This work is supported by the Air Force Office of Scientific Research (AFOSR FA9550-18-1-0503).

To ensure compliance with ethical standards, all animal procedures related to isolating cardiomyocytes from rodent hearts were first approved by the University of Chicago Institutional Animal Care and Use Committee (IACUC). Additionally, all animal experiments were conducted in complete accordance with guidance from the University of Chicago IACUC.
1. Preparation of cell-SiNWs hybrids
<ol>
	<li>Isolate primary cardiomyocytes (CMs) using a commercial kit following manufacturer&#8217;s guidelines.</li>
	<li>Prepare complete DMEM for primary cell isolation supplemented with 10% heat-inactivated fetal bovine serum, 1% penicillin-streptomycin, and 1% L-glutamine.</li>
	<li>To isolate myofibroblast (MFs) from the MFs-CMs suspension, pre-plate the isolated cells on a tissue culture dish (cells isolated from 2 hearts from step 1.1. per 100 mm dish) for 1 h. As CMs need a fibronectin or collagen treated surface to adhere, only MFs will attach to tissue culture surface.</li>
	<li>Aspirate the enriched CMs cell suspension. These CMs can be used for hetero-cellular coupling experiments as described in section 3. Rinse the MFs with DMEM to eliminate any remaining CMs from the MFs dish.</li>
	<li>Add fresh culture medium to MFs and allow them to proliferate until they are ~80% confluent (2-4 days). Change the medium every other day.</li>
	<li>When the cells are ready (80% confluent), prepare SiNWs for the hybridization step below (step 1.7). 
	NOTE: Many types of SiNWs can be used for this. In this experiment, SiNWs that were grown by chemical vapor deposition (CVD) with a core-shell p-i-n junction configuration were used as described previously16. During the CVD growth, the SiNWs are grown on a silicon wafer substrate, and are eventually kept as silicon chips covered with SiNWs.</li>
	<li>Cut a 3 mm x 3 mm chip from a wafer with CVD grown SiNWs using a diamond scribe. Use sharp forceps to handle the wafer and minimize the surface area that is touched with the forceps, as this may break the SiNWs.</li>
	<li>Sterilize the chip by rinsing it with 70% ethanol and allowing the ethanol to dry for 30 min under UV light in a biosafety laminar flow hood.</li>
	<li>Transfer the chip into a sterile microcentrifuge tube and rinse excess ethanol using complete culture media.</li>
	<li>Add 1 mL of culture media and sonicate the chip in sonication bath for 1-10 min. The media should turn cloudy as SiNWs are released into the media. 
	NOTE: Sonication time and power should be optimized for different sonicators or different cells, as shorter durations and lower powers will yield longer SiNWs.</li>
	<li>Add the SiNWs suspension into 5 mL of culture media and seed it onto the 100 mm tissue culture dish with MFs. Allow the SiNWs to internalize for 4 h and rinse the excess SiNWs off 5x with media. Allow partially internalized SiNWs to complete the internalization by allowing them to sit for another 1 h before use. 
	NOTE: Different cell types may need different SiNWs concentration and/or internalization times.</li>
	<li>Prepare collagen coating solution by diluting collagen stock solution (3 mg/mL) with sterile 20 mM acetic acid at a ratio of 1:50. Add 0.5 mL coating solution to a 35 mm glass bottom dish and allow it to sit for 1 h in 37 &#176;C. Remove the solution and rinse dish with sterile PBS.</li>
	<li>Harvest the cell-SiNWs hybrids by treating the cells with 3 mL of trypsin for 2 min at 37 &#176;C. Add 10 mL of culture media and rinse the hybrids vigorously by pipetting. Centrifuge the cells gently at 200 x g for 5 min to avoid damaging the cells with the internalized SiNWs. Remove excess media, suspend cells with 1 mL media and seed them onto the collagen treated glass bottom dish. 
	NOTE: The hybrids can be seeded alone, to investigate intracellular or intercellular coupling or with CMs to investigate hetero-cellular coupling in vitro.</li>
	<li>Perform a final verification of SiNW internalization by labeling cells&#8217; cytosol (calcein-AM, 4 &#181;M) and membrane (membrane marker, 2 &#181;M) for 30 min at 37 &#176;C, and imaging the cell using confocal microscopy. As SiNWs are highly reflective, reflected light can be used instead of fluorescence to visualize them.</li>
</ol>
2. Preparation of cells for intra- and intercellular investigations
<ol>
	<li>Prepare collagen coating solution as in 1.12</li>
