Ecological values of Hamilton urban streams (North Island, New Zealand): constraints and opportunities for restoration

Urban streams globally are characterised by degraded habitat conditions and low aquatic biodiversity, but are increasingly becoming the focus of restoration activities. We investigated habitat quality, ecological function, and fish and macroinvertebrate community composition of gully streams in Hamilton City, New Zealand, and compared these with a selection of periurban sites surrounded by rural land. A similar complement of fish species was found at urban and periurban sites, including two threatened species, with only one introduced fish widespread (Gambusia affinis). Stream macroinvertebrate community metrics indicated low ecological condition at most urban and periurban sites, but highlighted the presence of one high value urban site with a fauna dominated by sensitive taxa. Light-trapping around seepages in city gullies revealed the presence of several caddisfly species normally associated with native forest, suggesting that seepage habitats can provide important refugia for some aquatic insects in urban environments. Qualitative measures of stream habitat were not significantly different between urban and periurban sites, but urban streams had significantly lower hydraulic function and higher biogeochemical function than periurban streams. These functional differences are thought to reflect, respectively, (1) the combined effects of channel modification and stormwater hydrology, and (2) the influence of riparian vegetation providing shade and enhancing habitat in streams. Significant relationships between some macroinvertebrate community metrics and riparian vegetation buffering and bank protection suggest that riparian enhancement may have beneficial ecological outcomes in some urban streams. Other actions that may contribute to urban stream restoration goals include an integrated catchment approach to resolving fish passage issues, active reintroduction of wood to streams to enhance cover and habitat heterogeneity, and seeding of depauperate streams with native migratory fish to help initiate natural recolonisation

Mouse ooplasm confers context-specific reprogramming capacity

Enucleated oocytes have the distinctive ability to reprogram somatic nuclei back to totipotency. Here, we investigate genome-scale DNA methylation patterns after nuclear transfer and compare them to the dynamics at fertilization. We identify specific targets for DNA demethylation after nuclear transfer, such as germline-associated promoters, as well as unique limitations that include certain repetitive element classes.National Institutes of Health (U.S.) (Grant 5DP1OD003958

Mouse Ooplasm Confers Context-Specific Reprogramming Capacity

Enucleated oocytes have the remarkable ability to reprogram somatic nuclei back to totipotency. Here we investigate genome-scale DNA methylation patterns after nuclear transfer and compare them to the dynamics at fertilization. We identify specific targets for DNA demethylation after nuclear transfer such as germ-line associated promoters, as well as unique limitations that include certain repetitive element classes.Stem Cell and Regenerative Biolog

Aerial Inventories of Waterfowl in Illinois and Estimation of Moist-soil Plant Seed Abundance for Waterfowl on Lands Managed by Illinois Department of Natural Resources

Grant/Contract No: W-43-R 53-54-55Reports on progress and results of inventories of waterfowl along the Illinois and central Mississippi rivers during fall and winter and estimation of moist-soil plant seed abundance for waterfowl on lands managed by Illinois Department of Natural ResourcesINHS Technical Report Prepared for U.S. Fish & Wildlife Service, Illinois Department of Natural Resource

Childhood IQ and marriage by mid-life: the Scottish Mental Survey 1932 and the Midspan Studies

The study examined the influence of IQ at age 11 years on marital status by mid-adulthood. The combined databases of the Scottish Mental Survey 1932 and the Midspan studies provided data from 883 subjects. With regard to IQ at age 11, there was an interaction between sex and marital status by mid-adulthood (p = 0.0001). Women who had ever-married achieved mean lower childhood IQ scores than women who had never-married (p < 0.001). Conversely, there was a trend for men who had ever-married to achieve higher childhood IQ scores than men who had never-married (p = 0.07). In men, the odds ratio of ever marrying was 1.35 (95% CI 0.98–1.86&#59; p = 0.07) for each standard deviation increase in childhood IQ. Among women, the odds ratio of ever marrying by mid-life was 0.42 (95% CI 0.27–0.64; p = 0.0001) for each standard deviation increase in childhood IQ. Mid-life social class had a similar association with marriage, with women in more professional jobs and men in more manual jobs being less likely to have ever-married by mid-life. Adjustment for the effects of mid-life social class and height on the association between childhood IQ and later marriage, and vice versa, attenuated the effects somewhat, but suggested that IQ, height and social class acted partly independently

Regenerable DNA-Functionalized Hydrogels for Ultrasensitive, Instrument-Free Mercury(II) Detection and Removal in Water

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see Dave, N., Chan, M. Y., Huang, P.-J. J., Smith, B. D., & Liu, J. (2010). Regenerable DNA-Functionalized Hydrogels for Ultrasensitive, Instrument-Free Mercury(II) Detection and Removal in Water. Journal of the American Chemical Society, 132(36), 12668–12673. https://doi.org/10.1021/ja106098jMercury is a highly toxic environmental pollutant with bioaccumulative properties. Therefore, new materials are required to not only detect but also effectively remove mercury from environmental sources such as water. We herein describe a polyacrylamide hydrogel-based sensor functionalized with a thymine-rich DNA that can simultaneously detect and remove mercury from water. Detection is achieved by selective binding of Hg2+ between two thymine bases, inducing a hairpin structure where, upon addition of SYBR Green I dye, green fluorescence is observed. In the absence of Hg2+, however, addition of the dye results in yellow fluorescence. Using the naked eye, the detection limit in a 50 mL water sample is 10 nM Hg2+. This sensor can be regenerated using a simple acid treatment and can remove Hg2+ from water at a rate of ∼1 h−1. This sensor was also used to detect and remove Hg2+ from samples of Lake Ontario water spiked with mercury. In addition, these hydrogel-based sensors are resistant to nuclease and can be rehydrated from dried gels for storage and DNA protection. Similar methods can be used to functionalize hydrogels with other nucleic acids, proteins, and small molecules for environmental and biomedical applications.University of Waterloo || Natural Sciences and Engineering Research Council |

Molecular recording of mammalian embryogenesis.

