Formalization and separation: A systematic basis for interpreting approaches to summarizing science for climate policy.

In studies of environmental issues, the question of how to establish a productive interplay between science and policy is widely debated, especially in relation to climate change. The aim of this article is to advance this discussion and contribute to a better understanding of how science is summarized for policy purposes by bringing together two academic discussions that usually take place in parallel: the question of how to deal with formalization (structuring the procedures for assessing and summarizing research, e.g. by protocols) and separation (maintaining a boundary between science and policy in processes of synthesizing science for policy). Combining the two dimensions, we draw a diagram onto which different initiatives can be mapped. A high degree of formalization and separation are key components of the canonical image of scientific practice. Influential Science and Technology Studies analysts, however, are well known for their critiques of attempts at separation and formalization. Three examples that summarize research for policy purposes are presented and mapped onto the diagram: the Intergovernmental Panel on Climate Change, the European Union's Science for Environment Policy initiative, and the UK Committee on Climate Change. These examples bring out salient differences concerning how formalization and separation are dealt with. Discussing the space opened up by the diagram, as well as the limitations of the attraction to its endpoints, we argue that policy analyses, including much Science and Technology Studies work, are in need of a more nuanced understanding of the two crucial dimensions of formalization and separation. Accordingly, two analytical claims are presented, concerning trajectories, how organizations represented in the diagram move over time, and mismatches, how organizations fail to handle the two dimensions well in practice.

DNA binding to hydroxyapatite: a potential mechanism for preservation of microbial DNA.

INTRODUCTION: Molecular methods are increasingly being deployed for analysis of the microbial flora in the root canal. Such methods are based on the assumption that recovered DNA is associated with the active endodontic infection, yet paleomicrobiology research is based on the recovery of ancient DNA from centuries-old tooth and bone samples, which points to considerable longevity of the DNA molecule in these tissues. The main component of dentin and bone is the mineral hydroxyapatite. This study assessed DNA binding to hydroxyapatite and whether this binding affinity stabilizes the DNA molecule in various media. METHODS: DNA was extracted from Fusobacterium nucleatum and added to ceramic hydroxyapatite for 90 minutes. The DNA-bound hydroxyapatite was incubated in different media (ie, water, sera, and DNase I) for up to 3 months. At predetermined intervals, the recovery of detectable DNA was assessed by releasing the DNA from the hydroxyapatite using EDTA and evaluating the presence of DNA by gel electrophoresis and polymerase chain reaction (PCR) amplification. RESULTS: When incubated with hydroxyapatite, nonamplified DNA was detectable after 3 months in water, sera, and DNase I. In contrast, DNA incubated in the same media (without hydroxyapatite) decomposed to levels below the detection level of PCR within 3 weeks, with the exception of DNA in sera in which PCR revealed a weak positive amplification product. CONCLUSIONS: These results confirm a specific binding affinity of hydroxyapatite for DNA. Hydroxyapatite-bound DNA is more resistant to decay and less susceptible to degradation by serum and nucleases, which may account for the long-term persistence of DNA in bone and tooth.

Persistence of dead-cell bacterial DNA in ex vivo root canals and influence of nucleases on DNA decay in vitro.

OBJECTIVE: The fate of DNA from bacteria that do not survive in the root canal is uncertain, yet DNA longevity may confound recovery of authentic etiologic participants in the disease process. This study assessed the recovery of PCR-detectable DNA in ex vivo human root canals and some environmental factors on the decay of microbial DNA. STUDY DESIGN: Heat-killed Enterococcus faecalis cells were inoculated into instrumented human root canals ex vivo, and samples were taken at intervals over 2 years and analyzed by polymerase chain reaction. In an in vitro assay, heat-killed E. faecalis cells and extracted E. faecalis DNA were inoculated into various media, DNase, and culture of a DNase-producing species, Prevotella intermedia. Recovery of DNA was assessed by gel electrophoresis. RESULTS: In ex vivo human teeth, amplifiable DNA was recovered after 1 and 2 years (in 14/15 and 21/25 teeth, respectively). In vitro experiments showed that extracted DNA incubated in different media (water, 10%-50% sera, and DNase) progressively decomposed to levels below the detection limit. In corresponding assays, cell-bound DNA was more resistant to decay. CONCLUSION: Amplifiable DNA is preserved after cell death, but the critical determinant is the form of DNA. Free DNA undergoes spontaneous and enzymatic decomposition, whereas cell-bound E. faecalis DNA persists for long periods.

