Multi-omics responses in tree swallow (\u3ci\u3eTachycineta bicolor\u3c/i\u3e) nestlings from the Maumee Area of Concern, Maumee River, Ohio

A multi-omics approach was utilized to identify altered biological responses and functions, and to prioritize contaminants to assess the risks of chemical mixtures in the Maumee Area of Concern (AOC), Maumee River, OH, USA. The Maumee AOC is designated by the United States Environmental Protection Agency as having significant beneficial use impairments, including degradation of fish and wildlife populations, bird or animal deformities or reproduction problems, and loss of fish and wildlife habitat. Tree swallow (Tachycineta bicolor) nestlings were collected at five sites along the Maumee River, which included wastewater treatment plants (WWTPs) and industrial land-use sites. Polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo p dioxins and furans (PCDD/Fs), and chlorinated pesticide concentrations were elevated in Maumee tree swallows, relative to a remote reference site, Star Lake, WI, USA. Liver tissue was utilized for non-targeted transcriptome and targeted metabolome evaluation. A significantly differentially expressed gene cluster related to a downregulation in cell growth and cell cycle regulation was identified when comparing all Maumee River sites with the reference site. There was an upregulation of lipogenesis genes, such as PPAR signaling (HMGCS2, SLC22A5), biosynthesis of unsaturated fatty acids (FASN, SCD, ELOVL2, and FADS2), and higher lipogenesis related metabolites, such as docosapentaenoic acid (DPA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (AA) at two industrial land-use sites, Ironhead and Maumee, relative to WWTP sites (Perrysburg and SideCut), and the reference site. Toledo Water, in the vicinity of the other two industrial sites and also adjacent to a WWTP, showed a mix of signals between industrial land-use and WWTP land-use. PAHs, oxychlordane, and PBDEs were determined to be the most likely causes of the differentiation in biological responses, including de novo lipogenesis and biosynthesis of unsaturated fatty acids

Development of the morpholino gene knockdown technique in Fundulus heteroclitus : a tool for studying molecular mechanisms in an established environmental model

Author Posting. © Elsevier B.V., 2008. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Aquatic Toxicology 87 (2008): 289-295, doi:10.1016/j.aquatox.2008.02.010.A significant challenge in environmental toxicology is that many genetic and genomic tools available in laboratory models are not developed for commonly used environmental models. The Atlantic killifish (Fundulus heteroclitus) is one of the most studied teleost environmental models, yet few genetic or genomic tools have been developed for use in this species. The advancement of genetic and evolutionary toxicology will require that many of the tools developed in laboratory models be transferred into species more applicable to environmental toxicology. Antisense morpholino oligonucleotide (MO) gene knockdown technology has been widely utilized to study development in zebrafish and has been proven to be a powerful tool in toxicological investigations through direct manipulation of molecular pathways. To expand the utility of killifish as an environmental model, MO gene knockdown technology was adapted for use in Fundulus. Morpholino microinjection methods were altered to overcome the significant differences between these two species. Morpholino efficacy and functional duration were evaluated with molecular and phenotypic methods. A cytochrome P450-1A (CYP1A) MO was used to confirm effectiveness of the methodology. For CYP1A MO-injected embryos, a 70% reduction in CYP1A activity, a 86% reduction in total CYP1A protein, a significant increase in β-naphthoflavone-induced teratogenicity, and estimates of functional duration (50% reduction in activity 10 dpf, and 86% reduction in total protein 12 dpf) conclusively demonstrated that MO technologies can be used effectively in killifish and will likely be just as informative as they have been in zebrafish.This work was funded in part by the National Institute of Environmental Health Sciences through the Duke Superfund Basic Research Center (P42ES010356), the Boston University Superfund Basic Research Program (P42ES007381), and the Duke Integrated Toxicology and Environmental Health Program (ES-T32-0007031). Additional support was provided by a U.S. Environmental Protection Agency STAR fellowship awarded to C.R.F

