Customizable Arrays Research Articles

Construction of simple, customised, brain-spanning, multi-channel, linear microelectrode arrays

BackgroundThe construction of multichannel micro-electrode arrays (MEA) generally requires complex and expensive procedures. Here we describe a simple, cheap, flexible method of linear MEA construction. New methodOur method allows manufacture of linear MEA (cross section ∼ 375 × 250 μm with 12 electrodes) of any desired length, with customized spacing of the electrode tips (down to a minimum spacing of 200 μm or less) to suit different needs and experiments. We describe the following steps: (1) set-up for MEA construction; (2) building of a construction jig; (3) building the reference, ground and optional electrical stimulation electrodes; (4) treatment of the main recording microwires; (5) soldering of the microwires to the main connector plug and arrangement of the microwires in a customizable array; and (6) testing of the MEA resistance and correct connections. Finally, we describe methods for quick surgical implantation of multiple MEAs and bipolar micro-stimulation electrodes for in vivo experiments in free-moving rats. ResultsWe provide examples of multi-site local field potentials from prolonged recordings in awake and free-moving rodents, with recordings viable for months, as well as samples of electrical stimulation effects on cortical and hippocampal recordings. Hippocampal recordings showed clear phase reversal and amplitude changes across its layers. ConclusionsWe briefly discuss how the arrays can support other forms of stimulation such as optogenetic probes.

Manipulation and Deposition of Complex, Functional Block Copolymer Nanostructures Using Optical Tweezers.

Block copolymer self-assembly has enabled the creation of a range of solution-phase nanostructures with applications from optoelectronics and biomedicine to catalysis. However, to incorporate such materials into devices a method that facilitates their precise manipulation and deposition is desirable. Herein we describe how optical tweezers can be used to trap, manipulate, and pattern individual cylindrical micelles and larger hybrid micellar materials. Through the combination of TIRF imaging and optical trapping we can precisely control the three-dimensional motion of individual cylindrical block copolymer micelles in solution, enabling the creation of customizable arrays. We also demonstrate that dynamic holographic assembly enables the creation of ordered customizable arrays of complex hybrid block copolymer structures. By creating a program which automatically identifies, traps, and then deposits multiple assemblies simultaneously we have been able to dramatically speed up this normally slow process, enabling the fabrication of arrays of hybrid structures containing hundreds of assemblies in minutes rather than hours.

Modifying the strength and strain concentration profile within collagen scaffolds using customizable arrays of poly-lactic acid fibers

The tendon-to-bone junction is a highly specialized tissue which dissipates stress concentrations between mechanically dissimilar tendon and bone. Upon injury, the local heterogeneities across this insertion are not regenerated, leading to poor functional outcomes such as formation of scar tissue at the insertion and re-failure rates exceeding 90%. Although current tissue engineering methods are moving towards the development of spatially-graded biomaterials to begin to address these injuries, significant opportunities remain to engineer the often complex local mechanical behavior of such biomaterials to enhance their bioactivity. Here, we describe the use of three-dimensional printing techniques to create customizable arrays of poly-lactic acid (PLA) fibers that can be incorporated into a collagen scaffold under development for tendon bone junction repair. Notably, we use additive manufacturing concepts to generate arrays of spatially-graded fibers from biodegradable PLA that are incorporated into collagen scaffolds to create a collagen-PLA composite. We demonstrate the ability to tune the mechanical performance of the fiber-scaffold composite at the bulk scale. We also demonstrate the incorporation of spatially-heterogeneous fiber designs to establish non-uniform local mechanical performance of the composite biomaterial under tensile load, a critical element in the design of multi-compartment biomaterials for tendon-to-bone regeneration applications. Together, this work highlights the capacity to use multi-scale composite biomaterials to control local and bulk mechanical properties, and provides key insights into design elements under consideration for mechanically competent, multi-tissue regeneration platforms.

3D printing enables separation of orthogonal functions within a hydrogel particle.

Multifunctional particles with distinct physiochemical phases are required by a variety of applications in biomedical engineering, such as diagnostic imaging and targeted drug delivery. This motivates the development of a repeatable, efficient, and customizable approach to manufacturing particles with spatially segregated bioactive moieties. This study demonstrates a stereolithographic 3D printing approach for designing and fabricating large arrays of biphasic poly (ethylene glycol) diacrylate (PEGDA) gel particles. The fabrication parameters governing the physical and biochemical properties of multi-layered particles are thoroughly investigated, yielding a readily tunable approach to manufacturing customizable arrays of multifunctional particles. The advantage in spatially organizing functional epitopes is examined by loading superparamagnetic iron oxide nanoparticles (SPIONs) and bovine serum albumin (BSA) in separate layers of biphasic PEGDA gel particles and examining SPION-induced magnetic resonance (MR) contrast and BSA-release kinetics. Particles with spatial segregation of functional moieties have demonstrably higher MR contrast and BSA release. Overall, this study will contribute significant knowledge to the preparation of multifunctional particles for use as biomedical tools.

