Research was supported by seed funds from The Agricultural Research Organization to MK.

1. Growing the plants and root preparation
<ol>
	<li>Option 1: Prepare adventitious roots from stem.
	<ol>
		<li>Take a rooting tray for growing plants.</li>
		<li>Fill the tray with soil.</li>
		<li>Add one seed of M82 tomato cultivar to each cell in the tray.</li>
		<li>Cover the seeds with a little soil.</li>
		<li>Water the tray from the bottom with a dropper as the water fills the bottom of the tray and the soil absorbs water.</li>
		<li>Add 2 mL of fertilizer per 1 L of water to the bottom of the tray once a week.</li>
		<li>Grow in a growing chamber at 25 &#176;C.</li>
		<li>Use lighting conditions of 9 h light (7:00-16:00) alternated with 15 h of darkness.</li>
		<li>After 3 weeks remove the plant from the soil.</li>
		<li>Cut the root system from the plant at the point of interaction with the stem.</li>
		<li>Put the rootless plant in a beaker filled with water.</li>
		<li>After a few days, cut the adventitious roots that emerge from the stem and use them for replication.</li>
	</ol>
	</li>
	<li>Option 2: Prepare seed germinating roots.
	<ol>
		<li>Wet a Petri dish sized filter paper with water.</li>
		<li>Put several M82 seeds (no more than 10) on the paper, inside a Petri dish.</li>
		<li>Incubate the plate at 25 &#176;C.</li>
		<li>Hydrate the paper every day.</li>
		<li>After germinated roots are long enough (approximately 5 days), remove the seeds and use the roots for replication.</li>
	</ol>
	</li>
</ol>
2. Preparation of the root negative replica from polyurethane
<ol>
	<li>To generate negative replica solution, add 9.49 g of diurethane dimethacrylate to a 20 mL vial.
	<ol>
		<li>Add 1.45 mL of ethyl methacrylate to the vial.</li>
		<li>Stir at room temperature (RT) until the solution looks clear and becomes homogeneous. 
		NOTE: Approximately 2 h is sufficient to reach a homogeneous solution.</li>
		<li>Add 3 mL of the plasticizer, diethyl phthalate, and stir for 1 h at RT. 
		NOTE: Diethyl phthalate is miscible in acrylate monomer.</li>
		<li>Add 300 &#181;L of the photo initiator, 2-hydroxy-2-methylpropiophenone, and stir overnight at RT. Continue stirring until all bubbles are removed. 
		NOTE: The protocol can be paused here. The solution can be kept at RT.</li>
	</ol>
	</li>
	<li>To generate the negative replica of the root, take a clean glass slide and pour 1 mL of the negative replica solution on it.
	<ol>
		<li>Place 2&#8210;3 roots over the solution. Do not allow the roots to be fully covered by the solution.</li>
		<li>Keep the slide under 8 W ultra violet (UV) lamp for 8&#8210;10 min. Do not keep the solution under UV light for too long. 
		NOTE: It is important not to keep the solution under the UV light for too long as it makes the polyurethane too hard, making it impossible to remove the root.</li>
		<li>Switch off the UV lamp, remove the replica from the glass slide and put it in a Petri dish filled with ethanol, to remove unreacted monomer.</li>
		<li>To obtain the negative replica, remove the root from the replica very slowly using forceps.</li>
	</ol>
	</li>
</ol>
3. Prepare the root positive replica from PDMS.
<ol>
	<li>To generate the mixture for the positive replica, place 10 g of dimethyl siloxane in a paper cup.
	<ol>
		<li>Add 1 g of curing agent and mix thoroughly.</li>
		<li>Keep the mixture in a desiccator under vacuum for 2 h to remove air bubbles.</li>
	</ol>
	</li>
	<li>To generate the positive replica, place the polyurethane negative replica in a Petri dish.
	<ol>
		<li>Pour the PDMS mixture on top of the negative replica.</li>
		<li>Apply vacuum for 2 h to assure coverage of the microstructure.</li>
		<li>Keep the Petri dish overnight at RT.</li>
		<li>Separate the cured positive replica from the negative replica by hand.</li>
	</ol>
	</li>
</ol>
4. Prepare the root positive replica from ethyl cellulose.
<ol>
	<li>To generate the ethyl cellulose solution,&#160;put 1.32 ml of diethyl pthalate as a plasticizer in a 100 ml cup.
	<ol>
		<li>Add 20 mL of ethanol and stir at RT for 2 h.</li>
		<li>Add 3.3 g&#160;of ethyl cellulose and stir overnight.</li>
	</ol>
	</li>
	<li>To generate the positive replica, place the polyurethane negative replica in a Petri dish.
	<ol>
		<li>Pour the ethyl cellulose solution on top of the negative replica.</li>
		<li>Keep the Petri dish overnight at RT under the hood.</li>
		<li>Remove the positive replica from the negative replica very slowly by forceps.</li>
	</ol>
	</li>
</ol>

