Genetic perturbation of the maize methylome.

DNA methylation can play important roles in the regulation of transposable elements and genes. A collection of mutant alleles for 11 maize (Zea mays) genes predicted to play roles in controlling DNA methylation were isolated through forward- or reverse-genetic approaches. Low-coverage whole-genome bisulfite sequencing and high-coverage sequence-capture bisulfite sequencing were applied to mutant lines to determine context- and locus-specific effects of these mutations on DNA methylation profiles. Plants containing mutant alleles for components of the RNA-directed DNA methylation pathway exhibit loss of CHH methylation at many loci as well as CG and CHG methylation at a small number of loci. Plants containing loss-of-function alleles for chromomethylase (CMT) genes exhibit strong genome-wide reductions in CHG methylation and some locus-specific loss of CHH methylation. In an attempt to identify stocks with stronger reductions in DNA methylation levels than provided by single gene mutations, we performed crosses to create double mutants for the maize CMT3 orthologs, Zmet2 and Zmet5, and for the maize DDM1 orthologs, Chr101 and Chr106. While loss-of-function alleles are viable as single gene mutants, the double mutants were not recovered, suggesting that severe perturbations of the maize methylome may have stronger deleterious phenotypic effects than in Arabidopsis thaliana.

Genomic analyses reveal poaching hotspots and illegal trade in pangolins from Africa to Asia.

The white-bellied pangolin (Phataginus tricuspis) is the world's most trafficked mammal and is at risk of extinction. Reducing the illegal wildlife trade requires an understanding of its origins. Using a genomic approach for tracing confiscations and analyzing 111 samples collected from known geographic localities in Africa and 643 seized scales from Asia between 2012 and 2018, we found that poaching pressures shifted over time from West to Central Africa. Recently, Cameroon's southern border has emerged as a site of intense poaching. Using data from seizures representing nearly 1 million African pangolins, we identified Nigeria as one important hub for trafficking, where scales are amassed and transshipped to markets in Asia. This origin-to-destination approach offers new opportunities to disrupt the illegal wildlife trade and to guide anti-trafficking measures.

Genomic vulnerability and socio-economic threats under climate change in an African rainforest bird.

Preserving biodiversity under rapidly changing climate conditions is challenging. One approach for estimating impacts and their magnitude is to model current relationships between genomic and environmental data and then to forecast those relationships under future climate scenarios. In this way, understanding future genomic and environmental relationships can help guide management decisions, such as where to establish new protected areas where populations might be buffered from high temperatures or major changes in rainfall. However, climate warming is only one of many anthropogenic threats one must consider in rapidly developing parts of the world. In Central Africa, deforestation, mining, and infrastructure development are accelerating population declines of rainforest species. Here we investigate multiple anthropogenic threats in a Central African rainforest songbird, the little greenbul (Andropadus virens). We examine current climate and genomic variation in order to explore the association between genome and environment under future climate conditions. Specifically, we estimate Genomic Vulnerability, defined as the mismatch between current and predicted future genomic variation based on genotype-environment relationships modeled across contemporary populations. We do so while considering other anthropogenic impacts. We find that coastal and central Cameroon populations will require the greatest shifts in adaptive genomic variation, because both climate and land use in these areas are predicted to change dramatically. In contrast, in the more northern forest-savanna ecotones, genomic shifts required to keep pace with climate will be more moderate, and other anthropogenic impacts are expected to be comparatively low in magnitude. While an analysis of diverse taxa will be necessary for making comprehensive conservation decisions, the species-specific results presented illustrate how evolutionary genomics and other anthropogenic threats may be mapped and used to inform mitigation efforts. To this end, we present an integrated conceptual model demonstrating how the approach for a single species can be expanded to many taxonomically diverse species.

Has Toxicity Testing Moved into the 21st Century? A Survey and Analysis of Perceptions in the Field of Toxicology.

