Induced pluripotent stem cells (iPSC) have a high potential, for they can be differentiated into any cell type for regenerative medicine, drug discovery, developmental biology, and disease modeling. However, iPSC’s and their differentiated progeny display an undesired variability in their shape, contractile properties, growth rates, etc. Identifying subsets of phenotypes in iPSCs and their differentiated progeny will allow us to optimize tissue models for research. Here, we generated a rainbow reporter line in iPSCs that can track individual cells as they clonally expand and differentiate while providing phenotypic information. Knocking in four copies of a cassette containing three distinct fluorescent proteins allowed the expression of up to eighteen different colors. However, not all colors were present in equal proportion, increasing the probability that distinct lineages could have the same color. To achieve an equal color distribution, colored cells were isolated by sparsely plating a culture of mixed colored cells. After a week of expansion, individual colonies were picked and imaged under a spinning disk microscope to determine the color of the colony and whether it was single lineage or mixed. Viable cell lines were isolated and frozen in stock. These cells will be examined for markers of cell proliferation, pluripotency, apoptosis and quantitative RNA expression analysis to confirm that the color barcoded iPSCs act the same as non-engineered iPSCs. To date, we were able to create eight color barcoded iPSC lines for further experimentation, increasing the concentration limit of colored cells in non-colored cells by five-fold. The next step will engineer 3D tissues by growing iPSC-derived cardiac cells in a mold to simulate in vivo tissue development. Colored coded cells will allow us to track how the initial location/physical stresses/phenotype of an iPSC-derived cardiac cell in an engineered tissue determines its tissue layer and cell type.

 Recent studies have shown exposure to concentrations of carbon dioxide above a threshold ranging from 600 and 1000 parts per million (ppm) impairs human cognitive performance. Upon passing this threshold, a 400ppm increase is correlated with a 21% decline in cognitive performance. Classrooms and offices, two spaces where cognitive performance should be optimized, often exceed 1000 ppm, with one study of classrooms in Texas showing that over 20% exhibit peak CO² concentrations well above 3000 ppm. While one solution to this problem is increasing the rate of ventilation, this results in greater energy expenditure. The BioArchos project proposes the deployment of modular, wall-mounted, easily operated carbon sequestration devices. The apparatus utilizes the photosynthetic and metabolic processes of Chlorella vulgaris, a species of algae, as a means of addressing the cognitive, environmental, and cost issues that surround elevated CO² levels. We started this investigation with the design and assembly of a closed-loop bioreactor testbed, which tested the impact of CO² concentration, gas pressure, and light intensity on overall performance. Our initial tests seek to optimize the response time of the system to an increase in carbon concentration and the energy consumption of the device. Our findings from these tests, as well as the findings from other studies inform the development of an open-loop prototype, which is the first iteration of our proposed solution. We predict this prototype will remove approximately 350g of CO2 every day, using approximately 0.5 kW of energy. That is about the average CO2 output of one person’s 8-hour work day, with an energy usage less than half of a conventional microwave. Once the proof of concept is established, the focus of the BioArchos project will be to increase the volumetric efficiency of our device while reducing operational costs to make the final product more accessible and effective.

Higher concentrations of carbon dioxide have adverse cognitive effects, including reducing memory, impairing concentration, and lowering decision-making capabilities. To mitigate this we have designed and built a photobioreactor with a culture of Chlorella vulgaris, a species of green microalgae, with the purpose of reducing the concentration of carbon dioxide. We are developing a control system for the bioreactor that will manage the algae population, optimize oxygen output, and optimize energy consumption of the LED panels. For the system a control loop is being designed and tested. It will regulate the oxygen output rate using a light intensity controller. The rate of photosynthesis can be analyzed as a function of light intensity, and data from experimentally graphing this relation is used in the control loop to optimize the production of oxygen. Preliminary modelling and testing of this system is ongoing. Future research goals include full prototype testing and quantitative analysis of gas concentration over long-term cultivation cycles. Our research will allow more environmentally friendly air filtration with the purpose of being used commercially to reduce carbon dioxide concentration in indoor spaces.

