Matching Items (29)
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- All Subjects: Chemistry
- All Subjects: Photosynthesis
- Creators: School of Molecular Sciences
- Member of: Theses and Dissertations
- Resource Type: Text
Description
In oxygenic photosynthesis, conversion of solar energy to chemical energy is catalyzed by the<br/>pigment-protein complexes Photosystem II (PSII) and Photosystem I (PSI) embedded within the<br/>thylakoid membrane of photoautotrophs. The function of these pigment-protein complexes are<br/>conserved between all photoautotrophs, however, the oligomeric structure, as well as the<br/>spectroscopic properties of the PSI complex, differ. In early evolving photoautotrophs, PSI<br/>exists in a trimeric organization, but in later evolving species this was lost and PSI exists solely<br/>as a monomer. While the reasons for a change in oligomerization are not fully understood, one<br/>of the 11 subunits within cyanobacterial PSI, PsaL, is thought to be involved in trimerization<br/>through the coordination of a calcium ion in an adjacent monomer. Recently published<br/>structures have demonstrated that PSI complexes are capable of trimerization without<br/>coordinating the calcium ion within PsaL.<br/>5 Here we explore the role the calcium ion plays in both<br/>the oligomeric and spectroscopic properties in PSI isolated from Synechocystis sp. PCC 6803.
ContributorsVanlandingham, Jackson R (Author) / Mazor, Yuval (Thesis director) / Mills, Jeremy (Committee member) / School of Life Sciences (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Nucleosomes are the basic repetitive unit of eukaryotic chromatin and are responsible for packing DNA inside the nucleus of the cell. They consist of a complex of eight histone proteins (two copies of four proteins H2A, H2B, H3 and H4) around which 147 base pairs of DNA are wrapped in ~1.67 superhelical turns. Although the nucleosomes are stable protein-DNA complexes, they undergo spontaneous conformational changes that occur in an asynchronous fashion. This conformational dynamics, defined by the "site-exposure" model, involves the DNA unwrapping from the protein core and exposing itself transiently before wrapping back. Physiologically, this allows regulatory proteins to bind to their target DNA sites during cellular processes like replication, DNA repair and transcription. Traditional biochemical assays have stablished the equilibrium constants for the accessibility to various sites along the length of the nucleosomal DNA, from its end to the middle of the dyad axis. Using fluorescence correlation spectroscopy (FCS), we have established the position dependent rewrapping rates for nucleosomes. We have also used Monte Carlo simulation methods to analyze the applicability of FRET fluctuation spectroscopy towards conformational dynamics, specifically motivated by nucleosome dynamics. Another important conformational change that is involved in cellular processes is the disassembly of nucleosome into its constituent particles. The exact pathway adopted by nucleosomes is still not clear. We used dual color fluorescence correlation spectroscopy to study the intermediates during nucleosome disassembly induced by changing ionic strength. Studying the nature of nucleosome conformational change and the kinetics is very important in understanding gene expression. The results from this thesis give a quantitative description to the basic unit of the chromatin.
ContributorsGurunathan, Kaushik (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Woodbury, Neal (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2011
Description
This work demonstrated a novel microfluidic device based on direct current (DC) insulator based dielectrophoresis (iDEP) for trapping individual mammalian cells in a microfluidic device. The novel device is also applicable for selective trapping of weakly metastatic mammalian breast cancer cells (MCF-7) from mixtures with mammalian Peripheral Blood Mononuclear Cells (PBMC) and highly metastatic mammalian breast cancer cells, MDA-MB-231. The advantage of this approach is the ease of integration of iDEP structures in microfliudic channels using soft lithography, the use of DC electric fields, the addressability of the single cell traps for downstream analysis and the straightforward multiplexing for single cell trapping. These microfluidic devices are targeted for capturing of single cells based on their DEP behavior. The numerical simulations point out the trapping regions in which single cell DEP trapping occurs. This work also demonstrates the cell conductivity values of different cell types, calculated using the single-shell model. Low conductivity buffers are used for trapping experiments. These low conductivity buffers help reduce the Joule heating. Viability of the cells in the buffer system was studied in detail with a population size of approximately 100 cells for each study. The work also demonstrates the development of the parallelized single cell trap device with optimized traps. This device is also capable of being coupled detection of target protein using MALDI-MS.
ContributorsBhattacharya, Sanchari (Author) / Ros, Alexandra (Committee member) / Ros, Robert (Committee member) / Buttry, Daniel (Committee member) / Arizona State University (Publisher)
Created2013
Description
Though schizophrenia was categorized as a mental illness over 100 years ago, there is a plethora of knowledge that continues to perplex the scientific and medical community alike. This tragic mental disorder affects approximately 1% of the general population, and many of these individuals are homeless if left untreated. Each schizophrenia patient has a different set of symptoms, so all of these patients experience a variety of positive and negative symptoms. Negative symptoms are called so as they are in absence, and some examples include apathy, anhedonia, lack of motivation, reduced social drive, and reduced cognitive functioning. Positive behavior, on the other hand, is a change in behavior or thoughts such as visual or auditory hallucinations, delusions, confused thoughts, disorganized speech, and trouble concentrating. Because schizophrenia patients do not share the exact same set of symptoms, research in schizophrenia requires a tremendous amount of medical resources. Over the last few years, new studies have started in the field of schizophrenia involving proteomics, or the study of proteins and their function. This new frontier gives doctors and scientists alike a new opportunity to improve the quality of life of schizophrenia patients by providing a potential method through which patients would receive individualized treatment based on their specific symptoms.
