This study was supported by the United States (US) Department of Veterans Affairs Rehabilitation Research and Development Service awards: #RX001664-01A1 (CDA-1, Ereifej) and #RX002628-01A1 (CDA-2, Ereifej). The contents do not represent the views of the U.S. Department of Veterans Affairs or the United States Government. The authors would like to thank FEI Co. (Now part of Thermofisher Scientific) for staff assistance and use of instrumentation, which aided in developing the scripts used in this research.

The authors have nothing to disclose.

The fabrication protocol outlined here utilizes focused ion beam lithography to effectively and reproducibly etch nano-architectures into the surface of non-functional and functional single shank silicon microelectrodes. Focused ion beam (FIB) lithography allows for the selective ablation of the substrate surface by using a finely-focused ion beam50,51. FIB is a direct-write technique that can produce various features with nanoscale resolution and high aspect rat...

Intracortical Microelectrodes (IME) are invasive electrodes which provide a means of direct interfacing between external devices and the neuronal populations inside the cerebral cortex1,2. This technology is an invaluable tool for recording neural action potentials to improve scientists&#39; ability to explore neuronal function, advance understanding of neurological diseases and develop potential therapies. Intracortical microelectrode, used as a part of Brain Machine Interface (BMI) systems, enables recording of action potentials from an individual or small groups of neurons to detect motor intentions that can be used to produce functional outputs3. In fact, BMI systems have successfully been used for prosthetic and therapeutic purposes, such as acquired sensorimotor rhythm control to operate a computer cursor in patients with amyotrophic lateral sclerosis (ALS)4 and spinal cord injuries5 and restoring the movement in people suffering from chronic tetraplegia6.
Unfortunately, IMEs often fail to record consistently over time due to several failure modes that include mechanical, biological and material factors7,8. The neuroinflammatory response occurring after the electrode implantation is thought to be a considerable challenge contributing to electrode failure9,10,11,12,13,14. The neuroinflammatory response is initiated during the initial insertion of the IME which severs the blood brain barrier, damages the local brain parenchyma and disrupts glial and neuronal networks15,16. This acute response is characterized by the activation of glial cells (microglia/macrophages and astrocytes), which release pro-inflammatory and neurotoxic molecules around the implant site17,18,19,20. The chronic activation of glial cells results in a foreign body reaction characterized by the formation of a glial scar isolating the electrode from healthy brain tissue7,9,12,13,17,21,22. Ultimately, hindering the electrode&#39;s ability to record neuronal action potentials, due to the physical barrier between the electrode and the neurons and the degeneration and death of neurons23,24,25.
The early failure of intracortical microelectrodes has brought about considerable research in the development of next generation electrodes, with emphasis on biomimetic strategies26,27,28,29,30. Of particular interest to the protocol described here, is the use of nano-architecture as a class of biomimetic surface alterations for IMEs31. It has been established that surfaces mimicking the architecture of the natural in vivo environment have an improved biocompatible response32,33,34,35,36. Thus, the hypothesis compelling this protocol is that the discontinuity between the rough architecture of the brain tissue and smooth architecture of the intracortical microelectrodes may contribute to the neuroinflammatory and chronic foreign body response to implanted IMEs (for a full review refer to Kim et al.31). We have previously shown that the utilization of nano-architecture features similar to the brain&#39;s extracellular matrix architecture reduces astrocyte inflammatory markers from cells cultured on nano-architectured substrates, compared to flat control surfaces in both in vitro and ex vivo models of neuroinflammation37,38. Furthermore, we