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- Creators: Harrington Bioengineering Program
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A variety of different genes have been associated with cell fate. For example, the Nanog/Oct-4/Sox2 network forms the core interaction of a gene network that maintains stem cell pluripotency, and Oct-4 and Sox2 also play a role in the tissue types that stem cells eventually differentiate into. Using the CRISPR/cas9 based homology independent targeted integration (HITI) method developed by Suzuki et al., we can integrate fluorescent tags behind genes with reasonable efficiency via the non-homologous end joining (NHEJ) DNA repair pathway. With human embryonic kidney (HEK) 293T cells, which can be transfected with high efficiencies, we aim to create a three-parameter reporter cell line with fluorescent tags for three different genes related to cell fate. This cell line would provide several advantages for the study of cell fate, including the ability to quantitatively measure cell state, observe expression heterogeneity among a population of genetically identical cells, and easily monitor fluctuations in expression patterns.
The project is partially complete at this time. This report discusses progress thus far, as well as the challenges faced and the future steps for completing the reporter line.
This thesis is a tutorial for a MATLAB user-interface, known as EEGLAB. Cognitive and neural correlates of analytical and insight processes were evaluated and analyzed in the CRAT using EEG. It was hypothesized that different EEG signals will be measured for analytical versus insight problem solving, primarily observed in the gamma wave production. The data was interpreted using EEGLAB, which allows psychological processes to be quantified based on physiological response. I have written a tutorial showing how to process the EEG signal through filtering, extracting epochs, artifact detection, independent component analysis, and the production of a time – frequency plot. This project has combined my interest in psychology with my knowledge of engineering and expand my knowledge of bioinstrumentation.
X-ray phase contrast imaging (XPCI) is a novel imaging method that utilizes phase information of X-rays in order to produce images. XPCI allows for highly resolved features that traditional X-ray imaging modalities cannot discern. The objective of this experiment was to model initial simulations predicting the output signal of the future compact x-ray free electron laser (CXFEL) XPCI source. The signal was reported in tonal values (“counts”), where MATLAB and MATLAB App Designer were the computing environments used to develop the simulations. The experimental setup’s components included a yttrium aluminum garnet (YAG) scintillating screen, mirror, and Mako G-507C camera with a Sony IMX264 sensor. The main function of the setup was to aim the X-rays at the YAG screen, then measure its scintillation through the photons emitted that hit the camera sensor. The resulting quantity used to assess the signal strength was tonal values (“counts”) per pixel on the sensor. Data for X-ray transmission through water, air, and polyimide was sourced from The Center for X-ray Optics’s simulations website, after which the data was interpolated and referenced in MATLAB. Matrices were an integral part of the saturation calculations; field-of-view (FOV), magnification and photon energies were also necessary. All the calculations were compiled into a graphical user interface (GUI) using App Designer. The code used to build this GUI can be used as a template for later, more complex GUIs and is a great starting point for future work in XPCI research at CXFEL.