Assessing susceptibility for polycyclic aromatic hydrocarbon toxicity in an in vitro 3D respiratory model for asthma.

There is increased emphasis on understanding cumulative risk from the combined effects of chemical and non-chemical stressors as it relates to public health. Recent animal studies have identified pulmonary inflammation as a possible modifier and risk factor for chemical toxicity in the lung after exposure to inhaled pollutants; however, little is known about specific interactions and potential mechanisms of action. In this study, primary human bronchial epithelial cells (HBEC) cultured in 3D at the air-liquid interface (ALI) are utilized as a physiologically relevant model to evaluate the effects of inflammation on toxicity of polycyclic aromatic hydrocarbons (PAHs), a class of contaminants generated from incomplete combustion of fossil fuels. Normal HBEC were differentiated in the presence of IL-13 for 14 days to induce a profibrotic phenotype similar to asthma. Fully differentiated normal and IL-13 phenotype HBEC were treated with benzo[a]pyrene (BAP; 1-40 µg/mL) or 1% DMSO/PBS vehicle at the ALI for 48 h. Cells were evaluated for cytotoxicity, barrier integrity, and transcriptional biomarkers of chemical metabolism and inflammation by quantitative PCR. Cells with the IL-13 phenotype treated with BAP result in significantly (p < 0.05) decreased barrier integrity, less than 50% compared to normal cells. The effect of BAP in the IL-13 phenotype was more apparent when evaluating transcriptional biomarkers of barrier integrity in addition to markers of mucus production, goblet cell hyperplasia, type 2 asthmatic inflammation and chemical metabolism, which all resulted in dose-dependent changes (p < 0.05) in the presence of BAP. Additionally, RNA sequencing data showed that the HBEC with the IL-13 phenotype may have increased potential for uncontrolled proliferation and decreased capacity for immune response after BAP exposure compared to normal phenotype HBEC. These data are the first to evaluate the role of combined environmental factors associated with inflammation from pre-existing disease and PAH exposure on pulmonary toxicity in a physiologically relevant human in vitro model.

Leveraging Multiple Data Streams for Prioritization of Mixtures for Hazard Characterization.

There is a growing need to establish alternative approaches for mixture safety assessment of polycyclic aromatic hydrocarbons (PAHs). Due to limitations with current component-based approaches, and the lack of established methods for using whole mixtures, a promising alternative is to use sufficiently similar mixtures; although, an established framework is lacking. In this study, several approaches are explored to form sufficiently similar mixtures. Multiple data streams including environmental concentrations and empirically and predicted toxicity data for cancer and non-cancer endpoints were used to prioritize chemical components for mixture formations. Air samplers were analyzed for unsubstituted and alkylated PAHs. A synthetic mixture of identified PAHs was created (Creosote-Fire Mix). Existing toxicity values and chemical concentrations were incorporated to identify hazardous components in the Creosote-Fire Mix. Sufficiently similar mixtures of the Creosote-Fire Mix were formed based on (1) relative abundance; (2) toxicity values; and (3) a combination approach incorporating toxicity and abundance. Hazard characterization of these mixtures was performed using high-throughput screening in primary normal human bronchial epithelium (NHBE) and zebrafish. Differences in chemical composition and potency were observed between mixture formation approaches. The toxicity-based approach (Tox Mix) was the most potent mixture in both models. The combination approach (Weighted-Tox Mix) was determined to be the ideal approach due its ability to prioritize chemicals with high exposure and hazard potential.

Genetic analysis of Caenorhabditis elegans pry-1/Axin suppressors identifies genes involved in reproductive structure development, stress responses, and aging.

