Chemotaxonomic identification

Multiply charged proteins can also be partially sequenced, and microsequences of proteins isolated from several microorganisms have been reported, accomplished with electrospray ionization and FTMS.23,90 Nonadjacent fragment ions may be used to identify bacterial proteins in these top-down strategies.91 In all cases these sequences could be related by bioinformatics to the parent species. An obvious extension would be to characterize proteins from intact microorganisms in this way. In at least one instance a microsequence has been obtained from a protein released from a contaminated intact bacteriophage sample (MS2) to provide a chemotaxonomic identification.77 This work was carried out in an ion trap mass spectrometer. 

B. asahinai, B. germanica, and B. vaga. The same authors performed chemotaxonomic identification of different Blattella cockroaches in Taiwan and various Pacific Basin locations (Brenner et al 1993). 

Brenner, R. J., Carlson, D. A., Rothe, L.M. and Paterson, R. S. (1993). Morphological and chemotaxonomic identification ofBlatella cockroaches (Blattaria Blattellidae) from Taiwan and selected Pacific basin locations. Invertebrate taxonomy, 7, 1205-1219. 

Rosch P Harz M, Schmitt M, Peschke KD, Ronnebeiger O, Burkhardt H, Motzkus HW, Lankers M, Hofer S, Thiele H, Popp J. Chemotaxonomic identification of single bacteria by micro-Raman spectroscopy application to clean-room-relevant biological contaminations. Appl Environ Microbiol. 2005 71(3) 1626-37... 

B. anthracis and related species.41,44 6 Some of these peaks have been identified (e.g., as small acid soluble spore proteins and cyclic lipopeptides), but others remain uncharacterized. There is no agreement among different laboratories as to which markers are suitable for chemotaxonomic differentiata-tion of species (i.e., are consistently found in one species versus another) or for strain identification (i.e., are reproducibly found in one strain but not another). Further, although it might be anticipated that surface proteins can be preferentially ionized or extracted, the ultra-structural origin of some peptides within the cell is not always clear. 

The present chapter does not consider analysis of extracted protein biomarkers but rather focuses on strategies for rapid chemotaxonomic analysis of intact microorganisms with automated sample manipulation. Rapid means less than 5 minutes. Advantages of the application of bioinformatics and proteomics strategies for rapid identification of microorganisms include the following ... 

As noted with the chemotaxonomic studies, the limited resolving power and mass accuracy of MALDI-TOF complicates identification of unknown proteins. If the greatly improved resolving power and accuracy of MALDI-FTMS can be used to monitor overexpressed proteins, it could have significant advantages. Figure 13.12 is a MALDI-FTMS spectrum of E. coli whole cells that have been genetically altered to produce the soluble core domain mammalian cytochrome b5 protein, which consists of 98 amino acids. 

Chao, J. and Der Marderosian, A.H. (1973) Identification of ergoline alkaloids in the genus Argyreia and related genera and their chemotaxonomic implications in the Convolvulaceae. Phytochemistry, 12, 2435-2440. 

McDaniel, C.A., Howard, R. W., Blomquist, G. J. and Collins, A.M. (1984). Hydrocarbons of the cuticle, sting apparatus, and sting shaft of Apis mellifera L. Identification and preliminary evaluation as chemotaxonomic characters. Sociobiology, 8, 287-298. 

A number of Aspergillus spp. have been submitted to a chemical screening, pointing to the identification of possible chemotaxonomic indicators [43], The results indicated that A. campestris and A. taichungensis, producing both 7 and 13, should be placed in section Candidi. 

Monomethyl and dimethylalkanes in the range C16-C20 are prominent in many cultured cyanobacteria as well as most cyanobacterial mat communities that have been studied (Section 8.03.5.3). No specific physiological role has been assigned to these hydrocarbons. Because they have probably multiple origins in ancient sediments and petroleum, these monomethyl and dimethylalkanes alone probably have limited chemotaxonomic specificity. However, they may be very useful in multivariate approaches for linking isotopic and molecular-structure data for a less ambiguous identification of sedimentary cyanobacterial lipids. 

Three new diastereomers of 3-hexyl-5-methylindolizidine, (5Z,9Z)-, (5E,9E)- and (5Z,9 ), Fig. (8), were identified in different collections of thief ants Solenopsis (Diplorhoptrum) species from Cahfomia. The identification of these alkaloids resulted from the analysis of their MS spectra and comparison of their GC-FTIR spectra. The authors also emphasised the chemotaxonomic value of the stereochemistry of these alkaloids [23]. 

