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Description
Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative

Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative diseases are commonly misdiagnosed in live human subjects. Postmortem histopathological examination of a donor's brain, combined with premortem clinical criteria, is often the most robust approach to correctly classify an individual as a disease-specific case or unaffected control. We describe the establishment of primary dermal fibroblasts cells lines from 28 autopsy donors. These fibroblasts were used to examine the proliferative effects of establishment protocol, tissue amount, biopsy site, and donor age. As proof-of-principle, iPSCs were generated from fibroblasts from a 75-year-old male, whole body donor, defined as an unaffected neurological control by both clinical and histopathological criteria. To our knowledge, this is the first study describing autopsy donor-derived somatic cells being used for iPSC generation and subsequent neural differentiation. This unique approach also enables us to compare iPSC-derived cell cultures to endogenous tissues from the same donor. We utilized RNA sequencing (RNA-Seq) to evaluate the transcriptional progression of in vitro-differentiated neural cells (over a timecourse of 0, 35, 70, 105 and 140 days), and compared this with donor-identical temporal lobe tissue. We observed in vitro progression towards the reference brain tissue, supported by (i) a significant increasing monotonic correlation between the days of our timecourse and the number of actively transcribed protein-coding genes and long intergenic non-coding RNAs (lincRNAs) (P < 0.05), consistent with the transcriptional complexity of the brain, (ii) an increase in CpG methylation after neural differentiation that resembled the epigenomic signature of the endogenous tissue, and (iii) a significant decreasing monotonic correlation between the days of our timecourse and the percent of in vitro to brain-tissue differences (P < 0.05) for tissue-specific protein-coding genes and all putative lincRNAs. These studies support the utility of autopsy donors' somatic cells for iPSC-based neurological disease models, and provide evidence that in vitro neural differentiation can result in physiologically progression.
ContributorsHjelm, Brooke E (Author) / Craig, David W. (Thesis advisor) / Wilson-Rawls, Norma J. (Thesis advisor) / Huentelman, Matthew J. (Committee member) / Mason, Hugh S. (Committee member) / Kusumi, Kenro (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Skeletal muscles arise from the myotome compartment of the somites that form during vertebrate embryonic development. Somites are transient structures serve as the anlagen for the axial skeleton, skeletal muscle, tendons, and dermis, as well as imposing the metameric patterning of the axial musculoskeletal system, peripheral nerves, and vasculature. Classic

Skeletal muscles arise from the myotome compartment of the somites that form during vertebrate embryonic development. Somites are transient structures serve as the anlagen for the axial skeleton, skeletal muscle, tendons, and dermis, as well as imposing the metameric patterning of the axial musculoskeletal system, peripheral nerves, and vasculature. Classic studies have described the role of Notch, Wnt, and FGF signaling pathways in controlling somite formation and muscle formation. However, little is known about the transformation of myotome compartments into identifiable post-natal muscle groups. Using a mouse model, I have undertaken an evaluation of morphological events, including hypertrophy and hyperplasia, related to the formation of several muscles positioned along the dorsal surface of the vertebrae and ribs. Lunatic fringe (Lfng) deficient embryos and neonates were also examined to further understand the role of the Notch pathway in these processes as it is a modulator of the Notch receptor and plays an important role in defining somite borders and anterior-posterior patterning in many vertebrates. Lunatic fringe deficient embryos showed defects in muscle fiber hyperplasia and hypertrophy in the iliocostalis and longissimus muscles of the erector spinae group. This novel data suggests an additional role for Lfng and the Notch signaling pathway in embryonic and fetal muscle development.
ContributorsDe Ruiter, Corinne (Author) / Rawls, J. Alan (Thesis advisor) / Wilson-Rawls, Jeanne (Committee member) / Kusumi, Kenro (Committee member) / Fisher, Rebecca E. (Committee member) / Arizona State University (Publisher)
Created2012
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Description
The direct-to-consumer (DTC) stem cell industry is a novel industry in the United States offering experimental stem cell treatments to patients with little regulatory oversight. The rapid expansion of this industry over the last decade has drawn attention from a number of stakeholders, and there is heated debate about how