	<li>For intracellular electrical stimulation, culture hybrids with low seeding densities. Use a standard hemocytometer to count cells from section 1.11. and seed 50,000 cells on a 35 mm glass bottom dish in culture media. For intercellular investigations, use higher cell densities (500,000 cells per dish). For intercellular coupling between CMs and MFs, co-culture the hybrids with freshly isolated CMs.&#160;</li>
	<li>Allow cells to attach overnight before performing optical stimulation experiments. For intercellular investigations, allow 48 h at 37 &#176;C&#160;for the cells to express intercellular gap junctions before the experiment is conducted.</li>
	<li>Prepare calcium sensitive dye stock solution (may be kept in -20 &#176;C) by adding 50 &#181;L of DMSO to 50 &#181;g Fluo-4 AM. Prepare staining solution by diluting 1 &#181;L of dye in 1 mL of DMEM.</li>
	<li>Aspirate the culture medium from cells and add 1 mL of staining solution. Allow dye to internalize into cells for 20-30 min at 37 &#176;C. Aspirate the dye and rinse twice with sterile PBS.</li>
	<li>Finally, add 1 mL of pre-warmed phenol-red free DMEM Media, and allow the intracellular Fluo-4 to undergo de-esterification for 30 min in 37 &#176;C.</li>
	<li>Transfer cells to microscope for imaging and stimulation.</li>
</ol>
3. Optical imaging and stimulation
<ol>
	<li>Pre-heat a humidified microincubator to 37 &#176;C and bubble air-CO2 mixture (95:5).</li>
	<li>Use a microscope with a collimated laser line coupled into the light path for calcium imaging and optical stimulation. 
	NOTE: A scanning confocal microscope is the most straightforward option due to its point stimulation capabilities. However, this procedure can be done using any standard florescence microscope by coupling a collimated laser beam into the infinity space of the light path using a beam splitter. Any microscope objective is designed so that a collimated laser passed through it will be focused to a diffraction limited laser spot at the focal plane. The laser wavelength should be close to the excitation light, so it will be reflected by the dichroic mirror and passed by the excitation filter.</li>
	<li>Visualize the SiNWs and determine the stimulation site using brightfield microscopy, transmitted light, or reflective light. Then, reconfigure the light path to fluorescence mode, while maintaining the stimulation point at the predefined location of the SiNW.</li>
	<li>Validate the optimal stimulation power and pulse length for each SiNW size and cell type, to minimize photothermal damage to stimulated cells. For a typical stimulation protocol, perform a 2-10 s baseline recording of the intracellular calcium activity. Then, apply a single laser pulse of 1-10 mW power and 1-10 ms duration (corresponding to 30-300 kW/mm2) to stimulate the SiNW, and record the resulting calcium wave for another 2-10 s. 
	NOTE: It is essential to optimize the optical power and pulse length for each SiNW size and cells. This is necessary to minimize photothermal damage to the stimulated cells.</li>
	<li>Transfer the recorded movies of the optical stimulation, if necessary, for further analysis.</li>
</ol>
4. Video processing
<ol>
	<li>Visualize changes in Fluo-4 fluorescence using the &#8220;dF over F&#8221; macro17 available for ImageJ18, which calculates the change in fluorescence counts for each pixel, and normalizes by the average value of the resting baseline. Convert the output (floating point format) to 8 bits for further processing.</li>
	<li>Process the dF/F movie further using the &#8220;Remove outliers&#8221; selective median filter available in ImageJ. Define parameters to remove pixels where their value is more than 10 above the median value in a 2-pixel radius and replace that pixel value with the median.</li>
	<li>Calculate the optical flow in each frame via the Lucas-Kanade algorithm, as implemented in the Matlab Computer Vision toolbox. The output of this function was a vector field containing the x- and y-components of the optical flow at each point in each image (code is available in Supplementary File 1). 
	NOTE: The mean optical flow within a cell, &#60;&#957;&#62;, corresponds to the development of calcium flux within a cell. The differential of the optical flow, &#916;&#60;&#957;&#62; provides the time point at which calcium signaling was activated, by identifying where the signal was maximized. Additionally, the magnitude of &#916;&#60;&#957;&#62; at its maximum is correlated to the rate at which the calcium wave front progresses through the cell.</li>
	<li>Calculate the intercellular speed of calcium transmission according to the following equation. 
	vCa2+ = rij / ( tmax,j &#8722; tmax,i ), 
	where tmax,j and tmax,i are the times of activation for cells j and i, respectively, and rij is the distance between the centroids of the cells.</li>
</ol>

