Characterization of Glycation Sites on Human Serum Albumin using Mass Spectrometry

The modification of proteins by reducing sugars is a process that occurs naturally in the body. This process, which is known as glycation, has been linked to many of the chronic complications encountered during diabetes. Glycation has also been linked to changes in the binding of human serum albumin (HSA) to several drugs and small solutes in the body. While these effects are known, there is little information that explains why these changes in binding occur. The goal of this project was to obtain qualitative and quantitative information about glycation that occurs on HSA. The first section of this dissertation examined methods that could be used to quantify and identify glycation that occurs on HSA. The extent of glycation that occurred on HSA was quantified using oxygen-18 labeling mass spectrometry and the glycation sites were identified by observing the mass-to-charge (m/z) shifts that occurred in glycated HSA. This initial investigation revealed that oxygen-18 labeling based quantitation can be improved over previous methods if a relative comparison is done with oxygen-18 labeled peptides in a control HSA sample. Similarly, the process of making m/z shift-based assignments could be improved if only the peptides that were unique to the glycated HSA samples were used with internal calibration. These techniques were used in subsequent chapters for the assignment of early and late-stage glycation products on HSA. The regions of HSA that contained the highest amount of modification were identified, quantified, and ranked in order of their relative abundance. Of the commonly reported glycation sites, the N-terminus was found to have the highest extent of modification, followed by lysines 525, 199, and 439. The relative amount of modification on lysine 281, with respect to the aforementioned residues, varied with different degrees of glycation. The oxygen-18 labeling approach used for this analysis was novel because it allowed for the simultaneous quantification of all glycation-related modifications that were occurring on HSA. As such, several arginine residues were also found to have high amounts of modification on glycated HSA.

Selection of Switching Sites in All-Optical Nework Topology Design

In this paper, we consider the problem of topology design for optical networks. We investigate the problem of selecting switching sites to minimize total cost of the optical network. The cost of an optical network can be expressed as a sum of three main factors: the site cost, the link cost, and the switch cost. To the best of our knowledge, this problem has not been studied in its general form as investigated in this paper. We present a mixed integer quadratic programming (MIQP) formulation of the problem to find the optimal value of the total network cost. We also present an efficient heuristic to approximate the solution in polynomial time. The experimental results show good performance of the heuristic. The value of the total network cost computed by the heuristic varies within 2% to 21% of its optimal value in the experiments with 10 nodes. The total network cost computed by the heuristic for 51% of the experiments with 10 node network topologies varies within 8% of its optimal value. We also discuss the insight gained from our experiments.

State of the Arctic October 2006

This State of the Arctic Report presents a review of recent data by an international group of scientists who developed a consensus on the information content and reliability. The report highlights data primarily from 2000 to 2005 with a first look at winter 2006, providing an update to some of the records of physical processes discussed in the Arctic Climate Impact Assessment (ACIA, 2004, 2005). Of particular note: • Atmospheric climate patterns are shifting (Fig. 1). The late winter/spring pattern for 2000–2005 had new hot spots in northeast Canada and the East Siberian Sea relative to 1980–1999. Late winter 2006, however, shows a return to earlier climate patterns, with warm temperatures in the extended region near Svalbard. • Ocean salinity and temperature profiles at the North Pole and in the Beaufort Sea, which changed abruptly in the 1990s, show that conditions since 2000 have relaxed toward the pre-1990 climatology, although 2001–2004 has seen an increase in northward ocean heat transport through Bering Strait (Fig. 2), which is thought to impact sea ice loss. • Sea ice extent continues to decrease. The sea ice extent in September 2005 was the minimum observed in summer during the satellite era (beginning in 1979), marking an unprecedented series of extreme ice extent minima beginning in 2002 (Fig. 3). The sea ice extent in March 2006 was also the minimum observed in winter during the satellite era. • Tundra vegetation greenness increased, primarily due to an increase in the abundance of shrubs. Boreal forest vegetation greenness decreased, possibly due to drought conditions (Fig. 4). • There is increasing interest in the stability of the Greenland ice sheet. The velocity of outlet glaciers increased in 2005 relative to 2000 and 1995, but uncertainty remains with regard to the total mass balance. • Permafrost temperatures continue to increase. However, data on changes in the active layer thickness (the relatively thin layer of ground between the surface and permafrost that undergoes seasonal freezing and thawing) are less conclusive. While some of the sites show a barely noticeable increasing trend in the thickness of the active layer, most of them do not. • Globally, 2005 was the warmest year in the instrumental record (beginning in 1880), with the Arctic providing a large contribution toward this increase. Many of the trends documented in the ACIA are continuing, but some are not. Taken collectively, the observations presented in this report indicate that during 2000–2005 the Arctic system showed signs of continued warming. However, there are a few indications that certain elements may be recovering and returning to recent climatological norms (for example, the central Arctic Ocean and some wind patterns). These mixed tendencies further illustrate the sensitivity and complexity of the Arctic physical system. They underline the importance of maintaining and expanding efforts to observe and better understand this important component of the climate system to provide accurate predictions of its future state.

