The authors would like to acknowledge Aspen Walker at the University of Pennsylvania for her assistance in reactor maintenance and sample collection.

1. Reactor Assembly
<ol>
	<li>Arrange the reactor components according to the schematic in Figure 1.
	<ol>
		<li>Place the reactor (R) on a mixing plate, add a stir bar to the reactor. Place the recycle tank (RT) beside the stir plate and reactor so that the effluent (top) port of the tank is directed towards the edge of the lab bench.</li>
		<li>Place the waste container (W) underneath the effluent (top) port of the recycle tank (RT). Place the feed tank (FT) next to the recycle tank (RT). 
		Note: The feed tank has a total capacity of 5 L.</li>
	</ol>
	</li>
	<li>Secure the reactor (R) against tipping with an appropriately sized stand and clamp. Likewise, secure the recycle tank (RT) to prevent movement.</li>
	<li>Insert neoprene peristaltic pump tubing in the recycle (Pump A) and feed (Pump B) pump heads. Refer to the Materials table for additional tubing specifications. Install the pump heads onto the pump drives with the screws provided with the pump drives.</li>
	<li>Connect Pump A&#39;s tubing to the ports on the reactor and the recycle tank. Insert the end of Pump B&#39;s tubing into the feed tank and the recycle tank. Connect the top reactor port to the recycle tank with tubing. Apply clamps to the tubing at the reactor ports. 
	Note: Photosynthetic communities may benefit from artificial illumination provided by lamps.</li>
</ol>
2. Preparation of Stock Solutions, Influent/Feed Solutions, and Algae Inoculant
<ol>
	<li>Prepare the mineral stock solution. Add the following to a 1 L volumetric flask with 500 ml of deionized water: 200 g sodium bicarbonate, 40 g monobasic potassium phosphate, 4 g magnesium sulfate, 4 g ferric chloride, 4 g calcium chloride, 1 g copper chloride, 1 g cobalt chloride hexahydrate, 1 g nickel chloride hexahydrate, 1 g zinc sulfate heptahydrate. Add an additional 400 ml of deionized water. Swirl forcefully to encourage dissolution of salts. Following dissolution of salts, add deionized water to bring the total volume of solution to 1 L.</li>
	<li>Prepare the ammonia stock solution. In a 1 L volumetric flask, dissolve 38.214 grams of ammonium chloride in approximately 900 ml of deionized water. After dissolution, add deionized water to bring the total volume up to 1,000 ml. 
	Note: 1 ml of stock solution diluted to 1 L yields a 10 mg L-1 NH4+-N solution.</li>
	<li>Prepare the nitrate stock solution. In a 1 L volumetric flask, dissolve 72.413 g of potassium nitrate in approximately 900 ml of deionized water. After dissolution, add deionized water to bring the total volume up to 1,000 ml. 
	Note: 1 ml of stock solution diluted to 1 L yields a 10 mg L-1 NO3--N solution.</li>
	<li>Prepare feed/influent solution. To make a feed solution containing 20 mg L-1 NH4+-N and 20 mg L-1 NO3--N, dilute 2 ml of ammonia stock solution and 2 ml of nitrate stock solution to 1 L total volume. Prior to dilution, add 0.5 ml mineral solution/L of solution being made. Prepare 5 L of influent in total to start up the reactor.</li>
	<li>Prepare the algae inoculant.
	<ol>
		<li>Collect a large volume (at least 10 L) of water from an algae-containing water body such as a stream or pond. Allow the algae to settle by leaving the water samples undisturbed for 24 hr.</li>
		<li>Decant and discard the clear (non-algae containing) water at the top of the samples, leaving a concentrated algae suspension within the sample bottles. Combine the algae suspension from all of the samples into one container and repeat the settling and decanting steps.</li>
		<li>Measure the biomass within the concentrated sample.
		<ol>
