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- Creators: School of Life Sciences
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Description
Previous research has showed that auditory modulation may be affected by pure tone
stimuli played prior to the onset of speech production. In this experiment, we are examining the
specificity of the auditory stimulus by implementing congruent and incongruent speech sounds in
addition to non-speech sound. Electroencephalography (EEG) data was recorded for eleven adult
subjects in both speaking (speech planning) and silent reading (no speech planning) conditions.
Data analysis was accomplished manually as well as via generation of a MATLAB code to
combine data sets and calculate auditory modulation (suppression). Results of the P200
modulation showed that modulation was larger for incongruent stimuli than congruent stimuli.
However, this was not the case for the N100 modulation. The data for pure tone could not be
analyzed because the intensity of this stimulus was substantially lower than that of the speech
stimuli. Overall, the results indicated that the P200 component plays a significant role in
processing stimuli and determining the relevance of stimuli; this result is consistent with role of
P200 component in high-level analysis of speech and perceptual processing. This experiment is
ongoing, and we hope to obtain data from more subjects to support the current findings.
stimuli played prior to the onset of speech production. In this experiment, we are examining the
specificity of the auditory stimulus by implementing congruent and incongruent speech sounds in
addition to non-speech sound. Electroencephalography (EEG) data was recorded for eleven adult
subjects in both speaking (speech planning) and silent reading (no speech planning) conditions.
Data analysis was accomplished manually as well as via generation of a MATLAB code to
combine data sets and calculate auditory modulation (suppression). Results of the P200
modulation showed that modulation was larger for incongruent stimuli than congruent stimuli.
However, this was not the case for the N100 modulation. The data for pure tone could not be
analyzed because the intensity of this stimulus was substantially lower than that of the speech
stimuli. Overall, the results indicated that the P200 component plays a significant role in
processing stimuli and determining the relevance of stimuli; this result is consistent with role of
P200 component in high-level analysis of speech and perceptual processing. This experiment is
ongoing, and we hope to obtain data from more subjects to support the current findings.
ContributorsTaylor, Megan Kathleen (Author) / Daliri, Ayoub (Thesis director) / Liss, Julie (Committee member) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Phenotypic evolution is an essential topic within the general field of evolution. Theoretically, the outcome of phenotypic evolution may be influenced by factors such as genetic background and the interaction of natural selection and genetic drift. To gain empirical evidence for testing the effects of those factors, we used eight long-term evolved Escherichia coli populations as a model system. These populations differ in terms of genetic background (different mutation rates) as well as bottleneck size (small- and large-magnitude). Specifically, we used a plate reader to measure three growth-related traits: maximum growth rate (umax), carrying capacity (Kc), and lag time (Lt) for 40 clones within each population. For each trait we quantified the change in mean per generation, the change in variance per generation, and the correlation coefficient between pairs of traits. Interestingly, we found that the small and large bottleneck populations of one background displayed clear, distinguishing trends that were not present within the populations of the other background. This leads to the conclusion that the influence of selection and drift on a population’s phenotypic outcomes is itself influenced by the genetic background of that population. Additionally, we found a strong positive correlation between umax and Kc within each of the high-mutation populations that was not consistent with our neutral expectation. However, the other two pairs did not exhibit a similar pattern. Our results provide a novel understanding in the relationship between the evolution of E. coli growth-related phenotypes and the population-genetic environment.
ContributorsGonzales, Jadon (Co-author, Co-author) / Lynch, Michael (Thesis director) / Ho, Wei-Chin (Committee member) / Geiler-Samerotte, Kerry (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Humans have evolved in many ways. Just look at how life for mankind has changed over the past few decades. It is amazing how different life can be in just a short amount of time. While it is evident that we have impacts of the environment, it should be just as evident that we impact the animals around us. However, there are a few subtle ways in which we impact the evolution of life.
Through man-made structures, human interference, artificial lights at night, and electromagnetic fields we have caused animals and insects to evolve and fit these new environments. While we tail the world around us to convince ourselves, the animals also living in these environments need to adapt to survive. In this essay, I will discuss how the affects mentioned above have cause crows, moths, snails, bobcats, blackbirds, mosquitoes, elephants, diurnal animals, fireflies, dung beetles, birds and bats to evolve. The adaptations these organisms made were caused by the subtle ways in which we have impact the landscapes around us.
