Early-successional bird species are showing alarming declines across the Northeast and particularly in New England. Utilizing limited resources to the best advantage of these declining bird species is a vital task for land managers. In 2006 and 2007, I collected bird abundance and habitat information from 87 points in early-successional habitat in Connecticut. The objective of this effort was to evaluate the relationships between the habitat variables collected at a plot using the point intercept method and the associated bird abundance at the plot. A second objective was to compare two different methods of characterizing early-successional habitat in explaining the variance in bird abundance. A plot-based method based on the BBIRD protocol from Montana Cooperative Wildlife Research Unit and the point intercept method were compared. Finally, I designed and created a database written in Microsoft Access which was used to standardize data entry, aid in the sharing of data and to calculate summary statistics to assist habitat managers in making conservation decisions. The habitat variables were grouped according to composition and structure to analyze bird-habitat relationships. Low broadleaved shrubs, broadleaved shrubs, fern/forbs, conifers, broadleaved trees and invasives, as well as average height for shrubs and trees were used for the analysis. Nine focal early-successional species that are showing general trends of decline were chosen from the list of all birds seen or heard. Bird abundance and detectibility covariates were modeled with the habitat variables using N-mixture models (2004). Up to 24% of the variation of the best models (based upon AICc) was explained by the predictors I investigated. Five of the 9 birds showed a positive correlation to a shrub category variable. Fern/forbs, graminoids and invasives were found to exert less influence on the abundance of these scrub-shrub birds. Results indicated that the date of the survey affected the detectibility of only 5 of the species, and vegetation height only affected one of the species. Overall correlations indicate that these nine shrubland dependent species utilize a structurally complex habitat including broadleaved shrubs less 2 meters in height and than 2-5 meters in height and herbaceous forbs and graminoids. Invasive plants were found to be positively correlated to 2 of the 9 species possibly warranting additional work on the affects of these species on early-successional birds. Thirty-one of the total 87 point count points were selected for the comparison between the BBIRD and point intercept method. I choose six focal early-successional species for the analysis: indigo bunting, blue-winged warbler, chestnut-sided warbler, yellow warbler, prairie warbler and the common yellowthroat. The point intercept and BBIRD methods explained on average the same amount of variability in the data, and models from each data set included nearly the same number of variables, on average. Thus, we conclude these two vegetation sampling methodologies were essentially equivalent in summarizing important characteristics of scrub-shrub bird habitats. In the field, the BBIRD method took on average almost twice as long to complete as the point intercept method. Because in this study the two methods were similar in the amount of the bird abundance variance they explained and because the BBIRD method takes substantially longer to complete, I recommend that the point intercept method be considered an acceptable method for managers to use to characterize the relationships between early-successional bird species and their habitat. An important step in the successful conservation of declining early-successional bird species is the creation of database management systems and the coordination and cooperation amongst agencies that can stem from the use of these databases. The database I created ensures standardized data entry for data collected from multiple sites over many years. The database takes this data and can be queried for whatever particular information a manager needs. Percent cover of vegetation and invasives, average height of vegetation, and bird abundance are summarized and graphically displayed by the database. Ease of operation, ability to query and ability to share the information makes this database an important tool in the successful conservation of declining species

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In Arabidopsis thaliana, the development and the defense system are precisely controlled by some proteins to allocate energy and resources as needed. JASMONATE-ZIM domain 3 protein is the repressor of the jasmonic acid defense pathway. JACKDAW (JKD), SHORTSHOOT (SHR), and SCARECROW (SCR) bind together to form the BIRD complex, which regulates root patterning. The transcription factor Teosinte branched1/Cycloidea/Proliferating cell factor 14 (TCP14) also regulates plant development. Recent data shows that JAZ3 and TCP14 interact with JKD and may form a ternary complex, which reveals the study of the five proteins mentioned above may help to understand how defense signals are interpreted during plant growth. The interactions of these five proteins provide a theoretical base to maximize plant fitness and increase crop yield. Using protein purification, microscale thermophoresis, isothermal titration calorimetry, negative staining, X-ray crystallography in this project, we identified JKD interacted with JAZ3, and JKD interacted with TCP14, but they could not form a ternary complex in vitro; SHR/SCR interacted with JAZ3. Those binding results suggests TCP14 and SHR/SCR may have very similar binding site of JKD, and JAZ3 may guide the degradation of the BIRD complex. In structural studies, we resolved the 2D class average that showed the outline of the BIRD complex and it potentially helped to identify how JKD bound to DNA. We also determined the crystal structure of the TCP14 domain, which was an intertwined dimer that possibly uses arginine residues in the N terminus to interact with DNA. These interaction and structure studies of the five proteins provide the basis to understand how defense signals affect plant development.

Boreal forests in Europe are intensively managed for timber and pulp production, resulting in decreased biodiversity, and in the long-term leading to a reduced number of functioning ecosystem services. To develop a more sustainable forest management it is important to investigate what features and habitat types are needed to preserve a high diversity of species within the forestry landscapes. Birds are a suitable study taxon since their ecology is well known and their diversity often mirrors the diversity of other taxa. This study investigated how different habitat types, for example, forest stand composition and age of forest etc., influence the diversity, species richness and abundance of forest bird species in boreal forestry landscapes in Sweden. I expected that the percentage of deciduous forests and older forests would increase the diversity and richness of forest birds, while spruce forests and young forests would have negative effects. Further, I expected mixed forest stands to be more diverse regarding forest birds than pure forest stands. The sites for this study consisted of fiveforestry landscapes in south Sweden, with both active forestry and multifunctional forestry areas. The results showed positive effects of the percentage of deciduous forests, wetlands, older forests, mixed coniferous forests, and pine forests on species richness, abundance, and diversity of forest bird species. However, deciduous forests and older forests had the strongestpositive influence on species richness and diversity. Furthermore, I did not find evidence that mixed forest stands have a higher diversity or species richness than monocultures of only spruce and pine respectively.