Increasing the strength and bioactivity of collagen scaffolds using customizable arrays of 3D-printed polymer fibers

Tendon is a highly aligned connective tissue which transmits force from muscle to bone. Each year, people in the US sustain more than 32 million tendon injuries. To mitigate poor functional outcomes due to scar formation, current surgical techniques rely heavily on autografts. Biomaterial platforms and tissue engineering methods offer an alternative approach to address these injuries. Scaffolds incorporating aligned structural features can promote expansion of adult tenocytes and mesenchymal stem cells capable of tenogenic differentiation. However, appropriate balance between scaffold bioactivity and mechanical strength of these constructs remains challenging. The high porosity required to facilitate cell infiltration, nutrient and oxygen biotransport within three-dimensional constructs typically results in insufficient biomechanical strength. Here we describe the use of three-dimensional printing techniques to create customizable arrays of acrylonitrile butadiene styrene (ABS) fibers that can be incorporated into a collagen scaffold under development for tendon repair. Notably, mechanical performance of scaffold-fiber composites (elastic modulus, peak stress, strain at peak stress, and toughness) can be selectively manipulated by varying fiber-reinforcement geometry without affecting the native bioactivity of the collagen scaffold. Further, we report an approach to functionalize ABS fibers with activity-inducing growth factors via sequential oxygen plasma and carbodiimide crosslinking treatments. Together, we report an adaptable approach to control both mechanical strength and presence of biomolecular cues in a manner orthogonal to the architecture of the collagen scaffold itself. Statement of SignificanceTendon injuries account for more than 32 million injuries each year in the US alone. Current techniques use allografts to mitigate poor functional outcomes, but are not ideal platforms to induce functional regeneration following injury. Tissue engineering approaches using biomaterial substrates have significant potential for addressing these defects. However, the high porosity required to facilitate cell infiltration and nutrient transport often dictates that the resultant biomaterials has insufficient biomechanical strength. Here we describe the use of three-dimensional printing techniques to generate customizable fiber arrays from ABS polymer that can be incorporated into a collagen scaffold under development for tendon repair applications. Notably, the mechanical performance of the fiber-scaffold composite can be defined by the fiber array independent of the bioactivity of the collagen scaffold design. Further, the fiber array provides a substrate for growth factor delivery to aid healing.

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting

TALENs are important new tools for genome engineering. Fusions of transcription activator-like (TAL) effectors of plant pathogenic Xanthomonas spp. to the FokI nuclease, TALENs bind and cleave DNA in pairs. Binding specificity is determined by customizable arrays of polymorphic amino acid repeats in the TAL effectors. We present a method and reagents for efficiently assembling TALEN constructs with custom repeat arrays. We also describe design guidelines based on naturally occurring TAL effectors and their binding sites. Using software that applies these guidelines, in nine genes from plants, animals and protists, we found candidate cleavage sites on average every 35 bp. Each of 15 sites selected from this set was cleaved in a yeast-based assay with TALEN pairs constructed with our reagents. We used two of the TALEN pairs to mutate HPRT1 in human cells and ADH1 in Arabidopsis thaliana protoplasts. Our reagents include a plasmid construct for making custom TAL effectors and one for TAL effector fusions to additional proteins of interest. Using the former, we constructed de novo a functional analog of AvrHah1 of Xanthomonas gardneri. The complete plasmid set is available through the non-profit repository AddGene and a web-based version of our software is freely accessible online.

Quantitative miRNA Expression Analysis Using Fluidigm Microfluidics Dynamic Arrays

BackgroundMicroRNAs (miRNAs) represent a growing class of small non-coding RNAs that are important regulators of gene expression in both plants and animals. Studies have shown that miRNAs play a critical role in human cancer and they can influence the level of cell proliferation and apoptosis by modulating gene expression. Currently, methods for the detection and measurement of miRNA expression include small and moderate-throughput technologies, such as standard quantitative PCR and microarray based analysis. However, these methods have several limitations when used in large clinical studies where a high-throughput and highly quantitative technology needed for the efficient characterization of a large number of miRNA transcripts in clinical samples. Furthermore, archival formalin fixed, paraffin embedded (FFPE) samples are increasingly becoming the primary resource for gene expression studies because fresh frozen (FF) samples are often difficult to obtain and requires special storage conditions. In this study, we evaluated the miRNA expression levels in FFPE and FF samples as well as several lung cancer cell lines employing a high throughput qPCR-based microfluidic technology. The results were compared to standard qPCR and hybridization-based microarray platforms using the same samples.ResultsWe demonstrated highly correlated Ct values between multiplex and singleplex RT reactions in standard qPCR assays for miRNA expression using total RNA from A549 (R = 0.98; p < 0.0001) and H1299 (R = 0.95; p < 0.0001) lung cancer cell lines. The Ct values generated by the microfluidic technology (Fluidigm 48.48 dynamic array systems) resulted in a left-shift toward lower Ct values compared to those observed by ABI 7900 HT (mean difference, 3.79), suggesting that the microfluidic technology exhibited a greater sensitivity. In addition, we show that as little as 10 ng total RNA can be used to reliably detect all 48 or 96 tested miRNAs using a 96-multiplexing RT reaction in both FFPE and FF samples. Finally, we compared miRNA expression measurements in both FFPE and FF samples by qPCR using the 96.96 dynamic array and Affymetrix microarrays. Fold change comparisons for comparable genes between the two platforms indicated that the overall correlation was R = 0.60. The maximum fold change detected by the Affymetrix microarray was 3.5 compared to 13 by the 96.96 dynamic array.ConclusionThe qPCR-array based microfluidic dynamic array platform can be used in conjunction with multiplexed RT reactions for miRNA gene expression profiling. We showed that this approach is highly reproducible and the results correlate closely with the existing singleplex qPCR platform at a throughput that is 5 to 20 times higher and a sample and reagent usage that was approximately 50-100 times lower than conventional assays. We established optimal conditions for using the Fluidigm microfluidic technology for rapid, cost effective, and customizable arrays for miRNA expression profiling and validation.