O-GlcNAc: The Sweet Side of Epigenetics

In 1992 Edmond H. Fischer and Edwin G. Krebs won the Nobel Prize in Physiology or Medicine “for their discoveries concerning reversible protein phoshorylation as a biological regulatory mechanism.” Phosphorylation of proteins can essentially be thought of as the on/off switch that regulates protein activity inside of cells.

It became increasingly clear later on, however, that protein physiology was much more complex than regulation through just a simple on/off phosphorylation switch. It was eventually discovered by Johns Hopkins’ very own Dr. Gerald Hart that a very special sugar called N-acetylglucosamine (GlcNAc) can be added to the same places on proteins where phosphorylation often occurs. The addition of GlcNAc to these sites is now known as the O-GlcNAc modification. O-GlcNAc essentially serves as another layer of control over protein physiology by acting as a sort of “cap” that must be removed before a protein can be phosphorylated. In otherwords, phosphorylation and the O-GlcNAc modification cycle between each other to regulate how many important proteins behave. One amazing feature of the O-GlcNAc modification is the fact that it is performed by only two enzymes, OGT which adds it to proteins and OGA which removes it, and that’s it. This is in stark contrast to protein phosphorylation and dephosphorylation which needs hundreds of different enzymes to perform phosphorylation mechanics.

Fig 1.  Histones are modified by O-GlcNAc.

Fig 1. Histones are modified by O-GlcNAc.

To this day O-GlcNAc cycling remains an enigma, however, emerging evidence continues to mount that illustrates the very important physiological roles for O-GlcNAc. Two of some of the most important concepts within the realm of epigenetics are the modifications of histones and the methylation of DNA. It is now known that histones, which are proteins that help package DNA into the nucleus, are modified by O-GlcNAc 1 (fig 1.). The other major type of epigenetic regulation of gene expression– methylation of DNA–silences genes, but is also a reversible process. Proteins named TETs help to remove methyl groups on DNA to reverse this silencing. Recently it has also been shown that TETs have their activity regulated by O-GlcNAc 2. In otherwords, O-GlcNAc seems to have a very important role in regulating and interacting with two very important physiological mechanisms that write the epigenetic code.

Finally, glucose is most often thought of as fuel for the cell–and this is true–however, the substrate that is required to perform the O-GlcNAc modification (GlcNAc) happens to also be a byproduct of glucose metabolism. Major diseases such as cancer, diabetes, and Alzheimer’s are often associated with altered glucose metabolism and also have profound epigenetic changes. It is quite tempting, therefore, to postulate that O-GlcNAc may be the key that links environment, stress, nutrient availability, and metabolism to changes in epigenetics. Understanding carbohydrate metabolism and O-GlcNAc regulation of epigenetics may one day open new doors that will lead to breakthroughs in regenerative medicine, understanding embryological development, tissue engineering, and treating major diseases.

About the Author: Christopher Saeui is a fourth year Biomedical Engineering PhD student in the Kevin J. Yarema Laboratory for Cell and Carbohydrate Engineering studying the epigenetic and metabolic mechanisms that alter glycosylation in cancer.

1. Sakabe, K., Wang, Z. & Hart, G. W. Beta-N-acetylglucosamine (O-GlcNAc) is part of the histone code. Proc. Natl. Acad. Sci. U. S. A. 107, 19915-19920 (2010).
2. Shi, F. T. et al. Ten-eleven translocation 1 (Tet1) is regulated by O-linked N-acetylglucosamine transferase (Ogt) for target gene repression in mouse embryonic stem cells. J. Biol. Chem. 288, 20776-20784 (2013).

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

Seminar on bacterial and neuronal molecular communication nanonetworks

The seminar “Bacterial and Neuronal Molecular Communication Nanonetworks and Future Perspectives on the Internet of Nano Things” will be presented by Sasitharan Balasubramaniam, Tuesday, March 3, at noon in Barton Hall Room 117. The seminar is hosted by Johns Hopkins University, Whiting School of Engineering, Department of Electrical and Computer Engineering.

Balasubramaniam is visiting from the Nano Communication Centre, Department of Electronic and Communication Engineering, Tampere University of Technology, Tampere, Finland.


Sasitharan Balasubramaniam

Abstract: The field of nanotechnology, evolved over the last few decades, has resulted in the ability of engineering novel tools, materials, and components at the molecular and atomic scale, and it is expected to lead to the development of nanoscale machines, or nanomachines. A number of these devices are bio-inspired nanomachines created through synthetic biology that allows the ability to program, control, reuse, modify, and re-engineer biological cells (e.g., bacteria).

