Name: assembly and tracking of microbial community development within a microwell array platform
Uploaded: 2017-06-06T15:30:00
Description: Watch this Scientific Journal Video about Assembly and Tracking of Microbial Community Development within a Microwell Array Platform at JoVE.com

Microwell arrays were fabricated and characterized at the Center for Nanophase Materials Sciences User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. Financial support for this work was provided through the Oak Ridge National Laboratory Director&#39;s Research and Development Fund. The authors would also like to thank the J. Mougous Laboratory (University of Washington, Seattle, WA) for the supply of P. aeruginosa strains used in these studies.

1. Silicon Microwell-array Fabrication
<ol>
	<li>Parylene coating
	<ol>
		<li>Deposit between 1-1.5 &#181;m of parylene N on silicon wafers using a commercially available parylene coating system according to the manufacturer&#39;s specifications and instructions (settings: vaporizer set point = 160 &#176;C; furnace set point = 650 &#176;C). 
		NOTE: Approximately 6 g of parylene N loaded into a chamber yields coatings 1-1.5 &#181;m thick.</li>
	</ol>
	</li>
	<li>Photolithography
	...

<ol>
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S., Vlamakis, H., Kim, P., Khan, M., Kolter, R., Aizenberg, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bacterial+flagella+explore+microscale+hummocks+and+hollows+to+increase+adhesion.">Bacterial flagella explore microscale hummocks and hollows to increase adhesion.</a> Proc Natl Acad Sci USA. 110 (14), 5624-5629 (2013).</li><li>Zhou, J., Liu, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stochastic+Assembly+Leads+to+Alternative+Communities+with+Distinct+Functions+in+a+Bioreactor+Microbial+Community.">Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community.</a> MBio. 4 (2), 1-8 (2013).</li><li>van Vliet, S., Hol, F. J., Weenink, T., Galajda, P., Keymer, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effects+of+chemical+interactions+and+culture+history+on+the+colonization+of+structured+habitats+by+competing+bacterial+populations.">The effects of chemical interactions and culture history on the colonization of structured habitats by competing bacterial populations.</a> BMC Microbiol. 14 (1), 116 (2014).</li><li>Niepa, T. H. R., Hou, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+Nanoculture+as+an+Artificial+Microniche.">Microbial Nanoculture as an Artificial Microniche.</a> Sci Rep. 6, 30578 (2016).</li><li>Hansen, R. H., Timm, A. 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D., Singh, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Type+VI+Secretion+System+of+Pseudomonas+aeruginosa+Targets+a+Toxin+to+Bacteria.">A Type VI Secretion System of Pseudomonas aeruginosa Targets a Toxin to Bacteria.</a> Cell Host Microbe. 7 (1), 25-37 (2010).</li><li>LeRoux, M., Ja De Leon, ., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+single-cell+characterization+of+bacterial+interactions+reveals+type+VI+secretion+is+a+double-edged+sword.">Quantitative single-cell characterization of bacterial interactions reveals type VI secretion is a double-edged sword.</a> Proc Natl Acad Sci. 109 (48), 19804-19809 (2012).</li><li>Whitney, J. C., Beck, C. 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This article presented a microwell array device and experimental protocols designed to enable high-throughput and high-content live-cell imaging-based analysis of bacterial community development. While the focus of the demonstration here was to study the effects of contact-mediated Type VI secretion on community development, the arrays were designed to be flexible and accommodate the study of a broad range of microbial communities and microbe-microbe interactions. The work here focuses solely on the use of bacteria that ...

