Static capillary structures and their stability

This thesis examines the static equilibrium shapes and stability of various capillary surfaces. The equilibrium shapes are accurately approximated using asymptotic series solutions in the micro-gravity limit. The stability of two of these capillary surfaces is then examined using an energy functional method and these results corroborated using a linear stability analysis. Finally, a method of improving the stability of a vertical liquid bridge is examined numerically and experimentally. The problems considered in this thesis are motivated by a stent problem described in the rst chapter but, in fact, capillary phenomena are ubiquitous in science, nature and industry and the work here has wide reaching applications

Hypothesized adaptions of <i>R. mucilaginosa</i> to the CF lung environment.

<p>The model is based on the comparison between the reference genome DY-18 and the reconstructed genome CF1E. <i>rhs</i>: rearrangement hot spot; Type I R-M: Type I restriction modification; MdaB: Modular of drug activity B; ROS: reactive oxygen species; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats.</p

Prevalence of <i>Rothia mucilaginosa</i>, and the prototypical pathogen <i>Pseudomonas aeruginosa</i>, in eighteen microbiomes from six CF patients.

<p>Patients were sampled at times of differing health status (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064285#pone.0064285.s002" target="_blank">Table S1</a>; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064285#pone.0064285-Lim1" target="_blank">[12]</a>). Ex: Exacerbation; Tr: On treatment; Pt: Post treatment; St: Stable; *:present in <1% of the microbiome.</p

Predicted protein-coding sequences present in the CF1E scaffold annotated by RAST, but missing from the DY-18 reference (list excludes hypothetical proteins).

<p>See details in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064285#pone.0064285.s013" target="_blank">Table S12</a>.</p

Genomic regions present in the DY-18 reference genome but missing from the CF1E draft genome.

<p>See details in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064285#pone.0064285.s012" target="_blank">Table S11</a>.</p

Species-Specific Viromes in the Ancestral Holobiont <i>Hydra</i>

<div><p>Recent evidence showing host specificity of colonizing bacteria supports the view that multicellular organisms are holobionts comprised of the macroscopic host in synergistic interdependence with a heterogeneous and host-specific microbial community. Whereas host-bacteria interactions have been extensively investigated, comparatively little is known about host-virus interactions and viral contribution to the holobiont. We sought to determine the viral communities associating with different <i>Hydra</i> species, whether these viral communities were altered with environmental stress, and whether these viruses affect the <i>Hydra</i>-associated holobiont. Here we show that each species of <i>Hydra</i> harbors a diverse host-associated virome. Primary viral families associated with <i>Hydra</i> are <i>Myoviridae</i>, <i>Siphoviridae</i>, <i>Inoviridae</i>, and <i>Herpesviridae</i>. Most <i>Hydra</i>-associated viruses are bacteriophages, a reflection of their involvement in the holobiont. Changes in environmental conditions alter the associated virome, increase viral diversity, and affect the metabolism of the holobiont. The specificity and dynamics of the virome point to potential viral involvement in regulating microbial associations in the <i>Hydra</i> holobiont. While viruses are generally regarded as pathogenic agents, our study suggests an evolutionary conserved ability of viruses to function as holobiont regulators and, therefore, constitutes an emerging paradigm shift in host-microbe interactions.</p></div

The relative abundance of viral types and the bacterial class hosts of associating viruses to various <i>Hydra</i> species.

<p>A) Predicted host range of each <i>Hydra</i> associated virome, including eukaryotic and prokaryotic viruses. B) Predicted bacterial host range for the bacteriophages associating with <i>Hydra</i> species. The order in each column is equivalent to the order in the legend.</p

The <i>Hydra</i> viromes.

<p>The relative abundance and diversity of viral families associating with <i>Hydra</i> species in non-stressed and heat-stressed conditions reveals that each species of <i>Hydra</i> associates with a unique community of viruses. Results display the relative abundances of families of identified viruses (TBLASTX, E-value threshold ≤10⁻⁵) associating with the different species of <i>Hydra</i> under both non-stressed and heat-stressed conditions for all viral families (A), for prokaryotic viruses (B), and for eukaryotic viruses (C). The order of the viral family in each column is equivalent to the order of the viral family in the legend.</p

Effects of <i>Hydra</i>-associating viruses on metabolic subsystems.

<p>Relative abundances of sequences assigned to each cellular metabolic subsystem by MG-RAST. Assembled sequences were submitted to MG-RAST and TBLASTX was used to compare to a metabolic subsystem SEED database (E-value threshold ≤10⁻⁵). A) Values show the percent relative abundance of each SEED category assignment for each virome with respect to their effect on metabolism, genetic processing, and cellular regulation. The order of the subsystem in each column is equivalent to the order of the subsystem in the legend. B) Percent changes with heat-stress for each <i>Hydra</i> species of the three general groupings from (A). C) Percent changes with heat-stress for each <i>Hydra</i> species from three specific subsystems in (A).</p

<i>Hydra</i> species harbor specific viral communities.

<p>Viromes were cross-assembled into one file using MIRA and then each virome was compared to the cross-assembled file using crAss. A) CrAss Wootters formula cladogram output of each <i>Hydra</i> species virome. B) CrAss Wootters formula cladogram output of each <i>Hydra</i> species under non-stressed (NS) and heat-stressed (HS) conditions. The viral family in each pie chart is listed in the legend.</p