Nondestructive 3D pathology is poised to play a transformative role in biomedical research and precision medicine in the decades to come, helping to usher pathology into a digital 3D era. Recent improvements in high-throughput volumetric microscopy, including light-sheet microscopy, have made it feasible for large pre-clinical and clinical specimens to be imaged in toto within reasonable time frames [Glaser, et al., Nature BME, 2017; Glaser, et al., Nature Communications, 2019]. However, these imaging methods depend upon the quality and reproducibility with which fluorescent labeling and optical clearing of thick tissue specimens is performed. In particular, while high-quality volumetric datasets can be acquired with pain-staking optimization and iteration of manual tissue-preparation protocols, high-throughput imaging assays demand that these methods be highly consistent and require minimal labor. We developed a protocol for automated micro-controller-based labeling and clearing of clinical specimens in order to generate volumetric imaging datasets that consistently mimic the appearance of “gold-standard” H&E histology. Archived formalin-fixed paraffin-embedded (FFPE) tissue blocks are first de-paraffinized with a combination of heat and xylene removal of paraffin wax. Next, specimens are put in an acidic, ethanol and water solution so that an aqueous nuclear and eosin labeling step can be achieved. This otherwise labor-intensive, two-day procedure is a critical step for automation since manual processing can lead to variabilities that will affect downstream labeling and clearing performance. Finally, specimens are cleared with a non-toxic clearing agent for refractive index-matching and 3D microscopy. By using automated micro-controller-based buffer exchange hardware, we demonstrate the reliability of these low-cost and convenient methods for imaging a diverse range of tissues. These methods will facilitate pre-clinical and clinical studies with large numbers of tissue specimens, such as those needed to validate the benefits of 3D pathology for clinical decision support.

Escherichia coli (E. coli) bacteria are a source of food related illness. If irrigation water is contaminated by fecal matter runoff, crops may become infected prior to harvesting, processing, or packaging. Existing test methods require 16-48 hours for sufficient growth and subsequent confirmation of bacterial infection in the irrigation water. Therefore, providing a means for a rapid detection of water borne coliform and E. coli during this growth phase would allow a more preventative response. We have developed a method to determine bacteria presence by a measure of metabolic activity with a spectral analysis system. Byproducts of fermentation from the metabolic activity of live bacteria results in a solution pH drop within a relatively short time. The fluorophore fluorescein is added to the media, allowing optical detection of the solution pH due to its pH sensitive spectral properties within a pH range of 4-7. A blue LED is used to excite fluorescence, emitting peaks at 525 and 550 nm wavelength light depending on the ionization state equilibrium. Unmixing of the spectral profile yields the fluorescent contributions of the ionization states and determination of the pH. A pH drop from metabolic activity serves as a confirmatory test for a growing bacteria culture. Results can be provided within the early hours of growth instead of days, with time of detection depending on the initial concentration of living bacteria. The economical and biosafe characteristics of fluorescein and the testing materials would allow the use of the assay in low resource or rural areas.

Back contact solar cells improve on the standard geometry by arranging both the positive and negative electrodes on the back of the device. This significantly improves efficiency by eliminating three critical challenges faced by typical solar cells: (1) shading of the active layer by top contacts, (2) the conflicting requirement for conductive yet transparent top contact materials, and (3) difficulty in printing metallic contacts onto the sensitive photoactive layer. Electrodeposition is a disruptive method that offers an alternative pathway for solution processing manufacturing, but is relatively unexplored as a method of fabricating perovskite back contact solar cells. This study focuses on achieving selective electrodeposition of high quality nanoscale electron and hole transport layers (tin and nickel oxides respectively) onto interdigitated silver collectors. In this investigation, a silver working electrode and a nickel or tin counter electrode against a silver/silver chloride reference electrode comprise a three-probe system in nickel nitrate and tin chloride electrolyte baths. The conductivity and carrier mobility of the electrodeposited transport layers are discussed as a function of salt and dopant molecule concentrations in the electrolyte bath. High carrier mobility layers are desirable for increased solar cell efficiency. The microstructure and thickness of the transport layer are discussed as a function of bath temperature, stirring speed, and the magnitude and duration of the supplied current density. The transport layers are characterized using optical profilometry and scanning electron microscopy. Diode devices are fabricated to characterize the electrical properties of the oxide layers. Based on these results, an optimal electrodeposition procedure is recommended for producing high quality nickel- and tin-based charge transport layers for application in back contact perovskite solar cells. Achieving this device geometry via electrodeposition enables the production of more efficient solar modules using high throughput manufacturing methods - bringing novel photovoltaic materials one step closer to widespread use.