Matching Items (78)
Description
Though it is a widespread adaptation in humans and many other animals, parental care comes in a variety of forms and its subtle physiological costs, benefits, and tradeoffs related to offspring are often unknown. Thus, I studied the hydric, respiratory, thermal, and fitness dynamics of maternal egg-brooding behavior in Children's pythons (Antaresia childreni). I demonstrated that tight coiling detrimentally creates a hypoxic developmental environment that is alleviated by periodic postural adjustments. Alternatively, maternal postural adjustments detrimentally elevate rates of egg water loss relative to tight coiling. Despite ventilating postural adjustments, the developmental environment becomes increasingly hypoxic near the end of incubation, which reduces embryonic metabolism. I further demonstrated that brooding-induced hypoxia detrimentally affects offspring size, performance, locomotion, and behavior. Thus, parental care in A. childreni comes at a cost to offspring due to intra-offspring tradeoffs (i.e., those that reflect competing offspring needs, such as water balance and respiration). Next, I showed that, despite being unable to intrinsically produce body heat, A. childreni adjust egg-brooding behavior in response to shifts in nest temperature, which enhances egg temperature (e.g., reduced tight coiling during nest warming facilitated beneficial heat transfer to eggs). Last, I demonstrated that A. childreni adaptively adjust their egg-brooding behaviors due to an interaction between nest temperature and humidity. Specifically, females' behavioral response to nest warming was eliminated during low nest humidity. In combination with other studies, these results show that female pythons sense environmental temperature and humidity and utilize this information at multiple time points (i.e., during gravidity [egg bearing], at oviposition [egg laying], and during egg brooding) to enhance the developmental environment of their offspring. This research demonstrates that maternal behaviors that are simple and subtle, yet easily quantifiable, can balance several critical developmental variables (i.e., thermoregulation, water balance, and respiration).
ContributorsStahlschmidt, Zachary R (Author) / DeNardo, Dale F (Thesis advisor) / Harrison, Jon (Committee member) / McGraw, Kevin (Committee member) / Rutowski, Ronald (Committee member) / Walsberg, Glenn (Committee member) / Arizona State University (Publisher)
Created2011
Description
A synbody is a newly developed protein binding peptide which can be rapidly produced by chemical methods. The advantages of the synbody producing process make it a potential human proteome binding reagent. Most of the synbodies are designed to bind to specific proteins. The peptides incorporated in a synbody are discovered with peptide microarray technology. Nevertheless, the targets for unknown synbodies can also be discovered by searching through a protein mixture. The first part of this thesis mainly focuses on the process of target searching, which was performed with immunoprecipitation assays and mass spectrometry analysis. Proteins are pulled down from the cell lysate by certain synbodies, and then these proteins are identified using mass spectrometry. After excluding non-specific bindings, the interaction between a synbody and its real target(s) can be verified with affinity measurements. As a specific example, the binding between 1-4-KCap synbody and actin was discovered. This result proved the feasibility of the mass spectrometry based method and also suggested that a high throughput synbody discovery platform for the human proteome could be developed. Besides the application of synbody development, the peptide microarray technology can also be used for immunosignatures. The composition of all types of antibodies existing in one's blood is related to an individual's health condition. A method, called immunosignaturing, has been developed for early disease diagnosis based on this principle. CIM10K microarray slides work as a platform for blood antibody detection in immunosignaturing. During the analysis of an immunosignature, the data from these slides needs to be validated by using landing light peptides. The second part of this thesis focuses on the validation of the data. A biotinylated peptide was used as a landing light on the new CIM10K slides. The data was collected in several rounds of tests and indicated that the variation among landing lights was significantly reduced by using the newly prepared biotinylated peptide compared with old peptide mixture. Several suggestions for further landing light improvement are proposed based on the results.