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The authors declare that they have no competing financial interests.

We have demonstrated here a simple way to perform intracellular electrical stimulation of cells. In this demonstration, we used MFs that were prehybridized with SiNWs, then co-cultured with CMs. In general, most proliferating cells have the tendency to internalize SiNWs, which allows the use of this methodology with many other cell types. Moreover, while we demonstrated the intracellular stimulation of cells, the same principles can be used to perform extracellular stimulation of cells. This can be done by blocking endos...

All biological organisms use electricity, in the form of ions, to regulate the cellular behavior. Cell membranes contain various types of specific ion channels allowing the passive and active transport of ions. These ions govern the functions of excitable cells, such as neuronal activity and skeletal and cardiac muscle contractility. However, bioelectricity also plays an important role in non-excitable cells, governing many cellular functions such as cell proliferation1, neuroimmunity2,3,4, and stem cell differentiation5.
In recent decades, the field of bioelectricity has drawn an increasing level of interest, which has contributed to the development of numerous technologies for bioelectronic interfaces. Microelectrode patch pipettes are the gold standard of intracellular recording and stimulation6. In this methodology, a glass pipette is pulled under specific conditions to form a sharp edge with a pore size of few microns. This pipette is filled with a buffer and the pipette allows direct contact of the buffer with the intracellular volume. This results in a bioelectric interface that yields extremely high signal to noise ratios, precise control over cellular electrical activity, and extremely high temporal resolution. Although this methodology is an extremely powerful tool, which was recently downscaled to a nano-pipette configuration7, it is associated with several important technical limitations. The cytosol dilution effect8, as well as mechanical vibrations, limits its utility to short term interrogations, and it requires expensive specialized equipment and a high level of technical skill. Moreover, its bulkiness limits the number of cells that can be recorded or stimulated simultaneously, and due to its invasiveness, it cannot be reconfigured throughout an experiment. To overcome these limitations, microelectrode arrays were developed, but the size of the electrodes limits the spatial resolution as well as intracellular access. Nanoelectrode arrays allow intracellular recording and stimulation but require abrasive electroporation to access the cytosol9,10. In addition, all these methodologies are substrate bound and are thus limited to in vitro cell cultures, or to external superficial cells, with no access to cells that are inside a 3-dimensional (3D) tissue.
Optogenetics11 is widely used to address these 3D and in vivo limitations. However, optogenetic methods are based on the perturbations of light-activated plasma membrane ion channels that are distributed at the plasma membrane, limiting the 3D spatial resolution12 and intracellular capabilities.
We have recently shown that silicon nanowires (SiNWs) can be used to perform intracellular bioelectric interrogation with submicron spatial resolution with different non-excitable cells, namely cardiac myofibroblasts and oligodendrocytes13. Moreover, we used these SiNWs to perform ex-vivo cell specific interrogation within a 3D cardiac tissue, to investigate how cardiac cells electrically couple in vivo14. A major advantage of this methodology is its simplicity; it does not require any genetic modification or bulky instrumentation. Many cells will spontaneously internalize photo-responsive SiNWs with no need for sonication or electroporation15. In addition, they will spontaneously escape the endosomal encapsulation and form a seamless integration with the cytosol and intracellular organelles13,15. These cell-SiNWs composites, termed cell-silicon hybrids, possess the dynamic, soft and versatile nature of the original cell, as well as the optoelectric capabilities of the SiNWs. After hybridization, the cell-SiNW hybrid can be harvested using standard tissue culture techniques and used for various applications such as intracellular bioelectric stimulation; studying intercellular bioelectric coupling in vitro; and for in vivo cell specific interrogation. As an effective stimulation requires co-localization of high optical power densities and SiNWs, one can achieve high spatial resolution both in 2D and 3D. In this protocol we describe in detail the methodology, as well as how the results can be analyzed. The focus is placed on the intra- and intercellular investigation in vitro, but the in vivo implementation of this methodology can be directly utilized for many other biological scenarios.

<table border="0" cellpadding="0" cellspacing="0" style="width:666px;" width="665">
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	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">35 mm Glass bottom dishes</td>
			<td style="width:121px;">Cellvis</td>
			<td style="width:161px;">D35-10-0-N</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">3i Marianas Spinning Disk Confocal</td>
			<td style="width:121px;">3i</td>
			<td style="width:161px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Calcein-AM</td>
			<td style="width:121px;">Invitrogen</td>
			<td style="width:161px;">C1430</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">CellMask Orange Plasma membrane Stain</td>
			<td style="width:121px;">Invitrogen</td>
			<td style="width:161px;">C10045</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Collagen I, rat tail</td>
			<td style="width:121px;">Gibco</td>
			<td style="width:161px;">A1048301</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Deluxe Diamond Scribing Pen</td>
			<td style="width:121px;">Ted Pella</td>
			<td style="width:161px;">54468</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">DMEM, high glucose, pyruvate, no glutamine</td>
			<td style="width:121px;">Gibco</td>
			<td style="width:161px;">10313039</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">DMSO, Anhydrous</td>
			<td style="width:121px;">Invitrogen</td>
			<td style="width:161px;">D12345</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Falcon Standard Tissue Culture Dishes</td>
			<td style="width:121px;">Falcon</td>
			<td style="width:161px;">08-772E</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Fetal Bovine Serum, certified, heat inactivated,</td>
			<td style="width:121px;">Gibco</td>
			<td style="width:161px;">10082147</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Fibronectin Human Protein, Plasma</td>
			<td style="width:121px;">Gibco</td>
			<td style="width:161px;">33016015</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Fisherbrand 112xx Series Advanced Ultrasonic Cleaner</td>
			<td style="width:121px;">Fisher Scientific</td>
			<td style="width:161px;">FB11201</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Fluo-4, AM, cell permeant</td>
			<td style="width:121px;">Invitrogen</td>
			<td style="width:161px;">F14201</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">FluoroBrite DMEM Media</td>
			<td style="width:121px;">Gibco</td>
			<td style="width:161px;">A1896701</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">L-Glutamine (200 mM)</td>
			<td style="width:121px;">Gibco</td>
			<td style="width:161px;">25030081</td>
			<td></td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:216px;">OKO full environmental control chamber (constant temperature, humidity and CO2)</td>
			<td style="width:121px;">OKO</td>
			<td style="width:161px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">PBS, pH 7.4</td>
			<td style="width:121px;">Gibco</td>
			<td style="width:161px;">10010023</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Penicillin-Streptomycin (10,000 U/mL)</td>
			<td style="width:121px;">Gibco</td>
			<td style="width:161px;">15140122</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Pierce Primary Cardiomyocyte Isolation Kit</td>
			<td style="width:121px;">Thermo Scientific</td>
			<td style="width:161px;">88281</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Trypsin-EDTA (0.25%), phenol red</td>
			<td style="width:121px;">Gibco</td>
			<td style="width:161px;">25200056</td>
			<td></td>
		</tr>
	</tbody>
</table>

