Subtropical clouds key to Southern Ocean teleconnections to the tropical Pacific.

Excessive precipitation over the southeastern tropical Pacific is a major common bias that persists through generations of global climate models. While recent studies suggest an overly warm Southern Ocean as the cause, models disagree on the quantitative importance of this remote mechanism in light of ocean circulation feedback. Here, using a multimodel experiment in which the Southern Ocean is radiatively cooled, we show a teleconnection from the Southern Ocean to the tropical Pacific that is mediated by a shortwave subtropical cloud feedback. Cooling the Southern Ocean preferentially cools the southeastern tropical Pacific, thereby shifting the eastern tropical Pacific rainbelt northward with the reduced precipitation bias. Regional cloud locking experiments confirm that the teleconnection efficiency depends on subtropical stratocumulus cloud feedback. This subtropical cloud feedback is too weak in most climate models, suggesting that teleconnections from the Southern Ocean to the tropical Pacific are stronger than widely thought.

Novel In Vivo CometChip Reveals NDMA-Induced DNA Damage and Repair in Multiple Mouse Tissues.

The comet assay is a versatile assay for detecting DNA damage in eukaryotic cells. The assay can measure the levels of various types of damage, including DNA strand breaks, abasic sites and alkali-sensitive sites. Furthermore, the assay can also be modified to include purified DNA glycosylases so that alkylated and oxidized bases can be detected. The CometChip is a higher throughput version of the traditional comet assay and has been used to study cultured cells. Here, we have tested its utility for studies of DNA damage present in vivo. We show that the CometChip is effective in detecting DNA damage in multiple tissues of mice exposed to the direct-acting methylating agent methylmethane sulfonate (MMS) and to the metabolically activated methylating agent N-nitrosodimethylamine (NDMA), which has been found to contaminate food, water, and drugs. Specifically, results from MMS-exposed mice demonstrate that DNA damage can be detected in cells from liver, lung, kidney, pancreas, brain and spleen. Results with NDMA show that DNA damage is detectable in metabolically competent tissues (liver, lung, and kidney), and that DNA repair in vivo can be monitored over time. Additionally, it was found that DNA damage persists for many days after exposure. Furthermore, glycosylases were successfully incorporated into the assay to reveal the presence of damaged bases. Overall, this work demonstrates the efficacy of the in vivo CometChip and reveals new insights into the formation and repair of DNA damage caused by MMS and NDMA.

Rosa26-GFP direct repeat (RaDR-GFP) mice reveal tissue- and age-dependence of homologous recombination in mammals in vivo.

Homologous recombination (HR) is critical for the repair of double strand breaks and broken replication forks. Although HR is mostly error free, inherent or environmental conditions that either suppress or induce HR cause genomic instability. Despite its importance in carcinogenesis, due to limitations in our ability to detect HR in vivo, little is known about HR in mammalian tissues. Here, we describe a mouse model in which a direct repeat HR substrate is targeted to the ubiquitously expressed Rosa26 locus. In the Rosa26 Direct Repeat-GFP (RaDR-GFP) mice, HR between two truncated EGFP expression cassettes can yield a fluorescent signal. In-house image analysis software provides a rapid method for quantifying recombination events within intact tissues, and the frequency of recombinant cells can be evaluated by flow cytometry. A comparison among 11 tissues shows that the frequency of recombinant cells varies by more than two orders of magnitude among tissues, wherein HR in the brain is the lowest. Additionally, de novo recombination events accumulate with age in the colon, showing that this mouse model can be used to study the impact of chronic exposures on genomic stability. Exposure to N-methyl-N-nitrosourea, an alkylating agent similar to the cancer chemotherapeutic temozolomide, shows that the colon, liver and pancreas are susceptible to DNA damage-induced HR. Finally, histological analysis of the underlying cell types reveals that pancreatic acinar cells and liver hepatocytes undergo HR and also that HR can be specifically detected in colonic somatic stem cells. Taken together, the RaDR-GFP mouse model provides new understanding of how tissue and age impact susceptibility to HR, and enables future studies of genetic, environmental and physiological factors that modulate HR in mammals.

