Matching Items (157)
Description
Cleavage and polyadenylation is a step in mRNA processing in which the 3’UTR is cleaved and a polyA tail is added to create a final mature transcript. This process relies on RNA sequence elements that guide a large multimeric protein complex named the Cleavage and Polyadenylation Complex to dock on the 3’UTR and execute the cleavage reaction. Interactions of the complex with the RNA and specific dynamics of complex recruitment and formation still remain largely uncharacterized. In our lab we have identified an Adenosine residue as the nucleotide most often present at the cleavage site, although it is unclear whether this specific element is a required instructor of cleavage and polyadenylation. To address whether the Adenosine residue is necessary and sufficient for the cleavage and polyadenylation reaction, we mutated this nucleotide at the cleavage site in three C. elegans protein coding genes, forcing the expression of these wt and mutant 3’UTRs, and studied how the cleavage and polyadenylation machinery process these genes in vivo. We found that interrupting the wt sequence elements found at the cleavage site interferes with the cleavage and polyadenylation reaction, suggesting that the sequence close to the end of the transcript plays a role in modulating the site of the RNA cleavage. This activity is also gene-specific. Genes such as ges-1 showed little disruption in the cleavage of the transcript, with similar location occurring in both the wt and mutant 3’UTRs. On the other hand, mutation of the cleavage site in genes such as Y106G6H.9 caused the activation of new cryptic cleavage sites within the transcript. Taken together, my experiments suggest that the sequence elements at the cleavage site somehow participate in the reaction to guide the cleavage reaction to occur at an exact site. This work will help to better understand the mechanisms of transcription termination in vivo and will push forward research aimed to study post-transcriptional gene regulation in eukaryotes.
ContributorsSteber, Hannah Suzanne (Author) / Mangone, Marco (Thesis director) / Harris, Robin (Committee member) / LaBaer, Joshua (Committee member) / School of Life Sciences (Contributor, Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
In response to a national call within STEM to increase diversity within the sciences, there has been a growth in science education research aimed at increasing participation of underrepresented groups in science, such as women and ethnic/racial minorities. However, an underexplored underrepresented group in science are religious students. Though 82% of the United States population is religiously affiliated, only 52% of scientists are religious (Pew, 2009). Even further, only 32% of biologists are religious, with 25% identifying as Christian (Pew, 2009; Ecklund, 2007). One reason as to why Christian individuals are underrepresented in biology is because faculty may express biases that affect students' ability to persist in the field of biology. In this study, we explored how revealing a Christian student's religious identity on science graduate application would impact faculty's perception of the student during the biology graduate application process. We found that faculty were significantly more likely to perceive the student who revealed their religious identity to be less competent, hirable, likeable, and faculty would be less likely to mentor the student. Our study informs upon possible reasons as to why there is an underrepresentation of Christians in science. This further suggests that bias against Christians must be addressed in order to avoid real-world, negative treatment of Christians in science.
ContributorsTruong, Jasmine Maylee (Author) / Brownell, Sara (Thesis director) / Gaughan, Monica (Committee member) / Barnes, Liz (Committee member) / School of Life Sciences (Contributor) / W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Cancer is one of the leading causes of death globally according to the World Health Organization. Although improved treatments and early diagnoses have reduced cancer related mortalities, metastatic disease remains a major clinical challenge. The local tumor microenvironment plays a significant role in cancer metastasis, where tumor cells respond and adapt to a plethora of biochemical and biophysical signals from stromal cells and extracellular matrix (ECM) proteins. Due to these complexities, there is a critical need to understand molecular mechanisms underlying cancer metastasis to facilitate the discovery of more effective therapies. In the past few years, the integration of advanced biomaterials and microengineering approaches has initiated the development of innovative platform technologies for cancer research. These technologies enable the creation of biomimetic in vitro models with physiologically relevant (i.e. in vivo-like) characteristics to conduct studies ranging from fundamental cancer biology to high-throughput drug screening. In this review article, we discuss the biological significance of each step of the metastatic cascade and provide a broad overview on recent progress to recapitulate these stages using advanced biomaterials and microengineered technologies. In each section, we will highlight the advantages and shortcomings of each approach and provide our perspectives on future directions.
