1,436 research outputs found
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 -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
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
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
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
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
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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]
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
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