Microbial communities are shaped by both deterministic factors, such as the structure of the environment, and stochastic processes, which are associated with cell death, division, protein concentration, number of organelles, and mutation1. Within the natural environment, it can be nearly impossible to parse the individual impact of these influences on community composition and activity. Obscured by natural structures and buried within a chemical and biological milieu, identifying community members and further resolving their spatiotemporal distribution within the natural environment is extremely challenging. Nonetheless, recent efforts have underscored the importance of spatial organization on community function and point towards the need to account for both member abundance and organization in ongoing studies2,3,4.
It is clear that the local chemical environment (i.e.&#160;the availability of nutrients and secondary metabolites), the physical structure (e.g., soil architecture, plant roots, ocean particles, or the intestinal microvilli), the presence or absence of oxygen, and the introduction of pathogenic species all affect the composition, architecture, and function of microbial communities5,6,7,8,9,10,11. Nonetheless, traditional techniques for cultures that neglect to capture these factors continue to prevail. Community composition (e.g., the presence of co-dependent species), physical attachment, signaling molecule concentration, and direct cell-cell contact are all important factors for shaping a microbial community and can be lost in conventional culture conditions. These properties are difficult to replicate in a bulk liquid culture or on an agar plate. The availability of microfluidic, micropatterning, and nanofabrication techniques that allow for the replication of key physical and chemical features of natural environments has, however, enabled many researchers to build bacterial communities to study their interactions12,13,14 and to develop synthetic environments that mimic natural conditions4,15,16,17,18,19,20.
This protocol describes a method to fabricate a microwell array device and provides detailed experimental procedures that can be used to functionalize the wells in the array and to grow bacteria, both as single-species colonies and in multi-member communities. This work also demonstrates how bacteria modified to produce fluorescent reporter proteins can be used to monitor bacterial growth within wells over time. A similar array was presented previously and showed that it is possible to track the growth of single-species colonies of Pseudomonas aeruginosa (P. aeruginosa)&#160;in microwells. By modulating well size and seeding density, the starting conditions of thousands of growth experiments can be varied in parallel to determine how the initial inoculation conditions affect the ability of the bacteria to grow21. The current work uses a slightly modified version of the microwell array that builds on the previous work by enabling the simultaneous comparison of multiple arrays and by using a more robust experimental protocol. The array used in this work contains multiple subarrays, or array ensembles, containing wells of different sizes, ranging from 15 - 100 &#181;m in diameter, that are arranged at three different pitches (i.e.&#160;2x, 3x, and 4x the well diameter). The arrays are etched into silicon, and the growth of the bacteria seeded in the silicon arrays is enabled by sealing the arrays with a coverslip that has been coated with a medium-infused agarose gel. P. aeruginosa mutants designed to study the Type VI secretion system are used in this demonstration.
The results presented here build toward the ultimate goal of analyzing multimember communities within microwell arrays, enabling researchers to monitor the abundance and organization of bacteria in situ while controlling and probing the chemical environment. This should ultimately provide insights into the &#34;rules&#34; that govern community development and succession.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Parylene N</td>
			<td>Specialty Coating Systems</td>
			<td>CAS NO.:1633-22-3</td>
		</tr>
		<tr>
			<td>Parylene coater</td>
			<td>Specialty Coating Systems</td>
			<td>Labcoter 2 Parylene Deposition Unit PDS2010</td>
		</tr>
		<tr>
			<td>Silicon Wafer</td>
			<td>WRS Materials</td>
			<td>100mm diameter, 500-550&#956;m thickness, Prime, 10-20 resistivity, N/Phos&#60;100&#62;,</td>
		</tr>
		<tr>
			<td>adhesion promoter</td>
			<td>Shin-Etsu Microsci</td>
			<td>MicroPrime P20 adhesion promoter</td>
		</tr>
		<tr>
			<td>postive tone photoresist</td>
			<td>Rohm and Haas Electronics Materials LLC (Owned by Dow)</td>
			<td>Microposit S1818 Positive Photoresist (code 10018357)</td>
		</tr>
		<tr>
			<td>Quintel Contact Aligner</td>
			<td>Neutronix Quintel Corp</td>
			<td>NXQ 7500 Mask Aligner</td>
		</tr>
		<tr>
			<td>Reactive Ion Etching Tool</td>
			<td>Oxford Instruments</td>
			<td>Plasmalab System 100 Reactive Ion Etcher</td>
		</tr>
		<tr>
			<td>R2A Broth</td>
			<td>TEKnova</td>
			<td>R0005</td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin</td>
			<td>Sigma</td>
			<td>A9647</td>
		</tr>
		<tr>
			<td>Multimode Plate Reader</td>
			<td>Perkin Elmer</td>
			<td>Enspire, 2300-0000</td>
		</tr>
		<tr>
			<td>Fluorescent Microscope</td>
			<td>Nikon</td>
			<td>Eclipse Ti-U</td>
		</tr>
		<tr>
			<td>Automated Stage</td>
			<td>Prior</td>
			<td>ProScan III</td>
		</tr>
		<tr>
			<td>CCD camera</td>
			<td>Nikon</td>
			<td>DS-QiMc</td>
		</tr>
		<tr>
			<td>Stage-top environmental control chamber</td>
			<td>In Vivo Scientific</td>
			<td>STEV ECU-HOC</td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline</td>
			<td>ThermoFisher Scientific</td>
			<td>14190144</td>
		</tr>
		<tr>
			<td>UltraPure Agarose</td>
			<td>ThermoFisher Scientific</td>
			<td>16500500</td>
		</tr>
		<tr>
			<td>25 x 75 mm No. 1.5 coverslip</td>
			<td>Nexterion</td>
			<td>High performance #1.5H coverslips</td>
		</tr>
		<tr>
			<td>Fluorescence Reference Slides</td>
			<td>Ted Pella</td>
			<td>2273</td>
		</tr>
		<tr>
			<td>Physical Stylus Profilometer</td>
			<td>KLA Tencor</td>
			<td>P-6</td>
		</tr>
		<tr>
			<td>lab wipes</td>
			<td>Kimberly Clark</td>
			<td>Kimipe KIMTECH SCIENCE Brand, 34155</td>
		</tr>
		<tr>
			<td>commercial software</td>
			<td>Nikon</td>
			<td>NIS Elements</td>
		</tr>
		<tr>
			<td>Zeiss 710 Confocal Microscope</td>
			<td>Zeiss</td>
			<td></td>
		</tr>
		<tr>
			<td>filter cubes</td>
			<td>Nikon</td>
			<td>Nikon FITC (96311), Nikon Texas Red(96313)</td>
		</tr>
	</tbody>
</table>