<p> Two-dimensional C-H chemical shift correlation spectroscopy provides a large amount of information in a two dimensional matrix. Many variations of these experiments have been in an effort to enhance the information content of these experiments. Decoupling of multiplet signals is one method used to increase the sensitivity of an NMR experiment. Simple broadband decoupling in ω2 is done by irradiating the correlated channel during acquisition. Decoupling in ω1 must be done using less direct methods, one of which is to use bilinear rotation decoupling. The traditional description of the effect that a BIRD pulse has on the spin systems is based on a simple AX system which is at equilibrium at the beginning of the pulse, which does not apply in many real systems.</p> <p> This study uses the Superspin formalism to show in more detail the behaviour of more complex spin systems during the BIRD sequence, and the effect of varying parameters within the BIRD sequence. This treatment involved the derivation of complete spherical tensor descriptions of AX, AX2, and AX3 spin systems. This allowed the derivation of a mathematical description of an INEPT style pulse sequence, where the refocussing pulse in INEPT was replaced with the BIRD sequence. The derivation of the general evolution transformations of the spherical tensors in Liouville space also allowed the theoretical treatment to be done in a single basis, where earlier implementations of the Superspin formalism converted between a spherical tensor basis for the treatment of pulses and a Hamiltonian basis for the treatment of delays. This theoretical treatment allows the derivation of a functional form for the dependence of the carbon signal intensity on the variation of the interpulse delay in the BIRD sequence.</p> <p> This formalism was also used to analyze the occurrence of artifacts in two dimensional heteronuclear shift correlation spectra, due to strong coupling between methylene protons. These artifacts were studied in experiments that attempt broadband homonuclear decoupling in ω1 through the use of constant evolution time between the initial excitation pulse and polarization transfer. Two experiments were analyzed, the COLOC experiment and the HETRES experiment. The superspin formalism was used to deduce a functional form for the intensity of the artifact as a function of the strength of the coupling between the methylene protons.</p> / Thesis / Master of Science (MSc)

Due to the global loss of tidal marsh area, potential anthropogenic and natural disturbances to these systems, and coastal marshes’ affinity for trapping environmental pollutants, understanding how marsh birds inhabiting these ecosystems will adapt to these changes is paramount. To quantify future changes, I first needed to have something to compare against – baseline estimates. To this end, I performed distance sampling line transect surveys during the nonbreeding season to estimate species-specific population abundance, density, and habitat associations and captured two species of marsh bird, Clapper Rail (Rallus crepitans) and Seaside Sparrow (Ammospiza maritima), to estimate baseline ingestion of one such environmental pollutant – microplastics. By providing the first baseline population and density estimates for numerous nonbreeding marsh birds, my findings suggest that the tidal marshes of Mississippi provide critical habitat for many of these species. Additionally, I was able to document the first evidence of microplastic ingestion by resident tidal marsh birds.

Bottomland hardwood forests (BHF) are a disappearing habitat of importance to numerous migratory and non-migratory birds of conservation concern. Thus, understanding variables of bottomland hardwood forests that affect avian assemblage patterns are of great interest. I examined factors influencing avian assemblage and guild patterns in BHF of Noxubee National Wildlife Refuge in east-central Mississippi by conducting winter and spring fixed-radius avian point counts and vegetation surveys from 2002 ? 2004. The goals of this project were to 1) determine effects of greentree reservoir (GTR) management on breeding and wintering non-game bird community structure, 2) test hypotheses regarding plant structural complexity and avian assemblage patterns, and 3) examine the effects of landscapes on local bird assemblages within BHF. Greentree reservoirs have subtle effects on avian communities. Sites within GTRs, sites in BHF adjacent to GTRs, and random, unimpounded BHF sites differed significantly in breeding bird diversity, richness, and evenness. However, the patterns exhibited were a decreasing continuum of these variables with sites peripheral to GTRs demonstrating intermediate values. No differences were found among abundance, conservation status, or habitat specialization of breeding birds. Guild parameters did not differ except for a decreasing continuum in species richness among unimpounded BHF, BHF to GTRs, and GTR sites. The canopy nesting and ground gleaning foraging guilds were the only guilds found to differ among sites. Patterns could indicate that given the inherent structural variation of BHF, GTRs are within the expected range of variation, or GTR management could be indirectly affecting the surrounding landscape. GTR management did not affect community parameters for wintering birds, and only the bark gleaning foraging guild varied among sites (higher in GTRs). These results reflect the ubiquitous nature of wintering birds in east-central Mississippi forests. There was direct support for the structural vertical heterogeneity hypothesis; however, regression analyses of principal component scores derived from sixty structural descriptor metrics suggest that avian communities and guilds are more directly influenced by overall local plant structural complexity, as predicted by the spatial heterogeneity hypothesis. Avian community and guild parameters did not differ among the three landscape contexts defined by 1,000 and 1,500m buffers.

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