Published: January 27, 2017
Jan. 27, 2017 - Researchers from Tufts University's School of Arts and Sciences, the Allen Discovery Center at Tufts, and the University of Maryland, Baltimore County have had previously shown that pigment cells (melanocytes) in developing frogs could be converted to a cancer-like, metastatic form by disrupting their normal bioelectric and serotonergic signaling and had used AI to reverse-engineer a model that explained this complex process. However, during these extensive experiments, the biologists observed something remarkable: All the melanocytes in a single frog larva either converted to the cancer-like form or remained completely normal. In the new study, the researchers asked their AI-derived model to answer the question of how to achieve partial melanocyte conversion within the same animal using one or more interventions.
The AI model ultimately predicted that a precise combination of three reagents (altanserin, a 5HTR2 inhibitor; reserpine, a VMAT inhibitor, and VP16-XlCreb1, mRNA encoding constitutively active CREB) would achieve that outcome. When this pharmaceutical cocktail was used in vivo on real tadpoles, the result was, in fact, conversion of melanocytes in some regions but not others within individual frog larvae-something never before seen. "Even with the full model describing the exact mechanism that controls the system, a human scientist alone would not have been able to find the exact combination of drugs that would result in the desired outcome. This provides proof-of-concept of how an artificial intelligence system can help us find the exact interventions necessary to obtain a specific result," said the paper's first author, Dr. Daniel Lobo, assistant professor of biology and computer science at the University of Maryland, Baltimore County.
Plans for future research include extending the platform to incorporate time-series data that will enable even more accurate comparisons between computer and in vivo models. Researchers also hope to extend the approach to other aspects of regenerative medicine by discovering interventions that help reprogram tumors, kick start regeneration and control stem cell dynamics. Levin added, "Much of biomedicine boils down to this: We have a complex biological system, and a ton of data on what various perturbations have been seen to do to it. Now we want to do something different--cure a disease, control cell behavior, regenerate tissue. For almost any problem where a lot of data are available, we can use this model-discovery platform to find a model and then interrogate it to see what we have to do to achieve result X."
- Adapted from original article by Patrick Collins, Tufts Now
Published: January 26, 2017
Jan. 26, 2017 - Malfunctioning microtubules have been associated with various illnesses including cancer and Alzheimer's disease. However, studying a single dynamic microtubule, which measures 24 nanometers in diameter, and up to 10 microns in length, is complicated by established practices of using dyes or stains that are added in order to see the item more clearly, as they can affect the item that is to be scanned in unexpected ways, damaging or even killing biological materials. Researchers in the Quantitative Light Imaging Laboratory at the Beckman Institute, led by Mikhail Kandel, EBICS trainee and lead author on the study, recently published in ACS Nano their technique of using label-free spatial light interference microscopy (SLIM) and computer processing in order to image the microtubules in an assay.
Previous efforts at imaging the miniscule structures have used immunofluorescence, injecting antibodies into fluorescent dyes in order to clearly see the cell as it functions. However, the fluorescence can affect cell function and the length of time that the cell can be imaged. "We imaged them for a very long period of time, not two or three minutes, but more like eight hours," said Kandel. "The label-free aspect is the main breakthrough in my opinion," said Gabriel Popescu, associate professor of electrical and computer engineering. "There have been other efforts towards making this label-free, it's a very important class of challenges. Current techniques yield smaller fields of view, and the image contrast is not as good."
SLIM is a commercially manufactured product that can fit on to upgrade about any microscope, say the researchers. This allows biologists to use other microscopy techniques, including fluorescence, in addition to SLIM. The SLIM product is available through Phi Optics, a company that Popescu founded. The researchers plan to push the boundaries on imaging cells, hopefully imaging microtubules in live cells. "If we manage to push this in a living cell, that would be a real breakthrough," said Popescu.
- Adapted from original article by Maeve Reilly, Beckman Institute
EBICS Knowledge Transfer in Action!: Kara McCloskey delivers UIUC-developed bio-bot teaching module to UC Merced
Published: January 11, 2017
Jan. 11, 2017 - Kara McCloskey, EBICS faculty member at UC Merced, collaborates with Renuka Nandkishore and Rashid Bashir's lab at UIUC to teach students in her Tissue Engineering Design course to build living, walking robots, aka "bio-bots," out of engineered muscle cells. By harnessing the adaptive response behaviors of biological materials, bio-bots could accomplish more than traditional robots can, due to complex functionalities like self-assembly or self-healing. "Bio-bots have only been around since 2012, so this is really cutting-edge science with multiple technologies - natural materials assembly, 3-D printing, genetic engineering, cell patterning and self-assembly, mechanical force generation - all in a micro-scale platform," McCloskey said.
UIUC developed the bio-bot teaching curriculum and provided the most critical tools, protocols and lecture materials -- the molds for the muscle rings, the 3-D-printed skeletons and the original cell line -- to support delivering the course at collaborating EBICS institutions. McCloskey's UC Merced students are the first from another campus to learn this module as part of their coursework. In learning to assemble cells into functional tissue, McCloskey's students culture the cells in soft, gelatin-like polymers called hydrogels. They pattern the cells in the gel so they will self-assemble into muscle rings, attach the rings to 3D-printed "bones" to create the 7-millimeter-long, light-responsive bots, and then exercise biological machines to build strength called contractile forces.
With an altered design, the bio-bots could be customized for specific applications. Researchers in McCloskey's School of Engineering lab are using similar technology to pattern stem cell-derived heart cells into a sheath of living cardiac tissue that could patch areas of human heart muscle that have been damaged by heart attacks. The sheath would contract and expand just like natural tissue does, in rhythm with the heart. But they must figure out how to integrate patterned synchronously contracting muscle with vasculature to supply blood, and so far, the two have not integrated well.
Ritu Raman, EBICS postdoctoral fellow at UIUC helped design and co-lecture the bio-bot course, focusing on teaching students how to use 3-D printers to design and build their own biological machines. "We see many potential applications for bio-bots ranging from healthcare to national defense to environmental cleanup," Raman said. However, the focus of the curriculum isn't on applications, but on teaching future engineers the fundamental design rules and principles of building with biology. "We want to introduce biological materials into the toolkit of the next generation of makers by giving them hands-on experience with bio-bot design and manufacture," Raman said.