			<li>Dry a paper vacuum filter (0.45 &#181;m MCE vacuum filter) and aluminum weigh boat O/N in an oven which has been set to 103 &#176;C After cool-down in a desiccator for 30 min at RT measure the combined mass of the filter and weigh boat.</li>
			<li>Vacuum filter 20 ml of concentrated algae suspension and return the filter and weigh boat to oven to dry O/N.</li>
			<li>Measure the combined mass of the filter and weigh boat. Calculate the biomass density within the concentrated sample. 
			Note: The total volume of water sample that investigators will need to collect will depend upon the source water body.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
3. Seeding and Starting the Reactor
<ol>
	<li>Add 750 ml of feed solution to the reactor. Fill the recycle tank with 500 ml of feed solution.</li>
	<li>Use a long pipette to gently add an inoculate suspension containing 1.5 g of algae near the bottom of the reactor. Allow the inoculum to settle to the bottom of the reactor, ensure this by visual observation, before proceeding to the next step.</li>
	<li>Once the cells have settled, remove the tube clamps and turn on Pump A to a slow flow rate (10 revolutions min-1/38 ml min-1). Air trapped in the tubing will be expelled into the reactor. 
	Note: The addition of 750 ml to the reactor will prevent any biomass disturbed by the pump from leaving the reactor. Squeeze the tubing to ensure that all air has been expelled.</li>
	<li>Gradually add feed solution to the recycle tank as the solution is pumped into the reactor. Continue the addition until both the reactor and the recycle tank are at capacity and effluent starts to exit the recycle tank via the top port. 
	Note: The volume of feed solution to be added to the recycle tank will vary with the volume of the inoculant added to the reactor.</li>
	<li>Pour the remaining feed solution into the feed tank.</li>
	<li>Set the recycle pump (Pump A) to 19 revolutions min-1, establishing a recycle flow rate of 72.5 ml min-1. Observe the algae begin to loft from the bottom of the reactor. Using the gradations on the reactor, determine the algae biomass zone height. Ensure that the height is constant before proceeding to the next step.</li>
	<li>Turn on the mixing plate at very low speed; a setting of 1 or 2 is appropriate to start. The mixing bar will assist in lofting biomass further, but aggressive mixing will cause algae to leave the reactor, enter the recycle tank, and leave in the effluent. Set mixing speed at a setting needed to establish a clear algae boundary within the reactor (Figure 2A); the algal biomass zone should be approximately 10-15 cm in height.</li>
	<li>Start the feed pump after observing a clear boundary between the algal plug and the reactor fluid. Set the pump to 25 revolutions min-1, establishing a flow rate of 1.5 ml min-1. Observe the reactor fluid exit the effluent port due to gravity and displacement caused by the incoming influent stream.</li>
</ol>
4. Sample Collection and Analysis
<ol>
	<li>Carry out sample collection activities prior to performing maintenance on the reactor system. Collect 20 ml of effluent and influent samples daily. Collect effluent samples from within the recycle tank. Collect influent samples directly from the feed tank.</li>
	<li>Vacuum filter samples to remove suspended solids prior to storage and analysis.</li>
	<li>Store the influent and effluent samples at -20 &#176;C until further analysis. Limit the number of freeze thaw cycles samples are subjected to. If needed, samples can be split into aliquots to maintain sample integrity.</li>
	<li>Carry out sample analysis for nitrate, nitrite, and ammonia using standard techniques17. 
	Note: The authors utilized Ion Chromatography (IC) to produce the results presented herein. Refer to the Materials table for specification.</li>
</ol>