The direct-to-consumer (DTC) stem cell industry is a novel industry in the United States offering experimental stem cell treatments to patients with little regulatory oversight. The rapid expansion of this industry over the last decade has drawn attention from a number of stakeholders, and there is heated debate about how the industry should be regulated in order to maintain patient safety and treatment efficacy while also promoting innovation. Since 2009, the U.S. Food and Drug Administration (FDA) has been the main regulatory agency within the DTC stem cell industry, but it has been criticized for not taking stricter action. To develop a better understanding of the regulatory landscape in the DTC stem cell industry, this study provides a thorough analysis of five effective regulatory pathways: Food & Drug Administration (FDA), Federal Trade Commission (FTC), litigation, state legislation, and state medical boards. The operation of these pathways as regulatory agencies separately and together provide a clearer picture of future regulation in the DTC stem cell industry.
ContributorsWilliams, Paige (Author) / Frow, Emma (Thesis director) / Bowman, Diana (Committee member) / School of International Letters and Cultures (Contributor) / School of Human Evolution & Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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Description

The US President's Council on Bioethics was an organization headquartered in Washington D.C. that was chartered to advise then US President George W. Bush on ethical issues related to biomedical science and technology. In November 2001, US President George W. Bush created the President's Council on Bioethics (PCB). Convened during

The US President's Council on Bioethics was an organization headquartered in Washington D.C. that was chartered to advise then US President George W. Bush on ethical issues related to biomedical science and technology. In November 2001, US President George W. Bush created the President's Council on Bioethics (PCB). Convened during a nationwide cloning and embryonic stem cell research debate, the Council stated that it worked to address arguments about ethics from many different perspectives. The organization enacted a model for analyzing bioethical issues through deliberation instead of through the consensus approach. US President Barack Obama replaced the PCB in 2009 with his Presidential Commission for the Study of Bioethical Issues.

Created2014-02-18
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By 2011, researchers in the US had established that non-invasive blood tests can accurately determine the gender of a human fetus as early as seven weeks after fertilization. Experts predicted that this ability may encourage the use of prenatal sex screening tests by women interested to know the gender of

By 2011, researchers in the US had established that non-invasive blood tests can accurately determine the gender of a human fetus as early as seven weeks after fertilization. Experts predicted that this ability may encourage the use of prenatal sex screening tests by women interested to know the gender of their fetuses. As more people begin to use non-invasive blood tests that accurately determine the sex of the fetus at 7 weeks, many ethical questions pertaining to regulation, the consequences of gender-imbalanced societies, and altered meanings of the parent-child relationship.

Created2014-03-23
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Description

Established in tandem with Singapore's national Biomedical Sciences Initiatives, the Bioethics Advisory Committee (BAC) was established by the Singapore Cabinet in December 2000 to examine the potential ethical, legal, and social issues arising from Singapore's biomedical research sector, and to recommend policy to Singapore's government. BAC's deliberations on embryonic stem

Established in tandem with Singapore's national Biomedical Sciences Initiatives, the Bioethics Advisory Committee (BAC) was established by the Singapore Cabinet in December 2000 to examine the potential ethical, legal, and social issues arising from Singapore's biomedical research sector, and to recommend policy to Singapore's government. BAC's deliberations on embryonic stem cell research helped shape the government policies that helped Singapore pursue its goal of becoming one of the biggest investors of embryonic stem cell research in the early twenty-first century.

Created2014-03-14
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Ethical Issues in Human Stem Cell Research: Executive Summary was published in September 1999 by The US National Bioethics Advisory Commission in response to a national debate about whether or not the US federal government should fund embryonic stem cell research. Ethical Issues in Human Stem Cell Research recommended

Ethical Issues in Human Stem Cell Research: Executive Summary was published in September 1999 by The US National Bioethics Advisory Commission in response to a national debate about whether or not the US federal government should fund embryonic stem cell research. Ethical Issues in Human Stem Cell Research recommended policy to US President William Clinton's administration, which advocated for federal spending on the use of stem research on stem cells that came from embryos left over from in vitro fertilization (IVF) fertility treatments. Although NBAC's proposals never became legislation, the report helped shape public, private, and international discourse on stem cell research policy.

Created2014-04-01
Description
Wound healing is a complex tissue response that requires a coordinated interplay of multiple cells in orchestrated biological processes to restore the skin's barrier function post-injury. Proteolytic enzymes, in particular matrix metalloproteinases (MMPs), contribute to all phases of the healing process by regulating immune cell influx, clearing out the extracellular