- Adapted from the original article by Lorena Anderson, UC Merced University News
EBICS core principles: Ethics modules and Interdisciplinary modules are now fully updated on EBICS website!
Published: January 9, 2017
To date, EBICS has developed four Ethics Modules, which affiliates have presented to a wide range of audiences throughout the United States. Explore modules 1-4 on the EBICS website!
The major intellectual theme of EBICS is the integration of concepts from the applied fields of tissue-engineering, systems biology, and synthetic biology to: a) yield new analytical insights into emergent behaviors of integrated cellular systems and b) use this analytical framework as the basis to design and build new kinds of biological machines.
Each of the applied fields of EBICS research integrates approaches from several established engineering and science disciplines; as a result, EBICS research is highly interdisciplinary in nature. The EBICS Education team has curated lectures from EBICS faculty to bridge potential gaps in technical knowledge experienced by students from disparate engineering and science backgrounds and to provide continuing education for EBICS undergraduates, graduate students and postdocs. Explore the interdisciplinary modules on the EBICS website! We will continue to update the series of lectures going forward.
Prof. Laurie Boyer leads Journal Club discussion on "Developmental Engineering of Cell Fate Decisions"
Published: December 12, 2016
Dec. 12, 2016 - MIT hosted Journal Club where the EBICS community across 7 of its affiliated institutions and organizations tuned into Prof. Laurie Boyer's discussion of two papers "Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types" and "Tissue Mechanics Orchestrate Wnt-Dependent Human Embryonic Stem Cell Differentiation" to illustrate the importance of developmental engineering of cell fate decisions. In the context of EBICS, developmental engineering determines parameters that underpin generations of specific and homogeneous cell types, allows identification of key markers for quantifying in vitro emergent behavior in real time, and provides a critical roadmap, both for inferring synthetic circuits driving cell specification and for generating functional 3D-cell systems.
From "Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types," Boyer highlighted:
- Stepwise map of competing signals guiding mesoderm development
- Efficient human mesoderm induction by blocking formation of unwanted fates
- ESC-derived human bone progenitors and heart precursors engraft in vivo
- A transient segmentation program in human embryogenesis marked by HOPX
From "Tissue Mechanics Orchestrate Wnt-Dependent Human Embryonic Stem Cell Differentiation," Boyer highlighted:
- Compliant hydrogel substrates enhance mesoderm differentiation of human ESCs
- Stabilization of adherens junctions primes hESCs for mesoderm differentiation
- Junctional reorganization and Src activity promote nuclear translocation of b-catenin
- On stiff gels, b-catenin degradation inhibits mesodermal differentiation
Missed it? Listen to the discussion now!
Published: December 6, 2016
Dec. 6, 2016 - The "Stice Stice Lab produces a neurodevelopment model with potential to accelerate research on Zika-related birth defects" feature story from the November 2016 EBICS Newsletter landed the cover feature of Stem Cells and Development's 25th Anniversary issue in support of their paper, "Zika Virus Induced Mortality and Microcephaly in Chicken Embryos."
The research, led by Forrest Goodfellow, a 2012 EBICS REU student and mentored by professor Steven Stice since 2011, presents using a current circulating isolate of Zika virus, MEX1-44, to infect chick embryos, and results are analyzed to develop a neurodevelopmental chick model that could mimic the effects of Zika on the first trimester of pregnancy. This model demonstrates fetal death and brain damage in early chick embryos similar to microcephaly. While high dose infection resulted in embryo death, low dose infections resulted in a decrease in cortical volume. In addition, some embryos displayed structural malformations of the central nervous system, shown in the MRI image (boxed area) of a Zika-infected embryo at embryonic day 20.
- Adapted from original caption provided by Dr. Melinda A. Brindley of the Department of Infectious Diseases, Population Health, Center for Vaccines and Immunology, and Dr. Steven L. Stice of the Regenerative Bioscience Center, University of Georgia
Published: December 2, 2016
Dec. 2, 2016 - Caroline Cvetkovic defended her dissertation, "Biological Building Blocks for 3D-Printed Cellular Systems," at the University of Illinois Urbana-Champaign (UIUC) in front of peers and a defense committee of EBICS faculty members Rashid Bashir, Martha Gillette, Hyunjoon Kong, and Taher Saif.
In Bashir Lab, Cvetkovic's research focused on the development of neuromuscular-controlled biological machines ("bio-bots"). The work combined aspects of 3D-printing, tissue-engineering, and soft robotics, and led to co-authorship on 7 publications and over 15 conference and seminar presentations.
Cvetkovic was funded by EBICS, as well as an Integrative Graduate Education and Research Traineeship (IGERT) grant from NSF, and the Support for Under-Represented Groups in Engineering (SURGE) fellowship at UIUC. Accomplishments throughout her graduate study include a Top Presentation nomination at the Biomedical Engineering Society (BMES) Annual Meeting, an invitation to be a session co-chair at the Tissue Engineering and Regenerative Medicine (TERMIS) World Congress, an invitation to the Mechanobiology Institute at the National University of Singapore, and a certificate from the Clinical and Translational Research Course for PhD Students at the National Institutes of Health.
Throughout her time at UIUC, Cvetkovic participated in research pertaining to 3 separate NSF-funded centers and programs: EBICS, (IGERT), and Center for Nanoscale Science and Technology (CNST). She engaged young students in scientific experimentation at community outreach activities such as UIUC's Engineering Open House and Science at the Market. Additionally, she participated in activities of the Student Leadership Council, Girls' Adventures in Math, Engineering, and Science (G.A.M.E.S.) Camp, 1867 Society, Provost and Graduate College Student Advisory Board, and was a project manager at Learning in the Community (LINC) Partnership.
We would like to congratulate and recognize Dr. Caroline Cvetkovic on her many accomplishments, and we wish her great success as she moves forward in her career!
Lu Lab exposes masses of hidden traits and possible subtle genetic connections relevant to unseen influences on disease
Published: November 23, 2016
Nov. 23, 2016 - Hang Lu, EBICS faculty member at Georgia Tech, led researchers to develop algorithms and a special microscope slide to expose previously unseen neurological nuances and intricate mutations that may be behind them. Their findings, published in Nature Communications exposes some of the secrets behind gene mutations towards localizing genetic biomarkers for diseases in humans and understanding debilitating disorders, including schizophrenia, bipolar disorder, autism, and autoimmune disorders.
