Browsing by Subject "Aggregation"
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Item Characterization of marine exopolymeric substance (EPS) responsible for binding of thorium (IV) isotopes(Texas A&M University, 2005-08-29) Alvarado Quiroz, Nicolas GabrielThe functional group composition of acid polysaccharides was determined after isolation using cross-flow ultrafiltration, radiolabeling with 234Th(IV) and other isotopes, and separation using isoelectric focusing (IEF) and polyacrylamide gel electrophoresis (PAGE). Phosphate and sulphate concentrations were determined from cultured bacterial and phytoplankton colloid, particulate and colloidal samples collected from the Gulf of M??xico (GOM). Characterization of the 234Th(IV)-binding biomolecule was performed using ion chromatography (IC), and gas chromatography-mass spectrometry (GC-MS). Radiotracer experiments and culture experiments were conducted in determining the binding environment of the 234Th(IV)-binding ligand (i.e., sorption onto suspended particles), as well as the origin of the ligand in seawater systems. In all samples, 234Th(IV) isoelectric focusing profiles indicated that 49% to 65% of the 234Th(IV) labeled EPS from Roseobacter gallaeciensis, Sagittula stellata, Emiliania huxleyi, Synechococcus elongatus and GOM Station 4-72m was found at a pHIEF of 2 in the IEF spectrum. The carboxylic acid group appeared at the same pHIEF as 234Th(IV) for EPS from Roseobacter gallaeciensis, Emiliania huxleyi, Synechococcus elongatus and GOM colloidal organic matter sample. The phosphate group appeared at the same pHIEF as 234Th(IV) for EPS from Roseobacter gallaeciensis, and Synechococcus elongatus sample. The sulphate group was found at the same pHIEF as 234Th(IV) for EPS from S. elongatus and GOM colloidal organic matter sample. The total polysaccharide content was only 14% and 8%, uronic acids were approximately 5.4% and 87.1%, and total protein content was 2.6% and 6.2% of total carbon content of Sagittula stellata and Synechococcus elongatus, respectively. Monosaccharides identified in both Sagittula stellata and Synechococcus elongatus were galactose, glucose, and xylose in common. In addition, Sagittula stellata contained mannose and Synechococcus elongatus had galactoglucuronic acid. Thus, depending on the species, the size, structural composition, and functional groups of the 234Th(IV)-binding, acidic polysaccharides will vary. From these observations, it is concluded that the steric environment and not necessarily the exact functional group might actually be responsible for thorium-234 complexation to macromolecular organic matter. This research helped to improve our understanding of the observed variability in POC/234Th ratios in the ocean and provided insights into factors that regulate organic carbon export fluxes.Item Cytoplasmic foci at the crossroads of artifactual science and biological function(2016-05) Zhao, Alice; Marcotte, Edward M.; Ellington, Andrew D; Zhang, Yan J; Appling, Dean R; Iyer, Vishwanath RDeciphering protein interaction and compartmentalization is crucial to understanding the molecular mechanisms that drive biological processes. Using various high throughput approaches, we have managed to score subcellular dynamic protein re-organization into supramolecular structures and map physical association networks to discover protein complexes on a proteome-wide level. However, the case by case studies of some of these novel structures and interactions reveal difficulties in interpreting their biological basis. This study offers insights into limits inherent in the molecular techniques used to investigate subcellular structures and protein interactions, describing a set of cautionary tales and critical analysis for deciphering cases of confounding data from orthogonal approaches. This study also offers a new experimental technique for high-throughput imaging assays with mammalian cell lines.Item Increasing TLB reach using TCAM cells(Texas A&M University, 2005-02-17) Kumar, AnujWe propose dynamic aggregation of virtual tags in TLB to increase its coverage and improve the overall miss ratio during address translation. Dynamic aggregation exploits both the spatial and temporal locality inherent in most application programs. To support dynamic aggregation, we introduce the use of ternary-CAM (TCAM) cells at the second-level TLB. The modified TLB architecture results in an increase of TLB reach without additional CAM entries. We also adopt bulk prefetching concurrently with aggregation technique to enhance the benefits due to spatial locality. The performance of the proposed TLB architecture is evaluated using SPEC2000 benchmarks concentrating on those that show high data TLB miss ratios. Simulation results indicate a