Mehmet Fatih Yanik

Neurosurgery: Functional regeneration after laser axotomy

Understanding how nerves regenerate is an important step towards developing treatments for human neurological disease, but investigation has so far been limited to complex organisms (mouse and zebrafish) in the absence of precision techniques for severing axons (axotomy). Here we use femtosecond laser surgery for axotomy in the roundworm Caenorhabditis elegans and show that these axons functionally regenerate after the operation. Application of this precise surgical technique should enable nerve regeneration to be studied in vivo in its most evolutionarily simple form.

Stopping Light All-Optically

We show that light pulses can be stopped and stored coherently, with an all-optical adiabatic and reversible pulse bandwidth compression process. Such a process overcomes the fundamental bandwidth-delay constraint in optics and can generate arbitrarily small group velocities for any light pulse with a given bandwidth, without any coherent or resonant light-matter interactions. We exhibit this process in optical resonators, where the bandwidth compression is accomplished only by small refractive-index modulations performed at moderate speeds.

High-contrast all-optical bistable switching in photonic crystal microcavities

We present a bistable photonic crystal configuration consisting of a waveguide sided coupled to a single-mode cavity with instantaneous Kerr nonlinearity. We show that such a configuration can generate extremely high contrast between the bistable states in its transmission with low input power. We also provide an analytic theory that can completely account for the entire transient switching dynamics, as revealed by finite difference time domain simulations.

Microfluidic system for on-chip high-throughput whole-animal sorting and screening at subcellular resolution

We report a suite of key microfluidic devices for complex high-throughput whole-animal genetic and drug screens. We demonstrate a high-speed microfluidic sorter that can isolate and immobilize Caenorhabditis elegans in a well defined geometry for screening phenotypic features at subcellular resolution in physiologically active animals. We show an integrated chip containing individually addressable screening-chamber devices for incubation and exposure of individual animals to biochemical compounds and high-resolution time-lapse imaging of many animals on a single chip without the need for anesthesia. We describe a design for delivery of compound libraries in standard multiwell plates to microfluidic devices and also for rapid dispensing of screened animals into multiwell plates. When used in various combinations, these devices will facilitate a variety of high-throughput assays using whole animals, including mutagenesis and RNAi and drug screens at subcellular resolution, as well as high-throughput high-precision manipulations such as femtosecond laser microsurgery for large-scale in vivo neural degeneration and regeneration studies.

All-optical transistor action with bistable switching in a photonic crystal cross-waveguide geometry.

We demonstrate all-optical switching action in a nonlinear photonic crystal cross-waveguide geometry with instantaneous Kerr nonlinearity, in which the transmission of a signal can be reversibly switched on and off by a control input. Our geometry accomplishes both spatial and spectral separation between the signal and the control in the nonlinear regime. The device occupies a small footprint of a few micrometers squared and requires only a few milliwatts of power at a 10-Gbit/s switching rate by use of Kerr nonlinearity in AlGaAs below half the electronic bandgap. We also show that the switching dynamics, as revealed by both coupled-mode theory and finite-difference time domain simulations, exhibits collective behavior that can be exploited to generate high-contrast logic levels and all-optical memory.

Displacement-sensitive photonic crystal structures based on guided resonance in photonic crystal slabs

We introduce a mechanically tunable photonic crystal structure consisting of coupled photonic crystal slabs. Using both analytic theory, and first-principles finite-difference time-domain simulations, we demonstrate that a strong variation of transmission and reflection coefficients of light through such structures can be accomplished with only a nanoscale variation of the spacing between the slabs. Moreover, by specifically configuring the photonic crystal structures, high sensitivity can be preserved in spite of significant fabrication-related disorders. We expect such structures to play important roles in micromechanically tunable optical sensors and filters.