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The authors have nothing to disclose.

We present a novel method for the replication of root surface microstructure. This method relies on existing methods of leaf surface microstructure replication4. In order to develop this method, we had to tweak the existing method for leaves. We realized that the problematic step in copying the leaf replication method into roots involves the first step of the root molding. This is the most sensitive part of the method as it involves the biological tissue. As a result, we wanted to choose a polymer that would demand relatively gentle conditions for curing and hence causing minimal damage to the biological tissue. We chose polyurethane because it can be polymerized quickly (within 10 min) under UV light29. Additionally, it is very hard once polymerized30 and we hoped that this property would allow for the relatively easy removal of the root from the polyurethane mold.
The presented method is a two-step approach in which the negative image (negative replica) is formed in the first step and the replication is formed in the second step, based on the negative replica. This extends the range of materials we can work with. Leaf surface microstructure replication was mainly performed on PDMS or epoxy materials11,31. Some work was done with other materials, specifically materials supporting microorganism growth13,32. This is because in recent years this method has been used to study microorganism-surface interactions in the context of leaf surface structure. However, no cellulose-like materials have been used in this method in the context of leaves. We suggest the use of a polyurethane negative replica as a mold and a variety of materials for the positive replica. In other words, making the positive replica, from a variety of materials, is relatively easy once a good negative replica is made. We currently use cellulose derivatives, but are exploring the possibilities of using more relevant materials to root surface such as pectin and lignin33,34 in combination with cellulose derivatives.
The method also expands upon the existing method of leaf surface microstructure replication since the leaf is a 2D surface while the root surface is curved and hence is a 3D surface. Our method does not enable the replication of the whole surface since embedding the whole root in the polyurethane solution does not allow for its release. Therefore, one side of the root has to be chosen when replicating the root surface microstructure. The generated synthetic surface is curved and represents roughly half the surface, but not all of it. Our assumption is that the structural features of the root surface are mostly symmetrical about the axis along the root length. However, in studies where such symmetry is not assumed, one should be careful to choose the appropriate side root to replicate.
We present two options for roots to be used as molds. The first is the option of adventitious roots grown from the stem and the second is the option of germinated roots on paper. The first option is mostly meant to assist researchers in practicing the method as these roots are more robust and easier to work with. The second option represents the genetic differences that can be found between roots of different cultivars, regardless of the environmental conditions. These surfaces can be used as important research tools, however, one should be aware that the environment can have a strong influence on the root surface structure, specifically the soil in which the roots are grown35,36. Due to the mechanical stress inflicted by the soil, some morphological changes are bound to happen, in addition to wounds accruing on the surface as the root penetrates the soil37. Removal of roots from soil, as well as cleaning them, without damaging their structure is a very difficult task. Hence, we are not optimistic as to the ability to use this method to reliably mimic the root surface microstructure of roots grown in soil. However, for research that focuses on genetic differences or environmental differences where the change in microstructure is noticeably clear, this method can be used as a tool to study the influence of root surface microstructure.
Our method produces an inert surface mimicking of only the microstructural properties of the root surface. While this method is designed to separate the structural effects in root-environment interactions from all other effects, we cannot ignore the chemical compounds in those interactions. Some microorganisms may not survive or function on the surface without the addition of compounds, specifically nutrients. The next step in the development of this platform will be the controlled addition of chemical compounds to study their effects on the different interactions when combined with structure.
This method was developed as a first step in the development of a synthetic platform to study root-microorganism interactions. Here we mimic the microstructure of the root surface and this initial platform can be used to study the influence of surface microstructure on microorganism behavior. However, this platform is limited since it lacks many other elements from the natural system. This platform should be further developed with the use of the right materials to generate the surface and with the addition of other, critical, chemicals into the system. In a more advanced platform, we can also imagine spatial distribution of the chemicals. However, since currently no other method exists to isolate structural effects in root-microorganism interactions, we hope researchers could use this initial platform to ask structure-specific questions in those interactions.

