Intraspecific seed interactions alter seedling emergence of Lespedeza cuneata under field conditions

There is growing recognition that seeds influence one another prior to, or shortly after, germination. Both interspecific and intraspecific seed–seed interactions have been reported, but for the latter, the evidence is almost exclusively from laboratory and greenhouse studies so that it is unclear whether such intraspecific seed interactions occur under field conditions. We tested how Lespedeza cuneata seed density influenced seedling emergence within a native grassland located in Kansas, USA and whether this response was related to seed leachate. The percentage of L. cuneata seedlings that emerged under field conditions was negatively related to seed density. After confirming this pattern in the greenhouse, we found that at low seed densities, addition of seed leachate had similar effects on seedling emergence as high seed densities in the absence of leachate. Our results provide some of the best evidence to date, that intraspecific seed density can influence seedling emergence in the field and that these effects are likely linked to seed leachate.     

Validation of a DNA methylation reference panel for the estimation of nucleated cells types in cord blood

Cord blood is widely used as surrogate tissue in epigenome-wide association studies of prenatal conditions. Cell type composition variation across samples can be an important confounder of epigenome-wide association studies in blood that constitute a mixture of cells. We evaluated a newly developed cord blood reference panel to impute cell type composition from DNA methylation levels, including nucleated red blood cells (nRBCs). We estimated cell type composition from 154 unique cord blood samples with available DNA methylation data as well as direct measurements of nucleated cell types. We observed high correlations between the estimated and measured composition for nRBCs (r = 0.92, R² = 0.85), lymphocytes (r = 0.77, R² = 0.58), and granulocytes (r = 0.72, R² = 0.52), and a moderate correlation for monocytes (r = 0.51, R² = 0.25) as well as relatively low root mean square errors from the residuals ranging from 1.4 to 5.4%. These results validate the use of the cord blood reference panel and highlight its utility and limitations for epidemiological studies.     

DNA methylation arrays as surrogate measures of cell mixture distribution

ABSTRACT: BACKGROUND: There has been a long-standing need in biomedical research for a method that quantifies the normally mixed composition of leukocytes beyond what is possible by simple histological or flow cytometric assessments. The latter is restricted by the labile nature of protein epitopes, requirements for cell processing, and timely cell analysis. In a diverse array of diseases and following numerous immune-toxic exposures, leukocyte composition will critically inform the underlying immuno-biology to most chronic medical conditions. Emerging research demonstrates that DNA methylation is responsible for cellular differentiation, and when measured in whole peripheral blood, serves to distinguish cancer cases from controls. RESULTS: Here we present a method, similar to regression calibration, for inferring changes in the distribution of white blood cells between different subpopulations (e.g. cases and controls) using DNA methylation signatures, in combination with a previously obtained external validation set consisting of signatures from purified leukocyte samples. We validate the fundamental idea in a cell mixture reconstruction experiment, then demonstrate our method on DNA methylation data sets from several studies, including data from a Head and Neck Squamous Cell Carcinoma (HNSCC) study and an ovarian cancer study. Our method produces results consistent with prior biological findings, thereby validating the approach. CONCLUSIONS: Our method, in combination with an appropriate external validation set, promises new opportunities for large-scale immunological studies of both disease states and noxious exposures.     

Effects of Jack Pine Plantation Management on Barrens Flora and Potential Kirtland's Warbler Nest Habitat

Jack pine barrens, once common in northern lower Michigan, mostly have been converted to managed jack pine plantations. Management of the disturbances associated with logging provides the opportunity to maintain the unique plant assemblages of jack pine barrens and nest habitat of the federally endangered Kirtland's warbler. Studies indicate that Carex pensylvanica can develop into dense mats and strongly compete with other barrens species such as Vaccinium angustifolium, which seem to be important species for Kirtland's warbler nest locations. According to forest managers, the most important factors facilitating high cover of V. angustifolium and reducing cover of C. pensylvanica are the amount of shade produced by tree crowns before harvest (pre‐harvest shade), the length of time between harvest and planting (planting delay), and fire. We found that high or low levels of pre‐harvest shade had no effect on cover of either V. angustifolium or C. pensylvanica. Planting delays of at least three years following prescribed burns generally increased cover of V. angustifolium in forest plots, which are important for warbler nesting. Analysis of community composition in openings indicated that burning enhanced the growth of barrens species. We found only weak evidence for a negative correlation between the cover of V. angustifolium and C. pensylvanica on our study sites. The openings created in the jack pine plantation are important refugia for barrens flora that would likely be lost under forests managed strictly for jack pine. Maintenance of jack pine barrens flora and Kirtland's warbler nest habitat is possible within the context of a heavily managed forest plantation system.