Prevalence of Bacteria of Division TM7 in Human Subgingival Plaque and Their Association with Disease

Members of the uncultivated bacterial division TM7 have been detected in the human mouth, but little information is available regarding their prevalence and diversity at this site. Human subgingival plaque samples from healthy sites and sites exhibiting various stages of periodontal disease were analyzed for the presence of TM7 bacteria. TM7 ribosomal DNA (rDNA) was found in 96% of the samples, and it accounted for approximately 0.3%, on average, of all bacterial rDNA in the samples as determined by real-time quantitative PCR. Two new phylotypes of this division were identified, and members of the division were found to exhibit filamentous morphology by fluorescence in situ hybridization. The abundance of TM7 rDNA relative to total bacterial rDNA was higher in sites with mild periodontitis (0.54% ± 0.1%) than in either healthy sites (0.21% ± 0.05%, P \u3c 0.01) or sites with severe periodontitis (0.29% ± 0.06%, P \u3c 0.05). One division subgroup, the I025 phylotype, was detected in 1 of 18 healthy samples and 38 of 58 disease samples. These data suggest that this phylotype, and the TM7 bacterial division in general, may play a role in the multifactorial process leading to periodontitis

The irradiated ISM of ULIRGs

The nuclei of ULIRGs harbor massive young stars, an accreting central black hole, or both. Results are presented for molecular gas that is exposed to X-rays (1-100 keV, XDRs) and far-ultraviolet radiation (6-13.6 eV, PDRs). Attention is paid to species like HCO+, HCN, HNC, OH, H2O and CO. Line ratios of HCN/HCO+ and HNC/HCN discriminate between PDRs and XDRs. Very high J (>10) CO lines, observable with HIFI/Herschel, discriminate very well between XDRs and PDRs. In XDRs, it is easy to produce large abundances of warm (T>100 K) H2O and OH. In PDRs, only OH is produced similarly well.Comment: 5 pages, 6 figures, to appear in: IAU Symposium 242 Astrophysical Masers and their Environment

Methanogenic \u3cem\u3eArchaea\u3c/em\u3e and human periodontal disease

Archaea have been isolated from the human colon, vagina, and oral cavity, but have not been established as causes of human disease. In this study, we reveal a relationship between the severity of periodontal disease and the relative abundance of archaeal small subunit ribosomal RNA genes (SSU rDNA) in the subgingival crevice by using quantitative PCR. Furthermore, the relative abundance of archaeal small subunit rDNA decreased at treated sites in association with clinical improvement. Archaea were harbored by 36% of periodontitis patients and were restricted to subgingival sites with periodontal disease. The presence of archaeal cells at these sites was confirmed by fluorescent in situ hybridization. The archaeal community at diseased sites was dominated by a Methanobrevibacter oralis-like phylotype and a distinct Methanobrevibacter subpopulation related to archaea that inhabit the gut of numerous animals. We hypothesize that methanogens participate in syntrophic relationships in the subgingival crevice that promote colonization by secondary fermenters during periodontitis. Because they are potential alternative syntrophic partners, our finding of larger Treponema populations sites without archaea provides further support for this hypothesis

Analysis of Conserved Non-rRNA Genes of \u3ci\u3eTropheryma whipplei\u3c/i\u3e

The causative agent of Whipple’s disease, Tropheryma whipplei, is a slow-growing bacterium that remains poorly-understood. Genetic characterization of this organism has relied heavily upon rRNA sequence analysis. Pending completion of a complete genome sequencing effort, we have characterized several conserved non-rRNA genes from T. whipplei directly from infected tissue using broad-range PCR and a genome-walking strategy. Our goals were to evaluate its phylogenetic relationships, and to find ways to expand the strain typing scheme, based on rDNA sequence comparisons. The genes coding for the ATP synthase beta subunit (atpD), elongation factor Tu (tuf), heat shock protein GroEL (groEL), beta subunit of DNA-dependent RNA polymerase (rpoB), and RNase P RNA (rnpB) were analyzed, as well as the regions upstream and downstream of the rRNA operon. Phylogenetic analyses with all nonrRNA marker molecules consistently placed T. whipplei within the class, Actinobacteria. The arrangement of genes in the atpD and rpoB chromosomal regions was also consistent with other actinomycete genomes. Tandem sequence repeats were found upstream and downstream of the rRNA operon, and downstream of the groEL gene. These chromosomal sites and the 16S-23S rRNA intergenic spacer regions were examined in the specimens of 11 patients, and a unique combination of tandem repeat numbers and spacer polymorphisms was found in each patient. These data provide the basis for a more discriminatory typing method for T. whipplei

