Cancer risk assessment for 1,3-butadiene: dose-response modeling from an epidemiological perspective

The dose-response assessment of the association between 1,3-butadiene (BD) and leukemia mortality among workers in the North American synthetic rubber industry is explored. Analyses are based on the most recent University of Alabama at Birmingham epidemiological study and exposure estimation. The U.S. EPA Science Advisory Board recommendations of using the most recent data and giving consideration to peak exposures to BD have been followed. If cumulative BD ppm-years is to be used as the predictor of the leukemia rate ratio, then the performance of that predictor is statistically significantly improved if the slope in the predictor is estimated with age and the cumulative number of BD peaks (where a BD peak is any exposure, regardless of duration, to a BD concentration above 100 ppm) added as categorical covariates. After age and the cumulative number of BD peaks are incorporated as categorical covariates in the Poisson regression model, the estimated concentration (EC(001)) corresponding to an excess risk of 0.001 as a result of continuous environmental exposure is 11.2 ppm; however, the estimated slope for BD cumulative ppm-years in the linear rate ratio for leukemia used to derive this EC(001) is not statistically significantly different from zero. Sensitivity analyses using alternative models indicate either essentially no risk or estimated EC(001) values of 9 and 77 ppm. Analyses suggesting the absence of a statistically significant low-dose risk versus cumulative BD ppm-years are presented. Sensitivity analyses of other malignant neoplasms of lymphatic and hematopoietic tissue (specifically, lymphoid and myeloid neoplasms) resulted in conclusions about the dose-response modeling methodology that were supportive of the methodology used for leukemia.     

Relationships of the Insect-Pathogenic Order Entomophthorales (Zygomycota, Fungi) Based on Phylogenetic Analyses of Nuclear Small Subunit Ribosomal DNA Sequences (SSU rDNA)

We sequenced the nuclear small subunit of ribosomal DNA (SSU rDNA) from seven species within the insect-pathogenic order Entomophthorales. These sequences were aligned with other published SSU rDNA sequences and phylogenies were inferred using phenetic and cladistic methods. Based on three different phylogenetic methods the Entomophthorales (excludingBasidiobolus ranarum) is monophyletic;B. ranarumwas more closely related to chytrids from Chytridiales and Neocallimasticales than to Entomophthorales, as was proposed by Nagahamaet al.(Mycologia87:203–209, 1995). Nuclear characters (large nuclei containing conspicuous condensed chromatin and lack of a prominent nucleolus) were of predictive value for the monophyly of the family Entomophthoraceae. Conidial characters separate the Entomophthoraceae, which only includes obligate pathogens, into at least two lineages: one lineage with uninucleate conidia and another with multinucleate conidia. The two species ofConidiobolusstudied were paraphyletic in our analyses and only distantly related to each other. This information may prove to be important in the use of these fungi as biocontrol agents.     

The influence of arbuscular mycorrhizae and light on Wisconsin (USA) sand savanna understories 2. Plant competition

Wisconsin (USA) oak savannas are endangered plant communities that have remarkably high plant species diversity. To investigate factors underlying this richness, we experimentally investigated the potentially interacting effects of light gradients and arbuscular mycorrhizal fungi (AMF) on plant competition in the greenhouse, using a fully randomized block design. We used four plant species, soil, and AMF from a remnant sand savanna, under two light and five AMF treatments. Plants were grown four per pot under two competition treatments (either one or four species per pot) for 20 weeks. Using ANOVA, we found that all species showed significant treatment effects on total and shoot biomass, primarily due to differences in competition and light, less to AMF. However, effects were the opposite of predictions. Putatively mycorrhizal plants showed neutral to negative responses to AMF, and a nonmycorrhizal species outcompeted AMF species in infected pots. We concluded that our experimental setup of small pots, sandy soil, and long growing period had induced parasitism by the AMF on susceptible hosts. This unexpected result is consistent with field data from the sand savanna, and may help explain how nonmycorrhizal plants can compete successfully with AMF species in established, species-rich communities.     

