chemical and Biomolecular Engineering, where I characterized invasive breast cancer cell movement and compared those characterizations to the cell’s ability to metastasize in both 3D gels and on 2D substrates.

Kelcee Everette

Kelcee Everette

This project for me was especially exciting because I had never conducted research before. I learned a lot of skills that will be extremely valuable to me as I pursue my PhD.

The entire research experience was completely new to me, but my mentor, PI, and labmates were super helpful in teaching me the techniques I’d need to conduct my experiments.  Some of the skills I acquired included advanced microscopy, how to culture cells, and how create 3D collagen matrices, along with learning new programs like ImageJ and Metamorph.

I also learned a lot about the biological nature of cancer cells. The most interesting thing I learned, and the cornerstone of my project, was that cancer cells that are genetically identical can have vastly different motility profiles. The old saying “you learn something new every day” was a very applicable statement to my time in the lab.

Outside of the lab, my fellow interns and I had fun exploring the Inner Harbor, going to a food truck festival and a few other local and cultural festivals, and exploring local eateries and shopping centers. My experience this summer has been truly enjoyable both in and out of the lab, and I feel as if I have made great connections within the scientific community in just ten short weeks.

All press inquiries about this program or about INBT in general should be directed to Mary Spiro, INBT’s science writer and media relations director at mspiroATjhu.edu.

REU Profile: Microfluidics internship teaches patience, perseverance

Alex Chavez is a rising sophomore at University of Central Florida where he is studying Mechanical Engineering and Biomedical Sciences and minoring in Bio-Engineering and Mathematics. He spent the summer in the Materials Science and Engineering laboratories of Kalina Hristova and Peter C. Searson as part of the Johns Hopkins Institute for NanoBioTechnology Research Experience for Undergraduates program (INBT REU). His mentor was Alex Komin, a PhD candidate in the Searson group.

Alex wanted to write about his experience at Johns Hopkins in the INBT REU program in a blog post as follows:

This summer at the INBT REU has been a challenging and rewarding experience that has allowed me to investigate interesting topics at the interface of microfluidics, biological cells, and drug delivery. My research is focused on fabricating microfluidic devices, which allow to easily introduce the fluorescent molecules of interest to the cells and wash them out while doing live-cell fluorescence imaging.

Alex Chavez

Alex Chavez

While the main purpose of the device is to measure the rates at which fluorescent molecules can enter and exit cells, the applications of this microfluidic device may extend to the measurements of inhibition and cell viability without taking the cells out of the microscope. One of my research goals was to optimize the microfluidic device, such as the tube connection and battling with the bubbles that could ultimately stop the flow of the fluid in the microfluidic vessel. I have enjoyed learning how to fabricate microfluidic devices, work in the cleanroom, culture cells, seed cells, and to work with a confocal microscope.

This experience has given me the chance to learn from an expert in cell culture and learn more about the JHU community. Being mentored by an expert that can guide me and give me hints on what to do next, as well as to let me explore my own potential, has given me an incredible insight into the life of a graduate student. It has taught me the patience, diligence, and passion, to name a few skills, which a researcher should possess to perform their best in the laboratory. It has also showed me that sometimes experiments planned for a specific day may be delayed due to troubleshooting the device. It has also made me realize that if you keep on working and putting 100 percent of yourself, one day when you least expect it, you might be able to attain publishable results. This experience has ultimately taught me to keep on working and fighting for the love and advancement of science and drug delivery.

My experience at INBT has guided me and confirmed my thirst to pursue an advanced degree in biomedical engineering. My peers in the INBT REU program have inspired me to push myself to the limits and continue to work hard in order to know as much as them. I have visited Baltimore’s Inner Harbor and have had dinners with my peers. I’m blessed and truly privileged to have had this experience, including talking with my Puerto Rican roommate, Jean Rodriguez, about future goals and aspirations.

My mentor, Alexander Komin, has taught me invaluable skills that I will cherish and continue to further develop in the future. Thank you very much INBT for allowing me to further my research experience.

All press inquiries about this program or about INBT in general should be directed to Mary Spiro, INBT’s science writer and media relations director at mspiroATjhu.edu.

 

The Rosetta REU: software lets students collaborate at a distance

Johns Hopkins Institute for NanoBioTechnology (INBT) has launched a summer research undergraduate internship to train students to build new lifesaving drug molecules and create new biofuels, while testing the concept of a virtual research community. With the help of a $200,000, two-year grant to INBT from the National Science Foundation, Jeffrey Gray, professor of chemical and biomolecular engineering, spearheaded a first-of-its-kind training program where students collaborate with others from distant host university labs and use computer software to build vaccines, biofuels, and protein circuits in living cells.

