Matching Items (143)
Description
Finding life beyond Earth could change our understanding of life and habitability. The best place to look for life beyond Earth is Jupiter's moon, Europa. It has been estimated Europa may have a liquid, salt-water subsurface with 2 to 3 times the volume of all Earth's oceans. Knowing that all life requires water, it is in our best interest to explore Europa. This thesis explored the plausibility of life on Europa in four of its environments: on the surface, under the ice shell, in the liquid subsurface, and at the bottom of the liquid subsurface. Each of these environments were defined from science literature and compared to known Earth analogs. Europa's surface is not likely to support life, as there is not liquid water present. There is also extremely high radiation bombardment and extremely low surface temperatures that are estimated to be well out of the range for supporting life. It is more plausible that life could be under Europa's ice shell than on the surface. Under the surface, radiation exposure dramatically reduces. Researchers have found organisms on Earth that can live in similar environments as Europa's ice as well. These organisms require some interaction with liquid water though. Uncertainties about Europa's ice shell thickness and radiation load per depth it experiences, as well as there being limited research on organisms in ice environments, hinder us from definitively assessing the plausibility of life under the surface. The best environment on Europa to look for life on Europa is the subsurface. There remain a lot of uncertainties about the subsurface, however, that make it difficult to assess the plausibility of finding life. These uncertainties include its depth, water activity, salinity, temperature, pressure, and structure. This subsurface may be suitable for life, but until we can further understand the environment of the subsurface, we cannot make definite conclusions. As for assessing the plausibility of life at the bottom of Europa's subsurface, there is not much we know about this environment either. It has been suggested there may be hydrothermal vents, but no evidence has either supported or rejected this idea. Without a clear understanding of the environment at the bottom of the subsurface, the plausibility of life here cannot be definitively answered. It is apparent we need to further study Europa. In particular, we need to focus on understanding the subsurface. When the subsurface is better defined, we can better assess the plausibility of life being present. Fortunately, both NASA and the ESA are currently planning missions to Europa that are scheduled to launch in the 2020s.
ContributorsHoward, Cheyenne Whiffen (Author) / Farmer, Jack (Thesis director) / Shock, Everett (Committee member) / School of Earth and Space Exploration (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
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
Aberrant glycosylation has been shown to be linked to specific cancers, and using this idea, it was proposed that the levels of glycans in the blood could predict stage I adenocarcinoma. To track this glycosylation, glycan were broken down into glycan nodes via methylation analysis. This analysis utilized information from N-, O-, and lipid linked glycans detected from gas chromatography-mass spectrometry. The resulting glycan node-ratios represent the initial quantitative data that were used in this experiment.
For this experiment, two Sets of 50 µl blood plasma samples were provided by NYU Medical School. These samples were then analyzed by Dr. Borges’s lab so that they contained normalized biomarker levels from patients with stage 1 adenocarcinoma and control patients with matched age, smoking status, and gender were examined. An ROC curve was constructed under individual and paired conditions and AUC calculated in Wolfram Mathematica 10.2. Methods such as increasing size of training set, using hard vs. soft margins, and processing biomarkers together and individually were used in order to increase the AUC. Using a soft margin for this particular data set was proved to be most useful compared to the initial set hard margin, raising the AUC from 0.6013 to 0.6585. In regards to which biomarkers yielded the better value, 6-Glc/6-Man and 3,6-Gal glycan node ratios had the best with 0.7687 AUC and a sensitivity of .7684 and specificity of .6051. While this is not enough accuracy to become a primary diagnostic tool for diagnosing stage I adenocarcinoma, the methods examined in the paper should be evaluated further. . By comparison, the current clinical standard blood test for prostate cancer that has an AUC of only 0.67.