have shown the application of focused ion beam (FIB) lithography to etch nano-architectures directly onto silicon probes resulted in significantly increased neuronal viability and lower expression of pro-inflammatory genes from animals implanted with the nano-architecture probes compared to the smooth control group26. Therefore, the purpose of the protocol presented here is to describe the use of FIB lithography to etch nano-architectures on manufactured intracortical microelectrode devices. This protocol was designed to etch nano-architecture sized features into silicon surfaces of intracortical microelectrode shanks utilizing both automated and manual processes. These methods are uncomplicated, reproducible, and can certainly be optimized for various device materials and desired feature sizes.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>16-Channel ZIF-Clip Headstage</td>
			<td>Tucker Davis Technologies</td>
			<td>ZC16</td>
			<td>The headstage and headstage holder may need to be changed, depending on the electrode used. <a href="https://www.tdt.com/zif-clip-digital-headstages.html" target="_blank">https://www.tdt.com/zif-clip-digital-headstages.html</a></td>
		</tr>
		<tr>
			<td>1-meter cable, ALL spring wrapped</td>
			<td>Thomas Scientific</td>
			<td>1213F04</td>
			<td>Any non treated petri dish will suffice. <a href="https://www.thomassci.com/Laboratory-Supplies/Cell-Culture-Dishes/_/Non-Treated-Petri-Dishes?q=petri%20dish%20cell%20culture" target="_blank">https://www.thomassci.com/Laboratory-Supplies/Cell-Culture-Dishes/_/Non-Treated-Petri-Dishes?q=petri%20dish%20cell%20culture</a></td>
		</tr>
		<tr>
			<td>32-Channel ZIF-Clip Headstage Holder</td>
			<td>Tucker Davis Technologies</td>
			<td>Z-ROD32</td>
			<td>The headstage and headstage holder may need to be changed, depending on the electrode used. <a href="https://www.tdt.com/zif-clip-digital-headstages.html" target="_blank">https://www.tdt.com/zif-clip-digital-headstages.html</a></td>
		</tr>
		<tr>
			<td>Acetone, Thinner/Extender/Cleaner, 30ml</td>
			<td>Ted Pella</td>
			<td>16023</td>
			<td><a href="https://www.tedpella.com/SEMmisc_html/SEMpaint.htm#anchor16062" target="_blank">https://www.tedpella.com/SEMmisc_html/SEMpaint.htm#anchor16062</a></td>
		</tr>
		<tr>
			<td>Baby-Mixter Hemostat</td>
			<td>Fine Science Tools</td>
			<td>13013-14</td>
			<td>Any curved hemostat will suffice. <a href="https://www.finescience.com/en-US/Products/Forceps-Hemostats/Hemostats/Baby-Mixter-Hemostat" target="_blank">https://www.finescience.com/en-US/Products/Forceps-Hemostats/Hemostats/Baby-Mixter-Hemostat</a></td>
		</tr>
		<tr>
			<td>Carbon Conductive Tape, Double Coated</td>
			<td>Ted Pella</td>
			<td>16084-7</td>
			<td>The protocol suggested three options for mounting the functional electrode to the aluminum stub (copper or carbon conductive tape or a low profile clip. We utilized the carbon conductive tape in our study. <a href="https://www.tedpella.com/semmisc_html/semadhes.htm" target="_blank">https://www.tedpella.com/semmisc_html/semadhes.htm</a></td>
		</tr>
		<tr>
			<td>Corning Costar Not Treated Multiple Well Plates - 6 well</td>
			<td>Sigma Aldrich</td>
			<td>CLS3736-100EA</td>
			<td>Any non-treated 6 well plate will suffice. <a href="https://www.sigmaaldrich.com/catalog/substance/corningcostarnottreatedmultiplewellplates1234598765" target="_blank">https://www.sigmaaldrich.com/catalog/substance/</a></td>
		</tr>
		<tr>
			<td>Dumont #5 Fine Forceps</td>
			<td>Fine Science Tools</td>
			<td>11251-30</td>
			<td>Either this fine forceps or the vacuum pump will suffice. <a href="https://www.finescience.com/en-US/Products/Forceps-Hemostats/Dumont-Forceps/Dumont-5-Forceps/11251-30" target="_blank">https://www.finescience.com/en-US/Products/Forceps-Hemostats/Dumont-Forceps/Dumont-5-Forceps/11251-30</a></td>
		</tr>
		<tr>
			<td>Ethanol, 190 proof (95%), USP, Decon Labs</td>
			<td>Fisher Scientific</td>
			<td>22-032-600</td>
			<td>Any 95% ethanol will suffice. <a href="https://www.fishersci.com/shop/products/ethanol-190-proof-95-usp-decon-labs-10/22032600" target="_blank">https://www.fishersci.com/shop/products/ethanol-190-proof-95-usp-decon-labs-10/22032600</a></td>
		</tr>
		<tr>
			<td>Falcon Cell Strainer</td>