Ontogeny describes the emergence of complex multicellular organisms from single totipotent cells. This field is particularly challenging in mammals, owing to the indeterminate relationship between self-renewal and differentiation, variation in progenitor field sizes, and internal gestation in these animals. Here we present a flexible, high-information, multi-channel molecular recorder with a single-cell readout and apply it as an evolving lineage tracer to assemble mouse cell-fate maps from fertilization through gastrulation. By combining lineage information with single-cell RNA sequencing profiles, we recapitulate canonical developmental relationships between different tissue types and reveal the nearly complete transcriptional convergence of endodermal cells of extra-embryonic and embryonic origins. Finally, we apply our cell-fate maps to estimate the number of embryonic progenitor cells and their degree of asymmetric partitioning during specification. Our approach enables massively parallel, high-resolution recording of lineage and other information in mammalian systems, which will facilitate the construction of a quantitative framework for understanding developmental processes

Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta.

DNA methylation is an important regulator of gene function. Fetal sex is associated with the risk of several specific pregnancy complications related to placental function. However, the association between fetal sex and placental DNA methylation remains poorly understood. We carried out whole-genome oxidative bisulfite sequencing in the placentas of two healthy female and two healthy male pregnancies generating an average genome depth of coverage of 25x. Most highly ranked differentially methylated regions (DMRs) were located on the X chromosome but we identified a 225 kb sex-specific DMR in the body of the CUB and Sushi Multiple Domains 1 (CSMD1) gene on chromosome 8. The sex-specific differential methylation pattern observed in this region was validated in additional placentas using in-solution target capture. In a new RNA-seq data set from 64 female and 67 male placentas, CSMD1 mRNA was 1.8-fold higher in male than in female placentas (P value = 8.5 × 10-7, Mann-Whitney test). Exon-level quantification of CSMD1 mRNA from these 131 placentas suggested a likely placenta-specific CSMD1 isoform not detected in the 21 somatic tissues analyzed. We show that the gene body of an autosomal gene, CSMD1, is differentially methylated in a sex- and placental-specific manner, displaying sex-specific differences in placental transcript abundance

Use of waveform lidar and hyperspectral sensors to assess selected spatial and structural patterns associated with recent and repeat disturbance and the abundance of sugar maple (Acer saccharum Marsh.) in a temperate mixed hardwood and conifer forest.

Abstract Waveform lidar imagery was acquired on September 26, 1999 over the Bartlett Experimental Forest (BEF) in New Hampshire (USA) using NASA\u27s Laser Vegetation Imaging Sensor (LVIS). This flight occurred 20 months after an ice storm damaged millions of hectares of forestland in northeastern North America. Lidar measurements of the amplitude and intensity of ground energy returns appeared to readily detect areas of moderate to severe ice storm damage associated with the worst damage. Southern through eastern aspects on side slopes were particularly susceptible to higher levels of damage, in large part overlapping tracts of forest that had suffered the highest levels of wind damage from the 1938 hurricane and containing the highest levels of sugar maple basal area and biomass. The levels of sugar maple abundance were determined through analysis of the 1997 Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) high resolution spectral imagery and inventory of USFS Northern Research Station field plots. We found a relationship between field measurements of stem volume losses and the LVIS metric of mean canopy height (r2 = 0.66; root mean square errors = 5.7 m3/ha, p \u3c 0.0001) in areas that had been subjected to moderate-to-severe ice storm damage, accurately documenting the short-term outcome of a single disturbance event

A unique regulatory phase of DNA methylation in the early mammalian embryo

DNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of 5-methylcytosine at fertilization, followed by passive loss that reaches a minimum at the blastocyst stage. However, this model is based on limited data, and so far no base-resolution maps exist to support and refine it. Here we generate genome-scale DNA methylation maps in mouse gametes and from the zygote through post-implantation. We find that the oocyte already exhibits global hypomethylation, particularly at specific families of long interspersed element 1 and long terminal repeat retroelements, which are disparately methylated between gametes and have lower methylation values in the zygote than in sperm. Surprisingly, the oocyte contributes a unique set of differentially methylated regions (DMRs)—including many CpG island promoters—that are maintained in the early embryo but are lost upon specification and absent from somatic cells. In contrast, sperm-contributed DMRs are largely intergenic and become hypermethylated after the blastocyst stage. Our data provide a genome-scale, base-resolution timeline of DNA methylation in the pre-specified embryo, when this epigenetic modification is most dynamic, before returning to the canonical somatic pattern.Burroughs Wellcome (Career Award)National Institutes of Health (U.S.) (5RC1AA019317)National Institutes of Health (U.S.) (U01ES017155)National Institutes of Health (U.S.) (P01GM099117)National Human Genome Research Institute (U.S.) (1P50HG006193-01