Environmental bioinformatics

Figure 6.1 Evolving compendium of computational tools, databases, and literature information that make up the environmental bioinformatics Knowledge Base (ebKB).

The views presented in this article do not necessarily reflect those of the US Food and Drug Administration. Support for this work has been provided partially by the USEPA-funded Environmental Bioinformatics and Computational Toxicology Center (ebCTC), under STAR Grant number GAD R 832721-010. This work has not been reviewed by and does not represent the opinions of the funding agency. 

Panos G. Georgopoulos, Department of Environmental and Occupational Medicine Environmental and Occupational Health Sciences Institute, UMDNJ-RWJMS and Rutgers, the State University of New Jersey Environmental Bioinformatics and Computational Toxicology Center (ebCTC), Piscataway, NJ 08854, USA. 

The good programming practices described here reflect experience of the authors at the USEPA funded Center for Exposure and Risk Modeling (CERM), and the environmental bioinformatics and Computational Toxicology Center (ebCTC). 

Physiomics section of the Environmental Bioinformatics KnowledgeBase (ebKB ... 

Knudsen, T. B. (2008). The Virtual Embryo Project. In Environmental Bioinformatics Computational... 

Another application of bioinformatics is the use of pharmacogenomics. There are some diseases, such as sickle cell anemia (Exhibit 2.3), in which the difference of one amino acid group can have drastic consequences. These differences in nucleotides are termed single nucleotide polymorphisms (SNPs). SNPs, whether due to genetic origins or environmental factors, translate to individual differences. By understanding these SNPs using bioinformatics, more individualized medicines with better efficacy and less adverse effects can be prescribed. 

What can be done if there is not an exact literature precedent for the required enzymatic transformation In these cases some sort of screening procedure may be necessary, either by direct screening of commercial enzymes, culture collections and environmental isolates, or by using a bioinformatics-based approach to identify potential enzymes based on sequence information. 

The measurement and interpretation of expression levels of genes and proteins is at the center of today s attention in genomics, proteomics, and bioinformatics. The goal is to create a detailed differential functional picture of the cell s inner workings, as it is determined by the cell state at hand. Cell states can be influenced and determined by external environmental factors (temperature, pH, chemical stress factors), and by internal factors such as the cell belonging to a special tissue or be in a certain disease state. 

Li Y, Wang T, Xin J, Du X (2011) 5th hitemational conference on bioinformatics and biomedical engineering (iCBBE). Research Academy of Energy Environmental Studies, North China Electronics Power University, Beijing, China, pp 1-4... 

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