assembly and tracking of microbial community development within a microwell array platform

The development of microbial communities depends on a combination of complex deterministic and stochastic factors that can dramatically alter the spatial distribution and activities of community members. We have developed a microwell array platform that can be used to rapidly assemble and track thousands of bacterial communities in parallel. This protocol highlights the utility of the platform and describes its use for optically monitoring the development of simple, two-member communities within an ensemble of arrays within the platform. This demonstration uses two mutants of Pseudomonas aeruginosa, part of a series of mutants developed to study Type VI secretion pathogenicity. Chromosomal inserts of either mCherry or GFP genes facilitate the constitutive expression of fluorescent proteins with distinct emission wavelengths that can be used to monitor community member abundance and location within each microwell. This protocol describes a detailed method for assembling mixtures of bacteria into the wells of the array and using time-lapse fluorescence imaging and quantitative image analysis to measure the relative growth of each member population over time. The seeding and assembly of the microwell platform, the imaging procedures necessary for the quantitative analysis of microbial communities within the array, and the methods that can be used to reveal interactions between microbial species area all discussed.

The experimental platform presented here is designed for high-throughput and high-content studies of bacterial communities. The design enables thousands of communities, growing in wells of various sizes, to be analyzed simultaneously. With this microwell array design, the dependence of the final community composition on initial seeding densities, well size, and chemical environment can be determined. This work demonstrates the growth of a two-member community in the microwell array and pu...

Watch this Scientific Journal Video about Assembly and Tracking of Microbial Community Development within a Microwell Array Platform at JoVE.com

Assembly and Tracking of Microbial Community Development within a Microwell Array Platform

The development of microbial communities depends on a combination of factors, including environmental architecture, member abundance, traits, and interactions. This protocol describes a synthetic, microfabricated environment for the simultaneous tracking of thousands of communities contained in femtoliter wells, where key factors such as niche size and confinement can be approximated.

The development of microbial communities depends on a combination of complex deterministic and stochastic factors that can dramatically alter the spatial ...

