Barrett, The Honors College Thesis/Creative Project Collection

This paper describes a project involving the optimization of the analysis process of FreeSurfer and ANTS Registration for neuroscience analytics of patients at risk of cognitive decline using Nipype. The paper details the process of discovering more about Nipype, learning to use a supercomputer, and implementing the open-source python code to fit the needs of the research lab. Nipype is a python-based initiative to unify the various software packages used within the neuroscience community for data analysis. This paper also serves as documentation of the steps taken to complete the project so that future students are able to continue the optimization process to result in one cohesive workflow in which data is able to flow through a unified pipeline of analysis in the future.

Advancing the understanding and treatment of many neurological disorders can be achieved by improving methods of neuronal detection at increased depth in the mammalian brain. Different cell subtypes cannot be detected using non-invasive techniques beyond 1 mm from cortical surface, in the context of targeting particular cell types in vivo (Wang, 2012). These limitations in the depth of imaging and targeting are due to optical scattering (Ntziachristos, 2010). In order to overcome these restrictions, longer wavelength fluorescent proteins have been utilized by researchers to see tagged cells at depth. Optical techniques such as two-photon and confocal microscopy have been used in combination with fluorescent proteins to expand depth, but are still limited by the penetration depth of light due to optical scattering (Lee, 2015). This research aims to build on other detection methods, such as the photoacoustic effect and automated fluorescence-guided electrophysiology, to overcome this limitation.

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by the deterioration of upper and lower motor neurons in the brain, brain stem, and spinal cord. Multiple missense mutations have been connected to familial ALS, including those in the Matrin-3 protein. Matrin-3 is an RNA and DNA-binding protein encoded by the MATR3 gene. Normally found in the nuclear matrix, Matrin-3 plays several roles vital to RNA metabolism, including splicing, RNA degradation, mRNA transport, mRNA stability, and transcription. Mutations in MATR3 leading to familial ALS include P154S and S85C, but the mechanisms through which these mutations contribute to ALS pathology remain unknown. This makes mouse models particularly useful in elucidating pathology mechanisms, ultimately having the potential to serve as preclinical models for therapeutic drugs. Because of the importance of animal models, we worked to create ALS mouse models for the MATR3 P154S and S85C mutations. We specifically generated two CRISPR/Cas9 mediated knock-in mouse models containing the MATR3 P154S or S85C mutation expressed under the control of the endogenous promoter. Both the homozygous and heterozygous P154S mice developed no physical or motor defects or shortening of lifespan compared to the wildtype mice. They also exhibited no ALS-like pathology in either the muscle or spinal cord up to 24 months. In contrast, the homozygous S85C mice exhibited significant physical and motor differences, including smaller weight, impaired gait, and shortening of lifespan. Some ALS-like pathology was observed in the muscle, but pathology remained limited in the spinal cord of the homozygous mice up to 12 months. In conclusion, our data suggests that the MATR3 P154S mutation alone does not cause ALS in vivo, while the MATR3 S85C mutation induces significant motor deficits, with pathology in the spinal cord potentially beginning at older ages not examined in our study.

For my thesis, I conducted a study on a healthy pediatric cohort to investigate how DNA methylation of genes related to myelin may predict total white matter volume in a healthy pediatric cohort. The relatively new field of neuroimaging epigenetics investigates how methylation of genes in peripheral tissue samples is related to certain structural or functional features of the brain, as measured by neuroimaging data. Research has already demonstrated that methylation of genes in peripheral tissues is related to a variety of brain disorders. We hypothesized that methylation of myelin-related genes as measured in saliva samples would predict total white matter volume in a healthy pediatric cohort. After processing DNA methylation data from saliva samples from participants, multiple linear regressions were ran to determine if DNA methylation of myelin related genes was related to total white matter volume, as measured by data from structural MRIs. Results showed that these genes, which included MOG, MBP, and MYRF, significantly predicted total white matter volume. Two genes that were significant in our results have been previously shown to produce proteins that are essential to the structure of myelin.