However, a shortcoming of these nanomachines is the limited processing capabilities that allow them to only perform limited tasks. Enabling communication between nanomachines could further strengthen their capabilities and provide opportunities for new applications. The emerging field of molecular communication aims to enable nanomachines to communicate from an infrastructure that is constructed using biological components and systems that are found in nature.

The possibility of constructing bio-compatible communication systems using natural biological cells are at the basis of a plethora of application including, intra-body sensing and actuation as well as targeted drug delivery. However, unlike conventional communication systems that communicate through electromagnetic waves or optical light, this paradigm shift requires new design principles that comply with the properties, behavior, and constraints of biological systems.

The focus of this seminar is on two molecular communication systems, which include bacterial nanonetwork and neuronal nanonetwork. In the bacterial nanonetwork, we start by defining the physical communication model that can be achieved using flagellated bacteria to carry and transfer DNA encoded information between the nanomachines. This is followed by an analysis on the impact their natural motility behavior as well as interactions (e.g., conjugations) can have on the end-to-end delivery performance of the network.

Besides the motility properties of the bacteria, the seminar will also discuss the impact on network performance that result from their social behavior, and in particular through cooperation. This is followed by a discussion on the use of cooperative communication between the bacteria for localization application.

In the second part of the seminar on neuronal networks, multi-objective optimization problem for time-based transmission scheduling is discussed. The optimization solution maximizes the transmission of information by considering the constraints and properties of neurons, including their refractory periods, noise, as well as evolving connectivity.

The applications for each type of molecular communication systems are also briefly discussed, including bacterial nano sensor networks, as well as new opportunities for brain-machine interfaces for bio-hybrid neural interfaces. Lastly, the seminar presents future perspectives of applying molecular communication for the Internet of Nano Things.

Read more at http://www.cs.tut.fi/~balasubs/

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

Nano-bio lab course: photolithography

Editor’s note: Over the next several days, we will share the student impressions of some of the techniques learned in INBT’s nano-bio laboratory course (670.621). These reports demonstrate the wide variety of techniques students trained at the Johns Hopkins Institute for NanoBioTechnology are expected to understand. Each technique is taught in a different affiliated faculty lab. More lab techniques to come.

Photolithography (taught in the laboratory of Konstantinos Konstantopoulos)

photolithographyThis lab was interesting and informative, because I use similar techniques in lab, microfabrications and microfluidics, but I have not yet used photolithography to design a device. It was useful for me to learn about the different steps in fabrication, specifically finding out that smaller features need to be patterned before larger features. One drawback of this process is the inability to create tube-like geometries that resemble blood vessels in vivo.

One way I could incorporate photolithography into my microfluidic device would be to create a second port into the device so I could modify the media conditions during an experiment. For example, endothelial cells under shear stress could achieve a quiescent state in some basal media, then at a given time point, the media conditions could be modified and the response of the monolayer quantified. Photolithography and design can allow for better control over the flow through the device and allow for better experimental design.

About the author: Jackson DeStefano is a first year PhD candidate in the laboratory of Peter Searson, professor of materials science and engineering.

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

Neuro X symposium talk titles revealed

We know you are probably wondering what this Neuro X symposium is all about. It’s a pretty mysterious title for a research symposium. But we at the Johns Hopkins Institute for NanoBioTechnology like to keep you on your toes. Neuro is well, brain stuff, and X is, well, nearly anything you want it to be. And our talk titles reflect as much!

neuro-x-ad-2The Neuro X symposium (and poster session) is Friday, May 1 from 8 a.m. to 4 p.m. in the Owens Auditorium, between CRB I and CRB II  on the Johns Hopkins University medical campus. If you have not registered yet, please go to http://inbt.jhu.edu/news/symposium/ and register a poster or just let us know you are going to be there.

