COLONIZATION OF AND ADAPTATION TO TIDAL MARSHES IN THE SAVANNAH SPARROW (PASSERCULUS SANDWICHENSIS)

Intraspecific patterns of geographic variation reflect a dynamic history of colonization and divergence in response to spatially varying selective pressures. Analysis of this phenotypic variation has long stimulated biological thought, yet many outstanding questions remain regarding the ecological and evolutionary mechanisms driving patterns of geographic variation. In my dissertation, I collected data on demographic history, physiological traits contributing to salinity tolerance, and acclimation responses to different salinities to elucidate the mechanisms shaping colonization and adaptive divergence in tidal marsh populations of Savannah Sparrows (Passerculus sandwichensis). Specifically, I addressed two main questions related to adaptive divergence in this species: (1) how do demographic and ecological forces interact to shape spatial patterns of local adaptation? And (2) what role does ancestral plasticity play in adaptation to new environments? In Chapter 1, phylogeographic analyses of a population genomic dataset revealed that tidal marshes have been colonized twice by Savannah Sparrows and include a younger, less isolated tidal marsh lineage from the California coast, and an older, more isolated lineage from northwest Mexico. In the second chapter, I assessed how variation in demographic history and environmental factors interacted to shape patterns of divergence in physiological traits associated with salinity tolerance across multiple tidal marsh populations. Finally, in Chapter 3, I compared acclimation responses to salinity in freshwater-adapted and tidal marsh Savannah Sparrows to test whether ancestral plasticity may have contributed to tidal marsh adaptation in this species. The outcomes of adaptation to spatially varying selective pressures will be contingent on many interacting ecological, demographic, and evolutionary processes. The results of my dissertation show that demographic history, variation in selective pressures, and plasticity all contributed to patterns of adaptive divergence within tidal marsh Savannah Sparrows. This underscores the necessity of considering multiple interacting processes to thoroughly understand the evolution of geographic variation

Bubbles and denaturation in DNA

The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without the unwinding of the DNA double helix. Although these biological processes are driven by proteins, there might well be a relation between these biological openings and the spontaneous bubble formation due to thermal fluctuations. Mesoscopic models, like the Peyrard-Bishop-Dauxois model, have fairly accurately reproduced some experimental denaturation curves and the sharp phase transition in the thermodynamic limit. It is, hence, tempting to see whether these models could be used to predict the biological activity of DNA. In a previous study, we introduced a method that allows to obtain very accurate results on this subject, which showed that some previous claims in this direction, based on molecular dynamics studies, were premature. This could either imply that the present PBD should be improved or that biological activity can only be predicted in a more complex frame work that involves interactions with proteins and super helical stresses. In this article, we give detailed description of the statistical method introduced before. Moreover, for several DNA sequences, we give a thorough analysis of the bubble-statistics as function of position and bubble size and the so-called $l$-denaturation curves that can be measured experimentally. These show that some important experimental observations are missing in the present model. We discuss how the present model could be improved.Comment: 15 pages, 5 figures, published as Eur. Phys. J. E 20 : 421-434 AUG 200

Conformations of closed DNA

We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic expressions leading to the spatial configuration of a family of solutions representing distortions that interpolate between the circular form of DNA and a figure-eight form that represents the onset of interwinding. We are also able to generate knotted loops. We suggest ways to use our approach to produce other configurations relevant to studies of DNA structure. The stability of the distorted configurations is assessed, along with the effects of fluctuations on the free energy of the various configurations.Comment: 39 pages in REVTEX with 14 eps figures. Submitted to Phys. Rev. E. This manuscript updates, expands and revises, to a considerable extent, a previously posted manuscript, entitled "Conformations of Circular DNA," which appeared as cond-mat/970104

A stitch in time: Efficient computation of genomic DNA melting bubbles

Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic. Results: An efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a maximal bubble length. No approximations, such as windowing, have been introduced to reduce the time complexity. More than just finding the bubbles, the algorithm produces a stitch profile, which is a probabilistic graphical model of bubbles and helical regions. The algorithm applies a probability peak finding method based on a hierarchical analysis of the energy barriers in the Poland-Scheraga model. Conclusions: Exact and fast computation of genomic stitch profiles is thus feasible. Sequences of several megabases have been computed, only limited by computer memory. Possible applications are the genome-wide comparisons of bubbles with promotors, TSS, viral integration sites, and other melting-related regions.Comment: 16 pages, 10 figure

Superhelical Duplex Destabilization and the Recombination Position Effect

The susceptibility to recombination of a plasmid inserted into a chromosome varies with its genomic position. This recombination position effect is known to correlate with the average G+C content of the flanking sequences. Here we propose that this effect could be mediated by changes in the susceptibility to superhelical duplex destabilization that would occur. We use standard nonparametric statistical tests, regression analysis and principal component analysis to identify statistically significant differences in the destabilization profiles calculated for the plasmid in different contexts, and correlate the results with their measured recombination rates. We show that the flanking sequences significantly affect the free energy of denaturation at specific sites interior to the plasmid. These changes correlate well with experimentally measured variations of the recombination rates within the plasmid. This correlation of recombination rate with superhelical destabilization properties of the inserted plasmid DNA is stronger than that with average G+C content of the flanking sequences. This model suggests a possible mechanism by which flanking sequence base composition, which is not itself a context-dependent attribute, can affect recombination rates at positions within the plasmid