The overall goal of this method is high throughput parallel analysis of multi-member microbial communities in confined environments using silicon micro well arrays. The main advantage of this technique is that it allows for a high throughput highly parallel screening of finely localized microbial interactions that are significant to industry, medicine, and the environment. This method can help answer key questions in the biomedical and microbial ecology fields such as how do spacial constraints inherent at fine scales drive deterministic and stochastic parameters of community development and what are they key effects on microbial member abundance and organization?Begin with preparing the micro well arrays. First, cut individual micro well array chips from silicon wafers printed with multiple arrays using a diamond scribe. Each individual chip contains sub-arrays of wells with diameters ranging from five to 100 microns at three different spacing densities.On each chip, the complete motif of wells is also repeated four times. Next, make a humidified chamber using a pipette tip box and a PBS soaked wipe. Then apply a 150 microliter droplet of BSA solution to each chip and incubate the chips in the box for an hour at room temperature.Meanwhile prepare the bacteria. Spin down a culture and re-suspend it in 500 microliters of fresh R2A medium with two percent glycerol. Then measure the culture density at 600 nanometers and adjust the concentration to an optical density of 0.02.After the chip incubation, remove the BSA solution and rinse the chips three times with PBS. After the rinses, dry the chips with nitrogen gas and return them to the humidified chamber. Next, add 150 microliters of culture suspension to each dry chip and incubate the chips for an hour at four degrees Celsius so that the bacteria will have time to adhere to the wells, but the cell division of any possible contaminate is slow.To prepare a chip for imaging, first make an agarose-coated cover slip for each chip. Liquefy a small volume of agarose, about five milliliters is needed for each cover slip. Next, wash one side of a cover slip with ethanol and center it onto a glass slide with the washed side up.Then position two one millimeter thick PDMS spacers along the long edges of the cover slip and shift the cover slip so one millimeter hangs off the slide. Now, pour enough agarose onto the cover slip to completely cover it. Then use a second glass slide to flatten the agarose into a uniform thickness.Prepare several such slide assemblies in parallel. When the agarose begins to solidify, transfer the assemblies to four degrees Celsius. After 15 minutes of cooling, trim off the excess agarose around the cover slips.Then, put the assemblies in petri dishes and store them at four degrees Celsius. After the chips have incubated with the bacteria, dip the chips in ultra pure water one at a time for 10 seconds each. Then set the wet chips on their edges over a tissue until most of the liquid has drained off.Now, remove the bacteria that did not settle into the wells. Cut a piece of tape the length of the silicon chip and adhere it to the parylene coat on the silicon. Then peel off the tape to remove the parylene coat and immediately prepare to invert the chip.Now, place the chip onto a slide assembly such that the micro wells are in contact with the agarose. Be very careful not to move or shift the chip once in contact with the agarose. Now, transfer the complete assembly into the slide holder of a stagetop environmental control chamber and acquire time-lapse images over the next 24 hours at the desired interval and under 10x magnification.Process the image stacks using conventional, freely available software. First, import the image sequence. For averaging, load the correction or the dark field images.Then perform a background subtraction. Provide a radius value such as 135 pixels and select sliding paraboloid. Next, remove the average dark field image from the average illumination field image by selecting the two images and using the subtract operation.Now, apply an illumination correction as follows. Set the operation to divide, set i1 to the well image, set i2 to the correction image, set k1 to the correction image mean, and set k2 to zero. Then click Create New Window.To quantify the bacterial growth in the micro wells, first select the regions of interest with the micro array plug in. In the map menu, click reset grid and specify the rows, columns and well diameters. Then from the ROI shape menu, select circle.To adjust the ROI array to the image, the ROI array can be moved by pressing the ALT or ALT+SHIFT key and selecting the top left ROI with the mouse. To resize the ROIs, press the shift key while selecting the bottom right of the ROI array. To adjust the spacing between the ROIs, press the shift key while dragging the top or bottom side of the array.Once the ROI array fits over the wells of the image, click Measure RT.Then a table with all the measurements for each image or time point will be outputted and it can be copied into a spreadsheet for analysis. The growth of two strains of Pseudomonas aeruginosa was compared. One strain constitutively expresses toxic effector proteins associated with type six secretions.The other is susceptible to type six pathogenesis due to loss of function. Both express a different fluorescent protein. Co-cultures were studied longitudinally and in different well sizes.The bacteria were cultured individually and as a co-culture. 20 hours of growth was imaged in 30 minute intervals. After software corrections were performed on the imaging data, quantitative growth trajectories were plotted.In the co-culture, the data does not suggest too much of a change in growth. To advance the analysis, each trajectory was fitted to a modified logistic function with three parameters, maximum signal, maximum rate, and lag time. This analysis suggest that the co-culture of these species had a negligible effect on their overall growth and their variability seen in the growth curves is most likely due to environmental factors.Once mastered, the set up can be executed in just a few hours if it is performed properly. While attempting this procedure, it is important to have robustly growing cells to properly adjust the final cell OD values to have uniform auger layers in the chip assemblies and to be mindful during the parylene peel off step. Following this procedure, questions like how does gene expression within each community change as a function of community composition and organization, can be addressed by genetic material analysis.Don't forget that working with Pseudomonas aeruginosa can be potentially hazardous, and precautions such as gloves, jacket, goggles, and proper aseptic techniques should always be used while performing this procedure.