Typical summer internships bring students together to one host university, but students in the Computational Biomolecular training program use an open-source software called Rosetta to work together on problems no matter where they are. Participants are mentored by members of a global collaborative team known as the Rossetta Commons, and users analyze massive amounts of data to predict the structure of real and imagined proteins, enzymes, and other molecules.

ChemBE professor Jeff Gray (standing) confers with Rosetta Commons undergradutate intern, Morgan Nance (seated left), and her mentor, Rebecca Alford (seated right), undergraduate research assistant, as they video conference with Mingzhao Liu, an undergraduate interning at Vanderbilt University.

ChemBE professor Jeff Gray (standing) confers with Rosetta Commons undergraduate intern, Morgan Nance (seated left), and her mentor, Rebecca Alford (seated right), undergraduate research assistant, as they video conference with Mingzhao Liu, an undergraduate interning at Vanderbilt University. Photo by Will Kirk/Homewood Photography

“Computational biologists study known macromolecules or design new ones and use computers to predict how these molecules will fold in 3D and interact with cells or other molecules,” said Gray. “For example, researchers create computational algorithms to design a new drug molecule or use the Rosetta software to predict how molecules might behave in a living organism. And because the work is done using a computer, researchers can easily collaborate at a distance.”

The students in the pilot program began with a week-long boot camp at the University of North Carolina at the end of May. Then, they traveled to host universities, which included Johns Hopkins; University of California, Davis; Scripps Research Institute; Stanford University; New York University; Rensselaer Polytechnic Institute; and Vanderbilt.

Morgan Nance, a biochemistry and molecular biology major from the University of California, Davis, worked in the Gray Lab. “I hope to become more familiar with Rosetta to the point that I am able to utilize it in my home lab,” Nance said. “I want to gain the technical skills of how to use this new software and the knowledge of how to develop it further. “

With the pilot program, students quickly expand their skill set. “Each lab has different expertise,” Gray said. “One lab might specialize in protein docking, another in RNA structure and design, another in vaccine design or protein function. When students cross train in these laboratories, they learn to recognize the common themes. “

Each week, Nance and her colleagues “met” via video chat to discuss current published papers and to present updates from host labs. At the end of 10 weeks, the Rosetta cohort convened at the annual RosettaCON in Leavenworth, Washington. Though Nance was on her own at Hopkins, INBT staff included her in activities organized for their other summer research interns.

“If this distributed model works just as well as the traditional one, we would then be able to accept this kind of model and access the best labs in the country for doing research,” said Sally O’Connor, the NSF program director.

Story by Mary Spiro

All press inquiries about this program or about INBT in general should be directed to Mary Spiro, INBT’s science writer and media relations director at mspiroATjhu.edu.

Summer research symposium to feature INBT-hosted interns

The School of Medicine will host the second annual Hopkins Career Academic and Research Experiences for Students (C.A.R.E.S.) Summer Symposium on Thursday, July 30, from 10 a.m. to 3:30 p.m.in the Anne and Mike Armstrong Medical Education Building.

SOM150502 CARES Summer 2015 Program Poster 24x36-3 (1)_Page_2Johns Hopkins Institute for NanoBioTechnology has 15 Research Experience for Undergraduates participating in the symposium.  In addition to more than one dozen poster presenters, REU Ashley Williams will give an individual talk on her research project at 1:20 p.m. in the East Auditorium. High school students from the INBT supported SARE program (Summer Academic Research Experience) will also have posters, and two-time SARE scholar Assefa Akinwole will give a talk on his work at 12:50 p.m. in the West Auditorium. The symposium is free and open to the entire Hopkins Community.

In total, more than 150 high school students from Baltimore City and undergraduates from around the country will present posters and oral presentations. Peter Agre, M.D. (Med ’74), director of the Johns Hopkins Malaria Research Institute, will deliver the keynote address.

“This is an excellent opportunity for our Baltimore City scholars to showcase their talents, intellect, and passion for science and medicine and reaffirm that they can compete at the highest level with undergraduates from across the country,” said Danny Teraguchi, Ph.D., assistant dean for student affairs and director of the office for student diversity.

C.A.R.E.S. is grateful to the Office of the Vice Dean for Education, Pulmonary and Critical Care Medicine Summer Internship Program, Johns Hopkins Internship Program in Brain Sciences, and its corporate sponsor, PNC, for supporting the symposium, and for their commitment to advancing education opportunities and academic programming for Baltimore City youth.

