Frontiers in Bioengineering Conference: The Farthest Out in Front

Earlier this month, I attended the Frontiers in Bioengineering conference at the Beckman Institute (UIUC). It was an interesting event with diverse perspectives on the field of Bioengineering. The two-day event featured researchers from all over the world, but focused on the synergies between Engineering and Cell/Molecular Biology.

One way to summarize the proceedings is to discuss the three most interesting (at least to me) technological advances. So here they are, in no particular order:

1) tissue co-cultures: Roger Kamm and Kevin Healey discussed the use of co-cultures to synthetically grow new organs and/or repair scaffolds. Co-cultures [1] are ex vivo systems within which multiple cell types are established and grown in media. The benefit of this artificial system involves the endogenous production of growth factors and a microenvironment. Exogenously-delivered factors apparently do not have the same efficacy for applications such as nerve grafts and cardiac repair. In the case of nerve grafts, supplying a bona-fide microenvironment can increase the distance of nerve innervation across a denervated gap. Co-cultures can also provide target tissues and anterograde cells to better approximate neuronal communication.

2) SHAPEseq: this an up-and-coming technique that has been used by a number of research groups to sequence the secondary structure of RNA [2]. SHAPEseq, or Selective 2'-hydroxyl acylation analyzed by primer extension, involves several steps that are similar to or go beyond the basic RNAseq technology. These include: preparing a barcoded RNA library, preparing a structure-specific cDNA library, aligning the corresponding reads, and calculating shape reactivities [3]. As with RNAseq, the objective is to build sequence libraries. Unlike with RNAseq, these libraries are structure-dependent. This allows for important structural information (e.g. hairpins, loops) to be estimated from a sample with single-nucleotide resolution.

A graphical summary of the SHAPEseq protocol. COURTESY: protocol description in [3].

3) NiN (nonviral induced neuronal) cells: this is a technique that was presented by Kam Leong at Duke. The idea is to use a non-viral genetic engineering approach (such as CRISPR) to introduce reprogramming factors into a cell. Non-viral factor delivery, as opposed to viral-mediated delivery using polycistronic vectors (genetic elements), is supposedly safer for transplantation and other therapeutic uses [4]. Other non-viral techniques (such as RNA-mediated reprogramming) have been tried with a mixed record of success. But by using the gene editing method [5], a cell population can be reprogrammed to a level of efficiency approximating viral-mediated reprogramming techniques. Despite various issues with estimating reprogramming efficiency and diversity across source cells [6], NiN techniques might be a easy and relatively controllable way to produce highly-specialized types of induced Neurons.

Honorable mention by association: The technology enabling the NiN advance is called CRISPR, or clustered, regularly interspaced, short palindromic repeat technology [7]. By using RNA-guided nucleases such as members of the Cas protein family (Cas9 in particular) [8], CRISPR technology can enable precise targeting of gene regulation. This includes the introduction and control of transgenes, something for which CRISPR has a lot of potential. To be fair, there are other, similar methods such as Transcription Activator-Like Effector Nucleases (TALENs) and Zinc Finger Nucleases (ZFNs) [9]. So congratulations to all of our gene editing technologies as we look to the future.

A diagram of the Cas-mediated CRISPR protocol. COURTESY: James Atmos, Wikipedia.

NOTES:
[1] For examples, please see the following articles:
a) Paschos, N.K., Brown, W.E., Eswaramoorthy, R., Hu, J.C., and Athanasiou, K.A.   Advances in tissue engineering through stem cell-based co-culture. Journal of Tissue Engineering and Regenerative Medicine, doi:10.1002/term.1870 (2014) AND

b) Ma, J., Both, S.K., Yang, F., Cui, F-Z., Pan, J., Meijer, G.J., Jansen, J.A., and van den Beucken, J.J.J.P.   Cell-Based Strategies in Bone Tissue Engineering and Regenerative Medicine. Stem Cells and Translational Medicine, sctm.2013-0126 (2013).

c) Meijer, G.J., de Bruijn, J.D., Koole, R., van Blitterswijk, C.A.   Cell-Based Bone Tissue Engineering. PLoS Medicine, 4(2), e9. doi:10.1371/journal.pmed.0040009 (2007).

[2] For examples, please see the following articles:

a) Lucks, J.B., Mortimer, S.A., Trapnell, C., Luof, S., Aviran, S., Schroth, G.P., Pachter, L., Doudna, J.A., and Arkin, A.P.   Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). PNAS, 108(27), 11063-11068 (2011)

b) Steen, K.A., Malhotra, A., Weeks, K.M.   Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease. Journal of the American Chemical Society, 132(29), 9940-9943 (2010).