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SCIENTISTS IN ACTION

Tracking Hypoxic Signaling within Encapsulated Cell Aggregates

In Diabetes mellitus type 1, autoimmune destruction of the pancreatic &beta;-cells results in loss of insulin production and potentially lethal hyperglycemia. As an alternative treatment option to exogenous insulin injection, transplantation of functional pancreatic tissue has been explored1,2. This approach offers the promise of a more natural, long-term restoration of normoglycemia. Protection of the donor tissue from the host's immune system is required to prevent rejection and encapsulation is a method used to help achieve this aim.
Biologically-derived materials, such as alginate3 and agarose4, have been the traditional choice for capsule construction but may induce inflammation or fibrotic overgrowth5 which can impede nutrient and oxygen transport. Alternatively, synthetic poly(ethylene glycol) (PEG)-based hydrogels are non-degrading, easily functionalized, available at high purity, have controllable pore size, and are extremely biocompatible,6,7,8. As an additional benefit, PEG hydrogels may be formed rapidly in a simple photo-crosslinking reaction that does not require application of non-physiological temperatures6,7. Such a procedure is described here. In the crosslinking reaction, UV degradation of the photoinitiator, 1-[4-(2-Hydroxyethoxy)-phenyl]-2-hydroxy-2-methyl-1-propane-1-one (Irgacure 2959), produces free radicals which attack the vinyl carbon-carbon double bonds of dimethacrylated PEG (PEGDM) inducing crosslinking at the chain ends. Crosslinking can be achieved within 10 minutes. PEG hydrogels constructed in such a manner have been shown to favorably support cells7,9, and the low photoinitiator concentration and brief exposure to UV irradiation is not detrimental to viability and function of the encapsulated tissue10. While we methacrylate our PEG with the method described below, PEGDM can also be directly purchased from vendors such as Sigma.
An inherent consequence of encapsulation is isolation of the cells from a vascular network. Supply of nutrients, notably oxygen, is therefore reduced and limited by diffusion. This reduced oxygen availability may especially impact &beta;-cells whose insulin secretory function is highly dependent on oxygen11-13. Capsule composition and geometry will also impact diffusion rates and lengths for oxygen. Therefore, we also describe a technique for identifying hypoxic cells within our PEG capsules. Infection of the cells with a recombinant adenovirus allows for a fluorescent signal to be produced when intracellular hypoxia-inducible factor (HIF) pathways are activated14. As HIFs are the primary regulators of the transcriptional response to hypoxia, they represent an ideal target marker for detection of hypoxic signaling15. This approach allows for easy and rapid detection of hypoxic cells. Briefly, the adenovirus has the sequence for a red fluorescent protein (Ds Red DR from Clontech) under the control of a hypoxia-responsive element (HRE) trimer. Stabilization of HIF-1 by low oxygen conditions will drive transcription of the fluorescent protein (Figure 1). Additional details on the construction of this virus have been published previously15. The virus is stored in 10% glycerol at -80&deg; C as many 150 &mu;L aliquots in 1.5 mL centrifuge tubes at a concentration of 3.4 x 1010 pfu/mL. 
Previous studies in our lab have shown that MIN6 cells encapsulated as aggregates maintain their viability throughout 4 weeks of culture in 20% oxygen. MIN6 aggregates cultured at 2 or 1% oxygen showed both signs of necrotic cells (still about 85-90% viable) by staining with ethidium bromide as well as morphological changes relative to cells in 20% oxygen. The smooth spherical shape of the aggregates displayed at 20% was lost and aggregates appeared more like disorganized groups of cells. While the low oxygen stress does not cause a pronounced drop in viability, it is clearly impacting MIN6 aggregation and function as measured by glucose-stimulated insulin secretion15. Western blot analysis of encapsulated cells in 20% and 1% oxygen also showed a significant increase in HIF-1&alpha; for cells cultured in the low oxygen conditions which correlates with the expression of the DsRed DR protein.

A method for photo-encapsulation of cells in a crosslinked PEG hydrogel is described. Hypoxic signaling within encapsulated murine insulinoma (MIN6) aggregates is tracked using a fluorescent marker system. This system allows serial examination of cells within a hydrogel scaffold and correlation of hypoxic signaling with changes in cell phenotype.

In Diabetes mellitus type 1, autoimmune destruction of the pancreatic &beta;-cells results in loss of insulin production and potentially lethal ...

Environmentally-controlled Microtensile Testing of Mechanically-adaptive Polymer Nanocomposites for ex vivo Characterization

