Matching Items (54)
Description
The RASopathies are a collection of developmental diseases caused by germline mutations in components of the RAS/MAPK signaling pathway and is one of the world’s most common set of genetic diseases. A majority of these mutations result in an upregulation of RAS/MAPK signaling and cause a variety of both physical and neurological symptoms. Neurodevelopmental symptoms of the RASopathies include cognitive and motor delays, learning and intellectual disabilities, and various behavioral problems. Recent noninvasive imaging studies have detected widespread abnormalities within white matter tracts in the brains of RASopathy patients. These abnormalities are believed to be indicative of underlying connectivity deficits and a possible source of the behavioral and cognitive deficits. To evaluate these long-range connectivity and behavioral issues in a cell-autonomous manner, MEK1 loss- and gain-of-function (LoF and GoF) mutations were induced solely in the cortical glutamatergic neurons using a Nex:Cre mouse model. Layer autonomous effects of the cortex were also tested in the GoF mouse using a layer 5 specific Rbp4:Cre mouse. Immunohistochemical analysis showed that activated ERK1/2 (P-ERK1/2) was expressed in high levels in the axonal compartments and reduced levels in the soma when compared to control mice. Axonal tract tracing using a lipophilic dye and an adeno-associated viral (AAV) tract tracing vector, identified significant corticospinal tract (CST) elongation deficits in the LoF and GoF Nex:Cre mouse and in the GoF Rbp4:Cre mouse. AAV tract tracing was further used to identify significant deficits in axonal innervation of the contralateral cortex, the dorsal striatum, and the hind brain of the Nex:Cre GoF mouse and the contralateral cortex and dorsal striatum of the Rbp4:Cre mouse. Behavioral testing of the Nex:Cre GoF mouse indicated deficits in motor learning acquisition while the Rbp4:Cre GoF mouse showed no failure to acquire motor skills as tested. Analysis of the expression levels of the immediate early gene ARC in Nex:Cre and Rbp4:Cre mice showed a specific reduction in a cell- and layer-autonomous manner. These findings suggest that hyperactivation of the RAS/MAPK pathway in cortical glutamatergic neurons, induces changes to the expression patterns of P-ERK1/2, disrupts axonal elongation and innervation patterns, and disrupts motor learning abilities.
ContributorsBjorklund, George Reed (Author) / Newbern, Jason M (Thesis advisor) / Neisewander, Janet (Committee member) / Smith, Brian (Committee member) / Orchinik, Miles (Committee member) / Mangone, Marco (Committee member) / Arizona State University (Publisher)
Created2018
Description
Systems biology studies complex biological systems. It is an interdisciplinary field, with biologists working with non-biologists such as computer scientists, engineers, chemists, and mathematicians to address research problems applying systems’ perspectives. How these different researchers and their disciplines differently contributed to the advancement of this field over time is a question worth examining. Did systems biology become a systems-oriented science or a biology-oriented science from 1992 to 2013?
This project utilized computational tools to analyze large data sets and interpreted the results from historical and philosophical perspectives. Tools deployed were derived from scientometrics, corpus linguistics, text-based analysis, network analysis, and GIS analysis to analyze more than 9000 articles (metadata and text) on systems biology. The application of these tools to a HPS project represents a novel approach.
The dissertation shows that systems biology has transitioned from a more mathematical, computational, and engineering-oriented discipline focusing on modeling to a more biology-oriented discipline that uses modeling as a means to address real biological problems. Also, the results show that bioengineering and medical research has increased within systems biology. This is reflected in the increase of the centrality of biology-related concepts such as cancer, over time. The dissertation also compares the development of systems biology in China with some other parts of the world, and reveals regional differences, such as a unique trajectory of systems biology in China related to a focus on traditional Chinese medicine.
This dissertation adds to the historiography of modern biology where few studies have focused on systems biology compared with the history of molecular biology and evolutionary biology.