Replication of leaf surface microstructure is a known method in the biomimetics research field1,2,3,4. The earliest replications of the leaf surface microstructure were performed using nail polish and rubber materials applied on the leaf surface for better visualization of microstructure, specifically stomata5,6,7,8,9,10. The method was then improved, and advanced polymers were used to mimic leaf surface microstructure using soft lithography, especially in the context of biomimetics of super hydrophobic surfaces2,3,4,11,12. In recent years, this method was proven as a useful tool in the study of the interaction between the leaf surface and microorganisms residing on the surface whether they are pathogenic13,14 or beneficial, as part of the natural leaf phyllosphere15. Simplification of the natural system was proven extremely useful in the study of surface-microorganism interactions even when purely synthetic systems were used as surfaces15,16,17,18.
While replication of leaf surface microstructure was shown to be a useful tool for studying the interaction occurring on the surface of the leaf with different microorganisms, no such tool exists for plant roots. Plant roots are harder to study since they reside below the ground and all interactions occur within the soil. Similar to leaves, root surface microstructure is likely to play a role in root-microorganism interactions. However, currently no method exists to isolate the specific role of root surface microstructure in the complex root-microorganism interactions. The most studied root surface microstructural feature is the root hairs19,20,21. Root hairs have an important role in increasing the surface area and by that allowing more efficient intake of nutrients and water22, however their involvement as a structural feature in root-microorganism interactions has never been tested.
The most widely used polymer for soft lithography in leaves is polydimethyl siloxane (PDMS). PDMS properties resemble those of the leaf cuticle15,23. However, in plant roots, the most abundant material is cellulose24,25 which has different properties than those of PDMS26,27,28. Using PDMS to build a synthetic platform for studying the surface microstructure effects in root-environment interactions is, hence, less than ideal.
The protocol presented here enables the formation of synthetic root surface microstructure replica from various materials. Like the method for leaf surface microstructure replication this is a two-step process. The first step uses the biological tissue (root) as a source for molding into a polyurethane mold (a negative replica). The polyurethane mold, which represents the negative image of the root surface microstructure, can then be used as a base to generate the positive replication of the root surface microstructure from a variety of materials, including PDMS and cellulose derivatives. This root surface replication can later be used as a platform to understand the surface structure role in root-microorganism interactions.

