Effective/census population size ratio estimation: a compendium and appraisal

With an ecological-evolutionary perspective increasingly applied toward the conservation and management of endangered or exploited species, the genetic estimation of effective population size (N_e) has proliferated. Based on a comprehensive analysis of empirical literature from the past two decades, we asked: (i) how often do studies link N_e to the adult census population size (N)? (ii) To what extent is N_e correctly linked to N? (iii) How readily is uncertainty accounted for in both N_e and N when quantifying N_e/N ratios? and (iv) how frequently and to what degree might errors in the estimation of N_e or N affect inferences of N_e/N ratios? We found that only 20% of available N_e estimates (508 of 2617; 233 studies) explicitly attempted to link N_e and N; of these, only 31% (160 of 508) correctly linked N_e and N. Moreover, only 7% (41 of 508) of N_e/N ratios (correctly linked or not) reported confidence intervals for both N_e and N; for those cases where confidence intervals were reported for N_e only, 31% of N_e/N ratios overlapped with 1, of which more than half also reached below N_e/N = 0.01. Uncertainty in N_e/N ratios thus sometimes spanned at least two orders of magnitude. We conclude that the estimation of N_e/N ratios in natural populations could be significantly improved, discuss several options for doing so, and briefly outline some future research directions.     

Changes in aquatic vegetation and fish communities following 5 years of sustained low water levels in coastal marshes of eastern Georgian Bay,Lake Huron

Aquatic vegetation in the relatively pristine coastal wetlands of eastern Georgian Bay provides critical habitat for a diverse fish community. Declining water levels in Lake Huron over the past decade, however, have altered the wetland plant assemblages in favour of terrestrial (emergent and meadow) taxa and have thus reduced or eliminated this important ecosystem service. In this study, we compared IKONOS satellite images for two regions of eastern Georgian Bay (acquired in 2002 and 2008) to determine significant changes in cover of four distinct wetland vegetation groups [meadow (M), emergent (E), high‐density floating (HD) and low‐density floating (LD)] over the 6 years. While LD decreased significantly (mean ?2995.4 m²), M and HD increased significantly (mean +2020.9 m² and +2312.6 m², respectively) between 2002 and 2008. Small patches of LD had been replaced by larger patches of HD. These results show that sustained low water levels have led to an increasingly homogeneous habitat and an overall net loss of fish habitat. A comparison of the fish communities sampled between 2003 and 2005 with those sampled in 2009 revealed that there was a significant decline in species richness. The remaining fish communities were also more homogeneous. We suggest that the observed changes in the wetland plant community due to prolonged low water levels may have resulted in significant changes in the fish communities of coastal wetlands in eastern Georgian Bay.     

Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution.     

Darwin’s naturalization hypothesis up-close: Intermountain grassland invaders differ morphologically and phenologically from native community dominants

Darwin’s naturalization hypothesis predicts that successful invaders will tend to differ taxonomically from native species in recipient communities because less related species exhibit lower niche overlap and experience reduced biotic resistance. This hypothesis has garnered substantial support at coarse scales. However, at finer scales, the influence of traits and niche use on invasibility and invader impacts is poorly understood. Within grasslands of western Montana, USA, we compared morphological and phenological traits for five top exotic invasive forbs and five dominant native forbs using multivariate techniques to examine niche separation between exotics and natives. Exotic forbs differed from native forbs in multivariate space. Phenologically, native forbs synchronized vegetative growth with bolting and flowering early in spring. In contrast, exotics initiated vegetative growth concurrent with natives but bolted and flowered later. Morphologically, vegetative growth of exotics was three times shorter and narrower, but flowering stem growth was 35% taller and 65% wider than the natives. Collectively, these patterns suggest different strategies of resource uptake and allocation. Additionally, following wildfire, survival was four times higher for exotics compared to natives, and three times more of the surviving exotics flowered. The exotics we examined appeared to be exploiting an empty community-level niche. The resulting pattern of trait differences between exotics and natives suggests a predictable pattern of invasion and a predictable trajectory of community change. Our results illustrate how quantifying trait differences between invading exotics and natives at the within-community scale can improve understandings of community invasibility and invader impacts.     

Attitudes toward Infection Prophylaxis in Pediatric Oncology: A Qualitative Approach

Background

The risks and benefits of infection prophylaxis are uncertain in children with cancer and thus, preferences should be considered in decision making. The purpose of this report was to describe the attitudes of parents, children and healthcare professionals to infection prophylaxis in pediatric oncology.

Methods

The study was completed in three phases: 1) An initial qualitative pilot to identify the main attributes influencing the decision to use infection prophylaxis, which were then incorporated into a discrete choice experiment; 2) A think aloud during the discrete choice experiment in which preferences for infection prophylaxis were elicited quantitatively; and 3) In-depth follow up interviews. Interviews were recorded verbatim and analyzed using an iterative, thematic analysis. Final themes were selected using a consensus approach.

Results

A total of 35 parents, 22 children and 28 healthcare professionals participated. All three groups suggested that the most important factor influencing their decision making was the effect of prophylaxis on reducing the chance of death. Themes of importance to the three groups included antimicrobial resistance, side effects of medications, the financial impact of outpatient prophylaxis and the route and schedule of administration.