This project utilized computational tools to analyze large data sets and interpreted the results from historical and philosophical perspectives. Tools deployed were derived from scientometrics, corpus linguistics, text-based analysis, network analysis, and GIS analysis to analyze more than 9000 articles (metadata and text) on systems biology. The application of these tools to a HPS project represents a novel approach.
The dissertation shows that systems biology has transitioned from a more mathematical, computational, and engineering-oriented discipline focusing on modeling to a more biology-oriented discipline that uses modeling as a means to address real biological problems. Also, the results show that bioengineering and medical research has increased within systems biology. This is reflected in the increase of the centrality of biology-related concepts such as cancer, over time. The dissertation also compares the development of systems biology in China with some other parts of the world, and reveals regional differences, such as a unique trajectory of systems biology in China related to a focus on traditional Chinese medicine.
This dissertation adds to the historiography of modern biology where few studies have focused on systems biology compared with the history of molecular biology and evolutionary biology.
ContributorsZou, Yawen (Author) / Laubichler, Manfred (Thesis advisor) / Maienschein, Jane (Thesis advisor) / Creath, Richard (Committee member) / Ellison, Karin (Committee member) / Newfeld, Stuart (Committee member) / Arizona State University (Publisher)
Created2016
Description
Methyl-CpG binding protein 2 (MECP2) is a widely abundant, multifunctional regulator of gene expression with highest levels of expression in mature neurons. In humans, both loss- and gain-of-function mutations of MECP2 cause mental retardation and motor dysfunction classified as either Rett Syndrome (RTT, loss-of-function) or MECP2 Duplication Syndrome (MDS, gain-of-function). At the cellular level, MECP2 mutations cause both synaptic and dendritic defects. Despite identification of MECP2 as a cause for RTT nearly 16 years ago, little progress has been made in identifying effective treatments. Investigating major cellular and molecular targets of MECP2 in model systems can help elucidate how mutation of this single gene leads to nervous system and behavioral defects, which can ultimately lead to novel therapeutic strategies for RTT and MDS. In the work presented here, I use the fruit fly, Drosophila melanogaster, as a model system to study specific cellular and molecular functions of MECP2 in neurons. First, I show that targeted expression of human MECP2 in Drosophila flight motoneurons causes impaired dendritic growth and flight behavioral performance. These effects are not caused by a general toxic effect of MECP2 overexpression in Drosophila neurons, but are critically dependent on the methyl-binding domain of MECP2. This study shows for the first time cellular consequences of MECP2 gain-of-function in Drosophila neurons. Second, I use RNA-Seq to identify KIBRA, a gene associated with learning and memory in humans, as a novel target of MECP2 involved in the dendritic growth phenotype. I confirm bidirectional regulation of Kibra by Mecp2 in mouse, highlighting the translational utility of the Drosophila model. Finally, I use this system to identify a novel role for the C-terminus in regulating the function of MECP in apoptosis and verify this finding in mammalian cell culture. In summary, this work has established Drosophila as a translational model to study the cellular effects of MECP2 gain-of-function in neurons, and provides insight into the function of MECP2 in dendritic growth and apoptosis.
ContributorsWilliams, Alison (Author) / Duch, Carsten (Thesis advisor) / Orchinik, Miles (Committee member) / Gallitano, Amelia (Committee member) / Huentelman, Matthew (Committee member) / Narayanan, Vinodh (Committee member) / Newfeld, Stuart (Committee member) / Arizona State University (Publisher)
Created2015
Description
A central task for historians and philosophers of science is to characterize and analyze the epistemic practices in a given science. The epistemic practice of a science includes its explanatory goals as well as the methods used to achieve these goals. This dissertation addresses the epistemic practices in gene expression research spanning the mid-twentieth century to the twenty-first century. The critical evaluation of the standard historical narratives of the molecular life sciences clarifies certain philosophical problems with respect to reduction, emergence, and representation, and offers new ways with which to think about the development of scientific research and the nature of scientific change.