<table>
	<tbody>
		<tr>
			<td>2-hydroxy-2-methylpropiophenone</td>
			<td>Sigma</td>
			<td>405655</td>
			<td></td>
		</tr>
		<tr>
			<td>Diethyl phthalate</td>
			<td>Across</td>
			<td>114520010</td>
			<td></td>
		</tr>
		<tr>
			<td>Diurethane dimetharylate</td>
			<td>Sigma</td>
			<td>436909</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl cellulose</td>
			<td>Across</td>
			<td>232705000</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl methacrylate</td>
			<td>Sigma</td>
			<td>234893</td>
			<td></td>
		</tr>
		<tr>
			<td>Shaphir Solution</td>
			<td>GAT fertilizer</td>
			<td>6-2-4</td>
			<td></td>
		</tr>
		<tr>
			<td>Sylgard 184 kit</td>
			<td>Polymer-G</td>
			<td>510018400500</td>
			<td></td>
		</tr>
	</tbody>
</table>

biomimetic replication of root surface microstructure using alteration of soft lithography

Biomimetics is the use of chemistry and material sciences to mimic biological systems, specifically biological structures, to better humankind. Recently, biomimetic surfaces mimicking the microstructure of leaf surface, were used to study the effects of leaf microstructure on leaf-environment interactions. However, no such tool exists for roots. We developed a tool allowing the synthetic mimicry of the root surface microstructure into an artificial surface. We relied on the soft lithography method, known for leaf surface microstructure replication, using a two-step process. The first step is the more challenging one as it involves the biological tissue. Here, we used a different polymer and curing strategy, relying on the strong, rigid, polyurethane, cured by UV for the root molding. This allowed us to achieve a reliable negative image of the root surface microstructure including the delicate, challenging features such as root hairs. We then used this negative image as a template to achieve the root surface microstructure replication using both the well-established polydimethyl siloxane (PDMS) as well as a cellulose derivative, ethyl cellulose, which represents a closer mimic of the root and which can also be degraded by cellulase enzymes secreted by microorganisms. This newly formed platform can be used to study the microstructural effects of the surface in root-microorganism interactions in a similar manner to what has previously been shown in leaves. Additionally, the system enables us to track the microorganism&#8217;s locations, relative to surface features, and in the future its activity, in the form of cellulase secretion.