In the Lu lab's latest experiment, researchers track the faintest phenotype changes in roundworms, chosen because their nerves share strong similarities with humans, by marking nerve proteins to appear as dots on roundworms' undersides for the computer to scan. When mutations occur, the dots can change ever so slightly. "To the naked eye, they're just dots on a dark background," Lu said. But the computer sees in them phenotypical shifts.
Lu's technique works via a transparent slide with tiny tubes that suck in one worm at a time under the computer's microscope. The scientists freeze the worm for a moment to take its picture, then unfreezes it. There's a fork in the tube holding the worm. If the algorithm detects a mutant based on its marked pattern in the image - even if this is not visible to the eye - the worm gets sucked down the first path for further study. If it isn't a mutant, it gets sucked down the second path.
Using this technique, the scientists stumbled upon a very subtle allele - a variation of a gene caused by mutation. The worms that had the allele were real mutants, but to the eye, they were completely neat and normal. They even behaved normally at first glance, and the researchers thought the computer may have sorted them out as mutants by mistake -- until a hitch turned up. "After they swam for about 40 minutes, they got really, really weak and couldn't swim well anymore," Lu said. The allele seemed to be associated with some kind of neurological disorder.
"Seen as a metaphor, this is an example of how you might identify something that is relevant to a disease but incredibly subtle," Lu said, "and you would never have found it using eyes and a microscope."
- Adapted from the original article by Ben Brumfield, Georgia Tech News Center
Published: November 18, 2016
The National Science Foundation (NSF) Center on Emergent Behaviors of Integrated Cellular Systems (EBICS) invites all undergraduates who are U.S. citizens/permanent residents AND currently enrolled in a science/engineering undergraduate program to apply! We strongly encourage students from underrepresented minority groups, women, and individuals with disabilities to submit an application! Learn about what EBICS REU offers and APPLY! Deadline Friday February 17, 2017.
Published: November 3, 2016
Manu Platt, associate professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory, was recognized by the Atlanta area as one of 40 leaders under the age of 40 who have made significant career achievements and have demonstrated substantial involvement in community service.
One of Professor Platt's mottos is "think globally, act locally, then act globally." This has been enacted in his projects starting with developing a blood test to determine if HIV-positive patients in South Africa were adhering to their antiretroviral medication regimen. Through extension of this work, his lab started projects in Ethiopia, first on HIV-related studies, then later assisting with the training of Ethiopian graduate students to process cancer samples and characterize differences between tumors.
At Georgia Tech, Platt has been hosting and mentoring high school students working in his lab under the Project ENGAGES (Engaging the Next Generation At Georgia Tech in Engineering and Science) program - now in its fourth year. This is a high school research program started with Professor Emeritus Bob Nerem that has brought through 60 African-American students from the Atlanta Public School system.
- Adapted from original article by Walter Rich, GT News. Read to learn more about Professor Platt's work.
Carrie Kouadio showcases EBICS Knowledge Transfer efforts at National Science Teachers Association Conference
Published: October 27, 2016
Carrie Kouadio, EBICS Knowledge Transfer Program Manager, presented "Biological Machines: Bioengineering Activities for the Classroom" to over 50 educators at the National Science Teachers Association Conference in Minneapolis, MN. The teacher-focused presentation synthesizes the outreach work of EBICS trainees Brian Williams, Ritu Raman, Ghazal Naseri Kouzehgarani, Raymond Swetenburg, and EBICS faculty members Lizanne Destefano and Rashid Bashir. The potential health, security, and environmental applications of EBICS research were illustrated through demonstrations and interactive activities. Education resources developed by the team were shared with the participants, and included the light-simulated walking robot, biomimicry in a light-sensitive robot, soft robotics, emergent behaviors in complex systems, and the ethics modules.
Kouadio also presented at the Illinois Science and Math Conference on October 7, 2016 with primarily science and math educators.
Popescu and Gillette Labs collaboration develop new imaging method to analyze dynamics of cellular systems
Published: October 26, 2016
Led by professor Gabriel Popescu and professor Martha Gillette, researchers at their respective labs, including former EBICS trainees Ru Wang, Basanta Baduri, Shamira Sridharan, Mustafa Mir, and Raj Iyer, developed a dye and chemical-free imaging method, phase correlation imaging (PCI), to track cells over long periods of time. PCI uses only light to reveal dynamics and provide insight into how cells function, develop and interact.
The study, published in Scientific Reports also uses PCI to look at how elements of the cell's internal skeleton structure guide transportation within the cell. Cells and their internal structures are transparent so researchers commonly use chemicals, like colored or fluorescent stains, to see structures inside cells, but chemicals can disrupt activity, or even poison the cell, and only work for a limited time, making it difficult to track normal cellular activity.
Because PCI only uses light, the researchers can scan a cell culture over and over, creating a timeline of movement within the cell and highlighting hotspots of activity. They can also tell the difference between quiescent cells, cells that are dormant but can become active again when stimulated, and senescent cells, older cells that have stopped dividing. The distinction is important, because quiescent cells are crucial for healing and repair after injury, but are difficult to see without specific chemical labels.
The researchers are now applying PCI to study neurons. They hope to witness emergent behavior, such as neurons in a culture beginning to talk to each other and stem cells developing into neurons. Later on, they plan to apply these dynamic maps to large tissues, such as embryos, brain slices and whole organisms, like worms, to watch development.
- Adapted from original article by Liz Ahlberg Touchstone, UIUC News Bureau
Stice Lab produces neurodevelopmental model with potential to accelerate research on Zika-related birth defects
Published: October 19, 2016
Forrest Goodfellow, a 2012 EBICS REU student and mentored by professor Steven Stice since 2011, has been leading a team at University of Georgia's Regenerative Bioscience Center (RBC) since 2015 to develop a neurodevelopmental chick model that could mimic the effects of Zika on the first trimester of pregnancy. This model demonstrates fetal death and brain damage in early chick embryos similar to microcephaly -- a rare birth defect linked to the Zika virus, now alarming health experts worldwide.
