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    Concordance in wetland physicochemical conditions, vegetation, and surroundign land cover is robust to data extraction approach
    (Public Library of Science, 2019-05-31) Kraft, Adam J.; Robinson, Derek T.; Evans, Ian S.; Rooney, Rebecca C.
    Concordance among wetland physicochemical conditions, vegetation, and surrounding land cover may result from the influence of land cover on the sources of plant propagules, on physicochemical conditions, and their subsequent determination of growing conditions. Alternatively, concordance may result if differences in climate, soils, and species pools are spatially confounded with differences in human population density and land conversion. Further, we expect that land cover within catchment boundaries will be more predictive than land cover in symmetrical buffers if runoff is a major pathway. We measured concordance between land cover, wetland vegetation and physicochemical conditions in 48 prairie pothole wetlands, controlling for inter-wetland distance. We contrasted land-cover data collected over a four-year period by multiple extraction approaches including topographically-delineated catchments and nested 30 m to 5,000 m radius buffers. After factoring out inter-wetland distance, physiochemical conditions were significantly concordant with land cover. Vegetation was not significantly concordant with land cover, though it was strongly and significantly concordant with physicochemical conditions. More, concordance was as strong when land cover was extracted from buffers <500 m in radius as from catchments, indicating the mechanism responsible is not topographically constrained. We conclude that local landscape structure does not directly influence wetland vegetation composition, but rather that vegetation depends on 1) physicochemical conditions in the wetland that are affected by surrounding land cover and on 2) regional factors such as the vegetation species pool and geographic gradients in climate, soil type, and land use.
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    Exploring correlations between neuropsychological measures and domain-specific consistencty in associations with n-3 LCPUFA status in 8-9 year-old boys and girls
    (Public Library of Science, 2019-05-22) Teisen, Marie N.; Niclasen, Janni; Vuholm, Stine; Lundbye-Jensen, Jesper; Stark, Ken D.; Damsgaard, Camilla T.; Geertsen, Svend S.; Lauritzen, Lotte
    Long-chain n-3 polyunsaturated fatty acids (n-3 LCPUFA) have in some studies been associated with cognitive and socioemotional outcomes in children, but results are inconsistent possibly due to the use of different tests and potential gender-specific effects. The objective of this cross-sectional study was to explore overall patterns in neuropsychological scores as well as correlations between scores within specific domains, and to examine potential gender differences and consistency in associations with n-3 LCPUFA status. In 199 Danish 8–9 year-old children, we performed a large battery of tests and questionnaires on attention, processing speed, executive functions, memory, and socioemotional traits, and measured erythrocyte fatty acid composition. Principal component analyses (PCA) showed that most of the variation in both cognitive performance and socioemotional traits was explained by overall performance, followed by speed-accuracy trade off and externalizing vs. internalizing problems, respectively. Boys had higher speed, lower attention and higher externalizing problem scores than girls. Measures of performance within both processing speed and attention domains correlated moderately, whereas no correlations were found for measures of executive functions apart from some weak correlations for impulsivity. Parent-rated scores for both externalizing and internalizing problems correlated strongly, whereas correlations with child-rated scores were weak. Scores within specific domains did not consistently associate with n-3 LCPUFA, except for processing speed measures which all pointed to faster processing with increased n-3 LCPUFA status. Gender differences in the associations were observed for attention and impulsivity. Child- but not parent-rated internalizing and social problems tended to associate directly with n-3 LCPUFA, supported by increased internalizing problems measured by the PCA component. In conclusion, measures of speed and attention seem to represent these domains in general, whereas single measures of more complex cognitive functions should be interpreted with caution. One approach could be to use multiple tests and create multivariate scores to guide interpretations. Furthermore, the results indicate a need to consider both parent- and child-rated socioemotional scores and gender differences in neuropsychological functions e.g. in investigations of n-3 LCPUFA effects.
