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End date: 2016 × search.filters.applied.f.isOrgUnitOfPublicationTitle: College of Sciences × search.filters.applied.f.resourcesubtype: Thesis ×

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Now showing 1 - 10 of 150
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The interactive effects of environmental warming and habitat fragmentation on the structure of experimental protist communities

2016-08-01 , Tsai, Meng-Hsiu

Global biodiversity is threatened by substantial and increasing human activity, such as human-induced environmental warming and habitat fragmentation. The effects of warming and fragmentation on biodiversity have been carefully studied, yet their potential interactive effects are less understood. Using freshwater protist communities subject to warming and fragmentation, I present the first experimental evidence of the interactive effects of warming and fragmentation on biodiversity. Somewhat unexpectedly, I found that fragmentation positively affected biodiversity. The magnitude of the effects of fragmentation, however, varied with the warming treatments. In one of our experimental communities (Combination B), fragmentation showed a much stronger positive effect on protist richness when warming was not conducted, but it showed a weaker but significant positive effect under a warming scenario. In other communities (from Combination C), however, fragmentation showed a stronger positive effect on richness when warming was present than when it was absent in experimental treatments. I further show that these long-term effects may be due to the alternation of individual species growth rate affected by warming, fragmentation and their interaction in short-term projections. Moreover, these findings of positive effects of fragmentation and interactions with warming can be useful for understanding conservation strategies, especially in areas where biodiversity is currently threatened or will be in the future.

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From rivers to natural gas: The influence of allochthonous inputs on marine nitrogen fixation and the carbon cycle

2015-12-04 , Weber, Sarah C.

The Western Tropical North Atlantic (WTNA) was once thought to be a net source of carbon dioxide (CO₂) to the atmosphere, but recent studies have shown that this Amazon River influenced region may actually act as a net sink for CO₂. During a 2010 research cruise to the WTNA, we characterized the impact of the Amazon River on offshore diazotrophy (N₂-fixation) and the resulting stimulation of biological carbon export from surface waters. Through the delivery of phosphate- and silicate-replete waters to the nitrogen (N) limited surface waters of the WTNA, the aging Amazon River plume promotes the growth of diatom-diazotoph associations (DDAs). Regions supporting large DDA blooms were associated with increased pCO₂ and DIC drawdown in the surface waters, reflecting the net export of carbon from the mixed layer. The existence of this biologically mediated linkage between the C and N cycles in productive surface waters is well known, but we have only recently discovered a stimulatory relationship in deep waters between oil/gas release and N₂-fixation. This association was first observed after the Deepwater Horizon oil spill in 2010 and we again saw evidence for it in the days following the Hercules 265 natural gas blowout. This blowout event was characterized by the release of an unknown quantity of natural gas into the shelf waters of the Northern Gulf of Mexico, but we detected a response from the marine microbial community within days. We observed a significant drawdown of dissolved oxygen and found biogeochemical evidence for the incorporation of methane-carbon into the food web, along with a modest stimulation of N₂-fixation. The episodic nature of anthropogenic blowouts makes them difficult to study, so we use cold seeps in the Gulf of Mexico as natural analogues. Interestingly, we have measured both methane oxidation and N₂-fixation at depth above some of the more active seeps. Using NanoSIMS analyses, we have taken the first steps towards physically characterizing the organisms utilizing these metabolisms. It appears that different organisms are carrying out these processes, with CH₄-assimilation occurring primarily in individual particles or small aggregates, whereas N₂-fixtion was associated with larger, sulfur-containing aggregates. Continued NanoSIMS work in combination with the use of microbial ID techniques will help to further characterize these unique deepwater diazotrophs.

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Active methane oxidizing bacteria in a boreal peat bog ecosystem

