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

Four undergrad researchers working in Belgium

Each summer, Johns Hopkins Institute for NanoBioTechnology (INBT) has funding to support research internships abroad. The International Research Experience for Students (IRES) program, funded by the National Science Foundation, provides support for students to work with researchers at The Inter-University MircroElectronics Centre (IMEC) in Leuven, Belgium. Students work at IMEC’s world-class microfabrication facility and learn to design, fabricate and test a wide range of biomedical devices.

Over the next several weeks, each student will blog about their experiences both as researchers in an international laboratory, but also as a visitor to Europe. Expect to see some lab photos and some tourist trip photos.

For 2015, four students have arrived in Belgium. They include Rachel Bang, Sophomore in Mechanical Engineering; Rebecca Black, Junior in Molecular and Cell Biology; Gwendolyn Hoffmann, Senior in Materials Science and Engineering; and Victoria Laney, Senior on Chemical and Biomolecular Engineering. For more information about the IRES program through INBT, visit http://inbt.jhu.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. For information about INBT’s collaboration with IMEC, contact INBT’s director of corporate partnerships, Tom Fekete at tfekete1ATjhu.edu

A new wealth of applications for gold nanoparticles

Gold has been the currency of many civilizations because of its advantageous and attractive bulk properties. Many modern civilizations have left the gold standard, but the attractiveness of gold has not decreased. One reason is because of the development of gold nanoparticles.

goldcups

Figure 1: Picture of gold nanoparticles embedded within Roman cup. When light is shown through the cup the gold nanoparticles reflect the red making it appear to change color. Source: http://www.smithsonianmag.com/history/this-1600-year-old-goblet-shows-that-the-romans-were-nanotechnology-pioneers-787224/?no-ist

Although gold nanoparticles have been formed as early as the 4th century AD because of incorporation into cups such as shown in Figure 1, it has not been until the past 50 years that researchers have developed gold nanoparticle formation techniques and exceptionally characterized these particles enabling their usefulness.

Gold nanoparticles have found numerous applications both within and outside of biology. For example, the gold nanoparticles could be used as therapeutic delivery vehicles. Furthermore, specially shaped and sized nanorods can be exothermically excited by 700-800 nm light. This could be used to produce a hyperthermia treatment of tumors where the nanoparticles could be coated with a ligand for the tumor and then light shown only in the location of the tumor for site-specific therapy.

In addition, gold nanoparticles are commonly used in biological assays as detection agents for certain pathological conditions. Outside of biology, gold nanoparticles can serve as catalysts for chemical reactions and also be used in printable electronics. These and other currently investigated applications for gold nanoparticles provide a rich future for gold in our modern society.

About the author: John Hickey is a second year Biomedical Engineering PhD candidate in the Jon Schneck lab researching the use of different biomaterials for immunotherapies and microfluidics in identifying rare immune cells.

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

 

Summer professional development seminar series begins

The 2015 Summer Professional Development Seminars hosted by Johns Hopkins Institute for NanoBioTechnology will be held on select Wednesdays from 10:45 a.m. to noon in the Mason Hall Boardroom on the Johns Hopkins University Homewood Campus. Space is limited, so please RSVP to mspiro@jhu.edu.

PrintJune 10 – Career paths for STEM degrees: What’s next?

A panel discussion with:

  • Elad Firnberg, President and Co-Founder at Revolve Biotechnologies
  • Jacob Koskimaki, Clinical Data Analyst at American Society of Clinical Oncology
  • Laura Dickinson, Head of Research and Development at Gemstone Biotherapeutics LLC
  • Vanessa McMains, Communications Specialist at Johns Hopkins Medicine
  • Helena Zec, PhD candidate Biomedical Engineering

June 24 – What will be the direction of research for the next 20 years?

A conversation with:

  • Denis Wirtz, Vice Provost for Research Johns Hopkins University and Associate Director of INBT
  • John Toscano, Vice Dean for Science and Research Infrastructure and Professor of Chemistry

July 8 – Networking 101

A workshop with:

Tom Fekete, Director of Corporate Partnerships for INBT

School teaches you everything except how to get a job. And, with the average length of a job being just 18 months, every job is temporary. Which means, job search is now a skill every professional needs to survive. Even more important is the difference between a job and a career. Fekete is a 40-year veteran of the chemical and pharmaceuticals industries with high level positions in engineering, research, operations and strategic planning management will talk about careers, job searches and networking.