Lysate of engineered Escherichia coli supports high-level conversion of glucose to 2,3-butanediol.

Cell-free metabolic engineering (CFME) is emerging as a powerful approach for the production of target molecules and pathway debugging. Unfortunately, high cofactor costs, limited cofactor and energy regeneration, and low volumetric productivities hamper the widespread use and practical implementation of CFME technology. To address these challenges, we have developed a cell-free system that harnesses ensembles of catalytic proteins prepared from crude lysates, or extracts, of cells to fuel highly active heterologous metabolic conversions. As a model pathway, we selected conversion of glucose to 2,3-butanediol (2,3-BD), a medium level commodity chemical with many industrial applications. Specifically, we engineered a single strain of Escherichia coli to express three pathway enzymes necessary to make meso-2,3-BD (m2,3-BD). We then demonstrated that lysates from this strain, with addition of glucose and catalytic amounts of cofactors NAD+ and ATP, can produce m2,3-BD. Endogenous glycolytic enzymes convert glucose to pyruvate, the starting intermediate for m2,3-BD synthesis. Strikingly, with no strain optimization, we observed a maximal synthesis rate of m2,3-BD of 11.3 ± 0.1 g/L/h with a theoretical yield of 71% (0.36 g m2,3-BD/g glucose) in batch reactions. Titers reached 82 ± 8 g/L m2,3-BD in a 30 h fed-batch reaction. Our results highlight the ability for high-level co-factor regeneration in cell-free lysates. Further, they suggest exciting opportunities to use lysate-based systems to rapidly prototype metabolic pathways and carry out molecular transformations when bioconversion yields (g product/L), productivities (g product/L/h), or cellular toxicity limit commercial feasibility of whole-cell fermentation.

Application of the Key Characteristics Framework to Identify Potential Breast Carcinogens Using Publicly Available in Vivo, in Vitro, and in Silico Data.

BACKGROUND: Chemicals that induce mammary tumors in rodents or activate estrogen or progesterone signaling are likely to increase breast cancer (BC) risk. Identifying chemicals with these activities can prompt steps to protect human health. OBJECTIVES: We compiled data on rodent tumors, endocrine activity, and genotoxicity to assess the key characteristics (KCs) of rodent mammary carcinogens (MCs), and to identify other chemicals that exhibit these effects and may therefore increase BC risk. METHODS: Using authoritative databases, including International Agency for Research on Cancer (IARC) Monographs and the US Environmental Protection's (EPA) ToxCast, we selected chemicals that induce mammary tumors in rodents, stimulate estradiol or progesterone synthesis, or activate the estrogen receptor (ER) in vitro. We classified these chemicals by their genotoxicity and strength of endocrine activity and calculated the overrepresentation (enrichment) of these KCs among MCs. Finally, we evaluated whether these KCs predict whether a chemical is likely to induce mammary tumors. RESULTS: We identified 279 MCs and an additional 642 chemicals that stimulate estrogen or progesterone signaling. MCs were significantly enriched for steroidogenicity, ER agonism, and genotoxicity, supporting the use of these KCs to predict whether a chemical is likely to induce rodent mammary tumors and, by inference, increase BC risk. More MCs were steroidogens than ER agonists, and many increased both estradiol and progesterone. Enrichment among MCs was greater for strong endocrine activity vs. weak or inactive, with a significant trend. DISCUSSION: We identified hundreds of compounds that have biological activities that could increase BC risk and demonstrated that these activities are enriched among MCs. We argue that many of these should not be considered low hazard without investigating their ability to affect the breast, and chemicals with the strongest evidence can be targeted for exposure reduction. We describe ways to strengthen hazard identification, including improved assessments for mammary effects, developing assays for more KCs, and more comprehensive chemical testing. https://doi.org/10.1289/EHP13233.

