Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients.

Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25-50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.

Population dynamics and genome-wide selection scan for dogs in Chernobyl.

BACKGROUND: Natural and anthropogenic disasters can have long-lasting impacts on the genetics and structure of impacted populations. The 1986 Chernobyl Nuclear Power Plant disaster led to extensive contamination of the local environment and the wildlife therein. Several ecological, environmental, and genetic studies reported various effects of this disaster on animal, insect, and plant species; however, little work has been done to investigate the genetics of the free-breeding dogs that occupy the Chernobyl Exclusion Zone (CEZ). RESULTS: We define the population genetic structure of two groups of dogs that reside within the CEZ, one around the reactor site itself and another living within Chernobyl City. We found little evidence of gene flow and a significant degree of genetic differentiation between the two populations dogs, suggesting that these are two distinct populations despite occupying areas located just 16 km apart. With an FST-based outlier analysis, we then performed a genome-wide scan for evidence of directional selection within the dog populations. We found 391 outlier loci associated with genomic regions influenced by directional selection, from which we identified 52 candidate genes. CONCLUSIONS: Our genome scan highlighted outlier loci within or near genomic regions under directional selection, possibly in response to the multi-generational exposure faced. In defining the population structure and identifying candidate genes for these dog populations, we take steps towards understanding how these types of prolonged exposures have impacted these populations.

Wildlife populations can be greatly affected by disasters, whether they are natural or man-made. Disasters that result in contamination or habitat destruction can result in population declines or influence wildlife adaptation to these adverse environmental changes. The Chernobyl nuclear power plant disaster released an enormous quantity of ionizing radiation into the surrounding environment. Abandonment of military and industrial facilities, as well as subsequent cleanup and remediation efforts, resulted in further environmental contamination by a variety of non-radioactive toxic metals, chemicals, and compounds. Earlier studies investigated local wildlife responses to some of these exposures. In this study, we address the impact of this disaster on the population structure of free-breeding dogs that live around the power plant and in the nearby city of Chernobyl. In particular, we use genetic approaches to understand how these two populations of dogs interact and their breed composition, so that we may begin to understand how these populations have adapted to over 30 years of exposure to this harsh environment. In this foundational study we determined that while the two local populations of dogs are separated by only 16 km, they have very low rates of interpopulation migration. We also detected genetic evidence that suggests that these population may have adapted to exposures faced over many generations. In future studies, we aim to determine if the genetic variation detected is indeed a biological response to enable survival after multi-generational exposures to radiation, heavy metals, organic toxins, or other environmental contaminants. In this way, we then understand how the impact of environmental catastrophes such as the Chernobyl nuclear disaster can influence animal populations.

The dogs of Chernobyl: Demographic insights into populations inhabiting the nuclear exclusion zone.

The 1986 Chernobyl nuclear disaster initiated a series of catastrophic events resulting in long-term and widespread environmental contamination. We characterize the genetic structure of 302 dogs representing three free-roaming dog populations living within the power plant itself, as well as those 15 to 45 kilometers from the disaster site. Genome-wide profiles from Chernobyl, purebred and free-breeding dogs, worldwide reveal that the individuals from the power plant and Chernobyl City are genetically distinct, with the former displaying increased intrapopulation genetic similarity and differentiation. Analysis of shared ancestral genome segments highlights differences in the extent and timing of western breed introgression. Kinship analysis reveals 15 families, with the largest spanning all collection sites within the radioactive exclusion zone, reflecting migration of dogs between the power plant and Chernobyl City. This study presents the first characterization of a domestic species in Chernobyl, establishing their importance for genetic studies into the effects of exposure to long-term, low-dose ionizing radiation.

"I think that comes with experience": A thematic analysis exploring how dental students at a transitional stage of training understand and engage with reflection.

INTRODUCTION: Reflection is an important skill for dentists but there is little consensus about how reflection can most usefully be integrated into dental education. The aim of this study was to conduct focus groups to explore how students at a transitional point of dental education in one UK dental school had experienced, and conceptualised reflection. METHODS: Students at the beginning of their clinical studies were recruited by email and invited to attend a single focus group. Focus groups were co-facilitated by a team of staff and student researchers and analysed using thematic analysis. Students acted as research partners in planning a topic guide, recruiting students, conducting focus groups and considering the implications of research findings for the curriculum, and contributed their perspectives to other aspects of the research. RESULTS: Students primarily associated reflection with their clinical learning and valued the skill highly in this context. They were less familiar with the potential for reflection to support personal development and deeper learning. Themes were identified of learning, uncertainty, emotions and wellbeing, community and challenges and are discussed in detail. CONCLUSION: Reflection is highly valued within our dental education setting but many students may be missing out on using it to its' full potential. Changes to the undergraduate curriculum, including offering reflection from an early stage of education may be warranted.