For this experiment, two Sets of 50 µl blood plasma samples were provided by NYU Medical School. These samples were then analyzed by Dr. Borges’s lab so that they contained normalized biomarker levels from patients with stage 1 adenocarcinoma and control patients with matched age, smoking status, and gender were examined. An ROC curve was constructed under individual and paired conditions and AUC calculated in Wolfram Mathematica 10.2. Methods such as increasing size of training set, using hard vs. soft margins, and processing biomarkers together and individually were used in order to increase the AUC. Using a soft margin for this particular data set was proved to be most useful compared to the initial set hard margin, raising the AUC from 0.6013 to 0.6585. In regards to which biomarkers yielded the better value, 6-Glc/6-Man and 3,6-Gal glycan node ratios had the best with 0.7687 AUC and a sensitivity of .7684 and specificity of .6051. While this is not enough accuracy to become a primary diagnostic tool for diagnosing stage I adenocarcinoma, the methods examined in the paper should be evaluated further. . By comparison, the current clinical standard blood test for prostate cancer that has an AUC of only 0.67.
ContributorsDe Jesus, Celine Spicer (Author) / Taylor, Thomas (Thesis director) / Borges, Chad (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Yellowstone National Park has a vibrant variety of flora, fauna, and hydrothermal systems all collected together in one large and complex system. Studies have been conducted for at least several decades in order to make sense of this system in ways that may be relevant to other similar geologies around the world. The latest update in this ever-ongoing study involves the collection and analysis of water samples from 2016. These samples have been analyzed for conductivity, pH, temperature, dissolved organic carbon, dissolved inorganic carbon, carbon isotopes, dissolved oxygen, ferrous iron, sulfide, silica, and more. While not many trends were found in this data in regards to dissolved organic carbon values, this is a substantial addition to a growing body of information that could yield more impressive information in times to come. In addition, factors that have yet to analyzed for this 2016 data, such as concentrations of metals and metalloids, may provide some insights when put through a chloride vs sulfate framework to separate out different reaction regions.
ContributorsDoan, Cuong Le (Author) / Shock, Everett (Thesis director) / Gould, Ian (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
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
Description
Microfluidic platforms have been exploited extensively as a tool for the separation of particles by electric field manipulation. Microfluidic devices can facilitate the manipulation of particles by dielectrophoresis. Separation of particles by size and type has been demonstrated by insulator-based dielectrophoresis in a microfluidic device. Thus, manipulating particles by size has been widely studied throughout the years. It has been shown that size-heterogeneity in organelles has been linked to multiple diseases from abnormal organelle size. Here, a mixture of two sizes of polystyrene beads (0.28 and 0.87 μm) was separated by a ratchet migration mechanism under a continuous flow (20 nL/min). Furthermore, to achieve high-throughput separation, different ratchet devices were designed to achieve high-volume separation. Recently, enormous efforts have been made to manipulate small size DNA and proteins. Here, a microfluidic device comprising of multiple valves acting as insulating constrictions when a potential is applied is presented. The tunability of the electric field gradient is evaluated by a COMSOL model, indicating that high electric field gradients can be reached by deflecting the valve at a certain distance. Experimentally, the tunability of the dynamic constriction was demonstrated by conducting a pressure study to estimate the gap distance between the valve and the substrate at different applied pressures. Finally, as a proof of principle, 0.87 μm polystyrene beads were manipulated by dielectrophoresis. These microfluidic platforms will aid in the understanding of size-heterogeneity of organelles for biomolecular assessment and achieve separation of nanometer-size DNA and proteins by dielectrophoresis.