			<td>Fisher Scientific</td>
			<td>08-771-1</td>
			<td><a href="https://www.fishersci.com/shop/products/falcon-cell-strainers-4/087711" target="_blank">https://www.fishersci.com/shop/products/falcon-cell-strainers-4/087711</a></td>
		</tr>
		<tr>
			<td>FEI, Tescan, Zeiss (also for Philips, Leo, Cambridge, Leica, CamScan), aluminum, grooved edge, &#216;32mm</td>
			<td>Ted Pella</td>
			<td>16148</td>
			<td>Depending on the SEM machine used, you may need a different size stub. <a href="https://www.tedpella.com/SEM_html/SEMpinmount.htm#_16180" target="_blank">https://www.tedpella.com/SEM_html/SEMpinmount.htm#_16180</a></td>
		</tr>
		<tr>
			<td>Fisherbrand Aluminum Foil, Standard-gauge roll</td>
			<td>Fisher Scientific</td>
			<td>01-213-101</td>
			<td>Any aluminum foil will suffice. <a href="https://www.fishersci.com/shop/products/fisherbrand-aluminum-foil-7/p-306250" target="_blank">https://www.fishersci.com/shop/products/fisherbrand-aluminum-foil-7/p-306250</a></td>
		</tr>
		<tr>
			<td>Fisherbrand Low- and Tall-Form PTFE Evaporating Dishes</td>
			<td>Fisher Scientific</td>
			<td>02-617-149</td>
			<td>Any Teflon plate will suffice, this is used to dry the probes after washing on a surface they will not stick onto. <a href="https://www.fishersci.com/shop/products/fisherbrand-low-tall-form-ptfe-evaporating-dishes-12/p-88552" target="_blank">https://www.fishersci.com/shop/products/fisherbrand-low-tall-form-ptfe-evaporating-dishes-12/p-88552</a></td>
		</tr>
		<tr>
			<td>Michigan-style silicon functional electrode</td>
			<td>NeuroNexus</td>
			<td>A1x16-3mm-100-177</td>
			<td><a href="http://neuronexus.com/electrode-array/a1x16-3mm-100-177/" target="_blank">http://neuronexus.com/electrode-array/a1x16-3mm-100-177/</a></td>
		</tr>
		<tr>
			<td>Model 1772 Universal holder</td>
			<td>KOPF</td>
			<td>Model 1772</td>
			<td>Other stereotaxic frames and accessories will suffice. <a href="http://kopfinstruments.com/product/model-1772-universal-holder/" target="_blank">http://kopfinstruments.com/product/model-1772-universal-holder/</a></td>
		</tr>
		<tr>
			<td>Model 900-U Small Animal Stereotaxic Instrument</td>
			<td>KOPF</td>
			<td>Model 900-U</td>
			<td>Other stereotaxic frames and accessories will suffice. <a href="http://kopfinstruments.com/product/model-900-small-animal-stereotaxic-instrument1/" target="_blank">http://kopfinstruments.com/product/model-900-small-animal-stereotaxic-instrument1/</a></td>
		</tr>
		<tr>
			<td>Model 960 Electrode Manipulator with AP Slide Assembly</td>
			<td>KOPF</td>
			<td>Model 960</td>
			<td>Other stereotaxic frames and accessories will suffice. <a href="http://kopfinstruments.com/product/model-1772-universal-holder/" target="_blank">http://kopfinstruments.com/product/model-1772-universal-holder/</a></td>
		</tr>
		<tr>
			<td>Parafilm M 10cm x 76.2m (4&#34; x 250&#39;)</td>
			<td>Ted Pella</td>
			<td>807-5</td>
			<td><a href="https://www.tedpella.com/grids_html/807-2.htm" target="_blank">https://www.tedpella.com/grids_html/807-2.htm</a></td>
		</tr>
		<tr>
			<td>PELCO Vacuum Pick-Up System, 220V</td>
			<td>Ted Pella</td>
			<td>520-1-220</td>
			<td>Either this vacuum pump or the fine forceps will suffice. <a href="http://www.tedpella.com/grids_html/Vacuum-Pick-Up-Systems.htm#anchor-520" target="_blank">http://www.tedpella.com/grids_html/Vacuum-Pick-Up-Systems.htm#anchor-520</a></td>
		</tr>
		<tr>
			<td>PELCO Conductive Silver Paint</td>
			<td>Ted Pella</td>
			<td>16062</td>
			<td><a href="https://www.tedpella.com/SEMmisc_html/SEMpaint.htm#anchor16062" target="_blank">https://www.tedpella.com/SEMmisc_html/SEMpaint.htm#anchor16062</a></td>
		</tr>
		<tr>
			<td>SEM FIB FEI Helios 650 Nanolab</td>
			<td>Thermo Fisher Scientific</td>
			<td>Helios G2 650</td>
			<td>This is the specific focused ion beam and scanning electron microscope used in the protocol. The Nanobuilder software is what it comes with. If a different FIB instrument is used, it may not be completely compatible with the protocol, specifically the steps requiring the Nanobuilder software. <a href="https://www.fei.com/products/dualbeam/helios-nanolab/" target="_blank">https://www.fei.com/products/dualbeam/helios-nanolab/</a></td>
		</tr>
	</tbody>
</table>

