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- All Subjects: Immunology
- Creators: School of Life Sciences
- Status: Published
Description
Systemic lupus erytematosus (SLE) is an autoimmune disease where the immune system is reactive to self antigens resulting in manifestations like glomerulonephritis and arthritis. The immune system also affects the central nervous system (known as CNS-SLE) leading to neuropsychiatric manifestations such as depression, cognitive impairment, psychosis and seizures. A subset of pathogenic brain-reactive autoantibodies (BRAA) is hypothesized to bind to integral membrane brain proteins, affecting their function, leading to CNS-SLE. I have tested this BRAA hypothesis, using our lupus-mouse model the MRL/lpr mice, and have found it to be a reasonable explanation for some of the manifestations of CNS-SLE. Even when the MRL/lpr had a reduced autoimmune phenotype, their low BRAA sera levels correlated with CNS involvement. The correlation existed between BRAA levels to integral membrane protein and depressive-like behavior. These results were the first to show a correlation between behavioral changes and BRAA levels from brain membrane antigen as oppose to cultured neuronal cells. More accurate means of predicting and diagnosing lupus and CNS-SLE is necessary. Using microarray technology I was able to determine peptide sets that could be predictive and diagnostic of lupus and each specific CNS manifestation. To knowledge no test currently exists that can effectively diagnose lupus and distinguish between each CNS manifestations. Using the peptide sets, I was able to determine possible natural protein biomarkers for each set as well as for five monoclonal BRAA from one MRL/lpr. These biomarkers can provide specific targets for therapy depending on the manifestation. It was necessary to investigate how these BRAA enter the brain. I hypothesized that substance P plays a role in altering the blood-brain barrier (BBB) allowing these BRAA to enter and affect brain function, when bound to its neurokinin-1 receptor (NK-1R). Western blotting results revealed an increase in the levels of NK-1R in the brain of the MRL/lpr compared to the MRL/mp. These MRL/lpr with increased levels of both NK-1R and BRAA displayed CNS dysfunction. Together, these results demonstrate that NK-1R may play a role in CNS manifestations. Overall, the research conducted here, add to the role that BRAA are playing in CNS-lupus.
ContributorsWilliams, Stephanie (Author) / Hoffman, Steven A (Thesis advisor) / Conrad, Cheryl (Committee member) / Chen, Julian (Committee member) / Orchinik, Miles (Committee member) / Arizona State University (Publisher)
Created2011
Description
This paper explores the relationship between wildfire management and the consideration of ecological and environmental concerns in Arizona. To get a proper perspective on the current state of wildfire management in Arizona, information on two wildfire management programs, the Four Forests Restoration Initiative and FireScape, was researched and analyzed, as well as contemporary fire policy, a history of wildfire in Arizona, and two recent fires in Sedona, AZ. The two fires in Sedona, the Brins Fire of 2006 and the Slide Fire of 2014, act as a focal point for this ecological management transition, as even within an 8-year period, we can see the different ways the two fires were managed and the transition to a greater ecological importance in management strategies. These all came together to give a full spectrum for the factors that have led to more ecologically-prominent wildfire management strategies in Arizona.
ContributorsGeorge-Sills, Dylan (Author) / Pyne, Stephen (Thesis director) / Hirt, Paul (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Sustainability (Contributor)
Created2015-05
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
Water is the main driver of net primary productivity (NPP) in arid ecosystems, followed by nitrogen and phosphorous. Precipitation is the primary factor in determining water availability to plants, but other factors such as surface rocks could also have an impact. Surface rocks may positively affect water availability by preventing evaporation from soil, but at higher densities, surface rocks may also have a negative impact on water availability by limiting water infiltration or light availability. However, the direct relationship between rock cover and aboveground net primary productivity (ANPP), a proxy for NPP, is not well understood. In this research we explore the relationship between rock cover, ANPP, and soil nutrient availability. We conducted a rock cover survey on long-term fertilized plots at fifteen sites in the Sonoran Desert and used 4 years of data from annual plant biomass surveys to determine the relationship between peak plant biomass and surface rock cover. We performed factorial ANCOVA to assess the relationship among annual plant biomass, surface rocks, precipitation, and fertilization treatment. Overall we found that precipitation, nutrients, and rock cover influence growth of Sonoran Desert annual plants. Rock cover had an overall negative relationship with annual plant biomass, but did not show a consistent pattern of significance over four years of study and with varying average winter precipitation.
ContributorsShaw, Julea Anne (Author) / Hall, Sharon (Thesis director) / Sala, Osvaldo (Committee member) / Cook, Elizabeth (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (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
In today's world, critical thinking and using a systems approach to problem solving are skills that are far too rare. In the age of information, the truth has become muddled by "fake news" and a constant barrage of exaggerations or blatant falsehoods. Without critical thinking skills, "many members of our society do not command the scientific literacy necessary to address important societal issues and concerns" (NCES 2012, p.11). Additionally, far too many people are incapable of thinking long term and understanding how their actions affect others. Because of this shortsightedness our world is facing one of its biggest ecological crises \u2014 global warming confounded by overpopulation and overconsumption. Now, more than ever, it is critical "for our young people to have a basic understanding of the relevant scientific ideas, technologies and ethical issues and powers of reasoning, to be prepared to face these issues" (Harlen et al., 2015). I believe that investigating innovative ways to teach ecology could be an important step to accomplishing this. Learning to think like a scientist forces people to rely on facts, follow similar protocols to deduce these facts, and be able to think critically about misleading events. More specifically, ecology education will allow people to develop those skills while also learning about team work, open-mindedness, and their environment. Ecology is defined as "the branch of biology that deals with the relations of organisms to one another and to their physical surroundings" (Dictionary.com, 2018). It is clear that this subcategory of science could act as a powerful introduction to the scientific world and how we relate to it. Its introduction at a young age has the potential to create a generation of conscientious and curious lifelong learners. In an attempt to support effective ways to teach ecology, I developed an educational unit and applied it in different educational contexts. My target audience was elementary aged students and I tested this unit with children in Phoenix Metropolitan Area afterschool programs. I taught core concepts of ecology \u2014 the water cycle, the sun's energy, plants and photosynthesis, and food webs \u2014in a sequence of lesson plans that build upon each other. Finally, I determined the appropriate age group and setting for these lesson plans through research and in-class observations. In this document, I explain the process I went through in developing my lesson plans, why I felt compelled to make them, and my experiences in implementing them.
