Sensitivity of US Gulf of Mexico coastal marsh vegetation to crude oil: Comparison of greenhouse and field responses

Greenhouse and field studies were conducted to evaluate the effect of crude oil on selected US Gulf of Mexico coastal marsh species. Species showed different levels of sensitivity to oiling between greenhouse and field conditions. In greenhouse studies, two crude oils were used: South Louisiana crude oil (SLC) and Arabian Medium crude oil (AMC). The majority of Spartina patens plants died within one month following oiling with little or no recovery after three months. Panicum hemitomon and Spartina alterniflora were also adversely affected by oiling under greenhouse conditions but to a lesser extent than S. patens. The SLC or AMC oiling led to biomass reductions in S. alterniflora and S. patens. The dry biomass was not affected by oiling in P. hemitomon, Sagittaria lancifolia, Typha latifolia, and Scirpus olneyi. Results showed that S. patens plants were more sensitive to SLC as compared to AMC oil. Gross CO₂-C fixation data collected in the greenhouse indicated no differences in recovery among species across oiling treatments for S. lancifolia, S. olneyi, and T. latifolia. Field studies with S. alterniflora, S. patens and S. lancifolia demonstrated initial sensitivity of these species to oiling, and recovery following oiling with SLC. Our data also showed that caution must be employed whenever results from greenhouse studies are extrapolated to predict oil impact on vegetation under field conditions. Development of any sensitivity index of plant responses to oiling should not be based on greenhouse experiments only. Field evaluations should be included which best depict plant responses to oiling. Thus, restoration measures of US Gulf of Mexico coastal marshes following oiling should rely primarily on field studies. The field research suggests that the US Gulf of Mexico coastal marsh vegetation are likely to recover from oil spills naturally without the need for remediation procedures.     

Identification of a common gene expression response in different lung inflammatory diseases in rodents and macaques

To identify gene expression responses common to multiple pulmonary diseases we collected microarray data for acute lung inflammation models from 12 studies and used these in a meta-analysis. The data used include exposures to air pollutants; bacterial, viral, and parasitic infections; and allergic asthma models. Hierarchical clustering revealed a cluster of 383 up-regulated genes with a common response. This cluster contained five subsets, each characterized by more specific functions such as inflammatory response, interferon-induced genes, immune signaling, or cell proliferation. Of these subsets, the inflammatory response was common to all models, interferon-induced responses were more pronounced in bacterial and viral models, and a cell division response was more prominent in parasitic and allergic models. A common cluster containing 157 moderately down-regulated genes was associated with the effects of tissue damage. Responses to influenza in macaques were weaker than in mice, reflecting differences in the degree of lung inflammation and/or virus replication. The existence of a common cluster shows that in vivo lung inflammation in response to various pathogens or exposures proceeds through shared molecular mechanisms.     

Smokers and passive smokers gene expression profiles: correlation with the DNA oxidation damage

Healthy volunteers (n=50) were enrolled for studying the variation of gene expression induced by smoking in peripheral lymphocytes. RNAs from smokers (>3 cigarettes/day, n=20) and passive smokers (exposed to tobacco smoke >3 h/day, n=10) were hybridized versus a reference pool obtained by mixing equal amounts of RNA from 20 nonsmokers, and gene expression was analyzed using DNA microarrays containing 13,971 oligos. Principal component analysis showed that 99.7% of gene expression variability was related to plasma cotinine, age, and DNA oxidation damage. SAM and GenMAPP/MAPPFinder analyses showed that smokers, compared to nonsmokers, had 129 down-regulated and 87 up-regulated genes, whereas passive smokers, compared to nonsmokers, had 44 down-regulated and 159 up-regulated genes, mainly involved in pathways associated with the activation of defensive responses. Hierarchical cluster analysis identified two distinct clusters of smokers, characterized by different oxidative DNA damage: smokers with high DNA oxidation damage, compared to smokers with low DNA oxidation damage, had a large number (150) of down-regulated genes, mainly associated with xenobiotic metabolism, DNA damage and repair, inflammatory responses, lymphocyte activation, and cytokine activity, suggesting a reduced cellular response to toxic agents in this subset of smokers that could lead to an increased DNA oxidation damage.     

Osmoregulation-dependent expression of Yersinia enterocolitica virulence factors.

