Characterization of bacteriophage communities and CRISPR profiles from dental plaque.

BackgroundDental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type.ResultsWe found that the plaque was inhabited by a community of bacteriophage whose membership was mostly subject-specific. There was a significant proportion of viral homologues shared between plaque and salivary viromes within each subject, suggesting that some oral viruses were present in both sites. We also characterized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in oral streptococci, as their profiles provide clues to the viruses that oral bacteria may be able to counteract. While there were some CRISPR spacers specific to each sample type, many more were shared across sites and were highly subject specific. Many CRISPR spacers matched viruses present in plaque, suggesting that the evolution of CRISPR loci may have been specific to plaque-derived viruses.ConclusionsOur findings of subject specificity to both plaque-derived viruses and CRISPR profiles suggest that human viral ecology may be highly personalized

Transcriptome analysis of bacteriophage communities in periodontal health and disease.

BackgroundThe role of viruses as members of the human microbiome has gained broader attention with the discovery that human body surfaces are inhabited by sizeable viral communities. The majority of the viruses identified in these communities have been bacteriophages that predate upon cellular microbiota rather than the human host. Phages have the capacity to lyse their hosts or provide them with selective advantages through lysogenic conversion, which could help determine the structure of co-existing bacterial communities. Because conditions such as periodontitis are associated with altered bacterial biota, phage mediated perturbations of bacterial communities have been hypothesized to play a role in promoting periodontal disease. Oral phage communities also differ significantly between periodontal health and disease, but the gene expression of oral phage communities has not been previously examined.ResultsHere, we provide the first report of gene expression profiles from the oral bacteriophage community using RNA sequencing, and find that oral phages are more highly expressed in subjects with relative periodontal health. While lysins were highly expressed, the high proportion of integrases expressed suggests that prophages may account for a considerable proportion of oral phage gene expression. Many of the transcriptome reads matched phages found in the oral cavities of the subjects studied, indicating that phages may account for a substantial proportion of oral gene expression. Reads homologous to siphoviruses that infect Firmicutes were amongst the most prevalent transcriptome reads identified in both periodontal health and disease. Some genes from the phage lytic module were significantly more highly expressed in subjects with periodontal disease, suggesting that periodontitis may favor the expression of some lytic phages.ConclusionsAs we explore the contributions of viruses to the human microbiome, the data presented here suggest varying expression of bacteriophage communities in oral health and disease

Largeness and SQ-universality of cyclically presented groups

Largeness, SQ-universality, and the existence of free subgroups of rank 2 are measures of the complexity of a finitely presented group. We obtain conditions under which a cyclically presented group possesses one or more of these properties. We apply our results to a class of groups introduced by Prishchepov which contains, amongst others, the various generalizations of Fibonacci groups introduced by Campbell and Robertson

Electronic equipment vulnerability to fire released carbon fibers

The vulnerability of electronic equipment to damage by carbon fibers released from burning aircraft type structural composite materials was investigated. Tests were conducted on commercially available stereo power amplifiers which showed that the equipment was damaged by fire released carbon fibers but not by the composite resin residue, soot and products of combustion of the fuel associated with burning the carbon fiber composites. Results indicate that the failure rates of the equipment exposed to the fire released fiber were consistent with predictions based on tests using virgin fibers

Interacting damage models mapped onto Ising and percolation models

We introduce a class of damage models on regular lattices with isotropic interactions, as e.g. quasistatic fiber bundles. The system starts intact with a surface-energy threshold required to break any cell sampled from an uncorrelated quenched-disorder distribution. The evolution of this heterogeneous system is ruled by Griffith's principle which states that a cell breaks when the release in elastic energy in the system exceeds the surface-energy barrier necessary to break the cell. By direct integration over all possible realizations of the quenched disorder, we obtain the probability distribution of each damage configuration at any level of the imposed external deformation. We demonstrate an isomorphism between the distributions so obtained and standard generalized Ising models, in which the coupling constants and effective temperature in the Ising model are functions of the nature of the quenched-disorder distribution and the extent of accumulated damage. In particular, we show that damage models with global load sharing are isomorphic to standard percolation theory, that damage models with local load sharing rule are isomorphic to the standard Ising model, and draw consequences thereof for the universality class and behavior of the autocorrelation length of the breakdown transitions corresponding to these models. We also treat damage models having more general power-law interactions, and classify the breakdown process as a function of the power-law interaction exponent. Last, we also show that the probability distribution over configurations is a maximum of Shannon's entropy under some specific constraints related to the energetic balance of the fracture process, which firmly relates this type of quenched-disorder based damage model to standard statistical mechanics.Comment: 16 pages, 3 figure