2014-11-14 , Esson, Kaitlin Colleen

Boreal peatlands are important ecosystems to the global carbon cycle. Although they cover only 3% of the earth's land surface area, boreal peatlands store roughly one third of the world's soil carbon. Peatlands also comprise a large natural source of methane emitted to the atmosphere. Some methane in peatlands is oxidized before escaping to the atmosphere by aerobic methane oxidizing bacteria. With changing climate conditions, the fate of the stored carbon and emitted methane from these systems is uncertain. One important step toward better understanding the effects of climate change on carbon cycling in peatlands is to ascertain the microorganisms actively involved in carbon cycling. To investigate the active aerobic methane oxidizing bacteria in a boreal peat bog, a combination of microcosm experiments, DNA-stable isotope probing, and next generation sequencing technologies were employed. Studies were conducted on samples from the S1 peat bog in the Marcell Experimental Forest (MEF). Potential rates of methane oxidation were determined to be in the range of 13.85 to 17.26 μmol CH₄ g dwt⁻¹ d⁻¹. After incubating with ¹³C-CH₄, DNA was extracted from these samples, separated into heavy and light fractions with cesium chloride gradient formation by ultracentrifugation and needle fractionation, and fractions were fingerprinted with automated ribosomal intergenic spacer analysis (ARISA) and further interrogated with qPCR. Based on ARISA, distinct banding patterns were observed in heavy fractions in comparison to the light fractions indicating an incorporation of ¹³C into the DNA of active methane oxidizers. This was further supported by a relative enrichment in the functional gene pmoA, which encodes a subunit of the particulate methane monooxygenase, in heavy fractions from samples incubated for fourteen days. Within heavy fractions for samples incubated for 8 and 14 days, the relative abundance of methanotrophs increased to 37% and 25%, respectively, from an in situ abundance of approximately 4%. Phylogenetic analysis revealed that the methanotrophic community was composed of both Alpha and Gammaproteobacterial methanotrophs of the genera Methylocystis, Methylomonas, and Methylovulum. Both Methylocystis and Methylomonas have been detected in peatlands before, however, none of the phylotypes in this study were closely related to any known cultivated members of these groups. These data are the first to implicate Methylovulum as an active methane oxidizer in peatlands, though this organism has been detected in another cold aquatic ecosystem with consistent methane emissions. The Methylovulum sequences from this study, like Methylocystis and Methylomonas, were not closely related to the only cultivated member of this genus. While Methylocystis was dominant in ¹³C-enriched fractions with a relative abundance of 30% of the microbial community after an eight-day incubation, Methylomonas became dominant with a relative abundance of approximately 16% after fourteen days of incubation. The relative abundance of Methylovulum was maintained at 2% in ¹³C- enriched fractions after eight and fourteen days.

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Understanding the relation between RNase H and retrotransposition activity in the context of the Aicardi-Goutieres syndrome

2014-05-19 , Yang, Taehwan

Ribonucleases (RNases) H1 and H2 are endonucleases that hydrolyze the RNA strand of RNA-DNA hybrids forming at the chromosomal level as well as extra-chromosomal hybrids. Extra-chromosomal RNA-DNA hybrids can frequently occur in cells as intermediate structures in the process of reverse transcription and generation of cDNA by retrotransposition. It is known that mutations in RNase H2 are found in Aicardi-Goutières syndrome (AGS) patients. AGS is a rare but severe immune-mediated neurodevelopmental disorder. Currently, the mechanism by which defects in RNase H2 cause AGS is still unclear. We hypothesized that defects in RNases H, including those associated with AGS can trigger the accumulation of extra-chromosomal RNA-DNA hybrids. Thus, we speculate that increased stability of such free RNA-DNA hybrid structures could be a likely trigger for stimulating the autoimmune system, mimicking a viral infection in AGS patients. RNase H2 protein subunits of human and yeast Saccharomyces cerevisiae RNase H2 proteins have conserved amino acid sequences. Based on the similarity between human and yeast RNase H2, we thought to utilize S. cerevisiae as a research model to generate and study several AGS-related mutants. Initially, we set up an assay to detect retrotransposition activity in the budding yeast by introducing a recombinant DNA which includes a Ty1 retrotransposable element fused to an inactive his3 marker gene. To test whether the retrotransposition assay works in our yeast strains, we treated yeast cells with phosphonoformic acid (PFA) or knocked out DBR1 gene coding for the RNA lariat debranching enzyme. Both approaches strongly reduced the frequency of retrotransposition in our strains, demonstrating that the system was working as expected. Next, we examined whether yeast cells with defective forms of RNases H or AGS-orthologous mutants of RNase H2 had altered retrotransposition activity compared with cells with wild-type RNases H. Results showed that the retrotransposition activity was repressed in the absence of both types of RNase H. In addition, AGS-related mutants showed decreased retrotransposition frequencies when RNase H1 was also knocked-out. These findings are relevant to uncover the mechanism of the AGS.