[3] Mortimer, S.A., Trapnell, C., Aviran, C., Pachter, L., and Lucks, J.B.   SHAPE–Seq: High‐Throughput RNA Structure Analysis. Current Protocols in Chemical Biology, 10.1002/
9780470559277.ch120019 (2012).

[4] Park, H.J., Shin, J., Kim, J., and Cho, S.W.   Nonviral delivery for reprogramming to pluripotency and differentiation. Archives of Pharmacology Research, 37(1), 107-119 (2014).

[5] Perez-Pinera, P., Kocak, D.D., Vockley, C.M., Adler, A.F., Kabadi, A.M., Polstein, L.R., Thakore, P.I., Glass, K.A., Ousterout, D.G., Leong, K.W., Guilak, F., Crawford, G.E., Reddy, T.E., and Gersbach, C.A.   RNA-guided gene activation by CRISPR-Cas9–based transcription factors. Nature Methods, 10, 973-976 (2013).

[6] Alicea, B., Murthy, S., Keaton, S.A., Cobbett, P., Cibelli, J.B., and Suhr, S.T.   Defining phenotypic respecification diversity using multiple cell lines and reprogramming regimens. Stem Cells and Development, 22(19), 2641-2654.

[7] Hsu, P.D., Lander, E.S., and Zhang, F.   Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell, 157(6), 1262-1278 (2014).

[8] Sander, J.D. and Joung, J.K.   CRISPR-Cas systems for editing, regulating and targeting genomes. Nature Biotechnology, 32, 347-355 (2014).

[9] Gaj, T., Gersbach, C.A., and Barbas, C.F.   ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in Bioengineering, 31(7), 397-405 (2013).

Dynamics Days 2012 Report

Last week (January 3-7) I was an attendee at Dynamics Days, a complexity conference held this year in the Inner Harbor section of Baltimore, MD and hosted by the University of Maryland-College Park. The University of Maryland has an active research group studying chaotic systems and includes people such as Ed Ott, Wolgang Losert, and Michelle Girvan. In fact, this year's event featured a tribute to Ed Ott in honor of his 70th birthday.

I presented a poster on my own work, which was part of a very active poster session. There were also several overarching themes that were shared by a number of talks and poster presentations. One theme was using variations on Lagrangian analysis for understanding turbulent flows. One example is the calculation of finite size Lyapunov exponents (FSLEs) to understand the effects on scale in complex systems. Another example was in the use of second-order Lagrangian systems to understand the effects of turbulence on UAV aircraft. The third example involved incorporating a stochastic element into Lagrangian modeling through the use of an uncertainty estimator. In general, the use of Lagrangians to understand aggregations of particles due to flow field dynamics is currently at the cutting-edge of research in engineering and physics, most notably in the form of Lagrangian Coherent Structure (LCS) analysis.

Example of a Lorentz attractor (above) and a flow field containing Lagrangian Coherent Structures (LCSs) - (below).

A second theme was (of course) chaotic systems, or dynamical systems that are often operate far from equilibrium. Jim Yorke reminded us that there are several definitions of chaos, depending on the type of system under analysis. The best known form of chaos is "statistical regularity" chaos, the short hand of which is understood as a strange attractor. Other forms of chaos include: transient chaos, broad-band power spectra, and deterministic and bounded dynamic behavior. Chaos can be represented as either oscillatory regimes embodied in attractor maps or bifurcations and period doubling-type events embodied in Henon (horseshoe) and logistic maps. Yorke made the connection between each representation and how it relates to our understanding of chaos. He also briefly touched on an emerging application of chaos to system control, which involves a game of survival between the noise and control components of a system. In chaotic systems, where the noise is greater than the control component, the dataset first needs to be sculpted, which reveals a series of safe sets that can be further sculpted to increase controllability. A related presentation focused on the difference between "fast" and "slow" dynamics, and how they work together to define time dynamics.

Example of a Rossler attractor (above) and a logistic map (below).