The first chapter revisits some of the key experiments that contributed to the development of the repression model of genetic regulation in the lac operon and concludes that the early research on gene expression and genetic regulation depict an iterative and integrative process, which was neither reductionist nor holist. In doing so, it challenges a common application of a conceptual framework in the history of biology and offers an alternative framework. The second chapter argues that the concept of emergence in the history and philosophy of biology is too ambiguous to account for the current research in post-genomic molecular biology and it is often erroneously used to argue against some reductionist theses. The third chapter investigates the use of network representations of gene expression in developmental evolution research and takes up some of the conceptual and methodological problems it has generated. The concluding comments present potential avenues for future research arising from each substantial chapter.
In sum, this dissertation argues that the epistemic practices of gene expression research are an iterative and integrative process, which produces theoretical representations of the complex interactions in gene expression as networks. Moreover, conceptualizing these interactions as networks constrains empirical research strategies by the limited number of ways in which gene expression can be controlled through general rules of network interactions. Making these strategies explicit helps to clarify how they can explain the dynamic and adaptive features of genomes.
The first chapter revisits some of the key experiments that contributed to the development of the repression model of genetic regulation in the lac operon and concludes that the early research on gene expression and genetic regulation depict an iterative and integrative process, which was neither reductionist nor holist. In doing so, it challenges a common application of a conceptual framework in the history of biology and offers an alternative framework. The second chapter argues that the concept of emergence in the history and philosophy of biology is too ambiguous to account for the current research in post-genomic molecular biology and it is often erroneously used to argue against some reductionist theses. The third chapter investigates the use of network representations of gene expression in developmental evolution research and takes up some of the conceptual and methodological problems it has generated. The concluding comments present potential avenues for future research arising from each substantial chapter.
In sum, this dissertation argues that the epistemic practices of gene expression research are an iterative and integrative process, which produces theoretical representations of the complex interactions in gene expression as networks. Moreover, conceptualizing these interactions as networks constrains empirical research strategies by the limited number of ways in which gene expression can be controlled through general rules of network interactions. Making these strategies explicit helps to clarify how they can explain the dynamic and adaptive features of genomes.
ContributorsRacine, Valerie (Author) / Maienschein, Jane (Thesis advisor) / Laubichler, Manfred D (Thesis advisor) / Creath, Richard (Committee member) / Newfeld, Stuart (Committee member) / Morange, Michel (Committee member) / Arizona State University (Publisher)
Created2016
Description
Cell morphology and the distribution of voltage gated ion channels play a major role in determining a neuron's firing behavior, resulting in the specific processing of spatiotemporal synaptic input patterns. Although many studies have provided insight into the computational properties arising from neuronal structure as well as from channel kinetics, no comprehensive theory exists which explains how the interaction of these features shapes neuronal excitability. In this study computational models based on the identified Drosophila motoneuron (MN) 5 are developed to investigate the role of voltage gated ion channels, the impact of their densities and the effects of structural features.
First, a spatially collapsed model is used to develop voltage gated ion channels to study the excitability of the model neuron. Changing the channel densities reproduces different in situ observed firing patterns and induces a switch from resonator to integrator properties. Second, morphologically realistic multicompartment models are studied to investigate the passive properties of MN5. The passive electrical parameters fall in a range that is commonly observed in neurons, MN5 is spatially not compact, but for the single subtrees synaptic efficacy is location independent. Further, different subtrees are electrically independent from each other. Third, a continuum approach is used to formulate a new cable theoretic model to study the output in a dendritic cable with many subtrees, both analytically and computationally. The model is validated, by comparing it to a corresponding model with discrete branches. Further, the approach is demonstrated using MN5 and used to investigate spatially distributions of voltage gated ion channels.
First, a spatially collapsed model is used to develop voltage gated ion channels to study the excitability of the model neuron. Changing the channel densities reproduces different in situ observed firing patterns and induces a switch from resonator to integrator properties. Second, morphologically realistic multicompartment models are studied to investigate the passive properties of MN5. The passive electrical parameters fall in a range that is commonly observed in neurons, MN5 is spatially not compact, but for the single subtrees synaptic efficacy is location independent. Further, different subtrees are electrically independent from each other. Third, a continuum approach is used to formulate a new cable theoretic model to study the output in a dendritic cable with many subtrees, both analytically and computationally. The model is validated, by comparing it to a corresponding model with discrete branches. Further, the approach is demonstrated using MN5 and used to investigate spatially distributions of voltage gated ion channels.