To form the root surface microstructure replication, a root must be chosen for molding. We grow tomato plants in soil, making the use of the natural root from the root system extremely challenging. Removal of soil from the root system can be difficult and additionally, the root system roots are fragile and can break upon molding attempts. We therefore suggest to first use more rigid roots, to establish the protocol in the lab. The formation of such roots is described in Figure 1A. The plant root system is removed after the plant was grown for 3 weeks and the rootless plant is placed in water for about a week until adventitious roots emerge from the stem. Those roots can be used for replication during the protocol establishment. Once the protocol has been well established, a more realistic root surface structure is desired. Here we suggest avoiding roots grown in soil as the full removal of soil in extremely challenging. Instead we suggest the use of germinating roots, supplying valuable information on the root surface microstructure of a genetically specific plant. The growth of such roots is described in Figure 1B. The seeds are placed on a wet filter paper and incubated at 25 &#176;C. After approximately 5 days, during which the filter paper is kept moist, the germinated roots are long enough for replication. Those roots are more fragile than the previously suggested roots and require more delicate care.
The production of the root surface microstructure replica is a two-step process. In the first step the natural root is being molded into a polyurethane based mold (the negative replica). The advantage of this step is that all materials for the polyurethane mold are being prepared and the root is placed on top of the prepared solution at the very end for a 10 min exposure to UV. As a result, the biological tissue is not exposed to harsh conditions for too long and can be gently handled at the end of the process. If all protocol steps are followed, a good negative replica is generated. This replica will show the cell structure of the root surface as well as holes representing the location of the root hairs (Figure 2A). If some critical steps in the protocol are not being followed, the procedure will fail. One such step is the placement of the root on the polyurethane solution prior to curing. The root must be placed very gently to avoid the submergence of it in the polyurethane solution. Such submergence, of any part of the root, will cause the entrapment of the root in the hard polymer with no ability to remove it. If such an event occurs, the root will remain within the negative replica after it is cured (Figure 2B). Another crucial step is regarding the curing time by UV light. The recommended curing time is 8&#8210;10 min. Going past 10 min will result in an extremely hard polyurethane mold, making it impossible to remove the root without breaking it within the polyurethane mold. The breakage of the root can sometimes be visible to the naked eye, e.g., when a large piece is broken (Figure 2C, top, marked with purple arrows). However, sometimes small root pieces are left in the material which are difficult to spot by the naked eye and a microscope has to be used (Figure 2C, bottom, marked with purple arrows). We recommend carefully examining the polyurethane negative replica with a microscope prior to the continuation of the protocol to make sure no residual root is present.
Once the polyurethane negative replica is prepared; many materials can be used for the preparation of the positive replica. The preparation of the positive replica, using the polyurethane negative replica as a mold, is straight forward and depends completely on the quality of the polyurethane negative replica. To generate the positive replica we have used both PDMS&#8212;as it is well known in the field of soft lithography (Figure 3A)&#8212;and ethyl cellulose as a material that better mimics the properties of the root surface which is mostly composed of cellulose (Figure 3B). The SEM image of the PDMS replica shows the root hairs very clearly. The hairs are in the elongation zone, where they begin to emerge. Hence, the length of root hairs varies along the root surface as they become longer, much like in the natural root (Figure 3A). Ethyl cellulose generates harder and less flexible film than PDMS. Hence, the removal of it from the negative mold requires more care. However, some hairs and the surface microstructure are visible under the light microscope (Figure 3B). We used those two materials to generate the positive replica, however, any material that can form a film will be a good candidate for the positive replica, using the polyurethane negative replica.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/61437/61437fig01.jpg" /> 
Figure 1: Tomato plant roots for replication.&#160;(A) A tomato (M82) plant is grown at 25 &#176;C with 9 h of light and 15 h darkness. After 3 weeks, the plant is removed from the soil and the root system is cut off. The rootless plant is put in water until adventitious roots emerge from the stem after about a week. These roots do not show the exact structure as the roots from the root system, but they represent a good model. Those roots are less fragile than the root system roots and hence are preferred to work with when establishing the technique in the lab. (B) Tomato (M82) seeds are put on a wet filter paper in a Petri dish and incubated at 25 &#176;C. The paper is hydrated every day and the seeds are germinating. The roots are growing and after approximately 5 days are long enough to be used for replication. These roots are gentler and should be used once the method is well established. <a href="https://www.jove.com/files/ftp_upload/61437/61437fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/61437/61437fig2v2.jpg" /> 
Figure 2: Microscopy images of polyurethane negative replica.&#160;(A) SEM image of polyurethane negative replica made according to a protocol following all the steps. Cell structure is clearly visible. Yellow arrows point at holes formed by the hairs in the root. (B) Light microscopy images of polyurethane negative replica with a root inside of it as it was fully covered with the solution and the removal of it was impossible. The polyurethane negative was cured with the root inside. The root is visible by eye and using light microscopy. It is impossible to remove this root from the cured replica. (C) Light microscopy images of polyurethane negative replica that was kept under UV light for too long. As a result, root could not be fully removed from the polymer with either large particles visible by eye (top image, marked with purple arrows) or small fractions visible only by microscope (lower image, marked with purple arrows). <a href="https://www.jove.com/files/ftp_upload/61437/61437fig2v2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/61437/61437fig03.jpg" /> 
Figure 3: Microscope images of positive replica.&#160;(A) SEM micrograph of a positive replica made from PDMS. Enlargement shows root hairs. (B) Light microscopy images of a positive replica made from ethyl cellulose. Hairs are shown in the images on the right while surface texture is visible in the image on the left. <a href="https://www.jove.com/files/ftp_upload/61437/61437fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Biomimetic Replication of Root Surface Microstructure using Alteration of Soft Lithography at JoVE.com

Biomimetic Replication of Root Surface Microstructure using Alteration of Soft Lithography

Biomimetics has been previously used as a tool to study leaf-microorganism interactions. However, no such tool exists for roots. Here, we develop a protocol to form synthetic surfaces mimicking root surface microstructure for the study of root-environment interactions.