Letter frequency analysis of proprietary prescription drug names in the United States: Minding the Zs and Qs.

Background: Proprietary or brand names of prescription drugs are generally with letters that are unusual in common English. There is little academic research exploring if this perception is true, despite the fact that manufacturers pay millions of dollars to research and develop drug names that conform to regulatory standards while remaining marketable. Objectives: To assess the extent to which letters used in prescription drug names may deviate from common English and to test if prescription drug names show measurable trends in letter frequency over time. Methods: The names of all prescription drugs approved in the United States between 1985 and 2020 were downloaded. Duplicates were removed and products without a proprietary name were excluded. Letter frequency analyses were then conducted on all letters in these names as an aggregate and year-over-year. Letter frequencies were compared to a validated academic reference, a corpus derived from all Google Books data, and the scoring system from the board game Scrabble. Results: Regardless of the comparator, prescription drug names use letters that are not common in typical English. Letters A (11.96% of all observed letters), V (3.08%), X (2.31%), and Z (1.91%) are all overrepresented in prescription drug names, while E (10.23%), H (0.90%), T (6.30%), and S (4.21%) are underrepresented. The letters C and N are becoming less common over time (frequency decrease of 0.10 percentage points and 0.12 percentage points per year, respectively), while V, Y, and Z are becoming more common (frequency increases of 0.61 to 0.86 percentage points per year). Conclusions: Proprietary prescription names use letters that are unlike words used in everyday American English, and there are measureable trends in letter selection. It remains to be seen how drug manufacturers will cope with an increasingly-narrow naming space as more products continue to be approved over time.

The update and optimization of an eDNA assay to detect the invasive rusty crayfish (Faxonius rusticus).

Environmental DNA (eDNA) is nuclear or mitochondrial DNA shed into the environment, and amplifying this DNA can serve as a reliable, noninvasive way to monitor aquatic systems for the presence of an invasive species. Assays based on the collection of eDNA are becoming increasingly popular, and, when optimized, can aid in effectively and efficiently tracking invasion fronts. We set out to update an eDNA assay to detect the invasive rusty crayfish, Faxonius rusticus. We tested for species specificity compared to other stream crayfish and field tested the assay at sites with known presence (N = 3) and absence (N = 4) in the Juniata River watershed in central Pennsylvania, USA. To maximize sensitivity, we field tested different storage buffers (Longmire's buffer and ethanol), DNA extraction methods (Qiagen's DNEasy and PowerWater kits), and quantitative polymerase chain reaction (qPCR) chemistries (TaqMan and SYBR green). Our assay confirmed the presence data and performed optimally when filter samples were stored in Longmire's buffer, DNA was extracted with DNeasy Blood and Tissue Kit, and TaqMan qPCR chemistry was utilized. With proper sample processing, our assay allows for accurate, noninvasive detection of F. rusticus in streams.

Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica.

Ecological theories posit that heterogeneity in environmental conditions greatly affects community structure and function. However, the degree to which ecological theory developed using plant- and animal-dominated systems applies to microbiomes is unclear. Investigating the metabolic strategies found in microbiomes are particularly informative for testing the universality of ecological theories because microorganisms have far wider metabolic capacity than plants and animals. We used metagenomic analyses to explore the relationships between the energy and physicochemical gradients in Lake Fryxell and the metabolic capacity of its benthic microbiome. Statistical analysis of the relative abundance of metabolic marker genes and gene family diversity shows that oxygenic photosynthesis, carbon fixation, and flavin-based electron bifurcation differentiate mats growing in different environmental conditions. The pattern of gene family diversity points to the likely importance of temporal environmental heterogeneity in addition to resource gradients. Overall, we found that the environmental heterogeneity of photosynthetically active radiation (PAR) and oxygen concentration ([O2]) in Lake Fryxell provide the framework by which metabolic diversity and composition of the community is structured, in accordance with its phylogenetic structure. The organization of the resulting microbial ecosystems are consistent with the maximum power principle and the species sorting model.

Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica.

