Simple and efficient CRISPR/Cas9‐mediated targeted mutagenesis in Xenopus tropicalis

We have assessed the efficacy of the recently developed CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR‐associated) system for genome modification in the amphibian Xenopus tropicalis. As a model experiment, targeted mutations of the tyrosinase gene were verified, showing the expected albinism phenotype in injected embryos. We further tested this technology by interrupting the six3 gene, which is required for proper eye and brain formation. Expected eye and brain phenotypes were observed when inducing mutations in the six3 coding regions, as well as when deleting the gene promoter by dual targeting. We describe here a standardized protocol for genome editing using this system. This simple and fast method to edit the genome provides a powerful new reverse genetics tool for Xenopus researchers. genesis 51:835–843. © 2013 Wiley Periodicals, Inc.     

The Putative Thiosulfate Sulfurtransferases PspE and GlpE Contribute to Virulence of Salmonella Typhimurium in the Mouse Model of Systemic Disease

The phage-shock protein PspE and GlpE of the glycerol 3-phosphate regulon of Salmonella enterica serovar Typhimurium are predicted to belong to the class of thiosulfate sulfurtransferases, enzymes that traffic sulfur between molecules. In the present study we demonstrated that the two genes contribute to S. Typhimurium virulence, as a glpE and pspE double deletion strain showed significantly decreased virulence in a mouse model of systemic infection. However, challenge of cultured epithelial cells and macrophages did not reveal any virulence-associated phenotypes. We hypothesized that their contribution to virulence could be in sulfur metabolism or by contributing to resistance to nitric oxide, oxidative stress, or cyanide detoxification. In vitro studies demonstrated that glpE but not pspE was important for resistance to H₂O₂. Since the double mutant, which was the one affected in virulence, was not affected in this assay, we concluded that resistance to oxidative stress and the virulence phenotype was most likely not linked. The two genes did not contribute to nitric oxid stress, to synthesis of essential sulfur containing amino acids, nor to detoxification of cyanide. Currently, the precise mechanism by which they contribute to virulence remains elusive.     

How do low dispersal species establish large range sizes? The case of the water beetle Graphoderus bilineatus

Species’ dispersal abilities have been considered a major driving force in establishment and maintenance of large range sizes. However, recent studies question the general validity of this relationship because the relationship between dispersal ability and range size might in some cases be less important than species phylogeny or local spatial attributes. In this study we used the water beetle Graphoderus bilineatus a philopatric species of conservation concern in Europe as a model to explain large range size and to support effective conservation measures for such species that also have limited dispersal. We recorded the presence/absence of G. bilineatus and measured 14 habitat and 20 landscape variables at 228 localities in Estonia, Poland and Sweden within the core range of the species. Using information theory and average multivariate logistic regression models we determined that presence of G. bilineatus depended on landscape connectivity, distance to a possible source habitat, and stability of the site; however, specificity of habitat characteristics was not vital for the species. We reason that the large range of G. bilineatus is best explained by the historical combination of lakes, river systems and wetlands which used to be highly connected throughout the central plains of Europe. Our data suggest that a broad habitat niche can prevent landscape elements from becoming barriers for species like G. bilineatus. Therefore, we question the usefulness of site protection as conservation measures for G. bilineatus and similar philopatric species. Instead, conservation actions should be focused at the landscape level to ensure a long‐term viability of such species across their range.     

Deaths and Medical Visits Attributable to Environmental Pollution in the United Arab Emirates

Background

This study estimates the potential health gains achievable in the United Arab Emirates (UAE) with improved controls on environmental pollution. The UAE is an emerging economy in which population health risks have shifted rapidly from infectious diseases to chronic conditions observed in developed nations. The UAE government commissioned this work as part of an environmental health strategic planning project intended to address this shift in the nature of the country’s disease burden.

Methods and Findings

We assessed the burden of disease attributable to six environmental exposure routes outdoor air, indoor air, drinking water, coastal water, occupational environments, and climate change. For every exposure route, we integrated UAE environmental monitoring and public health data in a spatially resolved Monte Carlo simulation model to estimate the annual disease burden attributable to selected pollutants. The assessment included the entire UAE population (4.5 million for the year of analysis). The study found that outdoor air pollution was the leading contributor to mortality, with 651 attributable deaths (95% confidence interval [CI] 143–1,440), or 7.3% of all deaths. Indoor air pollution and occupational exposures were the second and third leading contributors to mortality, with 153 (95% CI 85–216) and 46 attributable deaths (95% CI 26–72), respectively. The leading contributor to health-care facility visits was drinking water pollution, to which 46,600 (95% CI 15,300–61,400) health-care facility visits were attributed (about 15% of the visits for all the diseases considered in this study). Major study limitations included (1) a lack of information needed to translate health-care facility visits to quality-adjusted-life-year estimates and (2) insufficient spatial coverage of environmental data.