July 22 – Financial Literacy

A workshop with:

Debbie Johnson of Johns Hopkins Federal Credit Union

Learn about budgeting, saving and what else you can do once you start earning a paycheck.

Hand-held device will quickly ID bacteria

Tza-Huei (Jeff)Wang, a mechanical engineering professor affiliated with Johns Hopkins Institute for NanoBioTechnology, received a $6 million grant from the National Institutes of Health to develop a hand-held device that will quickly indentify bacteria.

Droplet-chip-photo-Wang-Lab-crop-1020x1024

This illustration depicts a microfluidic chip for bacterial detection and drug testing in picoliter-sized droplets. Graphic by Jeff Wang Lab/Johns Hopkins University.

“We need to be faster and more precise in the way we diagnose and treat people with bacterial infections,” said Wang, who is leading the team that will build the new microfluidic testing devices. “Instead of waiting three days to figure out what the infection is and what’s the best drug to treat it, we believe our technology will deliver both answers within just three hours.”

Wang explained that delays in bacterial identification lead physicians to rely on broad spectrum antibiotics, which in turn can lead to drug resistance. Discovering quickly which bug is causing the infection, Wang said “should lead to more effective treatment and a lower risk of promoting antibiotic resistance.”

Wang’s award, which will be distributed over five years toward the development of this life-saving microfluidic device, came from National Institute of Allergy and Infectious Diseases (NIAID).

Read more here.

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

The challenge of accurately measuring drug permeability

In our seventh NanoBio Lab, Erin Gallagher, a predoctoral candidate from the lab of professor Peter Searson, demonstrated the use of a cell permeability assay as a means of modeling drug diffusion through the blood brain barrier (BBB) endothelium. Assays such as this one enable us to better understand the cellular processes that govern what drug molecules are able to cross the BBB and the role of efflux pumps and transporters. Development of more accurate in vitro models is a highly valuable avenue of research, as it will allow for rational drug design to more effectively treat diseases such as Alzheimer’s, Parkinson’s and mood disorders with potentially fewer side effects.

The blood brain barrier (BBB) presents a challenge for delivery of drug molecules to the central nervous system, as many of the mechanisms it employs were evolved specifically to prevent introduction of dangerous substances into the central nervous system. Understanding the mechanisms by which various substances are able to cross the BBB will allow for more rational design of future generations of drug molecules and carrier systems.

The blood brain barrier (BBB) presents a challenge for delivery of drug molecules to the central nervous system, as many of the mechanisms it employs were evolved specifically to prevent introduction of dangerous substances into the central nervous system. Understanding the mechanisms by which various substances are able to cross the BBB will allow for more rational design of future generations of drug molecules and carrier systems.

For the assay, canine kidney cells (MDCK II) were seeded on transwells in a 24 well plate, 24 hours prior to the assay to allow the cells to form a confluent endothelial layer with functional tight junctions. When cells have formed a confluent endothelial layer, ion movement must occur through the cells themselves instead of through the much higher resistivity tight junctions. As a result, the overall resistivity measured is higher than for non-confluent cells, for which ions are able to simply diffuse through the transwell. Therefore, assessment of the integrity of the endothelial layer was done to measure the conductivity through the layer of cells.

Following assessment of the endothelial layer integrity, we ran a permeability assay for the fluorescent molecule Lucifer Yellow (LY) to determine its apparent permeability as a model for drugs diffusing across the BBB. Utilizing a standard concentration curve of LY fluorescence, the amount of LY that diffused through the layer was determined at specific time points to imply apparent permeability. For more typical non-fluorescent drug molecules, high performance liquid chromatography (HPLC) can be used to measure the amount of drug having diffused.

As a tool, assays modeling the blood brain barrier are indispensible to the pharmaceutical industry, but finding a model system that effectively reproduces in vivo conditions for less expensive, high throughput in vitro testing is a challenge. Permeability models, such as the one used in this lab, also allow development of novel strategies for moving drugs across the BBB. These strategies include molecular engineering of drug molecules to take advantage of cellular active transport mechanisms or peptide engineering that facilitates vesicle transport across the endothelium.

David Wilson is a first year PhD student in biomedical engineering working in the drug delivery laboratory of associate professor Jordan Green in biomedical engineering.

Image Citation:  Wong, A. D., Ye, M., Levy, A. F., Rothstein, J. D., Bergles, D. E., & Searson, P. C. (2013). The blood-brain barrier: an engineering perspective. Frontiers in Neuroengineering, 6(August), 1–22. doi:10.3389/fneng.2013.00007

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