Implantable microdevices are gaining significant attention for several biomedical applications1-4. Such devices have been made from a range of materials, each offering its own advantages and shortcomings5,6. Most prominently, due to the microscale device dimensions, a high modulus is required to facilitate implantation into living tissue. Conversely, the stiffness of the device should match the surrounding tissue to minimize induced local strain7-9. Therefore, we recently developed a new class of bio-inspired materials to meet these requirements by responding to environmental stimuli with a change in mechanical properties10-14. Specifically, our poly(vinyl acetate)-based nanocomposite (PVAc-NC) displays a reduction in stiffness when exposed to water and elevated temperatures (e.g. body temperature). Unfortunately, few methods exist to quantify the stiffness of materials in vivo15, and mechanical testing outside of the physiological environment often requires large samples inappropriate for implantation. Further, stimuli-responsive materials may quickly recover their initial stiffness after explantation. Therefore, we have developed a method by which the mechanical properties of implanted microsamples can be measured ex vivo, with simulated physiological conditions maintained using moisture and temperature control13,16,17. 
To this end, a custom microtensile tester was designed to accommodate microscale samples13,17 with widely-varying Young's moduli (range of 10 MPa to 5 GPa). As our interests are in the application of PVAc-NC as a biologically-adaptable neural probe substrate, a tool capable of mechanical characterization of samples at the microscale was necessary. This tool was adapted to provide humidity and temperature control, which minimized sample drying and cooling17. As a result, the mechanical characteristics of the explanted sample closely reflect those of the sample just prior to explantation.
The overall goal of this method is to quantitatively assess the in vivo mechanical properties, specifically the Young's modulus, of stimuli-responsive, mechanically-adaptive polymer-based materials. This is accomplished by first establishing the environmental conditions that will minimize a change in sample mechanical properties after explantation without contributing to a reduction in stiffness independent of that resulting from implantation. Samples are then prepared for implantation, handling, and testing (Figure 1A). Each sample is implanted into the cerebral cortex of rats, which is represented here as an explanted rat brain, for a specified duration (Figure 1B). At this point, the sample is explanted and immediately loaded into the microtensile tester, and then subjected to tensile testing (Figure 1C). Subsequent data analysis provides insight into the mechanical behavior of these innovative materials in the environment of the cerebral cortex.

Environmentally-controlled Microtensile Testing of Mechanically-adaptive Polymer Nanocomposites for ex vivo Characterization

A method is discussed by which the in vivo mechanical behavior of stimuli-responsive materials is monitored as a function of time. Samples are tested ex vivo using a microtensile tester with environmental controls to simulate the physiological environment. This work further promotes understanding the in vivo behavior of our material.

Implantable microdevices are gaining significant attention for several biomedical applications1-4. Such devices have been made from a range of materials, ...

Polymeric Microneedle Array Fabrication by Photolithography

This manuscript describes the fabrication of polymeric microneedle (MN) arrays by photolithography. It involves a simple mold-free process by using a photomask consisting of embedded micro-lenses. Embedded micro-lenses were found to influence MN geometry (sharpness). Robust MN arrays with tip diameters ranging between 41.5 &#181;m &#177; 8.4 &#181;m and 71.6 &#181;m &#177; 13.7 &#181;m, with two different lengths (1,336 &#181;m &#177; 193 &#181;m and 957 &#181;m &#177; 171 &#181;m) were fabricated. These MN arrays may provide potential applications in delivery of low molecular and macromolecular therapeutic agents through skin.

Here, we present a protocol describing a mold-free fabrication process of the polymeric microneedles by photolithography.

This manuscript describes the fabrication of polymeric microneedle (MN) arrays by photolithography. It involves a simple mold-free process by using a ...

Development of an In Vitro Ocular Platform to Test Contact Lenses

Currently, in vitro evaluations of contact lenses (CLs) for drug delivery are typically performed in large volume vials,1-6 which fail to mimic physiological tear volumes.7 The traditional model also lacks the natural tear flow component and the blinking reflex, both of which are defining factors of the ocular environment. The development of a novel model is described in this study, which consists of a unique 2-piece design, eyeball and eyelid piece, capable of mimicking physiological tear volume. The models are created from 3-D printed molds (Polytetrafluoroethylene or Teflon molds), which can be used to generate eye models from various polymers, such as polydimethylsiloxane (PDMS) and agar. Further modifications to the eye pieces, such as the integration of an explanted human or animal cornea or human corneal construct, will permit for more complex in vitro ocular studies. A commercial microfluidic syringe pump is integrated with the platform to emulate physiological tear secretion. Air exposure and mechanical wear are achieved using two mechanical actuators, of which one moves the eyelid piece laterally, and the other moves the eyeballeyepiece circularly. The model has been used to evaluate CLs for drug delivery and deposition of tear components on CLs.

Development of an In Vitro Ocular Platform to Test Contact Lenses

Current in vitro models for evaluating contact lenses (CLs) and other eye-related applications are severely limited. The presented ocular platform simulates physiological tear flow, tear volume, air exposure and mechanical wear. This system is highly versatile and can be applied to various in vitro analyses with CLs.

Currently, in vitro evaluations of contact lenses (CLs) for drug delivery are typically performed in large volume vials,1-6 which fail to mimic ...