ContributorsPeela, Nitish (Author) / Nikkhah, Mehdi (Thesis director) / LaBaer, Joshua (Committee member) / Harrington Bioengineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Glioblastoma is the most aggressive and lethal brain tumor, due to its resistance to current conventional therapy. The resistance to chemo- and radiotherapy has been attributed to a special population of cells known as glioma stem cells. Previous literature has shown the importance of a Central Nervous System-restricted transcription factor OLIG2 in maintaining the tumor-propagating potential of these glioma stem cells. OLIG2's function was further elucidated, with its pro-mitogenic function due to its ability to negatively regulate the p53 pathway by suppressing the acetylation of the p53 protein's C terminal domain. Past work in our lab has confirmed that one of OLIG2's partner proteins is Histone Deacetylase 1 (HDAC1). In vitro experiments have also shown that targeting HDAC1 using hairpin RNA in glioma stem cells negatively impacts proliferation. In a survival study using a murine glioma model, targeting Hdac1 using hairpin RNA is shown to reduce tumor burden and increase survival. In this paper, we demonstrate that silencing Hdac1 expression reduces proliferation, increases cell death, likely a result of increased acetylation of p53. Olig2 expression levels seem to be unaffected in GSCs, demonstrating that the Hdac1 protein ablation is indeed lethal to GSCs. This work builds upon previously collected results, confirming that Hdac1 is a potential surrogate target for Olig2's pro-mitotic function in regulating the p53 pathway.
ContributorsLoo, Vincent You Wei (Author) / LaBaer, Joshua (Thesis director) / Mehta, Shwetal (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Learning student names has been promoted as an inclusive classroom practice, but it is unknown whether students value having their names known by an instructor. We explored this question in the context of a high-enrollment active-learning undergraduate biology course. Using surveys and semistructured interviews, we investigated whether students perceived that instructors know their names, the importance of instructors knowing their names, and how instructors learned their names. We found that, while only 20% of students perceived their names were known in previous high-enrollment biology classes, 78% of students perceived that an instructor of this course knew their names. However, instructors only knew 53% of names, indicating that instructors do not have to know student names in order for students to perceive that their names are known. Using grounded theory, we identified nine reasons why students feel that having their names known is important. When we asked students how they perceived instructors learned their names, the most common response was instructor use of name tents during in-class discussion. These findings suggest that students can benefit from perceiving that instructors know their names and name tents could be a relatively easy way for students to think that instructors know their names. Academic self-concept is one's perception of his or her ability in an academic domain compared to other students. As college biology classrooms transition from lecturing to active learning, students interact more with each other and are likely comparing themselves more to students in the class. Student characteristics, such as gender and race/ethnicity, can impact the level of academic self-concept, however this has been unexplored in the context of undergraduate biology. In this study, we explored whether student characteristics can affect academic self-concept in the context of a college physiology course. Using a survey, students self-reported how smart they perceived themselves in the context of physiology compared to the whole class and compared to the student they worked most closely with in class. Using logistic regression, we found that males and native English speakers had significantly higher academic self-concept compared to the whole class compared with females and non-native English speakers, respectively. We also found that males and non-transfer students had significantly higher academic self-concept compared to the student they worked most closely with in class compared with females and transfer students, respectively. Using grounded theory, we identified ten distinct factors that influenced how students determined whether they are more or less smart than their groupmate. Finally, we found that students were more likely to report participating less than their groupmate if they had a lower academic self-concept. These findings suggest that student characteristics can influence students' academic self-concept, which in turn may influence their participation in small group discussion.