Molecular origins of mutational spectra produced by the environmental carcinogen N-nitrosodimethylamine and SN1 chemotherapeutic agents.

DNA-methylating environmental carcinogens such as N-nitrosodimethylamine (NDMA) and certain alkylators used in chemotherapy form O 6-methylguanine (m6G) as a functionally critical intermediate. NDMA is a multi-organ carcinogen found in contaminated water, polluted air, preserved foods, tobacco products, and many pharmaceuticals. Only ten weeks after exposure to NDMA, neonatally-treated mice experienced elevated mutation frequencies in liver, lung and kidney of ∼35-fold, 4-fold and 2-fold, respectively. High-resolution mutational spectra (HRMS) of liver and lung revealed distinctive patterns dominated by GC→AT mutations in 5'-Pu-G-3' contexts, very similar to human COSMIC mutational signature SBS11. Commonly associated with alkylation damage, SBS11 appears in cancers treated with the DNA alkylator temozolomide (TMZ). When cells derived from the mice were treated with TMZ, N-methyl-N-nitrosourea, and streptozotocin (two other therapeutic methylating agents), all displayed NDMA-like HRMS, indicating mechanistically convergent mutational processes. The role of m6G in shaping the mutational spectrum of NDMA was probed by removing MGMT, the main cellular defense against m6G. MGMT-deficient mice displayed a strikingly enhanced mutant frequency, but identical HRMS, indicating that the mutational properties of these alkylators is likely owed to sequence-specific DNA binding. In sum, the HRMS of m6G-forming agents constitute an early-onset biomarker of exposure to DNA methylating carcinogens and drugs.

A retrospective mathematical analysis of controlled release design and experimentation.

The development and performance evaluation of new biodegradable polymer controlled release formulations relies on successful interpretation and evaluation of in vitro release data. However, depending upon the extent of empirical characterization, release data may be open to more than one qualitative interpretation. In this work, a predictive model for release from degradable polymer matrices was applied to a number of published release data in order to extend the characterization of release behavior. Where possible, the model was also used to interpolate and extrapolate upon collected released data to clarify the overall duration of release and also kinetics of release between widely spaced data points. In each case examined, mathematical predictions of release coincide well with experimental results, offering a more definitive description of each formulation's performance than was previously available. This information may prove particularly helpful in the design of future studies, such as when calculating proper dosing levels or determining experimental end points in order to more comprehensively evaluate a controlled release system's performance.

Transgenic mice harboring direct repeat substrates reveal key underlying causes of homologous recombination in vivo.

Homology directed repair is a critical process for maintaining the genome of mammalian cells. While considered to be relatively error free, homologous recombination (HR) can lead to insertions, deletions, translocations, and loss of heterozygosity. Furthermore, it is known that conditions that cause HR events are often carcinogenic, and that HR modulates susceptibility to cancer chemotherapeutics, making HR relevant to both cancer etiology and treatment. To learn about HR in vivo, several laboratories have developed mouse models that harbor direct repeat substrates for which HR yields a phenotype that can be visualized by either a change in pigmentation or by expression of a fluorescent protein. An exciting aspect of this work is that it is possible to detect recombinant cells within intact tissues and thus learn about how physiological changes, genes, and exposures modulate HR susceptibility in vivo, as well as which cell types are most susceptible to HR, and the extent to which recombinant cells have undergone clonal expansion. Here, we review progress in studying HR in vivo for four different mouse strains that harbor direct repeat substrates for HR detection, namely the pun mice, the fluorescent yellow direct repeat (FYDR) mice, the EGFP-DR mice, and the ROSA26 direct repeat (RaDR) mice. Key advances in our understanding of fundamental processes that modulate HR susceptibility in vivo are the focus of this review.

Anthropogenic aerosol and cryosphere changes drive Earth's strong but transient clear-sky hemispheric albedo asymmetry.