Population Genetics of Bowhead Whales (Baleana mysticetus) in the Western Arctic

Bowhead whales (Balaena mysticetus) in the Bering, Chukchi, and Beaufort seas experienced a severe reduction as a result of commercial whaling in the 19th century. Since the cessation of commercial whaling, the population has recovered to a size that is approaching pre-whaling estimates. Inupiat and Yupik communities in northern and western Alaska hunt these Western Arctic (WA) bowheads along their migratory path during spring and fall. This hunting is regulated by the International Whaling Commission. Recent but preliminary analysis of available genetic data (207 whales and 10 microsatellite markers) raised the question of the presence of multiple, genetically distinct populations within the WA bowheads. Here we re-examined this question on the basis of a study of 414 whales and 22 newly developed microsatellite loci. We identified widespread departures from Hardy-Weinberg equilibrium; however, we were unable to detect significant evidence of multiple genetic populations within the WA bowheads that could explain this Hardy-Weinberg disequilibrium, particularly when compared to the strength of evidence for differentiation between WA bowheads and other populations from distant regions such as the Okhotsk Sea and eastern Canada. There was conclusive evidence of genetic differentiation among the three regions. The statistical rejection of panmixia within the WA improves our understanding of bowhead whale biology, and the lack of evidence for multiple populations within the WA enables risk-averse management of aboriginal hunting of Western Arctic bowhead whales.La population de baleines boréales (Balaena mysticetus) des mers de Béring, de Tchoukotka et de Beaufort a enregistré un grave déclin en raison de la pêche commerciale à la baleine au XIXe siècle. Depuis que la pêche commerciale à la baleine a cessé, la population de baleines boréales a connu un certain essor au point où elle approche maintenant les estimations de la taille qu’elle avait avant la pêche commerciale à la baleine. Les collectivités Inupiat et Yupik du nord et de l’ouest de l’Alaska chassent les baleines boréales de l’ouest de l’Arctique le long de leur voie de migration au printemps et à l’automne. La chasse est réglementée par l’International Whaling Commission. Des analyses récentes, bien que préliminaires, des données génétiques disponibles (207 baleines et 10 marqueurs microsatellites) ont soulevé la question de la présence de multiples populations génétiquement distinctes au sein de la population de baleines boréales de l’ouest de l’Alaska. Ici, nous avons réexaminé cette question en fonction de l’étude de 414 baleines et de 22 locis microsatellites nouvellement mis au point. Nous avons remarqué d’importantes déviations de l’équilibre de Hardy-Weinberg; toutefois, nous n’avons pas pu trouver de preuve significative de populations génétiques multiples au sein des baleines boréales de l’ouest de l’Alaska qui pourrait expliquer ce déséquilibre de Hardy-Weinberg, plus particulièrement en comparaison avec la force de la preuve de différenciation entre les baleines boréales de l’ouest de l’Arctique et d’autres populations de régions distantes telles que la mer d’Okhotsk et l’est du Canada. Il y avait des preuves concluantes de différenciation génétique entre les trois régions. Le rejet statistique de la panmixie au sein de l’ouest de l’Arctique améliore notre compréhension de la biologie des baleines boréales, et le manque de preuves de populations multiples dans l’ouest de l’Arctique donne lieu à la gestion de l’aversion au risque de la chasse à la baleine boréale de l’ouest de l’Arctique par les Autochtones

Evolutionary Toxicology: Population-Level Effects of Chronic Contaminant Exposure on the Marsh Frogs (Rana ridibunda) of Azerbaijan

We used molecular methods and population genetic analyses to study the effects of chronic contaminant exposure in marsh frogs from Sumgayit, Azerbaijan. Marsh frogs inhabiting wetlands in Sumgayit are exposed to complex mixtures of chemical contaminants, including petroleum products, pesticides, heavy metals, and many other industrial chemicals. Previous results documented elevated estimates of genetic damage in marsh frogs from the two most heavily contaminated sites. Based on mitochondrial DNA (mtDNA) control region sequence data, the Sumgayit region has reduced levels of genetic diversity, likely due to environmental degradation. The Sumgayit region also acts as an ecological sink, with levels of gene flow into the region exceeding gene flow out of the region. Additionally, localized mtDNA heteroplasmy and diversity patterns suggest that one of the most severely contaminated sites in Sumgayit is acting as a source of new mutations resulting from an increased mutation rate. This study provides an integrated method for assessing the cumulative population impacts of chronic contaminant exposure by studying both population genetic and evolutionary effects

Genotoxicity in Atlantic killifish (Fundulus heteroclitus) from a PAH-contaminated Superfund site on the Elizabeth River, Virginia