From 8 to 9 a.m. there will be a free continental breakfast and time for networking. After a brief introduction from symposium chairs Peter Searson, director of the Institute for NanoBioTechnology, and Dwight Bergles, professor in the Solomon H. Snyder Department of Neuroscience, the speakers will begin as follows:

9:05 – 9:35 – Alfredo Quiñones-Hinojosa, MD, FAANS, “Cutting Edge: Chasing Migratory Cancer Cells”

Professor of Neurological Surgery and Oncology
Neuroscience and Cellular and Molecular Medicine, Johns Hopkins School of Medicine

9:35 – 10:05 – Jordan J. Green, PhD, “NanoBioTechnologies to Treat Brain Cancer”

Associate Professor of Biomedical Engineering, Ophthalmology, Neurosurgery,
Johns Hopkins School of Medicine; Materials Science & Engineering, Whiting School of Engineering

10:05 – 10:35 – Ahmet Hoke MD, PhD, FRCPC, “Electrospun nanofibers for nerve regeneration”

Professor, Neurology and Neuroscience, Johns Hopkins School of Medicine

10:35-10:45 – Break/Networking

10:45-11:15 – Patricia H. Janak, “Neural circuits for reward: new advances and future challenges”

Professor, Department of Psychological and Brain Sciences/Department of Neuroscience, Krieger School of Arts and Sciences Johns Hopkins University

11:15- 11:45 – Piotr Walczak, MD.PhD, “MRI-Guided Targeting of the Brain with Therapeutic Agents at High Efficiency and Specificity”

Associate Professor, Department of Radiology and Radiological Science, Division of MR Research, Johns Hopkins University School of Medicine

11:15 – 12:15 – Martin G. Pomper, MD, PhD, “Molecular Neuroimaging”

William R. Brody Professor of Radiology; Professor of Radiology and Radiological Science, Johns Hopkins School of Medicine

12:15 -1:15 – Lunch

1:15-2:15 – Poster Session A

2:15-3:15 – Poster Sessions B

3:30 – Prize Presentations/Photos



Join the Facebook event page here: https://www.facebook.com/events/640947002669229

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


Superconductor performance improved with nanowires

Superconducting materials have many useful applications, from magnetic resonance imaging (MRI) in medicine, to maglev trains, to particle accelerators. These materials are called superconductors because of their ability to carry electric current with minimal resistance. However, the conducting efficiency of these materials can be compromised when electrons get caught in swirling vortices. Researchers in the laboratory of Nina Markovic, a physicist affiliated with Johns Hopkins Institute for NanoBioTechnology, have discovered a way to use nanowires to prevent these disruptive electron tornados. Read more from Johns Hopkins News and Information below.

Superconductor materials are prized for their ability to carry an electric current without resistance, but this valuable trait can be crippled or lost when electrons swirl into tiny tornado-like formations called vortices. These disruptive mini-twisters often form in the presence of magnetic fields, such as those produced by electric motors.

To keep supercurrents flowing at top speed, Johns Hopkins scientists have figured out how to constrain troublesome vortices by trapping them within extremely short, ultra-thin nanowires. Their discovery was reported Feb. 18 in the journal Physical Review Letters.


This illustration depicts a short row of vortices held in place between the edges of a nanowire developed by Johns Hopkins scientists. (Graphic by Nina Markovic and Tyler Morgan-Wall)

“We have found a way to control individual vortices to improve the performance of superconducting wires,” said Nina Markovic, an associate professor in the Department of Physics and Astronomy in the university’s Krieger School of Arts and Sciences. Markovic is an affiliated faculty member of Johns Hopkins Institute for NanoBioTechnology.

Many materials can become superconducting when cooled to a temperature of nearly 460 below zero F, which is achieved by using liquid helium.

The new method of maintaining resistance-free current within these superconductors is important because these materials play a key role in devices such MRI medical scanners, particle accelerators, photon detectors and the radio frequency filters used in cell phone systems. In addition, superconductors are expected to become critical components in future quantum computers, which will be able to do more complex calculations than current machines.

Wider use of superconductors may hinge on stopping the nanoscopic mischief that electron vortices cause when they skitter from side to side across a conducting material, spoiling the zero-resistance current. The Johns Hopkins scientists say their nanowires keep this from happening.

Markovic, who supervised the development of these wires, said other researchers have tried to keep vortices from disrupting a supercurrent by “pinning” the twisters to impurities in the conducting material, which renders them unable to move.

“Edges can also pin the vortices, but it is more difficult to pin the vortices in the bulk middle area of the material, farther away from the edges,” she said. “To overcome this problem, we made a superconducting sample that consists mostly of edges: a very narrow aluminum nanowire.”

These nanowires, Markovic said, are flat strips about one-billionth as wide as a human hair and about 50 to 100 times longer than their width. Each nanowire forms a one-way highway that allows pairs of electrons to zip ahead at a supercurrent pace.

