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Item Techniques for improving activity based biosensors: a Kuhl platform for engineering(Montana State University - Bozeman, College of Agriculture, 2020) Thomas, Merrilee Anne; Chairperson, Graduate Committee: Thomas Hughes and Susy C. Kohout (co-chair); Thomas E. Hughes was a co-author of the article, 'Optically activated, customizable, excitable cells Kuhl platform for evolving next gen biosensors' submitted to the journal 'PLOS One' which is contained within this dissertation.According to Kuhn, ''there are three classes of problems - determination of significant facts, matching of facts with theory, and articulation of that theory (Kuhn 2012).'' The current paradigm in molecular neuroscience is that there is a need for revolutionary tool development in neuroscience. Interestingly, the need for better tools in neuroscience is to answer neuroscience theories and provide the determination and articulation of those theories. Currently, the neuroscientist's toolbox is growing and the ways in which those tools are used is rapidly changing. Neuroscience underwent a revolution when we were able to take single-cell recording in vivo and then assign field properties to individual neurons based upon those responses (O'Keefe and Bouma 1969; O'Keefe and Dostrovsky 1971; Moser et al. 1995). Scientists became adept at imaging increasingly smaller regions of the functioning human brain (Price 2012). We have since been able to genetically encode and manipulate proteins and pathways while recording from them using fluorescence (Southern and Berg 1982; Chalfie 2009). In vitro and in vivo we have harnessed the use of light to stimulate or inhibit specific neurons or ligands (Boyden 2011; Adamantidis et al. 2007). These tools are just the beginning and by no means is this an exhaustive list. We introduce the Kuhl synthetic cell system that provides a customizable de-novo excitable cell. The Kuhl system is activated using a blue light photo activated cyclase bPAC. It can be used to create better tools to image the brain and can be used to screen multi-color fluorescent sensors. Interestingly, sensors that are within bPACs activation spectrum can be used in these synthetic cells. We show that both red and green Ca 2+ sensors can be imaged simultaneously, and both Ca 2+ and Voltage sensors can be screened in the Kuhl system. The Kuhl system has the potential to be used to screen for drug compounds and in theory, they could be used in studying pathways that are less understood, such as the mTOR pathway.Item Large-scale spatiotemporal cortical dynamics in visual short-term memory: from spiking activity to oscillations(Montana State University - Bozeman, College of Agriculture, 2020) Hoffman, Steven Joseph; Chairperson, Graduate Committee: Charles M. Gray and Jamie Mazer (co-chair); Nicholas M. Dotson was an author and Baldwin Goodell and Charles M. Gray were co-authors of the article, 'A large-scale semi-chronic microdrive recording system for non-human primates' in the journal 'Neuron' which is contained within this dissertation.; Nicholas M. Dotson and Charles M. Gray were co-authors of the article, 'The cortical local field potential exhibits distinct spatial gradients that vary with frequency and time during visual short-term memory' which is contained within this dissertation.; Dissertation contains a article of which Steven Joseph Hoffman is not the main author.Cognitive processes occur through coordinated activity via disparate cortical and subcortical brain structures. Although these structures may be widely separated, evolutionary pressures dictate that cognition must occur rapidly and efficiently. In order to capture these brain-wide activity patterns the tools for measuring them need to be similarly capable of measurements of both high spatial coverage, and high temporal resolution. Additionally, the measurements would ideally be of the activity of the fundamental units involved in cognition, that is the neurons, rather than an extrapolation of their activity via a different signal source. However, outside of the work presented here, current technologies are rare that allow both the requisite coverage and spatiotemporal resolution to achieve these measurements. The results of the studies presented in Chapters 2-4 provide both the tools for making such measurements, and the initial analyses of the neuronal dynamics during short-term memory. In Chapter 2 we present the technological and methodological process for recording neural activity (both action potentials and local field potentials) from across roughly a hemisphere of cortex in the macaque monkey performing a visual short-term memory task. In visual short-term memory a visual percept must be maintained then recalled when it is no longer present. This cognitive process is one we use nearly incessantly in every-day life. In Chapter 3 we found task dependent spiking activity during short-term memory is wide-spread, and that most areas display a balanced state of both increases and decreases in firing rate. Within these areas we found a hierarchically organized subset of cortical areas that also showed stimulus specific activity during the memory period of the task. In Chapter 4 we used spectral analysis to investigate the oscillatory make-up of neural activity across the recorded areas. We found within specific frequency bands there are different gradients of amplitude of spectral power across cortex. Additionally, we found that we could use a small number of spectrally derived variables in order to decode the brain area origin of the signal. This shows that areas have a characteristic spectral composition, that varies systematically across the cortical mantle.