The Axin family of scaffolding proteins regulates a wide array of developmental and post-developmental processes in eukaryotes. Studies in the nematode Caenorhabditis elegans have shown that the Axin homolog PRY-1 plays essential roles in multiple tissues. To understand the genetic network of pry-1, we focused on a set of genes that are differentially expressed in the pry-1-mutant transcriptome and are linked to reproductive structure development. Knocking down eight of the genes (spp-1, clsp-1, ard-1, rpn-7, cpz-1, his-7, cdk-1, and rnr-1) via RNA interference efficiently suppressed the multivulva phenotype of pry-1 mutants. In all cases, the ectopic induction of P3.p vulval precursor cell was also inhibited. The suppressor genes are members of known gene families in eukaryotes and perform essential functions. Our genetic interaction experiments revealed that in addition to their role in vulval development, these genes participate in one or more pry-1-mediated biological events. Whereas four of them (cpz-1, his-7, cdk-1, and rnr-1) function in both stress response and aging, two (spp-1 and ard-1) are specific to stress response. Altogether, these findings demonstrate the important role of pry-1 suppressors in regulating developmental and post-developmental processes in C. elegans. Given that the genes described in this study are conserved, future investigations of their interactions with Axin and their functional specificity promises to uncover the genetic network of Axin in metazoans.

Linking Coregulated Gene Modules with Polycyclic Aromatic Hydrocarbon-Related Cancer Risk in the 3D Human Bronchial Epithelium.

Exposure to polycyclic aromatic hydrocarbons (PAHs) often occurs as complex chemical mixtures, which are linked to numerous adverse health outcomes in humans, with cancer as the greatest concern. The cancer risk associated with PAH exposures is commonly evaluated using the relative potency factor (RPF) approach, which estimates PAH mixture carcinogenic potential based on the sum of relative potency estimates of individual PAHs, compared to benzo[a]pyrene (BAP), a reference carcinogen. The present study evaluates molecular mechanisms related to PAH cancer risk through integration of transcriptomic and bioinformatic approaches in a 3D human bronchial epithelial cell model. Genes with significant differential expression from human bronchial epithelium exposed to PAHs were analyzed using a weighted gene coexpression network analysis (WGCNA) two-tiered approach: first to identify gene sets comodulated to RPF and second to link genes to a more comprehensive list of regulatory values, including inhalation-specific risk values. Over 3000 genes associated with processes of cell cycle regulation, inflammation, DNA damage, and cell adhesion processes were found to be comodulated with increasing RPF with pathways for cell cycle S phase and cytoskeleton actin identified as the most significantly enriched biological networks correlated to RPF. In addition, comodulated genes were linked to additional cancer-relevant risk values, including inhalation unit risks, oral cancer slope factors, and cancer hazard classifications from the World Health Organization's International Agency for Research on Cancer (IARC). These gene sets represent potential biomarkers that could be used to evaluate cancer risk associated with PAH mixtures. Among the values tested, RPF values and IARC categorizations shared the most similar responses in positively and negatively correlated gene modules. Together, we demonstrated a novel manner of integrating gene sets with chemical toxicity equivalence estimates through WGCNA to understand potential mechanisms.

The chemistry and toxicology of vaping.

Vaping is the process of inhaling and exhaling an aerosol produced by an e-cigarette, vape pen, or personal aerosolizer. When the device contains nicotine, the Food and Drug Administration (FDA) lists the product as an electronic nicotine delivery system or ENDS device. Similar electronic devices can be used to vape cannabis extracts. Over the past decade, the vaping market has increased exponentially, raising health concerns over the number of people exposed and a nationwide outbreak of cases of severe, sometimes fatal, lung dysfunction that arose suddenly in otherwise healthy individuals. In this review, we discuss the various vaping technologies, which are remarkably diverse, and summarize the use prevalence in the U.S. over time by youths and adults. We examine the complex chemistry of vape carrier solvents, flavoring chemicals, and transformation products. We review the health effects from epidemiological and laboratory studies and, finally, discuss the proposed mechanisms underlying some of these health effects. We conclude that since much of the research in this area is recent and vaping technologies are dynamic, our understanding of the health effects is insufficient. With the rapid growth of ENDS use, consumers and regulatory bodies need a better understanding of constituent-dependent toxicity to guide product use and regulatory decisions.

Classifying polycyclic aromatic hydrocarbons by carcinogenic potency using in vitro biosignatures.

