Distribution and Genetic Diversity of Salmonella enterica in the Upper Suwannee River

The Suwannee River spans the Florida/Georgia border to the Gulf of Mexico, and contributes to regional irrigation and recreational activities. Association of Salmonella enterica with these resources may result in the contamination of produce and disease outbreaks. Therefore, surface water was examined for the distribution of S. enterica at multiple time points from 4 sites on the upper Suwannee River. Isolates were confirmed by detection of the invA gene, and 96% of all samples were positive for the bacterium. Most probable number enumeration ranged from <18 to 5400 MPN/100 mL. Genetic diversity of these isolates (n=110) was compared to other environmental (n=47) or clinical (n=28) strains and to an online library (n=314) using DiversiLab rep-PCR. All strains showed >60% similarity and distributed into 16 rep-PCR genogroups. Most (74%) of the Suwannee River isolates were clustered into two genogroups that were comprised almost exclusively (97%) of just these isolates. Conversely, 85% of the clinical reference strains clustered into other genogroups. However, some Suwannee River isolates (12%) were clustered with these primarily clinically-associated genogroups, supporting the hypothesis that river water can serve as a disease reservoir and that pathogenic strains may persist or possibly originate from environmental sources

SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes

<p>Abstract</p> <p>Background</p> <p><it>Vibrio vulnificus </it>is the leading cause of reported death from consumption of seafood in the United States. Despite several decades of research on molecular pathogenesis, much remains to be learned about the mechanisms of virulence of this opportunistic bacterial pathogen. The two complete and annotated genomic DNA sequences of <it>V. vulnificus </it>belong to strains of clade 2, which is the predominant clade among clinical strains. Clade 2 strains generally possess higher virulence potential in animal models of disease compared with clade 1, which predominates among environmental strains. SOLiD sequencing of four <it>V. vulnificus </it>strains representing different clades (1 and 2) and biotypes (1 and 2) was used for comparative genomic analysis.</p> <p>Results</p> <p>Greater than 4,100,000 bases were sequenced of each strain, yielding approximately 100-fold coverage for each of the four genomes. Although the read lengths of SOLiD genomic sequencing were only 35 nt, we were able to make significant conclusions about the unique and shared sequences among the genomes, including identification of single nucleotide polymorphisms. Comparative analysis of the newly sequenced genomes to the existing reference genomes enabled the identification of 3,459 core <it>V. vulnificus </it>genes shared among all six strains and 80 clade 2-specific genes. We identified 523,161 SNPs among the six genomes.</p> <p>Conclusions</p> <p>We were able to glean much information about the genomic content of each strain using next generation sequencing. Flp pili, GGDEF proteins, and genomic island XII were identified as possible virulence factors because of their presence in virulent sequenced strains. Genomic comparisons also point toward the involvement of sialic acid catabolism in pathogenesis.</p

Single-cell gene and isoform expression analysis reveals signatures of ageing in haematopoietic stem and progenitor cells

Single-cell approaches have revealed that the haematopoietic hierarchy is a continuum of differentiation, from stem cell to committed progenitor, marked by changes in gene expression. However, many of these approaches neglect isoform-level information and thus do not capture the extent of alternative splicing within the system. Here, we present an integrated short- and long-read single-cell RNA-seq analysis of haematopoietic stem and progenitor cells. We demonstrate that over half of genes detected in standard short-read single-cell analyses are expressed as multiple, often functionally distinct, isoforms, including many transcription factors and key cytokine receptors. We observe global and HSC-specific changes in gene expression with ageing but limited impact of ageing on isoform usage. Integrating single-cell and cell-type-specific isoform landscape in haematopoiesis thus provides a new reference for comprehensive molecular profiling of heterogeneous tissues, as well as novel insights into transcriptional complexity, cell-type-specific splicing events and consequences of ageing

Density-driven structural transformations in B2O3 glass

The method of in situ high-pressure neutron diffraction is used to investigate the structure of B2O3 glass on compression in the range from ambient to 17.5(5) GPa. The experimental results are supplemented by molecular dynamics simulations made using a newly developed aspherical ion model. The results tie together those obtained from other experimental techniques to reveal three densification regimes. In the first, BO3 triangles are the predominant structural motifs as the pressure is increased from ambient to 6.3(5) GPa, but there is an alteration to the intermediate range order which is associated with the dissolution of boroxol rings. In the second, BO4 motifs replace BO3 triangles at pressures beyond 6.3 GPa and the dissolution of boroxol rings continues until it is completed at 11–14 GPa. In the third, the B-O coordination number continues to increase with pressure to give a predominantly tetrahedral glass, a process that is completed at a pressure in excess of 22.5 GPa. On recovery of the glass to ambient from a pressure of 8.2 GPa, triangular BO3 motifs are recovered but, relative to the uncompressed material, there is a change to the intermediate range order. The comparison between experiment and simulation shows that the aspherical ion model is able to provide results of unprecedented accuracy at pressures up to at least 10 GPa

Eighth Annual Conference of inVIVO Planetary Health: From Challenges to Opportunities

inVIVO Planetary Health (inVIVO) is a progressive scientific movement providing evidence, advocacy, and inspiration to align the interests and vitality of people, place, and planet. Our goal is to transform personal and planetary health through awareness, attitudes, and actions, and a deeper understanding of how all systems are interconnected and interdependent. Here, we present the abstracts and proceedings of our 8th annual conference, held in Detroit, Michigan in May 2019, themed “From Challenges, to Opportunities”. Our far-ranging discussions addressed the complex interdependent ecological challenges of advancing global urbanization, including the biopsychosocial interactions in our living environment on physical, mental, and spiritual wellbeing, together with the wider community and societal factors that govern these. We had a strong solutions focus, with diverse strategies spanning from urban-greening and renewal, nature-relatedness, nutritional ecology, planetary diets, and microbiome rewilding, through to initiatives for promoting resilience, positive emotional assets, traditional cultural narratives, creativity, art projects for personal and community health, and exploring ways of positively shifting mindsets and value systems. Our cross-sectoral agenda underscored the importance and global impact of local initiatives everywhere by contributing to new normative values as part of a global interconnected grass-roots movement for planetary health