ContributorsSun, Minyao (Author) / Johnston, Stephen Albert (Thesis advisor) / Diehnelt, Chris Wayne (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)
Created2011
Description
Immunosignaturing is a new immunodiagnostic technology that uses random-sequence peptide microarrays to profile the humoral immune response. Though the peptides have little sequence homology to any known protein, binding of serum antibodies may be detected, and the pattern correlated to disease states. The aim of my dissertation is to analyze the factors affecting the binding patterns using monoclonal antibodies and determine how much information may be extracted from the sequences. Specifically, I examined the effects of antibody concentration, competition, peptide density, and antibody valence. Peptide binding could be detected at the low concentrations relevant to immunosignaturing, and a monoclonal's signature could even be detected in the presences of 100 fold excess naive IgG. I also found that peptide density was important, but this effect was not due to bivalent binding. Next, I examined in more detail how a polyreactive antibody binds to the random sequence peptides compared to protein sequence derived peptides, and found that it bound to many peptides from both sets, but with low apparent affinity. An in depth look at how the peptide physicochemical properties and sequence complexity revealed that there were some correlations with properties, but they were generally small and varied greatly between antibodies. However, on a limited diversity but larger peptide library, I found that sequence complexity was important for antibody binding. The redundancy on that library did enable the identification of specific sub-sequences recognized by an antibody. The current immunosignaturing platform has little repetition of sub-sequences, so I evaluated several methods to infer antibody epitopes. I found two methods that had modest prediction accuracy, and I developed a software application called GuiTope to facilitate the epitope prediction analysis. None of the methods had sufficient accuracy to identify an unknown antigen from a database. In conclusion, the characteristics of the immunosignaturing platform observed through monoclonal antibody experiments demonstrate its promise as a new diagnostic technology. However, a major limitation is the difficulty in connecting the signature back to the original antigen, though larger peptide libraries could facilitate these predictions.
ContributorsHalperin, Rebecca (Author) / Johnston, Stephen A. (Thesis advisor) / Bordner, Andrew (Committee member) / Taylor, Thomas (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)
Created2011
Description
African Swine Fever (ASF), endemic in many African countries, is now spreading to other continents. Though ASF is capable of incurring serious economic losses in affected countries, no vaccine exists to provide immunity to animals. Disease control relies largely on rapid diagnosis and the implementation of movement restrictions and strict eradication programs. Developing a scalable, accurate and low cost diagnostic for ASF will be of great help for the current situation. CIM's 10K random peptide microarray is a new high-throughput platform that allows systematic investigations of immune responses associated with disease and shows promise as a diagnostic tool. In this study, this new technology was applied to characterize the immune responses of ASF virus (ASFV) infections and immunizations. Six sets of sera from ASFV antigen immunized pigs, 6 sera from infected pigs and 20 sera samples from unexposed pigs were tested and analyzed statistically. Results show that both ASFV antigen immunized pigs and ASFV viral infected pigs can be distinguished from unexposed pigs. Since it appears that immune responses to other viral infections are also distinguishable on this platform, it holds the potential of being useful in developing a new ASF diagnostic. The ability of this platform to identify specific ASFV antibody epitopes was also explored. A subtle motif was found to be shared among a set of peptides displaying the highest reactivity for an antigen specific antibody. However, this motif does not seem to match with any antibody epitopes predicted by a linear antibody epitope prediction.
ContributorsXiao, Liang (Author) / Sykes, Kathryn (Thesis advisor) / Zhao, Zhan-Gong (Committee member) / Stafford, Phillip (Committee member) / Arizona State University (Publisher)
Created2011
Description
Studies of animal contests often focus solely on a single static measurement of fighting ability, such as the size or the strength of the individual. However, recent studies have highlighted the importance of individual variation in the dynamic behaviors used during a fight, such as, assessment strategies, decision making, and fine motor control, as being strong predictors of the outcome of aggression. Here, I combined morphological and behavioral data to discover how these features interact during aggressing interactions in male virile crayfish, Faxonius virilis. I predicted that individual variation in behavioral skill for decision making (i.e., number of strikes thrown), would determine the outcome of contest success in addition to morphological measurements (e.g. body size, relative claw size). To evaluate this prediction, I filmed staged territorial interactions between male F. virilis and later analyzed trial behaviors (e.g. strike, pinches, and bout time) and aggressive outcomes. I found very little support for skill to predict win/loss outcome in trials. Instead, I found that larger crayfish engaged in aggression for longer compared to smaller crayfish, but that larger crayfish did not engage in a greater number of claw strikes or pinches when controlling for encounter duration. Future studies should continue to investigate the role of skill, by using finer-scale techniques such as 3D tracking software, which could track advanced measurements (e.g. speed, angle, and movement efficiency). Such studies would provide a more comprehensive understanding of the relative influence of fighting skill technique on territorial contests.