ContributorsBerger, Sandra (Author) / Crook, Sharon (Thesis advisor) / Baer, Steven (Committee member) / Hamm, Thomas (Committee member) / Smith, Brian (Committee member) / Arizona State University (Publisher)
Created2014
Description
Traumatic brain injury (TBI) most frequently occurs in pediatric patients and remains a leading cause of childhood death and disability. Mild TBI (mTBI) accounts for 70-90% of all TBI cases, yet its neuropathophysiology is still poorly understood. While a single mTBI injury can lead to persistent deficits, repeat injuries increase the severity and duration of both acute symptoms and long term deficits. In this study, to model pediatric repetitive mTBI (rmTBI) we subjected unrestrained juvenile animals (post-natal day 20) to repeat weight drop impact. Animals were anesthetized and subjected to sham or rmTBI once per day for 5 days. At 14 days post injury (PID), magnetic resonance imaging (MRI) revealed that rmTBI animals displayed marked cortical atrophy and ventriculomegaly. Specifically, the thickness of the cortex was reduced up to 46% beneath and the ventricles increased up to 970% beneath the impact zone. Immunostaining with the neuron specific marker NeuN revealed an overall loss of neurons within the motor cortex but no change in neuronal density. Examination of intrinsic and synaptic properties of layer II/III pyramidal neurons revealed no significant difference between sham and rmTBI animals at rest or under convulsant challenge with the potassium channel blocker, 4-Aminophyridine. Overall, our findings indicate that the neuropathological changes reported after pediatric rmTBI can be effectively modeled by repeat weight drop in juvenile animals. Developing a better understanding of how rmTBI alters the pediatric brain may help improve patient care and direct "return to game" decision making in adolescents.
ContributorsGoddeyne, Corey (Author) / Anderson, Trent (Thesis advisor) / Smith, Brian (Committee member) / Kleim, Jeffrey (Committee member) / Arizona State University (Publisher)
Created2014
Description
Food is an essential driver of animal behavior. For social organisms, the acquisition of food guides interactions with the environment and with group-mates. Studies have focused on how social individuals find and choose food sources, and share both food and information with group-mates. However, it is often not clear how experiences throughout an individual's life influence such interactions. The core question of this thesis is how individuals’ experience contributes to within-caste behavioral variation in a social group. I investigate the effects of individual history, including physical injury and food-related experience, on individuals' social food sharing behavior, responses to food-related stimuli, and the associated neural biogenic amine signaling pathways. I use the eusocial honey bee (Apis mellifera) system, one in which individuals exhibit a high degree of plasticity in responses to environmental stimuli and there is a richness of communicatory pathways for food-related information. Foraging exposes honey bees to aversive experiences such as predation, con-specific competition, and environmental toxins. I show that foraging experience changes individuals' response thresholds to sucrose, a main component of adults’ diets, depending on whether foraging conditions are benign or aversive. Bodily injury is demonstrated to reduce individuals' appetitive responses to new, potentially food-predictive odors. Aversive conditions also impact an individual's social food sharing behavior; mouth-to-mouse trophallaxis with particular groupmates is modulated by aversive foraging conditions both for foragers who directly experienced these conditions and non-foragers who were influenced via social contact with foragers. Although the mechanisms underlying these behavioral changes have yet to be resolved, my results implicate biogenic amine signaling pathways as a potential component. Serotonin and octopamine concentrations are shown to undergo long-term change due to distinct foraging experiences. My work serves to highlight the malleability of a social individual's food-related behavior, suggesting that environmental conditions shape how individuals respond to food and share information with group-mates. This thesis contributes to a deeper understanding of inter-individual variation in animal behavior.