Chick embryos have significant similarity to human fetal neurodevelopment and rapid embryonic process: "We wanted a complete animal model, closely to that of a human, which would recapitulate the microcephaly phenotype," said Goodfellow, who has worked extensively with eggs and chickens. In a previous project with Stice and Dr. Qun Zhao, the team developed a unique approach of marrying stem cell biology and MRI to track and label neural stem cells. Using the neurodevelopment chick model, researchers can take a closer look at a multitude of different Zika strains and possibly identify the critical window of susceptibility for Zika virus-induced birth defects, allowing further design and testing of therapeutic efficacy.
Goodfellow presented the findings at the 2016 Southern Translational Education and Research (STaR) Conference. The team's research was also recently featured on WSB-ATL (ABC) news, and the team will be designing the cover of Stem Cells and Development's November 2016 issue.
- Adapted from the original article by Charlene Betourney, UGA Today
Published: October 17, 2016
Paula Hammond, the David H. Koch Professor in Engineering and head of MIT's Department of Chemical Engineering, has been elected to the National Academy of Medicine (NAM) in recognition of her distinguished contributions to medicine and health. Membership in the NAM is considered one of the highest honors in the fields of health and medicine and recognizes individuals who have demonstrated outstanding professional achievements and commitment to service.
Professor Hammond, a member of MIT's Koch Institute for Integrative Cancer Research and a founding member of the Institute for Soldier Nanotechnologies, focuses on biomaterials and drug delivery, particularly the self-assembly of polymeric nanomaterials.The core of Hammond's work is the use of electrostatics, including a technique known as layer-by-layer assembly, to generate functional materials with highly controlled architectures. These materials are used to deliver drugs for cancer and regenerative medicine, including treatments for wound healing and bone repair. Some of her recent efforts include targeted nanomedicine approaches to address resistant cancers, such as advanced ovarian cancer. She has worked with clinicians and researchers at various Boston-area hospitals, and she and members of her lab have been involved with a range of biotech companies.
- Adapted from original article by Anne Trafton, MIT News. Read to learn more about Professor Hammond's awards and accomplishments.
Ritu Raman completes her PhD at the University of Illinois at Urbana-Champaign
Published: October 17, 2016
Ritu Raman defended her dissertation, entitled "3D Printed Muscle-Powered Bio-Bots," with co-advisors Rashid Bashir and Taher Saif. Her committee members included Gabriel Popescu and Hyun Joon Kong. "We have developed and optimized novel stereolithographic 3D printing technologies as enabling tools for 'building with biology.' Using these 3D printers, we have forward-engineered biohybrid robots, or bio-bots, capable of complex controllable locomotion in response to a range of dynamic environmental signals. We anticipate that, in collaboration with the EBICS community, we can design bio-bots that target the next generation of grand engineering challenges," Raman explains.
In her time at the University of Illinois at Urbana-Champaign, Raman has been very productive and engaged. To highlight a selection of her recognitions, in 2016, she became the most published graduate student in the Mechanical Science and Engineering Graduate Program, and won 1st Place in the ThinkChicago: Lollapalooza Civic Tech Challenge. In 2015, she won the Illinois Innovation 15K Prize. She was awarded the NSF GRFP in 2014 and the NSF IGERT fellowship in 2012.
Throughout her involvement with EBICS, Raman has been a valuable contributor to the SLC and to science outreach efforts to the public. As a lecturer for the Bioengineering course "Biofabrication Lab," Raman designed and co-lectured a course focused on teaching the fundamental design rules and principles of building biological machines. In this capacity, she disseminated a novel course curriculum and core philosophy of "building with biology" to instructors at partner institutions around the nation.
We would like to congratulate and recognize Dr. Ritu Raman on her many accomplishments, and we wish her great success as she moves forward in her career!
Brian Williams earns EBICS Knowledge Transfer Award
Published: October 11, 2016
Brian Williams, EBICS trainee based out of Saif Lab at UIUC, was recognized for his efforts in Knowledge Transfer, "For Leadership in Communicating Science to the Public." Brian was also awarded with $500 in recognition of his creativity, leadership, and hard work in STEM outreach. Brian has played a major role in the success of EBICS outreach activities at the University of Illinois at Urbana-Champaign such as Engineering Open House and Science at the Market. He has developed many of the activities now utilized in presentations for teachers to teach the public about EBICS research. Thank you Brian, for all your efforts!
EBICS REU alumni present their research at 2016 Biomedical Engineering Society (BMES) Annual Meeting
Published: October 8, 2016
EBICS REU alumni Marc Shuler, Steven Pirvu, Alyssa Mendenhall, and Kwasi Amofa, and Georgia Tech SURE alumnus Ken Brandon presented their research at 2016 BMES annual meeting in Minneapolis, MN and were active participants in the many organized activities throughout the 4-day conference. While presenting among 800+ other posters, the EBICS representatives were confident in discussing their research with others: "[We] had a blast at BMES! I met some interesting people and (hopefully) successfully talked to potential graduate professors. I also learned a lot from the sessions." says Mendenhall. Pirvu enthused about the networking potential granted: "BMES was great! I presented on the final day, and a few professors came up to give me their business cards!". All expressed gratitude for the EBICS support to make their attendance at the conference possible, and the advocacy towards their future goals.
Simone Douglas receives Sloan Fellowship
Published: August 26, 2016
Aug. 26, 2016 - Simone Douglas was named as a 2016 Sloan Scholar as part of the Alfred P. Sloan Foundation's Minority Ph.D. (MPHD) Program. Simone is a 2nd year Ph.D. student, mentored by Prof. Manu Platt, in the biomedical engineering program at Georgia Tech and Emory University. In EBICS, she is a member of the Student Leadership Council (SLC) and is currently researching alternative fibrinolysis pathways in the Vascularization Working Group, to characterize and control fibrin degradation in vascularized constructs.
The Sloan Foundation was created in 1995 to "assist efforts to diversify the U.S. Ph.D. degree-holding workforce by increasing the recruitment, retention, and graduation of underrepresented minority doctoral students in science, technology, engineering, and mathematics." This year's applicant pool was strong and competitive; only eight students were selected from Georgia Tech to be nominated to the Sloan Foundation. Congratulations Simone!