All press inquiries about this program or about INBT in general should be directed to Mary Spiro, INBT’s science writer and media relations director at mspiroATjhu.edu.

 

Assefa Akinwole

Assefa Akinwole

Ashley Williams

Ashley Williams

REU Profile: Hydrogels and stem cells

FranklynHall

Franklyn Hall

Franklyn Hall is a rising junior at Mississippi State University where he is studying Chemical Engineering with a Biomolecular Concentration. He is spending the summer in the chemical and biomolecular engineering laboratory of Sharon Gerecht as part of the Johns Hopkins Institute for NanoBioTechnology Research Experience for Undergraduates program (INBT REU).

Franklyn wanted to write about his experience thus far at Johns Hopkins in the INBT REU program in a blog post as follows:

This summer at the INBT REU has been an amazing experience that has allowed me to investigate interesting research topics such as hydrogels and stem cell growth. This experience has also given me the opportunity to learn more about the JHU community and the life of a graduate student.

My research is mainly focused on the characterization of the optimal conditions for vascular regeneration and growth within hydrogels. Hydrogels are unique 3-D environments that mimic in-vivo cell growth and allow researchers to study and adjust growth conditions, patterns, and cell interactions. These 3-D growth environments not only improve our understanding of stem cells, but they have applications in wound healing and tissue regeneration. I am specifically investigating hypoxia in hydrogels or the state of having low oxygen availability within the hydrogel. One of my research goals is to find the optimal hypoxic conditions and the effect of oxygen gradients within the hydrogel on cell growth and development. I have enjoyed learning how to make the hydrogel polymers, culture and stain cells, and look forward to producing results soon.

Outside of the laboratory I have had the opportunity to play on the departmental softball team with my graduate student mentor. It is common for graduate students to play different sports in the evening to socialize and have fun outside of the laboratory. During our semiweekly games, I have been able to talk to Masters, MD, and MD/PhD. students to learn about their graduate study experiences and future goals.  We have also had the opportunity to go out to eat and go to different events around Baltimore.

Graduate studies and research may be challenging. However, with people like the ones I have met, the support is there for you to persevere and make your mark on the scientific community.

All press inquiries about this program or about INBT in general should be directed to Mary Spiro, INBT’s science writer and media relations director at mspiroATjhu.edu.

 

High school students join ranks of summer researchers at INBT

Twelve high school students have joined the ranks of researchers working in labs affiliated with Johns Hopkins Institute for NanoBioTechnology this summer.

Nine of the students come to Hopkins via the Summer Academic Research Experience program (SARE), which pairs selected academically inclined students who attend Baltimore area schools, such as the SEED School of Maryland, with laboratory mentors at the Johns Hopkins School of Medicine. INBT has administered this program since 2009. Its funding comes from a variety of sources including, INBT, the Family League of Baltimore and private grants and donations.

SARE-2015-kids-web

SARE 2015 Cohort: Back row: Natalie Suarez-Perez, Adam Elsaidy, Princess Massaquoi, Ayende Watson, Stacey Alston. Front row: Assefa Akinwole, Siri Keyaka, Tashanna Sands, Grace Ayole,

Three of the students have joined INBT labs through a supplement to the National Science Foundation’s REU (Research Experience for Undergraduates) program and these students have been placed in INBT affiliated laboratories on the Homewood campus of the University.  This program is new to the Institute and students selected had applied directly to NSF via school recommendations. Students in this program come from outside the Baltimore area and live on campus in student housing.

INBT is dedicated to providing educational outreach opportunities to a variety of populations, especially students living in and around the Johns Hopkins University campuses. To find out about all of our educational program, visit the website http://inbt.jhu.edu/education/. Questions about our academic programs may be directed to INBT’s Academic Program Administrator Camille Bryant at cbryantATJHU.edu

All press inquiries about this program or about INBT in general should be directed to Mary Spiro, INBT’s science writer and media relations director at mspiroATjhu.edu.

NSF High School Cohort 2015: Nico Deshler, Nahom Yimam and Prathak Naidu

NSF High School Cohort 2015: Nico Deshler, Nahom Yimam and Prathak Naidu

REU student profile: Christopher Glover

Christopher Glover is a rising senior in bioengineering at the University of Missouri. He worked this summer as an REU intern in the laboratory of professor Jeff Tza-Huei Wang, who has joint appointments in mechanical engineering, biomedical engineering and oncology. The Research Experience for Undergraduates, hosted by Johns Hopkins Institute for NanoBioTechnology, attracts nearly 800 undergraduate applicants for just 10 research positions.