ContributorsFinkelstein, Abigail (Author) / Amdam, Gro V (Thesis advisor) / Conrad, Cheryl (Committee member) / Smith, Brian (Committee member) / Neisewander, Janet (Committee member) / Bimonte-Nelson, Heather A. (Committee member) / Arizona State University (Publisher)
Created2017
Description
The goal of the present study was to investigate whether a rest period following the end of chronic stress would impact fear extinction. Past research has indicated that chronic stress leads to impairments in the learning and recall of fear conditioning extinction. Moreover, the effects of chronic stress can return to levels similar to controls when a post-stress “rest” period (i.e., undisturbed except for normal husbandry) is given prior to testing. Male rats underwent chronic restraint stress for 6hr/day/21days (STR-IMM). Some rats, underwent a post-stress rest period for 6- or 3-weeks after the end of stress (STR-R6, STR-R3). Control (CON) rats were unrestrained for the duration of the experiment. In Experiment 1, following the stress or rest manipulation, all rats were acclimated to conditioning and extinction contexts, fear conditioned with 3 tone-foot shock pairings, and then had two days of extinction training. All groups froze similarly to the tone across all training sessions. However, STR-R6/R3 froze less in the non-shock context than did STR-IMM or CON. During extinction training, STR-IMM showed high levels of freezing to the non-shock context, leading to a concern they may be generalizing across contexts. Consequently, a follow-up experiment tested for context generalization. In Experiment 2, STR-IMM rats underwent a generalization test in an environment that was either different or the same as the conditioning environment, using STR-R6 as a comparison. STR-IMM and STR-R6 showed similar relative levels of freezing to tone and context, regardless of their conditioning environment to reveal that STR-IMM did not generalize and instead, maybe expressing hypervigilance. Thus, the present study demonstrated the novel finding that a rest period from chronic stress can lead to reduced fear responsiveness in a non-shock environment.
ContributorsJudd, Jessica M (Author) / Conrad, Cheryl D. (Thesis advisor) / Sanabria, Federico (Committee member) / Smith, Brian (Committee member) / Arizona State University (Publisher)
Created2018
Description
Desert ecosystems of the southwest United States are characterized by hot and arid climates, but hibernating bats can be found at high altitudes. The emerging fungal infection, white-nose syndrome, causes mortality in hibernating bat populations across eastern North America and the pathogen is increasingly observed in western regions. However, little is known about the ecology of hibernating bats in the southwest, which can help predict how these populations may respond to the fungus. My study investigated hibernating bats during two winters (2018-2019/2019-2020) at three caves in northern Arizona to: (1) describe diversity and abundance of hibernating bats using visual internal surveys and photographic documentation, (2) determine the duration of hibernation by recording bat echolocation call sequences outside caves and recording bat activity in caves using visual inspection, and (3) describe environmental conditions where hibernating bats are roosting. Adjacent to bats, I collected temperature and relative humidity, which I converted into absolute humidity. I documented hibernation status (i.e. active vs. not active) and roosting body position (i.e. open, partially hidden, and hidden). Between September 2018 and April 2019, 246 bat observations were recorded across the three caves. The majority of bats were identified as Myotis spp. (45.9\%, n=113), followed by Corynorhinus townsendii (45.5\%, n=112), Parastrellus hesperus (4.8\%, n=12), Eptesicus fuscus (3.6\%, n=9). Between September 2019 and April 2020, I documented a total of 361 bat observations across the three caves. C. townsendii was most prevalent (52.9\%, n=191), followed by the category P. hesperus/Myotis spp. (25.7\%, n=93), Myotis spp. (12.4\%, n=45), P. Hesperus (4.4\%, n=16), E. fuscus (3.6\%, n=13) and Unknown (0.8\%, n=3). Average conditions adjacent to bats were, temperature=12.5ºC, relative humidity=53\%, and absolute humidity=4.9 g/kg. Hibernating bats were never observed in large clusters and the maximum hibernating population size was 24, suggesting low risk for pathogen transmission among bats. Hibernation lasted approximately 120 days, with minimal activity documented inside and outside caves. Hibernating bats in northern Arizona may be at low risk for white-nose syndrome based on population size, hibernation length, roosting behavior, and absolute humidity, but other variables (e.g. temperature) indicate the potential for white-nose syndrome impacts on these populations.
