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- All Subjects: Immunology
- Creators: School of Life Sciences
Description
Space microbiology, or the study of microorganisms in space, has significant applications for both human spaceflight and Earth-based medicine. This thesis traces the evolution of the field of space microbiology since its creation in 1935. Beginning with simple studies to determine if terrestrial life could survive spaceflight, the field of space microbiology has grown to encompass a substantial body of work that is now recognized as an essential component of NASA' research endeavors. Part one provides an overview of the early period of space microbiology, from high-altitude balloon and rocket studies to work conducted during the Apollo program. Part two summarizes the current state of the field, with a specific focus on the revolutionary contributions made by the Nickerson lab at the Biodesign Institute at ASU using the NASA-designed Rotating Wall Vessel (RWV) Bioreactor. Finally, part three highlights the research I've conducted in the Nickerson lab, as well as continuing studies within the field of space microbiology.
ContributorsMcCarthy, Breanne E. (Author) / Lynch, John (Thesis director) / Foy, Joseph (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
While former New York Yankees pitcher Goose Gossage unleashed his tirade on the deterioration of the unwritten rules of baseball and nerds ruining the sport about halfway through my writing of the paper, sentiments like his were inspiration for my topic: the evolution of statistics and data in baseball. By telling the story of how baseball data and statistics have evolved, my goal was to also demonstrate how they have been intertwined since the beginning—which would essentially mean that nerds have always been ruining the sport (if you subscribe to that kind of thought).
In the quest to showcase this, it was necessary to document how baseball prospers from numbers and numbers prosper from baseball. The relationship between the two is mutualistic. Furthermore, an all-encompassing historical look at how data and statistics in baseball have matured was a critical portion of the paper. With a metric such as batting average going from a radical new measure that posed a threat to the status quo, to a fiercely cherished statistic that was suddenly being unseated by advanced analytics, it shows the creation of new and destruction of old has been incessant. Innovators like Pete Palmer, Dick Cramer and Bill James played a large role in this process in the 1980s. Computers aided their effort and when paired with the Internet, unleashed the ability to crunch data to an even larger sector of the population. The unveiling of Statcast at the commencement of the 2015 season showed just how much potential there is for measuring previously unquantifiable baseball acts.
Essentially, there will always be people who mourn the presence of data and statistics in baseball. Despite this, the evolution story indicates baseball and numbers will be intertwined into the future, likely to an even greater extent than ever before, as technology and new philosophies become increasingly integrated into front offices and clubhouses.
In the quest to showcase this, it was necessary to document how baseball prospers from numbers and numbers prosper from baseball. The relationship between the two is mutualistic. Furthermore, an all-encompassing historical look at how data and statistics in baseball have matured was a critical portion of the paper. With a metric such as batting average going from a radical new measure that posed a threat to the status quo, to a fiercely cherished statistic that was suddenly being unseated by advanced analytics, it shows the creation of new and destruction of old has been incessant. Innovators like Pete Palmer, Dick Cramer and Bill James played a large role in this process in the 1980s. Computers aided their effort and when paired with the Internet, unleashed the ability to crunch data to an even larger sector of the population. The unveiling of Statcast at the commencement of the 2015 season showed just how much potential there is for measuring previously unquantifiable baseball acts.
Essentially, there will always be people who mourn the presence of data and statistics in baseball. Despite this, the evolution story indicates baseball and numbers will be intertwined into the future, likely to an even greater extent than ever before, as technology and new philosophies become increasingly integrated into front offices and clubhouses.