Micropatterning and Assembly of 3D Microvessels

In vitro platforms to study endothelial cells and vascular biology are largely limited to 2D endothelial cell culture, flow chambers with polymer or glass based substrates, and hydrogel-based tube formation assays. These assays, while informative, do not recapitulate lumen geometry, proper extracellular matrix, and multi-cellular proximity, which play key roles in modulating vascular function. This manuscript describes an injection molding method to generate engineered vessels with diameters on the order of 100 &#181;m. Microvessels are fabricated by seeding endothelial cells in a microfluidic channel embedded within a native type I collagen hydrogel. By incorporating parenchymal cells within the collagen matrix prior to channel formation, specific tissue microenvironments can be modeled and studied. Additional modulations of hydrodynamic properties and media composition allow for control of complex vascular function within the desired microenvironment. This platform allows for the study of perivascular cell recruitment, blood-endothelium interactions, flow response, and tissue-microvascular interactions. Engineered microvessels offer the ability to isolate the influence from individual components of a vascular niche and precisely control its chemical, mechanical, and biological properties to study vascular biology in both health and disease.

This manuscript presents an injection molding method to engineer microvessels that recapitulate physiological properties of endothelium. The microfluidic-based process creates patent 3D vascular networks with tailorable conditions, such as flow, cellular composition, geometry, and biochemical gradients. The fabrication process and examples of potential applications are described.

In vitro platforms to study endothelial cells and vascular biology are largely limited to 2D endothelial cell culture, flow chambers with polymer or glass ...

Microfluidic Platform with Multiplexed Electronic Detection for Spatial Tracking of Particles

Microfluidic processing of biological samples typically involves differential manipulations of suspended particles under various force fields in order to spatially fractionate the sample based on a biological property of interest. For the resultant spatial distribution to be used as the assay readout, microfluidic devices are often subjected to microscopic analysis requiring complex instrumentation with higher cost and reduced portability. To address this limitation, we have developed an integrated electronic sensing technology for multiplexed detection of particles at different locations on a microfluidic chip. Our technology, called Microfluidic CODES, combines Resistive Pulse Sensing with Code Division Multiple Access to compress 2D spatial information into a 1D electrical signal. In this paper, we present a practical demonstration of the Microfluidic CODES technology to detect and size cultured cancer cells distributed over multiple microfluidic channels. As validated by the high-speed microscopy, our technology can accurately analyze dense cell populations all electronically without the need for an external instrument. As such, the Microfluidic CODES can potentially enable low-cost integrated lab-on-a-chip devices that are well suited for the point-of-care testing of biological samples.

We demonstrate a microfluidic platform with an integrated surface electrode network that combines resistive pulse sensing (RPS) with code division multiple access (CDMA), to multiplex detection and sizing of particles in multiple microfluidic channels.

Microfluidic processing of biological samples typically involves differential manipulations of suspended particles under various force fields in order to ...

Fabrication of a Multiplexed Artificial Cellular MicroEnvironment Array

Cellular microenvironments consist of a variety of cues, such as growth factors, extracellular matrices, and intercellular interactions. These cues are well orchestrated and are crucial in regulating cell functions in a living system. Although a number of researchers have attempted to investigate the correlation between environmental factors and desired cellular functions, much remains unknown. This is largely due to the lack of a proper methodology to mimic such environmental cues in vitro, and simultaneously test different environmental cues on cells. Here, we report an integrated platform of microfluidic channels and a nanofiber array, followed by high-content single-cell analysis, to examine stem cell phenotypes altered by distinct environmental factors. To demonstrate the application of this platform, this study focuses on the phenotypes of self-renewing human pluripotent stem cells (hPSCs). Here, we present the preparation procedures for a nanofiber array and the microfluidic structure in the fabrication of a Multiplexed Artificial Cellular MicroEnvironment (MACME) array. Moreover, overall steps of the single-cell profiling, cell staining with multiple fluorescent markers, multiple fluorescence imaging, and statistical analyses, are described.

This article describes the detailed methodology to prepare a Multiplexed Artificial Cellular MicroEnvironment (MACME) array for high-throughput manipulation of physical and chemical cues mimicking in vivo cellular microenvironments and to identify the optimal cellular environment for human pluripotent stem cells (hPSCs) with single-cell profiling.

Cellular microenvironments consist of a variety of cues, such as growth factors, extracellular matrices, and intercellular interactions. These cues are ...

