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Undergraduate Research Opportunities Program

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End date: 2020 × Start date: 2015 × Item Type: Publication × Has files: Yes × search.filters.applied.f.isOrgUnitOfPublicationTitle: School of Biological Sciences ×

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Now showing 1 - 10 of 64
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Decoding Disease Persistence in Pediatric Acute Lymphoblastic Leukemia One Single Cell at a Time

2020-12 , Imbach, Kathleen Jane

In order to understand the biological and molecular mechanisms underlying disease resistance to therapy in pediatric acute lymphoblastic leukemia (ALL), we performed an investigation utilizing single-cell RNA-sequencing (scRNA-seq) on the 10X Genomics Chromium platform. Bone marrow samples from seven patients were collected, four of whom exhibited measurable residual disease (MRD) after induction therapy, and three patients who did not. Cells from bone marrow tissue were extracted from each patient at the time of diagnosis, prior to treatment efforts. Leukemic cells were separated from peripheral immune cells using flow cytometry and ~1000 single cells were sequenced from each patients’ cell populations. The goal of this study was to discern how the immune and leukemic cell populations and gene expression therein vary at the time of diagnosis between patients who do or do not respond to induction. Our results demonstrate a comparative increase in immune exhaustion signatures in the immune cells of MRD-positive patients, corroborating previous findings that implicate the role of exhaustion in resistant disease. We also show a discrepancy of cell cycle states in the leukemic cell compartment according to disease outcome, with an enrichment of blasts from MRD-negative patients exhibiting genetic signatures of S- and G2/M-phase.

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Competition Dynamics between Ancestral Unicellular and Laboratory-Evolved Multicellular Chlamydomonas reinhardtii

2020-05 , Sukkestad, Sophia Marin

Life on Earth as humanity comprehends it would be unthinkable without multicellular organisms. Despite the pervasiveness of multicellularity, the mechanisms of its evolutionary origin remain largely a mystery. Fortunately, the advent of experimental evolution has enabled scientists to explore facets of organismal history indiscernible from the fossil record alone. Such studies have successfully facilitated in-lab evolution of multicellular morphs in many species. However, evaluation of selective pressures which increase multicellular fitness remain poorly understood, including whether multicellular organisms are more adept at homeostasis. In this study, I investigated the growth and fitness of undifferentiated Chlamydomonas reinhardtii descended from strains evolved under predation selection by Herron et. al (2019). These descendant strains were tested for homeostatic efficacy against a unicellular ancestor in a series of competition assays in control and pH-variable media. Overall, I found no significant difference in intrinsic growth rate between multicellular strains and the unicellular competitor in control or acidic mixed cultures. Fitness of all multicellular strains tested, though less than that of the single-celled ancestor, also did not significantly differ when cultivated in acidic versus ideal conditions. These results support previous hypotheses of fitness decrease with increasing body size due to growth constraints, and suggest further investigation into other environmental challenges for longer replicates are necessary.

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Quasi-Periodic Patterns of Resting-State Brain Activity in Individuals with Idiopathic Hypersomnia and Narcolepsy

2020-05 , Bassil, Yasmine

The brain’s overall organization of its networks is often studied through its functional connectivity, defined as the spatiotemporal dependency of neuronal activity in anatomically separated regions. Altered functional connectivity in cortical networks, such as the default mode and task positive networks, is often associated with neurological disorders and can be studied and measured through resting-state functional MRI (rs-fMRI). This study compares dynamic changes in functional connectivity between individuals with idiopathic hypersomnia, narcolepsy, and typically functioning controls. This comparison is conducted through the investigation of the quasi-periodic pattern (QPP), a low-frequency spatiotemporal pattern in the brain linked to infra-slow activity. This study showed that this spatiotemporal pattern of focus, the QPP, differed in strength, frequency, and spatial distribution between the three subject groups. These findings represent preliminary differences that can be expanded upon through further analyses, including additional functional connectivity analyses, QPP regression, and statistical testing. It can be concluded that quasi-periodic patterns provide insight into the mechanisms behind spatiotemporal pattern differences seen in individuals with sleep disorders. Further analysis of these patterns could help expand current knowledge of connectivity differences in individuals with neurological disorders, as well as allow for development of effective diagnoses.