A striking feature of the Earth system is that the Northern and Southern Hemispheres reflect identical amounts of sunlight. This hemispheric albedo symmetry comprises two asymmetries: The Northern Hemisphere is more reflective in clear skies, whereas the Southern Hemisphere is cloudier. Here we show that the hemispheric reflection contrast from differences in continental coverage is offset by greater reflection from the Antarctic than the Arctic, allowing the net clear-sky asymmetry to be dominated by aerosol. Climate model simulations suggest that historical anthropogenic aerosol emissions drove a large increase in the clear-sky asymmetry that would reverse in future low-emission scenarios. High-emission scenarios also show decreasing asymmetry, instead driven by declines in Northern Hemisphere ice and snow cover. Strong clear-sky hemispheric albedo asymmetry is therefore a transient feature of Earth's climate. If all-sky symmetry is maintained, compensating cloud changes would have uncertain but important implications for Earth's energy balance and hydrological cycle.

Best practices to quantify the impact of reproductive toxicants on development, function, and diseases of the rodent mammary gland.

Work from numerous fields of study suggests that exposures to hormonally active chemicals during sensitive windows of development can alter mammary gland development, function, and disease risk. Stronger links between many environmental pollutants and disruptions to breast health continue to be documented in human populations, and there remain concerns that the methods utilized to identify, characterize, and prioritize these chemicals for risk assessment and risk management purposes are insufficient. There are also concerns that effects on the mammary gland have been largely ignored by regulatory agencies. Here, we provide technical guidance that is intended to enhance collection and evaluation of the mammary gland in mice and rats. We review several features of studies that should be controlled to properly evaluate the mammary gland, and then describe methods to appropriately collect the mammary gland from rodents. Furthermore, we discuss methods for preparing whole mounted mammary glands and numerous approaches that are available for the analysis of these samples. Finally, we conclude with several examples where analysis of the mammary gland revealed effects of environmental toxicants at low doses. Our work argues that the rodent mammary gland should be considered in chemical safety, hazard and risk assessments. It also suggests that improved measures of mammary gland outcomes, such as those we present in this review, should be included in the standardized methods evaluated by regulatory agencies such as the test guidelines used for identifying reproductive and developmental toxicants.

Chemical Effects on Breast Development, Function, and Cancer Risk: Existing Knowledge and New Opportunities.

Population studies show worrisome trends towards earlier breast development, difficulty in breastfeeding, and increasing rates of breast cancer in young women. Multiple epidemiological studies have linked these outcomes with chemical exposures, and experimental studies have shown that many of these chemicals generate similar effects in rodents, often by disrupting hormonal regulation. These endocrine-disrupting chemicals (EDCs) can alter the progression of mammary gland (MG) development, impair the ability to nourish offspring via lactation, increase mammary tissue density, and increase the propensity to develop cancer. However, current toxicological approaches to measuring the effects of chemical exposures on the MG are often inadequate to detect these effects, impairing our ability to identify exposures harmful to the breast and limiting opportunities for prevention. This paper describes key adverse outcomes for the MG, including impaired lactation, altered pubertal development, altered morphology (such as increased mammographic density), and cancer. It also summarizes evidence from humans and rodent models for exposures associated with these effects. We also review current toxicological practices for evaluating MG effects, highlight limitations of current methods, summarize debates related to how effects are interpreted in risk assessment, and make recommendations to strengthen assessment approaches. Increasing the rigor of MG assessment would improve our ability to identify chemicals of concern, regulate those chemicals based on their effects, and prevent exposures and associated adverse health effects.

Enhanced simulated early 21st century Arctic sea ice loss due to CMIP6 biomass burning emissions.

