Assessment of Selected Reef Sites in Northern and South-Central Belize, Including Recovery from Bleaching and Hurricane Disturbances (Stony Corals, Algae and Fish)

The condition of coral. algal. and fish populations in fore reefs. patch reefs, and coral reef ridges was investigated at 13 sites along the northern and south-central Belize barrier reef during May 1999, documenting effects of the 1998 warming episode and Hurricane Mitch. We found high percentages of partial, or even complete, colony mortality of major reef-builders (Acropora palmata, the Montastraea annuluris species complex and Agaricia tenuifolia) that were rarely censused as recruits. A. tenuifolia, formerly a space-dominant coral in reef ridges, had incurred nearly 100% mortality after bleaching. Nearly 45% of the M. annurluris complex was still discolored (50% had been bleached in January 1999) on some south-central patch reefs where the total (recent + old) partial mortality exceeded 60% of colony surfaces. Although turf algae dominated patch reefs and coral reef ridges, macroalgae were quite prevalent representing \u3e30% cover at six sites. Parrotfish densities exceeded surgeontishes at most sites (11/13). Consistent patterns of lower partial-colony mortality of stony corals and greater fish densities and sizes near and within the Hol Chan Marine Reserve highlight the ecological benefits of protected areas for the maintenance of reef corals and attendant fish populations

The Canine Oral Microbiome

Determining the bacterial composition of the canine oral microbiome is of interest for two primary reasons. First, while the human oral microbiome has been well studied using molecular techniques, the oral microbiomes of other mammals have not been studied in equal depth using culture independent methods. This study allows a comparison of the number of bacterial taxa, based on 16S rRNA-gene sequence comparison, shared between humans and dogs, two divergent mammalian species. Second, canine oral bacteria are of interest to veterinary and human medical communities for understanding their roles in health and infectious diseases. The bacteria involved are mostly unnamed and not linked by 16S rRNA-gene sequence identity to a taxonomic scheme. This manuscript describes the analysis of 5,958 16S rRNA-gene sequences from 65 clone libraries. Full length 16S rRNA reference sequences have been obtained for 353 canine bacterial taxa, which were placed in 14 bacterial phyla, 23 classes, 37 orders, 66 families, and 148 genera. Eighty percent of the taxa are currently unnamed. The bacterial taxa identified in dogs are markedly different from those of humans with only 16.4% of oral taxa are shared between dogs and humans based on a 98.5% 16S rRNA sequence similarity cutoff. This indicates that there is a large divergence in the bacteria comprising the oral microbiomes of divergent mammalian species. The historic practice of identifying animal associated bacteria based on phenotypic similarities to human bacteria is generally invalid. This report describes the diversity of the canine oral microbiome and provides a provisional 16S rRNA based taxonomic scheme for naming and identifying unnamed canine bacterial taxa

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Assessment of Coral Reefs off San Salvador Island, Bahamas (Stony Coral, Algae and Fish Populations)

During assessments at 11 shallow reef sites on an Salvador Island, Bahamas in .iunc I998 we found low prevalence of disease, bleaching, and recent partial-colon1 mortality among stony corals (10 cm minimum dixncter). Old partial-colony mortalit) was \u3e50% in Acropora palmata; however, recent tissue losses were low and it had recruits at several sites. Total (recent + old) partial-colony mortality of the Montastraea annularis species complex exceeded 30% on leeward patch reefs and back reefs. Groupers (serranids), snappers (lutjanids), and grunts (haemulids) were rare. Parrotfishes (scarids) were uncommon at most sites and surgeonfishes (acanthurids) were the dominant herbivores. Macroalgae, particularly browns that are seldom grazed by surgeonfishes. were the dominant algal functional group. The green macroalga Microdictyon marinum was extremely abundant and overgrowing Porites porires on leeward patch reefs. To facilitate their conservation, an Salvador Island\u27s reef resources should be designated as a marine reserve

Fluoride Content of Ready-to-Eat Infant Foods and Drinks in Australia

The use of fluoride is effective in preventing dental caries. However, an excessive intake of fluoride leads to dental fluorosis, making it necessary to regularly monitor the fluoride intake especially for infants. There is hitherto a lack of information on fluoride content in infant foods from an Australian perspective. Therefore, this study aims to estimate the amount of fluoride content from a range of commercially available ready-to-eat (RTE) infant foods and drinks available in Australia. Based on an external calibration method, potentiometry involving a fluoride ion selective electrode and a silver|silver chloride reference electrode was conducted to analyse the fluoride content of a total of 326 solid food samples and 49 liquid food samples in this work. Our results showed an overall median (range) fluoride content of 0.16 (0.001–2.8) µg F/g of solid food samples, and 0.020 (0.002–1.2) µg F/mL of liquid food samples. In addition, ~77.5% of the liquid samples revealed a fluoride content < 0.05% µg F/mL. The highest variation of fluoride concentration (0.014–0.92 µg F/g) was found in formulas for ≥6 month-old infants. We have attributed the wide fluoride content variations in ready-to-eat infant foods and drinks to the processing steps, different ingredients and their origins, including water. In general, we found the fluoride content in most of the collected samples from Australian markets to be high and may therefore carry a risk of dental fluorosis. These results highlight the need for parents to receive appropriate information on the fluoride content of ready-to-eat infant food and drinks

Effects of Water Velocity and Trash Rack Architecture on Juvenile Fish Passage and Interactions: A Simulation

Many resident and migratory fish species have experienced population declines due tomodification of estuarine ecosystems. Fish screens (or louvers) have been designed to guide fishaway from the diversion pumps, and trash racks have been placed upstream of the screens tointercept aquatic plants and debris. Although small fish may aggregate around these structures,potentially increasing their vulnerability to predators, we know little about the behaviour,performance, and survival of fish near trash racks. To determine how trash rack flow regime andarchitecture influence fish behaviour, we exposed juvenile threadfin shad (Dorosoma petenense)and winter-run Chinook salmon (Oncorhynchus tshawytscha) to three water velocities and twobar spacing treatments in a circular tank bisected by a simulated trash rack. Our results suggestthat relatively small increases in water velocity at diversion facilities will result in the aggregationof juvenile fish near trash racks. In contrast, bar spacing did not influence fish passage frequencyor interaction in this study. We also found that threadfin shad selected higher velocities as watercurrent increased, whereas Chinook salmon consistently showed a preference for moderate tolow water velocities

Identity Profiles in Lesbian, Gay, and Bisexual Youth: The Role of Family Influences

Sexual identity development is a central task of adolescence and young adulthood and can be especially challenging for sexual minority youth. Recent research has moved from a stage model of identity development in lesbian, gay, and bisexual (LGB) youth to examining identity in a non-linear, multidimensional manner. In addition, although families have been identified as important to youth's identity development, limited research has examined the influence of parental responses to youth's disclosure of their LGB sexual orientation on LGB identity. The current study examined a multidimensional model of LGB identity and its links with parental support and rejection. One hundred and sixty-nine LGB adolescents and young adults (ages 14–24, 56% male, 48% gay, 31% lesbian, 21% bisexual) described themselves on dimensions of LGB identity and reported on parental rejection, sexuality-specific social support, and non-sexuality-specific social support. Using latent profile analysis (LPA), two profiles were identified, indicating that youth experience both affirmed and struggling identities. Results indicated that parental rejection and sexuality-specific social support from families were salient links to LGB identity profile classification, while non-sexuality specific social support was unrelated. Parental rejection and sexuality-specific social support may be important to target in interventions for families to foster affirmed LGB identity development in youth