This paper provides a multidisciplinary analysis of the relationship between beauty and addiction, with a focus on the emerging field of neuroaesthetics. Neuroaesthetics investigates the neural mechanisms that underlie aesthetic experiences and how the brain cognitively processes beauty. Since there is a biological foundation of this report, I will predominantly discuss neuroanatomy, neurological studies, and the overlap in neural circuitry between beauty and addiction. In addition, I will discuss the philosophical roots of beauty, as well as the environmental elements involved. Chapter 1 begins by explaining the history of beauty and its importance. I discuss the main constituents of beauty and differentiate between key terms involved in the beauty experience. In order to understand the link between beauty and addiction, it is essential to have a knowledgeable background on what beauty is. Next, I discuss the neurobiology of addiction. The main component of this chapter involves the mesolimbic and mesocortical reward pathways. I also describe neuroanatomical terms involved in addiction. The last chapter considers the implications of neuroaesthetics in various studies, which primarily involve the use of fMRIs. I discuss the sensory evaluations of beauty and the brain regions involved in the beauty experience. From this, I found that the experience of beauty activates these main brain regions: PFC, amygdala, striatum, NAcc, cingulate, VTA, and most remarkably, field A1 of the mOFC. By combining the neurological studies with studies of aesthetics, I reached the conclusion that there is an overlap in the neural pathways during the experience of beauty and during addiction. Although it is necessary for further research to be conducted to properly declare this, I discovered that the pursuit of beauty can lead to addictive behaviors, as the reward centers of the brain are activated by aesthetic experiences.

With millions of people living with a disease as restraining as migraines, there are no ways to diagnose them before they occur. In this study, a migraine model using nitroglycerin is used in rats to study the awake brain activity during the migraine state. In an attempt to search for a biomarker for the migraine state, we found multiple deviations in EEG brain activity across different bands. Firstly, there was a clear decrease in power in the delta, beta, alpha, and theta bands. A slight increase in power in the gamma and high frequency bands was also found, which is consistent with other pain-related studies12. Additionally, we searched for a decreased pain threshold in this deviation, in which we concluded that more data analysis is needed to eliminate the multiple potential noise influxes throughout each dataset. However, with this study we did find a clear change in brain activity, but a more detailed analysis will narrow down what this change could mean and how it impacts the migraine state.

Alzheimer’s disease (AD) is an irreversible brain disorder that plagues millions of people with no current cure. Current clinical research is slowly advancing to more definitive treatments in hopes of reducing the effects of progressive cognitive and behavioral decline, but none so far can slow AD’s onset. A brain area known as the nucleus incertus (NI) was recently discovered to potentially impact AD because of its connections to brain targets that degenerate; however, the NI’s role is unknown. This goal of this experiment was to use a transgenic mouse model (APP/PS1) that expresses AD pathology slowly as found in humans, and to test the mice in a variety of cognitive and anxiety assessments. Mice of both sexes and two different ages were used, with the first being young adult before AD pathology manifests (around 3-4 months old), and the second being around the cusp of when AD pathology manifests (late adult, 8-10 months old). The mice were tested in a variety of cognitive tasks that included the novel object recognition (NOR), Morris water maze (MWM), and the object placement (OP), with the latter being the focus of my thesis. Anxiety measures were taken from the open field (OF) and elevated plus maze (EPM) with the visible platform (VP) used to ensure mice could perform on the rigorous MWM task. In the OP, we found an age effect, where the older mice were less likely to explore the moved object during the OP compared to the younger mice; motor ability was unlikely to explain this effect. We did not find any significant age by genotype effects. These findings indicate that cognitive impairment only just started to affect the older cohort, since OP impairment was found on one measure and not another. Other measures currently being quantified will be helpful in understanding this data, and to see whether learning, memory, and anxiety are affected.