Vortices can form when a magnetic field is applied, but because of the material’s ultra-thin design, “only one short vortex row can fit within the nanowires,” Markovic said. “Because there is an edge on each side of them, the vortices are trapped in place and the supercurrent can just slip around them, maintaining the resistance-free speed.”

The ability to control the exact number of vortices in the nanowire may produce additional benefits, physics experts say. Future computers or other devices may someday use vortices instead of electrical charges to transmit information, they say.

The lead author of the Physical Review Letters article was Tyler Morgan-Wall, a doctoral student in Markovic’s lab. Along with Markovic, the co-authors were Benjamin Leith, who was an undergraduate at Johns Hopkins when the research took place; Nikolaus Hartman, a graduate student; and Atikur Rahman, who was a postdoctoral fellow in Markovic’s lab.

This research was support by National Science Foundation grants DMR-1106167 and PHYS-1066293. The Physical Review Letters journal article may be viewed at: http://journals.aps.org/prl/pdf/10.1103/PhysRevLett.114.077002.

Nina Markovic’s Lab Page: http://markoviclab.com/

Source: http://releases.jhu.edu/2015/02/24/ultra-thin-nanowires-can-trap-electron-twisters-that-disrupt-superconductors/

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


Protein teamwork drives successful cell division

Like a surgeon separating conjoined twins, cells have to be careful to get everything just right when they divide in two. Otherwise, the resulting daughter cells could be hobbled, particularly if they end up with too many or two few chromosomes. Successful cell division hangs on the formation of a dip called a cleavage furrow, a process that has remained mysterious. Now, researchers at Johns Hopkins have found that no single molecular architect directs the cleavage furrow’s formation; rather, it is a robust structure made of a suite of team players.

The finding is detailed in the March 2 issue of the journal Current Biology.

A cleavage furrow begins to separate a dividing cell into daughter cells. (Credit: Janet Effler/Johns Hopkins Medicine

A cleavage furrow begins to separate a dividing cell into daughter cells. (Credit: Janet Effler/Johns Hopkins Medicine

“We assumed the cleavage furrow was like a finely tuned Swiss watch, in that breaking a key component would bring it to a stop — we just didn’t know what that component was,” says Douglas Robinson, Ph.D., a professor of cell biology in the Institute for Basic Biomedical Sciences at the Johns Hopkins University School of Medicine, borrowing an analogy from the late Ray Rappaport, the founding father of modern cell division research. “But it turned out to be more like an old Maine fishing boat: almost indestructible.”

Cell division is how new cells form, both during development and throughout an organism’s life. To learn more about this process, Robinson and graduate student Vasudha Srivastava took the one-celled amoeba Dictyostelium as their model. One by one, they disabled genes for proteins known to be involved in the cleavage furrow to see whether doing so disrupted its assembly. But no matter which protein was taken out, other proteins still self-assembled to form the cleavage furrow.

“It’s not a house of cards — pulling out one protein doesn’t bring it down,” Srivastava says. Instead, she and Robinson found a robust process tuned not only by chemical signaling, but also by mechanical processes.

That makes sense, Robinson says, given the importance of the cleavage furrow to life itself. “Cells need to get division right in order to avoid ending up with the wrong number of chromosomes, which can be fatal,” he says.

The study was funded by the Hay Graduate Fellowship Fund, the National Institute for General Medical Sciences (grant number GM66817), the National Institutes of Health Office of the Director (grant number S10 OD016374) and the Johns Hopkins Physical Sciences-Oncology Center.

Douglas Robinson is an affiliated faculty member of Johns Hopkins Institute for NanoBioTechnology.

Reposted in its entirety from Johns Hopkins School of Medicine News.

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

Podcast: Shaping polymers for biomedical use

In this edition of the Johns Hopkins Institute for NanoBioTechnology Nanobyte podcast, Hai-Quan Mao, professor of materials science and engineering at Johns Hopkins University, discusses his work with polymers and their potential applications for medicine.

Slide1 In the Mao lab, researchers are using multi-molecule structures called polymers and forming them into different shapes for biomedical applications such as tissue engineering, nerve regeneration, and drug delivery. Mao uses natural models, such virus, as shape templates for designing nanoparticles with specific capabilities.

Listen to the podcast on Mixcloud here.

Visit the Mao Research Group here.

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

Finding new tasks for the disruptive proteins in bee venom

When a bee stings you, it leaves its stinger within your body releasing a peptide toxin called melittin. Melittin is toxic to cells because it is able to insert and bind to the cell membrane, which destabilizes the membrane.