One of the most difficult challenges for risk assessment is evaluation of chemicals that predominately co-occur in mixtures like polycyclic aromatic hydrocarbons (PAHs). We previously developed a classification model in which systems biology data collected from mice short-term after chemical exposure accurately predict tumor outcome. The present study demonstrates translation of this approach into a human in vitro model in which chemical-specific bioactivity profiles from 3D human bronchial epithelial cells (HBEC) classify PAHs by carcinogenic potency. Gene expression profiles were analyzed from HBEC exposed to carcinogenic and non-carcinogenic PAHs and classification accuracies were identified for individual pathway-based gene sets. Posterior probabilities of best performing gene sets were combined via Bayesian integration resulting in a classifier with four gene sets, including aryl hydrocarbon receptor signaling, regulation of epithelial mesenchymal transition, regulation of angiogenesis, and cell cycle G2-M. In addition, transcriptional benchmark dose modeling of benzo[a]pyrene (BAP) showed that the most sensitive gene sets to BAP regulation were largely dissimilar from those that best classified PAH carcinogenicity challenging current assumptions that BAP carcinogenicity (and subsequent mode of action) is reflective of overall PAH carcinogenicity. These results illustrate utility of using systems toxicology approaches to analyze global gene expression towards carcinogenic hazard assessment.

Comparative mechanisms of PAH toxicity by benzo[a]pyrene and dibenzo[def,p]chrysene in primary human bronchial epithelial cells cultured at air-liquid interface.

Current assumption for assessing carcinogenic risk of polycyclic aromatic hydrocarbons (PAHs) is that they function through a common mechanism of action; however, recent studies demonstrate that PAHs can act through unique mechanisms potentially contributing to cancer outcomes in a non-additive manner. Using a primary human 3D bronchial epithelial culture (HBEC) model, we assessed potential differences in mechanism of toxicity for two PAHs, benzo[a]pyrene (BAP) and dibenzo[def,p]chrysene (DBC), compared to a complex PAH mixture based on short-term biosignatures identified from transcriptional profiling. Differentiated bronchial epithelial cells were treated with BAP (100-500 µg/ml), DBC (10 µg/ml), and coal tar extract (CTE 500-1500 µg/ml, SRM1597a) for 48 h and gene expression was measured by RNA sequencing or quantitative PCR. Comparison of BAP and DBC gene signatures showed that the majority of genes (~60%) were uniquely regulated by treatment, including signaling pathways for inflammation and DNA damage by DBC and processes for cell cycle, hypoxia and oxidative stress by BAP. Specifically, BAP upregulated targets of AhR, NRF2, and KLF4, while DBC downregulated these same targets, suggesting a chemical-specific pattern in transcriptional regulation involved in antioxidant response, potentially contributing to differences in PAH potency. Other processes were regulated in common by all PAH treatments, BAP, DBC and CTE, including downregulation of genes involved in cell adhesion and reduced functional measurements of barrier integrity. This work supports prior in vivo studies and demonstrates the utility of profiling short-term biosignatures in an organotypic 3D model to identify mechanisms linked to carcinogenic risk of PAHs in humans.

Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration.

BACKGROUND: The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio rerio (zebrafish), and Macaca mulatta (macaque), as well as perform orthologous conversions among the supported species. In addition to providing a robust means of identifier conversion, BRM also incorporates a suite of microRNA (miRNA)-target databases upon which to query target genes or to perform reverse target lookups using gene identifiers. RESULTS: BRM has the capability to perform cross-species identifier lookups across common identifier types, directly integrate datasets across platform or species by performing identifier retrievals in the background, and retrieve miRNA targets from multiple databases simultaneously and integrate the resulting gene targets with experimental mRNA data. Here we use workflows provided in BRM to integrate RNA sequencing data across species to identify common biomarkers of exposure after treatment of human lung cells and zebrafish to benzo[a]pyrene (BAP). We further use the miRNA Target workflow to experimentally determine the role of miRNAs as regulators of BAP toxicity and identify the predicted functional consequences of miRNA-target regulation in our system. The output from BRM can easily and directly be uploaded to freely available visualization tools for further analysis. From these examples, we were able to identify an important role for several miRNAs as potential regulators of BAP toxicity in human lung cells associated with cell migration, cell communication, cell junction assembly and regulation of cell death. CONCLUSIONS: Overall, BRM provides bioinformatics tools to assist biologists having minimal programming skills with analysis and integration of high-content omics' data from various transcriptomic and proteomic platforms. BRM workflows were developed in Java and other open-source technologies and are served publicly using Apache Tomcat at https://cbb.pnnl.gov/brm/ .