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The authors have nothing to disclose and declare that they have no competing financial interests.

This section will start with a discussion of protocol variations needed to address possible operational issues as well as using different microbial communities. The strengths of this reactor design will be discussed, including the ability to govern control of oxygen flux and the formation of high density flocs within the reactor. Current challenges and possible avenues of investigation will also be mentioned.
Protocol nuances and variations 
The operation of HDBRs for cultivation...

Municipal wastewater is commonly treated with activated sludge processes in order to reduce the suspended solids (SS), biological oxygen demand (BOD), organic and inorganic nitrogen, and phosphorous content5,6. The activated sludge process, a means of secondary wastewater treatment, entails the oxidation of organic carbon in an aeration tank filled with a mixed liquor of incoming wastewater and recycled heterotrophic microorganism (commonly referred to as activated sludge)5-7. The mixed liquor then enters a relatively large clarifier (settling tank) where the sludge settles for easier collection, to either be disposed or recycled back to the aeration tank, while the clarified, treated wastewater can continue to tertiary treatment or disinfection before being released into receiving waters5-7. Efficient separation of the treated wastewater and solids (sludge) in the secondary clarifier is essential for the proper function of a wastewater treatment system, as any activated sludge continuing beyond the clarifiers will increase the BOD and SS in the effluent 5-8.
A number of alternative biological processes exist for secondary treatment of wastewater, which reduce or eliminate the need for large clarifying tanks, including attached-growth (biofilm) reactors, membrane bioreactors (MBRs), and granular sludge reactors. In biofilm reactors, the formation of biofilms, in which microorganisms naturally aggregate and attach as a layer on a solid surface, allows for biomass retention and accumulation without the need for a clarifying tank. Biofilm reactors can be classified into three types: packed bed reactors, fluidized bed reactors, and rotating biological contactors. Packed bed reactors, such as a trickling filters and biological towers, utilize a stationary solid growth surface5,6. Fluidized bed reactors (FBRs) depend on the attachment of microorganisms to particles, such as sand, granular activated carbon (GAC), or glass beads, which are kept in suspension by a high upward flow rate9,10. Rotating biological reactors depend on biofilms formed on media attached to a rotating shaft allowing the biofilm to be alternately exposed to air and the liquid being treated5,6. MBRs use membrane filtration units, either within the bioreactor (submerged configuration) or externally via recirculation (side-stream configuration)5,11. The membranes serve to achieve good separation of biomass and solid particles from the treated liquid11,12. Granular sludge reactors are upflow reactors in which the formation of extremely dense and well-settling granules of microorganisms occurs when they are exposed to high superficial air upflow velocities13.
As another alternative to the activated sludge process, a novel upflow reactor system, now called a high density bioreactor (HDBR), was designed and built by Sales and Shieh (2006) to study COD removal by activated sludge from synthetic waste streams in low F/M conditions that are known to cause the formation of poor settling sludge (i.e., bulking sludge)1,7,14. The HDBR system utilized modified fluidized bed reactors that typically consist of an upflow reactor and an external recycle tank. Fluidized bed reactors are typically operated with recycle stream flow rates high enough to keep the biofilm growth substratum suspended but low enough so that the biofilm-covered substrate is retained. Unlike fluidized bed reactors, the HDBR described in Sales and Shieh (2006) used relatively low recycle stream flow rates which, along with external aeration, prevented disruption of the biomass zone formed within the reactor1. Subsequent studies have demonstrated this reactor design&#39;s ability to successfully treat a range of nitrogen fluxes using nitrifying/denitrifying bacteria3,4. In all studies the formation of a stable, dense biomass zone within the HDBR eliminated the need for an external flocculation/sedimentation process1-4.
As we report here, the use of the HDBR to grow dense cultures has also been tested in a photobioreactor (PBR) configuration for the cultivation of algae. We discuss the benefits and drawbacks of this novel reactor system for algal cultivation and its potential for overcoming a large hurdle in the commercialization of algal biofuels associated with biomass harvesting (i.e., good solid-liquid separation15,16). The following protocol outlines the steps needed to assemble, startup, sample from, and maintain an HDBR with algae as the microbial community of interest. Variations in the startup and operation protocol of heterotrophic and nitrifying/denitrifying cultures will also be mentioned. Lastly, general advantages, disadvantages, and unknowns of this novel reactor design will be highlighted.

