Browsing by Subject "Methylation"

Now showing 1 - 6 of 6
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    The effect of high sulfate loading on methylmercury production, partitioning, and transport in mining-imapcted freshwater sediments and lakes in northeastern Minnesota
    (2015-02) Bailey, Logan Timothy
    Methylmercury (MeHg) is a highly toxic form of mercury with the ability to bioaccumulate in food webs. The bioaccumulation of MeHg leads to elevated MeHg levels in fish tissue and poses a threat to public health. Thus MeHg concentrations in surface waters - which may be a result of water column MeHg production, or sediment MeHg production and subsequent flux from sediment porewater - are of particular concern. The production of MeHg from inorganic mercury (iHg) is primarily a result of sulfate-reducing bacteria (SRB) activity in anoxic aquatic environments.Ongoing and historic mining activity on the Mesabi Iron Range (Minnesota, USA) has led to elevated sulfate levels in the downstream waters of the St. Louis River watershed. In an effort to understand the effect of mining-related sulfur-loading on the production and partitioning of MeHg, sediment samples were collected and analyzed from sulfur impacted and non sulfur-impacted lakes and wetlands within the watershed. Additionally, the water column and inlet and outlet streams of a mesotrophic lake (Lake McQuade) were sampled intensively during summer stratified conditions in order to identify the sources and sinks of MeHg to the lake system and determine the potential for MeHg export downstream.Results suggest that dissolved sulfide plays a large role in governing MeHg dynamics in sulfate-impacted freshwater sediment. Consistent with previous research, net MeHg production appeared to be inhibited in sediments with dissolved sulfide >60 uM. However, these high concentrations of dissolved sulfide were accompanied by increased partitioning of MeHg into the porewater phase, potentially increasing the fraction of MeHg available to be transported into surface waters.Sediment at sulfate-impacted sites was generally characterized by high dissolved sulfide and a low potential for long-term net MeHg production. However, the accumulation of dissolved sulfide in sediment porewaters can be limited by the availability of free labile iron (Fe2+) and consequent iron-sulfide precipitation reactions. In the results presented here, high sulfur-loading at two sites appeared to have consumed the available free labile iron and created conditions which allowed for the accumulation of dissolved sulfide and inhibition of MeHg production in the sediment. However, relatively high sulfur-loading(>100 mg/L) to a third site where iron remains in excess of sulfur in sediment may have led to robust net MeHg production, in absence of inhibitory dissolved sulfide concentrations. Accumulation of MeHg in the hypolimnion of Lake McQuade occurred during summer 2012 during a time when bottom water sulfate was being consumed. Though some uncertainty remains as to the ultimate source of the MeHg, estimates of MeHg inputs and outputs to the hypolimnion suggest that water column production was a primary source of MeHg to the hypolimnion during the stratified summer months. Following the wet spring months when inputs were dominated by upstream flows, the flux of MeHg across the limnetic surface was estimated to be the primary source of MeHg to the epilimnion during the stratified summer months. However, most of MeHg input to the epilimnion was apparently degraded prior to being exported to the outlet stream. Thus, despite mid-summer accumulation of MeHg in the hypolimnion, the combination of stratification and substantial degradation in the epilimnion acted to limit export of MeHg out of Lake McQuade.As a whole, Lake McQuade acted as small net source of MeHg to the surrounding water system during the summer months of 2012. Evidence points to a brief rise in MeHg export immediately following lake turnover in Mid-August due to the release of hypolimnetic MeHg to surface waters during lake mixing.
