Browsing by Author "Marrs, Kathleen"

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    Dyrk1a Dynamics: The Influence of Gene Copy Number on Neurodevelopment in the Ts65dn Mouse Model of Down Syndrome
    (2024-05) Hawley, Laura E.; Roper, Randall; Belecky-Adams, Teri; Cummins, Theodore; Goodlett, Charles; Hardy, Tabitha; Marrs, Kathleen
    Down syndrome (DS) arises from the triplication of human chromosome 21 (Hsa21), leading to a spectrum of phenotypes characterized by neurodevelopmental and cognitive abnormalities. The Ts65Dn mouse model emulates DS by harboring three copies of genes found on Hsa21 resulting in trisomy 21 (Ts21)- like traits, including disruptions in neuronal pathways, delays in sensorimotor and behavior milestones, and deficits in learning and memory tasks. There is no cure for DS and available therapies primarily address symptoms stemming from Ts21-associated phenotypes. DYRK1A, a gene triplicated in Ts21, has a pivotal role in pathways of neurodevelopment and has been a focus of inhibition treatment research aimed at preempting abnormal brain phenotypes. This study aimed to find a point of substantial Dyrk1a expression dysregulation during a period of critical neonatal neurodevelopment and employ targeted pharmacological and genetic knockdown methods to alleviate the presence or severity of characteristically abnormal brain and behavior phenotypes. The hypothesis of this study was that administering a targeted intervention prior to a point of known overexpression in trisomic pups would ameliorate molecular, sensorimotor, and neurobehavioral deficits, redirecting growth trajectories of Ts65Dn neonatal pups towards more neurotypical outcomes. To test this hypothesis, the spatiotemporal pattern of DYRK1A expression was quantified during the first three weeks of neonatal development across the hippocampus, cerebral cortex, and cerebellum of the Ts65Dn mouse model and found to fluctuate according to the genotype, age, sex, and brain region of the subject. Dyrk1a protein and mRNA expression levels were delineated in trisomic animals by age, exploring the correlation between expression and age, sex, genotype, and brain region. Next a constitutive Dyrk1a knockdown model was integrated with the Ts65Dn model to investigate the impact of gene copy number reduction on protein and mRNA expression levels during phases of known DYRK1A dysregulation. On postnatal day 6, protein expression was rescued in all three brain regions of male animals but was rescued only in the cerebellum of females. There were no significant differences in mRNA transcript levels in either sex at this age. Finally, genetic elements were introduced into the Ts65Dn model to facilitate a spatiotemporally controlled functional reduction of Dyrk1a and discern how the timing of gene copy number reduction affects molecular and neurobehavioral development in a trisomic system. Results from these studies suggest that only functionally reducing Dyrk1a gene copy number on the day of birth is not sufficient to rescue the majority of deficits and delays present in the Ts65Dn mouse model of DS. These findings significantly enhance the understanding of trisomic Dyrk1a expression dynamics during neonatal development and shed light on tailored therapeutic approaches to modulate intrinsic DS characteristics based on age, sex, and phenotypic considerations.
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    An Exploration of Irish Surname History through Patrilineal Genetics
    (2018-12) Farmer, Stephanie Kay; Walsh, Susan; Marrs, Kathleen; Balakrishnan, Lata
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    Quantifying Dyrk1a During Perinatal Development in the Hippocampus, Cerebral Cortex and Cerebellum of the Ts65Dn
    (2020-05) Hawley, Laura Elizabeth; Roper, Randall J.; Goodlett, Charles R.; Belecky-Adams, Teri; Marrs, Kathleen; Hardy, Tabitha
    The relationship between gene copy number and protein expression levels has not thoroughly been examined in humans or mouse models of Down syndrome (DS) in relationship to developmental changes in the trisomic brain. Found on human chromosome 21 (Hsa21) and triplicated in DS, Dual-specificity tyrosine-phosphorylated regulated kinase 1A (DYRK1A) has been linked in DS to neurological deficits by restricting cell growth and proliferation. Little information exists regarding DYRK1A during perinatal development and how its expression may lead to cognitive deficits, and none exists that explores the gene-to-protein relationship during these critical time periods. This study aims to 1) Quantify variable DYRK1A expression across development as a function of age, sex, and brain region in trisomic Ts65Dn mice compared to euploid counterparts and 2) establish that the spatiotemporal pattern of developmental DYRK1A in the brain is not influenced solely by gene copy number, and that reduction of Dyrk1a in euploid and trisomic mice does not result in a corresponding global reduction of DYRK1A expression. DYRK1A was quantified in three areas of the postnatal brain at seven ages using the Ts65Dn mouse, the most studied model of DS, and found that trisomic expression is significantly increased on postnatal day ([P]6), declining by the third week to near euploid levels. We also uncovered a sexual dimorphic expression of DYRK1A when comparing animals of different sexes within the same genotype. Data from Dyrk1a knockdown mice indicated that reducing only Dyrk1a in euploid and in otherwise trisomic animals yields highly variable levels of DYRK1A, dependent on sex and tissue type, supporting the non-intuitive relationship between gene dosage and protein expression. These data emphasize the need to understand the age-dependent regulation of antecedent conditions that are causing changes in Dyrk1a expression in the brain.