ContributorsPeterson, Rozabel (Author) / Brian, Jennifer (Thesis director) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Tempe Town Lake is the site of fifteen years’ worth of chemical data collection by ASU researchers. In 2018 the dataSONDE, an instrument capable of measuring different water quality parameters every thirty minutes for a month at a time was installed in the lake. The SONDE has the potential to completely reduce the need for sampling by hand. Before the SONDE becomes the sole means of gathering data, it is important to verify its accuracy. In this study, the measurements gathered by the SONDE (pH, dissolved oxygen, temperature, conductivity and colored dissolved organic matter) were compared to measurements gathered using the verified methods from the past fifteen years.
ContributorsSauer, Elinor Rayne (Author) / Hartnett, Hilairy (Thesis director) / Glaser, Donald (Committee member) / Shock, Everett (Committee member) / Historical, Philosophical & Religious Studies (Contributor) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
Description
Coral reefs are diverse marine ecosystems, where reef building corals provide both the structure of the habitat as well as the primary production through their symbiotic algae, and alongside algae living on the reef itself, are the basis of the food web of the reef. In this way, coral reefs are the ocean's "forests" and are estimated to support 25% of all marine species. However, due to the large size of a coral reef, the relative inaccessibility and the reliance on in situ surveying methods, our current understanding of reefs is spatially limited. Understanding coral reefs from a more spatially complete perspective will offer insight into the ecological factors that contribute to coral reef vitality. This has become a priority in recent years due to the rapid decline of coral reefs caused by mass bleaching. Despite this urgency, being able to assess the entirety of a coral reef is physically difficult and this obstacle has not yet been overcome. However, similar difficulties have been addressed in terrestrial ecosystems by using remote sensing methods, which apply hyperspectral imaging to assess large areas of primary producers at high spatial resolutions. Adapting this method of remote spectral sensing to assess coral reefs has been suggested, but in order to quantify primary production via hyper spectral imaging, light-use efficiencies (LUEs) of coral reef communities need to be known. LUEs are estimations of the rate of carbon fixation compared to incident absorbed light. Here, I experimentally determine LUEs and report on several parameters related to LUE, namely net productivity, respiration, and light absorbance for the main primary producers in coral reefs surrounding Bermuda, which consist of algae and coral communities. The derived LUE values fall within typical ranges for LUEs of terrestrial ecosystems, with LUE values for coral averaging 0.022 ± 0.002 mol O2 mol photons-1 day-1 at a water flow rate of 17.5 ± 2 cm s^(-1) and 0.049 ± 0.011 mol O2 mol photons-1 day-1 at a flow rate of 32 ± 4 cm s^(-1) LUE values for algae averaged 0.0335 ± 0.0048 mol O2 mol photons-1 day-1 at a flow rate of 17.5 ± 2 cm s^(-1). These values allow insight into coral reef productivity and opens the door for future remote sensing applications.
ContributorsFlesher, David A (Author) / Neuer, Susanne (Thesis director) / Redding, Kevin (Committee member) / School of Molecular Sciences (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Enzyme Replacement Therapy (ERT) is a treatment often used for patients with disorders that affect the production of various enzymes within the body, such as Cystic Fibrosis and Fabry Disease. ERT involves the use of artificially-produced enzymes, which can be derived from humans, pigs, and bacteria. Generally, enzymes derived from porcine and bacterial sources are much less expensive and more accessible than those derived from a human source. This, and the ethical implications that porcine enzymes carry, make the decision of choosing treatment simple to some and complex to others. Ethically, human-derived enzymes are often considered more ethical, while not conflicting with religious beliefs and practices as porcine-derived enzymes do.
In order to further compare porcine and human-derived enzymes, a determination of the enzyme effectiveness was done via digestion simulation. The digestion for both the human and porcine-derived enzymes consisted of three steps: oral, gastric, and intestinal. After the digestion, the absorbance for each enzyme class as well as a dilution curve of the formula used was read and recorded. Using the standard dilution curve and the absorbance values for each unknown, the formula and thus enzyme concentration that was lost through the reaction was able to be calculated.
The effectiveness of both the human and porcine enzymes, determined by the percent of formula lost, was 18.2% and 19.7%, respectively, with an error of 0.6% from the spectrophotometer, and an error of about 10% from the scale used for measuring the enzymes. This error was likely due to the small mass required of the enzymes and can be prevented in the future by performing the experiment at a larger scale.
In order to further compare porcine and human-derived enzymes, a determination of the enzyme effectiveness was done via digestion simulation. The digestion for both the human and porcine-derived enzymes consisted of three steps: oral, gastric, and intestinal. After the digestion, the absorbance for each enzyme class as well as a dilution curve of the formula used was read and recorded. Using the standard dilution curve and the absorbance values for each unknown, the formula and thus enzyme concentration that was lost through the reaction was able to be calculated.