Starvation response and growth in serum of Fusobacterium nucleatum, Peptostreptococcus anaerobius, Prevotella intermedia, and Pseudoramibacter alactolyticus.

The microbiota inhabiting the untreated root canal differ markedly from those found in post-treatment disease, yet there is limited information on the microbial characteristics distinguishing the different infections. We hypothesized that starvation survival is a key microbial property in species selection. This study analyzed starvation-survival behavior over 60 days of species representative of the untreated root canal infection: Fusobacterium nucleatum, Peptostreptococcus anaerobius, Prevotella intermedia and Pseudoramibacter alactolyticus. All species did not survive 1 day in water. In 1% serum, the 4 species could not survive beyond 2-3 weeks. They required a high initial cell density and >or=10% serum to survive the observation period. The results highlight a poor starvation-survival capacity of these 4 species compared with species prevalent in post-treatment infection, which are well equipped to endure starvation and survive in low numbers on minimal serum. These findings point to starvation-survival capacity as a selection factor for microbial participation in post-treatment disease.

Building biofilms in vital host tissues: a survival strategy of Actinomyces radicidentis.

OBJECTIVE: To investigate the ability of Actinomyces radicidentis to survive and establish in soft connective tissue that grew into subcutaneously implanted tissue cages in Sprague-Dawley rats. STUDY DESIGN: Known concentrations of A. radicidentis suspension, grown on blood agar and broth cultures, were inoculated into tissue cages in rats. The cage contents were retrieved after 7, 14, and 28 days for culturing and correlative light and transmission electron microscopy. RESULTS: Cell suspensions harvested from both types of cultures showed substantial decline in numbers in tissue cages during the observation period. However, correlative light and transmission electron microscopy revealed numerous aggregates of coccoid bacteria already by 7 days of observation compared with the formation of well established colonies with characteristic actinomycotic features by 14 days after inoculation. CONCLUSIONS: These results suggest that the pathogenicity of A. radicidentis is due to its ability to form large aggregates of cells held together by embedding themselves in an extracellular matrix in vital host tissues. Thus, A. radicidentis, like other pathogenic Actinomyces, existing in the protected biofilm-environment can collectively evade destruction and elimination by host defenses, including phagocytosis.

Experimental evidence supports the abscess theory of development of radicular cysts.

OBJECTIVE: The objective of this study was to experimentally induce inflammatory cysts in an animal model so as to test the hypothesis that radicular cysts develop via the "abscess pathway." METHODOLOGY: Twenty-eight perforated custom-made Teflon cages were surgically implanted into defined locations in the back of 7 Sprague Dawley rats. A week after the implantation of the cages, a known quantity of freshly grown, close allogeneic oral keratinocytes in phosphate buffer solution (PBS) was injected into each cage. One cage per animal was treated as the control that received only epithelial cells. The remaining 3 cages of each animal were trials. Seven days post epithelial cell inoculation; a suspension of 0.2 mL of Fusobacterium nucleatum (10(8) bacteria per mL) was injected into each of the 3 trial cages. Two, 12, and 24 weeks after the inoculation of the bacteria, the cages were taken out, and the tissue contents were fixed and processed by correlative light and transmission electron microscopy. Sixteen of the 21 trial cages could be processed and yielded results. RESULTS: Inoculations of epithelial cells followed 1 week later by F. nucleatum into tissue cages resulted in the development inflammatory cysts in 2 of the 16 cages. The 2 cages contained a total of 4 cystic sites. None of the control cages showed the presence of any cyst-like pathology. CONCLUSIONS: Inflammatory cysts were induced by initiating acute inflammatory foci (abscess/necrotic area) by bacterial injection that got enclosed by a proliferating epithelium. This finding provides strong experimental evidence in support of the "abscess theory" of development of radicular cysts.

Bacterial DNA persists for extended periods after cell death.

The fate of DNA from bacteria that infect the root canal but cannot survive is currently unknown, yet such information is essential in establishing the validity of polymerase chain reaction (PCR)-based identification methods for root canal samples. This in vitro study tested the hypothesis that PCR-detectable DNA from dead bacteria might persist after cell death and investigated the efficiency of sodium hypochlorite (NaOCl) as a field decontamination agent. Using heat-killed Enterococcus faecalis, the persistence of DNA encoding the 16S rRNA gene was monitored by PCR. While most probable number analysis showed an approximate 1000-fold decay in amplifiable template, E. faecalis DNA was still PCR-detectable 1 year after cell death. NaOCl (1%) eliminated amplifiable DNA within 60 seconds of exposure. Our findings also disclosed a previously overlooked problem of concentration-dependent inhibition of the PCR reaction by thiosulfate-inactivated NaOCl. These results highlight the challenges of reliably identifying the authentic living root canal flora with PCR techniques.