DNA-based detection of the fungal pathogen Geomyces destructans in soils from bat hibernacula

White-nose syndrome (WNS) is an emerging disease causing unprecedented morbidity and mortality among bats in eastern North America. The disease is characterized by cutaneous infection of hibernating bats by the psychrophilic fungus Geomyces destructans. Detection of G. destructans in environments occupied by bats will be critical for WNS surveillance, management and characterization of the fungal lifecycle. We initiated an rRNA gene region-based molecular survey to characterize the distribution of G. destructans in soil samples collected from bat hibernacula in the eastern United States with an existing PCR test. Although this test did not specifically detect G. destructans in soil samples based on a presence/absence metric, it did favor amplification of DNA from putative Geomyces species. Cloning and sequencing of PCR products amplified from 24 soil samples revealed 74 unique sequence variants representing 12 clades. Clones with exact sequence matches to G. destructans were identified in three of 19 soil samples from hibernacula in states where WNS is known to occur. Geomyces destructans was not identified in an additional five samples collected outside the region where WNS has been documented. This study highlights the diversity of putative Geomyces spp. in soil from bat hibernacula and indicates that further research is needed to better define the taxonomy of this genus and to develop enhanced diagnostic tests for rapid and specific detection of G. destructans in environmental samples.     

New measures of topological stability in phylogenetic trees - Taking taxon composition into account

In phylogenetic trees the addition and removal of taxa has large effects on tree topology, hence measures of branch support and tree stability should account for taxonomic composition. Currently no comprehensive system of composition-dependent parameters exists in any cladistic or phenetic strategy. We introduce several values and indices based on a modification of the original jackknife resampling. Their advantage is a complete evaluation and optimization of taxon composition in phylogenetic data. While related to the Jackknife Monophyly Index (JMI), our system of support measures expands beyond parsimony analyses, and includes indices estimating support for the entire phylogenetic tree based on individual branch supports.     

Using ITS2 secondary structure to create species-specific oligonucleotide probes for fungi

Oligonucleotide microarray based on ITS2 rDNA sequences would be extremely useful in identifying fungi within soil samples. However ITS2 contains phylogenetic information and duplication of sequences among taxa make false positive detections likely unless a way could be found to identify taxon-specific portions of the ITS2 sequence a priori. Examination of component ITS2 sequences suggested one method of identifying species-specific probes. Analysis of 168 fungal ITS2 sequences showed that all 168 ITS2 rRNA sequences could be folded to produce similar secondary structures of 3-4 loops. Unique probes occurred most often in the second loop. While the loop 2 sequence was unique in all taxa, there were partial congeneric and intergeneric duplicates. Evidence for a decrease in duplicates with increasing phylogenetic distance was mixed. From the evidence, 2 or 3 disjunct oligonucleotide probes from the loop 2 sequence might be sufficient to identify most fungal species. This combination appears minimally susceptible to false positives and conceivably could be extended to design probes to identify any eukaryotic species.     

Multiclavula ichthyiformis (Fungi: Basidiomycota: Cantharellales: Clavulinaceae), a remarkable new basidiolichen from Costa Rica

The new basidiolichen Multiclavula ichthyiformis Nelsen, Lücking, Uma?a, Trest & Will-Wolf is described from Costa Rica. The new species differs from other species of Multiclavula in having a basidiocarp with tomentose stipe and flattened lamina with nonamphigenous hymenium. Molecular sequence data (ITS) confirmed its placement within Multiclavula in the Clavulinaceae (Cantharellales, Agaricomycetes). The new lichen was discovered in a Central American paramo remnant, illustrating the importance of biotic inventories of fungi and lichens to increase our knowledge of the diversity of these groups in endangered tropical ecosystems. The new species was found as part of the TICOLICHEN project in Costa Rica.     

Positions of multiple insertions in SSU rDNA of lichen-forming fungi

Lichen-forming fungi, in symbiotic associations with algae, frequently have nuclear small subunit ribosomal DNA (SSU rDNA) longer than the 1,800 nucleotides typical for eukaryotes. The lichen-forming ascomycetous fungus Lecanora dispersa contains insertions at eight distinct positions of its SSU rDNA; the lichen-forming fungi Calicium tricolor and Porpidia crustulata each contain one insertion. Insertions are not limited to fungi that form lichens; the lichen ally Mycocalicium albonigrum also contains two insertions. Of the 11 insertion positions now reported for lichen-forming fungi and this ally, 6 positions are known only from lichen-forming fungi. Including the 4 newly reported in this study, insertions are now known from at least 17 positions among all reported SSU rDNA sequences. Insertions, most of which are Group I introns, are reported in fungal and protistan lineages and occur at corresponding positions in genomes as phylogenetically distant as the nuclei of fungi, green algae, and red algae. Many of these positions are exposed in the mature rRNA tertiary structure and may be subject to independent insertion of introns. Insertion of introns, accompanied by their sporadic loss, accounts for the scattered distribution of insertions observed within the SSU rDNA of these diverse organisms.