focused ion beam lithography to etch nano-architectures into microelectrodes

With advances in electronics and fabrication technology, intracortical microelectrodes have undergone substantial improvements enabling the production of sophisticated microelectrodes with greater resolution and expanded capabilities. The progress in fabrication technology has supported the development of biomimetic electrodes, which aim to seamlessly integrate into the brain parenchyma, reduce the neuroinflammatory response observed after electrode insertion and improve the quality and longevity of electrophysiological recordings. Here we describe a protocol to employ a biomimetic approach recently classified as nano-architecture. The use of focused ion beam lithography (FIB) was utilized in this protocol to etch specific nano-architecture features into the surface of non-functional and functional single shank intracortical microelectrodes. Etching nano-architectures into the electrode surface indicated possible improvements of biocompatibility and functionality of the implanted device. One of the benefits of using FIB is the ability to etch on manufactured devices, as opposed to during the fabrication of the device, facilitating boundless possibilities to modify numerous medical devices post-manufacturing. The protocol presented herein can be optimized for various material types, nano-architecture features, and types of devices. Augmenting the surface of implanted medical devices can improve the device performance and integration into the tissue.

FIB Etched Nano-architecture on the Surfaces of Single Shank Intracortical Probes 
Utilizing the methods described here, intracortical probes were etched with specific nano-architectures following established protocols39. Dimensions and shape of the nano-architecture design described in these methods were implemented from previous in vitro results depicting a decrease in glial cell reactivity when cultured with the nano-architecture design described here37</...

Watch this Scientific Journal Video about Focused Ion Beam Lithography to Etch Nano-architectures into Microelectrodes at JoVE.com

Focused Ion Beam Lithography to Etch Nano-architectures into Microelectrodes

We have shown that the etching of nano-architecture into intracortical microelectrode devices may reduce the inflammatory response and has the potential to improve electrophysiological recordings. The methods described herein outline an approach to etch nano-architectures into the surface of non-functional and functional single shank silicon intracortical microelectrodes.

With advances in electronics and fabrication technology, intracortical microelectrodes have undergone substantial improvements enabling the production of ...

focused-ion-beam-lithography-to-etch-nano-architectures-into

Research

JoVE Journal

Bioengineering

6.6K Views.  University of Michigan. We have shown that the etching of nano-architecture into intracortical microelectrode devices may reduce the inflammatory response and has the potential to improve electrophysiological recordings. The methods described herein outline an approach to etch nano-architectures into the surface of non-functional and functional single shank silicon intracortical microelectrodes.

Video: Focused Ion Beam Lithography to Etch Nano-architectures into Microelectrodes

Fluorescent Nanoparticles for the Measurement of Ion Concentration in Biological Systems

Tightly regulated ion homeostasis throughout the body is necessary for the prevention of such debilitating states as dehydration.1 In contrast, rapid ion fluxes at the cellular level are required for initiating action potentials in excitable cells.2 Sodium regulation plays an important role in both of these cases; however, no method currently exists for continuously monitoring sodium levels in vivo 3 and intracellular sodium probes 4 do not provide similar detailed results as calcium probes. In an effort to fill both of these voids, fluorescent nanosensors have been developed that can monitor sodium concentrations in vitro and in vivo.5,6 These sensors are based on ion-selective optode technology and consist of plasticized polymeric particles in which sodium specific recognition elements, pH-sensitive fluorophores, and additives are embedded.7-9 Mechanistically, the sodium recognition element extracts sodium into the sensor. 10 This extraction causes the pH-sensitive fluorophore to release a hydrogen ion to maintain charge neutrality within the sensor which causes a change in fluorescence. The sodium sensors are reversible and selective for sodium over potassium even at high intracellular concentrations.6 They are approximately 120 nm in diameter and are coated with polyethylene glycol to impart biocompatibility. Using microinjection techniques, the sensors can be delivered into the cytoplasm of cells where they have been shown to monitor the temporal and spatial sodium dynamics of beating cardiac myocytes.11 Additionally, they have also tracked real-time changes in sodium concentrations in vivo when injected subcutaneously into mice.3 Herein, we explain in detail and demonstrate the methodology for fabricating fluorescent sodium nanosensors and briefly demonstrate the biological applications our lab uses the nanosensors for: the microinjection of the sensors into cells; and the subcutaneous injection of the sensors into mice.

Fluorescent nanoparticles produced in our lab are used for imaging ion concentrations and ion fluxes in biological systems such as cells during signaling and interstitial fluid during physiological homeostasis.

Tightly regulated ion homeostasis throughout the body is necessary for the prevention of such debilitating states as dehydration.1 In contrast, rapid ion ...