Clare Ko receives training grant, The Tissue Microenvironment (TiMe) Training Program, supported by NIH
Published: August 25, 2016
Aug. 25, 2016 - Clare Ko, EBICS trainee at UIUC mentored by Prof. Hyunjoon Kong, was selected from a strong applicant pool across UIUC to receive one of eight TiMe Training Program grants, which awards recipients up to two years of funding from the NIH, and provides recipients with curricular, extracurricular, professional development, and career development activities. The TiMe Training program aims to integrate three technological approaches: sensing and imaging to measure biochemical and biophysical parameters, bioengineering to recapitulate the tissue microenvironment, and computational modeling. Currently, Clare contributes to two EBICS Working Groups: Pump-Bot, in which her project is assembling a self-activated pump system that can transfer fluid, and Neuron-Muscle, in which she is engineering NMJ in vitro using nano-patterned substrates. Congratulations Clare!
Cali Callaway acknowledges her experiences working in the Stice and Kamm labs for shaping her academic trajectory
Published: August 14, 2016
Aug. 14, 2016 - As a freshman, Cali joined Prof. Stice's lab to work on the development of a neural tube injury model in chickens incorporating mouse pluripotent stem cells, then spent summer 2015 after her sophomore year at MIT in Prof. Kamm's lab to research a microfluidics platform for the study of neuromuscular junction formation. In her profile for UGA's "Amazing Students" column, Cali expresses gratitude to the Stice and Kamm labs for the skill-building opportunities they provided her, and commends Dr. Stice's mentorship throughout her time at UGA. Now starting her senior year, Cali plans on attending medical school in Fall 2017.
Meghan Ferrall-Fairbanks and Dayne West lead teams to receive top prize at PrePARE Professional Development Workshop
Published: August 13, 2016
Aug. 7-12, 2016 - EBICS trainees Meghan Ferrall-Fairbanks (GT), Nicole Madfis (UC Merced), Tanya Singh (CCNY), and Dayne West (GT) attended the Paths Afforded by the Research Enterprise (PrePARE) Professional Development Workshop in Indianapolis, IN. During this week-long workshop, trainee representatives from all the NSF STCs were taught a wide range of important professional skills, including communicating your science in presentations and interviews, creating individualized development plans, and dining interview etiquette, to succeed in both academic and industrial careers. In addition to these skills, participants divided into six multi-institutional interdisciplinary teams to each write an NSF RFA proposal to address a grand challenge. Meghan's team proposed to develop a new biomaterial that can be used to protect against coastal erosion. Dayne's team proposed improvements to the reduce-reuse-recycle triangle, by making all plastics recyclable. After all six teams presented their proposals, Meghan and Dayne's teams were selected as winners of the Amazon gift card prize. Congratulations to both!
Published: August 8, 2016
Aug. 8, 2016 - Brian Williams defended his dissertation "Low Reynolds Number Biohybrid Swimming" at the University of Illinois Urbana-Champaign in front of advisor, Taher Saif, and the rest of his defense committee Hyunjoon Kong, Rhanor Gillette, and Gabriel Juarez.
In Saif Lab, Williams built multicellular biohybrid machines with networks of neurons and myocytes, including a flagellar swimmer that uses the contractions of one to several cardiac myocytes to generate propulsion at low Reynolds number. To achieve the goal of using the complex internal machinery of the eukaryotic cell to build programmable, self-powered, biohybrid robotics, Williams also microfabricated characterizable, compliant platforms to probe specific biological mechanisms, such as the role of mechanical coupling in the collective behavior of large populations of cardiac myocytes. Finally, he analyzed and studied vesicle dynamics in various cell types, and used their transport characteristics to probe the intracellular environment.
Williams was one of EBICS's most prolific developers of outreach demonstrations, used in community events in Champaign, to present core EBICS research concepts, highlights of which include the soft robotics inchworm, the optogenetic bot, and most recently, the Elementary Braitenberg vehicle.
Congratulations to Dr. Brian Williams, who is currently a mechanical engineer at Lam Research in Portland Oregon, and we wish him great success as he moves forward in his career!
Published: August 4, 2016
Aug. 3-4, 2016 - The 1st International Workshop on Engineering Living Systems convened a cadre of 60 forward-looking thought-leaders across a variety of expertise including: industry, stem cell biology, developmental biology, synthetic biology, tissue chip engineering, robotics, and ethics, whose primary goal is the exploration of the ethical and research implications that arise from the EBICS mission to develop the capability to design, engineer and produce complex integrated cellular systems or "biological machines" that solve real-world problems in health, security, and the environment.
Critical to the successful design of such engineered cellular systems is a fundamental understanding of the interactions between cells and their environment, their control by biochemical and mechanical cues, and the coordinated behavior of functional cell clusters. Examples range from biological robots to organs-on-a-chip, and have broad applications across medicine, manufacturing, agriculture, and energy management, among other disciplines. Whether we achieve this through a "bottom-up" or a "top-down" approach, the basic cellular building blocks can all be derived from pluripotent sources.
In discussing the ethical and research implications of these complex biological interactions, the emergent behaviors they produce, and the ultimate creation of biological machines engineered to perform specific, targeted functions, 2016 Workshop participants agreed to leverage the following broader impacts:
- A position paper on Engineered Living Systems for wide dissemination
- A proposal for a new EFRI call on:
- Advanced manufacturing processes for multicellular machines
- Reduced functionality cells for ELSs
- New collaborations and potential partnerships
- Avenues for continuing EBICS activities
- Transitioning to a regular meeting (e.g. GRC)
- Possibility for a new journal
- Recruiting EBICS Distinguished Visiting Scholars
- Forging new international collaborations (a "virtual center")
- Providing trainees a broader perspective of EBICS-centric activities worldwide
The Workshop on Engineering Living Systems will tentatively next assemble in 2018.
MIT REU engages in Poster Session and Closing Luncheon of 30th Annual MIT Summer Research Programs
Published: August 4, 2016
Aug. 4, 2016 - Upon returning from the 2016 EBICS Annual Retreat, MIT REU immediately began preparations to present their research two days later at the 30th Annual MIT Summer Research Programs Poster Session. 103 students across 4 summer research programs at MIT, including EBICS, discussed their research with, and fielded questions from, a diverse audience of peers, faculty, mentors, graduate students, distinguished guests, staff, and program alumni that altogether formed an audience of ~250 guests. At the Closing Luncheon, Minerva Marcano had the honor of introducing the Keynote Speaker, Dr. Christopher Jones, who served as the Assistant Dean for Graduate Education at MIT for nearly a decade.