Thirty-three known iridoid and secoiridoid glucosides have been analysed by gas chromatography of their trimethylsilyl derivatives. G.c.-m.s. analysis of several representative compounds e.g. 4-CO2H, 4-C02Me, 4-unsubstituted) demonstrated the feasibility of iridoid-containing plant extract analysis and resulted in the identification of secologanoside 11-methyl ester (99 R = H, X = CH2) from Lonicera morrowii the sixth paper in a series of chemotaxonomic studies on iridoids illustrates the need for accurate analysis of minor components. ... 

The early chemotaxonomic studies of Erdtman (1952) showed that the heartwood of pines contained flavonoid (Ce-Cs-Ce) and stilbene (C6-C2-Ce) compounds, which could aid species identification. Although the two sections of the pine genus, Haploxylon and Diploxylon, both contain the stilbenes pinosylvin and pinosylvin monomethyl ether, the groups can be distinguished since the Diploxylon group (pines with two or three needles per cluster) contains only flavanones whereas... 

The isolation and identification of germacrane lactones from a host of plant sources is an area of continuing interest particularly in the laboratories of Professors Herz and Bohlmann. The search for biologically active compounds and the chemotaxonomic classification of plant species are the two major driving forces for this research. The sub-division of these lactones into germacranolides (479)—... 

For species characterization, whole-cell and extracellular proteins (CUnk and Pennington 1987 Berber et al. 2(X)3) or cellular fatty acid analysis and/or combined with gas chromatography may be applied. In general, fatty acid profiles correlate with the data on DNA homology and phenotype features (Behme et al. 1996). Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDl-TOF MS) was experimentally applied to intact bacterial cells or specimens prepared nsing extraction procedures. This chemotaxonomic method was used for identification of the staphylococcal species and MRSA strains (Du et al. 2(X)2 Carbonnelle et al. 2007). 

Several strategies and philosophies are available for the identification of bioactive compounds from natural sources. Different aspects of these strategies have been reviewed [44-47]. Several such approaches have been used previously for this purpose 1) ethnobotany, 2) serendipity, 3) random sampling, and 4) exploitation of chemotaxonomic knowledge. 

Source indicators-As source indicators, molecular markers are applied either qualitatively (source identification) or quantitatively (source apportionment). The requirements for quantitative source apportionment are considerably more stringent and the number of examples in the literature is fewer than for source identification (e.g. Schauer et al., 1996 Eganhouse and Sherblom, 2001 Takada et al., 1997). Specific biogenic markers have been used for chemotaxonomic purposes (Kates, 1997) and to characterize the composition of benthic and pelagic communities present in aquatic ecosystems (Findlay and Watling, 1997). Many fossil biomarkers have served as indicators of organic matter provenance (Peters and Moldowan, 1993) or for paleoclimate reconstruction (Brassel et al., 1986). Biomarkers are also used frequently to identify sources of fossil fuel contamination in the contemporary environment (Kaplan et al., 1997 Volkman et al., 1997). Finally, there are numerous studies in which molecular markers associated with municipal wastes, urban mnoff, or combustion of fossil fuels have been used to infer the effect of various point and non-point sources of contamination (see references in Takada and Eganhouse, 1998). 

PA is the most abimdant saturated fatty acid found in most animal products, for example meat. Palmitic acid has been reported to account for approximately 27% of the saturated fatty acid content of beef (Whetsell et al., 2003). PA occurrences in animal s tissues are likely to be influence by environmental and nutritional factors. This imique feature makes PA an essential chemotaxonomic tool for identification of species of animals and poultry and even plant related species. 

This paper described the chemotaxonomy characteristics of two C2o-diterpenoid alkaloids and five C 19-diterpenoid alkaloids from Delphinium albocoeruleum Maxim of Chinese origin. The study indicated that the compound delelatine may be considered as a chemotaxonomic marker for the Delphinium genus as it occurs in Delphinium elatum. Delphinium barbeyi, D. tatsinenense [66], and Delphinium giraldii [67], Delphinine, a major compound, may possibly be utihzed for identification of D. albocoeruleum Maxim. 

Classification and identification of microorganisms based on rapid and specific methods for determining the chemical composition have proved to be a valuable approach in microbiology. The identification of many chemical constituents that show a degree of specificity suitable for chemotaxonomic and/or diagnostic purposes made it clear that improvements in methods of sample preparation play an important role in fully utilizing the high speed and specificity offered by MS. 

For the application of both culture-dependent and culture-independent approaches, molecular, phenotypic, and chemotaxonomic data have allowed researchers the unequivocal identification of AAB from many varieties of traditional and industrial vinegar niches (SF and SC acetifications) as well as the classification of new isolates (Cleenwerck and de Vos 2008 Yamada and Yukphan 2008 De Veto et al. 2006 Gullo et al. 2009). 

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