Effectiveness of Milorganite® as a Repellent to Protect Ornamental and Agronomic Plants From Deer Over-Browsing

When deer populations become locally overabundant, browsing of ornamental and agronomic plants negatively affects plant establishment, survival, and productivity. Milorganite® is a slow-release, organic fertilizer produced from human sewage. We tested Milorganite® as a deer repellent on chrysanthemums (Chrysanthemums morifolium) in an urban/suburban environment, and soybeans (Gycine max) in a rural agriculture environment. Six beds of chrysanthemums at two sites were monitored for 28 to 35 days. Treatment plants received a top dressing of 104 grams of Milorganite® (1120.9 kg/ha). Milorganite® treated plants had more (P < 0.001) terminal buds and achieved greater height (P < 0.002) compared to controls at one site, however damage observed was similar at the second site. In a second experiment, 0.2-ha plots of soybeans (Glycine max) were planted on five rural properties in northeastern Georgia and monitored for ≥ 30 days. Treated areas received 269 kg/ha of Milorganite®. In 4 of 5 sites, Milorganite® delayed browsing on treated plants from 1 week to > 5 weeks post-planting. Duration of the protection appeared to be related to the difference in deer density throughout most of the study areas. Results of this study indicate Milorganite® has potential use as a deer repellent.

Use of Natural Vegetative Barriers to Limit Expansion of Blacktailed Prairie Dog Towns

Prairie dog (Cynomys ludovicianus) control has historically consisted of lethal methods to maintain, reduce, or eliminate populations in South Dakota and throughout the species range. Non-lethal methods of control are desired to meet changing management objectives for the black-tailed prairie dog. The use of naturally occurring buffer strips as vegetative barriers may be effective in limiting prairie dog town expansion. The objectives of this study were: 1) to evaluate effective width of vegetative barriers in limiting prairie dog towns expansion in western South Dakota; and 2) to document effect native vegetation height on expansion of prairie dog towns in western South Dakota. Five study sites were established in western South Dakota on rangelands containing prairie dog towns of adequate size. Electric fences were constructed for the purpose of excluding cattle and creating buffer strips of native grasses and shrubs. Prairie dogs were poisoned to create a prairie dog free buffer zone adjacent to active prairie dog towns. Grazing was allowed on both sides of the buffer strip. When grazing pressure was not sufficient, mowing was used to simulate grazing. Buffer strips were 100 meters long and 10, 25, and 40 meters in width. A zero meter control was included on all study sites. Quadrats (25) were randomly distributed throughout the buffer strips. Evaluation of study sites included visual obstruction, vegetation cover, vegetation frequency, vegetation height, and vegetation identification. Barrier penetration was evaluated by the presence of new active burrows behind vegetative barriers. Significant relationships were documented for both VOR and vegetation height. No significant difference was found between frequency of breakthroughs and buffer widths.

Ecology, stable isotopes, and management of grassland songbirds at National Park Service properties on the Great Plains

Grassland ecosystems have been severely reduced and grassland bird populations have experienced consistent declines. National Park Service (NPS) properties on the Great Plains provide breeding habitat for grassland songbirds, though little is known about the quality of this habitat. A short-term study on songbirds at three NPS properties complemented current monitoring, providing an among park comparison addressing grassland bird productivity and fidelity relative to NPS property size. During 2008-2009, I assessed avian species richness, and estimated bird density and grassland songbird nest success. Bird species richness was greatest at small and medium sites, while number of nesting obligate species was greatest at the large site. Species-specific densities varied among sites, with few grassland obligates occurring at all three sites. Nest success estimates for grassland obligates were highest at the small site and lower at the large site. Another method to quantify habitat quality is assessment of breeding site fidelity. Current extrinsic markers used in monitoring site fidelity are inadequate for small birds; stable isotope analyses provide an alternative. I compared two techniques for assigning stable isotope tissue origin and measured grassland songbird site fidelity. My method of assigning origin provided site-specific variances of expected stable isotope values, an improvement over the most commonly used method. Fidelity tended to be higher at the large site, which may indicate a more robust breeding community of grassland birds. The small size of two of my sites precluded large sample sizes and made strong inferences difficult. To quantify how scientists cope with weak inference, I conducted a literature review. Strong inference was rarely observed, and most authors of weak-inference papers provided specific management recommendations. I suggest that adaptive management is an ideal method to resolve uncertainty from weak inference. Managers should consider my results within the context of regional and global management and the extent to which their unit might aide songbird conservation.