Plasma Lithography Surface Patterning for Creation of Cell Networks

Systematic manipulation of a cell microenvironment with micro- and nanoscale resolution is often required for deciphering various cellular and molecular phenomena. To address this requirement, we have developed a plasma lithography technique to manipulate the cellular microenvironment by creating a patterned surface with feature sizes ranging from 100 nm to millimeters. The goal of this technique is to be able to study, in a controlled way, the behaviors of individual cells as well as groups of cells and their interactions.
This plasma lithography method is based on selective modification of the surface chemistry on a substrate by means of shielding the contact of low-temperature plasma with a physical mold. This selective shielding leaves a chemical pattern which can guide cell attachment and movement. This pattern, or surface template, can then be used to create networks of cells whose structure can mimic that found in nature and produces a controllable environment for experimental investigations. The technique is well suited to studying biological phenomenon as it produces stable surface patterns on transparent polymeric substrates in a biocompatible manner. The surface patterns last for weeks to months and can thus guide interaction with cells for long time periods which facilitates the study of long-term cellular processes, such as differentiation and adaption. The modification to the surface is primarily chemical in nature and thus does not introduce topographical or physical interference for interpretation of results. It also does not involve any harsh or toxic substances to achieve patterning and is compatible for tissue culture. Furthermore, it can be applied to modify various types of polymeric substrates, which due to the ability to tune their properties are ideal for and are widely used in biological applications. The resolution achievable is also beneficial, as isolation of specific processes such as migration, adhesion, or binding allows for discrete, clear observations at the single to multicell level.
This method has been employed to form diverse networks of different cell types for investigations involving migration, signaling, tissue formation, and the behavior and interactions of neurons arraigned in a network.

A versatile plasma lithography technique has been developed to generate stable surface patterns for guiding cellular attachment. This technique can be applied to create cell networks including those that mimic natural tissues and has been used for studying several, distinct cell types.

Systematic manipulation of a cell microenvironment with micro- and nanoscale resolution is often required for deciphering various cellular and molecular ...

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic valve leaflets are composed of interstitial cells suspended within an extracellular matrix (ECM) and are lined with an endothelial cell monolayer. The valve withstands a harsh, dynamic environment and is constantly exposed to shear, flexion, tension, and compression. Research has shown calcific lesions in diseased valves occur in areas of high mechanical stress as a result of endothelial disruption or interstitial matrix damage1-3. Hence, it is not surprising that epidemiological studies have shown high blood pressure to be a leading risk factor in the onset of aortic valve disease4. 
The only treatment option currently available for valve disease is surgical replacement of the diseased valve with a bioprosthetic or mechanical valve5. Improved understanding of valve biology in response to physical stresses would help elucidate the mechanisms of valve pathogenesis. In turn, this could help in the development of non-invasive therapies such as pharmaceutical intervention or prevention. Several bioreactors have been previously developed to study the mechanobiology of native or engineered heart valves6-9. Pulsatile bioreactors have also been developed to study a range of tissues including cartilage10, bone11 and bladder12. The aim of this work was to develop a cyclic pressure system that could be used to elucidate the biological response of aortic valve leaflets to increased pressure loads. 
The system consisted of an acrylic chamber in which to place samples and produce cyclic pressure, viton diaphragm solenoid valves to control the timing of the pressure cycle, and a computer to control electrical devices. The pressure was monitored using a pressure transducer, and the signal was conditioned using a load cell conditioner. A LabVIEW program regulated the pressure using an analog device to pump compressed air into the system at the appropriate rate. The system mimicked the dynamic transvalvular pressure levels associated with the aortic valve; a saw tooth wave produced a gradual increase in pressure, typical of the transvalvular pressure gradient that is present across the valve during diastole, followed by a sharp pressure drop depicting valve opening in systole. The LabVIEW program allowed users to control the magnitude and frequency of cyclic pressure. The system was able to subject tissue samples to physiological and pathological pressure conditions. This device can be used to increase our understanding of how heart valves respond to changes in the local mechanical environment.

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

A cyclic pressure bioreactor capable of subjecting heart valve tissue to physiological and pathological pressure conditions has been designed. A LabVIEW program allows users to control pressure magnitude, amplitude and frequency. This device can be used to study the mechanobiology of heart valve tissue or isolated cells.

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic ...

Continuously-stirred Anaerobic Digester to Convert Organic Wastes into Biogas: System Setup and Basic Operation