ContributorsGarcia, Jacob Michael (Author) / Kurland, Brett (Thesis director) / Doig, Stephen (Committee member) / Jackson, Victoria (Committee member) / Walter Cronkite School of Journalism and Mass Communication (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Introduction: Human papillomavirus (HPV) infection is seen in up to 90% of cases of cervical cancer, the third leading cancer cause of death in women. Current HPV screening focuses on only two HPV types and covers roughly 75% of HPV-associated cervical cancers. A protein based assay to test for antibody biomarkers against 98 HPV antigens from both high and low risk types could provide an inexpensive and reliable method to screen for patients at risk of developing invasive cervical cancer. Methods: 98 codon optimized, commercially produced HPV genes were cloned into the pANT7_cGST vector, amplified in a bacterial host, and purified for mammalian expression using in vitro transcription/translation (IVTT) in a luminescence-based RAPID ELISA (RELISA) assay. Monoclonal antibodies were used to determine immune cross-reactivity between phylogenetically similar antigens. Lastly, several protein characteristics were examined to determine if they correlated with protein expression. Results: All genes were successfully moved into the destination vector and 86 of the 98 genes (88%) expressed protein at an adequate level. A difference was noted in expression by gene across HPV types but no correlation was found between protein size, pI, or aliphatic index and expression. Discussion: Further testing is needed to express the remaining 12 HPV genes. Once all genes have been successfully expressed and purified at high concentrations, DNA will be printed on microscope slides to create a protein microarray. This microarray will be used to screen HPV-positive patient sera for antibody biomarkers that may be indicative of cervical cancer and precancerous cervical neoplasias.
ContributorsMeshay, Ian Matthew (Author) / Anderson, Karen (Thesis director) / Magee, Mitch (Committee member) / Katchman, Benjamin (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Guided by the Obama administration, NASA has begun developing commercial launch capabilities. For both cargo and crew delivery to the International Space Station, NASA has selected companies to build and operate the vehicles at a fixed price. Alexander McDonald suggests that this continues a trend in space exploration established by large observatory projects, and that the Apollo-era style of funding and operation was a historical anomaly. This paper attempts to discover if historical analog can support or weaken this thesis. The analogs chosen are two episodes in the history of terrestrial exploration: the experience of the Spanish and British empires in North America. These are compared to the history of space exploration up until today, focusing on how the role of private enterprise has changed in each instance. While the analogies between historical episodes are weak in a few areas, they do possess a common narrative concerning the shifting balance between private and government interests. This narrative supports McDonald's thesis, and shows that NASA's current policy anticipates an expected transition towards a private-public hybrid model of exploration and expansion.
ContributorsRobb, Daniel Robert (Author) / Pyne, Stephen (Thesis director) / Bell, Jim (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2015-05
Description
Efforts to quantify the diversity of the T cell repertoire have generally been unsuccessful because not all factors accounting for diversity have been considered. In order to get an accurate representation of the T cell repertoire, one must incorporate analysis of germline gene diversity, diversity from somatic recombination, joining diversity from N- and P- nucleotides, and TCR chain pairing diversity. Because of advances in high-throughput sequencing techniques, estimates have been able to account for diversity from TCR genes. However the ability to account for chain pairing diversity has been more difficult. In order to do so, single cell sorting techniques must be employed. These techniques, though effective, are time consuming and expensive. For this reason, no large-scale analyses have been done on the immune repertoires using these techniques. In this study, we propose a novel method for linking the two TCR chain sequences from an individual cell. DNA origami nanostructure technology is employed to capture and bind the TCRγ and TCRδ chain mRNA inside individual cells using probe strands complementary to the C-region of those sequences. We then use a dual-primer RT and ligation molecular strategy to link the two sequences together. The result is a single amplicon containing the CDR3 region of the TCRγ and TCRδ. This amplicon can then be easily PCR amplified using sequence specific primers, and sequenced. DNA origami nanostructures offer a rapid, cost-effective method alternative to conventional single cell sorting techniques, as both TCR mRNA can be captured on one origami molecule inside a single cell. At present, this study outlines a proof-of-principle analysis of the method to determine its functionality. Using known TCRγ and TCRδ sequences, the DNA origami and RT/PCR method was tested and resulting sequence data proved the effectiveness of the method. The original TCRγ and TCRδ sequences were linked together as a single amplicon containing both CDR3 regions of the genes. Thus, this method can be employed in further research to elucidate the γδ T cell repertoire. This technology is also easily adapted to any gene target or cell type and therefore presents a large opportunity to be used in other immune repertoire analysis and other immunological studies (such as the rapid identification and subsequent production of antibodies).