ContributorsNguyen, Phillip Huy (Author) / Angilletta, Michael (Thesis director) / McGraw, Kevin (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Human-induced rapid environmental change (HIREC) influences nearly all of Earth's ecosystems through processes such as urbanization. Previous studies have found that urbanization influences biodiversity patterns, often yielding an increase in the abundance of a few urban-adapted taxa at the expense of native species diversity. The western black widow spider, Latrodectus hesperus, is a medically-important pest species that often forms dense urban subpopulations (i.e., infestations) relative to the low-density subpopulations found throughout undisturbed, desert habitat. Here, I employ field and laboratory studies to examine the population ecology and stoichiometry of this urban pest to increase our understanding of the mechanisms underlying its success. The population ecology of ten black widow subpopulations spread across metropolitan Phoenix, AZ was examined during the peak breeding season (June-August). This study revealed that arthropod prey abundance, female mass and population density of females showed significant spatial variation across the ten subpopulations. Additionally, prey abundance and foraging success, measured as the number of carcasses found in webs, were a strong determinant of female mass and population density within each subpopulation. To test the mechanisms that drive black widow infestations, I used ecological stoichiometry to examine the nutrient (nitrogen and phosphorus) composition of spiders and arthropod prey from urban habitat, desert habitat and a laboratory diet regime. These studies revealed that (1) spiders are more nutrient rich than cricket prey in the field, (2) spider subpopulations exhibit significant spatial variation in their nitrogen composition, (3) nutrient composition of urban spider subpopulations does not differ significantly from Sonoran desert subpopulations, (4) laboratory-reared spiders fed a diet of only laboratory-reared crickets are more nitrogen and phosphorus limited than field-captured spiders, and (5) cannibalism by laboratory-reared spiders alleviated phosphorus limitation, but not nitrogen limitation, when compared to field-captured spiders. This work highlights the need to examine the population ecology of species relationships, such as predator-prey dynamics, to fully understand the fecundity and population growth of urban pest species. Moreover, the integration of population ecology and stoichiometry illustrates the need to address mechanisms like nutrient limitation that may explain why urban pest populations thrive and native species diversity suffers following HIREC.
ContributorsTrubl, Patricia (Author) / Johnson, James C. (Thesis advisor) / Rutowski, Ronald (Thesis advisor) / McGraw, Kevin (Committee member) / Arizona State University (Publisher)
Created2012
Description
We propose a novel solution to prevent cancer by developing a prophylactic cancer. Several sources of antigens for cancer vaccines have been published. Among these, antigens that contain a frame-shift (FS) peptide or viral peptide are quite attractive for a variety of reasons. FS sequences, from either mistake in RNA processing or in genomic DNA, may lead to generation of neo-peptides that are foreign to the immune system. Viral peptides presumably would originate from exogenous but integrated viral nucleic acid sequences. Both are non-self, therefore lessen concerns about development of autoimmunity. I have developed a bioinformatical approach to identify these aberrant transcripts in the cancer transcriptome. Their suitability for use in a vaccine is evaluated by establishing their frequencies and predicting possible epitopes along with their population coverage according to the prevalence of major histocompatibility complex (MHC) types. Viral transcripts and transcripts with FS mutations from gene fusion, insertion/deletion at coding microsatellite DNA, and alternative splicing were identified in NCBI Expressed Sequence Tag (EST) database. 48 FS chimeric transcripts were validated in 50 breast cell lines and 68 primary breast tumor samples with their frequencies from 4% to 98% by RT-PCR and sequencing confirmation. These 48 FS peptides, if translated and presented, could be used to protect more than 90% of the population in Northern America based on the prediction of epitopes derived from them. Furthermore, we synthesized 150 peptides that correspond to FS and viral peptides that we predicted would exist in tumor patients and we tested over 200 different cancer patient sera. We found a number of serological reactive peptide sequences in cancer patients that had little to no reactivity in healthy controls; strong support for the strength of our bioinformatic approach. This study describes a process used to identify aberrant transcripts that lead to a new source of antigens that can be tested and used in a prophylactic cancer vaccine. The vast amount of transcriptome data of various cancers from the Cancer Genome Atlas (TCGA) project will enhance our ability to further select better cancer antigen candidates.
