CITE seminar series
CITE - Chemicals In the Environment - is a research topic within the Helmholtz programm oriented funding. CITE addresses multiple aspects of the impact of chemicals in the environment. We aim to have a monthly regular seminar series addressing issues related to our activities.
01.11.2012, 3 p.m., Building 1, 1st floor, lecture hall (left)
Prof. Antonia Concetta Elia
University of Perugia, Department of Cellular and Environmental Biology, Italy
Biomarkers for contaminant-mediated oxidative stress in freshwater organisms: an overview of field and laboratory studies
Balance between prooxidants and antioxidants is extremely important for biological functions. Oxidative stress results when the antioxidant defenses are overcome by prooxidant forces, and reactive oxygen species (ROS) are not adequately removed. Antioxidant, enzymatic and non enzymatic systems are biomarkers for contaminant-mediated oxidative stress and can also indicate the magnitude of response in organisms exposed to contaminants. Heavy metals, organochlorine and organophosphate pesticides, polychlorinated biphenyls, antibiotics and additives in diets fed in aquaculture play important roles in the mechanistic aspects of oxidative damage. The role of the antioxidant systems and their sensitivity in freshwater organisms can be of great importance in environmental toxicology studies.
In this presentation we expose our current knowledge and advancement in the understanding of oxidative processes in freshwater organisms caused by the contaminants listed above, and specific applications carried out in field and laboratory studies will be presented. For example, oxidative stress biomarkers in aquatic organisms can also be applied to evaluate the human healthiness of several disinfectants employed to make drinkable superficial water. Moreover, we will introduce some target species and tissues of aquatic pollution and show that their biochemical antioxidant alterations can provide useful information for the implementation of biomarker-based monitoring programs in freshwater biotopes. Furthermore, a multiple biomarker approach is recommended as an integrated tool to evaluate different short and long-term toxic effects of aquatic contaminants.
Host: Stefan Scholz (BIOTOX)
23.11.2012, 10 a.m., Building 1, 1st floor, lecture hall (left)
Prof. Takaaki Nishioka
Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
Sharing Mass Spectra in Research Community on MassBank
MassBank is a public repository of mass spectrometry (MS) data of endogenous and exogenous small molecules in cells and biological systems. A total of 25 research groups (17 Japan, 4 EU, 2 USA, 1 Switzerland and China groups) deposit 31,153 data (August 2012). Among the data, about eight thousands ESI-MS/MS data are of high mass accuracy analyzed on hybrid-tandem MSs. MassBank project manually annotated the molecular formula to product ions in these data. It provides such highly precise peak data not only by the conventional numerical m/z but also by the molecular formula. The latter data, “chemically exact” data, are useful to analyze the relationships between product ions and chemical substructures.
On the other, some users are afraid of the quality of MS data on the public repository. MassBank project carefully searches and deletes the data poor in the quality. However, users could easily find such poor data, if any. Different laboratories deposit more than five ESI-MS/MS data for each chemical compound on average. By comparing all the data of an identical chemical compound on a viewer, users could find MS data poor in the quality as those of unlike to the others.
Another feature of MassBank is a distributed database. Contributors prepare their data in the common record format and make the formatted data open to the public from their own local data servers distributed on the internet. Thus by a part of their research expenses, the contributors share most of the cost that should be necessary to manage MassBank if this is a centralized database. Currently 10 data servers are distributed on the internet. Researchers of a small data set contribute from either one of 10 data servers. In the distributed database, its users obtain search results in a shorter time because the data are searched in parallel on all the data servers. This is suitable for a large data sets such as MS data of unknowns. However, the time necessary to obtain search results might be longer by the data servers of a poor CPU. Additionally search results would be affected when a data server might be occasionally unavailable.
Other topics including a batch spectral search, a API service connected to KEGG PATHWAY API, consensus reference MS data, and “Bio-MassBank” that is a public repository of MS data of unknown and unidentified chemical compounds will be reported in the lecture.
Host: Tobias Schulze (WANA)