Determinants of headwater stream condition in central Iowa: An empirical study

Headwater streams constitute the majority of stream length of river systems, and have important roles in terms of landscape processes and as habitat for organisms. These bodies of water are also tightly coupled with the local terrestrial landscape, making them ideal for studying linkages between land use and stream condition. Despite the ubiquity and importance of these streams, they are often overlooked and damaged. Previous research has shown that both urban and agricultural land use negatively impact stream condition, and that the magnitude of anthropogenic effects is generally greater in urban landscapes. Understanding of agricultural and urban land use impacts on streams depends on identifying cause and effect linkages between human system (demographic) features, terrestrial landscape features, and biophysical characteristics of streams. Using correlation analysis, path analysis, and non-metric multidimensional scaling, I simultaneously investigated these relationships in 29 central Iowa watersheds that collectively represented a strong urban-rural gradient. These analyses enabled me to quantify the impact of human land use on headwater streams, and identify direct and indirect mechanisms for human impacts on benthic macroinvertebrate communities. Aquatic macroinvertebrates were a primary focus of this study because they have well-established utility as indicators of stream condition due to their diverse environmental requirements, and importance in food webs. Results suggested that urban land use had a greater negative impact than agricultural land use on stream condition, as indicated by spatial variation in total invertebrate taxon richness and the percentage of the total number of invertebrates that were mayflies (Ephemeroptera), stoneflies (Plecoptera), and caddisflies (Trichoptera). Urban impacts appeared to be caused by pollutants delivered to streams by impervious surfaces, while agricultural effects were the result of nitrogen enrichment from croplands. Regardless of land use, watershed area had a positive impact on the invertebrate community through its effects on stream discharge. Similarly, the effect of coarse substrate on the invertebrate community was also positive regardless of watershed land use. My study therefore provided valuable insight into the direct and indirect effects of social and biophysical factors impacting headwater streams affected by urban and rural land uses in central Iowa

Perspectives on ENCODE

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.11Nsciescopu

Expanded encyclopaedias of DNA elements in the human and mouse genomes

AbstractThe human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.11Nsciescopu