The mechanisms underlying decadal variability in Arctic sea ice remain actively debated. Here, we show that variability in boreal biomass burning (BB) emissions strongly influences simulated Arctic sea ice on multidecadal time scales. In particular, we find that a strong acceleration in sea ice decline in the early 21st century in the Community Earth System Model version 2 (CESM2) is related to increased variability in prescribed BB emissions in the sixth phase of the Coupled Model Intercomparison Project (CMIP6) through summertime aerosol-cloud interactions. Furthermore, we find that more than half of the reported improvement in sea ice sensitivity to CO2 emissions and global warming from CMIP5 to CMIP6 can be attributed to the increased BB variability, at least in the CESM. These results highlight a new kind of uncertainty that needs to be considered when incorporating new observational data into model forcing while also raising questions about the role of BB emissions on the observed Arctic sea ice loss.

Reactive Oxygen Species in the Adverse Outcome Pathway Framework: Toward Creation of Harmonized Consensus Key Events.

Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are formed as a result of natural cellular processes, intracellular signaling, or as adverse responses associated with diseases or exposure to oxidizing chemical and non-chemical stressors. The action of ROS and RNS, collectively referred to as reactive oxygen and nitrogen species (RONS), has recently become highly relevant in a number of adverse outcome pathways (AOPs) that capture, organize, evaluate and portray causal relationships pertinent to adversity or disease progression. RONS can potentially act as a key event (KE) in the cascade of responses leading to an adverse outcome (AO) within such AOPs, but are also known to modulate responses of events along the AOP continuum without being an AOP event itself. A substantial discussion has therefore been undertaken in a series of workshops named "Mystery or ROS" to elucidate the role of RONS in disease and adverse effects associated with exposure to stressors such as nanoparticles, chemical, and ionizing and non-ionizing radiation. This review introduces the background for RONS production, reflects on the direct and indirect effects of RONS, addresses the diversity of terminology used in different fields of research, and provides guidance for developing a harmonized approach for defining a common event terminology within the AOP developer community.

Analysis of mutations in tumor and normal adjacent tissue via fluorescence detection.

Inflammation is a major risk factor for many types of cancer, including colorectal. There are two fundamentally different mechanisms by which inflammation can contribute to carcinogenesis. First, reactive oxygen and nitrogen species (RONS) can damage DNA to cause mutations that initiate cancer. Second, inflammatory cytokines and chemokines promote proliferation, migration, and invasion. Although it is known that inflammation-associated RONS can be mutagenic, the extent to which they induce mutations in intestinal stem cells has been little explored. Furthermore, it is now widely accepted that cancer is caused by successive rounds of clonal expansion with associated de novo mutations that further promote tumor development. As such, we aimed to understand the extent to which inflammation promotes clonal expansion in normal and tumor tissue. Using an engineered mouse model that is prone to cancer and within which mutant cells fluoresce, here we have explored the impact of inflammation on de novo mutagenesis and clonal expansion in normal and tumor tissue. While inflammation is strongly associated with susceptibility to cancer and a concomitant increase in the overall proportion of mutant cells in the tissue, we did not observe an increase in mutations in normal adjacent tissue. These results are consistent with opportunities for de novo mutations and clonal expansion during tumor growth, and they suggest protective mechanisms that suppress the risk of inflammation-induced accumulation of mutant cells in normal tissue.

CometChip enables parallel analysis of multiple DNA repair activities.

DNA damage can be cytotoxic and mutagenic, and it is directly linked to aging, cancer, and other diseases. To counteract the deleterious effects of DNA damage, cells have evolved highly conserved DNA repair pathways. Many commonly used DNA repair assays are relatively low throughput and are limited to analysis of one protein or one pathway. Here, we have explored the capacity of the CometChip platform for parallel analysis of multiple DNA repair activities. Taking advantage of the versatility of the traditional comet assay and leveraging micropatterning techniques, the CometChip platform offers increased throughput and sensitivity compared to the traditional comet assay. By exposing cells to DNA damaging agents that create substrates of Base Excision Repair, Nucleotide Excision Repair, and Non-Homologous End Joining, we show that the CometChip is an effective method for assessing repair deficiencies in all three pathways. With these applications of the CometChip platform, we expand the utility of the comet assay for precise, high-throughput, parallel analysis of multiple DNA repair activities.