Through man-made structures, human interference, artificial lights at night, and electromagnetic fields we have caused animals and insects to evolve and fit these new environments. While we tail the world around us to convince ourselves, the animals also living in these environments need to adapt to survive. In this essay, I will discuss how the affects mentioned above have cause crows, moths, snails, bobcats, blackbirds, mosquitoes, elephants, diurnal animals, fireflies, dung beetles, birds and bats to evolve. The adaptations these organisms made were caused by the subtle ways in which we have impact the landscapes around us.
ContributorsFikse, Sydney D (Author) / Sterner, Beckett (Thesis director) / Pfeifer, Susanne (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Transcranial Current Stimulation (TCS) is a long-established method of modulating neuronal activity in the brain. One type of this stimulation, transcranial alternating current stimulation (tACS), is able to entrain endogenous oscillations and result in behavioral change. In the present study, we used five stimulation conditions: tACS at three different frequencies (6Hz, 12Hz, and 22Hz), transcranial random noise stimulation (tRNS), and a no-stimulation sham condition. In all stimulation conditions, we recorded electroencephalographic data to investigate the link between different frequencies of tACS and their effects on brain oscillations. We recruited 12 healthy participants. Each participant completed 30 trials of the stimulation conditions. In a given trial, we recorded brain activity for 10 seconds, stimulated for 12 seconds, and recorded an additional 10 seconds of brain activity. The difference between the average oscillation power before and after a stimulation condition indicated change in oscillation amplitude due to the stimulation. Our results showed the stimulation conditions entrained brain activity of a sub-group of participants.
ContributorsChernicky, Jacob Garrett (Author) / Daliri, Ayoub (Thesis director) / Liss, Julie (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Many factors are at play within the genome of an organism, contributing to much of the diversity and variation across the tree of life. While the genome is generally encoded by four nucleotides, A, C, T, and G, this code can be expanded. One particular mechanism that we examine in this thesis is modification of bases—more specifically, methylation of Adenine (m6A) within the GATC motif of Escherichia coli. These methylated adenines are especially important in a process called methyl-directed mismatch repair (MMR), a pathway responsible for repairing errors in the DNA sequence produced by replication. In this pathway, methylated adenines identify the parent strand and direct the repair proteins to correct the erroneous base in the daughter strand. While the primary role of methylated adenines at GATC sites is to direct the MMR pathway, this methylation has also been found to affect other processes, such as gene expression, the activity of transposable elements, and the timing of DNA replication. However, in the absence of MMR, the ability of these other processes to maintain adenine methylation and its targets is unknown.
To determine if the disruption of the MMR pathway results in the reduced conservation of methylated adenines as well as an increased tolerance for mutations that result in the loss or gain of new GATC sites, we surveyed individual clones isolated from experimentally evolving wild-type and MMR-deficient (mutL- ;conferring an 150x increase in mutation rate) populations of E. coli with whole-genome sequencing. Initial analysis revealed a lack of mutations affecting methylation sites (GATC tetranucleotides) in wild-type clones. However, the inherent low mutation rates conferred by the wild-type background render this result inconclusive, due to a lack of statistical power, and reveal a need for a more direct measure of changes in methylation status. Thus as a first step to comparative methylomics, we benchmarked four different methylation-calling pipelines on three biological replicates of the wildtype progenitor strain for our evolved populations.
While it is understood that these methylated sites play a role in the MMR pathway, it is not fully understood the full extent of their effect on the genome. Thus the goal of this thesis was to better understand the forces which maintain the genome, specifically concerning m6A within the GATC motif.
