Multilocus analysis of extracellular putative virulence proteins made by group A Streptococcus: Population genetics, human serologic response, and gene transcription

Species of pathogenic microbes are composed of an array of evolutionarily distinct chromosomal genotypes characterized by diversity in gene content and sequence (allelic variation). The occurrence of substantial genetic diversity has hindered progress in developing a comprehensive understanding of the molecular basis of virulence and new therapeutics such as vaccines. To provide new information that bears on these issues, 11 genes encoding extracellular proteins in the human bacterial pathogen group A Streptococcus identified by analysis of four genomes were studied. Eight of the 11 genes encode proteins with a LPXTG(L) motif that covalently links Gram-positive virulence factors to the bacterial cell surface. Sequence analysis of the 11 genes in 37 geographically and phylogenetically diverse group A Streptococcus strains cultured from patients with different infection types found that recent horizontal gene transfer has contributed substantially to chromosomal diversity. Regions of the inferred proteins likely to interact with the host were identified by molecular population genetic analysis, and Western immunoblot analysis with sera from infected patients confirmed that they were antigenic. Real-time reverse transcriptase–PCR (TaqMan) assays found that transcription of six of the 11 genes was substantially up-regulated in the stationary phase. In addition, transcription of many genes was influenced by the covR and mga trans-acting gene regulatory loci. Multilocus investigation of putative virulence genes by the integrated approach described herein provides an important strategy to aid microbial pathogenesis research and rapidly identify new targets for therapeutics research.

Development of a bovine X chromosome linkage group and painting probes to assess cattle, sheep, and goat X chromosome segment homologies.

The X chromosome linkage group is conserved in placental mammals. However, X chromosome morphological differences, due to internal chromosome rearrangements, exist among mammalian species. We have developed bovine chromosome painting probes for Xp and Xq to assess segment homologies between the submetacentric bovine X chromosome and the acrocentric sheep and goat X chromosomes. These painting probes and their corresponding DNA libraries were developed by chromosome micromanipulation, DNA micropurification, microcloning, and PCR amplification. The bovine Xp painting probe identified an interstitially located homologous segment in the sheep and goat Xq region, most probably resulting from chromosome inversion. Ten type II (microsatellite) markers obtained from the bovine Xq library and five other X chromosome assigned, but unlinked, markers were used to generate a linkage map for Xq spanning 89.4 centimorgans. The chromosome painting probes and molecular markers generated in this study would be useful for comparative mapping and tracing of internal X chromosome rearrangements in all ruminant species and would contribute to the understanding of mammalian sex chromosome evolution.

Amphibian Hotspots and Conservation Priorities in Eastern Cuba Identified by Species Distribution Modeling

The high rate of amphibian endemism and the severe habitat modification in the Caribbean islands make them an ideal place to test if the current protected areas network might protect this group. In this study, we model distribution and map species richness of the 40 amphibian species from eastern Cuba with the objectives of identify hotspots, detect gaps in species representation in protected areas, and select additional areas to fill these gaps. We used two modeling methods, Maxent and Habitat Suitability Models, to reach a consensus distribution map for each species, then calculate species richness by combining specific models and finally performed gap analyses for species and hotspots. Our results showed that the models were robust enough to predict species distributions and that most of the amphibian hotspots were represented in reserves, but 50 percent of the species were incompletely covered and Eleutherodactylus rivularis was totally uncovered by the protected areas. We identified 1441 additional km2 (9.9% of the study area) that could be added to the current protected areas, allowing the representation of every species and all hotspots. Our results are relevant for the conservation planning in other Caribbean islands, since studies like this could contribute to fill the gaps in the existing protected areas and to design a future network. Both cases would benefit from modeling amphibian species distribution using available data, even if they are incomplete, rather than relying only in the protection of known or suspected hotspots.

Saproxylic Beetle Assemblage Selection as Determining Factor of Species Distributional Patterns: Implications for Conservation

The knowledge of the distributional patterns of saproxylic beetles is essential for conservation biology due to the relevance of this fauna in the maintenance of ecological processes and the endangerment of species. The complex community of saproxylic beetles is shaped by different assemblages that are composed of species linked by the microhabitats they use. We evaluate how different the species distribution patterns that are obtained can be, depending on the analyzed assemblage and to what extent these can affect conservation decisions. Beetles were sampled using hollow emergence and window traps in three protected areas of the Iberian Peninsula. Species richness, composition, and diversity turnover were analyzed for each sampling method and showed high variation depending on the analyzed assemblage. Beta diversity was clearly higher among forests for the assemblage captured using window traps. This method collects flying insects from different tree microhabitats and its captures are influenced by the forest structuring. Within forests, the assemblages captured by hollow emergence traps, which collect the fauna linked to tree hollows, showed the largest turnover of species, as they are influenced by the characteristics of each cavity. Moreover, the selection of the forest showing the highest species richness strongly depended on the studied assemblage. This study demonstrates that differences in the studied assemblages (group of species co-occurring in the same habitat) can also lead to significant differences in the identified patterns of species distribution and diversity turnover. This fact will be necessary to take into consideration when making decisions about conservation and management.