Ecological communities are regulated by the flow of energy through environments. Energy flow is typically limited by access to photosynthetically active radiation (PAR) and oxygen concentration (O2). The microbial mats growing on the bottom of Lake Fryxell, Antarctica, have well-defined environmental gradients in PAR and (O2). We analyzed the metagenomes of layers from these microbial mats to test the extent to which access to oxygen and light controls community structure. We found variation in the diversity and relative abundances of Archaea, Bacteria and Eukaryotes across three (O2) and PAR conditions: high (O2) and maximum PAR, variable (O2) with lower maximum PAR, and low (O2) and maximum PAR. We found distinct communities structured by the optimization of energy use on a millimeter-scale across these conditions. In mat layers where (O2) was saturated, PAR structured the community. In contrast, (O2) positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. Microbial communities changed across covarying gradients of PAR and (O2). The comprehensive metagenomic analysis suggests that the benthic microbial communities in Lake Fryxell are structured by energy flow across both meter- and millimeter-scales.

Systematic review of patient-reported measures of treatment burden in stroke.

OBJECTIVES: Treatment burden is the workload of healthcare for people with long-term conditions (LTC) and its impact on well-being. A method of measurement is required to identify those experiencing high burden and to measure intervention efficacy. Our aim was to identify, examine and appraise validated patient-reported measures (PRMs) of treatment burden in stroke. Here, stroke serves as an exemplar LTC of older adults. DESIGN: A systematic review of published studies that describe the development and validation of PRMs measuring treatment burden in stroke survivors. DATA SOURCES: We searched MEDLINE, Embase, CINAHL and PsycINFO electronic databases. ELIGIBILITY CRITERIA: Studies published between January 2000 and 12 April 2019 inclusive, in English language. No restrictions were set based on clinical setting or geographical location. DATA EXTRACTION AND SYNTHESIS: Screening, data extraction and quality appraisal were conducted by two independent reviewers. Content of the PRMs was compared with a published taxonomy of treatment burden. Quality appraisal was conducted using International Society for Quality of Life Research standards. RESULTS: From 3993 articles, 6 relevant PRMs were identified: 3 were stroke specific: The Satisfaction with Stroke Care questionnaire; The Stroke Patient-Reported Outcome Measure and The Barriers to Physical Activity after Stroke scale. Three were generic but validated in stroke: The WHO Quality of Life-100; The Patient's Questionnaire on Participation in Discharge Planning and The Chao Perception of Continuity scale. None comprehensively measured treatment burden. Examples of omitted burdens included developing coping strategies, managing finances and returning to driving. The most notable issue regarding quality appraisal was that three PRMs lacked any underpinning qualitative research relevant to the sample. CONCLUSION: There is a need to develop a comprehensive PRM of treatment burden for use in stroke, with potential for use in other older populations.

Environmental and Biological Influences on Carbonate Precipitation Within Hot Spring Microbial Mats in Little Hot Creek, CA.

Microbial mats are found in a variety of modern environments, with evidence for their presence as old as the Archean. There is much debate about the rates and conditions of processes that eventually lithify and preserve mats as microbialites. Here, we apply novel tracer experiments to quantify both mat biomass addition and the formation of CaCO3. Microbial mats from Little Hot Creek (LHC), California, contain calcium carbonate that formed within multiple mat layers, and thus constitute a good test case to investigate the relationship between the rate of microbial mat growth and carbonate precipitation. The laminated LHC mats were divided into four layers via color and fabric, and waters within and above the mat were collected to determine their carbonate saturation states. Samples of the microbial mat were also collected for 16S rRNA analysis of microbial communities in each layer. Rates of carbonate precipitation and carbon fixation were measured in the laboratory by incubating homogenized samples from each mat layer with δ13C-labeled HCO3- for 24 h. Comparing these rates with those from experimental controls, poisoned with NaN3 and HgCl2, allowed for differences in biogenic and abiogenic precipitation to be determined. Carbon fixation rates were highest in the top layer of the mat (0.17% new organic carbon/day), which also contained the most phototrophs. Isotope-labeled carbonate was precipitated in all four layers of living and poisoned mat samples. In the top layer, the precipitation rate in living mat samples was negligible although abiotic precipitation occurred. In contrast, the bottom three layers exhibited biologically enhanced carbonate precipitation. The lack of correlation between rates of carbon fixation and biogenic carbonate precipitation suggests that processes other than autotrophy may play more significant roles in the preservation of mats as microbialites.

Tracheole investment does not vary with body size among bumblebee (Bombus impatiens) sisters.