To determine if the disruption of the MMR pathway results in the reduced conservation of methylated adenines as well as an increased tolerance for mutations that result in the loss or gain of new GATC sites, we surveyed individual clones isolated from experimentally evolving wild-type and MMR-deficient (mutL- ;conferring an 150x increase in mutation rate) populations of E. coli with whole-genome sequencing. Initial analysis revealed a lack of mutations affecting methylation sites (GATC tetranucleotides) in wild-type clones. However, the inherent low mutation rates conferred by the wild-type background render this result inconclusive, due to a lack of statistical power, and reveal a need for a more direct measure of changes in methylation status. Thus as a first step to comparative methylomics, we benchmarked four different methylation-calling pipelines on three biological replicates of the wildtype progenitor strain for our evolved populations.
While it is understood that these methylated sites play a role in the MMR pathway, it is not fully understood the full extent of their effect on the genome. Thus the goal of this thesis was to better understand the forces which maintain the genome, specifically concerning m6A within the GATC motif.
ContributorsBoyer, Gwyneth (Author) / Lynch, Michael (Thesis director) / Behringer, Megan (Committee member) / Geiler-Samerotte, Kerry (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
The aim of this study was to determine whether IUD administration, with and without the presence of Levo, and with and without the presence of the ovaries, impacts cognition in a rat model. Rats received either Sham or Ovariectomy (Ovx) surgery (removal of the ovaries), plus either no IUD, a Blank IUD (without Levo), or a Levo-releasing IUD (Levo IUD), enabling us to evaluate the effects of Ovx and the effects of IUD administration on cognition. Two weeks after surgery, all treatment groups were tested on the water radial arm maze, Morris water maze, and visible platform task to evaluate cognition. At sacrifice, upon investigation of the uteri, it was determined that some of the IUDs were no longer present in animals from these groups: Sham\u2014Blank IUD, Ovx\u2014Blank IUD, and Sham\u2014Levo IUD. Results from the remaining three groups showed that compared to Sham animals with no IUDs, Ovx animals with no IUDs had marginally impaired working memory performance, and that Ovx animals with Levo IUDs as compared to Ovx animals with no IUDs had marginally enhanced memory performance, not specific to a particular memory type. Results also showed that Ovx animals with Levo IUDs had qualitatively more cells in their vaginal smears and increased uterine horn weight compared to Ovx animals with no IUDs, suggesting local stimulation of the Levo IUDs to the uterine horns. Overall, these results provide alternative evidence to the hypothesis that the Levo IUD administers Levo in solely a localized manner, and suggests that the possibility for the Levo IUD to affect reproductive cyclicity in ovary-intact animals is not rejected. The potential for the Levo IUD to exert effects on cognition suggests that either the hormone does in fact systemically circulate, or that the Levo IUD administration affects cognition by altering an as yet undetermined hormonal or other feedback between the uterus and the brain.
ContributorsStrouse, Isabel Martha (Author) / Bimonte-Nelson, Heather (Thesis director) / Glenberg, Arthur (Committee member) / Sirianni, Rachael (Committee member) / Conrad, Cheryl (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
Lactase persistence is the ability of adults to digest lactose in milk (Segurel & Bon, 2017). Mammals are generally distinguished by their mammary glands which gives females the ability to produce milk and feed their newborn children. The new born therefore requires the ability to breakdown the lactose in the milk to ensure its proper digestion (Segurel & Bon, 2017). Generally, humans lose the expression of lactase after weaning, which prevents them being able to breakdown lactose from dairy (Flatz, 1987).
