Matching Items (73)
Description
Duchenne Muscular Dystrophy (DMD) is an X-linked recessive disease characterized by progressive muscle loss and weakness. This disease arises from a mutation that occurs on a gene that encodes for dystrophin, which results in observable muscle death and inflammation; however, the genetic changes that result from dystrophin's dysfunctionality remain unknown. Current DMD research uses mdx mice as a model, and while very useful, does not allow the study of cell-autonomous transcriptome changes during the progression of DMD due to the strong inflammatory response, perhaps hiding important therapeutic targets. C. elegans, which has a very weak inflammatory response compared to mdx mice and humans, has been used in the past to study DMD with some success. The worm ortholog of the dystrophin gene has been identified as dys-1 since its mutation phenocopies the progression of the disease and a portion of the human dystrophin gene alleviates symptoms. Importantly, the extracted RNA transcriptome from dys-1 worms showed significant change in gene expression, which needs to be further investigated with the development of a more robust model. Our lab previously published a method to isolate high-quality muscle-specific RNA from worms, which could be used to study such changes at higher resolution. We crossed the dys-1 worms with our muscle-specific strain and demonstrated that the chimeric strain exhibits similar behavioral symptoms as DMD patients as characterized by a shortened lifespan, difficulty in movement, and a decrease in speed. The presence of dys-1 and other members of the dystrophin complex in the body muscle were supported by the development of a resulting phenotype due to RNAi knockdown of each component in the body muscle; however, further experimentation is needed to reinforce this conclusion. Thus, the constructed chimeric C. elegans strain possesses unique characteristics that will allow the study of genetic changes, such as transcriptome rearrangements and dysregulation of miRNA, and how they affect the progression of DMD.
ContributorsNguyen, Thuy-Duyen Cao (Author) / Mangone, Marco (Thesis director) / Newbern, Jason (Committee member) / Duchaine, Thomas (Committee member) / School of Social Transformation (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Alternative polyadenylation (APA) is the biological mechanism in which the same gene can have multiple 3'untranslated region (3'UTR) isoforms due to the presence of multiple polyadenylation signal (PAS) elements within the pre mRNAs. Because APA produces mRNA transcripts that have different 3'UTR isoforms, certain transcripts may be subject to post-transcriptional regulation by regulatory non-coding RNAs, such as microRNAs or RNA binding proteins defects of which have been implicated in diseases such as cancer. Despite the increasing level of information, functional understanding of the molecular mechanisms involved in transcription is still poorly understood, nor is it clear why APA is necessary at a cell or tissue-specific level. To address these questions I wanted to develop a set of sensor strain plasmids capable of detecting cleavage and polyadenylation in vivo, inject the complete sensor strain plasmid into C. elegans and prepare stable transgenic lines, and perform proof-of-principle RNAi feeding experiments targeting genes associated with the cleavage and polyadenylation complex machinery. I demonstrated that it was possible to create a plasmid capable of detecting cleavage and polyadenylation in C. elegans; however, issues arose during the RNAi assays indicating the sensor strain plasmid was not sensitive enough to the RNAi to effectively detect in the worms. Once the problems involved with sensitivity and variability in the RNAi effects are resolved, the plasmid would be able to better address questions regarding the functional understanding of molecular mechanisms involved in transcription termination.
ContributorsWilky, Henry Patrick (Author) / Mangone, Marco (Thesis director) / Newbern, Jason (Committee member) / Blazie, Stephen (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Research implemented by Luthar and colleagues over the past decade has revealed serious levels of maladjustment among youth growing up in affluent and upwardly mobile communities across the country. Contrary to what was previously believed, these youth often fare much worse on measures of both internalizing and externalizing problems when compared to their inner-city counterparts (Luthar, Barkin & Crossman, 2013). In an attempt to differentiate affluent youth with levels of maladjustment from their peers who are more well adjusted, the present study examines the relationship between internalizing problems and goal-setting, with analyses separated by gender. In a culture where there is such a focus on extrinsic goals, is it possible that goal-setting influences feelings of anxiety and depression? Multiple regression analyses were conducted with two goal-setting measures predicting to various internalizing dimensions of the Youth Self Report (Achenbach & Rescorla). The sample included 252 senior year high school students participating in the New England Study on Suburban Youth (NESSY). Statistically significant results supported our hypothesis that a higher ratio of extrinsic goals would predict to internalizing problems, for both males and females. Future research that implements an experimental design would be beneficial in understanding more fully whether changing one's goals and values decreases internalizing problems.