ContributorsMaldonado Perez, Nubia Erandi (Author) / Moore, Marianne S (Thesis advisor) / DeNardo, Dale (Committee member) / Deviche, Pierre (Committee member) / Smith, Brian (Committee member) / Arizona State University (Publisher)
Created2020
Description
Ant colonies provide numerous opportunities to study communication systems that maintain the cohesion of eusocial groups. In many ant species, workers have retained their ovaries and the ability to produce male offspring; however, they generally refrain from producing their own sons when a fertile queen is present in the colony. Although mechanisms that facilitate the communication of the presence of a fertile queen to all members of the colony have been highly studied, those studies have often overlooked the added challenge faced by polydomous species, which divide their nests across as many as one hundred satellite nests resulting in workers potentially having infrequent contact with the queen. In these polydomous contexts, regulatory phenotypes must extend beyond the immediate spatial influence of the queen.
This work investigates mechanisms that can extend the spatial reach of fertility signaling and reproductive regulation in three polydomous ant species. In Novomessor cockerelli, the presence of larvae but not eggs is shown to inhibit worker reproduction. Then, in Camponotus floridanus, 3-methylheptacosane found on the queen cuticle and queen-laid eggs is verified as a releaser pheromone sufficient to disrupt normally occurring aggressive behavior toward foreign workers. Finally, the volatile and cuticular hydrocarbon pheromones present on the cuticle of Oecophylla smaragdina queens are shown to release strong attraction response by workers; when coupled with previous work, this result suggests that these chemicals may underly both the formation of a worker retinue around the queen as well as egg-located mechanisms of reproductive regulation in distant satellite nests. Whereas most previous studies have focused on the short-range role of hydrocarbons on the cuticle of the queen, these studies demonstrate that eusocial insects may employ longer range regulatory mechanisms. Both queen volatiles and distributed brood can extend the range of queen fertility signaling, and the use of larvae for fertility signaling suggest that feeding itself may be a non-chemical mechanism for reproductive regulation. Although trail laying in mass-recruiting ants is often used as an example of complex communication, reproductive regulation in ants may be a similarly complex example of insect communication, especially in the case of large, polydomous ant colonies.
This work investigates mechanisms that can extend the spatial reach of fertility signaling and reproductive regulation in three polydomous ant species. In Novomessor cockerelli, the presence of larvae but not eggs is shown to inhibit worker reproduction. Then, in Camponotus floridanus, 3-methylheptacosane found on the queen cuticle and queen-laid eggs is verified as a releaser pheromone sufficient to disrupt normally occurring aggressive behavior toward foreign workers. Finally, the volatile and cuticular hydrocarbon pheromones present on the cuticle of Oecophylla smaragdina queens are shown to release strong attraction response by workers; when coupled with previous work, this result suggests that these chemicals may underly both the formation of a worker retinue around the queen as well as egg-located mechanisms of reproductive regulation in distant satellite nests. Whereas most previous studies have focused on the short-range role of hydrocarbons on the cuticle of the queen, these studies demonstrate that eusocial insects may employ longer range regulatory mechanisms. Both queen volatiles and distributed brood can extend the range of queen fertility signaling, and the use of larvae for fertility signaling suggest that feeding itself may be a non-chemical mechanism for reproductive regulation. Although trail laying in mass-recruiting ants is often used as an example of complex communication, reproductive regulation in ants may be a similarly complex example of insect communication, especially in the case of large, polydomous ant colonies.
ContributorsEbie, Jessica (Author) / Liebig, Jürgen (Thesis advisor) / Hölldobler, Bert (Thesis advisor) / Pratt, Stephen (Committee member) / Smith, Brian (Committee member) / Rutowski, Ronald (Committee member) / Arizona State University (Publisher)
Created2020