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    Quantitatively Assessing the Genetics of Hair Color in Addition to Identifying Regulatory Elements Impacting Body-Mass Index in the FTO Gene
    (2020-08) Hopkins, Racquel; Walsh, Susan; Berbari, Nicolas; Marrs, Kathleen
    Obesity is a medical condition whose rates have seen a rise in both the United States and worldwide in recent decades. Numerous studies have been done to understand obesity, and through the use of GWAS researchers have been able to find multiple genetic factors that can contribute to obesity in mammals. One proposed cause of obesity are genetic impacts on cilia formation in the CNS, which causes downstream effects on food intake and energy expenditure, causing obesity via overeating and decreased activity. In the first half of this thesis, I describe a study, in collaboration with the Berbari Lab at IUPUI, that explored the human chromosome 16:53801550-53808600 (GRCh37/hg19), an intron of the FTO alpha-ketoglutarate Dependent Dioxygenase (FTO) gene for transcriptional regulators that impact BMI and obesity. First, using control DNA, PCR, and gel-electrophoresis, we created an assay for 44 primer sets (forward and reverse) covering the genomic region. After optimizing the assay, we then selected 111 human DNA samples across three weight groups (underweight, normal weight, and obese) to sequence using the assay. The samples were selected from subjects enrolled in the Walsh Lab FDP study. Sequencing was completed using the Illumina MiSeq System, and sequenced results were viewed using the Integrative Genomics Viewer (IGV) program. Variants that showed in the results were analyzed across and within the weight groups, and their locations were researched for previously known BMI or enhancer activity using online genome browsers Ensembl and UCSC Genome Browser. The results of this study revealed two SNPs, rs8055197 and rs11642015, that provided the best correlation with the weight categories among the samples. These results were consistent with literature that previously linked these single-nucleotide polymorphisms (SNPs) to obesity, particularly in relation to genes that are regulated by FTO (CUX1, POMC, and IRX3/5). Both SNPs lie within areas that show high enhancer activity in neural crest cells, important cells for cilia formation. Although there were SNPs in high LD within both regions, these two SNPs were chosen due to their homologous variant locations within the mouse genome (rs8055197 - GRCm38/mm10 8:91376305; rs11642015 - GRCm38/mm10 8:91375651), which provides a means of testing this obesity correlation, with a proposed enhancer relationship through FTO, in mouse models. In the second half of this thesis, I explored new methods for quantitatively defining natural hair color categories, and attempted to find novel SNPs impacting hair color in a GWAS using the quantitative values as phenotypes. In previous publications, the development and validation of the HIrisPlex-S Prediction Tool for hair prediction was made using categorical hair colors, which were defined and classified by individual researchers or lab personnel. Using spectrophotometer measurements and HSV color values, we used a machine-learning tool to objectively classify sample hair photos into natural hair color classes. We then used this quantitative data as the input phenotype for a GWAS, using both linear regression and linear mixed model regression, to search for new genetic associations with these objectively defined hair color classes. Lastly, we also measured correlations between these hair color phenotypes and a SNP array consisting of all currently known pigment SNPs cited in recent literature. The results of this study showed that quantitative values can be used as a means of classifying human hair colors. Both models used in the GWAS highlighted previously known SNPs that contributed to quantitative hair color. By utilizing the linear mixed model approach which has the ability to generate more power due to the normalization of hidden population structure, there was one near genome-wide significant SNP found that is currently not linked with hair color, rs2037697 (IQUB), which showed strong associations with light brown hair (p-value = 1.83192E-07), however this would need to be confirmed with increased numbers to validate its association. The results of the correlation analysis showed that SNPs cited as having impacts on pigmentation (eye, skin, and hair) also show strong associations with these objectively defined quantitative hair color classes and these rankings may prove very useful as the field moves towards quantitative hair color prediction.