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Effects of competition, disturbance and productivity on the dynamics of inducible trophic polymorphism in tetrahymena vorax

2016-08-01 , Yin, Yi

Inducible trophic polymorphism enables organisms to alter their trophic level when facing environmental changes, and therefore can ameliorate the intensity of competition. The freshwater ciliated protist Tetrahymena vorax was found to have three distinct phenotypic morphs with two trophic levels. Its carnivorous macrostomes consume intraspecific competitors and its bacterivorous pyriform microstome morph and tailed microstome morph indiscriminately. Cannibalism here indicates an extreme case of niche differentiation and resource utilization via phenotypic plasticity and significantly affects the dynamic equilibrium of T. vorax’s three morphs. By manipulating productivity level, disturbance frequency and the presence or absence of an interspecific competitor species Colpdium striatum, I demonstrated the dynamic transformations of T. vorax’s three morphs and endeavored to explain the underlying mechanisms. In this study, I also tested some classic assumptions about phenotypic tradeoffs in T. vorax and hence clarified some misunderstandings and proposed novel hypotheses.

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Moderately lower temperatures greatly extend the lifespan of Brachionus manjavacas (Rotifera): thermodynamics or gene regulation?

2015-11-20 , Johnston, Rachel Kelsey

Environmental temperature greatly affects lifespan in a wide variety of animals, but the exact mechanisms underlying this effect are still largely unknown. A moderate temperature decrease from 22°C to 16°C extends the lifespan of the monogonont rotifer Brachionus manjavacas by up to 163%. Thermodynamic effects on metabolism contribute to this increase in longevity, but are not the only cause. When rotifers are exposed to 16°C for four days and then transferred to 22°C, they survive until day 13 at nearly identical rates as rotifers maintained at 16°C continuously. This persistence of the higher survival for nine days after transfer to 22°C suggests that low temperature exposure alters the expression of genes that affect the rate of aging. The relative persistence of the gene regulation effect suggests that it may play an even larger role in slowing aging than the thermodynamic effects. The life extending effects of these short-term low temperature treatments are largest when the exposure happens early in the life cycle, demonstrating the importance of early development. There is no advantage to lowering the temperature below 16°C to 11° or 5°C. Rotifers exposed to 16°C also displayed increased resistance to heat, starvation, oxidative and osmotic stress. Reproductive rates at 16°C were lower than those at 22°C, but because they reproduce longer, there is no significant change in the lifetime fecundity of females. To investigate which genes contribute to these effects, the expression of specific temperature sensing genes was knocked down using RNAi. Of 12 genes tested, RNAi knockdown of four eliminated the survival enhancing effects of the four-day cold treatment: TRP7, forkhead box C, Y-box factor, and ribosomal protein S6. This demonstrates that active gene regulation is an important factor in temperature mediated life extension, and that these particular genes play an integral role in these pathways. As a thermoresponsive sensor, TRP7 may be responsible for triggering the signaling cascade contributing to temperature mediated life extension. The TRP genes may also provide especially promising candidates for targeted gene manipulations or pharmacological interventions capable of mimicking the effects of low temperature exposure. These results support recent theories of aging that claim rate of aging is determined by an actively regulated genetic program rather than an accumulation of molecular damage.

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Calibration of phenol oxidase measurement in acidic wetland environments

2014-07-22 , Chanton, Patrick

Phenol oxidases mediate the degradation of recalcitrant compounds, polyphenolics, in wetland soils and are considered to play a key role in the microbial carbon cycle of peatlands which predominate in boreal biomes. In order to validate a method for quantification of oxidative enzyme activity in acidic wetland environments, the relationship between pH and substrate oxidation was studied using the standard enzyme tyrosinase and in soils collected from six freshwater wetlands including three marshes in north Florida and peatlands of northern Minnesota. Phenol oxidase (PO) activity was quantified with two commonly used assay substrates, ABTS (2,2'-azino-bis(3-ethylobenzthiazoline-6-sulfonic acid) and L-DOPA (L-3,4-dihydroxyphenylalanine), across a pH range of 4 to 7 which matched the in situ pH range of the studied wetlands. The PO assay is sensitive and activity could be detected with either substrate across a pH range of 4 to 7. However, with the standard enzyme tyrosinase, it was shown that a large change or threshold in oxidation rates occurred at pH 5. At pH < 5, L-DOPA oxidation rates were greatly diminished and ABTS oxidation was at a maximum. Above pH 5, ABTS oxidation occurred at much slower rates and L-DOPA oxidation was at a maximum. The pH response of PO activity in wetland soils corroborated observations made with tyrosinase. Thus, ABTS is recommended to be an effective substrate for the quantification of PO activity at an in situ pH of < 5, while L-DOPA is recommended at an in situ pH of > 5. In soils collected from a northern Minnesota peatland, assays conducted at an in situ pH of 4 showed one to two orders of magnitude higher rates of PO activity in solid phase peat in comparison to porewater, indicating that the majority of PO activity is associated with the peat. At three Minnesota peatland sites, PO activity was shown to attenuate with depth in agreement with the activities of other enzymes and with rates of peat decomposition.