silicon nanowires and optical stimulation for investigations of intra- and intercellular electrical coupling

Myofibroblasts can spontaneously internalize silicon nanowires (SiNWs), making them an attractive target for bioelectronic applications. These cell-silicon hybrids offer leadless optical modulation capabilities with minimal perturbation to normal cell behavior. The optical capabilities are obtained by the photothermal and photoelectric properties of SiNWs. These hybrids can be harvested using standard tissue culture techniques and then applied to different biological scenarios. We demonstrate here how these hybrids can be used to study the electrical coupling of cardiac cells and compare how myofibroblasts couple to one another or to cardiomyocytes. This process can be accomplished without special equipment beyond a fluorescent microscope with coupled laser line. Also shown is the use of a custom-built MATLAB routine that allows the quantification of calcium propagation within and between the different cells in the culture. Myofibroblasts are shown to have a slower electrical response than that of cardiomyocytes. Moreover, the myofibroblast intercellular propagation shows slightly slower, though comparable velocities to their intracellular velocities, suggesting passive propagation through gap junctions or nanotubes. This technique is highly adaptable and can be easily applied to other cellular arenas, for in vitro as well as in vivo or ex vivo investigations.

The ability of this methodology to allow direct access to the intracellular cytosol depends on the spontaneous internalization of the SiNW into the cells. Although SiNWs will undergo spontaneous internalization into many cell types15, some cells, such as cardiomyocytes and neurons, will need the SiNWs to be treated to allow their internalization19. In this protocol we describe the internalization process of p-i-n SiNWs with 200-300 nm diameter and ~1-3 &#181;m long into car...

Watch this Scientific Journal Video about Silicon Nanowires and Optical Stimulation for Investigations of Intra- and Intercellular Electrical Coupling at JoVE.com

Silicon Nanowires and Optical Stimulation for Investigations of Intra- and Intercellular Electrical Coupling

This protocol describes the use of silicon nanowires for intracellular optical bio-modulation of cell in a simple and easy to perform method. The technique is highly adaptable to diverse cell types and can be used for in vitro as well as in vivo applications.

Myofibroblasts can spontaneously internalize silicon nanowires (SiNWs), making them an attractive target for bioelectronic applications. These ...

silicon-nanowires-optical-stimulation-for-investigations-intra

Research

JoVE Journal

Bioengineering

4.4K Views.  The University of Chicago. This protocol describes the use of silicon nanowires for intracellular optical bio-modulation of cell in a simple and easy to perform method. The technique is highly adaptable to diverse cell types and can be used for in vitro as well as in vivo applications.

Video: Silicon Nanowires and Optical Stimulation for Investigations of Intra- and Intercellular Electrical Coupling

Soft Lithographic Functionalization and Patterning Oxide-free Silicon and Germanium