<table border="0" cellpadding="0" cellspacing="0" width="686">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Aeration stone</td>
			<td style="width:96px;">Alita</td>
			<td style="width:119px;">AS-3015C</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Aerator</td>
			<td style="width:96px;">Top Fin</td>
			<td style="width:119px;">Air-1000</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Ammonium chloride</td>
			<td style="width:96px;">Sigma Aldrich</td>
			<td style="width:119px;">A9434</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Anion analysis column</td>
			<td style="width:96px;">Shodex</td>
			<td style="width:119px;">IC SI-52 4E</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:213px;">Beaker (600 mL)</td>
			<td style="width:96px;">Corning Pyrex</td>
			<td style="width:119px;">1000-600</td>
			<td style="width:259px;">Used as mixing vessel (MV). Addition of hose barbs at the bottom and 500 mL levels. Outside diameter of hose barbs 3/8&#34;.&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Calcium chloride</td>
			<td style="width:96px;">Sigma Aldrich</td>
			<td style="width:119px;">C5670</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Cation analysis column</td>
			<td style="width:96px;">Shodex</td>
			<td style="width:119px;">IC YS-50</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Cobalt chloride hexahydrate</td>
			<td style="width:96px;">Sigma Aldrich</td>
			<td style="width:119px;">C8661</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Copper chloride</td>
			<td style="width:96px;">Sigma Aldrich</td>
			<td style="width:119px;">222011</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Ferric chloride</td>
			<td style="width:96px;">Sigma Aldrich</td>
			<td style="width:119px;">157740</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:213px;">Filter (vacuum)</td>
			<td style="width:96px;">Fisherbrand</td>
			<td style="width:119px;">09-719-2E</td>
			<td style="width:259px;">0.45 um membrane filter, MCE, 47 mm diameter</td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:213px;">Graduated cylinder (1000 mL)</td>
			<td style="width:96px;">Corning Pyrex</td>
			<td style="width:119px;">3025-1L</td>
			<td style="width:259px;">Used as reactor vessel (R). Addition of hose barbs at bottom, 500 mL, and 1 L levels. Outside diameter of hose barbs 3/8&#34;.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">HPLC/IC</td>
			<td style="width:96px;">Shimadzu</td>
			<td style="width:119px;">Prominence</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Magnesium sulfate</td>
			<td style="width:96px;">Sigma Aldrich</td>
			<td style="width:119px;">M2643</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:213px;">Masterflex L/S variable speed drive</td>
			<td style="width:96px;">Masterflex</td>
			<td style="width:119px;">07553-50</td>
			<td style="width:259px;">Drive for recycle and feed pumps (2 needed)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Nickel chloride hexahydrate</td>
			<td style="width:96px;">Sigma Aldrich</td>
			<td style="width:119px;">N6136</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Potassium nitrate</td>
			<td style="width:96px;">Sigma Aldrich</td>
			<td style="width:119px;">P8291</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:213px;">(Monobasic) Potassium phosphate</td>
			<td style="width:96px;">Sigma Aldrich</td>
			<td style="width:119px;">P5655</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Pump head</td>
			<td style="width:96px;">Masterflex</td>
			<td style="width:119px;">07018-20</td>
			<td style="width:259px;">Recycle pump head</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Pump head</td>
			<td style="width:96px;">Masterflex</td>
			<td style="width:119px;">07013-20</td>
			<td style="width:259px;">Feed pump head</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Pump tubing</td>
			<td style="width:96px;">Masterflex</td>
			<td style="width:119px;">6404-18</td>
			<td style="width:259px;">Recycle pump tubing</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Pump tubing</td>
			<td style="width:96px;">Masterflex</td>
			<td style="width:119px;">6404-13</td>
			<td style="width:259px;">Feed pump tubing</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Sodium bicarbonate</td>
			<td style="width:96px;">Sigma Aldrich</td>
			<td style="width:119px;">S5761</td>
			<td style="width:259px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:213px;">Zinc sulfate heptahydrate</td>
			<td style="width:96px;">Sigma Aldrich</td>
			<td style="width:119px;">Z0251</td>
			<td style="width:259px;"></td>
		</tr>
	</tbody>
</table>

a novel bioreactor for high density cultivation of diverse microbial communities

A novel reactor design, coined a high density bioreactor (HDBR), is presented for the cultivation and study of high density microbial communities. Past studies have evaluated the performance of the reactor for the removal of COD1 and nitrogen species2-4 by heterotrophic and chemoautotrophic bacteria, respectively. The HDBR design eliminates the requirement for external flocculation/sedimentation processes while still yielding effluent containing low suspended solids. In this study, the HDBR is applied as a photobioreactor (PBR) in order to characterize the nitrogen removal characteristics of an algae-based photosynthetic microbial community. As previously reported for this HDBR design, a stable biomass zone was established with a clear delineation between the biologically active portion of the reactor and the recycling reactor fluid, which resulted in a low suspended solid effluent. The algal community in the HDBR was observed to remove 18.4% of total nitrogen species in the influent. Varying NH4+ and NO3- concentrations in the feed did not have an effect on NH4+ removal (n=44, p=0.993 and n=44, p=0.610 respectively) while NH4+ feed concentration was found to be negatively related with NO3- removal (n=44, p=0.000) and NO3- feed concentration was found to be positively correlated with NO3- removal (n=44, p=0.000). Consistent removal of NH4+, combined with the accumulation of oxidized nitrogen species at high NH4+ fluxes indicates the presence of ammonia- and nitrite-oxidizing bacteria within the microbial community.