Caenorhabditis elegans neuronal regeneration is influenced by life stage, ephrin signaling, and synaptic branching

We previously reported functional regeneration of Caenorhabditis elegans motor neurons after femtosecond laser axotomy. We report here that multiple neuronal types can regrow after laser axotomy using a variety of lasers. The precise pattern of regrowth varies with cell type, stage of animal, and position of axotomy. Mechanosensory axons cut in late larval or adult stages displayed extensive regrowth, yet failed to reach their target area because of guidance errors in the anteroposterior axis. By contrast, mechanosensory axons cut in early larval stages regrew at the same rate but with fewer anteroposterior guidance errors, and were more likely to reach their target area. In adult animals lacking the VAB-1 Eph receptor tyrosine kinase, mechanosensory axon regrowth was more accurate than in the wild type, suggesting that guidance errors of regrowing touch neuron axons are the result of Eph signaling. Kinase-dependent and kinase-independent Eph signaling influenced outgrowth and guidance of regrowing touch neurons, respectively. Mechanosensory neurons regrew when severed proximal to their collateral synaptic branch but did not regrow when severed distal to the branch point. However, the distal axon could regrow if the branch is removed surgically at the same time as distal axotomy, or at a later time. The touch neuron synaptic branch point may act as a sorting area to regulate growth. These findings reveal that multiple influences affect regenerative growth in C. elegans neurons.

Large-scale in vivo femtosecond laser neurosurgery screen reveals small-molecule enhancer of regeneration

Discovery of molecular mechanisms and chemical compounds that enhance neuronal regeneration can lead to development of therapeutics to combat nervous system injuries and neurodegenerative diseases. By combining high-throughput microfluidics and femtosecond laser microsurgery, we demonstrate for the first time large-scale in vivo screens for identification of compounds that affect neurite regeneration. We performed thousands of microsurgeries at single-axon precision in the nematode Caenorhabditis elegans at a rate of 20 seconds per animal. Following surgeries, we exposed the animals to a hand-curated library of approximately one hundred small molecules and identified chemicals that significantly alter neurite regeneration. In particular, we found that the PKC kinase inhibitor staurosporine strongly modulates regeneration in a concentration- and neuronal type-specific manner. Two structurally unrelated PKC inhibitors produce similar effects. We further show that regeneration is significantly enhanced by the PKC activator prostratin.

Innate Immune Suppression Enables Frequent Transfection with RNA Encoding Reprogramming Proteins

Background Generating autologous pluripotent stem cells for therapeutic applications will require the development of efficient DNA-free reprogramming techniques. Transfecting cells with in vitro-transcribed, protein-encoding RNA is a straightforward method of directly expressing high levels of reprogramming proteins without genetic modification. However, long-RNA transfection triggers a potent innate immune response characterized by growth inhibition and the production of inflammatory cytokines. As a result, repeated transfection with protein-encoding RNA causes cell death. Methodology/Principal Findings RNA viruses have evolved methods of disrupting innate immune signaling by destroying or inhibiting specific proteins to enable persistent infection. Starting from a list of known viral targets, we performed a combinatorial screen to identify siRNA cocktails that could desensitize cells to exogenous RNA. We show that combined knockdown of interferon-β (Ifnb1), Eif2ak2, and Stat2 rescues cells from the innate immune response triggered by frequent long-RNA transfection. Using this technique, we were able to transfect primary human fibroblasts every 24 hours with RNA encoding the reprogramming proteins Oct4, Sox2, Klf4, and Utf1. We provide evidence that the encoded protein is active, and we show that expression can be maintained for many days, through multiple rounds of cell division. Conclusions/Significance Our results demonstrate that suppressing innate immunity enables frequent transfection with protein-encoding RNA. This technique represents a versatile tool for investigating expression dynamics and protein interactions by enabling precise control over levels and timing of protein expression. Our finding also opens the door for the development of reprogramming and directed-differentiation methods based on long-RNA transfection.

Omnidirectional resonance in a metal–dielectric–metal geometry

We show that a planar metallic microcavity structure can exhibit an omnidirectional resonance, i.e., a resonance for which the resonance wavelength is independent of the incidence angle of light. The structure consists of a metal–dielectric–metal configuration. The omnidirectional resonance occurs when the reflection phase shift cancels the propagation shift. We numerically demonstrate such an omnidirectional resonance in an Ag–SiO2–Ag structure with realistic material parameters. Such omnidirectionally resonant structures are important for all-angle efficiency enhancement in light emitting diodes and photodetectors.We show that a planar metallic microcavity structure can exhibit an omnidirectional resonance, i.e., a resonance for which the resonance wavelength is independent of the incidence angle of light. The structure consists of a metal–dielectric–metal configuration. The omnidirectional resonance occurs when the reflection phase shift cancels the propagation shift. We numerically demonstrate such an omnidirectional resonance in an Ag–SiO2–Ag structure with realistic material parameters. Such omnidirectionally resonant structures are important for all-angle efficiency enhancement in light emitting diodes and photodetectors.