Layer Analysis of the Structure of Water Confined in Vycor Glass

A Molecular Dynamics simulation of the microscopic structure of water confined in a silica pore is presented. A single cavity in the silica glass has been modeled as to reproduce the main features of the pores of real Vycor glass. A layer analysis of the site-site radial distribution functions evidence the presence in the pore of two subsets of water molecules with different microscopic structure. Molecules which reside in the inner layer, close to the center of the pore, have the same structure as bulk water but at a temperature of 30 K higher. On the contrary the structure of the water molecules in the outer layer, close to the substrate, is strongly influenced by the water-substrate hydrophilic interaction and sensible distortions of the H-bond network and of the orientational correlations between neighboring molecules show up. Lowering the hydration has little effect on the structure of water in the outer layer. The consequences on experimental determinations of the structural properties of water in confinement are discussed.Comment: 6 pages, 8 figures included in the text, one figure added, changes in the tex

Minerals information GIS for regional development and inward investment in Northern Highlands of Scotland

The principal aim of this project, funded by the Department of Trade and Industry (DTI), is to stimulate exploration for metalliferous minerals in the Northern Highlands of Scotland, thereby promoting inward investment, job creation and the development of infrastructure in the region. The Northern Highlands study area occupies about 27,000 km2 located to the north and west of the Great Glen, including the Hebrides, Orkney and Shetland. The regional geology is highly varied, comprising mainly Archaean and Proterozoic metamorphic rocks and Palaeozoic sedimentary rocks. Intrusive igneous rocks are also widely developed. This geological diversity enhances the potential of the region for the occurrence of a wide range of mineral deposit types. The Northern Highlands are under-explored, relative to other parts of Scotland; nevertheless, this study has documented more than 350 recorded mineral occurrences

Real-world questions and concerns about disease-modifying antirheumatic drugs (DMARDs): A retrospective analysis of questions to a medicine call center

Background: Disease-modifying antirheumatic drugs (DMARDs) have transformed the treatment of numerous autoimmune and inflammatory diseases but their perceived risk of harm may be a barrier to use. Methods: In a retrospective mixed-methods study, we analysed conventional (c) and biologic (b) DMARDs-related calls and compared them with rest of calls (ROC) from consumers to an Australian national medicine call center operated by clinical pharmacists from September 2002 to June 2010. This includes the period where bDMARDs became available on the Pharmaceutical Benefits Scheme, the government-subsidized prescription medicines formulary. We compared caller and patient demographics, enquiry types and motivation to information-seek for both cDMARDs and bDMARDs with ROC, using a t-test for continuous data and a chi-square test for categorical data. We explored call narratives to identify common themes. Results: There were 1547 calls involving at least one DMARD. The top three cDMARD enquiry types were side effects (27.2%), interactions (21.9%), and risk versus benefit (11.7%). For bDMARDs, the most common queries involved availability and subsidized access (18%), mechanism and profile (15.8%), and side effects (15.1%). The main consumer motivations to information-seek were largely independent of medicines type and included: inadequate information (44%), wanting a second opinion (23.6%), concern about a worrying symptom (18.8%), conflicting information (6.9%), or information overload (2.3%). Question themes common to conventional and biological DMARDs were caller overemphasis on medication risk and the need for reassurance. Callers seeking information about bDMARDs generally overestimated effectiveness and focused their attention on availability, cost, storage, and medicine handling. Conclusion: Consumers have considerable uncertainty regarding DMARDs and may overemphasise risk. Patients cautiously assess the benefits and risks of their DMARDs but when new treatments emerge, they tend to overestimate their effectivenes

Exploring the stability of communication network metrics in a dynamic nursing context

Network stability is of increasing interest to researchers as they try to understand the dynamic processes by which social networks form and evolve. Because hospital patient care units (PCUs) need flexibility to adapt to environmental changes (Vardaman et al., 2012), their networks are unlikely to be uniformly stable and will evolve over time. This study aimed to identify a metric (or set of metrics) sufficiently stable to apply to PCU staff information sharing and advice seeking communication networks over time. Using Coefficient of Variation, we assessed both Across Time Stability (ATS) and Global Stability over four data collection times (Baseline and 1, 4, and 7 months later). When metrics were stable using both methods, we considered them "super stable." Nine metrics met that criterion (Node Set Size, Average Distance, Clustering Coefficient, Density, Weighted Density, Diffusion, Total Degree Centrality, Betweenness Centrality, and Eigenvector Centrality). Unstable metrics included Hierarchy, Fragmentation, Isolate Count, and Clique Count. We also examined the effect of staff members' confidence in the information obtained from other staff members. When confidence was high, the "super stable" metrics remained "super stable," but when low, none of the "super stable" metrics persisted as "super stable." Our results suggest that nursing units represent what Barker (1968) termed dynamic behavior settings in which, as is typical, multiple nursing staff must constantly adjust to various circumstances, primarily through communication (e.g., discussing patient care or requesting advice on providing patient care), to preserve the functional integrity (i.e., ability to meet patient care goals) of the units, thus producing the observed stability over time of nine network metrics. The observed metric stability provides support for using network analysis to study communication patterns in dynamic behavior settings such as PCUs.National Institute of General Medical Sciences of the National Institutes of HealthOpen access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]