The Atlantic Wood Industries Superfund site (AWI) on the Elizabeth River in Portsmouth, VA is heavily contaminated with polycyclic aromatic hydrocarbons (PAHs) from a wood treatment facility. Atlantic killifish, or mummichog (Fundulus heteroclitus), at this Superfund site are exposed to very high concentrations of several carcinogens. In this study, we measured PAH concentrations in both fish tissues and sediments. Concurrently, we assessed different aspects of genotoxicity in the killifish exposed in situ. Both sediment and tissue PAH levels were significantly higher in AWI samples, relative to a reference site, but the chemistry profile was different between sediments and tissues. Killifish at AWI exhibited higher levels of DNA damage compared to reference fish, as measured via the flow cytometric method (FCM), and the damage was consistent with sediment PAH concentrations. Covalent binding of benzo[a]pyrene (BaP) metabolites to DNA, as measured via LC-MS/MS adduct detection methods, were also elevated and could be partially responsible for the DNA damage. Using similar LC-MS/MS methods, we found no evidence that oxidative DNA adducts had a role in observed genotoxicity

Enzymatic Activities and DNA Substrate Specificity of Mycobacterium tuberculosis DNA Helicase XPB

XPB, also known as ERCC3 and RAD25, is a 3′→5′ DNA repair helicase belonging to the superfamily 2 of helicases. XPB is an essential core subunit of the eukaryotic basal transcription factor complex TFIIH. It has two well-established functions: in the context of damaged DNA, XPB facilitates nucleotide excision repair by unwinding double stranded DNA (dsDNA) surrounding a DNA lesion; while in the context of actively transcribing genes, XPB facilitates initiation of RNA polymerase II transcription at gene promoters. Human and other eukaryotic XPB homologs are relatively well characterized compared to conserved homologs found in mycobacteria and archaea. However, more insight into the function of bacterial helicases is central to understanding the mechanism of DNA metabolism and pathogenesis in general. Here, we characterized Mycobacterium tuberculosis XPB (Mtb XPB), a 3′→5′ DNA helicase with DNA-dependent ATPase activity. Mtb XPB efficiently catalyzed DNA unwinding in the presence of significant excess of enzyme. The unwinding activity was fueled by ATP or dATP in the presence of Mg2+/Mn2+. Consistent with the 3′→5′ polarity of this bacterial XPB helicase, the enzyme required a DNA substrate with a 3′ overhang of 15 nucleotides or more. Although Mtb XPB efficiently unwound DNA model substrates with a 3′ DNA tail, it was not active on substrates containing a 3′ RNA tail. We also found that Mtb XPB efficiently catalyzed ATP-independent annealing of complementary DNA strands. These observations significantly enhance our understanding of the biological roles of Mtb XPB

Reconciling carbon-cycle concepts, terminology, and methods

Author Posting. © The Author(s), 2006. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Ecosystems 9 (2006): 1041-1050, doi:10.1007/s10021-005-0105-7.Recent patterns and projections of climatic change have focused increased scientific and public attention on patterns of carbon (C) cycling and its controls, particularly the factors that determine whether an ecosystem is a net source or sink of atmospheric CO2. Net ecosystem production (NEP), a central concept in C-cycling research, has been used to represent two different concepts by C-cycling scientists. We propose that NEP be restricted to just one of its two original definitions—the imbalance between gross primary production (GPP) and ecosystem respiration (ER), and that a new term—net ecosystem carbon balance (NECB)—be applied to the net rate of C accumulation in (or loss from; negative sign) ecosystems. NECB differs from NEP when C fluxes other than C fixation and respiration occur or when inorganic C enters or leaves in dissolved form. These fluxes include leaching loss or lateral transfer of C from the ecosystem; emission of volatile organic C, methane, and carbon monoxide; and soot and CO2 from fire. C fluxes in addition to NEP are particularly important determinants of NECB over long time scales. However, even over short time scales, they are important in ecosystems such as streams, estuaries, wetlands, and cities. Recent technological advances have led to a diversity of approaches to measuring C fluxes at different temporal and spatial scales. These approaches frequently capture different components of NEP or NECB and can therefore be compared across scales only by carefully specifying the fluxes included in the measurements. By explicitly identifying the fluxes that comprise NECB and other components of the C cycle, such as net ecosystem exchange (NEE) and net biome production (NBP), we provide a less ambiguous framework for understanding and communicating recent changes in the global C cycle. Key words: Net ecosystem production, net ecosystem carbon balance, gross primary production, ecosystem respiration, autotrophic respiration, heterotrophic respiration, net ecosystem exchange, net biome production, net primary production