Published: August 3, 2016
July 31 - Aug. 2, 2016 - 87 members of the EBICS community including faculty, trainees, REUs, External Advisory Committee (EAC), Industry Advisory Committee (IAC), and staff, participated in the 2016 EBICS Annual Retreat at the Q Center in St. Charles, IL. Highlights of the Retreat include:
- Presentations on diversity and education in EBICS, the Student Leadership Council (SLC), and all seven working group research presentations
- Natasha Arora and Marianna Sofman's presentation of their Technology Conceptualization Plan
- Discussion of Ethics Module 4: Emergent Behavior
- Trainee and REU poster presentations
- Discussion within working group breakout sessions
- Keynote Address by Dr. Kristin Fabre, AstraZeneca
For your entertainment - watch the trainee & REU Knockerball activity! Video courtesy of Simone Douglas.
Sebastien Uzel led development of a microfluidic device that replicates the connection between muscles and nerves
Published: August 3, 2016
Aug. 3, 2016 - During his graduate studies at MIT, Sebastien Uzel, now a postdoc at Harvard, led the work on creating a quarter-sized microfluidic device, that allows researchers to influence and observe the interactions between the muscle tissue and motor neurons within a realistic, three-dimensional matrix.
Previously, to simulate the neuromuscular junction in the lab, researchers grew muscle and nerve cells in shallow Petri dishes or on small glass substrates. To recreate more realistic in vitro neuromuscular junctions, Uzel and his colleagues, which includes EBICS faculty Prof. Roger Kamm, Prof. Laurie Boyer, and former EBICS trainee Vincent Chan, fabricated two important features in their microfluidic device: a three-dimensional environment, and compartments that separate muscles from nerves to mimic their natural separation in the human body. The researchers suspended muscle and neuron cells in the millimeter-sized compartments, which they then filled with gel to mimic a three-dimensional environment.
The research results, published online in Science Advances, may help scientists understand and identify drugs to treat amyotrophic lateral sclerosis (ALS), as well as other neuromuscular-related conditions, and could even be tailored to individual patients.
Sebastien and his coauthors have submitted a patent application for their microfluidic device.
- Adapted from the original article by Jennifer Chu, MIT News
UIUC REU presents their posters at the Illinois Summer Research Symposium
Published: July 23, 2016
July 21-22, 2016 - EBICS REU students at Illinois participated in the Illinois Summer Research Symposium (ISRS). This annual event brings together nine summer research programs that support the inclusion and participation of students from U.S. populations underrepresented in graduate study. All members of UIUC REU presented their research through presentations and poster sessions and participated in networking and social activities. The ISRS draws more than 120 students from across a variety of disciplines.
NPR's Science Friday interviews Ritu Raman about UIUC's bio-bot research in their segment "Predicting the Future of Robotics"
Published: July 22, 2016
July 22, 2016 - "And as engineers build squishy biological-machine hybrids, with mouse muscles and sea slug mouthparts, how far are we from creating truly living machines? A look at the future of 'bio-bots' and the unintended consequences of combining flesh, neurons, and mechanical parts." - Science Friday
Caroline Cvetkovic completes the Clinical and Translational Research Course at the NIH Clinical Center
Published: July 22, 2016
July 22, 2016 - Caroline Cvetkovic was selected as part of a 28-member cohort to participate in the two-week intensive Clinical and Translational Research course at the NIH campus in Bethesda, Maryland.
"The purpose of the course is to demonstrate the role of PhD scientists in clinical and translational research, provide an overview and examples of how basic science and clinical observations lead to translational research, and increase awareness and access to Ph.D. role models, research resources, and potential career opportunities at the NIH." - NIH Clinical Center
MIT EBICS REU cultivates "Chalk Talk" best practices at Novartis
Published: July 5, 2016
July 5, 2016 - MIT EBICS REU started off their Week 5 with a science overview and industry tour of Novartis. They impressed organizers of Novartis's highly competitive Summer Scholars program with their thoughtful and active participation during the Lunch Seminar discussing best practices in presenting Chalk Talks. Aside from working on their individual projects alongside their mentors, REUs have also explored the "Journey to the Ph.D." through a workshop with MIT faculty from a sampling of departments, and a lunch networking event with a diverse group of Biological Engineering graduate students.
Speakers confirmed for the EBICS Annual Retreat, and the Workshop on Engineering Living Systems
Published: July 5, 2016
July 5, 2016 - Kristin Fabre, Ph.D., Scientific Program Manager for the Tissue Chip Initiative, and Tom Skalak, Ph.D., Executive Director of Science and Technology of the Paul G. Allen Frontiers Group have been confirmed as speakers for the EBICS Retreat, and the Workshop on Engineering Living Systems respectively.
Dr. Fabre received her BS in Biology from the University of Wyoming, followed by her MS and PhD from Colorado State University in Cell and Molecular Biology. Fabre joined NIH National Center for Advancing Translational Sciences (NCATS) in November 2012 and is the Scientific Program Manager for the Tissue Chip Initiative. The Tissue Chip Program is comprised of several academic and government entities, aimed to bioengineer microphysiological platforms (or chips) that mimic human organ systems. These MPS platforms would be utilized for predicting efficacy and toxicity of candidate compounds faster, cheaper and with less use of animal models compared with current methods.
Dr. Skalak was educated as a bioengineer at Johns Hopkins University (B.E.S. 1979) and at the University of California, San Diego (Ph.D. 1984), is a Fellow of the National Academy of Inventors. Previously, he was the Vice President for Research and Professor of Biomedical Engineering at the University of Virginia, where he led research and innovation programs spanning biosciences, environmental sustainability, physical sciences, engineering and technology, arts, design, and humanities. He is a past President of both the American Institute of Medical and Biological Engineering (AIMBE) and the Biomedical Engineering Society (BMES). Skalak is a frequent speaker on innovation and creativity at Fortune 500, venture capital, major art museums, and government partners, including The White House.
Sebastian Palacios recognized for his leadership in the MIT community, and his research accomplishments
Published: July 1, 2016
Sebastian Palacios, a 3rd year Ph.D. candidate in Ron Weiss's lab, recently received three recognitions: the 2016 Golden Beaver Award, an honorable mention for his research and poster in the category of Biomedical Devices at the 2016 Health, Science, and Technology (HST) Forum, and the MIT UCEM Sloan Award.
