CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome

Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. For this purpose, a phylogenetically curated 16S rDNA database of the core oral microbiome, CORE, was developed. The goal was to include a comprehensive and minimally redundant representation of the bacteria that regularly reside in the human oral cavity with computationally robust classification at the level of species and genus. Clades of cultivated and uncultivated taxa were formed based on sequence analyses using multiple criteria, including maximum-likelihood-based topology and bootstrap support, genetic distance, and previous naming. A number of classification inconsistencies for previously named species, especially at the level of genus, were resolved. The performance of the CORE database for identifying clinical sequences was compared to that of three publicly available databases, GenBank nr/nt, RDP and HOMD, using a set of sequencing reads that had not been used in creation of the database. CORE offered improved performance compared to other public databases for identification of human oral bacterial 16S sequences by a number of criteria. In addition, the CORE database and phylogenetic tree provide a framework for measures of community divergence, and the focused size of the database offers advantages of efficiency for BLAST searching of large datasets. The CORE database is available as a searchable interface and for download at http://microbiome.osu.edu.     

Synthesis of an immunoconjugate of camptothecin.

The first immunoconjugate of camptothecin has been synthesized wherein the drug is attached to the tumor-recognizing antibody BR96 via a Cathepsin B cleavable linker. Endocytosis of the immunoconjugate upon binding to the tumor cell followed by enzymatic cleavage of the linker inside the endosome ensures tumor-specific release of the drug. In this way, it is hoped that the dose-limiting side effects associated with camptothecin can be eliminated while the antitumor activity is preserved.     

Anion effects on ionogel formation in N,N′-dialkylimidazolium-based ionic liquids

Addition of an appropriate concentration of water to either 1-decyl-3-methylimidazolium bromide or its nitrate analog is shown to trigger the self-assembly of the ionic liquid (IL) and the concomitant formation of gel (“ionogel”) phases adopting a rich variety of structural motifs. Infrared and ¹H nuclear magnetic resonance studies indicate that water addition disrupts hydrogen bonding between the imidazolium ring and the IL anion, and that gelation involves the partial replacement of these bonds with H-bonds between the anion and water. Using small angle X-ray scattering, the relationship of the water content and the nature of the IL anion to the mesoscopic structure of the ionogels has been determined. Of particular note is the observation that by adjustment of the ionogel composition (water content or anion), near-monodomain materials can be formed with either lamellar, 2-D hexagonal or 3-D cubic structures with tunable lattice dimensions.     

The relative importance of autotrophic and heterotrophic nitrification in a conifer forest soil as measured by 15N tracer and pool dilution techniques

The importance of heterotrophic nitrification was studied in soil from a mixed-conifer forest. Three sites in the forest were sampled: a clear cut area, a young stand and a mature stand. In the mature stand, the mineral soil (0–10 cm) and the organic layer were sampled separately. Gross rates of N mineralization and nitrification were measured by¹⁵NH ₄ ⁺ and¹⁵NO ₃ ^– isotopic pool dilution, respectively. The rates of autotrophic and heterotrophic nitrification were distinguished by use of acetylene as a specific inhibitor of autotrophic nitrification. In samples supplemented with¹⁵NH ₄ ⁺ and treated with acetylene, no¹⁵NO ₃ ^– was detectable showing that the acetylene treatment effectively blocked the autotrophic nitrification, and that NH ₄ ⁺ was not a substrate for heterotrophic nitrification. In the clear cut area, autotrophic nitrification was the most important NO ₃ ^– generating process with total nitrification (45 ug N kg^–1h^–1) accounting for about one-third of gross N mineralization (140 ug N kg^–1 h^–1). In the young and mature forested sites, gross nitrification rates were largely unaffected by acetylene treatment indicating that heterotrophic nitrification dominated the NO ₃ ^– generating process in these areas. In the mature forest mineral and organic soil, nitrification (heterotrophic) was equal to only about 5% of gross mineralization (gross mineralization rates of 90 ug N kg^–1 h^–1 mineral; 550 ug N kg^–1 h^–1 organic). The gross nitrification rate decreased from the clear cut area to the young forest area to the mineral soil of the mature forest (45; 17; 4.5 ug kg^–1 h^–1 respectively). The¹⁵N isotope pool dilution method, combined with acetylene as an inhibitor of autotrophic nitrification provided an effective technique for assessing the importance of heterotrophic nitrification in the N-cycle of this mixed-conifer ecosystem.     

Respiratory syncytial virus (RSV) F, G, M2 (22K), and N proteins each induce resistance to RSV challenge, but resistance induced by M2 and N proteins is relatively short-lived.

The ability of recombinant vaccinia viruses that separately encoded 9 of the 10 known respiratory syncytial virus (RSV) proteins to induce resistance to RSV challenge was studied in BALB/c mice. Resistance was examined at two intervals following vaccination to examine early (day 9) as well as late (day 28) immunity. BALB/c mice were inoculated simultaneously by the intranasal and intraperitoneal routes with a recombinant vaccinia virus encoding one of the following RSV proteins: F, G, N, P, SH, M, 1B, 1C, or M2 (22K). A parainfluenza virus type 3 HN protein recombinant (Vac-HN) served as a negative control. One half of the mice were challenged with RSV intranasally on day 9, and the remaining animals were challenged on day 28 postvaccination. Mice previously immunized by infection with RSV, Vac-F, or Vac-G were completely or almost completely resistant to RSV challenge on both days. In contrast, immunization with Vac-HN, -P, -SH, -M, -1B, or -1C did not induce detectable resistance to RSV challenge. Mice previously infected with Vac-M2 or Vac-N exhibited significant but not complete resistance on day 9. However, in both cases resistance had largely waned by day 28 and was detectable only in mice immunized with Vac-M2. These results demonstrate that F and G proteins expressed by recombinant vaccinia viruses are the most effective RSV protective antigens. This study also suggests that RSV vaccines need only contain the F and G glycoproteins, because the immunity conferred by the other proteins is less effective and appears to wane rapidly with time.