reduction in miss ratios between 59% and 99.99% for all the considered bench-marks except for one benchmark, which has a reduction of 10%. We show that the L2 TLB when enhanced using TCAM cells is an attractive solution to high miss ratios exhibited by applications.Item Mechanisms and consequences of ATM activation(2015-05) Mand, Michael Rodgers; Paull, Tanya T.; Dalby, Kevin; Huibregtse, Jon; Marcotte, Edward; Miller, KyleMutations in the ataxia telangiectasia mutated (ATM) gene cause the disease ataxia-telangiectasia (A-T). Patients with this disease have multiple symptoms, including the eponymous ataxia and telangiectasia as well as immunodeficiency, radiation sensitivity, and increased cancer rates. The ATM protein is a kinase and is activated by multiple types of stress to affect many cellular processes. At sites of DNA double-strand breaks (DSBs), ATM is activated by the protein complex Mre11/Rad50/Nbs1 (MRN). As part of this complex, Rad50 binds and hydrolyzes ATP and causes large conformational changes in the complex. However, the importance of this enzymatic activity in the activation of ATM has been unknown. Here I show ATP binding by Rad50 is required for ATM activation while ATP hydrolysis is dispensable. ATM is also activated in the presence of oxidative stress. Separation-of-function mutations for the activation of ATM by DSBs and oxidative stress have been characterized in vitro. Here, the effects of expressing wild-type ATM or ATM with these different separation-of-function mutations in an ATM-deficient lymphoblast cell line have been characterized. Analysis of the proteomes of these cells and a control cell line revealed that non-functional ATM resulted in the loss of a large group of proteins by mass spectrometry. The levels of these proteins were similar in the cells, but in the presence of non-functional ATM they showed increased levels of aggregation. Thus my results suggest ATM may function to prevent aggregation in these conditions. Notably neurodegeneration is often associated with aggregation. In the phosphoproteomes of cells expressing the various ATM constructs, the parental cell line and cells with ATM unable to be activated by oxidative stress had lower levels of phosphopeptides predicted to be phosphorylated by CK2. This decrease in CK2 activity was also associated with increased aggregation, specifically a subunit of CK2 known as CK2β. This work provides insights into the mechanism of ATM activation by MRN and the potential involvement of ATM in the prevention of protein aggregation.Item Search for selection pressures associated with aggregation propensity following whole genome duplication in S.cerevisiae.(2011-12) Wittig, Michael David; Press, William H.; Marcotte, Edward M.It has been theorized that most proteins are under selection pressure to be soluble in crowded cellular spaces. To maintain solubility a proteins’ aggregation propensity should be inversely proportional to their maximum likely concentration. This theory was examined by comparing the proteome of the model organism S. cerevisiae, which has previously undergone a Whole Genome Duplication (WGD) event to the proteome of the closely related yeast K. waltii, which has not undergone WGD. This comparison revealed the following: 1) Predicted aggregation propensities are higher in S. cerevisiae than K. waltii. 2) Aggregation propensity does not predict which genes reverted to a single copy after WGD. 3) In genes which were retained as duplicates in S. cerevisiae after WGD, aggregation propensities rose from the inferred common ancestral protein. 4) Genes retained as duplicates showed less of an increase relative to their homologues in K. waltii than genes which were not retained as duplicates. 5) The relationship between the log predicted aggregation propensity and log mRNA expression level or log protein abundance was not linear as previously predicted. These results suggest that while there is broad selection pressure for reduced aggregation pressure for genes which have been duplicated, the precise relationship between aggregation propensity and gene expression is more complicated than previously predicted. These results also allow speculation that the whole genome duplication in S.cerevisiae may have been made possible by a general relaxation of aggregation-related selection pressure.Item Telling secondhand stories : news aggregation and the production of journalistic knowledge(2015-08) Coddington, Mark Allen; Reese, Stephen D.; Anderson, C W; Bock, Mary A; Lawrence, Regina G; Strover, Sharon LNews aggregation has become one of the most widely practiced forms of newswork, as more news is characterized by information taken from other published sources and displayed in a single abbreviated space. This form of