Rodent Behavioral Testing to Assess Functional Deficits Caused by Microelectrode Implantation in the Rat Motor Cortex

Medical devices implanted in the brain hold tremendous potential. As part of a Brain Machine Interface (BMI) system, intracortical microelectrodes demonstrate the ability to record action potentials from individual or small groups of neurons. Such recorded signals have successfully been used to allow patients to interface with or control&#160;computers, robotic limbs, and their own limbs. However, previous animal studies have shown that a microelectrode implantation in the brain not only damages the surrounding tissue but can also result in functional deficits. Here, we discuss a series of behavioral tests to quantify potential motor impairments following the implantation of intracortical microelectrodes into the motor cortex of a rat. The methods for open field grid, ladder crossing, and grip strength testing provide valuable information regarding the potential complications resulting from a microelectrode implantation. The results of the behavioral testing are correlated with endpoint histology, providing additional information on the pathological outcomes and impacts of this procedure on the adjacent tissue.

We have shown that a microelectrode implantation in the motor cortex of rats causes immediate and lasting motor deficits. The methods proposed herein outline a microelectrode implantation surgery and three rodent behavioral tasks to elucidate potential changes in the fine or gross motor function due to implantation-caused damage to the motor cortex.

Medical devices implanted in the brain hold tremendous potential. As part of a Brain Machine Interface (BMI) system, intracortical microelectrodes ...

Prospecting Microbial Strains for Bioremediation and Probiotics Development for Metaorganism Research and Preservation

Pollution affects all biomes. Marine environments have been particularly impacted, especially coral reefs, one of the most sensitive ecosystems on Earth. Globally, 4.5 billion people are economically dependent on the sea, where most of their livelihood is provided by coral reefs. Corals are of great importance and therefore their extinction leads to catastrophic consequences. There are several possible solutions to remediate marine pollutants and local contamination, including bioremediation. Bioremediation is the capacity of organisms to degrade contaminants. The approach presents several advantages, such as sustainability, relatively low cost, and the fact that it can be applied in different ecosystems, causing minimal impacts to the environment. As an extra advantage, the manipulation of endogenous microbiomes, including putative beneficial microorganisms for corals (pBMCs), may have probiotic effects for marine animals. In this context, the use of the two approaches, bioremediation and pBMC inoculation combined, could be promising. This strategy would promote the degradation of specific pollutants that can be harmful to corals and other metaorganisms while also increasing host resistance and resilience to deal with pollution and other threats. This method focuses on the selection of pBMCs to degrade two contaminants: the synthetic estrogen 17a-ethinylestradiol (EE2) and crude oil. Both have been reported to negatively impact marine animals, including corals, and humans. The protocol describes how to isolate and test bacteria capable of degrading the specific contaminants, followed by a description of how to detect some putative beneficial characteristics of these associated microbes to their coral host. The methodologies described here are relatively cheap, easy to perform, and highly adaptable. Almost any kind of soluble target compound can be used instead of EE2 and oil.

Pollution affects all biomes. Marine environments have been particularly impacted, especially coral reefs, one of the most sensitive ecosystems on Earth. Bioremediation is the capacity of organisms to degrade contaminants. Here, we describe methodologies to isolate and test microbes presenting bioremediation ability and potential probiotic characteristics for corals.

Pollution affects all biomes. Marine environments have been particularly impacted, especially coral reefs, one of the most sensitive ecosystems on Earth. ...

Formulating and Characterizing Lipid Nanoparticles for Gene Delivery using a Microfluidic Mixing Platform

Lipid-based drug carriers have been used for clinically and commercially available delivery systems due to their small size, biocompatibility, and high encapsulation efficiency. Use of lipid nanoparticles (LNPs) to encapsulate nucleic acids is advantageous to protect the RNA or DNA from degradation, while also promoting cellular uptake. LNPs often contain multiple lipid components including an ionizable lipid, helper lipid, cholesterol, and polyethylene glycol (PEG) conjugated lipid. LNPs can readily encapsulate nucleic acids due to the ionizable lipid presence, which at low pH is cationic and allows for complexation with negatively charged RNA or DNA. Here LNPs are formed by encapsulating messenger RNA (mRNA) or plasmid DNA (pDNA) using rapid mixing of the lipid components in an organic phase and the nucleic acid component in an aqueous phase. This mixing is performed using a precise microfluidic mixing platform, allowing for nanoparticle self-assembly while maintaining laminar flow. The hydrodynamic size and polydispersity are measured using dynamic light scattering (DLS). The effective surface charge on the LNP is determined by measuring the zeta potential. The encapsulation efficiency is characterized using a fluorescent dye to quantify entrapped nucleic acid. Representative results demonstrate the reproducibility of this method and the influence that different formulation and process parameters have on the developed LNPs.

Lipid nanoparticles are developed using a microfluidic mixing platform approach for mRNA and DNA encapsulation.

Lipid-based drug carriers have been used for clinically and commercially available delivery systems due to their small size, biocompatibility, and high ...