The development of hybrid electronic devices relies in large part on the integration of (bio)organic materials and inorganic semiconductors through a stable interface that permits efficient electron transport and protects underlying substrates from oxidative degradation. Group IV semiconductors can be effectively protected with highly-ordered self-assembled monolayers (SAMs) composed of simple alkyl chains that act as impervious barriers to both organic and aqueous solutions. Simple alkyl SAMs, however, are inert and not amenable to traditional patterning techniques. The motivation for immobilizing organic molecular systems on semiconductors is to impart new functionality to the surface that can provide optical, electronic, and mechanical function, as well as chemical and biological activity. 
Microcontact printing (&mu;CP) is a soft-lithographic technique for patterning SAMs on myriad surfaces.1-9 Despite its simplicity and versatility, the approach has been largely limited to noble metal surfaces and has not been well developed for pattern transfer to technologically important substrates such as oxide-free silicon and germanium. Furthermore, because this technique relies on the ink diffusion to transfer pattern from the elastomer to substrate, the resolution of such traditional printing is essentially limited to near 1 &mu;m.10-16
In contrast to traditional printing, inkless &mu;CP patterning relies on a specific reaction between a surface-immobilized substrate and a stamp-bound catalyst. Because the technique does not rely on diffusive SAM formation, it significantly expands the diversity of patternable surfaces. In addition, the inkless technique obviates the feature size limitations imposed by molecular diffusion, facilitating replication of very small (&lt;200 nm) features.17-23 However, up till now, inkless &mu;CP has been mainly used for patterning relatively disordered molecular systems, which do not protect underlying surfaces from degradation.
Here, we report a simple, reliable high-throughput method for patterning passivated silicon and germanium with reactive organic monolayers and demonstrate selective functionalization of the patterned substrates with both small molecules and proteins. The technique utilizes a preformed NHS-reactive bilayered system on oxide-free silicon and germanium. The NHS moiety is hydrolyzed in a pattern-specific manner with a sulfonic acid-modified acrylate stamp to produce chemically distinct patterns of NHS-activated and free carboxylic acids. A significant limitation to the resolution of many &mu;CP techniques is the use of PDMS material which lacks the mechanical rigidity necessary for high fidelity transfer. To alleviate this limitation we utilized a polyurethane acrylate polymer, a relatively rigid material that can be easily functionalized with different organic moieties. Our patterning approach completely protects both silicon and germanium from chemical oxidation, provides precise control over the shape and size of the patterned features, and gives ready access to chemically discriminated patterns that can be further functionalized with both organic and biological molecules. The approach is general and applicable to other technologically-relevant surfaces.

Here we describe a simple method for patterning oxide-free silicon and germanium with reactive organic monolayers and demonstrate functionalization of the patterned substrates with small molecules and proteins. The approach completely protects surfaces from chemical oxidation, provides precise control over feature morphology, and provides ready access to chemically discriminated patterns.

The development of hybrid electronic devices relies in large part on the integration of (bio)organic materials and inorganic semiconductors through a ...

Attaching Biological Probes to Silica Optical Biosensors Using Silane Coupling Agents

In order to interface with biological environments, biosensor platforms, such as the popular Biacore system (based on the Surface Plasmon Resonance (SPR) technique), make use of various surface modification techniques, that can, for example, prevent surface fouling, tune the hydrophobicity / hydrophilicity of the surface, adapt to a variety of electronic environments, and most frequently, induce specificity towards a target of interest.1-5 These techniques extend the functionality of otherwise highly sensitive biosensors to real-world applications in complex environments, such as blood, urine, and wastewater analysis.2,6-7 While commercial biosensing platforms, such as Biacore, have well-understood, standard techniques for performing such surface modifications, these techniques have not been translated in a standardized fashion to other label-free biosensing platforms, such as Whispering Gallery Mode (WGM) optical resonators.8-9
WGM optical resonators represent a promising technology for performing label-free detection of a wide variety of species at ultra-low concentrations.6,10-12 The high sensitivity of these platforms is a result of their unique geometric optics: WGM optical resonators confine circulating light at specific, integral resonance frequencies.13 Like the SPR platforms, the optical field is not totally confined to the sensor device, but evanesces; this "evanescent tail" can then interact with species in the surrounding environment. This interaction causes the effective refractive index of the optical field to change, resulting in a slight, but detectable, shift in the resonance frequency of the device. Because the optical field circulates, it can interact many times with the environment, resulting in an inherent amplification of the signal, and very high sensitivities to minor changes in the environment.2,14-15
To perform targeted detection in complex environments, these platforms must be paired with a probe molecule (usually one half of a binding pair, e.g. antibodies / antigens) through surface modification.2 Although WGM optical resonators can be fabricated in several geometries from a variety of material systems, the silica microsphere is the most common. These microspheres are generally fabricated on the end of an optical fiber, which provides a "stem" by which the microspheres can be handled during functionalization and detection experiments. Silica surface chemistries may be applied to attach probe molecules to their surfaces; however, traditional techniques generated for planar substrates are often not adequate for these three-dimensional structures, as any changes to the surface of the microspheres (dust, contamination, surface defects, and uneven coatings) can have severe, negative consequences on their detection capabilities. Here, we demonstrate a facile approach for the surface functionalization of silica microsphere WGM optical resonators using silane coupling agents to bridge the inorganic surface and the biological environment, by attaching biotin to the silica surface.8,16 Although we use silica microsphere WGM resonators as the sensor system in this report, the protocols are general and can be used to functionalize the surface of any silica device with biotin.

Biosensors interface with complex, biological environments and perform targeted detection by combining highly sensitive sensors with highly specific probes attached to the sensor via surface modification. Here, we demonstrate the surface functionalization of silica optical sensors with biotin using silane coupling agents to bridge the sensor and the biological environment.

In order to interface with biological environments, biosensor platforms, such as the popular Biacore system (based on the Surface Plasmon Resonance (SPR) ...