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    The role of Stat3 in skeletal development
    (2017-06-30) Davidson, Rebecca; Li, Jiliang; Yokota, Hiroki; Marrs, Kathleen
    Many factors are present in the development of skeletal tissue. Some factors lead to an increase in bone mass while some lead to a decrease. One factor that is known to have an influence on skeletal development is Signal Transducer and Activator of Transcription 3 (Stat3). This knowledge arose because of a mutation in the Stat3 gene in humans causing a disease called Hyper-IgE Syndrome. This mutation leads to a variety of issues, including decreased bone mass. Because of this, our lab has sought to study Stat3 in its relation to bone. Many studies have already been conducted that discern how Stat3 influences skeletal biology by observing its role in osteoclasts, osteoblasts, and other bone cells. Its role is still unclear, and many studies have provided seemingly contradictory results in how it works on bone tissue. Our lab set up several different studies in order to further elucidate what role Stat3 plays in skeletal development by looking at its effects on osteoblasts and osteoclasts, the bone-forming and bone-destroying cells of the body, respectively. We conditionally knocked out Stat3 in the osteoblasts of mice and compared several different bone parameters to their wild type counterparts at 8 weeks of age. Differences were noted in bone phenotype, including decreased femur length, weight, bone mineral density, and bone mineral content in the cKO compared to their WT counterparts. While no significant difference in trabecular integrity was noted, several differences were observed in cortical bone. These differences indicate that Stat3 has a positive role in osteoblast differentiation, leading to an overall positive effect on bone mass. To observe the role of Stat3 in osteoclasts, in vitro experiments were set up in which pre-osteoclast RAW 264.7 cells were manipulated with Stat3 siRNA or a Stat3 overexpression construct and RANKL to induce differentiation. Using qPCR and western blot assays, it was determined that when Stat3 is knocked down, several important genes in osteoclastogenesis and osteoclast function are more highly expressed than in the control groups. When Stat3 is overexpressed, a similar pattern is observed where these same genes are downregulated in the presence of higher Stat3 levels. These results indicate that Stat3 has an overall inhibitory effect on osteoclastogenesis and osteoclast function, indicating it has a positive effect on bone mass. Future studies could be performed to further elucidate the effects of Stat3 on skeletal development. Isolating the osteoblasts from cKO and WT mice and performing qPCR and western blot assays could be useful in finding out how Stat3 is influencing these cells. Further studies could also be done on the RAW 264.7 cells to find where Stat3 is interacting with the RANKL pathway. A resorption assay could be done with these cells to better understand how function might be influenced by Stat3.
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    Role of Stenotrophomonas Maltophilia Pili Iin Biofilm And Virulence
    (2024-08) Bhaumik, Radhika; Marrs, Kathleen; Anderson, Gregory; Berbari, Nicolas; Marrs, James A.; Gregory, Richard L.
    Stenotrophomonas maltophilia is an emerging multidrug-resistant, Gram-negative opportunistic pathogen. It causes many hospital-acquired infections such as sepsis, endocarditis, meningitis, and catheter-related urinary tract infections. It also affects individuals with cystic fibrosis, exacerbating their lung condition. S. maltophilia often causes pathogenesis through the formation of biofilms. However, the molecular mechanisms S. maltophilia uses to carry out these pathogenic steps are unclear. The SMF-1 chaperone/usher pilus has been thought to mediate S. maltophilia attachment. To confirm this role, we created an isogenic deletion of the smf-1 pilin gene and observed a defect in biofilm compared to wild type. We also discovered 2 additional chaperone/usher pilus operons, mutation of which also caused attenuation in biofilm levels. Analysis of S. maltophilia clinical strains and S. maltophilia complete genomes listed in NCBI showed that these three pili are prevalent and highly conserved, suggesting a vital role in infection. Intriguingly, through TEM studies, we found that the mutation of one pilus is not phenotypically compensated by another. Infection of Galleria mellonella larvae revealed increased virulence of the pilus mutants. Additionally, we also demonstrated a relationship between pilus and flagella contributing to the overall biofilm development of S. maltophilia. Understanding their activity may help identify therapeutic targets for this pathogen.