ContributorsOrtiz, Ricardo (Author) / Ros, Alexandra (Thesis advisor) / Hayes, Mark (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2021
Description
The ability to find evidence of life on early Earth and other planets is constrained by the current understanding of biosignatures and our ability to differentiate fossils from abiotic mimics. When organisms transition from the living realm to the fossil record, their morphological and chemical characteristics are modified, usually resulting in the loss of information. These modifications can happen during early and late diagenesis and differ depending on local geochemical properties. These post-depositional modifications need to be understood to better interpret the fossil record. Siliceous hot spring deposits (sinters) are of particular interest for biosignature research as they are early Earth analog environments and targets for investigating the presence of fossil life on Mars. As silica-supersaturated fluids flow from the vent to the distal apron, they precipitate non-crystalline opal-A that fossilizes microbial communities at a range in scales (μm-cm). Therefore, many studies have documented the ties between the active microbial communities and the morphological and chemical biosignatures in hot springs. However, far less attention has been placed on understanding preservation in systems with complex mineralogy or how post-depositional alteration affects the retention of biosignatures. Without this context, it can be challenging to recognize biosignatures in ancient rocks. This dissertation research aims to refine our current understanding of biosignature preservation and retention in sinters. Biosignatures of interest include organic matter, microfossils, and biofabrics. The complex nature of hot springs requires a comprehensive understanding of biosignature preservation that is representative of variable chemistries and post-depositional alterations. For this reason, this dissertation research chapters are field site-based. Chapter 2 investigates biosignature preservation in an unusual spring with mixed opal-A-calcite mineralogy at Lýsuhóll, Iceland. Chapter 3 tracks how silica diagenesis modifies microfossil morphology and associated organic matter at Puchuldiza, Chile. Chapter 4 studies the effects of acid fumarolic overprinting on biosignatures in Gunnuhver, Iceland. To accomplish this, traditional geologic methods (mapping, petrography, X-ray diffraction, bulk elemental analyses) were combined with high-spatial-resolution elemental mapping to better understand diagenetic effects in these systems. Preservation models were developed to predict the types and styles of biosignatures that can be present depending on the depositional and geochemical context. Recommendations are also made for the types of deposits that are most likely to preserve biosignatures.
ContributorsJuarez Rivera, Marisol (Author) / Farmer, Jack D (Thesis advisor) / Hartnett, Hilairy E (Committee member) / Shock, Everett (Committee member) / Garcia-Pichel, Ferran (Committee member) / Trembath-Reichert, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2021
Description
In cold chain tracking systems, accuracy and flexibility across different temperatures ranges plays an integral role in monitoring biospecimen integrity. However, while two common cold chain tracking systems are currently available (electronic and physics/chemical), there is not an affordable cold chain tracking mechanism that can be applied to a variety of temperatures while maintaining accuracy for individual vials. Hence, our lab implemented our understanding of biochemical reaction kinetics to develop a new cold chain tracking mechanism using the permanganate/oxalic acid reaction. The permanganate/oxalic acid reaction is characterized by the reduction of permanganate (MnVII) to Mn(II) with Mn(II)-autocatalyzed oxidation of oxalate to CO2, resulting in a pink to colorless visual indicator change when the reaction system is not in the solid state (i.e., frozen or vitrified). Throughout our research, we demonstrate, (i) Improved reaction consistency and accuracy along with extended run times with the implementation of a nitric acid-based labware washing protocol, (ii) Simulated reaction kinetics for the maximum length reaction and 60-minute reaction based on previously developed MATLAB scripts (iii) Experimental reaction kinetics to verify the simulated MATLAB maximum and 60-minute reactions times (iv) Long-term stability of the permanganate/oxalic acid reaction with water or eutectic solutions of sodium perchlorate and magnesium perchlorate at -80°C (v) Reaction kinetics with eutectic solvents, sodium perchlorate and magnesium perchlorate, at 25°C, 4°C, and -8°C (vi) Accelerated reaction kinetics after the addition of varying concentrations of manganese perchlorate (vii) Reaction kinetics of higher concentration reaction systems (5x and 10x; for darker colors), at 25°C (viii) Long-term stability of the 10x higher concentration reaction at -80°C.