Engineering Skeletal Muscle Tissues from Murine Myoblast Progenitor Cells and Application of Electrical Stimulation

Engineered muscle tissues can be used for several different purposes, which include the production of tissues for use as a disease model in vitro, e.g. to study pressure ulcers, for regenerative medicine and as a meat alternative 1. The first reported 3D muscle constructs have been made many years ago and pioneers in the field are Vandenburgh and colleagues 2,3. Advances made in muscle tissue engineering are not only the result from the vast gain in knowledge of biochemical factors, stem cells and progenitor cells, but are in particular based on insights gained by researchers that physical factors play essential roles in the control of cell behavior and tissue development. State-of-the-art engineered muscle constructs currently consist of cell-populated hydrogel constructs. In our lab these generally consist of murine myoblast progenitor cells, isolated from murine hind limb muscles or a murine myoblast cell line C2C12, mixed with a mixture of collagen/Matrigel and plated between two anchoring points, mimicking the muscle ligaments. Other cells may be considered as well, e.g. alternative cell lines such as L6 rat myoblasts 4, neonatal muscle derived progenitor cells 5, cells derived from adult muscle tissues from other species such as human 6 or even induced pluripotent stem cells (iPS cells) 7. Cell contractility causes alignment of the cells along the long axis of the construct 8,9 and differentiation of the muscle progenitor cells after approximately one week of culture. Moreover, the application of electrical stimulation can enhance the process of differentiation to some extent 8. Because of its limited size (8 x 2 x 0.5 mm) the complete tissue can be analyzed using confocal microscopy to monitor e.g. viability, differentiation and cell alignment. Depending on the specific application the requirements for the engineered muscle tissue will vary; e.g. use for regenerative medicine requires the up scaling of tissue size and vascularization, while to serve as a meat alternative translation to other species is necessary.

Engineered muscle tissue has great potential in regenerative medicine, as disease model and also as an alternative source for meat. Here we describe the engineering of a muscle construct, in this case from mouse myoblast progenitor cells, and the stimulation by electrical pulses.

Engineered muscle tissues can be used for several different purposes, which include the production of tissues for use as a disease model in vitro, e.g. to ...

In vitro Synthesis of Native, Fibrous Long Spacing and Segmental Long Spacing Collagen

Collagen fibrils are present in the extracellular matrix of animal tissue to provide structural scaffolding and mechanical strength. These native collagen fibrils have a characteristic banding periodicity of ~67 nm and are formed in vivo through the hierarchical assembly of Type I collagen monomers, which are 300 nm in length and 1.4 nm in diameter. In vitro, by varying the conditions to which the monomer building blocks are exposed, unique structures ranging in length scales up to 50 microns can be constructed, including not only native type fibrils, but also fibrous long spacing and segmental long spacing collagen. Herein, we present procedures for forming the three different collagen structures from a common commercially available collagen monomer. Using the protocols that we and others have published in the past to make these three types typically lead to mixtures of structures. In particular, unbanded fibrils were commonly found when making native collagen, and native fibrils were often present when making fibrous long spacing collagen. These new procedures have the advantage of producing the desired collagen fibril type almost exclusively. The formation of the desired structures is verified by imaging using an atomic force microscope.

In vitro Synthesis of Native, Fibrous Long Spacing and Segmental Long Spacing Collagen

Simple and reproducible procedures are described for making three structurally distinct collagen assemblies from a common commercially available Type I collagen monomer. Native type, fibrous long spacing or segmental long spacing collagen can be constructed by varying the conditions to which the 300 nm long and 1.4 nm diameter monomer building block is exposed.

Collagen fibrils are present in the  extracellular matrix of animal tissue to provide structural scaffolding and  mechanical strength. These native ...

Optical Detection of E. coli Bacteria by Mesoporous Silicon Biosensors

A label-free optical biosensor based on a nanostructured porous Si is designed for rapid capture and detection of Escherichia coli K12 bacteria, as a model microorganism. The biosensor relies on direct binding of the target bacteria cells onto its surface, while no pretreatment (e.g.&#160;by cell lysis) of the studied sample is required. A mesoporous Si thin film is used as the optical transducer element of the biosensor. Under white light illumination, the porous layer displays well-resolved Fabry-P&#233;rot fringe patterns in its reflectivity spectrum. Applying a fast Fourier transform (FFT) to reflectivity data results in a single peak. Changes in the intensity of the FFT peak are monitored. Thus, target bacteria capture onto the biosensor surface, through antibody-antigen interactions, induces measurable changes in the intensity of the FFT peaks, allowing for a &#39;real time&#39; observation of bacteria attachment.
The mesoporous Si film, fabricated by an electrochemical anodization process, is conjugated with monoclonal antibodies, specific to the target bacteria. The immobilization, immunoactivity and specificity of the antibodies are confirmed by fluorescent labeling experiments. Once the biosensor is exposed to the target bacteria, the cells are directly captured onto the antibody-modified porous Si surface. These specific capturing events result in intensity changes in the thin-film optical interference spectrum of the biosensor. We demonstrate that these biosensors can detect relatively low bacteria concentrations (detection limit of 104 cells/ml) in less than an hour.