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    Epidemiology of childhood germ cell tumors (GCT): epigenome-wide methylation, differential MiRNA expression, and catchment quality of the CCRN
    (2013-09) Musselman, Jessica
    Epidemiology of Childhood Germ Cell Tumors (GCT): Epigenome-Wide Methylation, Differential MiRNA Expression, and Catchment Quality of the CCRN Germ cell tumors (GCTs) represent a heterogeneous group of neoplasms classified together through a common precursor cell, the primordial germ cell. The etiology of GCTs is not well elucidated, although genetic and epigenetic pathways are implicated. In this dissertation, I completed three complementary projects to further our understanding of these tumors. Project 1: I performed an epi-genome wide analysis of methylation in a large sample of childhood GCT (n = 111) to assess methylation with respect to survival, time to recurrence, and tumor histology. A semi-supervised recursively partitioned mixture modeling (SS-RPMM) algorithm segregated the GCTs into four methylation classes. Class membership was not significantly associated with tumor histology (p=0.06) or survival (p = 0.23), but was associated with disease recurrence (p = .02). These findings provide a strong rationale for future studies of methylation in GCT. Project 2: Particular interest has been paid to the role of miRNA in cancer in recent years, including studies in adult testicular GCTs. I conducted an evaluation of miRNA in GCTs by tumor and patient subgroups. Six miRNAs were differentially expressed by tumor histology after correction for multiple comparisons. These findings could provide insights into potential new targeted therapies. Project 3: The Childhood Cancer Research Network was established to ameliorate some of the difficulties associated with the study of childhood cancer; however, the quality of catchment in the CCRN has not been evaluated. I used data from the NCI's Surveillance, Epidemiology, and End Results (SEER) program and the 2010 U.S. Census to determine the ascertainment completeness of GCT cases over a 3-year period. Overall, enrollment was much lower than expected, particularly in the 15-19 year age group. These results provide useful insight into the completeness of case ascertainment of childhood GCT in the CCRN.
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    Functional characterization of two anaplasma phagocytophilum genes required for infection of mammalian host and tick vectors, respectively
    (2014-01) Oliva Chavez, Adela Sarahi
    Anaplasma phagocytophilum is a tick-borne pathogen and the causative agent of Human Granulocytic Anaplasmosis (HGA). A. phagocytophilum is not transovarially transmitted from the mother to the progeny of infected ticks and therefore needs to survive in both a mammalian and the arthropod vector in order to complete its life cycle. To adapt to different environments, A. phagocytophilum relies on differential gene expression as well as the post-translational modification of proteins. However, little is known about what A. phagocytophilum genes and enzymes are required for the infection of human or tick cells. I used random mutagenesis to generate knock-out strains of Ap for functional genomics studies. One of the mutated strains presented an insertion within the coding region of an O-methyltranferase (OMT) family 3, which affects the ability of A. phagocytophilum to infect tick cells. Studies in the function of this enzyme suggest that it is involved in the methylation of an outer membrane protein (Major Surface Protein 4), which appears to be involved in bacterial binding and entry. The second mutant presents an insertion within the coding region of a hypothetical protein in the locus APH_0906 and is unable to infect HL-60 cells and is impaired in its ability to grow in endothelial cells. Localization analysis of the protein showed that the protein is secreted into the cytoplasm and then translocated into the nucleus of host cells. Bioinformatic analyses demonstrated differences in Nuclear Localization Signals (NLSs) as well as binding residues within the protein homolog of human and non-human strains. Herein, I present the results from the functional analyses of both gene products.
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    Identification and characterization of DNA methylation variation within maize
    (2013-05) Eichten, Steven Richard
    DNA methylation is a genetic modification known to repress the activity of transposable elements, repetitive sequences, and in some cases genes. Although DNA methylation is often found in common locations across different individuals, evidence has shown that DNA methylation can vary between individuals at certain loci and can therefore have the opportunity to create a unique regulatory environment for the surrounding sequence. Beyond this, the relationship between DNA methylation state and the genetic content of an individual is still unclear. DNA methylation may act as a downstream effect of certain genetic signals, or it may act independently of genetic state as an epigenetic modification. The goal of this thesis is to profile the DNA methylation landscape across maize (Zea mays) and identify the genomic regions that display differential DNA methylation patterns. These regions of differential methylation are then further studied to understand their stability across generations, their influences on gene expression, as well as their connection to the genetic context they are found. The chapters describe the identification of thousands of differentially methylated regions (DMRs) between maize lines. These DMRs are shown to occur throughout the genome and have high stability across generations. In contrast, few DMRs are found across different tissues within the same genotype. DMRs are shown to often be associated with the local genetic variation. This genetic relationship is highlighted, along with the discovery of a mechanism of genetic control by the spreading of DNA methylation from certain retrotransposable elements. These results indicate that DMRs are present in maize and are created through both epigenetic and genetic means.
