STATE OF THE ART TAXONOMIC DATABASES – hierarchical and sequence based

Overview:

A database is defined as a structured collection of data which is managed to meet the needs of a community of users.

Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high throughput experiment technology, and computational analyses. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics.

Conventional taxonomic databases are databases consisting of scientific and common names for species of taxa from all biological kingdoms

Modern Taxonomic database is hierarchical and sequence-based, aiming to centralize the classification of all organisms represented in the databases with at least one nucleotide or protein sequence.


Phylogenetic Principles:

Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, hybridize together, or terminate by extinction.

The problem posed by phylogenetics is that genetic data are only available for the present, and fossil records (osteometric data) are sporadic and less reliable and our knowledge of how evolution operates is used to reconstruct the full tree.


Various other efforts exist at different places and different portals to create a taxonomy resource, such as:

NEWT
NCBI taxonomy browser
The Tree of Life project
Species 2000
International Organization for Plant Information
Integrated Taxonomic Information System to reconstruct the full tree.

Biosurfactants

Pseudomonas aeruginosa is a Gram-negative organism ubiquitously available in both soil and water is referred notoriously as opportunistic pathogen, because of its capability of causing diseases such as: infections, cancers, cystic fibrosis and acute pneumonia by taking the advantage of well equipped target disruption mechanisms (Favre-Bonté, 2007). It establishes infection by producing remarkable group of virulent products that may be cell associated or even extracellular. However, these virulent products are regulated by a complex and interlinked quorum sensing systems (genes), that seems to be responsible for other metabolisms at the same time. Besides, this kind of advanced communication helps the bacteria to proceed in a much organized regulatory patterns of gene expression, which is actually believed to give the bacteria a discerning advantage over the defense mechanisms of the host (Smith and Iglewski, 2003).

References:


Rahman, K.S.M., Rahman, T.J., McClean, S., Marchant, R., and Banat, I.M. (2002). Rhamnolipid biosurfactants production by strains of Pseudomonas aeruginosa using low cost raw materials. Biotechnol. Prog. 18, 277-281.

Rahman, K.S.M., Vasudevan, N., and Lakshmanaperumalsamy, P. (1999). Enhancement of biosurfactant production to emulsify different hydrocarbons, J. Environ. Poll. 6, 87-93.

Moran, A.C., Olivera, N., Commendatore, M., Esteves, J.L. and Sineriz, F. (2000). Enhancement of hydrocarbon waste biodegradation by addition of a biosurfactant from Bacillus subtilis O9. Biodegradation. 11, 65-71.

Maneerat. S., (2005). Production of biosurfactants using substrates from renewable-resources. J. Sci. Technol. 27, 675-683.

Mukherjee, S., Das, P., and Sen, R. (2006). Towards the commercial production of microbial surfactants. Trends Biotechnol. 24, 509-515.

Oliveira, F.J.S., Vazquez, L., de Campos, N.P., and de Franca, F.P. (2009). Production of rhamnolipids by a Pseudomonas alcaligenes strain. Process Biochem. 44, 383-389.

Favre-Bonté,S. (2007). Autoinducer production and quorum-sensing dependent phenotypes of Pseudomonas aeruginosa vary according to isolation site during colonization of intubated patients. BMC Microbiology 7(33), 1-12.

Smith, R. S., and Iglewski, B.H. (2003). Pseudomonas aeruginosa quorum sensing as a potential antimicrobial target. J. Clin. Invest. 112,1460–1465.