The HDBR was used to cultivate algae over several ratios of influent ammonia and nitrate concentrations, while maintaining a total nitrogen content in the feed at 40 mg &#8211;N L-1. Influent and effluent samples were taken daily; biomass density samples were taken at the beginning and end of each condition. The reactor took on average 3-5 days to reach steady state equilibrium after conditions were changed. Over a wide range of influent conditions a distinct biomass zone was established, as observed previous ...

Watch this Scientific Journal Video about A Novel Bioreactor for High Density Cultivation of Diverse Microbial Communities at JoVE.com

A Novel Bioreactor for High Density Cultivation of Diverse Microbial Communities

A novel reactor design, coined a high density bioreactor (HDBR), is presented for the cultivation and study of high density microbial communities. Here, the HDBR is successfully applied in a photobioreactor (PBR) configuration for the study of nitrogen metabolism by a mixed high density algal community.

A novel reactor design, coined a high density bioreactor (HDBR), is presented for the cultivation and study of high density microbial communities. Past ...

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Research

JoVE Journal

Bioengineering

16.9K Views.  Drexel University. A novel reactor design, coined a high density bioreactor (HDBR), is presented for the cultivation and study of high density microbial communities. Here, the HDBR is successfully applied in a photobioreactor (PBR) configuration for the study of nitrogen metabolism by a mixed high density algal community.

Video: A Novel Bioreactor for High Density Cultivation of Diverse Microbial Communities

Density Gradient Multilayered Polymerization (DGMP): A Novel Technique for Creating Multi-compartment, Customizable Scaffolds for Tissue Engineering

Complex tissue culture matrices, in which types and concentrations of biological stimuli (e.g. growth factors, inhibitors, or small molecules) or matrix structure (e.g. composition, concentration, or stiffness of the matrix) vary over space, would enable a wide range of investigations concerning how these variables affect cell differentiation, migration, and other phenomena. The major challenge in creating layered matrices is maintaining the structural integrity of layer interfaces without diffusion of individual components from each layer1. Current methodologies to achieve this include photopatterning2-3, lithography4, sequential functionalization5, freeze drying6, microfluidics7, or centrifugation8, many of which require sophisticated instrumentation and technical skills. Others rely on sequential attachment of individual layers, which may lead to delamination of layers9. 
DGMP overcomes these issues by using an inert density modifier such as iodixanol to create layers of varying densities10. Since the density modifier can be mixed with any prepolymer or bioactive molecule, DGMP allows each scaffold layer to be customized. Simply varying the concentration of the density modifier prevents mixing of adjacent layers while they remain aqueous. Subsequent single step polymerization gives rise to a structurally continuous multilayered scaffold, in which each layer has distinct chemical and mechanical properties. The density modifier can be easily removed with sufficient rinsing without perturbation of the individual layers or their components. This technique is therefore well suited for creating hydrogels of various sizes, shapes, and materials.
A protocol for fabricating a 2D-polyethylene glycol (PEG) gel, in which alternating layers incorporate RGDS-350, is outlined below. We use PEG because it is biocompatible and inert. RGDS, a cell adhesion peptide11, is used to demonstrate spatial restriction of a biological cue, and the conjugation of a fluorophore (Alexa Fluor 350) enables us to visually distinguish various layers. This procedure can be adapted for other materials (e.g. collagen, hyaluronan, etc.) and can be extended to fabricate 3D gels with some modifications10.

Density Gradient Multilayered Polymerization DGMP: A Novel Technique for Creating Multi-compartment, Customizable Scaffolds for Tissue Engineering

Here we describe a unique strategy for creating biocompatible, layered matrices with continuous interfaces between distinct layers for tissue engineering. Such a scaffold could provide an ideal customizable environment to modulate cell behavior by various biological, chemical or mechanical cues

Complex tissue culture matrices, in which types and concentrations of biological stimuli (e.g. growth factors, inhibitors, or small molecules) or matrix ...