Optical Detection of E. coli Bacteria by Mesoporous Silicon Biosensors

A label-free optical biosensor for rapid bacteria detection is introduced. The biosensor is based on a nanostructured porous Si, which is designed to directly capture the target bacteria cells onto its surface. We use monoclonal antibodies, immobilized onto the porous transducer, as the capture probes. Our studies demonstrate the applicability of these biosensors for the detection of low bacterial concentrations within minutes with no prior sample processing (such as cell lysis).

A label-free optical biosensor based on a nanostructured porous Si is designed for rapid capture and detection of Escherichia coli K12 bacteria, as a ...

Porous Silicon Microparticles for Delivery of siRNA Therapeutics

Small interfering RNA (siRNA) can be used to suppress gene expression, thereby providing a new avenue for the treatment of various diseases. However, the successful implementation of siRNA therapy requires the use of delivery platforms that can overcome the major challenges of siRNA delivery, such as enzymatic degradation, low intracellular uptake and lysosomal entrapment. Here, a protocol for the preparation and use of a biocompatible and effective siRNA delivery system is presented. This platform consists of polyethylenimine (PEI) and arginine (Arg)-grafted porous silicon microparticles, which can be loaded with siRNA by performing a simple mixing step. The silicon particles are gradually degraded over time, thereby triggering the formation of Arg-PEI/siRNA nanoparticles. This delivery vehicle provides a means for protecting and internalizing siRNA, without causing cytotoxicity. The major steps of polycation functionalization, particle characterization, and siRNA loading are outlined in detail. In addition, the procedures for determining particle uptake, cytotoxicity, and transfection efficacy are also described.

Delivery remains the main challenge for the therapeutic implementation of small interfering RNA (siRNA). This protocol involves the use of a multifunctional and biocompatible siRNA delivery platform, consisting of arginine and polyethylenimine grafted porous silicon microparticles.

Small interfering RNA (siRNA) can be used to suppress gene expression, thereby providing a new avenue for the treatment of various diseases. However, the ...

Computed Tomography and Optical Imaging of Osteogenesis-angiogenesis Coupling to Assess Integration of Cranial Bone Autografts and Allografts

A major parameter determining the success of a bone-grafting procedure is vascularization of the area surrounding the graft. We hypothesized that implantation of a bone autograft would induce greater bone regeneration by abundant blood vessel formation. To investigate the effect of the graft on neovascularization at the defect site, we developed a micro&#8211;computed tomography (&#181;CT) approach to characterize newly forming blood vessels, which involves systemic perfusion of the animal with a polymerizing contrast agent. This method enables detailed vascular analysis of an organ in its entirety. Additionally, blood perfusion was assessed using fluorescence imaging (FLI) of a blood-borne fluorescent agent. Bone formation was quantified by FLI using a hydroxyapatite-targeted probe and &#181;CT analysis. Stem cell recruitment was monitored by bioluminescence imaging (BLI) of transgenic mice that express luciferase under the control of the osteocalcin promoter. Here we describe and demonstrate preparation of the allograft, calvarial defect surgery, &#181;CT scanning protocols for the neovascularization study and bone formation analysis (including the in vivo perfusion of contrast agent), and the protocol for data analysis.
The 3D high-resolution analysis of vasculature demonstrated significantly greater angiogenesis in animals with implanted autografts, especially with respect to arteriole formation. Accordingly, blood perfusion was significantly higher in the autograft group by the 7th day after surgery. We observed superior bone mineralization and measured greater bone formation in animals that received autografts. Autograft implantation induced resident stem cell recruitment to the graft-host bone suture, where the cells differentiated into bone-forming cells between the 7th and 10th postoperative day. This finding means that enhanced bone formation may be attributed to the augmented vascular feeding that characterizes autograft implantation. The methods depicted may serve as an optimal tool to study bone regeneration in terms of tightly bounded bone formation and neovascularization.

Implantation of autologous and allogeneic bone grafts constitute accepted approaches to treat major craniofacial bone loss. Yet the effect of graft composition on the interplay among neovascularization, cell differentiation and bone formation is unclear. We present a multimodal imaging protocol aimed to elucidate the angiogenesis-osteogenesis interdependence at the graft proximity.

A major parameter determining the success of a bone-grafting procedure is vascularization of the area surrounding the graft. We hypothesized that ...

Optical Control of Living Cells Electrical Activity by Conjugated Polymers

Hybrid interfaces between organic semiconductors and living tissues represent a new tool for in-vitro and in-vivo applications. In particular, conjugated polymers display several optimal properties as substrates for biological systems, such as good biocompatibility, excellent mechanical properties, cheap and easy processing technology, and possibility of deposition on light, thin and flexible substrates. These materials have been employed for cellular interfaces like neural probes, transistors for excitation and recording of neural activity, biosensors and actuators for drug release. Recent experiments have also demonstrated the possibility to use conjugated polymers for all-optical modulation of the electrical activity of cells. Several in-vitro study cases have been reported, including primary neuronal networks, astrocytes and secondary line cells. Moreover, signal photo-transduction mediated by organic polymers has been shown to restore light sensitivity in degenerated retinas, suggesting that these devices may be used for artificial retinal prosthesis in the future. All in all, light sensitive conjugated polymers represent a new approach for optical modulation of cellular activity.
In this work, all the steps required to fabricate a bio-polymer interface for optical excitation of living cells are described. The function of the active interface is to transduce the light stimulus into a modulation of the cell membrane potential. As a study case, useful for in-vitro studies, a polythiophene thin film is used as the functional, light absorbing layer, and Human Embryonic Kidney (HEK-293) cells are employed as the biological component of the interface. Practical examples of successful control of the cell membrane potential upon stimulation with light pulses of different duration are provided. In particular, it is shown that both depolarizing and hyperpolarizing effects on the cell membrane can be achieved depending on the duration of the light stimulus. The reported protocol is of general validity and can be straightforwardly extended to other biological preparations.