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Development of an Assay for Sphingomyelinase D Products in Venom from Loxosceles reclusa and Other Spiders

2020-05 , Lachmayr, Hannah Lowndes

The venoms of Loxosceles reclusa, the brown recluse spider, and some other Loxosceles species cause dermonecrotic lesions—a dying of the flesh—and in severe cases, systemic injury and death. Since this type of injury results from a bite, diagnosis can be cryptic unless the culprit spider is available to be identified by an expert. The distribution of Loxosceles reclusa is also not well known, which further complicates diagnosis. These spiders are of additional interest because one of the agents in the venom is a sphingomyelinase D (SMase D) that cleaves the head group of sphingomyelin (SM) and causes intramolecular transphosphatidylation to produce ceramide 1,3-cyclic phosphate (Cer(1,3)P), a lipid that is not known to be present in humans otherwise. Therefore, a simple assay to analyze the presence of SMase D, by either activity assays or detection of its product Cer(1,3)P, could aid in identification of spider bites and possibly facilitate development of a treatment. A key reagent for such studies is Cer(1,3)P which is currently not commercially available, so we have developed a method for its synthesis and identified conditions for distinguishing Cer(1,3)P from the substrate SM and alternative hydrolysis products (ceramide-1-phosphate and ceramide) by thin-layer chromatography. The availability of this chemical and its synthesis procedure enables an assay of SMase D for better characterization of this important component of brown recluse spider venom (and possibly other organisms). Moreover, the assay could be used to search for enzymes that hydrolyze Cer(1,3)P, and such enzymes might prove useful in the development of a treatment for these wounds.

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Effect of Hydrodynamic Regime on Snowflake Yeast Evolution

2020-05 , Holt, Jacob D.

Experimental evolution of S. cerevisiae has unlocked new avenues in the study of the transition from uni- to multicellularity and how selection moves from the level of the individual cell to the multicellular-level. Selection for large size, proxied by selecting for settling speed, quickly leads to clusters of cells, coined ‘snowflake yeast’, and adaptations at the cluster level. While selecting for settling speed is a good proxy for selection of large size because it is simple to implement, settling, or sedimentation, is a complex process with the potential for unforeseen impacts on this model system. By changing the hydrodynamic regime during settling speed selection, the selection process, and its effects on the snowflake yeast system other than selection for increased size, is explored. It is found that size distributions change in response to differing hydrodynamic regimes during settling speed selection. However, the path to larger size remains relatively constant, showing that the major findings of the snowflake yeast system are robust to changes in hydrodynamic regime during settling speed selection.

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The Effects of Ocean Acidification on Molt Rate and Carapace Area in Juvenile Dungeness Crabs (Cancer magister)

2020-05 , Reinhardt, Emma

Ocean acidification, the consequence of atmospheric CO2 dissolving in the ocean to form carbonic acid, is rapidly intensifying. A wealth of marine wildlife is known to be vulnerable to the expected drop in pH, including a number of crab species. The Dungeness crab (Cancer magister), the target of a commercially important fishery in the Pacific Northwest, is known to be sensitive to elevated CO2 levels. In an effort to better characterize the degree to which C. magister is sensitive to ocean acidification, this study examined the carapace areas, the distance between the eyes, and the molt rates of juveniles reared for over three hundred days in ambient (low) and future (high) CO2 conditions across six instars. Statistical analysis indicates that carapace areas and eye distances were significantly smaller in crabs reared in high-CO2 relative to crabs reared in low-CO2. Effects on carapace area were detectable at the third through the sixth instar, and effects on eye distance were detectable at the second, third, and fifth instar. Molt rates were significantly slower for crabs in high-CO2 treatments for the periods of J1 to J2, J2 to J3, and J3 to J4. If dissolved CO2 levels continue to rise in the ocean, wild juveniles Dungeness crabs may be smaller at each stage and display delays in development. These sensitivities have the potential to affect the crabs’ role in US West Coast food webs and their recruitment into fisheries.