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    Mercury Methylation in Denitrifying Bioreactors: An Investigation in Pollution Swapping
    (2015-08) Natarajan, Michelle
    Woodchip and corn cob filled bioreactors have been shown repeatedly to be effective at reducing nitrate pollution from agricultural fields by supporting denitrifying bacteria. Little attention has been paid, however, to other microorganisms that may also proliferate in these environments. Of particular concern are sulfate reducing bacteria and other organisms known to convert mercury to highly toxic methylmercury, since supporting such organisms could lead to increased levels of methylmercury in downstream rivers and lakes. To investigate this concern, we conducted two studies. We measured total and methylmercury concentrations and related parameters in upflow column bioreactors filled with either woodchips or corn cobs. The temperature of the water pumped into the column bioreactors was in the range of 1.8�C to 18.6�C to simulate cooler autumn and winter weather. There was no significant mercury methylation detected at these temperatures. The concentration of methylmercury flowing out of the column bioreactors filled with corn cobs showed greater variability than that of woodchip filled bioreactors. The second study was set up to pump water with low concentrations of nitrate into four edge-of-field woodchip bioreactors to produce a residence time of 24 hours or more. We measured total and methylmercury concentrations along with other indicators of water chemistry and biological activity. While the conditions monitored in the bioreactors were consistent with documented conditions that support mercury methylating bacteria, we did not find evidence of methylmercury being generated within the bioreactors. These studies indicate that the production of methylmercury is not likely in Minnesota edge-of-field woodchip bioreactors or in woodchip or corn cob bioreactors where water temperatures are below 18.6�C and nitrates are not completely reduced.
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    Studies on apple peel color regulation.
    (2009-05) Rabinovich, Adriana Telias
    One of the most important factors determining apple [Malus pumila P. Mill.] market acceptance is peel color. Most apple cultivars (e.g. `Royal Gala') produce fruit with a defined fruit pigment pattern, but in the case of `Honeycrisp' apple, trees can produce fruits of two different kinds: striped and blushed. The causes of this phenomenon are unknown. We compared 'Honeycrisp' fruit from trees that were propagated from buds occurring on branches carrying only blushed or only striped fruit and concluded that blushed trees tend to produce a higher percentage of blushed fruit than striped trees, indicating a mechanism conserved through cell division. The percentage of blushed fruit on any given tree changed from year to year. Blushed and striped fruit occurred together on the same branch, and even on the same spur, with fruits located in the outer canopy being more likely to be striped. Higher crop loads were associated with a lower percentage of blushed fruit on the tree. Blushed and striped fruit do not consistently differ in their maximum pigment accumulation before ripening. The comparison of average hue angle for the whole peel at harvest indicates that blushed fruit are redder on average. We have also shown that striped areas of `Honeycrisp' and `Royal Gala' are due to sectorial increases in anthocyanin concentration. Transcript levels of the major biosynthetic genes and MdMYB10, a transcription factor that upregulates apple anthocyanin production, correlated with increased anthocyanin concentration in stripes. However, changes in the promoter and coding sequence of MdMYB10 do not correlate with skin pattern in `Honeycrisp' and other cultivars differing in peel pigmentation patterns. A survey of methylation levels throughout the coding region of MdMYB10 and a 2.5 kb region 5' of the ATG translation start site indicated that an area 900 bp long, starting 1400 bp upstream of the translation start site, is highly methylated. Comparisons of methylation levels of red and green stripes indicated that the degree of methylation of the MdMYB10 promoter is likely to be associated with the presence of stripes in these cultivars, with red stripes having lower methylation levels. Methylation may be associated with the presence of a TRIM retrotransposon within the promoter region, but the presence of the TRIM element alone cannot explain the phenotypic variability observed in `Honeycrisp'. We suggest that methylation in the MdMYB10 promoter is more variable in `Honeycrisp' than in `Royal Gala', leading to more variable color patterns in the peel of this cultivar.