A method for stimulation of in-vitro cell cultures electrical activity with visible light, based on the use of organic semiconducting polymers is described.

Hybrid interfaces between organic semiconductors and living tissues represent a new tool for in-vitro and in-vivo applications. In particular, conjugated ...

Preparation of Silicon Nanowire Field-effect Transistor for Chemical and Biosensing Applications

Surveillance using biomarkers is critical for the early detection, rapid intervention, and reduction in the incidence of diseases. In this study, we describe the preparation of polycrystalline silicon nanowire field-effect transistors (pSNWFETs) that serve as biosensing devices for biomarker detection. A protocol for chemical and biomolecular sensing by using pSNWFETs is presented. The pSNWFET device was demonstrated to be a promising transducer for real-time, label-free, and ultra-high-sensitivity biosensing applications. The source/drain channel conductivity of a pSNWFET is sensitive to changes in the environment around its silicon nanowire (SNW) surface. Thus, by immobilizing probes on the SNW surface, the pSNWFET can be used to detect various biotargets ranging from small molecules (dopamine) to macromolecules (DNA and proteins). Immobilizing a bioprobe on the SNW surface, which is a multistep procedure, is vital for determining the specificity of the biosensor. It is essential that every step of the immobilization procedure is correctly performed. We verified surface modifications by directly observing the shift in the electric properties of the pSNWFET following each modification step. Additionally, X-ray photoelectron spectroscopy was used to examine the surface composition following each modification. Finally, we demonstrated DNA sensing on the pSNWFET. This protocol provides step-by-step procedures for verifying bioprobe immobilization and subsequent DNA biosensing application.

We describe key steps for biosensing by using polysilicon nanowire field-effect transistors, including the preparation of the device and the immobilization and confirmation of a DNA molecular probe on the nanowire surface, as well as conditions for DNA sensing.

Surveillance using biomarkers is critical for the early detection, rapid intervention, and reduction in the incidence of diseases. In this study, we ...

Transmission of Multiple Signals through an Optical Fiber Using Wavefront Shaping

The transmission of multiple independent optical signals through a multimode fiber is accomplished using wavefront shaping in order to compensate for the light distortion during the propagation within the fiber. Our methodology is based on digital optical phase conjugation employing only a single spatial light modulator, where the optical wavefront is individually modulated at different regions of the modulator, one region per light signal. Digital optical phase conjugation approaches are considered to be faster than other wavefront shaping approaches, where (for example) a complete determination of the wave propagation behavior of the fiber is performed. In contrast, the presented approach is time-efficient since it only requires one calibration per light signal. The proposed method is potentially appropriate for spatial division multiplexing in communications engineering. Further application fields are endoscopic light delivery in biophotonics, especially in optogenetics, where single cells in biological tissue have to be selectively illuminated with high spatial and temporal resolution.

We demonstrate the transmission of multiple independent signals through a multimode fiber using wavefront shaping employing a single spatial light modulator. By modulating the wavefront for each signal individually, spatially separated foci are transmitted. Potential applications are multiplexed data transfer in communications engineering and endoscopic light delivery in biophotonics.

The transmission of multiple independent optical signals through a multimode fiber is accomplished using wavefront shaping in order to compensate for the ...

Silicon Nanowires and Optical Stimulation for Investigations of Intra- and Intercellular Electrical Coupling

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Soft Lithographic Functionalization and Patterning Oxide-free Silicon and Germanium

Attaching Biological Probes to Silica Optical Biosensors Using Silane Coupling Agents

Engineering Skeletal Muscle Tissues from Murine Myoblast Progenitor Cells and Application of Electrical Stimulation

In vitro Synthesis of Native, Fibrous Long Spacing and Segmental Long Spacing Collagen

Optical Detection of E. coli Bacteria by Mesoporous Silicon Biosensors

Porous Silicon Microparticles for Delivery of siRNA Therapeutics

Computed Tomography and Optical Imaging of Osteogenesis-angiogenesis Coupling to Assess Integration of Cranial Bone Autografts and Allografts

Optical Control of Living Cells Electrical Activity by Conjugated Polymers

Preparation of Silicon Nanowire Field-effect Transistor for Chemical and Biosensing Applications

Transmission of Multiple Signals through an Optical Fiber Using Wavefront Shaping