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Uncovering the peatland root microbiome: Environmental factors shaping microbial community structure

2020-05 , Verlander, Sarah Elizabeth

This study examines the effects of simulated whole-ecosystem warming and elevated levels of carbon dioxide on the microbial communities within the root-soil microbiomes of vascular plants in peatlands. Root samples obtained from the SPRUCE site in Minnesota will be used to carefully characterize the microbial communities in the root tissue and the surrounding rhizosphere. The microbial communities can then be examined for any effects of whole ecosystem warming and the enrichment of carbon dioxide in the atmosphere, creating a glimpse into the future of peatlands and the associated effects of climate change drivers. This study marks an important step on a path to a greater understanding of peatland root microbiomes and climate driven effects on these microbial communities.

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Single Cell Analysis of Patients with Perianal Chron’s Disease

2020-05 , Ferguson, Katherine Elizabeth

Perianal Chron’s Disease is a debilitating form of Chron’s Disease that often involves rectal tissue in its manifestation in the body. There is a greater need for understanding of the role of the epithelial tissue in the rectum in the pathology of Chron’s Disease. This study aims to determine cellular make-up of rectal-derived organoids grown from Chron’s Disease patients. Through the use of single-cell transcriptomics, this study will determine the cell types present in four rectal-derived organoids and use differential expression to analyze differences in epithelial tissue of Chron’s Disease patients in comparison to a healthy individual.

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Implicit awareness during skilled motor learning and the implications for rehabilitation

2020-05 , Turner, Emma M.

Motor skills and sequential motor learning are essential in our day to day lives, however, little behind the brain regions involved is known. This means that when someone has a deficiency in their motor skills or their ability to learn motor skills, treatments may not address the actual problem at hand. The purpose of this study is to determine what regions of the brains are active during learning in those who are successful at motor learning and how that differs from those who do not prove to be successful. It was found from examining the electro-encephalography (EEG) data that there were three main areas of the brain that are active during the serial reaction time task (SRTT) that was used to assess the subjects implicit motor learning. These regions were the right precuneus, the right angular gyrus and the right medial frontal gyrus. There war significant difference in these regions between the subject that showed ability to transfer their motor learning and those who were not. These results indicate that there is a difference in brain activation between successful and unsuccessful learners. Better understanding how people learn and the brain regions involved will allow medical professionals to better address those with motor learning deficiencies. This can help lead to the development of more affective treatments.

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scRNA-seq dropouts serve as a signal for tissue heterogeneity in autism spectrum disorder

2020-05 , Spencer, Collin

Analysis of single-cell RNA-sequencing (scRNA-seq) data is plagued by dropouts, zero counts for mRNA transcripts due to low mRNA in individual cells and inefficient mRNA capture. Dropouts are traditionally treated as an error to be corrected through normalization while performing unsupervised clustering of single cells based on highly expressed, variable transcripts. A novel algorithm, co-occurrence clustering, treats dropouts as a signal and binarizes scRNA-seq data for cell clustering, producing the same clusters as Seurat. Previous application of Seurat to single nuclear RNA-sequencing (snRNA-seq) data taken from the prefrontal cortex (PFC) and anterior cingulate cortex (ACC) of patients with autism spectrum disorder (ASD) found no difference in clusters between brain regions. This seems at odds with literature suggesting tissue-specific emergence of co-expression networks and regional specialization in the brain. We applied co-occurrence clustering to ASD samples to parse interregional heterogeneity between the PFC and ACC and identify novel cell clusters.

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