Biomimetics is the use of chemistry and material sciences to mimic biological systems, specifically biological structures, to better humankind. Recently, ...

biomimetic-replication-root-surface-microstructure-using-alteration

Research

JoVE Journal

Bioengineering

5.6K Views.  Agricultural Research Organization (Volcani Center). Biomimetics has been previously used as a tool to study leaf-microorganism interactions. However, no such tool exists for roots. Here, we develop a protocol to form synthetic surfaces mimicking root surface microstructure for the study of root-environment interactions.

Video: Biomimetic Replication of Root Surface Microstructure using Alteration of Soft Lithography

Demonstrating the Uses of the Novel Gravitational Force Spectrometer to Stretch and Measure Fibrous Proteins

The study of macromolecular structure has become critical to the elucidation of molecular mechanisms and function. There are several limited, but important bioinstruments capable of testing the force dependence of structural features in proteins. Scale has been a limiting parameter on how accurately researchers can peer into the nanomechanical world of molecules, such as nucleic acids, enzymes, and motor proteins that perform life-sustaining work. Atomic force microscopy (AFM) is well tuned to determine native structures of fibrous proteins with a distance resolution on par with electron microscopy. However, in AFM force studies, the forces are typically much higher than a single molecule might experience 1, 2. Optical traps (OT) are very good at determining the relative distance between the trapped beads and they can impart very small forces 3. However, they do not yield accurate absolute lengths of the molecules under study. Molecular simulations provide supportive information to such experiments, but are limited in the ability to handle the same large molecular sizes, long time frames, and convince some researchers in the absence of other supporting evidence2, 4.
The gravitational force spectrometer (GFS) fills a critical niche in the arsenal of an investigator by providing a unique combination of abilities. This instrument is capable of generating forces typically with 98% or better accuracy from the femtonewton range to the nanonewton range. The distance measurements currently are capable of resolving the absolute molecular length down to five nanometers, and relative bead pair separation distances with a precision similar to an optical trap. Also, the GFS can determine stretching or uncoiling where the force is near equilibrium, or provide a graded force to juxtapose against any measured structural changes. It is even possible to determine how many amino acid residues are involved in uncoiling events under physiological force loads 2. Unlike in other methods where there is extensive force calibration that must precede any assay, the GFS requires no such force calibration 5. By complementing the strengths of other methods, the GFS will bridge gaps in understanding the nanomechanics of vital proteins and other macromolecules.

This is a step-by step guide showing the purpose, operation, and representative results from the novel gravitational force spectrometer.

The study of macromolecular structure has become critical to the elucidation of molecular mechanisms and function. There are several limited, but ...

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 ...

Time-lapse Fluorescence Imaging of Arabidopsis Root Growth with Rapid Manipulation of The Root Environment Using The RootChip

The root functions as the physical anchor of the plant and is the organ responsible for uptake of water and mineral nutrients such as nitrogen, phosphorus, sulfate and trace elements that plants acquire from the soil. If we want to develop sustainable approaches to producing high crop yield, we need to better understand how the root develops, takes up a wide spectrum of nutrients, and interacts with symbiotic and pathogenic organisms. To accomplish these goals, we need to be able to explore roots in microscopic detail over time periods ranging from minutes to days.
We developed the RootChip, a polydimethylsiloxane (PDMS)- based microfluidic device, which allows us to grow and image roots from Arabidopsis seedlings while avoiding any physical stress to roots during preparation for imaging1 (Figure 1). The device contains a bifurcated channel structure featuring micromechanical valves to guide the fluid flow from solution inlets to each of the eight observation chambers2. This perfusion system allows the root microenvironment to be controlled and modified with precision and speed. The volume of the chambers is approximately 400 nl, thus requiring only minimal amounts of test solution.
Here we provide a detailed protocol for studying root biology on the RootChip using imaging-based approaches with real time resolution. Roots can be analyzed over several days using time lapse microscopy. Roots can be perfused with nutrient solutions or inhibitors, and up to eight seedlings can be analyzed in parallel. This system has the potential for a wide range of applications, including analysis of root growth in the presence or absence of chemicals, fluorescence-based analysis of gene expression, and the analysis of biosensors, e.g. FRET nanosensors3.

