Data from: An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina

In the inner plexiform layer of the mouse retina, ~70 neuronal subtypes form a stereotyped circuit that underlies visual processing. During development, subtypes organize into an intricate laminar structure. This organization is choreographed by extracellular interactions that mediate cell recognition events. To identify recognition proteins involved in lamination, we utilized microarray data from 13 subtypes to identify differentially-expressed cell surface and secreted proteins. Using these candidates, we performed a biochemical screen and identified ~50 previously-unknown receptor-ligand pairs. We tested the response of retinal neurons to several candidates and found that both members of one interaction pair, FLRT2-Unc5C, induce repulsion; each in a different neuronal subtype(s). Consistent with a repulsive role in mediating lamination, we observed a complementary expression pattern of FLRT2 and Unc5C in vivo. We identified that Starburst amacrine cells express FLRT2 and are repelled by Unc5C. These data support a repulsive mechanism for laminar restriction of Starburst amacrines

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States

The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1–2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices – perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.</p

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States.

The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1-2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices - perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions

Mouse retina extracellular receptor-ligand biochemical screen

Biochemical screen for extracellular receptor-ligand interactions in the developing mouse retina. The extracellular domain (ECD) region of 126 cell surface or secreted proteins were tested for pairwise binding in a matrix. ECDs along the x-axis were C-terminally fused to the Fc region of human IgG1. ECDs along the y-axis were C-terminally fused to alkaline phosphatase (AP). Proteins were tested for binding using a high-throughput, ELISA-based binding assay. In this assay, ECD-AP receptor protein is captured on an ELISA plate using an anti-AP antibody. Binding of ECD-Fc ligand protein to the ECD-AP receptor protein is detected by inclusion of an anti-Fc antibody conjugated to HRP. HRP activity is measured using O.D. 650 nm one hour following addition of substrate. Raw data values are reported