Design of a Biaxial Mechanical Loading Bioreactor for Tissue Engineering

We designed a loading device that is capable of applying uniaxial or biaxial mechanical strain to a tissue engineered biocomposites fabricated for transplantation. While the device primarily functions as a bioreactor that mimics the native mechanical strains, it is also outfitted with a load cell for providing force feedback or mechanical testing of the constructs. The device subjects engineered cartilage constructs to biaxial mechanical loading with great precision of loading dose (amplitude and frequency) and is compact enough to fit inside a standard tissue culture incubator. It loads samples directly in a tissue culture plate, and multiple plate sizes are compatible with the system. The device has been designed using components manufactured for precision-guided laser applications. Bi-axial loading is accomplished by two orthogonal stages. The stages have a 50 mm travel range and are driven independently by stepper motor actuators, controlled by a closed-loop stepper motor driver that features micro-stepping capabilities, enabling step sizes of less than 50 nm. A polysulfone loading platen is coupled to the bi-axial moving platform. Movements of the stages are controlled by Thor-labs Advanced Positioning Technology (APT) software. The stepper motor driver is used with the software to adjust load parameters of frequency and amplitude of both shear and compression independently and simultaneously. Positional feedback is provided by linear optical encoders that have a bidirectional repeatability of 0.1 &mu;m and a resolution of 20 nm, translating to a positional accuracy of less than 3 &mu;m over the full 50 mm of travel. These encoders provide the necessary position feedback to the drive electronics to ensure true nanopositioning capabilities. In order to provide the force feedback to detect contact and evaluate loading responses, a precision miniature load cell is positioned between the loading platen and the moving platform. The load cell has high accuracies of 0.15% to 0.25% full scale.

We designed a novel mechanical loading bioreactor that can apply uniaxial or biaxial mechanical strain to a cartilage biocomposite prior to transplantation into an articular cartilage defect.

We  designed a loading device that is capable of applying uniaxial or biaxial  mechanical strain to a tissue engineered biocomposites fabricated for  ...

Microfluidic Picoliter Bioreactor for Microbial Single-cell Analysis: Fabrication, System Setup, and Operation

In this protocol the fabrication, experimental setup and basic operation of the recently introduced microfluidic picoliter bioreactor (PLBR) is described in detail. The PLBR can be utilized for the analysis of single bacteria and microcolonies to investigate biotechnological and microbiological related questions concerning, e.g.&#160;cell growth, morphology, stress response, and metabolite or protein production on single-cell level. The device features continuous media flow enabling constant environmental conditions for perturbation studies, but in addition allows fast medium changes as well as oscillating conditions to mimic any desired environmental situation. To fabricate the single use devices, a silicon wafer containing sub micrometer sized SU-8 structures served as the replication mold for rapid polydimethylsiloxane casting. Chips were cut, assembled, connected, and set up onto a high resolution and fully automated microscope suited for time-lapse imaging, a powerful tool for spatio-temporal cell analysis. Here, the biotechnological platform organism Corynebacterium glutamicum&#160;was seeded into the PLBR and cell growth and intracellular fluorescence were followed over several hours unraveling time dependent population heterogeneity on single-cell level, not possible with conventional analysis methods such as flow cytometry. Besides insights into device fabrication, furthermore, the preparation of the preculture, loading, trapping of bacteria, and the PLBR cultivation of single cells and colonies is demonstrated. These devices will add a new dimension in microbiological research to analyze time dependent phenomena of single bacteria under tight environmental control. Due to the simple and relatively short fabrication process the technology can be easily adapted at any microfluidics lab and simply tailored towards specific needs.

In this protocol the fabrication, setup and basic operation of a microfluidic picoliter bioreactor (PLBR) for single-cell analysis of prokaryotic microorganisms is introduced. Industrially relevant microorganisms were analyzed as proof of principle allowing insights into growth rate, morphology, and phenotypic heterogeneity over certain time periods, hardly possible with conventional methods.

In this protocol the fabrication, experimental setup and basic operation of the recently introduced microfluidic picoliter bioreactor (PLBR) is described ...

Operation of a Benchtop Bioreactor

Fermentation systems are used to provide an optimal growth environment for many different types of cell cultures. The ability afforded by fermentors to carefully control temperature, pH, and dissolved oxygen concentrations in particular makes them essential to efficient large scale growth and expression of fermentation products. This video will briefly describe the advantages of the fermentor over the shake flask. It will also identify key components of a typical benchtop fermentation system and give basic instruction on setup of the vessel and calibration of its probes. The viewer will be familiarized with the sterilization process and shown how to inoculate the growth medium in the vessel with culture. Basic concepts of operation, sampling, and harvesting will also be demonstrated. Simple data analysis and system cleanup will also be discussed.