The links between leaf hydraulic vulnerability to drought and key aspects of leaf venation and xylem anatomy among 26 Australian woody angiosperms from contrasting climates.

Background and Aims: The structural properties of leaf venation and xylem anatomy strongly influence leaf hydraulics, including the ability of leaves to maintain hydraulic function during drought. Here we examined the strength of the links between different leaf venation traits and leaf hydraulic vulnerability to drought (expressed as P50leaf by rehydration kinetics) in a diverse group of 26 woody angiosperm species, representing a wide range of leaf vulnerabilities, from four low-nutrient sites with contrasting rainfall across eastern Australia. Methods: For each species we measured key aspects of leaf venation design, xylem anatomy and leaf morphology. We also assessed for the first time the scaling relationships between hydraulically weighted vessel wall thickness (th) and lumen breadth (bh) across vein orders and habitats. Key Results: Across species, variation in P50leaf was strongly correlated with the ratio of vessel wall thickness (th) to lumen breadth (bh) [(t/b)h; an index of conduit reinforcement] at each leaf vein order. Concomitantly, the scaling relationship between th and bh was similar across vein orders, with a log-log slope less than 1 indicating greater xylem reinforcement in smaller vessels. In contrast, P50leaf was not related to th and bh individually, to major vein density (Dvmajor) or to leaf size. Principal components analysis revealed two largely orthogonal trait groupings linked to variation in leaf size and drought tolerance. Conclusions: Our results indicate that xylem conduit reinforcement occurs throughout leaf venation, and remains closely linked to leaf drought tolerance irrespective of leaf size.

A Validation of the Group-Based Medical Mistrust Scale in Formerly Incarcerated Black and Latino Men.

While there is a growing body of literature on medical mistrust and its relevance to public health, research on formerly incarcerated Black and Latino men and their perception of mistrust toward medical providers and medical institutions remains scant. Very little is known about whether formerly incarcerated Black and Latino men mistrust medical and clinical providers given their previous experiences with the criminal justice system. It is important to determine whether medical mistrust play a key role in the health and health behaviors of released Black and Latino men. The purpose of this study is to validate and assess the psychometric properties of the Group-Based Medical Mistrust Scale for use among formerly incarcerated Black and Latino men in New York City. The findings of the exploratory and confirmatory factor analyses state that a two-factor structure fit the data best. Two dimensions emerged as important subscales: discrimination and suspicion. The current findings suggest the two-factor Group-Based Medical Mistrust Scale is a valid and reliable assessment tool to discern medical mistrust levels among formerly incarcerated Black and Latino men.

HIV risk inside U.S. prisons: a systematic review of risk reduction interventions conducted in U.S. prisons.

HIV prevalence in correctional populations is approximately five times that of the general adult population. This systematic review examines the broad question of HIV prevention and interventions to reduce inmate HIV-related risk behaviors in U.S. federal and state prisons. We conducted a systematic review of multiple databases and Google Scholar to identify behavioral, biomedical, social, and policy studies related to HIV among U.S. prison populations from 1980-2014. Studies were excluded if they did not focus on HIV, prison inmates, if they were conducted outside of the U.S., if they involved juvenile offenders, or if they included post-release outcomes. Twenty-seven articles met the study criteria. Evidence suggests that research related to the HIV care continuum, risk behaviors, gender, prevention (e.g., peer education), and policy are key topics to enhance HIV prevention interventions in the criminal justice system. This review provides a prison-specific overview of HIV in U.S. correctional populations and highlight effective interventions, including inmate peer education. There is an urgent need to continue to implement HIV prevention interventions across all prisons and improve the quality of life among those at heightened risk of HIV infection.