My research is focused on the people of Turkana, a human pastoral population inhabiting Northwest Kenya. The people of Turkana are Nilotic people that are native to the Turkana district. There are currently no conclusive studies done on evidence for genetic lactase persistence in Turkana. Therefore, my research will be on the evolution of lactase persistence in the people of Turkana. The goal of this project is to investigate the evolutionary history of two genes with known involvement in lactase persistence, LCT and MCM6, in the Turkana. Variants in these genes have previously been identified to result in the ability to digest lactose post-weaning age. Furthermore, an additional study found that a closely related population to the Turkana, the Massai, showed stronger signals of recent selection for lactase persistence than Europeans in these genes. My goal is to characterize known variants associated with lactase persistence by calculating their allele frequencies in the Turkana and conduct selection scans to determine if LCT/MCM6 show signatures of positive selection. In doing this, we conducted a pilot study consisting of 10 female Turkana individuals and 10 females from four different populations from the 1000 genomes project namely: the Yoruba in Ibadan, Nigeria (YRI); Luhya in Webuye, Kenya; Utah Residents with Northern and Western European Ancestry (CEU); and the Southern Han Chinese. The allele frequency calculation suggested that the CEU (Utah Residents with Northern and Western European Ancestry) population had a higher lactase persistence associated allele frequency than all the other populations analyzed here, including the Turkana population. Our Tajima’s D calculations and analysis suggested that both the Turkana population and the four haplotype map populations shows signatures of positive selection in the same region. The iHS selection scans we conducted to detect signatures of positive selection on all five populations showed that the Southern Han Chinese (CHS), the LWK (Luhya in Webuye, Kenya) and the YRI (Yoruba in Ibadan, Nigeria) populations had stronger signatures of positive selection than the Turkana population. The LWK (Luhya in Webuye, Kenya) and the YRI (Yoruba in Ibadan, Nigeria) populations showed the strongest signatures of positive selection in this region. This project serves as a first step in the investigation of lactase persistence in the Turkana population and its evolution over time.
My research is focused on the people of Turkana, a human pastoral population inhabiting Northwest Kenya. The people of Turkana are Nilotic people that are native to the Turkana district. There are currently no conclusive studies done on evidence for genetic lactase persistence in Turkana. Therefore, my research will be on the evolution of lactase persistence in the people of Turkana. The goal of this project is to investigate the evolutionary history of two genes with known involvement in lactase persistence, LCT and MCM6, in the Turkana. Variants in these genes have previously been identified to result in the ability to digest lactose post-weaning age. Furthermore, an additional study found that a closely related population to the Turkana, the Massai, showed stronger signals of recent selection for lactase persistence than Europeans in these genes. My goal is to characterize known variants associated with lactase persistence by calculating their allele frequencies in the Turkana and conduct selection scans to determine if LCT/MCM6 show signatures of positive selection. In doing this, we conducted a pilot study consisting of 10 female Turkana individuals and 10 females from four different populations from the 1000 genomes project namely: the Yoruba in Ibadan, Nigeria (YRI); Luhya in Webuye, Kenya; Utah Residents with Northern and Western European Ancestry (CEU); and the Southern Han Chinese. The allele frequency calculation suggested that the CEU (Utah Residents with Northern and Western European Ancestry) population had a higher lactase persistence associated allele frequency than all the other populations analyzed here, including the Turkana population. Our Tajima’s D calculations and analysis suggested that both the Turkana population and the four haplotype map populations shows signatures of positive selection in the same region. The iHS selection scans we conducted to detect signatures of positive selection on all five populations showed that the Southern Han Chinese (CHS), the LWK (Luhya in Webuye, Kenya) and the YRI (Yoruba in Ibadan, Nigeria) populations had stronger signatures of positive selection than the Turkana population. The LWK (Luhya in Webuye, Kenya) and the YRI (Yoruba in Ibadan, Nigeria) populations showed the strongest signatures of positive selection in this region. This project serves as a first step in the investigation of lactase persistence in the Turkana population and its evolution over time.
ContributorsJobe, Ndey Bassin (Author) / Wilson Sayres, Melissa (Thesis director) / Paaijmans, Krijn (Committee member) / Taravella, Angela (Committee member) / School of Earth and Space Exploration (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The world of podcasting has exploded in popularity in recent years. This medium is being used in education as well as in the public sector to share ideas, news, and stories. This paper reviews the research behind podcast success as a news form and in the educational sector and the implications of these findings for the future. Podcast listeners tend to listen to podcasts for entertainment and, notably, to diversify their time while completing other tasks. New ways to directly stream media from portable devices and advances in the internet have helped bolster the popularity of this media form. Podcasting proved to be successful in higher education as students tended to perform better when given access to podcasts. However, they were only successful when using podcasts as classroom adjuncts. This implies that educational podcasts must be produced differently than ones intended for the public. By reviewing the neuroscience behind language, emotion and memory, it was found that narrative formats that also evoked emotions had a positive ability in enhancing the listeners learning and memory. Keeping this in mind, the developed podcast aimed to bridge educational material to the general public by utilizing narrative as a vessel in which to deliver complex information about medicine, science and neuroscience. The accessibility and virtually non-existent barriers to the podcasting world offer a breadth of knowledge and opinions that have numerous factors of social influence. The impact of podcasting on the modern world deserves more research in sociology and psychology as it continues to grow in popularity.