Wound healing is a complex tissue response that requires a coordinated interplay of multiple cells in orchestrated biological processes to restore the skin's barrier function post-injury. Proteolytic enzymes, in particular matrix metalloproteinases (MMPs), contribute to all phases of the healing process by regulating immune cell influx, clearing out the extracellular matrix (ECM), and remodeling scar tissue. As a result of these various functions in the healing of skin wounds, uncontrolled activities of MMPs are associated with impaired wound healing. The MMP gene family consists of a highly conserved set of genes. Deleterious mutations in MMP genes cause developmental phenotypes that affect the heart, skeleton, and immune system response. The availability of contiguous draft genomes of non-model organisms enables the study of gene families through analysis of synteny and sequence identity. My project is aimed at conducting a comparative genomic analysis of the MMP gene family from the genomes of 29 tetrapod species—with an emphasis on reptiles. Results regarding the similarities and differences among MMP protein sequences can be further investigated to shed light on the causes which give rise to various adaptive mutations for specific species groups.
ContributorsYu, Alexander (Author) / Kusumi, Kenro (Thesis director) / Dolby, Greer (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2022-12
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Description

Structural Equation Modeling (SEM) is a multivariate analysis methodology that could potentially be utilized to examine the barrier effect that river systems have on genetic differentiation. In this project, river systems are split into the variables of Daily Average Discharge, Average River Width, and Seasonality measurements and regressed onto the

Structural Equation Modeling (SEM) is a multivariate analysis methodology that could potentially be utilized to examine the barrier effect that river systems have on genetic differentiation. In this project, river systems are split into the variables of Daily Average Discharge, Average River Width, and Seasonality measurements and regressed onto the genetic differentiation, measured as Fst. This data was collected from the USGS database (U.S. Geological Survey, 2020), sequencing files from differing literature, or Google Earth measurements. Different Structural Equation Modeling models are used to model different system structures as well as compare it to more traditional methodologies like Generalized Linear Modeling and Generalized Linear Mixed Modeling. Ultimately results were limited by the small sample size, however, interesting patterns still emerged from the models. The SE models indicate that Discharge plays a primary role in the genetic differentiation of adjacent river populations. In addition to this, the results demonstrate how quantification of indirect effects, particularly those relating to discharge, give more informative interpretations than traditional multivariate statistics alone. These findings prompt further investigations into this potential methodology.

ContributorsMaag, Garett (Author) / Dolby, Greer A. (Thesis advisor) / Kusumi, Kenro (Thesis advisor) / Stokes, Maya F. (Committee member) / Barly, Anthony (Committee member) / Arizona State University (Publisher)
Created2023
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Description
The most abundantly studied societies, with the exception of humans, are those of the eusocial insects, which include all ants. Eusocial insect societies are typically composed of many dozens to millions of individuals, referred to as nestmates, which require some form of communication to maintain colony cohesion and coordinate the

The most abundantly studied societies, with the exception of humans, are those of the eusocial insects, which include all ants. Eusocial insect societies are typically composed of many dozens to millions of individuals, referred to as nestmates, which require some form of communication to maintain colony cohesion and coordinate the activities within them. Nestmate recognition is the process of distinguishing between nestmates and non-nestmates, and embodies the first line of defense for social insect colonies. In ants, nestmate recognition is widely thought to occur through olfactory cues found on the exterior surfaces of individuals. These cues, called cuticular hydrocarbons (CHCs), comprise the overwhelming majority of ant nestmate profiles and help maintain colony identity. In this dissertation, I investigate how nestmate recognition is influenced by evolutionary, ontogenetic, and environmental factors. First, I contributed to the sequencing and description of three ant genomes including the red harvester ant, Pogonomyrmex barbatus, presented in detail here. Next, I studied how variation in nestmate cues may be shaped through evolution by comparatively studying a family of genes involved in fatty acid and hydrocarbon biosynthesis, i.e., the acyl-CoA desaturases, across seven ant species in comparison with other social and solitary insects. Then, I tested how genetic, developmental, and social factors influence CHC profile variation in P. barbatus, through a three-part study. (1) I conducted a descriptive, correlative study of desaturase gene expression and CHC variation in P. barbatus workers and queens; (2) I explored how larger-scale genetic variation in the P. barbatus species complex influences CHC variation across two genetically isolated lineages (J1/J2 genetic caste determining lineages); and (3) I experimentally examined how CHC development is influenced by an individual’s social environment. In the final part of my work, I resolved discrepancies between previous findings of nestmate recognition behavior in P. barbatus by studying how factors of territorial experience, i.e., spatiotemporal relationships, affect aggressive behaviors among red harvester ant colonies. Through this research, I was able to identify promising methodological approaches and candidate genes, which both broadens our understanding of P. barbatus nestmate recognition systems and supports future functional genetic studies of CHCs in ants.
ContributorsCash, Elizabeth I (Author) / Gadau, Jürgen (Thesis advisor) / Liebig, Jürgen (Thesis advisor) / Fewell, Jennifer (Committee member) / Hölldobler, Berthold (Committee member) / Kusumi, Kenro (Committee member) / Arizona State University (Publisher)
Created2016