BACKGROUND: Ten years ago, leaders in the field of toxicology called for a transformation of the discipline and a shift from primarily relying on traditional animal testing to incorporating advances in biotechnology and predictive methodologies into alternative testing strategies (ATS). Governmental agencies and academic and industry partners initiated programs to support such a transformation, but a decade later, the outcomes of these efforts are not well understood. OBJECTIVES: We aimed to assess the use of ATS and the perceived barriers and drivers to their adoption by toxicologists and by others working in, or closely linked with, the field of toxicology. METHODS: We surveyed 1,381 toxicologists and experts in associated fields regarding the viability and use of ATS and the perceived barriers and drivers of ATS for a range of applications. We performed ranking, hierarchical clustering, and correlation analyses of the survey data. RESULTS: Many respondents indicated that they were already using ATS, or believed that ATS were already viable approaches, for toxicological assessment of one or more end points in their primary area of interest or concern (26-86%, depending on the specific ATS/application pair). However, the proportions of respondents reporting use of ATS in the previous 12 mo were smaller (4.5-41%). Concern about regulatory acceptance was the most commonly cited factor inhibiting the adoption of ATS, and a variety of technical concerns were also cited as significant barriers to ATS viability. The factors most often cited as playing a significant role (currently or in the future) in driving the adoption of ATS were the need for expedited toxicology information, the need for reduced toxicity testing costs, demand by regulatory agencies, and ethical or moral concerns. CONCLUSIONS: Our findings indicate that the transformation of the field of toxicology is partly implemented, but significant barriers to acceptance and adoption remain. https://doi.org/10.1289/EHP1435.

Advancing alternatives analysis: The role of predictive toxicology in selecting safer chemical products and processes.

Alternatives analysis (AA) is a method used in regulation and product design to identify, assess, and evaluate the safety and viability of potential substitutes for hazardous chemicals. It requires toxicological data for the existing chemical and potential alternatives. Predictive toxicology uses in silico and in vitro approaches, computational models, and other tools to expedite toxicological data generation in a more cost-effective manner than traditional approaches. The present article briefly reviews the challenges associated with using predictive toxicology in regulatory AA, then presents 4 recommendations for its advancement. It recommends using case studies to advance the integration of predictive toxicology into AA, adopting a stepwise process to employing predictive toxicology in AA beginning with prioritization of chemicals of concern, leveraging existing resources to advance the integration of predictive toxicology into the practice of AA, and supporting transdisciplinary efforts. The further incorporation of predictive toxicology into AA would advance the ability of companies and regulators to select alternatives to harmful ingredients, and potentially increase the use of predictive toxicology in regulation more broadly. Integr Environ Assess Manag 2017;13:915-925. © 2017 SETAC.

Advancing Alternative Analysis: Integration of Decision Science.

BACKGROUND: Decision analysis-a systematic approach to solving complex problems-offers tools and frameworks to support decision making that are increasingly being applied to environmental challenges. Alternatives analysis is a method used in regulation and product design to identify, compare, and evaluate the safety and viability of potential substitutes for hazardous chemicals. OBJECTIVES: We assessed whether decision science may assist the alternatives analysis decision maker in comparing alternatives across a range of metrics. METHODS: A workshop was convened that included representatives from government, academia, business, and civil society and included experts in toxicology, decision science, alternatives assessment, engineering, and law and policy. Participants were divided into two groups and were prompted with targeted questions. Throughout the workshop, the groups periodically came together in plenary sessions to reflect on other groups' findings. RESULTS: We concluded that the further incorporation of decision science into alternatives analysis would advance the ability of companies and regulators to select alternatives to harmful ingredients and would also advance the science of decision analysis. CONCLUSIONS: We advance four recommendations: a) engaging the systematic development and evaluation of decision approaches and tools; b) using case studies to advance the integration of decision analysis into alternatives analysis; c) supporting transdisciplinary research; and d) supporting education and outreach efforts. https://doi.org/10.1289/EHP483.