ContributorsLjungberg, Emil (Author) / Borges, Chad (Thesis director) / Levitus, Marcia (Committee member) / Williams, Peter (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor) / Department of Psychology (Contributor)
Created2022-12
Description
I present results of field and laboratory experiments investigating the habitability of one of Earth’s driest environments: the Atacama Desert. This Desert, along the west coast of South America spanning Perú and Chile, is one of the driest places on Earth and has been exceedingly arid for millions of years. These conditions create the perfect natural laboratory for assessing life at the extremes of habitability. All known life needs water; however, the extraordinarily dry Atacama Desert is inhabited by well-adapted microorganisms capable of colonizing this hostile environment. I show field and laboratory evidence of an environmental process, water vapor adsorption, that provides a daily, sustainable input of water into the near (3 - 5 cm) subsurface through water vapor-soil particle interactions. I estimate that this water input may rival the yearly average input of rain in these soils (~2 mm).
I also demonstrate, for the first time, that water vapor adsorption is dependent on mineral composition via a series of laboratory water vapor adsorption experiments. The results of these experiments provide evidence that mineral composition, and ultimately soil composition, measurably and significantly affect the equilibrium soil water content. This suggests that soil microbial communities may be extremely heterogeneous in distribution depending on the distribution of adsorbent minerals.
Finally, I present changes in biologically relevant gasses (i.e., H2, CH4, CO, and CO2) over long-duration incubation experiments designed to assess the potential for biological activity in soils collected from a hyperarid region in the Atacama Desert. These long-duration experiments mimicked typical water availability conditions in the Atacama Desert; in other words, the incubations were performed without condensed water addition. The results suggest a potential for methane-production in the live experiments relative to the sterile controls, and thus, for biological activity in hyperarid soils. However, due to the extremely low biomass and extremely low rates of activity in these soils, the methods employed here were unable to provide robust evidence for activity. Overall, the hyperarid regions of the Atacama Desert are an important resource for researchers by providing a window into the environmental dynamics and subsequent microbial responses near the limit of habitability.
ContributorsGlaser, Donald M (Author) / Hartnett, Hilairy E (Thesis advisor) / Anbar, Ariel (Committee member) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2022
Description
Plasma and serum are the most commonly used liquid biospecimens in biomarker research. These samples may be subjected to several pre-analytical variables (PAVs) during collection, processing and storage. Exposure to thawed conditions (temperatures above -30 °C) is a PAV that is hard to control, and track and could provide misleading information, that fail to accurately reveal the in vivo biological reality, when unaccounted for. Hence, assays that can empirically check the integrity of plasma and serum samples are crucial. As a solution to this issue, an assay titled ΔS-Cys-Albumin was developed and validated. The reference range of ΔS-Cys-Albumin in cardio vascular patients was determined and the change in ΔS-Cys-Albumin values in different samples over time course incubations at room temperature, 4 °C and -20 °C were evaluated. In blind challenges, this assay proved to be successful in identifying improperly stored samples individually and as groups. Then, the correlation between the instability of several clinically important proteins in plasma from healthy and cancer patients at room temperature, 4 °C and -20 °C was assessed. Results showed a linear inverse relationship between the percentage of proteins destabilized and ΔS-Cys-Albumin regardless of the specific time or temperature of exposure, proving ΔS-Cys-Albumin as an effective surrogate marker to track the stability of clinically relevant analytes in plasma. The stability of oxidized LDL in serum at different temperatures was assessed in serum samples and it stayed stable at all temperatures evaluated. The ΔS-Cys-Albumin requires the use of an LC-ESI-MS instrument which limits its availability to most clinical research laboratories. To overcome this hurdle, an absorbance-based assay that can be measured using a plate reader was developed as an alternative to the ΔS-Cys-Albumin assay. Assay development and analytical validation procedures are reported herein. After that, the range of absorbance in plasma and serum from control and cancer patients were determined and the change in absorbance over a time course incubation at room temperature, 4 °C and -20 °C was assessed. The results showed that the absorbance assay would act as a good alternative to the ΔS-Cys-Albumin assay.
ContributorsJehanathan, Nilojan (Author) / Borges, Chad (Thesis advisor) / Guo, Jia (Committee member) / Van Horn, Wade (Committee member) / Arizona State University (Publisher)
Created2022