Table 1. - Estimated numbers of marine zooplnaktonic species for the World Oceanand for the South Atlantic

In total, ca. 7000 zooplanktonic species have been described for the World Ocean. This figure represents less than 4% of the total number of known marine organisms. Of the 7000 zooplanktonic species world-wide, some 60% are present in the South Atlantic; about one third of the latter have been recorded in its Subantarctic waters, and ca. 20% south of the Polar Front. When compared with those of benthic animals, these figures indicate that proportions of the overall inventories that are present in the cold waters are almost two times higher among the zooplankton. In agreement with this pattern, the proportions of Antarctic endemics in the benthos are very significantly higher than those in the plankton. For the water-column dwelling animals, the Polar Front boundary is more important than the Tropical-Subtropical limit, but almost equivalent to the Subtropical-Transitional limit, and weaker in biogeographic terms than the Transitional-Subantarctic boundary. Some of the implications of these dissimilarities, both for ecological theory and for resource allocation strategies, are discussed.

(Table 1) Abundances of Discoaster species in ODP Hole 130-806C

Members of the calcareous nannofossil genus Discoaster have been used extensively to subdivide Tertiary deep-sea sediments into biostratigraphic zones or subzones (e.g., Martini, 1971; Bukry, 1973). Haq and Lohmann (1976) mapped biogeographic migrations of this group through time and over latitude. They suggested that expansions and contractions of Discoaster-dominated assemblages across latitudes reflect sea-surface temperature changes. Subsequently, late Pliocene Discoaster species were counted at closely spaced sample intervals from various Atlantic sites (Backman et al., 1986; Backman and Pestiaux, 1987; Chepstow-Lusty et al., 1989, 1991), and Indian Ocean as well as Pacific Ocean sites (Chepstow-Lusty, 1990). In addition to the biostratigraphic information revealing positions and the precision by which the different late Pliocene Discoaster species can be determined, these studies also demonstrated that discoasters strongly fluctuate in abundance as a function of time. These abundance variations occur in equatorial as well as temperate temperature regimes, and show periodicities that reflect orbital frequencies. Chepstow-Lusty et al. (1989, 1991) also suggested that the oscillating abundances partly represent productivity pressure, because discoasters tend to show low abundances under high productivity conditions and vice versa. In the Pacific Ocean, counts showing late Pliocene Discoaster abundances exist from three sites, namely Ocean Drilling Program (ODP) Site 677 in the eastern equatorial upwelling region, Core V28-179 from the central equatorial region, and Core V32-127 from the mid-latitude Hess Rise. The two Vema cores are condensed and show sedimentation rates below 0.5 cm/1000 yr, thus offering a poorly resolved stratigraphy. Hole 806C from the Ontong Java Plateau provided an opportunity to establish a highly resolved Discoaster record from the western extreme of the equatorial Pacific under an environmental setting that differed from ODP Site 677 by being less influenced by intense upwelling. The Discoaster counting technique is described by Backman and Shackleton (1983).

(Table 1) Dominant species and total biomass of macrozoobenthos communities in the southwestern Kara Sea

The structure and distribution of the macrobenthic communities were studied in the southwestern Kara Sea. The material was collected in Baidaratskaya Bay in July 2007 and in a section running westward of the Yamal Peninsula in September 2007. The depths of the sampling stations ranged from 5 to 25 m in the Baidaratskaya Bay area and between 16 and 46 m in the Yamal section. A total of 212 benthic invertebrate species were recorded. In both areas, Bivalvia was the group with the highest biomass (54.88 g/m**2 in the Yamal section and 59.71 g/m**2 in the Baidaratskaya Bay area), while polychaetes were the group with the highest number of species (45 in the Yamal section and 64 the Baidaratskaya Bay area). Three major macrozoobenthic communities were recognized: the Astarte borealis community (20-46 m, the deepest sampling stations in both areas); the 'medium-depth' community (10-20 m, extremely mosaic, usually dominated by Serripes groenlandicus); and the Nephtys longosetosa community (depth smaller than 10 m, characterized by low biomass and the absence of large bivalves and echinoderms). The western Yamal shallow-water communities were shown to be generally similar to those of Baidaratskaya Bay. The comparison of these results with those of the benthos censuses performed in 1927-1945, 1975, and 1993 showed that the benthic communities in the southwestern Kara Sea remained relatively stable during the second half of the 20th century and the early 21st century.