Influence of residual bacteria on periapical tissue healing after chemomechanical treatment and root filling of experimentally infected monkey teeth.

The purpose of this study was twofold: first, to determine the influence on the healing of the periapical tissues when selected bacterial strains and combinations thereof remain after root canal treatment; and, second, the relationship to healing of the quality of the root filling. In eight monkeys, 175 root canals, previously infected with combinations of four or five bacterial strains and with radiographically verified apical periodontitis, were endodontically treated, bacteriologically controlled, and permanently obturated. After 2-2.5 yr, the periapical regions were radiographically and histologically examined. Of these teeth, 48 root canals were also examined for bacteria remaining after removal of the root fillings. When bacteria remained after the endodontic treatment, 79% of the root canals showed non-healed periapical lesions, compared with 28% where no bacteria were found. Combinations of residual bacterial species were more frequently related to non-healed lesions than were single strains. When no bacteria remained, healing occurred independently of the quality of the root filling. In contrast, when bacteria remained, there was a greater correlation with non-healing in poor-quality root fillings than in technically well-performed fillings. In root canals where bacteria were found after removal of the root filling, 97% had not healed, compared with 18% for those root canals with no bacteria detected. The present study demonstrates the importance of obtaining a bacteria-free root canal system before permanent root filling in order to achieve optimal healing conditions for the periapical tissues.

Apical periodontitis development and bacterial response to endodontic treatment. Experimental root canal infections in monkeys with selected bacterial strains.

In six monkeys, 160 root canals were inoculated with a combination of four bacterial strains belonging to species Streptococcus milleri, Peptostreptococcus anaerobius, Prevotella oralis, and Fusobacterium nucleatum. In two other monkeys, 24 root canals were inoculated with a five-strain combination consisting of these strains and a strain of Enterococcus faecalis. All strains were previously isolated from an infected monkey root canal. After 8-12 months, survival of the strains was recorded bacteriologically, and the reaction in the periapical region was radiographed. From 180 of 184 root canals, one or more of the bacterial strains were reisolated. The two facultative strains were more frequently reisolated than the anaerobic strains. Apical periodontitis was registered in the periapical region of more than 96% of root canals with reisolated bacteria but in none of those without reisolated bacteria. Endodontic treatment was carried out in two sessions with an interval of 14 d without interappointment dressings, and the effect was evaluated bacteriologically before and after each treatment. The chemo-mechanical treatment reduced significantly the number of strains and bacterial cells. The facultative bacteria were more resistant to the treatment than the anaerobic bacteria. The five-strain combination had a higher survival rate than the four-strain combination.

Taxonomic characterization of Mogibacterium diversum sp. nov. and Mogibacterium neglectum sp. nov., isolated from human oral cavities.

Novel isolates, strains HM-7, HM-6, HH-31, P9a-hT and UJB13-d, which were isolated from tongue plaque and necrotic dental pulp, were studied taxonomically and phylogenetically. These organisms were anaerobic, non-spore-forming, gram-positive, rod-shaped bacteria that were inert in most of the conventional biochemical tests and phenotypically resemble Mogibacterium species or asaccharolytic Eubacterium species. The G+C contents of the DNAs from the novel isolates ranged from 41 to 42 mol %. DNA-DNA hybridization studies demonstrated that these strains might be assigned to the genus Mogibacterium but not to the previously described species. It was also apparent that strain HM-7 belonged to the same species as strains HM-6 and HH-31, and that strains P9a-hT and UJB13-d belonged to a second species. The levels of DNA-DNA relatedness to asaccharolytic Eubacterium species, including Eubacterium brachy, Eubacterium nodatum, Eubacterium saphenum and the more recently proposed Eubacterium minutum and Eubacterium exiguum (reclassified as Slackia exigua), are less than 2%. The results of 16S rDNA sequence comparisons revealed that these organisms represent novel lineages distinct from all previously described species of gram-positive, rod-shaped bacteria. On the basis of phenotypic characteristics, DNA-DNA hybridization data and phylogenetic analysis with 16S rRNA gene sequence data, new species are proposed, namely Mogibacterium diversum (for strains HM-7, HM-6 and HH-31) and Mogibacterium neglectum (for strains P9a-hT and UJB13-d). HM-7T (= ATCC 700923T = JCM 11205T) is the type strain of the former and P9a-hT (= ATCC 700924T = JCM 11204T) is the type strain for the latter.