This article provides a protocol for cultivation of Arabidopsis seedlings in the RootChip, a microfluidic imaging platform that combines automated control of growth conditions with microscopic root monitoring and FRET-based measurement of intracellular metabolite levels.

The root functions as the physical anchor of the plant and is the organ responsible for uptake of water and mineral nutrients such as nitrogen, ...

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 ...

Surface Potential Measurement of Bacteria Using Kelvin Probe Force Microscopy

Surface potential is a commonly overlooked physical characteristic that plays a dominant role in the adhesion of microorganisms to substrate surfaces. Kelvin probe force microscopy (KPFM) is a module of atomic force microscopy (AFM) that measures the contact potential difference between surfaces at the nano-scale. The combination of KPFM with AFM allows for the simultaneous generation of surface potential and topographical maps of biological samples such as bacterial cells. Here, we employ KPFM to examine the effects of surface potential on microbial adhesion to medically relevant surfaces such as stainless steel and gold. Surface potential maps revealed differences in surface potential for microbial membranes on different material substrates. A step-height graph was generated to show the difference in surface potential at a boundary area between the substrate surface and microorganisms. Changes in cellular membrane surface potential have been linked with changes in cellular metabolism and motility. Therefore, KPFM represents a powerful tool that can be utilized to examine the changes of microbial membrane surface potential upon adhesion to various substrate surfaces. In this study, we demonstrate the procedure to characterize the surface potential of individual methicillin-resistant Staphylococcus aureus USA100 cells on stainless steel and gold using KPFM.

Here, we present a protocol explaining the use of Kelvin probe force microscopy as a tool for generating high resolution nano-scale surface potential maps. This tool was applied to assess the role of surface potential on the binding capacity of microorganisms to substrate surfaces.

Surface potential is a commonly overlooked physical characteristic that plays a dominant role in the adhesion of microorganisms to substrate surfaces. ...

Biomechanical Characterization of Human Soft Tissues Using Indentation and Tensile Testing

Regenerative medicine aims to engineer materials to replace or restore damaged or diseased organs. The mechanical properties of such materials should mimic the human tissues they are aiming to replace; to provide the required anatomical shape, the materials must be able to sustain the mechanical forces they will experience when implanted at the defect site. Although the mechanical properties of tissue-engineered scaffolds are of great importance, many human tissues that undergo restoration with engineered materials have not been fully biomechanically characterized. Several compressive and tensile protocols are reported for evaluating materials, but with large variability it is difficult to compare results between studies. Further complicating the studies is the often destructive nature of mechanical testing. Whilst an understanding of tissue failure is important, it is also important to have knowledge of the elastic and viscoelastic properties under more physiological loading conditions.
This report aims to provide a minimally destructive protocol to evaluate the compressive and tensile properties of human soft tissues. As examples of this technique, the tensile testing of skin and the compressive testing of cartilage are described. These protocols can also be directly applied to synthetic materials to ensure that the mechanical properties are similar to the native tissue. Protocols to assess the mechanical properties of human native tissue will allow a benchmark by which to create suitable tissue-engineered substitutes.

Tissue biomechanics is important for maintaining cell shape and function and for determining phenotype. This report demonstrates non-destructive mechanical protocols for characterizing elastic and viscoelastic properties of human soft tissues, which can be directly applied to tissue-engineered substrates to allow a close matching of engineered materials to native tissue.

Regenerative medicine aims to engineer materials to replace or restore damaged or diseased organs. The mechanical properties of such materials should ...