ContributorsLauer, Emma Miller (Author) / Luthar, Suniya (Thesis director) / Knight, George (Committee member) / Meier, Madeline (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor) / Department of English (Contributor)
Created2014-12
Description
Neurological manifestations may be more prominent and have a larger role in ankylosing spondylitis than previously thought. Ankylosing Spondylitis is a rheumatic disease primarily identified by its autoinflammatory characteristics and is highly associated with the HLA-B27 gene. While it’s cause is not yet fully understood and it’s symptoms widely vary, neurological impairment is not uncommon. The neurological manifestations of Ankylosing Spondylitis include but are not limited to pain sensitization, altered brain phenotype, and disrupted cardiac conduction. Central and peripheral nervous system involvement may be more significant than previously thought and have the potential to cause demyelinating diseases, spinal cord, and nerve root injuries. Altered connectivity throughout various regions within the brain further exemplify the need for a better understanding of the disease and better treatment development. Higher instances of depression and dementia were also reported and coincide with not only a less active lifestyle, but altered brain activity. Studies on cardiac conduction and arrhythmias in AS patients revealed parasympathetic and sympathetic nervous system dysregulation. These studies have explored the possibility of new targets for treatment involving cardiac mechanisms. Treatments for diseases of a similar suspected pathology, new prospective targets for therapy, and a more thorough understanding of current treatments for the disease may be the key in providing more substantial relief. By further investigation in the role of the nervous system in Ankylosing Spondylitis, the disease may become more manageable for patients and greatly increase quality of life in the future.
ContributorsHill, Jordan (Author) / Newbern, Jason (Thesis director) / Anderson, Karen (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
This is a descriptive study looking at the management of patients with hypoplastic aortic arch and interrupted aortic arch, which are obstructive anomalies of the aortic arch. I will specifically be looking at patient specific factors such as chromosomal abnormalities and other comorbidities associated with aortic arch conditions as well as outcomes following aortic arch repairs.
ContributorsMenon, Tushar (Author) / Newbern, Jason (Thesis director) / Nigro, John (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Traumatic brain injury (TBI) consists of the primary mechanical forces to the head followed by secondary inflammatory cascades. This inflammatory cascade consists of neuroinflammation characterized by microglial activation as the first line of defense. Another component of secondary inflammation comprises of activation of peripheral immune cells that can infiltrate the compromised blood brain barrier and susceptible organs such as the lungs. Acute inflammatory processes in the lungs include a disruption of the epithelial barriers allowing infiltration of neutrophils, and edema build up in the alveoli. This is known as acute lung injury (ALI) and it dampens respiratory function in approximately 20-25% of TBI patients necessitating an intervention. Remote ischemic conditioning (RIC) is an intervention consisting of repeated intervals of cessation and reperfusion of blood flow to a distal limb and has treated ALI, myocardial infarction, and neurological injury. TBI was hypothesized to induce ALI through degradation of alveolar-capillary membrane and infiltration of peripheral leukocytes. Furthermore, RIC was hypothesized to protect the integrity of the alveolar-capillary membrane, reduce infiltration of peripheral immune cells, and reduce microglial activation in the brain through myokine recruitment. Male CD1 mice were subject to either midline fluid percussion or sham injury and further randomized into 4 groups: sham, sham RIC, TBI, TBI RIC. RIC was administered on proximal thigh for 4x5 minutes, with 5-minute reperfusion one hour prior to TBI. One-hour post-injury, brain, lung, BAL fluid, and blood were collected. Lung histopathology showed RIC reduced hydrostatic edema in the alveoli by protecting the alveolar capillary membrane. BAL findings revealed TBI mice had increased neutrophil counts, RIC lowered neutrophil counts. In the brain, RIC increased cortex microglial endpoints were observed with no other significant differences in microglial morphology as well as plasma myokine levels across all sham, sham RIC, TBI, and TBI RIC animals. While underlying mechanisms still have to be further studied, this current study provides evidence that RIC can be used as a therapeutic intervention to ameliorate TBI-induce ALI.