Melittin is able to interact with the hydrophobic lipid layer of the cell membrane by forming unique helixes where hydrogen bonding occurs between both peptides. Consequently, charged (polar) amino acid residues are generally not observed in such proteins and pH can change the binding affinity. Such proteins are called membrane active proteins (MAPs).

Now this is not good for your bee-stung cells, but researchers are looking to repurpose nature’s disruptive proteins as anti-microbial drugs, cancer therapeutics, and HIV drugs. Specifically, researchers in the Kalina Hristova lab in the Department of Materials Science and Engineering at Johns Hopkins are engineering proteins based off of the melittin protein.

Figure 1: Membrane Active Peptide Schematic (Source: http://ins.sjtu.edu.cn/people/jakob/)

Figure 1: Membrane Active Peptide Schematic (Source: http://ins.sjtu.edu.cn/people/jakob/)

The Hristova lab researchers study their developed MAPs by using lab-produced vesicles from phosphatidylcholine (the major component of a cell membrane). They use the natural fluorescence from tryptophan (which increases in a hydrophobic environment), and circular dichroism spectroscopy (which is able to detect the chiral structure of proteins) to verify the peptide’s interactions with the vesicles, and what affinity they will bind.

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.

Engineering bacteria for medical uses

According to the National Institutes of Health and Centers for Disease Control, drug resistant pathogens are responsible for 2 million illnesses, 23,000 premature deaths, and an estimated $20 billion dollars in health care costs per year (1,2). The rapid emergence of drug resistant pathogens threatens to undo nearly a century’s worth of biomedical advances, and the situation has become so dire that President Obama has recently made fighting antibiotic resistant pathogens a top national priority.

Engineering Bacteria

Figure 1. Azido modified KDO was used to metabolically glycoengineer the LPS core of E. Coli

Newly emerging molecular engineering techniques may lead the way for next generation therapies designed to attack resistant microbes. One such strategy is metabolic glycoengineering, which is using unnatural monosaccharides to intercept the metabolic machinery of a cell to artificially install chemical “handles” on the surface. These chemical handles can then be exploited by performing reactions known as “click chemistry” to connect almost anything a researcher can think of to the surface of any cell.

Some of the most important structures of bacteria such as the peptidoglycan layer, lipopolysaccharides (LPS), teichoic acids, and capsule are comprised of extensive amounts of carbohydrates. Using glycoengineering, a physician may one day be able engineer those structures with unnatural monosaccharides to disrupt the adhesive properties, directly image, or target drugs to bacteria in a species specific manner–an unprecedented level of selectivity currently unachievable with our current regimen of antibiotics (Fig. 1).

For further reading:
(1) http://www.cdc.gov/drugresistance/national-strategy/
(2) http://www.niaid.nih.gov/topics/antimicrobialResistance/understanding/Pages/quickFacts.aspx

About the Author: Christopher Saeui is a fourth year Biomedical Engineering PhD student in the Kevin J. Yarema Laboratory for Cell and Carbohydrate Engineering studying the epigenetic and metabolic mechanisms that alter glycosylation in cancer.


What is microfluidics?

Microfluidics continues to find applications in many fields as researchers are realizing the benefits of scaling down to micron scales. This has implications in saving money from reagents and time from completing lengthy assays.

It also means that researchers are able to control experimental parameters at the micron scale more effectively, and use the fluidic flow to provide a dynamic environment. Applications for these devices include, but are not limited to, examples such as pathogen and cancer detection from blood, forming microparticles, studying antibiotic drug-resistant bacteria, understanding nanoparticle blood transport, and observation of the kinetics of chemical reactions.


Figure 1: A picture of a general microfluidic device. Source: http://blogs.nature.com/spoonful/2012/02/chip-promises-better-diagnosis-for-common-blood-disorder.html)

One reason that microfluidics has become so widespread is that the process to develop and create these devices is relatively simple and inexpensive. The process, called photolithography, is based off of a technology developed for the semiconductor industry in developing small features for circuits.

Photolithography uses special polymers that are reactive to certain wavelengths of light to create the forms used to make the device. Then another polymer, typically polydimethylsiloxane (PDMS), is poured into the casted photo-cured polymer mold to produce the microfluidic device. Many devices can be made from this mold and used in research and diagnostics for low-volume, high-throughput experiments.

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.