The Effects of UV Continuum and Lyman alpha Radiation on the Chemical Equilibrium of T Tauri Disks

We show in this Letter that the spectral details of the FUV radiation fields have a large impact on the chemistry of protoplanetary disks surrounding T Tauri stars. We show that the strength of a realistic stellar FUV field is significantly lower than typically assumed in chemical calculations and that the radiation field is dominated by strong line emission, most notably Lyman alpha radiation. The effects of the strong Lyman alpha emission on the chemical equilibrium in protoplanetary disks has previously been unrecognized. We discuss the impact of this radiation on molecular observations in the context of a radiative transfer model that includes both direct attenuation and scattering. In particular, Lyman alpha radiation will directly dissociate water vapor and may contribute to the observed enhancements of CN/HCN in disks.Comment: 14 pages, 4 figures, accepted by ApJ Letter

Rate coefficients for rovibrational transitions in H_2 due to collisions with He

We present quantum mechanical and quasiclassical trajectory calculations of cross sections for rovibrational transitions in ortho- and para-H_2 induced by collisions with He atoms. Cross sections were obtained for kinetic energies between 10^-4 and 3 eV, and the corresponding rate coefficients were calculated for the temperature range 100<T<4000 K. Comparisons are made with previous calculations.Comment: 21 pages, 2 figures, AAS, eps

Rhinosporidium seeberi: a human pathogen from a novel group of aquatic protistan parasites.

Rhinosporidium seeberi, a microorganism that can infect the mucosal surfaces of humans and animals, has been classified as a fungus on the basis of morphologic and histochemical characteristics. Using consensus polymerase chain reaction (PCR), we amplified a portion of the R. seeberi 18S rRNA gene directly from infected tissue. Analysis of the aligned sequence and inference of phylogenetic relationships showed that R. seeberi is a protist from a novel clade of parasites that infect fish and amphibians. Fluorescence in situ hybridization and R. seeberi- specific PCR showed that this unique 18S rRNA sequence is also present in other tissues infected with R. seeberi. Our data support the R. seeberi phylogeny recently suggested by another group. R. seeberi is not a classic fungus, but rather the first known human pathogen from the DRIPs clade, a novel clade of aquatic protistan parasites (Ichthyosporea)

Molecular fluorine chemistry in the early Universe

Some models of Big Bang nucleosynthesis suggest that very high baryon density regions were formed in the early Universe, and generated the production of heavy elements other than lithium such as fluorine F. We present a comprehensive chemistry of fluorine in the post-recombination epoch. Calculation of F, F- and HF abundances, as a function of redshift z, are carried out. The main result is that the chemical conditions in the early Universe can lead to the formation of HF. The final abundance of the diatomic molecule HF is predicted to be close to 3.75 10(-17) when the initial abundance of neutral fluorine F is 10(-15). These results indicate that molecules of fluorine HF were already present during the dark age. This could have implications on the evolution of proto-objects and on the anisotropies of cosmic microwave background radiation. Hydride of fluorine HF may affect enhancement of the emission line intensity from the proto-objects and could produce spectral-spatial fluctuations.Comment: Accepted in Astronomy and Astrophysics, 7 pages, 2 figure

On the relative abundance of LiH and LiH+ molecules in the early universe: new results from quantum reactions

The relative efficiencies of the chemical pathways that can lead to the destruction of LiH and LiH+ molecules, conjectured to be present in the primordial gas and to control molecular cooling processes in the gravitational collapse of the post-recombination era, are revisited by using accurate quantum calculations for the several reactions involved. The new rates are employed to survey the behavior of the relative abundance of these molecules at redshifts of interest for early universe conditions. We find significant differences with respect to previous calculations, the present ones yielding LIH abundances higher than LiH+ at all redshifts.Comment: The Astrophysical Journal, in pres