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    Severe wildfire affects the thermal and moisture regimes of at-risk turtle nesting habitat
    (BioOne, 2024-06) Markle, Chantel; Simone, Kyra; Wilkinson, Sophie; Freeman, Hope; Wiebe, Sarah; Sherwood, Emma; Waddington, James
    Natural wildfire regimes are important for ecosystem succession, but increased frequency and severity of wildfire due to climate change can negatively alter habitat characteristics. In 2018, over 11,000 ha of a granite rock barrens landscape that extends along the eastern shoreline of Georgian Bay, Lake Huron, burned in a wildfire. This landscape is a biodiversity hotspot providing habitat for many species at risk, including Emydoidea blandingii (Blanding's Turtle) and Clemmys guttata (Spotted Turtle), where turtles nest in shallow soil deposits in cracks and crevices in the bedrock. The burned, open rock-barren habitat had ∼70% fewer available nesting sites, but suitability of remaining nest habitat was unknown. To assess the impact of the wildfire on the suitability of turtle nesting habitat, we compared soil properties and in situ thermal and moisture regimes at turtle-selected nest sites, burned and unburned rock barren habitat, and burned forested uplands that may provide newly available habitat as a result of increased canopy openness following fire. Burned and unburned rock barren habitats drained quickly following rainfall, similar to turtle-selected sites, whereas burned forested uplands drained more slowly and provided wetter incubation conditions. Burned forested uplands provided a comparable thermal regime to turtle-selected nest sites and were often moss-dominated, with a relatively open canopy. Hatch success was estimated to be 20% lower at burned rock-barren habitats compared to unburned sites. Our findings suggest that severe wildfire affects soil thermal and moisture regimes, which can negatively alter the suitability of nest habitat, but burned upland forests are likely to provide suitable nesting habitat for at-risk turtles in the first years following fire.
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    Designer Sinorhizobium meliloti strains and multi-functional vectors enable direct inter-kingdom DNA transfer
    (Public Library of Science, 2019-06-17) Brumwell, Stephanie L.; MacLeod, Michael R.; Huang, Tony; Cochrane, Ryan R.; Meaney, Rebecca S.; Zamani, Maryam; Matysiakiewicz, Ola; Dan, Kaitlyn N.; Janakirama, Preetam; Edgell, David R.; Charles, Trevor C.; Finan, Turlough M.; Karas, Bogumil J.
    Storage, manipulation and delivery of DNA fragments is crucial for synthetic biology applications, subsequently allowing organisms of interest to be engineered with genes or pathways to produce desirable phenotypes such as disease or drought resistance in plants, or for synthesis of a specific chemical product. However, DNA with high G+C content can be unstable in many host organisms including Saccharomyces cerevisiae. Here, we report the development of Sinorhizobium meliloti, a nitrogen-fixing plant symbioticα-Proteobacterium, as a novel host that can store DNA, and mobilize DNA to E. coli, S. cerevisiae, and the eukaryotic microalgae Phaeodactylum tricornutum. To achieve this, we deleted the hsdR restriction-system in multiple reduced genome strains of S. meliloti that enable DNA transformation with up to 1.4 x 105 and 2.1 x 103 CFU μg-1 of DNA efficiency using electroporation and a newly developed polyethylene glycol transformation method, respectively. Multi-host and multi-functional shuttle vectors (MHS) were constructed and stably propagated in S. meliloti, E. coli, S. cerevisiae, and P. tricornutum. We also developed protocols and demonstrated direct transfer of these MHS vectors via conjugation from S. meliloti to E. coli, S. cerevisiae, and P. tricornutum. The development of S. meliloti as a new host for inter-kingdom DNA transfer will be invaluable for synthetic biology research and applications, including the installation and study of genes and biosynthetic pathways into organisms of interest in industry and agriculture.
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    Statistical methods for classification of 5hmC levels based on the Illumina Inifinium HumanMethylation450 (450k) array data, under the paired bisulfite (BS) and oxidative bisulfite (oxBS) treatment
    (Public Library of Science, 2019-06-13) Slynko, Alla; Benner, Axel
    Hydroxymethylcytosine (5hmC) methylation is a well-known epigenetic mark that is involved in gene regulation and may impact genome stability. To investigate a possible role of 5hmC in cancer development and progression, one must be able to detect and quantify its level first. In this paper, we address the issue of 5hmC detection at a single base resolution, starting with consideration of the well-established 5hmC measure Δβ and, in particular, with an analysis of its properties, both analytically and empirically. Then we propose several alternative hydroxymethylation measures and compare their properties with those of Δβ. In the absence of a gold standard, the (pairwise) resemblance of those 5hmC measures to Δβ is characterized by means of a similarity analysis and relative accuracy analysis. All results are illustrated on matched healthy and cancer tissue data sets as derived by means of bisulfite (BS) and oxidative bisulfite converting (oxBS) procedures.