ContributorsVotaw, Alexandra Lindsay (Author) / Larson, Kelli (Thesis director) / Herrmann, Lisa (Committee member) / York, Abigail (Committee member) / School of Art (Contributor) / The Design School (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Peatlands are a type of wetlands where the rate of accumulation of organic matter exceed the rate of decomposition and have accumulated more than 30 cm of peat (Joosten and Clark, 2002). Peatlands store approximately 30% of all terrestrial carbon as recalcitrant peat, partially decomposed plant and microbial biomass, while simultaneously producing almost 40% of the globally emitted methane (Schmidt et al., 2016), making peatlands an important component of the carbon budgets. Published research indicates that the efficiency of carbon usage among microbial communities can determine the soil-carbon response to rising temperatures (Allison et al. 2010). By determining carbon consumption in peatland soils, total community respiration response, and community structure change with additions, models of carbon use efficiency in permafrost peatlands will be well-informed and have a better understanding of how the peatlands will respond to, and utilize, increased availability of carbon compounds due to the melting permafrost. To do this, we will sequence Lutose deep core samples to observe baseline microbial community structure at different depths and different age-gradients, construct substrate incubations of glucose and propionate and observe community respiration response via a gas chromatography flame ionization detector, track the glucose and propionate additions with high-performance liquid chromatography (HPLC), and sequence the samples once more to determine if there was a deviation from the initial community structure obtained prior to the incubations. We found that our initial sequencing data was supported by previous work (Lin et al., 2014), however we were unable to sequence samples post-incubation due to time constraints. In this sequencing analysis we found that the strongest variable that made samples biologically similar was the age-gradient site in which they were extracted. We found that the group with glucose additions produced the most carbon dioxide compared with the other treatments, but was not the treatment that dominated the production of methane. Finally, in the HPLC samples that were analyzed, we found that glucose is likely forming the most by-product accumulation from mass balance calculations, while propionate is likely forming the least. Future experimentation should focus on the shortcomings of this experiment. Further analysis of 16S rRNA sequencing data from after the incubations should be analyzed to determine the change in microbial community structure throughout the experiment. Furthermore, HPLC analysis for the several samples need to be done and followed up with mass balance to determine where the added glucose and propionate are being allocated within the soil. Once these pieces of the puzzle are put into place, our original question of how the microbial community structure changes at different depths and age-gradients within permafrost peatlands will be conclusively answered.
ContributorsFrese, Alexander Nicholas (Author) / Cadillo-Quiroz, Hinsby (Thesis director) / van Paassen, Leon (Committee member) / Sarno, Analissa (Committee member) / School of Life Sciences (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Ephemeral and intermittent streams are valuable sources of surface water support in the arid ecosystems of the Southwestern United States. These streams account for over 80% of the streams in the American Southwest and their importance has been indicated in many studies. Ephemeral and intermittent streams support a wide range of plant and animal species in both continuous and episodic fashions. This study aimed to gain a better understanding of the relationship between streamflow permanence and patterns of biomass and secondary production of the riparian fauna these ecosystems support. This was accomplished through a yearlong survey in the Huachuca Mountains of Southeastern, Arizona where macroinvertebrates were collected at various sites along a gradient of streamflow permanence before, during, and after the three month monsoon season that supplies most of the annual rainfall in this region. The results of my surveys indicate that 1) Sites characterized by low streamflow permanence were more responsive to changes in precipitation than sites characterized by relatively high streamflow permanence 2) In ephemeral streams, there is a significant peak in terrestrial macroinvertebrate production and biomass both during and after the monsoon season 3) streamflow permanence may convey consistent but not exceptional secondary production whereas seasonality in rainfall may convey exceptional but episodic secondary production—more so in sites where streamflow is not consistent.
ContributorsMcCartin, Michael Patrick (Author) / Sabo, John (Thesis director) / Stromberg, Juliet (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
It is well known that deficiencies in key chemical elements (such as phosphorus, P) can reduce animal growth; however, recent empirical data have shown that high levels of dietary nutrients can also reduce animal growth. In ecological stoichiometry, this phenomenon is known as the "stoichiometric knife edge," but its underlying mechanisms are not well-known. Previous work has suggested that the crustacean zooplankter Daphnia reduces its feeding rates on phosphorus-rich food, causing low growth due to insufficient C (energy) intake. To test for this mechanism, feeding rates of Daphnia magna on algae (Scenedesmus acutus) differing in C:P ratio (P content) were determined. Overall, there was a significant difference among all treatments for feeding rate (p < 0.05) with generally higher feeding rates on P-rich algae. These data indicate that both high and low food C:P ratio do affect Daphnia feeding rate but are in contradiction with previous work that showed that P-rich food led to strong reductions in feeding rate. Additional experiments are needed to gain further insights.
ContributorsSchimpp, Sarah Ann (Author) / Elser, James (Thesis director) / Neuer, Susanne (Committee member) / Peace, Angela (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Sustainability (Contributor)
Created2014-05