ContributorsKrieg, Anna Florence (Author) / Brownell, Sara (Thesis director) / Stout, Valerie (Committee member) / Cooper, Katelyn (Committee member) / School of Life Sciences (Contributor) / School of Politics and Global Studies (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
CREB3L1 has been previously shown to auto-acetylate itself when prepared from HeLa cell based in vitro protein expression lysates. To circumvent the concerns of the contamination of co-purified human proteins from HeLa lysates, the protein was purified through insect cell transfection in vitro. The objective of this study was to assay the auto-acetylation activity of CREB3L1 prepared from insect cells using the baculovirus expression vector system (BEVS). To this end, His-tagged CREB3L1 was affinity purified from Hi5 cells using an IMAC column and used for acetylation assay. Samples were taken different time points and auto-acetylation was by western using antibodies specific to acetylated lysines. Auto-acetylation activity was observed after overnight incubation. Future experiments will focus on the improvement of purification yield and the identification of the substrates and interacting proteins of CREB3L1 to better understand the biological functions of this novel acetyltransferase.
ContributorsSchwab, Anna (Author) / LaBaer, Joshua (Thesis director) / Qiu, Ji (Committee member) / Barrett, The Honors College (Contributor)
Created2017-05
Description
The growing urban heat island (UHI) phenomenon is having detrimental effects on urban populations and the environment, and therefore, must be addressed. The purpose of this research is to investigate possible strategies that could be utilized to reduce the effects of the urban heat island for the city of Phoenix. Current strategies, case studies, and the ENVI-Met modeling software were used to finalize conclusions and suggestions to further progress Phoenix's goals in combating its urban heat island. Results from the studies found that there is much potential in reducing daytime and evening temperatures through improving infrastructure by means of increased vegetation in the forms of green roofs and walls, reducing anthropogenic heat release, improving artificial surface coverage, and implementing lasting policies for further development. Results from the ENVI-met microclimate program shows areas for further research in urban heat island mitigation strategies.
ContributorsShqalsi, Ema (Author) / Pijawka, David (Thesis director) / Middel, Ariane (Committee member) / Civil, Environmental and Sustainable Engineering Programs (Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Almost every form of cancer deregulates the expression and activity of anabolic glycosyltransferase (GT) enzymes, which incorporate particular monosaccharides in a donor acceptor as well as linkage- and anomer-specific manner to assemble complex and diverse glycans that significantly affect numerous cellular events, including tumorigenesis and metastasis. Because glycosylation is not template-driven, GT deregulation yields heterogeneous arrays of aberrant intact glycan products, some in undetectable quantities in clinical bio-fluids (e.g., blood plasma). Numerous glycan features (e.g., 6 sialylation, β-1,6-branching, and core fucosylation) stem from approximately 25 glycan “nodes:” unique linkage specific monosaccharides at particular glycan branch points that collectively confer distinguishing features upon glycan products. For each node, changes in normalized abundance (Figure 1) may serve as nearly 1:1 surrogate measure of activity for culpable GTs and may correlate with particular stages of carcinogenesis. Complementary to traditional top down glycomics, the novel bottom-up technique applied herein condenses each glycan node and feature into a single analytical signal, quantified by two GC-MS instruments: GCT (time-of-flight analyzer) and GCMSD (transmission quadrupole analyzers). Bottom-up analysis of stage 3 and 4 breast cancer cases revealed better overall precision for GCMSD yet comparable clinical performance of both GC MS instruments and identified two downregulated glycan nodes as excellent breast cancer biomarker candidates: t-Gal and 4,6-GlcNAc (ROC AUC ≈ 0.80, p < 0.05). Resulting from the activity of multiple GTs, t-Gal had the highest ROC AUC (0.88) and lowest ROC p‑value (0.001) among all analyzed nodes. Representing core-fucosylation, glycan node 4,6-GlcNAc is a nearly 1:1 molecular surrogate for the activity of α-(1,6)-fucosyltransferase—a potential target for cancer therapy. To validate these results, future projects can analyze larger sample sets, find correlations between breast cancer stage and changes in t-Gal and 4,6-GlcNAc levels, gauge the specificity of these nodes for breast cancer and their potential role in other cancer types, and develop clinical tests for reliable breast cancer diagnosis and treatment monitoring based on t-Gal and 4,6-GlcNAc.