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Sustainable tilapia feed derived from urban food waste

2015-12-08 , Chaddick, Justin Garrett

Finding an alternative to fishmeal and fish oil in animal feeds has been a topic of increasing interest due to the pressures being put on the ocean’s fisheries and the increasing world demand for animal protein. An often-overlooked source of nutrients is in the form of food waste. One third of all food produced globally ends up in landfills, wasting a huge amount of nutrients and embodied energy that could otherwise be redirected towards productive use. This study investigated the feasibility of feeding Hermetia illucens, the black soldier fly larvae (BSFL), grown on urban food waste, and Lemna minor, a species of duckweed, to tilapia in a recirculating aquaponic system as a compound feed. The study compared the growth of two groups of 58 tilapia over 44 days; one group was fed commercial pellets and the other a compound feed composed of BSFL and duckweed. The group fed the commercial pellets achieved heavier weight gain than the group fed the experimental feed but both groups resulted in steady weight gain and had similar mortality rates. Feeding the experimental feed composed of BSFL and duckweed to tilapia in an aquaponics system is an effective method of diverting food waste from the landfill and further research should be done to optimize this process.

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INTERACTIVE EFFECTS OF DISTURBANCE AND DISPERSAL ON COMMUNITY ASSEMBLY

2015-11-18 , Bannister, Miriam Nozomi Ojima

The traditional debate on alternative community states has been over whether or not they exist. Recent studies have focused on the role of assembly history in dictating community divergence, but the context in which assembly history becomes important is a continued topic of interest. In this study, we created communities of bacterivorous ciliated protists in laboratory microcosms and manipulated assembly history, disturbance frequency, and the presence of dispersal among local communities to investigate the mechanisms behind community divergence. Specifically, we sought to understand how the role of assembly history changed in response to disturbance, dispersal, and the combination of the two. Assembly history determined the identity of the dominant species through priority effects, and dispersal and disturbance showed interactive effects on both alpha and beta diversity. Dispersal increased alpha diversity, but only in the absence of disturbance, and it reduced beta diversity, but not in the presence of low or mixed disturbance treatments. These results show that the role of assembly history and the strength of priority effects are dependent on community context. Each factor cannot be viewed in isolation, and understanding the interaction between them is important for understanding how communities assemble, which lends insight into how ecological restoration should be approached.

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Functional Analysis Of The Inhibition Of Topoisomerase II Alpha By Linker Histone H1

2014-07-02 , Hamdan, Hiba

In higher eukaryotes, DNA is progressively packaged into chromatin. In these varying levels of compaction, linker histone H1 is a key player for mediating chromatin folding. As a result, linker histone H1 is involved in regulating cellular activities, such as gene transcription. Also essential for multiple cellular processes, topoisomerase II alpha (Top2a) is an enzyme that regulates DNA topology and thus is a target in cancer therapeutics. Previous studies in our lab have identified Top2a as an H1.3 binding partner by immunoprecipitation in embryonic stem cells. Further studies have shown that mouse histone H1.3 inhibits Top2a enzymatic activity in vitro. In this thesis, I pursued a functional analysis to confirm and analyze the inhibitory effect of human H1.3 on Top2a in vivo. We found that overexpression of hH1.3 significantly suppressed the growth of HeLa cancer cells and resulted in an increased cell population with abnormal mitotic chromosomes. These analyses may lead to a better understanding of the role of H1 and Top2a in chromatin structure and function.

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