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- All Subjects: Genomics
- All Subjects: Green anole--Evolution.
- Genre: Academic theses
- Status: Published
Description
The purpose of this dissertation was 1) to develop noninvasive strategies to assess skeletal muscle size, architecture, and composition in young and old adults (study #1) and 2) evaluate the impact of chemotherapeutic treatment on skeletal muscle satellite cells and capillaries (study #2). For study #1 ultrasound images were obtained from the quadriceps muscles of young (8 m, 8 f) and older (7 m, 5 f) participants on two occasions, separated by 5-15 days. Images were collected while the participants were both standing and supine, and were analyzed for muscle thickness, pennation angle, and echogenicity. In addition, test-retest reliability and ICCs were evaluated for each posture and when imaging sites remained marked or were re-measured from visit #1 to visit #2. Generally, in both younger and older adults muscle thickness was greater and echogenicity was lower in the anterior quadriceps when images were collected standing versus supine. Maintaining the imaging site between visits did not influence test re-test reliability for either age group. Older adults exhibited smaller muscle thickness, lower pennation angle and increased echogenicity. Further, variability for the use of ultrasound to determine muscle thickness and pennation angle was greater in older versus younger adults. Findings from study #1 highlight several methodological considerations for US-based assessment of skeletal muscle characteristics that should be considered for improving reproducibility and generalizability of US to assess skeletal muscle characteristics and function across the aging spectrum. This is particularly relevant given the emerging use of ultrasound to assess skeletal muscle characteristics in healthy and clinical populations. In the second study, ovariectomized female Sprague-Dawley rats were randomized to receive three bi-weekly intraperitoneal injections of the chemotherapeutic drug, Doxorubicin (DOX) (4mg/kg; cumulative dose 12mg/kg) or vehicle (VEH; saline). Animals were euthanized 5d following the last injection, and the soleus (SOL) and extensor digitorum longus (EDL) muscles were dissected and prepared for immunohistochemical and RT-qPCR analyses. Relative to VEH, cross-sectional area (CSA) of the SOL and EDL muscle fibers were 26% and 33% smaller, respectively, in DOX animals (P<0.05). In the SOL satellite cell and capillary densities were 39% and 35% lower, respectively, in DOX animals (P<0.05), whereas in the EDL satellite cell and capillary densities were unaffected by DOX administration (P>0.05). In the SOL MYF5 mRNA expression was increased in DOX animals (P<0.05), while in the EDL MGF mRNA expression was reduced in DOX animals (P<0.05). Chronic DOX administration is associated with reduced fiber size in multiple skeletal muscles, however DOX appears to impact the satellite cell and capillary densities in a muscle-specific manner. These findings from study #2 highlight that therapeutic targets to protect skeletal muscle from DOX may vary across muscles. Collectively, these findings 1) improve the ability to examine muscle size and function in younger and older adults, and 2) identify promising therapeutic targets to protect skeletal muscle from the harmful effects of chemotherapy treatment.
ContributorsD'Lugos, Andrew (Author) / Dickinson, Jared M (Thesis advisor) / Buman, Matthew P (Committee member) / Gaesser, Glenn A (Committee member) / Huentelman, Matthew J (Committee member) / Katsanos, Christos S (Committee member) / Arizona State University (Publisher)
Created2018
Description
In species with highly heteromorphic sex chromosomes, the degradation of one of the sex chromosomes can result in unequal gene expression between the sexes (e.g., between XX females and XY males) and between the sex chromosomes and the autosomes. Dosage compensation is a process whereby genes on the sex chromosomes achieve equal gene expression which prevents deleterious side effects from having too much or too little expression of genes on sex chromsomes. The green anole is part of a group of species that recently underwent an adaptive radiation. The green anole has XX/XY sex determination, but the content of the X chromosome and its evolution have not been described. Given its status as a model species, better understanding the green anole genome could reveal insights into other species. Genomic analyses are crucial for a comprehensive picture of sex chromosome differentiation and dosage compensation, in addition to understanding speciation.