ContributorsChristie, Immaculate (Author) / Newbern, Jason (Thesis director) / Lifshitz, Jonathan (Committee member) / Saber, Maha (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Immediate early genes (IEGs) are rapidly activated in response to an environmental stimulus, and most code for transcription factors that mediate processes of synaptic plasticity, learning, and memory. EGR3, an immediate early gene transcription factor, is a mediator of biological processes that are disrupted in patients with schizophrenia (SCZ). A microarray experiment conducted by our lab revealed that Egr3 also regulates genes involved in DNA damage response. A recent study revealed that physiological neuronal activity results in the formation of DNA double-stranded breaks (DSBs) in the promoters of IEGs. Additionally, they showed that these DSBs are essential for inducing the expression of IEGs, and failure to repair these DSBs results in the persistent expression of IEGs. We hypothesize that Egr3 plays a role in repairing activity- induced DNA DSBs, and mice lacking Egr3 should have an abnormal accumulation of these DSBs. Before proceeding with that experiment, we conducted a preliminary investigation to determine if electroconvulsive stimulation (ECS) is a reliable method of inducing activity- dependent DNA damage, and to measure this DNA damage in three subregions of the hippocampus: CA1, CA3, and dentate gyrus (DG). We asked the question, are levels of DNA DSBs different between these hippocampal subregions in animals at baseline and following electroconvulsive stimulation (ECS)? To answer this question, we quantified γ-H2AX, a biomarker of DNA DSBs, in the hippocampal subregions of wildtype mice. Due to technical errors and small sample size, we were unable to substantiate our preliminary findings. Despite these shortcomings, our experimental design can be modified in future studies that investigate the role of Egr3 in activity-induced DNA damage repair.
ContributorsKhoshaba, Rami Samuel (Author) / Newbern, Jason (Thesis director) / Gallitano, Amelia (Committee member) / Marballi, Ketan (Committee member) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Damage to DNA can affect the genes it encodes; if this damage is not repaired, abnormal proteins may be produced and cellular functions may be disturbed. DNA damage has been implicated in the initiation and progression of a variety of diseases. Conversely, DNA damage has also been discovered to contribute to beneficial biological processes. Madabhushi and colleagues (2015) determined that activity-dependent DNA double strand breaks (DSBs) in the promoter region of immediate early genes (IEGs) induced their expression. EGR3 is an IEG transcription factor which regulates the expression of growth factors and synaptic plasticity-associated genes. In a previously conducted microarray experiment, it was revealed that EGR3 regulates the expression of genes associated with DNA repair such as Cenpa and Nr4a2. These findings inspired us to investigate if EGR3 affects DNA repair in vivo. Before conducting this experiment, we sought to standardize and optimize a method of inducing DNA damage in the hippocampus. Electroconvulsive stimulation (ECS) is utilized to induce neuronal activity. Since neuronal activity leads to the formation of DNA DSBs, we theorized that ECS could be used to induce DNA DSBs in the hippocampus. We predicted that mice that receive ECS would have more DNA DSBs than those that receive the sham treatment. Gamma H2AX, a biomarker for DNA damage, was utilized to quantify DNA DSBs. Gamma H2AX expression in the dentate gyrus, CA1 and CA3 regions of the hippocampus was compared between mice that received the sham treatment and mice that received ECS. Mice that received ECS were sacrificed either 1 or 2 hours post-administration, constituting treatment conditions of 1 hr post-ECS and 2 hrs post-ECS. Our results suggest that ECS has a statistically significant effect exclusively in the CA1 region of the hippocampus. However, our analyses may have been limited due to sample size. A power analysis was conducted, and the results suggest that a sample size of n=4 mice will be sufficient to detect significant differences across treatments in all three regions of the hippocampus. Ultimately, future studies with an increased sample size will need to be conducted to conclusively assess the use of ECS to induce DNA damage within the hippocampus.