The Golden Beaver Award commends excellence in leadership for creating a positive change within the MIT graduate community, which Sebastian demonstrated through his leadership roles in Synberc, the MIT graduate residences, and being one of the founders of the MIT Biotechnology Report.
Sebastian received his HST honorable mention for his design of a new type of advanced medical technology that combines synthetic biology, neuroscience, control theory, semiconductor technology and computer science to repair the nervous system.
The MIT UCEM (University Center of Exemplary Mentoring) Awards are presented to select MIT students in recognition of outstanding performance in their graduate program and a promising future.
EBICS is excited to welcome Sebastian into the EBICS Student Leadership Council (SLC), as of July 2016. His experience on the SLC of Synberc, an NSF center, his leadership in the MIT community, and his passion for professional growth, mentoring and the engineering disciplines are valuable assets in cultivating the growth of EBICS.
Georgia Tech EBICS REU tours Axion Biosystems
Published: June 29, 2016
June 29, 2016 - After 6 weeks of diving into research, cell-culturing and proposal writing, the EBICS REU students at Georgia Tech decided to kick back for some rest and relaxation at the campus student center where they enjoyed pizza, games, and bonding with one another. The group went on their first industry tour to Axion Biosystems in Atlanta, in which some described the experience as "eye-opening," giving them a different perspective on what it would be like to work in industry versus academia. The students have often expressed a high level of gratitude for the overall experience of being an EBICS REU student and the opportunities it affords. The next four weeks will no doubt be more intense as the students prepare for their final essays and oral/poster presentations before attending the EBICS retreat.
Published: June 19, 2016
June 19, 2016 - In his feature, Raymond reflects on his experience working with Dr. Steve Stice (his mentor and EBICS faculty member), his involvement with the EBICS Student Leadership Council, and the opportunities opened to him through EBICS. Read the full Q & A style feature article.
Raymond and his family also recently welcomed their second son, Jack. After an 8 week stay in the NICU, Jack is now at home. Congratulations to the Swetenburg family!
Levin Lab discovery of bioelectric signaling role in channelopathies of embryogenesis featured on June cover of The Journal of Physiology
Published: June 15, 2016
June 15, 2016 - Levin lab research showing the bioelectric mechanism by which rare genetic disorder Andersen-Tawil Syndrome causes facial deformities, published online in advance of print, and featured in the March EBICS newsletter, is now in print, with a research micrograph on the June cover.
The Levin Lab also citied EBICS support in the following recent publications:
- In Frontiers in Bioengineering and Biotechnology: Exploring Instructive Physiological Signaling with the Bioelectric Tissue Simulation Engine (BETSE)
- In Developmental Neurobiology: Gap Junctional Signaling in Pattern Regulation: physiological network connectivity instructs growth and form
Published: June 1, 2016
June 1, 2016 - Congratulations to Dr. Hyunjoon Kong, EBICS faculty at UIUC, who received a 2016 Campus Distinguished Promotion Award. The award, given by the Campus Committee on Promotion and Tenure, identifies scholars whose contributions and achievements within their respective fields are particularly excellent.
Dr. Kong's promotion to the rank of full professor takes effect Aug. 16, 2016. He also holds the title of College of Liberal Arts & Sciences Centennial Scholar.
Dr. Kong is also a new member of the International Editorial Board of Biomaterials.
Published: June 1, 2016
June 1, 2016 - Georgia Tech welcomed the fourth cohort of Project ENGAGES research scholars on June 1, 2016. After two weeks of intense preparation through the program's "cell biology boot-camp," the 12 new high school students were able to participate in a lab speed-dating event to be matched with a mentor for the duration of the year. The end result was phenomenal and all of the students and mentors were extremely happy with their choices. The students finished boot-camp as of June 28, and are now working full-time in a lab with their respective mentor. In addition to research, the remainder of the summer will include industry tours, intense SAT/ACT prep, professional development and a finale oral and poster presentation.
UIUC EBICS REU hosts STEM outreach activity for Urbana, IL community
Published: May 28, 2016
May 28, 2016 - The University of Illinois - Urbana Champaign EBICS REU students and research team leader hosted a STEM educational booth at the Illinois Farmers' Market in Urbana, IL from 8:00am - 12:00pm on Saturday, May 28, 2016. Visitors to the booth designed shapes with clay and bb-gun pellets to either race them to the bottom of the water tank or keep them afloat - all while learning surface tension science! Thank you to Brian Williams, EBICS trainee, for organizing the demonstrations on surface tension and the sink tank race!
Published: April 28, 2016
April 28, 2016 - Yuhong Fan, EBICS faculty at Georgia Tech, presented 3 papers, related to epigenetic heterogeneity, a theme that is critical to EBICS research.
Read the articles:
Professor Kara McCloskey to lead graduate education outreach efforts for new $5 million interdisciplinary research center awarded to UC Merced Merced
Published: April 26, 2016
April 26, 2016 - Over five years, NSF's Centers of Research Excellence in Science and Technology (CREST) program will fund research on how biological matter, like proteins or cells, come together to perform specific tasks, effectively behaving as machines.
The center is built around three research emphases:
- biomolecular machines, which focuses on designing and characterizing nanoscale instruments based on protein molecules;
- macromolecular assemblies and hybrid devices that combine the benefits of synthetic and biological materials for functional devices; and
- cellular and multicellular systems such as tissue and bacterial swarms.
The grant allows UC Merced researchers to create the new CREST Center for Cellular and Biomolecular Machines (CCBM), which brings together more than a dozen faculty members from multiple units across campus, including bioengineering, physics, chemistry and chemical biology, materials science and engineering.
- Excerpts selected from original article by Lorena Anderson, UC Merced University Communications.
Published: April 12, 2016
April 12, 2016 - George Daley, Professor of Biological Chemistry and Molecular Pharmacology, Medicine, and Pediatrics at Harvard Medical School, presented his lecture, "Engineering cell fates in vitro," to an audience of over 100, and across EBICS members at MIT, GT, UIUC, BU, UGA and the Gladstone Institute. Discussion targeted current efforts to differentiate pluripotent stem cells to specific lineages by mimicking embryonic programs, and modes of assessing the fidelity of these cells relative to efforts to directly engineer cells via synthetic biology.