Anaerobic digestion (AD) is a bioprocess that is commonly used to convert complex organic wastes into a useful biogas with methane as the energy carrier 1-3. Increasingly, AD is being used in industrial, agricultural, and municipal waste(water) treatment applications 4,5. The use of AD technology allows plant operators to reduce waste disposal costs and offset energy utility expenses. In addition to treating organic wastes, energy crops are being converted into the energy carrier methane 6,7. As the application of AD technology broadens for the treatment of new substrates and co-substrate mixtures 8, so does the demand for a reliable testing methodology at the pilot- and laboratory-scale.
Anaerobic digestion systems have a variety of configurations, including the continuously stirred tank reactor (CSTR), plug flow (PF), and anaerobic sequencing batch reactor (ASBR) configurations 9. The CSTR is frequently used in research due to its simplicity in design and operation, but also for its advantages in experimentation. Compared to other configurations, the CSTR provides greater uniformity of system parameters, such as temperature, mixing, chemical concentration, and substrate concentration. Ultimately, when designing a full-scale reactor, the optimum reactor configuration will depend on the character of a given substrate among many other nontechnical considerations. However, all configurations share fundamental design features and operating parameters that render the CSTR appropriate for most preliminary assessments. If researchers and engineers use an influent stream with relatively high concentrations of solids, then lab-scale bioreactor configurations cannot be fed continuously due to plugging problems of lab-scale pumps with solids or settling of solids in tubing. For that scenario with continuous mixing requirements, lab-scale bioreactors are fed periodically and we refer to such configurations as continuously stirred anaerobic digesters (CSADs).
This article presents a general methodology for constructing, inoculating, operating, and monitoring a CSAD system for the purpose of testing the suitability of a given organic substrate for long-term anaerobic digestion. The construction section of this article will cover building the lab-scale reactor system. The inoculation section will explain how to create an anaerobic environment suitable for seeding with an active methanogenic inoculum. The operating section will cover operation, maintenance, and troubleshooting. The monitoring section will introduce testing protocols using standard analyses. The use of these measures is necessary for reliable experimental assessments of substrate suitability for AD. This protocol should provide greater protection against a common mistake made in AD studies, which is to conclude that reactor failure was caused by the substrate in use, when really it was improper user operation 10.

Laboratory-scale anaerobic digesters allow scientists to research new ways of optimizing existing applications of anaerobic biotechnology and to evaluate the methane producing potential of various organic wastes. This article introduces a generalized model for the construction, inoculation, operation, and monitoring of a laboratory-scale continuously stirred anaerobic digester.

Anaerobic digestion (AD) is a bioprocess that is commonly used to convert complex organic wastes into a useful biogas with methane as the energy carrier ...

Capillary Force Lithography for Cardiac Tissue Engineering

Cardiovascular disease remains the leading cause of death worldwide1. Cardiac tissue engineering holds much promise to deliver groundbreaking medical discoveries with the aims of developing functional tissues for cardiac regeneration as well as in vitro screening assays. However, the ability to create high-fidelity models of heart tissue has proven difficult. The heart&#8217;s extracellular matrix (ECM) is a complex structure consisting of both biochemical and biomechanical signals ranging from the micro- to the nanometer scale2. Local mechanical loading conditions and cell-ECM interactions have recently been recognized as vital components in cardiac tissue engineering3-5.
A large portion of the cardiac ECM is composed of aligned collagen fibers with nano-scale diameters that significantly influences tissue architecture and electromechanical coupling2. Unfortunately, few methods have been able to mimic the organization of ECM fibers down to the nanometer scale. Recent advancements in nanofabrication techniques, however, have enabled the design and fabrication of scalable scaffolds that mimic the in vivo structural and substrate stiffness cues of the ECM in the heart6-9.
Here we present the development of two reproducible, cost-effective, and scalable nanopatterning processes for the functional alignment of cardiac cells using the biocompatible polymer poly(lactide-co-glycolide) (PLGA)8 and a polyurethane (PU) based polymer. These anisotropically nanofabricated substrata (ANFS) mimic the underlying ECM of well-organized, aligned tissues and can be used to investigate the role of nanotopography on cell morphology and function10-14.
Using a nanopatterned (NP) silicon master as a template, a polyurethane acrylate (PUA) mold is fabricated. This PUA mold is then used to pattern the PU or PLGA hydrogel via UV-assisted or solvent-mediated capillary force lithography (CFL), respectively15,16. Briefly, PU or PLGA pre-polymer is drop dispensed onto a glass coverslip and the PUA mold is placed on top. For UV-assisted CFL, the PU is then exposed to UV radiation (&#955; = 250-400 nm) for curing. For solvent-mediated CFL, the PLGA is embossed using heat (120 &#176;C) and pressure (100 kPa). After curing, the PUA mold is peeled off, leaving behind an ANFS for cell culture. Primary cells, such as neonatal rat ventricular myocytes, as well as human pluripotent stem cell-derived cardiomyocytes, can be maintained on the ANFS2.

In this protocol, we demonstrate the fabrication of biomimetic cardiac cell culture substrata made from two distinct polymeric materials using capillary force lithography. The described methods provide a scalable, cost-effective technique to engineer the structure and function of macroscopic cardiac tissues for in vitro and in vivo applications.

Cardiovascular disease remains the leading cause of death worldwide1. Cardiac tissue engineering holds much promise to deliver groundbreaking medical ...