Fermentors are used to increase culture yield and productivity of bioengineered cells. After screening multiple microbial or animal cell culture candidates in shake flasks, the next logical step is to increase the selected culture&#x2019;s biomass with the fermentor. This video demonstrates the setup and operation of a typical benchtop bioreactor system.

Fermentation systems are used to provide an optimal growth environment for many different types of cell cultures. The ability afforded by fermentors to ...

Construction and Characterization of a Novel Vocal Fold Bioreactor

In vitro engineering of mechanically active tissues requires the presentation of physiologically relevant mechanical conditions to cultured cells. To emulate the dynamic environment of vocal folds, a novel vocal fold bioreactor capable of producing vibratory stimulations at fundamental phonation frequencies is constructed and characterized. The device is composed of a function generator, a power amplifier, a speaker selector and parallel vibration chambers. Individual vibration chambers are created by sandwiching a custom-made silicone membrane between a pair of acrylic blocks. The silicone membrane not only serves as the bottom of the chamber but also provides a mechanism for securing the cell-laden scaffold. Vibration signals, generated by a speaker mounted underneath the bottom acrylic block, are transmitted to the membrane aerodynamically by the oscillating air. Eight identical vibration modules, fixed on two stationary metal bars, are housed in an anti-humidity chamber for long-term operation in a cell culture incubator. The vibration characteristics of the vocal fold bioreactor are analyzed non-destructively using a Laser Doppler Vibrometer (LDV). The utility of the dynamic culture device is demonstrated by culturing cellular constructs in the presence of 200-Hz sinusoidal vibrations with a mid-membrane displacement of 40 &#181;m. Mesenchymal stem cells cultured in the bioreactor respond to the vibratory signals by altering the synthesis and degradation of vocal fold-relevant, extracellular matrix components. The novel bioreactor system presented herein offers an excellent in vitro platform for studying vibration-induced mechanotransduction and for the engineering of functional vocal fold tissues.

A novel vocal fold bioreactor capable of delivering physiologically relevant, vibratory stimulation to cultured cells is constructed and characterized. This dynamic culture device, when combined with a fibrous poly(&#949;-caprolactone) scaffold, creates a vocal fold-mimetic environment that modulates the behaviors of mesenchymal stem cells.

In vitro engineering of mechanically active tissues requires the presentation of physiologically relevant mechanical conditions to cultured cells. To ...

Cultivation of Mammalian Cells Using a Single-use Pneumatic Bioreactor System

Recent advances in mammalian, insect, and stem cell cultivation and scale-up have created tremendous opportunities for new therapeutics and personalized medicine innovations. However, translating these advances into therapeutic applications will require in vitro systems that allow for robust, flexible, and cost effective bioreactor systems. There are several bioreactor systems currently utilized in research and commercial settings; however, many of these systems are not optimal for establishing, expanding, and monitoring the growth of different cell types. The culture parameters most challenging to control in these systems include, minimizing hydrodynamic shear, preventing nutrient gradient formation, establishing uniform culture medium aeration, preventing microbial contamination, and monitoring and adjusting culture conditions in real-time. Using a pneumatic single-use bioreactor system, we demonstrate the assembly and operation of this novel bioreactor for mammalian cells grown on micro-carriers. This bioreactor system eliminates many of the challenges associated with currently available systems by minimizing hydrodynamic shear and nutrient gradient formation, and allowing for uniform culture medium aeration. Moreover, the bioreactor&#8217;s software allows for remote real-time monitoring and adjusting of the bioreactor run parameters. This bioreactor system also has tremendous potential for scale-up of adherent and suspension mammalian cells for production of a variety therapeutic proteins, monoclonal antibodies, stem cells, biosimilars, and vaccines.

Using a pneumatic bioreactor, we demonstrate the assembly, operation, and performance of this single-use bioreactor system for the growth of mammalian cells.

Recent advances in mammalian, insect, and stem cell cultivation and scale-up have created tremendous opportunities for new therapeutics and personalized ...