ContributorsZaare, Sahba (Author) / Borges, Chad (Thesis director) / LaBaer, Joshua (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Course-Based Undergraduate Research Experiences, or CUREs have become an increasingly popular way to integrate research opportunities into the undergraduate biology curriculum. Unlike traditional cookbook labs which provide students with a set experimental design and known outcome, CUREs offer students the opportunity to participate in novel and interesting research that is of interest to the greater biology community. While CUREs have been championed as a way to provide more students with the opportunity to experience, it is unclear whether students benefit differently from participating in different CURE with different structural elements. In this study we focused in on one proposed element of a CURE, collaboration, to determine whether student's perception of this concept change over the course of a CURE and whether it differs among students enrolled in different CUREs. We analyzed pre and post open-ended surveys asking the question "Why might collaboration be important in science?" in two CUREs with different structures of collaboration. We also compared CURE student responses to the responses of senior honors thesis students who had been conducting authentic research. Five themes emerged in response to students' conceptions of collaboration. Comparing two CURE courses, we found that students' conceptions of collaboration were varied within each individual CURE, as well as what students were leaving with compared to the other CURE course. Looking at how student responses compared between 5 different themes, including "Different Perspectives", "Validate/Verify Results", "Compare Results", "Requires Different Expertise", and "Compare results", students appeared to be thinking about collaboration in distinct different ways by lack of continuity in the amount of students discussing each of these among the classes. In addition, we found that student responses in each of the CURE courses were not significantly different for any of the themes except "Different Expertise" compared to the graduating seniors. However, due to the small (n) that the graduating seniors group had, 22, compared to each of the CURE classes composing of 155 and 98 students, this comparison must be taken in a preliminary manner. Overall, students thought differently about collaboration between different CUREs. Still, a gap filling what it means to "collaborate", and whether the structures of CUREs are effective to portray collaboration are still necessary to fully elaborate on this paper's findings.
ContributorsWassef, Cyril Alexander (Author) / Brownell, Sara (Thesis director) / Stout, Valerie (Committee member) / Cooper, Katelyn (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Disturbances in the protein interactome often play a large role in cancer progression. Investigation of protein-protein interactions (PPI) can increase our understanding of cancer pathways and will disclose unknown targets involved in cancer disease biology. Although numerous methods are available to study protein interactions, most platforms suffer from drawbacks including high false positive rates, low throughput, and lack of quantification. Moreover, most methods are not compatible for use in a clinical setting. To address these limitations, we have developed a multiplexed, in-solution protein microarray (MISPA) platform with broad applications in proteomics. MISPA can be used to quantitatively profile PPIs and as a robust technology for early detection of cancers. This method utilizes unique DNA barcoding of individual proteins coupled with next generation sequencing to quantitatively assess interactions via barcode enrichment. We have tested the feasibility of this technology in the detection of patient immune responses to oropharyngeal carcinomas and in the discovery of novel PPIs in the B-cell receptor (BCR) pathway. To achieve this goal, 96 human papillomavirus (HPV) antigen genes were cloned into pJFT7-cHalo (99% success) and pJFT7-n3xFlag-Halo (100% success) expression vectors. These libraries were expressed via a cell-free in vitro transcription-translation system with 93% and 96% success, respectively. A small-scale study of patient serum interactions with barcoded HPV16 antigens was performed and a HPV proteome-wide study will follow using additional patient samples. In addition, 15 query proteins were cloned into pJFT7_nGST expression vectors, expressed, and purified with 93% success to probe a library of 100 BCR pathway proteins and detect novel PPIs.
ContributorsRinaldi, Capria Lakshmi (Author) / LaBaer, Joshua (Thesis director) / Mangone, Marco (Committee member) / Borges, Chad (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12