FAUNMAP : a database documenting Late Quaternary distributions of mammal species in the United States /

Includes bibliographical references and indexes.

Formal group laws and hypergraph colorings

Thesis (Ph.D.)--University of Washington, 2016-06

Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis

Aim: The aim of this study was to characterize the bacterial community adhering to the mucosa of the terminal ileum, and proximal and distal colon of the human digestive tract. Methods and Results: Pinch samples of the terminal ileum, proximal and distal colon were taken from a healthy 35-year-old, and a 68-year-old subject with mild diverticulosis. The 16S rDNA genes were amplified using a low number of PCR cycles, cloned, and sequenced. In total, 361 sequences were obtained comprising 70 operational taxonomic units (OTU), with a calculated coverage of 82.6%. Twenty-three per cent of OTU were common to the terminal ileum, proximal colon and distal colon, but 14% OTU were only found in the terminal ileum, and 43% were only associated with the proximal or distal colon. The most frequently represented clones were from the Clostridium group XIVa (24.7%), and the Bacteroidetes (Cytophaga-Flavobacteria-Bacteroides ) cluster (27.7%). Conclusion: Comparison of 16S rDNA clone libraries of the hindgut across mammalian species confirms that the distribution of phylogenetic groups is similar irrespective of the host species. Lesser site-related differences within groups or clusters of organisms, are probable. Significance and Impact: This study provides further evidence of the distribution of the bacteria on the mucosal surfaces of the human hindgut. Data contribute to the benchmarking of the microbial composition of the human digestive tract.

A morphological study of the Anopheles punctulatus group (Diptera: Culicidae) in the Solomon Islands, with a description of Anopheles (Cellia) irenicus Schmidt, sp.n.

A description of Anopheles (Cellia) irenicus Schmidt, sp.n. (formerly A. farauti No. 7) is provided. This species is one of six recorded from the Solomon Islands within the A. punctulatus group, which contains the major vectors of the causative agents of malaria and lymphatic filariasis in the southwest Pacific. Morphological markers are described for adult females, fourth-instar larvae and pupae that identify most specimens of A. irenicus. Keys are presented to distinguish members of the A. punctulatus group in the Solomon Islands.

Reproductive isolation of a new hybrid species, Senecio eboracensis Abbott & Lowe (Asteraceae)

The nature and extent of reproductive isolation was examined between a new self-compatible hybrid species Senecio eboracensis (2n = 40) and its parents, self-incompatible S. squalidus (2n = 20) and self-compatible S. vulgaris (2n = 40). The triploid F-1 of S. eboracensis x S. squalidus exhibited very low seed set ((x) over bar = 0.63%), and F-2 and F-3 progeny were able to recover nominal levels of fertility ((x) over bar = 23.9 and 9.7%), while F-1 and F-2 offspring of S. eboracensis x S. vulgaris showed reduced seed set ((x) over bar = 63.8 and 58.8%). In both cases, evidence from previous work indicates that reduced fertility is associated with meiotic chromosome mispairing, and is a likely consequence of recombining both parental genomes within this new taxon. No hybrid offspring between S. eboracensis and S. squalidus were found in the wild, and only one such hybrid was recorded among 769 progeny produced by S. eboracensis surrounded by S. squalidus on an experimental plot. Natural crossing between S. eboracensis and S. vulgaris was recorded to be very low (between 0 and 1.46%) in the wild, but rose to 18.3% when individuals of S. eboracensis were surrounded by plants of S. vulgaris. It was concluded that strong breeding barriers exist between the new hybrid species and its two parents. Prezygotic isolation between S. eboracensis and S. vulgaris is likely to be largely due to both species reproducing by predominant self-fertilisation. However, differences recorded for germination, seedling survival, time of flowering and characters associated with pollinator attraction, plus significant clumping of juvenile and adult conspecifics in the wild, probably also contribute to reproductive isolation and ecological differentiation.