ContributorsPoindexter, Morgan Elizabeth (Author) / Blattman, Joseph (Thesis director) / Yan, Hao (Committee member) / Schoettle, Louis (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Cancer poses a significant burden on the global health system and represents a leading cause of death worldwide. For late-stage cancers, the traditional treatments of chemotherapy, radiation, and surgery are not always viable, and they can pose unnecessary health risks to the patients. New immunotherapies, such as adoptive cell transfer, are being developed and refined to treat such cancers. T cell immunotherapies in particular, where a patient’s T cell lymphocytes are isolated and amplified to be re-infused into the patient or where human cell lines are engineered to express T cell receptors for the recognition of common cancer antigens, are being expanded on because for some cancers, they could be the only option. Constructing an optimal pipeline for cloning and expression of antigen-specific TCRs has significant bearing on the efficacy of engineered cell lines for ACT. Adoptive T cell transfer, while making great strides, has to overcome a diverse T cell repertoire – cloning and expressing antigen-specific TCRs can mediate this understanding. Having identified the high frequency FluM1-specific TCR sequences in stimulated donor PBMCs, it was hypothesized that the antigen-specific TCR could be reconstructed via Gateway cloning methods and tested for expression and functionality. Establishing this pipeline would confirm an ability to properly pair and express the heterodimeric chains. In the context of downstream applications, neoantigens would be used to stimulate T cells, the α and β chains would be paired via single-cell or bulk methods, and instead of Gateway cloning, the CDR3 hypervariable regions α and β chains alone would be co-expressed using Golden Gate assembly methods.
ContributorsHirneise, Gabrielle Rachel (Author) / Anderson, Karen (Thesis director) / Mason, Hugh (Committee member) / Hariadi, Hugh (Committee member) / School of Life Sciences (Contributor, Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The essay conducts a wide review of the existing modern scholarship on plague, caused by Yersinia pestis, during the second plague pandemic in the Islamicate Mediterranean. A historiographical approach was taken to analyze the terminology recorded in scholarly plague treatises across the timeline of the historical narrative, from the centuries before during and after the 1348 plague pandemic known as the Black Death. Focus is given to the medical and symptom-based terminology that was used by medieval scholars to describes plagues arrival, appearance, and effects. Modern authors writing about regions from Anatolia and the Ottoman lands in the eastern Mediterranean, to the Andalusian region in Spanish Granada have translated and discussed major medieval treatises by scholars who were contemporary to the disease epidemics and this essay explores the medieval terminology using modern scholarship. An analysis of the detailed modern plague scholarship in the eastern Islamicate Mediterranean explores the interpretations and discussions generated by the numerous sources who wrote historical and religious treatises on plague during the initial pandemic and subsequent epidemic events. In the western Islamicate Mediterranean a trio of detailed treatises describe the symptoms and treatments for an unprecedented pandemic, providing unparalleled descriptive confirmation of the presence of plague related mortality. This western record is limited, however, by its finite temporal range, as no plague treatise arise from the Islamicate scholars in the western Mediterranean kingdoms to describe the events before or after the famous 1348 pandemic. Between the kingdoms in the east and west is a wasteland in the medieval scholarship on plague, its plague experience largely explained only in comparison with the adjacent regions. With this background the essay will seek the patterns and notable features in scholarly terminology, in order to create a coherent picture of the plague experience across the Islamicate Mediterranean.
ContributorsHayton, Jacob Raymond (Author) / Green, Monica (Thesis director) / El Hamel, Chouki (Committee member) / School of Historical, Philosophical and Religious Studies (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Viral infections are a significant cause of disease in humans. While some viral diseases have been eliminated, many more continue to infect millions. Viral infections are challenging to treat because viruses use host cell machinery to replicate, so it is difficult to develop drugs that can target viruses. Normally, the host’s immune system is capable of destroying the virus, but during chronic infections it becomes exhausted and T cells lose their effector functions necessary for the clearance of the virus. IL-2 can help relieve this exhaustion, but causes toxicity to the body. In mice infected with chronic LCMV, IL-2 administration causes death due to pulmonary hemorrhage. CD4 deficient mice were infected with chronic LCMV and then dosed with IL-2 and survived, but mice that were deficient for CD8 T cells died, indicating that toxicity was mediated by CD8 T cells. CD8 T cells can kill infected host cells directly by producing perforin, or can produce cytokines like IFN-γ and TNF to further activate the immune system and mediate killing. Mice that were deficient in perforin died after IL-2 administration, as well as mice that were deficient in IFN-γ. Mice deficient in TNF, however, survived, indicating that TNF was mediating the toxicity in response to IL-2. There are two different receptors for TNF, p55 and p75. p55 is known as TNFR1 and has been implicated in apoptosis of virally infected cells. P75 is known as TNFR2 and is associated more with inflammation in response to infection. My hypothesis was that if TNFR2 was knocked out, infected mice would survive IL-2 dosing. When single knockouts of TNFR1 and 2 were used in an experiment however, it was found that either receptor is capable of mediating toxicity, as both experimental groups failed to survive. This is relevant to current IL-2 therapies because there is no way to eliminate a single receptor in order to reduce toxicity. Further studies exploring the anti-viral capabilities of IFN-γ are suggested.