The effects of hyperosmotic stress on expression of plasmid coded Yop and Yad A proteins--virulence factors of Y.enterocolitica serotype 0:9 were characterized. When cells were shifted to high osmolarity and cultured at 37 degrees C in medium without Ca2+ the production of Yops was inhibited. In contrast, the amount of Yad A protein was unaffected. Addition of glycine betaine to this culture alleviated the effect of high osmolarity. It was also found that hyperosmotic stress causes increased negative supercoiling of DNA in Y. enterocolitica 0:9. Changes in DNA supercoiling coincided with expression of Yop proteins. These results suggest that in high osmolarity the expression of yop genes may be regulated by DNA supercoiling.     

Exposure to ultraviolet radiation (290-400 nm) causes oxidative stress, DNA damage, and expression of p53/p73 in laboratory experiments on embryos of the spotted salamander, Ambystoma maculatum

Developing embryos of the spotted salamander, Ambystoma maculatum, exposed to ultraviolet radiation (UVR; 290-400 nm) in the laboratory show a significant sensitivity to UVB (290-320 nm) radiation. Embryos in laboratory experiments exhibited significant DNA damage during exposures to UVR despite a significant increase in the production of the protective pigment melanin in response to UVR exposure. DNA damage occurs as a result of both the direct effects of exposure to UVR, and the indirect effects are mediated by the production of reduced oxygen intermediates. The production of reactive oxygen species initiates the expression of p53/p73 that leads to either DNA repair or apoptosis. When similar experiments are conducted on salamander embryos exposed to solar UVR in vernal pools, the embryos show significantly less sensitivity and higher survivorship. The differences between laboratory and field experiments are a result of the attenuation of UVR caused by the accumulation of dissolved organic carbon within the pools of these wooded areas. These findings suggest that northeastern populations of spotted salamanders are sensitive to UVR but are not significantly affected by present-day irradiances of UVR in the field. These results do suggest that continued decreases in stratospheric ozone over temperate latitudes have the potential to affect spotted salamanders in their natural habitats.     

Studying stress responses in the post-genomic era: its ecological and evolutionary role

Most investigations on the effects of and responses to stress exposures have been performed on a limited number of model organisms in the laboratory. Here much progress has been made in terms of identifying and describing beneficial and detrimental effects of stress, responses to stress and the mechanisms behind stress tolerance. However, to gain further understanding of which genes are involved in stress resistance and how the responses are regulated from an ecological and evolutionary perspective there is a need to combine studies on multiple levels of biological organization from DNA to phenotypes. Furthermore, we emphasize the importance of studying ecologically relevant traits and natural or semi-natural conditions to verify whether the results obtained are representative of the ecological and evolutionary processes in the field. Here, we will review what we currently know about thermal adaptation and the role of different stress responses to thermal challenges in insects, particularly Drosophila. Furthermore, we address some key questions that require future attention.     

Responses of hyperthermophilic crenarchaea to UV irradiation

Background  

DNA damage leads to cellular responses that include the increased expression of DNA repair genes, repression of DNA replication and alterations in cellular metabolism. Archaeal information processing pathways resemble those in eukaryotes, but archaeal damage response pathways remain poorly understood.     

Cancer pharmacogenomics: role of DNA repair genetic polymorphisms in individualizing cancer therapy

The evolving field of cancer pharmacogenomics uses genetic profiling to predict the response of tumor and normal tissue to therapy. The narrow therapeutic index and heterogeneity of patient responses to chemotherapy and radiotherapy implies that the efficacy of these treatments could, potentially, be significantly enhanced by improving our understanding of the genetic bases for interindividual differences in their effects. The cytotoxicity of both chemotherapy and radiotherapy is to a large extent directly related to their ability to induce DNA damage. The ability of cancer cells to recognize and repair this damage contributes to therapeutic resistance. On the other hand, suboptimal DNA repair in normal tissue may negatively impact on normal tissue tolerance.More than 130 genes have been identified that are associated with human DNA repair, and single nucleotide polymorphisms of several of the DNA repair genes have been described recently. In this article, we present the current evidence implicating variations within DNA repair genes as important predictive and prognostic markers in cancer. We review evidence suggesting DNA repair genetic polymorphisms may significantly influence the clinical response to chemotherapy and radiotherapy, and may influence normal tissue tolerance to cancer treatments.