A third theme was Biophysics. There were a number of posters on actin scaffoldings in cells and cell motility. In particular, actinomyosin elements in the cell are used for rigidity sensing and can be understood as a small-scale muscular machine. There was a presentation on the study of quorum sensing in bacteria using populations of magnetic dipoles as a physical analogues to biological signaling processes and spatiotemporal gradient sensing, and a related presentation on the statistical mechanics of chemotactic movements. There was also an interesting presentation by Theo Geisel on the perception of beat in music. We learned that derivations in drumbeat during the course of a song acts to "humanize" a given song, and that this information can be used to build audio editing technologies. There were several other presentations on neuroscience, including new directions in modeling the dynamical chaos of sleep/wake cycles (Victoria Booth) and the modeling of fast and slow neuronal dynamics using ion concentrations. Finally, Tomas Bohr gave a presentation on how plants are dynamical systems. In particular, the passive and active transport of water and sugars from the leaves to the root systems can be modeled using a series of mathematical techniques and predicts the growth and size limitations of plants.

Example of a Henon map, representing a horseshoe bifurcation.

A fourth theme was evolutionary game theory and the evolution of information and computation. This includes a wide range of approaches such as autonomous boolean networks, discontinuous percolation to model group selection, and encodings for regulatory networks. One notable presentation focused on a stochastic framework for understanding transcriptional dynamics. The major features of this model included relations between timescales and the role of oscillations, dampening, and excitability in the transcriptional process. Another talk involves using the rock-paper-scissors game to model the nonlinear hierarchical dynamics (where there is no dominant strategy) of viral infection and virulence. Jim Crutchfield's group had several posters on the nature of information and the role of entropy in biological complexity. One up-and-coming researcher by the name of Garrett Michener presented on his work encodings for regulatory networks that combines genetic algorithms, neural networks, regulatory networks, and computational linguistics. His models produce some interesting complex behaviors.

Example of active transport of water and sugars in a plant.

One obscure idea that interested me the most were various approaches to extreme events. While in many cases extreme events are treated as outliers, it is also known that not all data are normally-distributed. As a result, we need methods for understanding value that exhibit large variation from the mean in proper context. There was a poster than focused explicitly on how to measure extreme events in a system, and a presentation that discussed the phenomenon of rogue waves in optical systems with applications to rogue waves in other physical systems (such as the surface of the ocean). Next year's Dynamics Days (2013), obscure ideas and all, will be held in Boulder, Colorado.

Advances in Neuroengineering

A recent event put on by the IEEE EMBS focused on recent advances in Neuroengineering, or the interfacing of the nervous systems. Neuroengineering is an emerging approach to treating disabilities, understanding the brain, and building closed-loop control systems for brain-machine computer applications. Here are the sessions (on IEEE.tv):

Advances in neuroengineering

Understanding and treating conditions of the brain

One interesting topic brought up at these session was "microsleeps". Using advanced monitoring techniques, the presence of signatures akin to attentional lapses have been discovered. Microsleeps are sleep states that last on very short time scales. The presence of microsleeps could only be detected using electrophysiological techniques. This might be useful in predicting the onset of apnea episodes, or instances when a driver or heavy machine operator is about to deficus from their
task.

There are also therapeutic applications of these methods. The most intriguing would be to couple the real-time monitoring of muscle and brain activity with cutting edge gene and cell therapy treatments. The videos are worth the watch.

Biology and Physics: how one hand washes the other

Today at Soft Active Materials there were a lot of interesting talks, and after each session (morning and afternoon) there was a discussion panel.

For the afternoon panel, the following question was posed: what does Physics have to offer Biology, and vice versa? The question did not elicit much discussion, perhaps because it is so philosophical. So that is the question of the day -- what can Physics and Biology contribute to each other? I am not talking about in areas such as biophysics. I am referring to, say, the marriage of genomics and how cells/organisms respond to pressure gradients.

One concern was the nature of funding agencies. Another comment suggested that physics can provide a mimimal set of criterion and parameterization for understanding biological systems. My opinion is that physics can contribute two things of value: a set of tools to tackle hard and potentially intractable problems, and a way to look at old problems anew. This second point is of no small consequence -- paradigm shifts occur this way, and is extraordinarily valuable to the advancement of technological applications.

So, what do other people think? Please let me know in the comments section. Otherwise, good first day, and look forward to tommorrow.

Soft Active Materials Conference I

This week (5-18 through 5-21) I will be attending "Soft Active Materials: from granular rods to flocks, cells, and tissues" in Syracuse, NY.

Here is the program for more information. Here are a set of lecture notes for the session. I participated with a brief slideshow called "Emergent Natural Selection and the Evolution of Novel Biological Surfaces". Enjoy.