Bacterial database

TIGR Bacterial database(s) of The Institute of Genome Research (TIGR)... 

Other pattern recognition strategies have been used for bacterial identification and data interpretation from mass spectra. Bright et al. have recently developed a software product called MUSE, capable of rapidly speciating bacteria based on matrix-assisted laser desorption ionization time-of-flight mass spectra.13 MUSE constructs a spectral database of representative microbial samples by using single point vectors to consolidate spectra of similar (not identical) microbial strains. Sample unknowns are then compared to this database and MUSE determines the best matches for identification purposes. In a... 

Wang, Z. Dunlop, K. Long, S. R. Li, L. Mass spectrometric methods for generation of protein mass database used for bacterial identification. Anal. Chem. 2002, 74,3174-3182. 

Bacterial proteins from MALDI FTMS experiments are identifiable using the Swiss-Prot database.53 In order to identify any microorganism, it is neces-... 

Dare, D. I Sutton, H. E. Keys, C. J. Shah, H. N. Wells, G. McDowall, M. A. Optimisation of a database for rapid identification of intact bacterial cells of Escherichia coli by matrix-assisted desorption ionization time-of-flight mass spectrometry, Proc. 51st ASMS Conference, Montreal, Quebec, Canada, June 8-12, 2003. 

Variations on the spectral peaks from different species of the same genus were also observed. Three species of Pseudomonas produced the spectra shown in Figure 14.2. These spectra are clearly unique and were used to correctly identify unknown samples. Because of peak ratio reproducibility issues in bacterial protein profiles obtained by MALDI MS,11 a fingerprint approach that had been used for other mass spectrometry approaches has not been used. The profile reproducibility problem was first recognized by Reilly et al.12,13 and later researched by others in the field.14,15 As a later alternative, a direct comparison of the mass-to-charge ratio (m/z) of the unknown mass spectral peaks with a database of known protein masses has been used to identify unknown samples.14... 

For PyMS to be used for (1) routine identification of microorganisms and (2) in combination with ANNs for quantitative microbiological applications, new spectra must be comparable with those previously collected and held in a data base.127 Recent work within our laboratory has demonstrated that this problem may be overcome by the use of ANNs to correct for instrumental drift. By calibrating with standards common to both data sets, ANN models created using previously collected data gave accurate estimates of determi-nand concentrations, or bacterial identities, from newly acquired spectra.127 In this approach calibration samples were included in each of the two runs, and ANNs were set up in which the inputs were the 150 new calibration masses while the outputs were the 150 old calibration masses. These associative nets could then by used to transform data acquired on that one day to data acquired at an earlier data. For the first time PyMS was used to acquire spectra that were comparable with those previously collected and held in a database. In a further study this neural network transformation procedure was extended to allow comparison between spectra, previously collected on one machine, with spectra later collected on a different machine 129 thus calibration transfer by ANNs was affected. Wilkes and colleagues130 have also used this strategy to compensate for differences in culture conditions to construct robust microbial mass spectral databases. 

Soares-Weiser K, Brezis M, Leibovici L Antibiotics for spontaneous bacterial peritonitis in cirrhotics. Cochrane Database Syst Rev 2001 3 CD002232. 

McDonald H, Brocklehurst P, Parsons J, Vig-neswaran R Antibiotics for treating bacterial vaginosis in pregnancy. Cochrane Database Syst Rev 2003 2 CD000262. 

An extensive database has demonstrated that many chemicals that are positive in this test also exhibit mutagenic activity in other tests. There are, however, examples of mutagenic substances, which are not detected by this test reasons for these shortcomings can be ascribed to the specific nature of the endpoint detected, differences in metabolic activation, or differences in bioavailability. On the other hand, factors which enhance the sensitivity of the bacterial reverse mutation test can lead to an overestimation of mutagenic activity. The bacterial reverse mutation test may not be appropriate for the evaluation of certain classes of chemicals for example, highly bactericidal compounds (e.g., certain antibiotics) and those which are thought (or known) to interfere specifically with the mammalian cell replication system (e.g., some topoisomerase inhibitors and some nucleoside analogues). In such cases, mammalian mutation tests may be more appropriate. 

Positive results from the bacterial DNA damage or repair tests indicate that the test substance causes DNA damage, which is expressed as differential cell killing or growth inhibition of repair deficient bacteria. The DNA damage tests do not measure DNA repair per se nor do they measure mutations. A positive result in a DNA damage test in the absence of a positive result in another system is difficult to evaluate in the absence of a better database. 

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