Published: April 1, 2016
Catherine "Cali" Callaway, a junior at University of Georgia's Franklin College of Arts and Sciences, is majoring in biology with a concentration in neuroscience and pursuing a combined master's degree in artificial intelligence. She aims to earn a doctorate and a medical degree and to pursue a career conducting research in regenerative bioscience. Callaway has spent extensive time in a laboratory through UGA's Center for Undergraduate Research Opportunities, working with Georgia Research Alliance Eminent Scholar Steven Stice, director of the UGA Regenerative Bioscience Center, as well as during an intensive summer research experience for undergrads (REU) at the Massachusetts Institute for Technology.
Published: March 31, 2016
March 31, 2016 - As part of EBICS Knowledge Transfer efforts, Carrie Kouadio, EBICS Knowledge Transfer Program Manager, presented "Bioengineering Activities for the Classroom" at the National Science Teachers Association Conference in Nashville, TN. Other contributors included EBICS faculty Rashid Bashir, Lizanne DeStefano, and UIUC trainees Brian Williams, Ritu Raman, Ghazal Naseri Kouzehgarani, and UGA trainee Raymond Swetenburg. The presentation featured activities that have been developed by EBICS trainees and faculty to focus on EBICS-related concepts. Some of the highlights included the Light-stimulated Walking Robot, Biomimicry in a Light-sensitive Robot, Soft Robotics, Emergent Behaviors in Complex Systems, and the EBICS Ethics Modules.
Published: March 23, 2016
Philanthropist and Microsoft co-founder Paul Allen announced he will devote $100 million to launch the Paul G. Allen Frontiers Group. “We wanted to find people who might not be where the herd is going,’’ said Tom Skalak, executive director of the new Paul G. Allen Frontiers Group, a $100 million initiative to back risky, cutting-edge science that more conventional funders might avoid. The Frontiers Group, launched March 23, 2016, will start by bankrolling two Allen Discovery Centers; each will receive about $30 million over eight years. One of the two centers is at Tufts University, led by biologist Michael Levin, aims to understand the “morphogenic code,’’ or the signals inside organisms that choreograph networks of cells into functional tissues and organs. Levin has found that electric fields and electric signaling between cells help give tissues, organs, and other body parts (like arms) their shapes. That’s called an “emergent’’ phenomenon because it cannot be predicted from genes and molecules or the other mainstays of reductionist biology.
Michael Levin leads new Allen Discovery Center at Tufts University, with $30 million in funding, aiming to understand the "morphogenic code"
Published: March 23, 2016
March 23, 2016 - The Allen Discovery Center at Tufts University, led by EBICS faculty Michael Levin, is one of only two new centers funded by the Paul G. Allen Frontiers Group,a $100 million initiative to back risky, cutting-edge science that more conventional funders might avoid. The Center at Tufts will receive about $30 million over eight years towards understanding the "morphogenic code," the bioelectric signals inside organisms that choreograph networks of cells into functional tissues and organs. Levin has found that electric fields and electric signaling between cells help give tissues, organs, and other body parts (like arms) their shapes. That's called an "emergent'' phenomenon because it cannot be predicted from genes and molecules or the other mainstays of reductionist biology. Dr. Thomas Skalak, head of EBICS External Advisory Committee (EAC), is the founding executive director of the Frontiers Group.
Published: March 20, 2016
March 20, 2016 - Jasmin Imran Alsous, EBICS trainee and 4th year Ph.D. candidate in Stanislav Shvartsman Lab at Princeton, won the Autodesk Art and Biology Award at the Conference onVizualizing of Biological Data (VIBZI), with her entry "Picasso's Bulls and Drosophila's Eggs." Her winning entry compares an image sequence of cells that make up a Drosophila germ line cyst, a conserved structure from fruit flies to mammals that gives rise to eggs or sperm, to the progression of Picasso's bull drawings, in which a realistic picture transforms into a famous stick figure abstraction. The Autodesk award is for the most popular VIZBI Art and Biology submission, and the winner receives a three-year subscription to Autodesk Maya, a 3D animation, modeling, simulation, and rendering software.
Published: March 7, 2016
UIUC members of the EBICS biobots working group, engineered 8-10 mm biobots that mimic the muscle-tendon-bone complex, resulting in inchworm-like movement.
They can be controlled with electrical or optical signals and use muscle tissue for power. Currently, researchers are focused on biobots that mimic the body, but, perhaps one day, biological machines could replace animals for drug testing, or be used to detect and neutralize toxins in the environment, or even sequester carbon dioxide (CO2) from the atmosphere.
Published: March 3, 2016
Farren Isaacs, Assistant Professor of Molecular, Cellular and Developmental Biology and Systems Biology at Yale University, spoke about genomic engineering to 85 attendees across the GT, UIUC, and MIT communities. His presentation, "Programming Genomes to Expand Life's Functional Repertoire" covered:
- One application of MAGE (multiplex automated genome engineering) to generate combinatorial genomic variants from a complex pool of synthetic DNA to diversify multiple genes for biosynthetic pathway optimization.
- The integration of MAGE and CAGE (conjugative assembly genome engineering) to construct GROs (Genomically Recoded Organisms), replacing all 321 UAG stop codons with the synonymous UAA stop codon in E. coli.
- Engineering the GRO to depend on synthetic amino acids aimed at construction of safe GMOs unable to grow in the wild.
Kong Lab engineering cell matrix discovery promises innovation for fundamental applied studies on biological cells
Published: February 12, 2016
Paper by EBICS trainees Eunkyung Ko (UIUC) and Ellen Qin (UIUC), EBICS faculty Hyunjoon Kong (UIUC), et al. was published in Chemical Communications. Their research demonstrates that a hydrogel coupled with integrin-binding deoxyribonucleic acid (DNA) tethered with pre-defined rupture forces can modulate cell adhesion, differentiation, and secretion activities due to the changes in the number and, likely, force of cells adhered to a gel. Such innovative cell-matrix interface engineering would be broadly useful for a series of materials used for fundamental and applied studies on biological cells.
Published: February 10, 2016
Paper by EBICS faculty Michael Levin (Tufts), EBICS trainee Sebastien Uzel (MIT), et al. was published in The Journal of Physiology. Their research shows the bioelectric mechanism by which the rare genetic disorder Andersen-Tawil Syndrome (ATS) causes facial deformities, a finding that could lead to preventative measures and treatments from disorders ranging from birth defects to cancer.