Christopher Glover

Christopher Glover

Christopher’s project involved a proof-of-concept experiment to test a device used to digitally sort and amplify DNA samples.

The device consists of a silicone chip imprinted with 3,000 tiny wells to contain DNA. A thermoplastic lid covers the top of the chip to keep the DNA in place in the wells. After a segment of DNA is added to the chip, the number of copies of that DNA segment is amplified using a device called a thermal cycler. “The goal is to either get zero or one copy of the DNA segment in each well, which makes the device “digital,” he said.

“We aren’t concerned about the type of DNA we are amplifying but just to see if it will work,” Christopher said. “This could be used for medical screening where a specific allele could be detected within a gene to see if someone is more susceptible to getting a disease,” he said.

Christopher said that working in the Wang lab has helped him learn much more about nanotechnology than he had previously known. His future plans include earning a PhD in biomedical engineering.

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.

REU student Profile: Florencia Velez-Cortes

Florencia Velez-Cortes is a rising senior in physics and chemistry at The Ohio State University. As part of INBT’s REU program, she spent her summer as a research intern the chemical and biomolecular engineering laboratory of professor David Gracias. REU stands for Research Experience for Undergraduates and is a National Science Foundation program hosted by the Johns Hopkins Institute for NanoBioTechnology.

Florencia Velez-Cortes

Florencia Velez-Cortes

Florencia worked constructing bi-layers out of DNA and acrylamide gel. The combination of the two materials could be used the make biocompatible devices, such as microgrippers that could be used in tether-less surgery, she explained.

“The best part about this project is that we are working on something complete new and biocompatible that could even be responsive to chemical signals,” she explained.

Also because the material is composed of DNA, “it could be responsive to certain DNA sequences.”

Florencia said the most challenging thing for her this summer was working with people who are engineers, when she is not. “It’s been a steep learning curve for me but everyone has been really helpful and receptive to working with someone who is outside of their field.”

She also noted that the pace of research in the Gracias lab is a lot faster than what she is used to in her previous laboratory experiences. She said having a mentor she could talk to was integral to her success.

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.

REU student profile: Alexa Wnorowski

Alexa Wnorowski

Alexa Wnorowski

Alexa Wnorowski is a rising senior in Biological Engineering studying at Cornell University. Her summer REU at Johns Hopkins University involved studying the blood brain barrier in the materials science and engineering laboratory of Peter Searson. Searson directs the Institute for NanoBioTechnology that hosts the Research Experience for Undergraduates (REU).

“The goal is to figure out how to move drugs across this tight junction of cells that protects the brain,” Alexa explained. Alexa used a four-channel microfluidic device fabricated in the Searson lab.

“Each channel has a slightly different shear stress because it has a slightly different height,” she explained. “We seed a culture of cells at the bottom of the channel and let them grow so that they are confluent. Then we run media through the device and we see how the different shear stresses affects proliferation of the cells.”

Although she conducted research before, Alexa said she had never worked with microfluidic devices before. She said to gain a broader perspective on research, it’s important to work in several different laboratories. “Every lab is run in different ways and have very different atmospheres, “ she said. “This experience has shown me how research in conducted in different labs.”

Alexa’s goal is to earn a PhD in biomedical engineering.

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.

 

REU student profile: Rebecca Majewski

DNA, the genetic sequence that tells cells what proteins to manufacture, typically resides inside the nucleus of a cell, but not always. Rebecca Majewski is studying the uptake of DNA into cell nuclei using a different polymer chains. Rebecca is a rising senior in BioMolecular Engineering from the Milwaukee School of Engineering and is working as a summer intern in the Johns Hopkins Institute for Nanobiotechnology’s REU program.

“We are interested in how much of the DNA with the polyplex can get into the nucleus,” she said, but explains that DNA associated outside of the nucleus can cause false higher measurements.

Rebecca Majewski. Photo by Mary Spiro

Rebecca Majewski. Photo by Mary Spiro

Rebecca is washing the cells with the nuclei to get rid of DNA outside the nucleus and then comparing the measurement of uptake of the DNA by the cell versus the measurement of the uptake of DNA by the nucleus.

“We are interested in what DNA gets inserted into the nucleus because that is what is ultimately expressed. It is important to find out how much makes it to the final destination and then is expressed. The goal of this work is to test different polymer chains to see which one actually does the better job of getting the DNA into the nucleus,” she said.

Rebecca works alongside PhD students and postdoctoral fellows in the biomedical engineering lab of Jordan Green lab at the Johns Hopkins School of Medicine. She says she highly values the opportunity for a research experience through INBT’s REU because her undergraduate institution does not train graduate students.

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.