Excision of mutagenic replication-blocking lesions suppresses cancer but promotes cytotoxicity and lethality in nitrosamine-exposed mice.

N-Nitrosodimethylamine (NDMA) is a DNA-methylating agent that has been discovered to contaminate water, food, and drugs. The alkyladenine DNA glycosylase (AAG) removes methylated bases to initiate the base excision repair (BER) pathway. To understand how gene-environment interactions impact disease susceptibility, we study Aag-knockout (Aag-/-) and Aag-overexpressing mice that harbor increased levels of either replication-blocking lesions (3-methyladenine [3MeA]) or strand breaks (BER intermediates), respectively. Remarkably, the disease outcome switches from cancer to lethality simply by changing AAG levels. To understand the underlying basis for this observation, we integrate a suite of molecular, cellular, and physiological analyses. We find that unrepaired 3MeA is somewhat toxic, but highly mutagenic (promoting cancer), whereas excess strand breaks are poorly mutagenic and highly toxic (suppressing cancer and promoting lethality). We demonstrate that the levels of a single DNA repair protein tip the balance between blocks and breaks and thus dictate the disease consequences of DNA damage.

A cell-free system for production of 2,3-butanediol is robust to growth-toxic compounds.

The need for sustainable, low-cost production of bioenergy and commodity chemicals is increasing. Unfortunately, the engineering potential of whole-cell catalysts to address this need can be hampered by cellular toxicity. When such bottlenecks limit the commercial feasibility of whole-cell fermentation, cell-free, or in vitro, based approaches may offer an alternative. Here, we assess the impact of three classes of growth toxic compounds on crude extract-based, cell-free chemical conversions. As a model system, we test a metabolic pathway for conversion of glucose to 2,3-butanediol (2,3-BDO) in lysates of Escherichia coli. First, we characterized 2,3-BDO production with different classes of antibiotics and found, as expected, that the system is uninhibited by compounds that prevent cell growth by means of cell wall replication and DNA, RNA, and protein synthesis. Second, we considered the impact of polar solvent addition (e.g., methanol, n-butanol). We observed that volumetric productivities (g/L/h) were slowed with increasing hydrophobicity of added alcohols. Finally, we investigated the effects of using pretreated biomass hydrolysate as a feed stock, observing a 25% reduction in 2,3-BDO production as a result of coumaroyl and feruloyl amides. Overall, we find the cell-free system to be robust to working concentrations of antibiotics and other compounds that are toxic to cell growth, but do not denature or inhibit relevant enzymes.

Arctic Clouds and Precipitation in the Community Earth System Model Version 2.

The Arctic climate is changing rapidly, warming at about twice the rate of the planet. Global climate models (GCMs) are invaluable tools both for understanding the drivers of these changes and predicting future Arctic climate evolution. While GCMs are continually improving, there remain difficulties in representing cloud processes which occur on scales smaller than GCM resolution. Since clouds influence the Arctic energy and water cycles, their accurate representation in models is critical for robust future projections. In this work, we examine the representation of Arctic clouds and precipitation in the Community Earth System Model (CESM) with the Community Atmosphere Model (CAM), comparing the newly released version (CESM2 with CAM6) with its predecessor (CESM1 with CAM5). To isolate changes in the Arctic mean state, we compare preindustrial control runs. Arctic cloud ice has decreased slightly, while cloud water has increased dramatically in CESM2. Annual mean liquid-containing cloud (LCC) frequency has increased from 19% in CESM1 to 51% in CESM2. Since LCCs strongly modulate downwelling radiation at the surface, their increase has led to an increase in mean downwelling longwave (+22 W m-2) and corresponding decrease in downwelling shortwave (-23 W m-2) radiation. The mean Arctic surface temperature increased from 257 K in CESM1 to 260 K in CESM2, with the largest seasonal difference in winter (+6 K). Annual average snowfall has decreased slightly (-1 mm month-1), while rainfall has increased (+5 mm month-1).