The dynamic genetic repertoire of microbial communities

Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. In the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. A major unresolved question is how much of the observed variation is due to neutral vs. adaptive processes. Limited experimental data hint that some of this fine-scale variation may be in part functionally relevant, whereas sequence-based and modeling analyses suggest that much of it may be neutral. While methods for interpreting population genomic data are still in their infancy, we discuss current interpretations of existing datasets in the light of evolutionary processes and models. Finally, we highlight the importance of virus–host dynamics in generating and shaping within-population diversity

Building Resilience Through Strengths-Based Learning During Graduate Study Abroad: An Exploratory Study

Resilience has been identified as an essential skill for leaders (Basso, Gruendel, Key, MacBlaine, & Reynolds, 2015) and as crucial for navigating both school and life challenges (Yeager & Dweck, 2012). Research indicates that there are a variety of ways to build resilience, including in educational settings (Yeager & Dweck, 2012). Higher education institutions utilize pedagogical practices to maximize student learning and growth opportunities (Rennick, 2015). One pedagogical frame often employed is experiential education. College and university faculty have embedded experiential learning pedagogy in the curriculum to facilitate learning outside the classroom (Liang, Caton, & Hill, 2015; Jordan, Gagnon, Anderson, & Pilcher, 2018; Towers & Loyness, 2018). Additionally, experiential education principles have been integrated with study abroad curriculum to support student learning (Harper, 2018; Pipitone and Raghaven, 2017; Pipitone, 2018). Educators are interested in learning more about the potential effect of strengths-based initiatives in higher education (Soria & Stubblefield, 2015a). While scholars have reported on the benefits of utilizing a strengths-based curriculum for personal development (Passerilli, Hall, & Anderson, 2010), much work is still needed to explore the potential outcomes of strengths-based education on resilience development. This research sought to address the gap in the literature using a short-term graduate study abroad program embedded with experiential education practices to examine how the pedagogy design contributed to students’ perceived growth in resilience. The strengths-based curricular design included approximately sixty hours of strengths-based instruction prior to the trip and fourteen days of applying the common strengths language to enhance learning experiences and mitigate challenges

Gradient nonlinearity correction to improve apparent diffusion coefficient accuracy and standardization in the american college of radiology imaging network 6698 breast cancer trial

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113725/1/jmri24883.pd

Comparison of low--energy resonances in 15N(alpha,gamma)19F and 15O(alpha,gamma)19Ne and related uncertainties

A disagreement between two determinations of Gamma_alpha of the astro- physically relevant level at E_x=4.378 MeV in 19F has been stated in two recent papers by Wilmes et al. and de Oliveira et al. In this work the uncertainties of both papers are discussed in detail, and we adopt the value Gamma_alpha=(1.5^{+1.5}_{-0.8})10^-9eV for the 4.378 MeV state. In addition, the validity and the uncertainties of the usual approximations for mirror nuclei Gamma_gamma(19F) approx Gamma_gamma(19Ne), theta^2_alpha(19F) approx theta^2_alpha(19Ne) are discussed, together with the resulting uncertainties on the resonance strengths in 19Ne and on the 15O(alpha,gamma)19Ne rate.Comment: 9 pages, Latex, To appear in Phys. Rev.

A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes

During microbial evolution, genome rearrangement increases with increasing sequence divergence. If the relationship between synteny and sequence divergence can be modeled, gene clusters in genomes of distantly related organisms exhibiting anomalous synteny can be identified and used to infer functional conservation. We applied the phylogenetic pairwise comparison method to establish and model a strong correlation between synteny and sequence divergence in all 634 available Archaeal and Bacterial genomes from the NCBI database and four newly assembled genomes of uncultivated Archaea from an acid mine drainage (AMD) community. In parallel, we established and modeled the trend between synteny and functional relatedness in the 118 genomes available in the STRING database. By combining these models, we developed a gene functional annotation method that weights evolutionary distance to estimate the probability of functional associations of syntenous proteins between genome pairs. The method was applied to the hypothetical proteins and poorly annotated genes in newly assembled acid mine drainage Archaeal genomes to add or improve gene annotations. This is the first method to assign possible functions to poorly annotated genes through quantification of the probability of gene functional relationships based on synteny at a significant evolutionary distance, and has the potential for broad application

SARS-CoV-2 transmission risk from asymptomatic carriers: Results from a mass screening programme in Luxembourg.

