Technical guide for the development, evaluation, and modification of stream assessment methods for the Corps Regulatory Program

The U.S. Army Corps Regulatory Program considers the loss (impacts) and gain (compensatory mitigation) of aquatic resource functions as part of Clean Water Act Section 404 permitting and compensatory mitigation decisions. To better inform this regulatory decision-making, the Regulatory Program needs transparent and objective approaches to assess the function and condition of aquatic resources, including streams. Therefore, the Regulatory Program needs function-based stream assessments (1) to characterize a stream’s condition or function, (2) to improve understanding of the impact of a proposed action on an aquatic resource, and/or (3) to inform the development of stream compensatory mitigation tools rooted in stream condition and/or function. A function-based stream assessment can provide regulatory decision makers with the resources to objectively consider alternatives, minimize impacts, assess unavoidable impacts, determine mitigation requirements, and monitor the success of mitigation projects. A multiagency National Committee on Stream Assessment (NCSA) convened to create these guidelines to inform the development of new methods and evaluation of both national-level and regional methods currently in use. The resulting guidelines present nine phases, including rationale and recommendations to facilitate work efforts. The NCSA hopes that this technical guide promotes transparency, technical defensibility, and consistent application of stream assessments in the Regulatory Program.

Abstract 436: Maternal Pregestational Diabetes Alters Fetal Gene Regulatory Program to Cause Spectrum of Congenital Heart Defects

Maternal pre-gestational diabetes results in range of congenital malformations with significantpreponderance of congenital heart defects (CHD). We and others have previously demonstratedthat maternal high glucose (HG) acts as primary teratogen in diabetes and in combination withgenetic susceptibility loci, it increases the incidence of CHD ranging from mild ventricular septaldefects (VSD) to complex outflow tract (OFT) abnormalities. However, the underlying cellularand molecular basis of maternal HG dose-response on fetal cardiac development remainselusive. In this study, we have utilized Streptozotocin-induced murine model of maternal type1diabetes and demonstrated that spectrum of CHD in HG exposed developing embryos in utero ,is dose-dependent. We have performed histological analysis of hearts at embryonic (E) day 9.5,11.5, 13.5 and 15.5 exposed to different levels of maternal HG and compared them withuntreated normoglycemic controls. Analysis of E9.5, E11.5 and E13.5 embryos displayedtrabeculation and touchdown defects, thinning of right and left ventricular myocardium, VSD,OFT misalignment, double outlet right ventricle with increasing levels of maternal glucose.Whereas, E15.5 embryos exposed to maternal HG exhibited VSD, cardiac hypertrophy andhyper-trabeculation phenotypes in comparison to normoglycemic controls. To test cell-specificgene-regulatory program in response to hyperglycemia stress, we performed in vivo 10X singlecell transcriptomics and in vitro global RNA-sequencing on murine embryonic cell-lines culturedin normal and increasing doses of HG. RNA-seq analysis revealed differential gene expressionchanges associated with metabolic dysfunction, oxidative stress response, endothelial tomesenchymal transition, cardiomyocytes proliferation and impaired neural crest cell migration.Cardiomyocytes and endothelial cell proliferation (PHH3) and apoptosis (TUNEL) weremeasured using immunohistochemical analysis at E9.5-E15.5 embryonic hearts exposed tomaternal HG. In summary, more in-depth analysis of this study is warranted to indicate howmaternal intrauterine hyperglycemic environment disrupts the fine tuning of fetal cardiogenicgene/epigenetic program to cause CHD.

Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of the gene regulatory program in cancers

ABSTRACTBackgroundMost cancer alterations occur in the noncoding portion of the human genome, which contains important regulatory regions acting as genetic switches to ensure gene expression occurs at correct times and intensities in correct tissues. However, large scale discovery of noncoding events altering the gene expression regulatory program has been limited to a few examples with high recurrence or high functional impact.ResultsWe focused on transcription factor binding sites (TFBSs) that show similar mutation loads than what is observed in protein-coding exons. By combining cancer somatic mutations in TFBSs and expression data for protein-coding and miRNA genes, we evaluated the combined effects of transcriptional and post-transcriptional alteration on the dysregulation of the regulatory programs in cancer. The analysis of seven cancer cohorts culminated with the identification of protein-coding and miRNA genes linked to mutations at TFBSs that were associated with a cascading trans-effect deregulation on the cells’ regulatory program. Our analyses of cis-regulatory mutations associated with miRNAs recurrently predicted 17 miRNAs as pan-cancer-associated through deregulation of their target gene networks. Overall, our predictions were enriched for protein-coding and miRNA genes previously annotated as cancer drivers. Functional enrichment analyses highlighted that cis-regulatory mutations are associated with the dysregulation of key pathways associated with carcinogenesisConclusionsThese pan-cancer results suggest that our method predicts cis-regulatory mutations related to the dysregulation of key gene regulatory networks in cancer patients. It highlights how the gene regulatory program is disrupted in cancer cells by combining transcriptional and post-transcriptional regulation of gene expression.

Climate beyond Borders

This chapter reveals the international dimensions and contradictions of California’s climate change regulatory program. It provides an account of the rise of a coalition of translocal justice actors—California-based environmental justice activists and Indigenous rights leaders in Chiapas, Mexico and Acre Brazil—who mobilized against linking California’s forest carbon offsets in the Global South.