ContributorsLee, HoJoon (Author) / Johnston, Stephen A. (Thesis advisor) / Kumar, Sudhir (Committee member) / Miller, Laurence (Committee member) / Stafford, Phillip (Committee member) / Sykes, Kathryn (Committee member) / Arizona State University (Publisher)
Created2012
Description
Immunosignaturing is a technology that allows the humoral immune response to be observed through the binding of antibodies to random sequence peptides. The immunosignaturing microarray is based on complex mixtures of antibodies binding to arrays of random sequence peptides in a multiplexed fashion. There are computational and statistical challenges to the analysis of immunosignaturing data. The overall aim of my dissertation is to develop novel computational and statistical methods for immunosignaturing data to access its potential for diagnostics and drug discovery. Firstly, I discovered that a classification algorithm Naive Bayes which leverages the biological independence of the probes on our array in such a way as to gather more information outperforms other classification algorithms due to speed and accuracy. Secondly, using this classifier, I then tested the specificity and sensitivity of immunosignaturing platform for its ability to resolve four different diseases (pancreatic cancer, pancreatitis, type 2 diabetes and panIN) that target the same organ (pancreas). These diseases were separated with >90% specificity from controls and from each other. Thirdly, I observed that the immunosignature of type 2 diabetes and cardiovascular complications are unique, consistent, and reproducible and can be separated by 100% accuracy from controls. But when these two complications arise in the same person, the resultant immunosignature is quite different in that of individuals with only one disease. I developed a method to trace back from informative random peptides in disease signatures to the potential antigen(s). Hence, I built a decipher system to trace random peptides in type 1 diabetes immunosignature to known antigens. Immunosignaturing, unlike the ELISA, has the ability to not only detect the presence of response but also absence of response during a disease. I observed, not only higher but also lower peptides intensities can be mapped to antigens in type 1 diabetes. To study immunosignaturing potential for population diagnostics, I studied effect of age, gender and geographical location on immunosignaturing data. For its potential to be a health monitoring technology, I proposed a single metric Coefficient of Variation that has shown potential to change significantly when a person enters a disease state.
ContributorsKukreja, Muskan (Author) / Johnston, Stephen Albert (Thesis advisor) / Stafford, Phillip (Committee member) / Dinu, Valentin (Committee member) / Arizona State University (Publisher)
Created2012
Description
Parental care provides many benefits to offspring. One widely realized benefit is enhanced regulation of offspring's thermal environment. The developmental thermal environment during development can be optimized behaviorally through nest site selection and brooding, and it can be further enhanced by physiological heat production. In fact, enhancement of the developmental thermal environment has been proposed as the initial driving force for the evolution of endothermy in bird and mammals. I used pythons (Squamata: Pythonidae) to expand existing knowledge of behavioral and physiological parental tactics used to regulate offspring thermal environment. I first demonstrated that brooding behavior in the Children's python (Antaresia childreni) is largely driven by internal mechanisms, similar to solitary birds, suggesting that the early evolution of the parent-offspring association was probably hormonally driven. Two species of python are known to be facultatively thermogenic (i.e., are endothermic during reproduction). I expand current knowledge of thermogenesis in Burmese pythons (Python molurus) by demonstrating that females use their own body temperature to modulate thermogenesis. Although pythons are commonly cited as thermogenic, the actual extent of thermogenesis within the family Pythonidae is unknown. Thus, I assessed the thermogenic capability of five previously unstudied species of python to aid in understanding phylogenetic, morphological, and distributional influences on thermogenesis in pythons. Results suggest that facultative thermogenesis is likely rare among pythons. To understand why it is rare, I used an artificial model to demonstrate that energetic costs to the female likely outweigh thermal benefits to the clutch in species that do not inhabit cooler latitudes or lack large energy reserves. In combination with other studies, these results show that facultative thermogenesis during brooding in pythons likely requires particular ecological and physiological factors for its evolution.
ContributorsBrashears, Jake (Author) / DeNardo, Dale (Thesis advisor) / Harrison, Jon (Committee member) / Deviche, Pierre (Committee member) / McGraw, Kevin (Committee member) / Smith, Andrew (Committee member) / Arizona State University (Publisher)
Created2012
Description
Lung cancer is the leading cause of cancer-related deaths in the US. Low-dose computed tomography (LDCT) scans are speculated to reduce lung cancer mortality. However LDCT scans impose multiple risks including false-negative results, false- positive results, overdiagnosis, and cancer due to repeated exposure to radiation. Immunosignaturing is a new method proposed to screen and detect lung cancer, eliminating the risks associated with LDCT scans. Known and blinded primary blood sera from participants with lung cancer and no cancer were run on peptide microarrays and analyzed. Immunosignatures for each known sample collectively indicated 120 peptides unique to lung cancer and non-cancer participants. These 120 peptides were used to determine the status of the blinded samples. Verification of the results from Vanderbilt is pending.
ContributorsNguyen, Geneva Trieu (Author) / Woodbury, Neal (Thesis director) / Zhao, Zhan-Gong (Committee member) / Stafford, Phillip (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Department of Psychology (Contributor)
Created2015-05