BACKGROUND: To accompany the lifting of COVID-19 lockdown measures, Luxembourg implemented a mass screening (MS) programme. The first phase coincided with an early summer epidemic wave in 2020. METHODS: rRT-PCR-based screening for SARS-CoV-2 was performed by pooling of samples. The infrastructure allowed the testing of the entire resident and cross-border worker populations. The strategy relied on social connectivity within different activity sectors. Invitation frequencies were tactically increased in sectors and regions with higher prevalence. The results were analysed alongside contact tracing data. FINDINGS: The voluntary programme covered 49% of the resident and 22% of the cross-border worker populations. It identified 850 index cases with an additional 249 cases from contact tracing. Over-representation was observed in the services, hospitality and construction sectors alongside regional differences. Asymptomatic cases had a significant but lower secondary attack rate when compared to symptomatic individuals. Based on simulations using an agent-based SEIR model, the total number of expected cases would have been 42·9% (90% CI [-0·3, 96·7]) higher without MS. Mandatory participation would have resulted in a further difference of 39·7% [19·6, 59·2]. INTERPRETATION: Strategic and tactical MS allows the suppression of epidemic dynamics. Asymptomatic carriers represent a significant risk for transmission. Containment of future outbreaks will depend on early testing in sectors and regions. Higher participation rates must be assured through targeted incentivisation and recurrent invitation. FUNDING: This project was funded by the Luxembourg Ministries of Higher Education and Research, and Health

Multi-omics analysis of mouse fecal microbiome reveals supplier-dependent functional differences and novel metagenome-assembled genomes

AbstractHost genetics, sex, and other within-source factors have been associated with characteristic effects on the fecal microbiome in mice, however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes in particular confer differences in disease susceptibility in models of inflammatory conditions, as well as baseline behavior and body morphology. However, current knowledge regarding the compositional differences between suppliers is based on 16S rRNA amplicon sequencing data, and functional differences between these communities remain poorly defined. Here, we applied a meta-omic (metagenomic and metatranscriptomic) approach to biomolecules (DNA/RNA) extracted from murine fecal samples representative of two large U.S. suppliers of research mice, which differ in composition, and influence baseline physiology and behavior as well as disease severity in mouse models of intestinal disease. We reconstructed high-quality metagenome-assembled genomes (MAGs), frequently containing genomic content unique to each supplier. These differences were observed both within pangenomes of dominant taxa as well as the epibiontSaccharimonadaceae. Additionally, transcriptional activity and pathway analyses revealed key functional differences between the metagenomes associated with each supplier, including differences in carbohydrate enzyme activity and dissimilatory sulfate reduction by sulfate-reducing bacteria (SRB). These data provide a detailed characterization of the baseline differences in the fecal metagenome of laboratory mice from two U.S. commercial suppliers suggesting that these functional differences are influenced by differences in the initial inoculum of colony founders, as well as additional taxa gained during growth of the production colony

Ecological distribution and population physiology defined by proteomics in a natural microbial community

Community proteomics applied to natural microbial biofilms resolves how the physiology of different populations from a model ecosystem change with measured environmental factors in situ.The initial colonists, Leptospirillum Group II bacteria, persist throughout ecological succession and dominate all communities, a pattern that resembles community assembly patterns in some macroecological systems.Interspecies interactions, and not abiotic environmental factors, demonstrate the strongest correlation to physiological changes of Leptospirillum Group II.Environmental niches of subdominant populations seem to be determined by combinations of specific sets of abiotic environmental factors