ContributorsAden, Aisha Abubakar (Author) / Newbern, Jason (Thesis director) / Gallitano, Amelia (Thesis director) / Marballi, Ketan (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Traumatic brain injury (TBI) is a major cause of disability, with approximately 1.7 million incidents reported annually. Following a TBI, patients are likely to sustain sensorimotor and cognitive impairments and are at an increased risk of developing neurodegenerative diseases later in life. Despite this, robust therapies that treat TBI neuropathology are not available in the clinic. One emerging therapeutic approach is to target epigenetic mediators that modulate a variety of molecular regulatory events acutely following injury. Specifically, previous studies demonstrated that histone deacetylase inhibitor (HDACi) administration following TBI reduced inflammation, enhanced functional outcomes, and was neuroprotective. Here, we evaluated a novel quisinostat-loaded PLA-PEG nanoparticle (QNP) therapy in treating TBI as modeled by a controlled cortical impact. We evaluated initial pharmacodynamics within the injured cortex via histone acetylation levels following QNP treatment. We observed that QNP administration acutely following injury increased histone acetylation specifically within the injury penumbra, as detected by Western blot analysis. Given this effect, we evaluated QNP therapeutic efficacy. We observed that QNP treatment dampened motor deficits as measured by increased rotarod latency to fall relative to blank nanoparticle- and saline-treated controls. Additionally, open field results show that QNP treatment altered locomotion following injury. These results suggest that HDACi therapies are a beneficial therapeutic strategy following neural injury and demonstrate the utility for nanoparticle formulations as a mode for HDACi delivery following TBI.
ContributorsMousa, Gergey (Author) / Stabenfeldt, Sarah (Thesis director) / Newbern, Jason (Committee member) / Sirianni, Rachael (Committee member) / School of Life Sciences (Contributor) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The highly conserved Notch signaling pathway regulates cell-cell communication pathways, cell fate, cell determination, cell death, embryonic development, and adult tissue pathways in metazoans. The Notch receptors and ligands that bind to Notch are single pass, transmembrane proteins that communicate cell to cell via juxtacrine signaling. There are reports of the divergent function and localization of the Deltalike 3 (Dll3) ligand. In Mus musculus (an eutherin mammal) the DLL3 protein inhibits the Notch signaling pathway and is localized in the Golgi apparatus. In contrast, the DLL3 protein from zebrafish, Danio rerio (a teleost) activates Notch and is located on the cell surface. This study will focus on examining the evolutionary pathway/evolutionary similarities, localization, and function of the A. carolinensis dll3 gene in comparison to other vertebrate species. This is important because there is not much known about the evolutionary divergence of the DLL3 A. carolinensis protein, its function in Notch signaling, and its subcellular localization.
Evolutionary analysis of vertebrate DLL3 protein sequences using phylogenetic trees showed that D. rerio and A. carolinensis are more evolutionarily similar in comparison to M. musculus suggesting that they may have similar intracellular localization. However, immunofluorescence staining experiments showed that the A. carolinensis DLL3 protein co-localized significantly with an endoplasmic reticulum (ER) specific primary antibody. Since this protein is localized in the secretory system, similar to that of M. musculus DLL3, it suggests that its function is to inhibit the Notch signaling pathway. Protein sequence alignments were created that suggested that there is a region in the protein sequences where the lizard and mouse sequence are conserved, while the zebrafish sequence simultaneously varies. This region of the amino acid sequence could be responsible for the difference in localization and function of the protein in these two species.
Evolutionary analysis of vertebrate DLL3 protein sequences using phylogenetic trees showed that D. rerio and A. carolinensis are more evolutionarily similar in comparison to M. musculus suggesting that they may have similar intracellular localization. However, immunofluorescence staining experiments showed that the A. carolinensis DLL3 protein co-localized significantly with an endoplasmic reticulum (ER) specific primary antibody. Since this protein is localized in the secretory system, similar to that of M. musculus DLL3, it suggests that its function is to inhibit the Notch signaling pathway. Protein sequence alignments were created that suggested that there is a region in the protein sequences where the lizard and mouse sequence are conserved, while the zebrafish sequence simultaneously varies. This region of the amino acid sequence could be responsible for the difference in localization and function of the protein in these two species.
ContributorsBoschi, Alexis (Author) / Wilson-Rawls, Jeanne (Thesis director) / Newbern, Jason (Committee member) / Wilson Sayres, Melissa (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05