Shifting Winds: Using Ancestry DNA to Explore Multiracial Individuals\u27 Patterns of Articulating Racial Identity

This study explored how genotype information affects identification narratives of multiracial individuals. Twenty-one multiracial individuals completed individual interviews before and after receiving a DNA analysis to clarify their genetically based racial ancestry. Based on results, this article proposes patterns of articulating racial identity by multiracial individuals. Four patterns extend evolving research in multiracial identification, namely (1) the individual articulates a monoracial identity; (2) the individual articulates one identity, but this can shift in response to various conditions; (3) the individual articulates an extraracial identity, opting out of traditional categories applied to race; and (4) the person distinguishes traditional categories of race from culture and owns the two identities in different ways. Implications of these findings are discussed. First, adding new ancestry DNA information further muddles the neat categories of race, consistent with the view of race as socially constructed. Second, results emphasize the fluidity of identification for multiracial individuals. Third, DNA information challenges the neat percentages people tend to associate with their backgrounds. Particularly for younger multiracial individuals, there was less of a sense that race was a real thing and more that culture played a big part in how they saw themselves

A Population-Based Study of Childhood Cancer Survivors’ Body Mass Index

Background. Population-based studies are needed to estimate the prevalence of underweight or overweight/obese childhood cancer survivors. Procedure. Adult survivors (diagnosed ≤20 years) were identified from the linked Utah Cancer Registry and Utah Population Database. We included survivors currently aged ≥20 years and ≥5 years from diagnosis (N=1060), and a comparison cohort selected on birth year and sex (N=5410). BMI was calculated from driver license data available from 2000 to 2010. Multivariable generalized linear regression models were used to calculate prevalence relative risks (RR) and 95% confidence intervals (95% CI) of BMI outcomes for survivors and the comparison cohort. Results. Average time since diagnosis was 18.5 years (SD=7.8), and mean age at BMI for both groups was 30.5 (survivors SD=7.7, comparison SD=8.0). Considering all diagnoses, survivors were not at higher risk for being underweight or overweight/obese than the comparison. Male central nervous system tumor survivors were overweight (RR=1.12, 95% CI 1.01–1.23) more often than the comparison. Female survivors, who were diagnosed at age 10 and under, had a 10% higher risk of being obese than survivors diagnosed at ages 16–20 (P<0.05). Conclusion. While certain groups of childhood cancer survivors are at risk for being overweight/obese, in general they do not differ from population estimates

Nitrogen Increases Early-Stage and Slows Late-Stage Decomposition Across Diverse Grasslands

To evaluate how increased anthropogenic nutrient inputs alter carbon cycling in grasslands, we conducted a litter decomposition study across 20 temperate grasslands on three continents within the Nutrient Network, a globally distributed nutrient enrichment experiment We determined the effects of addition of experimental nitrogen (N), phosphorus (P) and potassium plus micronutrient (Kμ) on decomposition of a common tree leaf litter in a long-term study (maximum of 7 years; exact deployment period varied across sites). The use of higher order decomposition models allowed us to distinguish between the effects of nutrients on early- versus late-stage decomposition. Across continents, the addition of N (but not other nutrients) accelerated early-stage decomposition and slowed late-stage decomposition, increasing the slowly decomposing fraction by 28% and the overall litter mean residence time by 58%. Synthesis. Using a novel, long-term cross-site experiment, we found widespread evidence that N enhances the early stages of above-ground plant litter decomposition across diverse and widespread temperate grassland sites but slows late-stage decomposition. These findings were corroborated by fitting the data to multiple decomposition models and have implications for N effects on soil organic matter formation. For example, following N enrichment, increased microbial processing of litter substrates early in decomposition could promote the production and transfer of low molecular weight compounds to soils and potentially enhance the stabilization of mineral-associated organic matter. By contrast, by slowing late-stage decomposition, N enrichment could promote particulate organic matter (POM) accumulation. Such hypotheses deserve further testing

Influence of Socioeconomic Status Trajectories on Innate Immune Responsiveness in Children

Lower socioeconomic status (SES) is consistently associated with poor health, yet little is known about the biological mechanisms underlying this inequality. In children, we examined the impact of early-life SES trajectories on the intensity of global innate immune activation, recognizing that excessive activation can be a precursor to inflammation and chronic disease.Stimulated interleukin-6 production, a measure of immune responsiveness, was analyzed ex vivo for 267 Canadian schoolchildren from a 1995 birth cohort in Manitoba, Canada. Childhood SES trajectories were determined from parent-reported housing data using a longitudinal latent-class modeling technique. Multivariate regression was conducted with adjustment for potential confounders.SES was inversely associated with innate immune responsiveness (p=0.003), with persistently low-SES children exhibiting responses more than twice as intense as their high-SES counterparts. Despite initially lower SES, responses from children experiencing increasing SES trajectories throughout childhood were indistinguishable from high-SES children. Low-SES effects were strongest among overweight children (p<0.01). Independent of SES trajectories, immune responsiveness was increased in First Nations children (p<0.05) and urban children with atopic asthma (p<0.01).These results implicate differential immune activation in the association between SES and clinical outcomes, and broadly imply that SES interventions during childhood could limit or reverse the damaging biological effects of exposure to poverty during the preschool years