Fracture of disordered solids in compression as a critical phenomenon: II. Model Hamiltonian for a population of interacting cracks

To obtain the probability distribution of 2D crack patterns in mesoscopic regions of a disordered solid, the formalism of Paper I requires that a functional form associating the crack patterns (or states) to their formation energy be developed. The crack states are here defined by an order parameter field representing both the presence and orientation of cracks at each site on a discrete square network. The associated Hamiltonian represents the total work required to lead an uncracked mesovolume into that state as averaged over the initial quenched disorder. The effect of cracks is to create mesovolumes having internal heterogeneity in their elastic moduli. To model the Hamiltonian, the effective elastic moduli corresponding to a given crack distribution are determined that includes crack-to-crack interactions. The interaction terms are entirely responsible for the localization transition analyzed in Paper III. The crack-opening energies are related to these effective moduli via Griffith's criterion as established in Paper I.Comment: 9 pages, 1 figur

Three dimensional hysdrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic flow through porous media

We report the results of a study of multiphase flow in porous media. A Darcy's law for steady multiphase flow was investigated for both binary and ternary amphiphilic flow. Linear flux-forcing relationships satisfying Onsager reciprocity were shown to be a good approximation of the simulation data. The dependence of the relative permeability coefficients on water saturation was investigated and showed good qualitative agreement with experimental data. Non-steady state invasion flows were investigated, with particular interest in the asymptotic residual oil saturation. The addition of surfactant to the invasive fluid was shown to significantly reduce the residual oil saturation.Comment: To appear in Phys. Rev.

Developing a sense of place toolkit: Identifying destination uniqueness

It has long been recognised that the tangible and intangible characteristics that make a location distinctive and memorable, contribute significantly to destination image. How this destination feel is communicated, has largely been the domain of place branding and destination marketing, which have the potential to miss stakeholder voices. Recently though, practitioners are starting to carefully consider ‘sense of place’; that is an emotional attachment to place, which is defined more carefully in the literature review of this article, and which corresponds with long-running academic discussions. This paper attempts to identify some of these and bridge the gap between academic theory on sense of place and practice. In the UK, many rural areas are now seeking to operationalise sense of place through toolkit documents that might inform landscape interpretation and destination branding. A scenario echoed internationally, where local distinctiveness features in both rural and urban planning. However, sense of place in a tourism context, and more specifically the development of these toolkits, has received limited academic attention. Hence, this paper presents the case of Morecambe Bay, and the development of a dedicated sense of place toolkit. The subsequent case emerges from a collaboration between academics and practitioners and draws on participant observation, semi-structured interviews and document analysis. Specifically, the paper outlines a series of workshop activities developed with destination stakeholders and identifies how these inform subsequent toolkit design. It offers a critical analysis of the benefits and potential pitfalls of employing this approach. This case is of value to academics and destination stakeholders interested in identifying and communicating the uniqueness and emotional tone of the destination. Key lessons and recommendations are identified for those engaging in similar toolkit development initiatives

Human oral viruses are personal, persistent and gender-consistent.

Viruses are the most abundant members of the human oral microbiome, yet relatively little is known about their biodiversity in humans. To improve our understanding of the DNA viruses that inhabit the human oral cavity, we examined saliva from a cohort of eight unrelated subjects over a 60-day period. Each subject was examined at 11 time points to characterize longitudinal differences in human oral viruses. Our primary goals were to determine whether oral viruses were specific to individuals and whether viral genotypes persisted over time. We found a subset of homologous viral genotypes across all subjects and time points studied, suggesting that certain genotypes may be ubiquitous among healthy human subjects. We also found significant associations between viral genotypes and individual subjects, indicating that viruses are a highly personalized feature of the healthy human oral microbiome. Many of these oral viruses were not transient members of the oral ecosystem, as demonstrated by the persistence of certain viruses throughout the entire 60-day study period. As has previously been demonstrated for bacteria and fungi, membership in the oral viral community was significantly associated with the sex of each subject. Similar characteristics of personalized, sex-specific microflora could not be identified for oral bacterial communities based on 16S rRNA. Our findings that many viruses are stable and individual-specific members of the oral ecosystem suggest that viruses have an important role in the human oral ecosystem