Weak coordination among petiole, leaf, vein, and gas-exchange traits across Australian angiosperm species and its possible implications.

Close coordination between leaf gas exchange and maximal hydraulic supply has been reported across diverse plant life forms. However, it has also been suggested that this relationship may become weak or break down completely within the angiosperms. We examined coordination between hydraulic, leaf vein, and gas-exchange traits across a diverse group of 35 evergreen Australian angiosperms, spanning a large range in leaf structure and habitat. Leaf-specific conductance was calculated from petiole vessel anatomy and was also measured directly using the rehydration technique. Leaf vein density (thought to be a determinant of gas exchange rate), maximal stomatal conductance, and net CO 2 assimilation rate were also measured for most species (n = 19-35). Vein density was not correlated with leaf-specific conductance (either calculated or measured), stomatal conductance, nor maximal net CO 2 assimilation, with r (2) values ranging from 0.00 to 0.11, P values from 0.909 to 0.102, and n values from 19 to 35 in all cases. Leaf-specific conductance calculated from petiole anatomy was weakly correlated with maximal stomatal conductance (r (2) = 0.16; P = 0.022; n = 32), whereas the direct measurement of leaf-specific conductance was weakly correlated with net maximal CO 2 assimilation (r (2) = 0.21; P = 0.005; n = 35). Calculated leaf-specific conductance, xylem ultrastructure, and leaf vein density do not appear to be reliable proxy traits for assessing differences in rates of gas exchange or growth across diverse sets of evergreen angiosperms.

Conducting Health Disparities Research with Criminal Justice Populations: Examining Research, Ethics, and Participation.

This study explored the challenges of informed consent and understanding of the research process among Black and Latino men under community supervision (e.g., parole and/or probation). Between February and October 2012, we conducted cognitive face-to-face interviews using open-ended questions on the significant areas of research participation (i.e., the informed consent process, confidentiality, compensation, what is meant by human subject and clinical trials) among 259 men aged 35 to 67 under community supervision in Bronx, New York. Content analysis of the open-ended questions revealed limited knowledge concerning the understanding of research participation. The study participants appeared to generally understand concepts such as compensation after research participation and confidentiality. Participants demonstrated a lack of understanding of certain aspects of the research process-informed consent, human subject, Institutional Review Board, and clinical trials. These findings are informative to researchers conducting studies with criminal justice populations and Institutional Review Boards reviewing research studies.

Leaf hydraulic vulnerability to drought is linked to site water availability across a broad range of species and climates.

BACKGROUND AND AIMS: Vulnerability of the leaf hydraulic pathway to water-stress-induced dysfunction is a key component of drought tolerance in plants and may be important in defining species' climatic range. However, the generality of the association between leaf hydraulic vulnerability and climate across species and sites remains to be tested. METHODS: Leaf hydraulic vulnerability to drought (P50leaf, the water potential inducing 50 % loss in hydraulic function) was measured in a diverse group of 92 woody, mostly evergreen angiosperms from sites across a wide range of habitats. These new data together with some previously published were tested against key climate indices related to water availability. Differences in within-site variability in P50leaf between sites were also examined. KEY RESULTS: Values of hydraulic vulnerability to drought in leaves decreased strongly (i.e. became more negative) with decreasing annual rainfall and increasing aridity across sites. The standard deviation in P50leaf values recorded within each site was positively correlated with increasing aridity. P50leaf was also a good indicator of the climatic envelope across each species' distributional range as well as their dry-end distributional limits within Australia, although this relationship was not consistently detectable within sites. CONCLUSIONS: The findings indicate that species sorting processes have influenced distributional patterns of P50leaf across the rainfall spectrum, but alternative strategies for dealing with water deficit exist within sites. The strong link to aridity suggests leaf hydraulic vulnerability may influence plant distributions under future climates.

Bark functional ecology: evidence for tradeoffs, functional coordination, and environment producing bark diversity.