Real-time Monitoring of High Intensity Focused Ultrasound (HIFU) Ablation of In Vitro Canine Livers Using Harmonic Motion Imaging for Focused Ultrasound (HMIFU)

Harmonic Motion Imaging for Focused Ultrasound (HMIFU) is a technique that can perform and monitor high-intensity focused ultrasound (HIFU) ablation. An oscillatory motion is generated at the focus of a 93-element and 4.5 MHz center frequency HIFU transducer by applying a 25 Hz amplitude-modulated signal using a function generator. A 64-element and 2.5 MHz imaging transducer with 68kPa peak pressure is confocally placed at the center of the HIFU transducer to acquire the radio-frequency (RF) channel data. In this protocol, real-time monitoring of thermal ablation using HIFU with an acoustic power of 7 W on canine livers in vitro is described. HIFU treatment is applied on the tissue during 2 min and the ablated region is imaged in real-time using diverging or plane wave imaging up to 1,000 frames/second. The matrix of RF channel data is multiplied by a sparse matrix for image reconstruction. The reconstructed field of view is of 90&#176; for diverging wave and 20 mm for plane wave imaging and the data are sampled at 80 MHz. The reconstruction is performed on a Graphical Processing Unit (GPU) in order to image in real-time at a 4.5 display frame rate. 1-D normalized cross-correlation of the reconstructed RF data is used to estimate axial displacements in the focal region. The magnitude of the peak-to-peak displacement at the focal depth decreases during the thermal ablation which denotes stiffening of the tissue due to the formation of a lesion. The displacement signal-to-noise ratio (SNRd) at the focal area for plane wave was 1.4 times higher than for diverging wave showing that plane wave imaging appears to produce better displacement maps quality for HMIFU than diverging wave imaging.

Real-time Monitoring of High Intensity Focused Ultrasound HIFU Ablation of In Vitro Canine Livers Using Harmonic Motion Imaging for Focused Ultrasound HMIFU

This article describes real-time monitoring of HIFU ablation in canine liver with high frame rate ultrasound imaging using diverging and plane wave imaging. Harmonic Motion Imaging for Focused Ultrasound is used to image the decrease of acoustic radiation force induced displacement in the ablated region.

Harmonic Motion Imaging for Focused Ultrasound (HMIFU) is a technique that can perform and monitor high-intensity focused ultrasound (HIFU) ablation. An ...

Merging Ion Concentration Polarization between Juxtaposed Ion Exchange Membranes to Block the Propagation of the Polarization Zone

The ion concentration polarization (ICP) phenomenon is one of the most prevailing methods to preconcentrate low-abundance biological samples. The ICP induces a noninvasive region for charged biomolecules (i.e., the ion depletion zone), and targets can be preconcentrated on this region boundary. Despite the high preconcentration performances with ICP, it is difficult to find the operating conditions of non-propagating ion depletion zones. To overcome this narrow operating window, we recently developed a new platform for spatiotemporally fixed preconcentration. Unlike preceding methods that only use ion depletion, this platform also uses the opposite polarity of the ICP (i.e., ion enrichment) to stop the propagation of the ion depletion zone. By confronting the enrichment zone with the depletion zone, the two zones merge together and stop. In this paper, we describe a detailed experimental protocol to build this spatiotemporally defined ICP platform and characterize the preconcentration dynamics of the new platform by comparing them with those of the conventional device. Qualitative ion concentration profiles and current-time responses successfully capture the different dynamics between the merged ICP and the stand-alone ICP. In contrast to the conventional one that can fix the preconcentration location at only ~5 V, the new platform can produce a target-condensed plug at a specific location in the broad ranges of operating conditions: voltage (0.5-100 V), ionic strength (1-100 mM), and pH (3.7-10.3).

The protocol for a novel ion concentration polarization (ICP) platform that can stop the propagation of the ICP zone, regardless of the operating conditions is described. This unique ability of the platform lies in the use of merging ion depletion and enrichment, which are two polarities of the ICP phenomenon.

The ion concentration polarization (ICP) phenomenon is one of the most prevailing methods to preconcentrate low-abundance biological samples. The ICP ...

Functional Surface-immobilization of Genes Using Multistep Strand Displacement Lithography

Immobilization of genes on lithographically structured surfaces allows the study of compartmentalized gene expression processes in an open microfluidic bioreactor system. In contrast to other approaches towards artificial cellular systems, such a setup allows for a continuous supply with gene expression reagents and simultaneous draining of waste products. This facilitates the implementation of cell-free gene expression processes over extended periods of time, which is important for the realization of dynamic gene regulatory feedback systems. Here we provide a detailed protocol for the fabrication of genetic biochips using a simple-to-use lithographic technique based on DNA strand displacement reactions, which exclusively uses commercially available components. We also provide a protocol on the integration of compartmentalized genes with a polydimethylsiloxane (PDMS)-based microfluidic system. Furthermore, we show that the system is compatible with total internal reflection fluorescence (TIRF) microscopy, which can be used for the direct observation of molecular interactions between DNA and molecules contained in the expression mix.