ContributorsJarvis, Jordan Alisa (Author) / Blattman, Joseph (Thesis director) / Denzler, Karen (Committee member) / McAfee, Megan (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
This thesis documentary film takes a look at the dysfunctional but ongoing relationship between Twitter and sports journalism. The foundation of this relationship's dysfunction is what I have coined as the Twitter Outrage Cycle. In this cycle a sports broadcasting personality comments on a matter while on-air. Next, the program's audience where the comments were spoken becomes offended by the statement. After that, the offended audience members express their outrage on social media, most namely Twitter. Finally the cycle culminates with the public outrage pressuring networks and its executives to either suspended or fire the individual that said the controversial statements. This cycle began to occur on a more consistent basis starting in 2012. It became such a regular occurrence that many on-air talent figures have noticed and taken precautionary measures to either avoid or confront the Outrage Cycles. This documentary uses the voice of seven figures within the sports media and online interaction forum. Notable using the voices of three notable individuals that currently have a prominent voice in sports journalism. As well as a neutral social media curator who clearly explains the psyche behind these outraged viewer's mindsets. Through these four main voices their ideals and opinions on the matter weave together, disagree with each other at times but ultimately help the viewer come to an understanding of why these Outrage Cycles occur and what needs to be done in order for them to cease. We Should Talk: The Relationship Between Twitter and Sports Journalism is a documentary film that looks to illustrate a seemingly minimal part of many people's lives that when taken into perspective many people look at in a very serious light.
ContributorsNeely, Cammeron Allen Douglas (Author) / Kurland, Brett (Thesis director) / Fergus, Tom (Committee member) / Walter Cronkite School of Journalism and Mass Communication (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Background: Coccidioidomycosis (Valley Fever) is a respiratory disease that is caused by the soil-dwelling fungi Coccidioides immitis and Coccidioides posadasii. Because fungal glycosylation patterns are distinct from mammalian glycosylation patterns, we hypothesized that certain lectins (carbohydrate-binding proteins) might have differential binding properties to coccidioidal glycoproteins, and therefore serve as a tool for the purification and characterization of these glycoproteins from patient specimens. Materials and Methods: To identify potential Coccidioides-binding lectins, lectin-based immunohistochemistry was performed using a panel of 21 lectins on lung tissue from human patients infected with Coccidioides. Enzyme-Linked Immunosorbent Assays (ELISAs) were used to confirm and test candidate Coccidioides-binding lectins for their ability to bind to proteins from antigen preparations of laboratory-grown Coccidioides. Inhibition IHC and ELISAs were used to confirm binding properties of these lectins. SDS-PAGE and mass spectrometry were performed on eluates from coccidioidal antigen preparations run through lectin-affinity chromatography columns to characterize and identify lectin-binding coccidioidal glycoproteins. Results: Two GlcNAc-binding lectins, GSLII and sWGA, bound specifically to spherules and endospores in infected human lung tissue, and not to adjacent lung tissue. The binding of these lectins to both Coccidioides proteins in lung tissue and to coccidioidal antigen preparations was confirmed to have lectin-like characteristics. SDS-PAGE analysis of eluates from lectin-affinity chromatography demonstrated that GSLII and sWGA bind to coccidioidal glycoproteins. Mass spectrometric identification of the top ten lectin affinity-purified glycoproteins demonstrated that GSLII and sWGA share affinity to a common set of coccidioidal glycoproteins. Conclusion: This is the first report of lectins that bind specifically to Coccidioides spherules and endospores in infected humans. These lectins may have the potential to serve as tools for a better method of detection and diagnosis of Valley Fever.
ContributorsChowdhury, Yasmynn (Author) / Lake, Douglas (Thesis director) / Grys, Thomas (Committee member) / Magee, Mitchell (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2015-05