The causes underlying bark diversity are unclear. Variation has been frequently attributed to environmental differences across sites. However, variation may also result from tradeoffs and coordination between bark's multiple functions. Bark traits may also covary with wood and leaf traits as part of major dimensions of plant variation. To assess hypotheses regarding tradeoffs and functional coordination, we measured bark traits reflecting protection, storage, mechanics, and photosynthesis in branches of 90 species spanning a wide phylogenetic and environmental range. We also tested associations between bark, wood, and leaf traits. We partitioned trait variation within species, and within and across communities to quantify variation associated with across-site differences. We observed associations between bark mechanics and storage, density and thickness, and thickness and photosynthetic activity. Increasing bark thickness contributed significantly to stiffer stems and greater water storage. Bark density, water content, and mechanics covaried strongly with the equivalent wood traits, and to a lesser degree with leaf size, xylem conductivity, and vessel diameter. Most variation was observed within sites and had low phylogenetic signal. Compared with relatively minor across-site differences, tradeoffs and coordination among functions of bark, leaves, and wood are likely to be major and overlooked factors shaping bark ecology and evolution.

Hoxa-5 acts in segmented somites to regulate cervical vertebral morphology.

The vertebrate axial skeleton (vertebral column and ribs) is derived from embryonic structures called somites. Mechanisms of somite formation and patterning are largely conserved along the length of the body axis, but segments acquire different morphologies in part through the action of Hox transcription factors. Although Hox genes' roles in axial skeletal patterning have been extensively characterized, it is still not well understood how they interact with somite patterning pathways to regulate different vertebral morphologies. Here, we investigated the role of Hoxa-5 in after somite segmentation in chick. Hoxa-5 mRNA is expressed in posterior cervical somites, and within them is restricted mainly to a sub-domain of lateral sclerotome. RNAi-based knockdown leads to cartilage defects in lateral vertebral elements (rib homologous structures) whose morphologies vary within and outside of the Hoxa-5 expression domain. Both knockdown and misexpression suggest that Hoxa-5 acts via negative regulation of Sox-9. Further, Hoxa-5 misexpression suggests that spatial and/or temporal restriction of Hoxa-5 expression is necessary for proper vertebral morphology. Finally, the restriction of Hoxa-5 expression to lateral sclerotome, which we hypothesize is important for its patterning function, involves regulation by signaling pathways that pattern somites, Fgf-8 and Shh.

Co-induction of hepatic IGF-I and progranulin mRNA by growth hormone in tilapia, Oreochromis mossambiccus.

Like IGF-I, progranulin (pgrn) is a growth factor involved in tumorigenesis and wound healing. We report here the identification and characterization of pgrn cDNA in tilapia and the regulation of its expression by growth hormone (GH). The tilapia pgrn cDNA was cloned by RT-PCR amplification, using gene specific oligonucleotides as amplification primers. The cDNA contains an open reading frame encoding a peptide of 206 amino acid residues (aa) that contains a presumptive signal peptide (23 aa) and two repeat units of granulin (grn, 51 and 52 aa, respectively) franked by a GAP of 49 aa and the carboxyl terminus with 31 aa. The two predicted grn peptides are arranged in tandem repeats interrupted by a GAP peptide. RT-PCR analysis revealed that high levels of prgn mRNA were present in several tissues such as spleen, gastric cecum, intestine, fat tissue, gill, kidney, eye and pancreas, and lower levels in liver, muscle, heart, brain, skin and stomach. Administration of a single dose (500 ng/g body weight) of recombinant seabream growth hormone (rbGH) by intraperitoneal (ip) injection into one-month-old tilapia resulted in an obvious increase of IGF-I and pgrn mRNA (2.7-fold and 2.5-fold, respectively) in the liver at three hours post-GH treatment. The peptide levels of pgrn in the liver of GH-treated fish also were substantially induced over controls at 12h post-GH treatment as detected by western immuno-blot analysis. The co-induction of IGF-I and pgrn following GH treatment may suggest the involvement of pgrn in GH regulated growth in tilapia.