Body size is a key organism trait with critical implications for the physiology, life history, and ecology of organisms. Modern insects vary in body mass by over 6 orders of magnitude, but are small by comparison to many other metazoan taxa. The small size of modern insects may reflect limitations imposed by their open respiratory systems which rely, in part, on diffusion. Diffusion rates decline with distance such that, absent compensation, the capacity for larger insects to deliver oxygen to their tissues may be compromised. To compensate, larger grasshoppers, beetles, and bumblebees devote proportionally more of their body volume to the respiratory system, as demonstrated by hypermetric scaling of tracheal volume with body mass(>1). Among bumblebee sisters, total respiratory volume scaled with mass(2.6), but it is unclear at what level or levels of the tracheal system (main tracheal trunks, air sacs, tracheoles) bumblebees express this extreme hypermetry. Here we use transmission electron microscopy to examine the morphology of tracheoles in bumblebee flight muscle among sister bumblebees varying nearly four-fold in body mass. Neither tracheole density nor tracheole diameter changed with body mass. The total cross-sectional area of tracheoles was also invariant with body mass. Together, these results reveal that bumblebees do not compensate for size-related limitations on oxygen delivery by increasing investment at the level of the tracheoles.

Expression of the GPI-anchored receptor Prv-1 enhances thrombopoietin and IL-3-induced proliferation in hematopoietic cell lines.

Prv-1 is a hematopoietic cell surface receptor that has been shown to be overexpressed in patients diagnosed with polycythemia vera (PV) and essential thrombocythemia (ET), yet its cellular function remains unclear. In this study, we assessed the role of Prv-1 in thrombopoietin (Tpo)/Mpl signaling with the goal of identifying molecular mechanisms which augment Tpo-induced proliferation. By engineering the cytokine-dependent hematopoietic cell line BaF3 to express both Prv-1 and wild-type or mutant forms of Mpl, we were able to follow the time course of Tpo-dependent proliferation. We report that the overexpression of Prv-1 increased Tpo as well as IL-3-induced proliferation of BaF3/Mpl and BaF3 cells. Cells co-expressing Prv-1 and an Mpl receptor containing a Box 1 motif mutation, which fails to activate Jak2, was completely deficient in Tpo-dependent proliferation. In addition, BaF3 and BaF3/Prv-1 cells stimulated with IL-3 in the presence of the Jak2 inhibitor, AG490, abrogated the proliferative response, indicating that Prv-1 requires a functional Jak2 for its signaling activities. Western blot analysis showed an increase in Tpo and IL-3-induced Stat3 and Stat5 tyrosine phosphorylation in BaF3/Mpl and BaF3 cells expressing Prv-1. These results indicate a novel function for Prv-1 as a signaling molecule in cytokine signaling cascades and may lead to a greater understanding of the mechanism of overexpression of Prv-1 in myeloproliferative disorders.

Hitchhiking and recombination in birds: evidence from Mhc-linked and unlinked loci in Red-winged Blackbirds (Agelaius phoeniceus).

Hitchhiking phenomena and genetic recombination have important consequences for a variety of fields for which birds are model species, yet we know virtually nothing about naturally occurring rates of recombination or the extent of linkage disequilibrium in birds. We took advantage of a previously sequenced cosmid clone from Red-winged Blackbirds (Agelaius phoeniceus) bearing a highly polymorphic Mhc class II gene, Agph-DABI, to measure the extent of linkage disequilibrium across approximately 40 kb of genomic DNA and to determine whether non-coding nucleotide diversity was elevated as a result of physical proximity to a target of balancing selection. Application of coalescent theory predicts that the hitchhiking effect is enhanced by the larger effective population size of blackbirds compared with humans, despite the presumably higher rates of recombination in birds. We surveyed sequence polymorphism at three Mhc-linked loci occurring 1.5-40 kb away from Agph-DAB1 and found that nucleotide diversity was indistinguishable from that found at three presumably unlinked, non-coding introns (beta-actin intron 2, beta-fibrinogen intron 7 and rhodopsin intron 2). Linkage disequilibrium as measured by Lewontin's D' was found only across a few hundred base pairs within any given locus, and was not detectable among any Mhc-linked loci. Estimated rates of the per site recombination rate p derived from three different analytical methods suggest that the amounts of recombination in blackbirds are up to two orders of magnitude higher than in humans, a discrepancy that cannot be explained entirely by the higher effective population size of blackbirds relative to humans. In addition, the ratio of the number of estimated recombination events per mutation frequently exceeds 1, as in Drosophila, again much higher than estimates in humans. Although the confidence limits of the blackbird estimates themselves span an order of magnitude, these data suggest that in blackbirds the hitchhiking effect for this region is negligible and may imply that the per site per individual recombination rate is high, resembling those of Drosophila more than those of humans.