Surface Functionalization of Hepatitis E Virus Nanoparticles Using Chemical Conjugation Methods

Virus-like particles (VLPs) have been used as nanocarriers to display foreign epitopes and/or deliver small molecules in the detection and treatment of various diseases. This application relies on genetic modification, self-assembly, and cysteine conjugation to fulfill the tumor-targeting application of recombinant VLPs. Compared with genetic modification alone, chemical conjugation of foreign peptides to VLPs offers a significant advantage because it allows a variety of entities, such as synthetic peptides or oligosaccharides, to be conjugated to the surface of VLPs in a modulated and flexible manner without alteration of the VLP assembly.
Here, we demonstrate how to use the hepatitis E virus nanoparticle (HEVNP), a modularized theranostic capsule, as a multifunctional delivery carrier. Functions of HEVNPs include tissue-targeting, imaging, and therapeutic delivery. Based on the well-established structural research of HEVNP, the structurally independent and surface-exposed residues were selected for cysteine replacement as conjugation sites for maleimide-linked chemical groups via thiol-selective linkages. One particular cysteine-modified HEVNP (a Cys replacement of the asparagine at 573 aa (HEVNP-573C)) was conjugated to a breast cancer cell-specific ligand, LXY30 and labeled with near-infrared (NIR) fluorescence dye (Cy5.5), rendering the tumor-targeted HEVNPs as effective diagnostic capsules (LXY30-HEVNP-Cy5.5). Similar engineering strategies can be employed with other macromolecular complexes with well-known atomic structures to explore potential applications in theranostic delivery.

We have engineered the capsid protein of hepatitis E virus as a theranostic nanoparticle (HEVNP). HEVNP self-assembles into a stable icosahedral cage in mucosal delivery. Here, we describe the modification of HEVNPs for tumor targeting by mutating surface-exposed residues to cysteines, which conjugate synthetic ligands that specifically bind tumor cells.

Virus-like particles (VLPs) have been used as nanocarriers to display foreign epitopes and/or deliver small molecules in the detection and treatment of ...

Stiffness Measurement of Soft Silicone Substrates for Mechanobiology Studies Using a Widefield Fluorescence Microscope

Soft tissues in the human body typically have stiffness in the kilopascal (kPa) range. Accordingly, silicone and hydrogel flexible substrates have been proven to be useful substrates for culturing cells in a physical microenvironment that partially mimics in vivo conditions. Here, we present a simple protocol for characterizing the Young's moduli of isotropic linear elastic substrates typically used for mechanobiology studies. The protocol consists of preparing a soft silicone substrate on a Petri dish or stiff silicone, coating the top surface of the silicone substrate with fluorescent beads, using a millimeter-scale sphere to indent the top surface (by gravity), imaging the fluorescent beads on the indented silicone surface using a fluorescence microscope, and analyzing the resultant images to calculate the Young's modulus of the silicone substrate. Coupling the substrate's top surface with a moduli extracellular matrix protein (in addition to the fluorescent beads) allows the silicone substrate to be readily used for cell plating and subsequent studies using traction force microscopy experiments. The use of stiff silicone, instead of a Petri dish, as the base of the soft silicone, enables the use of mechanobiology studies involving external stretch. A specific advantage of this protocol is that a widefield fluorescence microscope, which is commonly available in many labs, is the major equipment necessary for this procedure. We demonstrate this protocol by measuring the Young's modulus of soft silicone substrates of different elastic moduli.

Substrates with stiffness in the kilopascal-range are useful to study the response of cells to physiologically relevant micro-environment stiffness. Using just a widefield fluorescence microscope, the Young's modulus of soft silicone gels can be determined using an indentation with a suitable sphere.

Soft tissues in the human body typically have stiffness in the kilopascal (kPa) range. Accordingly, silicone and hydrogel flexible substrates have been ...

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 ...

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.

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 ...