Conclusion

Effect of prophylaxis on risk of death was a key factor in decision making. Other identified factors were antimicrobial resistance, side effects of medication, financial impact and administration details. Better understanding of factors driving decision making for infection prophylaxis will help facilitate future implementation of prophylactic regiments.     

Resurgence of HIV Infection among Men Who Have Sex with Men in Switzerland: Mathematical Modelling Study

Background

New HIV infections in men who have sex with men (MSM) have increased in Switzerland since 2000 despite combination antiretroviral therapy (cART). The objectives of this mathematical modelling study were: to describe the dynamics of the HIV epidemic in MSM in Switzerland using national data; to explore the effects of hypothetical prevention scenarios; and to conduct a multivariate sensitivity analysis.

Methodology/Principal Findings

The model describes HIV transmission, progression and the effects of cART using differential equations. The model was fitted to Swiss HIV and AIDS surveillance data and twelve unknown parameters were estimated. Predicted numbers of diagnosed HIV infections and AIDS cases fitted the observed data well. By the end of 2010, an estimated 13.5% (95% CI 12.5, 14.6%) of all HIV-infected MSM were undiagnosed and accounted for 81.8% (95% CI 81.1, 82.4%) of new HIV infections. The transmission rate was at its lowest from 1995–1999, with a nadir of 46 incident HIV infections in 1999, but increased from 2000. The estimated number of new infections continued to increase to more than 250 in 2010, although the reproduction number was still below the epidemic threshold. Prevention scenarios included temporary reductions in risk behaviour, annual test and treat, and reduction in risk behaviour to levels observed earlier in the epidemic. These led to predicted reductions in new infections from 2 to 26% by 2020. Parameters related to disease progression and relative infectiousness at different HIV stages had the greatest influence on estimates of the net transmission rate.

Conclusions/Significance

The model outputs suggest that the increase in HIV transmission amongst MSM in Switzerland is the result of continuing risky sexual behaviour, particularly by those unaware of their infection status. Long term reductions in the incidence of HIV infection in MSM in Switzerland will require increased and sustained uptake of effective interventions.     

Modelling the Arrival of Invasive Organisms via the International Marine Shipping Network: A Khapra Beetle Study

Species can sometimes spread significant distances beyond their natural dispersal ability by anthropogenic means. International shipping routes and the transport of shipping containers, in particular are a commonly recognised pathway for the introduction of invasive species. Species can gain access to a shipping container and remain inside, hidden and undetected for long periods. Currently, government biosecurity agencies charged with intercepting and removing these invasive species when they arrive to a county's border only assess the most immediate point of loading in evaluating a shipping container's risk profile. However, an invasive species could have infested a container previous to this point and travelled undetected before arriving at the border. To assess arrival risk for an invasive species requires analysing the international shipping network in order to identify the most likely source countries and the domestic ports of entry where the species is likely to arrive. We analysed an international shipping network and generated pathway simulations using a first-order Markov chain model to identify possible source ports and countries for the arrival of Khapra beetle (Trogoderma granarium) to Australia. We found Kaohsiung (Taiwan) and Busan (Republic of Korea) to be the most likely sources for Khapra beetle arrival, while the port of Melbourne was the most likely point of entry to Australia. Sensitivity analysis revealed significant stability in the rankings of foreign and Australian ports. This methodology provides a reliable modelling tool to identify and rank possible sources for an invasive species that could arrive at some time in the future. Such model outputs can be used by biosecurity agencies concerned with inspecting incoming shipping containers and wishing to optimise their inspection protocols.     

SIRT1 and c-Myc Promote Liver Tumor Cell Survival and Predict Poor Survival of Human Hepatocellular Carcinomas

The increased expression of SIRT1 has recently been identified in numerous human tumors and a possible correlation with c-Myc oncogene has been proposed. However, it remains unclear whether SIRT1 functions as an oncogene or tumor suppressor. We sought to elucidate the role of SIRT1 in liver cancer under the influence of c-Myc and to determine the prognostic significance of SIRT1 and c-Myc expression in human hepatocellular carcinoma. The effect of either over-expression or knock down of SIRT1 on cell proliferation and survival was evaluated in both mouse and human liver cancer cells. Nicotinamide, an inhibitor of SIRT1, was also evaluated for its effects on liver tumorigenesis. The prognostic significance of the immunohistochemical detection of SIRT1 and c-Myc was evaluated in 154 hepatocellular carcinoma patients. SIRT1 and c-Myc regulate each other via a positive feedback loop and act synergistically to promote hepatocellular proliferation in both mice and human liver tumor cells. Tumor growth was significantly inhibited by nicotinamide in vivo and in vitro. In human hepatocellular carcinoma, SIRT1 expression positively correlated with c-Myc, Ki67 and p53 expression, as well as high á-fetoprotein level. Moreover, the expression of SIRT1, c-Myc and p53 were independent prognostic indicators of hepatocellular carcinoma. In conclusion, this study demonstrates that SIRT1 expression supports liver tumorigenesis and is closely correlated with oncogenic c-MYC expression. In addition, both SIRT1 and c-Myc may be useful prognostic indicators of hepatocellular carcinoma and SIRT1 targeted therapy may be beneficial in the treatment of hepatocellular carcinoma.