Construction and Setup of a Bench-scale Algal Photosynthetic Bioreactor with Temperature, Light, and pH Monitoring for Kinetic Growth Tests

The optimal design and operation of photosynthetic bioreactors (PBRs) for microalgal cultivation is essential for improving the environmental and economic performance of microalgae-based biofuel production. Models that estimate microalgal growth under different conditions can help to optimize PBR design and operation. To be effective, the growth parameters used in these models must be accurately determined. Algal growth experiments are often constrained by the dynamic nature of the culture environment, and control systems are needed to accurately determine the kinetic parameters. The first step in setting up a controlled batch experiment is live data acquisition and monitoring. This protocol outlines a process for the assembly and operation of a bench-scale photosynthetic bioreactor that can be used to conduct microalgal growth experiments. This protocol describes how to size and assemble a flat-plate, bench-scale PBR from acrylic. It also details how to configure a PBR with continuous pH, light, and temperature monitoring using a data acquisition and control unit, analog sensors, and open-source data acquisition software.

This paper describes the assembly process and operation of a bench-scale photosynthetic bioreactor that can be used, in conjunction with other methods, to estimate pertinent kinetic growth parameters. This system continuously monitors the pH, light, and temperature using sensors, a data acquisition and control unit, and open-source data acquisition software.

The optimal design and operation of photosynthetic bioreactors (PBRs) for microalgal cultivation is essential for improving the environmental and economic ...

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. ...

Process Optimization using High Throughput Automated Micro-Bioreactors in Chinese Hamster Ovary Cell Cultivation

Optimization of bioprocesses to increase the yield of desired products is of importance in the biopharmaceutical industry. This can be achieved by strain selection and by developing bioprocess parameters. Shake flasks have been used for this purpose. They, however, lack the capability to control the process parameters such as pH and dissolved oxygen (DO). This limitation can be overcome with the help of an automated micro-bioreactor. These bioreactors mimic cultivation at a larger scale. One of the major advantages of this system is the integration of the Design of Experiment (DOE) in the software. This integration enables establishing a design where multiple process parameters can be varied simultaneously. The critical process parameters and optimum bioprocess conditions can be analyzed within the software. The focus of the work presented here is to introduce the user to the steps involved in process design in the software and incorporation of the DOE within the cultivation run.

Here, we present a detailed procedure to run a Design of Experiment in an automated micro-bioreactor followed by cell harvest and protein quantification using a Protein A column.

Optimization of bioprocesses to increase the yield of desired products is of importance in the biopharmaceutical industry. This can be achieved by strain ...

High-Throughput Identification of Resistance to Pseudomonas syringae pv. Tomato in Tomato using Seedling Flood Assay

Tomato is an agronomically important crop that can be infected by Pseudomonas syringae, a Gram-negative bacterium, resulting in bacterial speck disease. The tomato-P. syringae pv. tomato pathosystem is widely used to dissect the genetic basis of plant innate responses and disease resistance. While disease was successfully managed for many decades through the introduction of the Pto/Prf gene cluster from Solanum pimpinellifolium into cultivated tomato, race 1 strains of P. syringae have evolved to overcome resistance conferred by the Pto/Prf gene cluster and occur worldwide.
Wild tomato species are important reservoirs of natural diversity in pathogen recognition, because they evolved in diverse environments with different pathogen pressures. In typical screens for disease resistance in wild tomato, adult plants are used, which can limit the number of plants that can be screened due to their extended growth time and greater growth space requirements. We developed a method to screen 10-day-old tomato seedlings for resistance, which minimizes plant growth time and growth chamber space, allows a rapid turnover of plants, and allows large sample sizes to be tested. Seedling outcomes of survival or death can be treated as discrete phenotypes or on a resistance scale defined by amount of new growth in surviving seedlings after flooding. This method has been optimized to screen 10-day-old tomato seedlings for resistance to two P. syringae strains and can easily be adapted to other P. syringae strains.

High-Throughput Identification of Resistance to Pseudomonas syringae pv. Tomato in Tomato using Seedling Flood Assay

The seedling flood assay facilitates rapid screening of wild tomato accessions for the resistance to the Pseudomonas syringae bacterium. This assay, used in conjunction with the seedling bacterial growth assay, can assist in further characterizing the underlying resistance to the bacterium, and can be used to screen mapping populations to determine the genetic basis of resistance.

Tomato is an agronomically important crop that can be infected by Pseudomonas syringae, a Gram-negative bacterium, resulting in bacterial speck disease. ...