Conclusions

Based on international comparisons, the UAE’s environmental disease burden is low for all factors except outdoor air pollution. From a public health perspective, reducing pollutant emissions to outdoor air should be a high priority for the UAE’s environmental agencies.     

Barn owls (<Emphasis Type="Italic">Tyto alba</Emphasis>) in western North America: phylogeographic structure,connectivity, and genetic diversity

The barn owl (Tyto alba) is a non-migratory species widely distributed across much of North America in areas with extensive old-field and grassland habitat and without extensive winter snow cover. We investigated the genetic diversity and phylogeographic patterns of barn owl populations in western North America, ranging from British Columbia (BC) to southern California, and one eastern population from Pennsylvania. We also determined the genetic distinctiveness of a population off the coast of southern California, Santa Barbara Island, as management plans to control the local owl population are being considered to decrease predation rate on the now threatened Scripps’s Murrelet (Synthliboramphus scrippsi). Using 8 polymorphic microsatellite markers (N = 126) and ND2 mitochondrial sequences (N = 37), we found little to no genetic structure among all sampled regions, with the exception of Santa Barbara Island. The BC mainland population, despite its northwestern geographically peripheral location and ongoing habitat degradation, is not genetically depauperate. However, individuals from Vancouver Island, likewise a peripheral population in BC, exhibited the lowest genetic diversity of all sampled locations. The low global F_ST value (0.028) estimated from our study suggests that old-field agricultural habitats are well connected in North America. Since the BC population has declined by about 50 % within the last three decades, it is vital to focus on preserving the remaining barn owl habitats in BC to allow successful establishment from neighbouring populations. Additionally, our microsatellite data revealed that the population on Santa Barbara Island showed genetic divergence from its continental counterpart. Mitochondrial data, however, demonstrated that this island population is not a monophyletic lineage containing unique haplotypes, and hence cannot be designated as an Evolutionarily Significant Unit.     

Evidence of Inbreeding in Hodgkin Lymphoma

Genome-wide association studies (GWASs) have identified several, mainly co-dominantly acting, single-nucleotide polymorphisms (SNPs) associated with Hodgkin lymphoma (HL). We searched for recessively acting disease loci by performing an analysis of runs of homozygosity (ROH) based on windows of homozygous SNP-blocks and by calculating genomic inbreeding coefficients on a SNP-wise basis. We used data from a previous GWAS with 906 cases and 1217 controls from a population with a long history of no matings between relatives. Ten recurrent ROHs were identified among 25 055 ROHs across all individuals but their association with HL was not genome-wide significant. All recurrent ROHs showed significant evidence for natural selection. As a novel finding genomic inbreeding among cases was significantly higher than among controls (P = 2.11*10⁻¹⁴) even after correcting for covariates. Higher inbreeding among the cases was mainly based on a group of individuals with a higher average length of ROHs per person. This result suggests a correlation of higher levels of inbreeding with higher cancer incidence and might reflect the existence of recessive alleles causing HL. Genomic inbreeding may result in a higher expression of deleterious recessive genes within a population.     

Predator‐mediated effects of severe drought associated with poor reproductive success of a seabird in a cross‐ecosystem cascade

Despite the profound impacts of drought on terrestrial productivity in coastal arid ecosystems, only a few studies have addressed how drought can influence ecological cascades across ecosystem boundaries. In this study, we examine the consequences of rainfall pulses and drought that subsequently impact the breeding success of a threatened nocturnal seabird, the Scripps's Murrelet (Synthliboramphus scrippsi). On an island off the coast of southern California, the main cause of reduced nest success for one of their largest breeding colonies is egg predation by an endemic deer mouse (Peromyscus maniculatus elusus). Mice on the island have an opportunistic diet of primarily terrestrial sources, but drastic declines in terrestrial productivity from drought might be expected to increase their reliance on marine resources, including murrelet eggs. We compiled data on terrestrial and marine productivity between 1983 and 2013 to determine how conditions in these ecosystems influence murrelet nest success. We found that the severity of drought had the strongest negative impact on murrelet nest success. We calculated that the reduction in fecundity during drought years due to increased egg predation by mice was substantial enough to produce a declining population growth rate. Nest success was much higher under normal or high rainfall conditions, depending on whether oceanic conditions were favorable to murrelets. Therefore, the more frequent and severe drought that is projected for this region could lead to an increased risk of murrelet population decline on this island. Our study highlights the need for understanding how species interactions will change through the effects of increasing drought and altered rainfall regimes under global change.