Self-reported sex differences in high-functioning adults with autism: a meta-analysis

Background: Sex differences in autistic symptomatology are believed to contribute to the mis- and missed diagnosis of many girls and women with an autism spectrum condition (ASC). Whilst recent years have seen the emergence of clinical and empirical reports delineating the profile of young autistic girls, recognition of sex differences in symptomatology in adulthood is far more limited. Methods: We chose here to focus on symptomatology as reported using a screening instrument, the Ritvo Autism Asperger Diagnostic Scale-Revised (RAADS-R). In a meta-analysis, we pooled and analysed RAADS-R data from a number of experimental groups. Analysis of variance (ANOVA) searched for the presence of main effects of Sex and Diagnosis and for interactions between these factors in our sample of autistic and non-autistic adults. Results: In social relatedness and circumscribed interests, main effects of Diagnosis revealed that as expected, autistic adults reported significantly greater lifetime prevalence of symptoms in these domains; an effect of Sex, in circumscribed interests, also suggested that males generally reported more prevalent symptoms than females. An interaction of Sex and Diagnosis in language symptomatology revealed that a normative sex difference in language difficulties was attenuated in autism. An interaction of Sex and Diagnosis in the sensorimotor domain revealed the opposite picture: a lack of sex differences between typically-developing men and women and a greater prevalence of sensorimotor symptoms in autistic women than autistic men. Conclusions: We discuss the literature on childhood sex differences in relation to those which emerged in our adult sample. Where childhood sex differences fail to persist in adulthood, several interpretations exist, and we discuss, for example, an inherent sampling bias that may mean that only autistic women most similar to the male presentation are diagnosed. The finding that sensorimotor symptomatology is more highly reported by autistic women is a finding requiring objective confirmation, given its potential importance in diagnosis

Cortical Mechanics and Meiosis II Completion in Mammalian Oocytes Are Mediated by Myosin-II and Ezrin-Radixin-Moesin (ERM) Proteins

Analysis of mouse oocyte mechanics shows that effective tension drops 6-fold from prophase I to metaphase II; the metaphase II egg has a 2.5-fold tension differential between the cortex over the spindle and the opposite cortex. Manipulation of actin, myosin-II, or ERMs alters tension levels and induces spindle abnormalities during meiosis II

Evolutionary toxicology : meta-analysis of evolutionary events in response to chemical stressors

The regulatory decision-making process regarding chemical safety is most often informed by evidence based on ecotoxicity tests that consider growth, reproduction and survival as end-points, which can be quantitatively linked to short-term population outcomes. Changes in these end-points resulting from chemical exposure can cause alterations in micro-evolutionary forces (mutation, drift, selection and gene flow) that control the genetic composition of populations. With multi-generation exposures, anthropogenic contamination can lead to a population with an altered genetic composition, which may respond differently to future stressors. These evolutionary changes are rarely discussed in regulatory or risk assessment frameworks, but the growing body of literature that documents their existence suggests that these important population-level impacts should be considered. In this meta-analysis we have compared existing contamination levels of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) that have been documented to be associated with evolutionary changes in resident aquatic organisms to regulatory benchmarks for these contaminants. The original intent of this project was to perform a meta-analysis on evolutionary events associated with PCB and PAH contamination. However, this effort was hindered by a lack of consistency in congener selection for "total" PCB or PAH measurements. We expanded this manuscript to include a discussion of methods used to determine PCB and PAH total contamination in addition to comparing regulatory guidelines and contamination that has caused evolutionary effects. Micro-evolutionary responses often lead populations onto unique and unpredictable trajectories. Therefore, to better understand the risk of population-wide alterations occurring, we need to improve comparisons of chemical contamination between affected locations. In this manuscript we offer several possibilities to unify chemical comparisons for PCBs and PAHs that would improve comparability among evolutionary toxicology investigations, and with regulatory guidelines. In addition, we identify studies documenting evolutionary change in the presence of PCB and PAH contamination levels below applicable regulatory benchmarks