In order to address this, multiple comparative genomics and bioinformatics analyses were conducted to elucidate patterns of evolution in the green anole and across multiple anole species. Comparative genomics analyses were used to infer additional X-linked loci in the green anole, RNAseq data from male and female samples were anayzed to quantify patterns of sex-biased gene expression across the genome, and the extent of dosage compensation on the anole X chromosome was characterized, providing evidence that the sex chromosomes in the green anole are dosage compensated.
In addition, X-linked genes have a lower ratio of nonsynonymous to synonymous substitution rates than the autosomes when compared to other Anolis species, and pairwise rates of evolution in genes across the anole genome were analyzed. To conduct this analysis a new pipeline was created for filtering alignments and performing batch calculations for whole genome coding sequences. This pipeline has been made publicly available.
In order to address this, multiple comparative genomics and bioinformatics analyses were conducted to elucidate patterns of evolution in the green anole and across multiple anole species. Comparative genomics analyses were used to infer additional X-linked loci in the green anole, RNAseq data from male and female samples were anayzed to quantify patterns of sex-biased gene expression across the genome, and the extent of dosage compensation on the anole X chromosome was characterized, providing evidence that the sex chromosomes in the green anole are dosage compensated.
In addition, X-linked genes have a lower ratio of nonsynonymous to synonymous substitution rates than the autosomes when compared to other Anolis species, and pairwise rates of evolution in genes across the anole genome were analyzed. To conduct this analysis a new pipeline was created for filtering alignments and performing batch calculations for whole genome coding sequences. This pipeline has been made publicly available.
ContributorsRupp, Shawn Michael (Author) / Wilson Sayres, Melissa A (Thesis advisor) / Kusumi, Kenro (Committee member) / DeNardo, Dale (Committee member) / Arizona State University (Publisher)
Created2016
Description
Rapid advancements in genomic technologies have increased our understanding of rare human disease. Generation of multiple types of biological data including genetic variation from genome or exome, expression from transcriptome, methylation patterns from epigenome, protein complexity from proteome and metabolite information from metabolome is feasible. "Omics" tools provide comprehensive view into biological mechanisms that impact disease trait and risk. In spite of available data types and ability to collect them simultaneously from patients, researchers still rely on their independent analysis. Combining information from multiple biological data can reduce missing information, increase confidence in single data findings, and provide a more complete view of genotype-phenotype correlations. Although rare disease genetics has been greatly improved by exome sequencing, a substantial portion of clinical patients remain undiagnosed. Multiple frameworks for integrative analysis of genomic and transcriptomic data are presented with focus on identifying functional genetic variations in patients with undiagnosed, rare childhood conditions. Direct quantitation of X inactivation ratio was developed from genomic and transcriptomic data using allele specific expression and segregation analysis to determine magnitude and inheritance mode of X inactivation. This approach was applied in two families revealing non-random X inactivation in female patients. Expression based analysis of X inactivation showed high correlation with standard clinical assay. These findings improved understanding of molecular mechanisms underlying X-linked disorders. In addition multivariate outlier analysis of gene and exon level data from RNA-seq using Mahalanobis distance, and its integration of distance scores with genomic data found genotype-phenotype correlations in variant prioritization process in 25 families. Mahalanobis distance scores revealed variants with large transcriptional impact in patients. In this dataset, frameshift variants were more likely result in outlier expression signatures than other types of functional variants. Integration of outlier estimates with genetic variants corroborated previously identified, presumed causal variants and highlighted new candidate in previously un-diagnosed case. Integrative genomic approaches in easily attainable tissue will facilitate the search for biomarkers that impact disease trait, uncover pharmacogenomics targets, provide novel insight into molecular underpinnings of un-characterized conditions, and help improve analytical approaches that use large datasets.
ContributorsSzelinger, Szabolcs (Author) / Craig, David W. (Thesis advisor) / Kusumi, Kenro (Thesis advisor) / Narayan, Vinodh (Committee member) / Rosenberg, Michael S. (Committee member) / Huentelman, Matthew J (Committee member) / Arizona State University (Publisher)
Created2015