The effectiveness of both the human and porcine enzymes, determined by the percent of formula lost, was 18.2% and 19.7%, respectively, with an error of 0.6% from the spectrophotometer, and an error of about 10% from the scale used for measuring the enzymes. This error was likely due to the small mass required of the enzymes and can be prevented in the future by performing the experiment at a larger scale.
ContributorsBlevins, Brianna R (Author) / Martin, Thomas (Thesis director) / McILwraith, Heide (Committee member) / College of Integrative Sciences and Arts (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
The heliobacteria, a family of anoxygenic phototrophs, are significant to photosynthesis evolution research, as they possess the simplest known photosynthetic apparatus. Although they are photoheterotrophs in the light, the heliobacteria may also grow chemotrophically via pyruvate metabolism in the absence of light. In Heliobacterium modesticaldum, the cytochrome bc complex is responsible for oxidizing menaquinol and reducing cytochrome c553 in the electron flow cycle used for phototrophy. However, there is no known electron acceptor for cytochrome c553 other than the photosynthetic reaction center. Therefore, it was hypothesized that the cytochrome bc complex is necessary for phototrophy, but unnecessary for chemotrophic growth in the dark. Under this hypothesis, a mutant of H. modesticaldum lacking the cytochrome bc complex was predicted to be viable, but non-phototrophic. In this project, a two-step method for CRISPR-based genome editing was used in H. modesticaldum to delete the genes encoding the cytochrome bc complex. Genotypic analysis verified the deletion of the petC, B, D, and A genes encoding the catalytic components of complex. Spectroscopic studies revealed that re-reduction of cytochrome c553 after flash-induced photo-oxidation was ~130 to 190 times slower in the ∆petCBDA mutant compared to wildtype, phenotypically confirming the removal of the cytochrome bc complex. The resulting ∆petCBDA mutant was unable to grow phototrophically, instead relying on pyruvate metabolism to grow chemotrophically as does wildtype in the dark.
ContributorsLeung, Sabrina (Author) / Redding, Kevin (Thesis director) / Liu, Wei (Committee member) / Vermaas, Wim (Committee member) / School of Molecular Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
As a child passes through the birth canal, they become inoculated with vital gram positive and gram-negative bacteria, aerobes and anaerobes. Breast milk helps to support this growing microbiome by providing oligosaccharides that support its proliferation. Breast milk can be considered the most nutritious source of food available to a growing infant by providing the necessary nutrients, growth hormones and antibodies to promote digestive health, growth, and a strong immune system. The Developmental Origins of Health and Disease Theory (DOHaD) is a theory that suggests a growing fetus and nursing child's nutrients and immune system are dependent on the mother's exposure to nutrients and toxins. Studies have shown a positive correlation between the length of nursing and a child's overall health through life. In addition, consuming an enriched diet after weaning builds a strong immunological and nutritional basis from which the child can grow. This leads to improvements in a child's overall health, which has beneficial long-term effects on morbidity and mortality. This project applied the theory to two Middle Horizon (AD500-1100) individuals from Akapana, Tiwanaku, in the Lake Titicaca Basin, Bolivia. Stable nitrogen and carbon isotope analysis was applied to first molar serial samples of these two individuals to determine weaning age and early childhood diet. Both individuals were male; one male died in adolescence between the age of 9-15 years, and the other died as an elderly adult around the age of 50-59 years. The results showed that the male who died in adulthood was provisioned with supplemental and post-weaning foods high in animal protein, and received breast milk until around 37 months of age. The adolescent male was weaned between 11-12 months and consumed a diet dominated by C4 plants \u2014 most likely maize \u2014 with much less protein. The correlation between prolonged access to breast milk and a healthier and more nutritious childhood diet and longevity are consistent with the theory discussed above.
ContributorsCampbell, Sibella Sweelin (Author) / Knudson, Kelly (Thesis director) / Marsteller, Sara (Committee member) / Greenwald, Alexandra (Committee member) / School of Human Evolution & Social Change (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
The Heliobacterial Reaction Center (HbRC) is the simplest Type I Reaction Center (RC) known today. However, upon illumination it has been found to produce menaquinol, and this has led to experiments investigating the function of this reduction scheme. The goal of the experiment was to investigate the mechanisms of menaquinol production through the use of Photosystem II (PSII) herbicides that are known to inhibit the QB quinone site in Type II RCs. Seven herbicides were chosen, and out of all of them terbuthylazine showed the greatest effect on the RC in isolated membranes when Transient Absorption Spectroscopy was used. In addition, terbuthylazine decreased menaquinone reduction to menaquinol by ~72%, slightly more than the reported effect of teburtryn (68%)1. In addition, terbuthylazine significantly impacted growth of whole cells under high light more than terbutryn.
ContributorsOdeh, Ahmad Osameh (Author) / Redding, Kevin (Thesis director) / Woodbury, Neal (Committee member) / Allen, James (Committee member) / School of Molecular Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05