ContributorsCharbel, Milad (Author) / Sirven, Joseph (Thesis director) / Reddy, Swapna (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Aberrant signaling through the canonical RAS/RAF/MEK/ERK (ERK/MAPK) pathway leads to the pathology of a group of neurodevelopmental disorders called RASopathies. RASopathies are caused by germline mutations in the ERK/MAPK pathway and have an incidence of approximately 1:2000 births. The majority of RASopathies stem from mutations that cause gain-of-function in the ERK/MAPK pathway. In this study, we have begun to unravel the roles that GABAergic interneurons play in the pathology of RASopathies. Our data demonstrate that gain-of-function ERK/MAPK signaling expressed in a GABAergic interneuron-specific fashion leads to forebrain hyperexcitability in mutant mice. Further, some GABAergic interneurons experience activated-caspase 3 mediated apoptosis in the embryonic subpallium, leading to a loss of PV-expressing interneurons in the somatosensory cortex. We found that pharmaceutical intervention during embryogenesis using a MEK1 inhibitor may be effective in preventing apoptosis of these neurons. Future work is still needed to understand the mechanism of the death of GABAergic interneurons and to further pursue therapeutic approaches. Taken together, this study suggests potential roles of cortical GABAergic interneurons in ERK/MAPK-linked pathologies and indicates possible approaches to provide therapy for these conditions.
ContributorsShah, Shiv (Author) / Newbern, Jason (Thesis director) / Gipson-Reichardt, Cassandra (Committee member) / School of Life Sciences (Contributor) / Economics Program in CLAS (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Egr3 is an immediate early gene transcription factor that shows genetic association with schizophrenia, and is found in decreased levels in the brains of schizophrenia patients. Schizophrenia patients also exhibit cognitive and memory deficits, both of which Egr3 has been shown to play a crucial role in. Additionally, high levels of DNA damage are found in the brains of schizophrenia patients. A recent study has shown that DNA damage occurs as a result of normal physiological activity in neurons and is required for induction of gene expression of a subset of early response genes. Also, failure to repair this damage can lead to gene expression in a constitutive switched on state. Egr3 knockout (Egr3-/-) mice show deficits in hippocampal synaptic plasticity and memory. We were interested in characterizing downstream targets of EGR3 in the hippocampus. To determine these targets, electroconvulsive seizure (ECS) was carried out in Egr3 -/- versus wild type (WT) mice, and a microarray study was first done in our lab. ECS maximally stimulates Egr3 expression and we hypothesized that there would be gene targets that are differentially expressed between Egr3 -/- and WT mice that had been subjected to ECS. Two separate analyses of the microarray yielded 65 common genes that were determined as being differentially expressed between WT and Egr3 -/- mice after ECS. Further Ingenuity Pathway Analysis of these 65 genes indicated the Gadd45 signaling pathway to be the top canonical pathway, with the top four pathways all being associated with DNA damage or DNA repair. A literature survey was conducted for these 65 genes and their associated pathways, and 12 of the 65 genes were found to be involved in DNA damage response and/or DNA repair. Validation of differential expression was then conducted for each of the 12 genes, in both the original male cohort used for microarray studies and an additional female cohort of mice. 7 of these genes validated through quantitative real time PCR (qRT-PCR) in the original male cohort used for the microarray study, and 4 validated in both the original male cohort and an independent female cohort. Bioinformatics analysis yielded predicted EGR3 binding sites in promoters of these 12 genes, validating their role as potential transcription targets of EGR3. These data reveal EGR3 to be a novel regulator of DNA repair. Further studies will be needed to characterize the role of Egr3 in repairing DNA damage.
ContributorsBarkatullah, Arhem Fatima (Author) / Newbern, Jason (Thesis director) / Gallitano, Amelia (Committee member) / Marballi, Ketan (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05