We describe a simple lithographic procedure for the immobilization of gene-length DNA molecules on a surface, which can be used to perform cell-free gene expression experiments on biochips.

Immobilization of genes on lithographically structured surfaces allows the study of compartmentalized gene expression processes in an open microfluidic ...

Assembly and Characterization of Biomolecular Memristors Consisting of Ion Channel-doped Lipid Membranes

The ability to recreate synaptic functionalities in synthetic circuit elements is essential for neuromorphic computing systems that seek to emulate the cognitive powers of the brain with comparable efficiency and density. To date, silicon-based three-terminal transistors and two-terminal memristors have been widely used in neuromorphic circuits, in large part due to their ability to co-locate information processing and memory. Yet these devices cannot achieve the interconnectivity and complexity of the brain because they are power-hungry, fail to mimic key synaptic functionalities, and suffer from high noise and high switching voltages. To overcome these limitations, we have developed and characterized a biomolecular memristor that mimics the composition, structure, and switching characteristics of biological synapses. Here, we describe the process of assembling and characterizing biomolecular memristors consisting of a 5 nm-thick lipid bilayer formed between lipid-functionalized water droplets in oil and doped with voltage-activated alamethicin peptides. While similar assembly protocols have been used to investigate biophysical properties of droplet-supported lipid membranes and membrane-bound ion channels, this article focuses on key modifications of the droplet interface bilayer method essential for achieving consistent memristor performance. Specifically, we describe the liposome preparation process and the incorporation of alamethicin peptides in lipid bilayer membranes, and the appropriate concentrations of each constituent as well as their impact on the overall response of the memristors. We also detail the characterization process of biomolecular memristors, including measurement and analysis of memristive current-voltage relationships obtained via cyclic voltammetry, as well as short-term plasticity and learning in response to step-wise voltage pulse trains.

Soft, low-power, biomolecular memristors leverage similar composition, structure, and switching mechanisms of bio-synapses. Presented here is a protocol to assemble and characterize biomolecular memristors obtained from insulating lipid bilayers formed between water droplets in oil. The incorporation of voltage-activated alamethicin peptides results in memristive ionic conductance across the membrane.

The ability to recreate synaptic functionalities in synthetic circuit elements is essential for neuromorphic computing systems that seek to emulate the ...

Bioinspired Soft Robot with Incorporated Microelectrodes

Bioinspired soft robotic systems that mimic living organisms using engineered muscle tissue and biomaterials are revolutionizing the current biorobotics paradigm, especially in biomedical research. Recreating artificial life-like actuation dynamics is crucial for a soft-robotic system. However, the precise control and tuning of actuation behavior still represents one of the main challenges of modern soft robotic systems. This method describes a low-cost, highly scalable, and easy-to-use procedure to fabricate an electrically controllable soft robot with life-like movements that is activated and controlled by the contraction of cardiac muscle tissue on a micropatterned sting ray-like hydrogel scaffold. The use of soft photolithography methods makes it possible to successfully integrate multiple components in the soft robotic system, including micropatterned hydrogel-based scaffolds with carbon nanotubes (CNTs) embedded gelatin methacryloyl (CNT-GelMA), poly(ethylene glycol) diacrylate (PEGDA), flexible gold (Au) microelectrodes, and cardiac muscle tissue. In particular, the hydrogels alignment and micropattern are designed to mimic the muscle and cartilage structure of the sting ray. The electrically conductive CNT-GelMA hydrogel acts as a cell scaffold that improves the maturation and contraction behavior of cardiomyocytes, while the mechanically robust PEGDA hydrogel provides structural cartilage-like support to the whole soft robot. To overcome the hard and brittle nature of metal-based microelectrodes, we designed a serpentine pattern that has high flexibility and can avoid hampering the beating dynamics of cardiomyocytes. The incorporated flexible Au microelectrodes provide electrical stimulation across the soft robot, making it easier to control the contraction behavior of cardiac tissue.

A bioinspired scaffold is fabricated by a soft photolithography technique using mechanically robust and electrically conductive hydrogels. The micropatterned hydrogels provide directional cardiomyocyte cell alignment, resulting in a tailored direction of actuation. Flexible microelectrodes are also integrated into the scaffold to bring electrical controllability for a self-actuating cardiac tissue.

Bioinspired soft robotic systems that mimic living organisms using engineered muscle tissue and biomaterials are revolutionizing the current biorobotics ...