newsgathering has deep roots in journalism history, but creates significant tension with modern journalism's primary newsgathering practice, reporting. Aggregation's reliance on secondhand information challenges journalism's valorization of firsthand evidence-gathering through the reporter's use of observation, interviews, and documents. This dissertation examines the epistemological practices and professional values of news aggregation, exploring how aggregators gather and verify evidence and present it as factual to audiences. It looks at aggregation in relationship to the dominant values and practices of modern professional journalism, particularly those of reporting. The study employs participant observation at three news aggregation operations as well as in-depth interviews with aggregators to understand the practices of news aggregation as well as the epistemological and professional values behind them. I found that aggregation proceeds by gathering textual evidence of the forms of evidence gathered through reporting work, positioning it as a form of second-order newswork built atop the epistemological practices and values of modern journalistic reporting. Aggregators' distance from the evidence on which they base their reports lends them a profound sense of uncertainty, which they attempt to mitigate by using textual means to communicate their epistemological ambivalence to their audiences and by seeking out technologically afforded means to get closer to news evidence. Aggregators' uncertainty extends to their professional identity, where they attempt to improve their marginal professional status by articulating their own ethical values but also by emphasizing their connections to traditional reporting. Narratively speaking, however, their work does not break down traditional journalistic forms, but instead broadens the narrative horizon to conceive of individual news accounts primarily as part of larger story arcs. The study illuminates the fraught relationship between aggregation and reporting, finding that while aggregation is heavily dependent on reporting, it can be developed as a valid, professionally valued form of newswork. Ultimately, both forms of work have a crucial role to play in providing vital, engaging news to the public.Item Uncertainty quantification for risk assessment of loss-of-coolant accident frequencies in nuclear power plants(2013-08) Pan, Ying-An; Morton, David P.This research presents the methodologies used to resolve the Nuclear Regulatory Commission Generic Safety Issue 191. The presented results are specific to South Texas Project Nuclear Operating Company (STPNOC). However, the proposed methodologies may be applicable to other nuclear power plants given the appropriate plant-specific frequencies. This research provides important inputs to CASA Grande, a computer program used to model physical phenomena and quantify uncertainties to obtain estimates of failure probabilities for post-loss-of-coolant accident events at the STPNOC containment. We provide modeling and sampling methods for loss-of-coolant accident (LOCA) frequencies and break sizes. We focus on a study known as NUREG-1829 (Tregoning et al., 2008), which includes an expert elicitation of quantiles governing the (annual) frequency of a LOCA in boiling water reactors and pressurized water reactors. We propose to model LOCA frequencies with bounded Johnson distributions and to sample break sizes using uniform distributions. We then develop a new method to distribute LOCA frequencies to different locations within a plant to account for the location-dependent differences while preserving the NUREG-1829 frequencies. We also propose to linearly interpolate the NUREG-1829 LOCA frequencies to obtain the frequencies for any break sizes other than those from NUREG-1829. In addition, we present a method to obtain the distribution of LOCA frequency within a break-size interval providing important inputs to the probabilistic risk assessment quantification for STPNOC. We review methods of combining the probability distributions of multiple experts to obtain a single probability distribution. More specifically, we describe the relative merits of the arithmetic mean (AM) and geometric mean (GM) as ways of performing this aggregation in the context of probabilities associated with rare events. Examining a set of pressurized water reactor results from NUREG-1829, we conclude that the GM represents a consistently sensible notion of the middle of the opinions expressed by nine experts. We further conclude that the AM is inappropriate for representing the center of the group's opinion for large effective break sizes. Instead, as the break size grows large a single expert's opinion dominates the combination produced by the AM.