Top-down strategy

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. 

Tandem mass spectrometry (see Chapter 3) can be applied to structural studies of various types of compounds, provided their molecular weights do not exceed approximately 2 to 4 kDa (there are also ways to analyze the sequence of larger molecules (proteins) by MS in the top-down strategy—see Figs. 6.2 and 6.3). In general, the larger... 

As such, the top-down strategy is a tool to recognize errors in the DNA-derived sequence, to identify (post-translational) modifications, or to evaluate modifications among complementary sets of the protein, e.g., in order to confirm the identity of a recombinant product. Further study with digestion and/or MS-MS then lows identification of the modification and its locatioa... 

The top-down strategy avoids a disadvantage of the bottom-up strategy in principle, it verifies the complete DNA-predicted sequence of the protein, as both the intact proteins and the sum of the fragments are measured. 

Fig. 1 Bottom-up and top-down strategies for analyzing proteomic samples. A description of these two processes can be found in Sect. 2. 2-DE two dimensional electrophoresis, n-D-LC multidimensional liquid chromatography, PMF Peptide mass fingerprinting, PTM Post-transla-tional modification, db database. Adapted with permission from Schliiter et al. [21]...

Most restriction mapping can be carried out using a top-down strategy that preserves an overview of the target and that reaches a nearly complete map relatively quickly. 

Divisive clustering represents a top-down strategy. It starts with one, all-object-inclusive cluster and splits the cluster until either each object forms its own cluster or a certain termination condition is reached. 

This objective is best approached using a top-down strategy, because the mass of the intact protein is an important constraint in the database searches, and can define mutations and modifications. Top-down protein analysis has been successfully carried out on all tandem high-resolution analyzers, and with both MALDl and ESI. 

A highly structured top-down strategy for applying folding and unfolding, guided by a recursion schema provided by the specifier, is proposed by [Lau 89] [Lau and Prestwich 90, 91]. This approach is amenable to mechanization. 

Arias, T. B. C., Avgeriou, P, America, P, Blom, K. Bachynskyyc, S. (2011). A top-down strategy to reverse architecting execution views for a large and complex software-intensive system An experience report. Science of Computer Programming 76(12) 1098-1112. 

Two top-down strategies have been developed for the production of pSi. The most widely used strategy is electrochemical etch, while the other approach, stain etch, is rarely used in practice due to its severe lack of flexibility [19]. The most widely employed top-down approach produces pSi through electrochemical etch of a bulk siUcon wafer. The pSi can then be oxidized to take advantage of silane chemistry. Alternatively, its surface can be carbon-terminated to obtain a hydrophilic chemically stable interface [20]. 

The persistent difficulties we have in the planned approaches to protein design point towards an intrinsic problem. At its root is the strong context dependence of the building blocks nature - and we - assemble. Rational approaches may be described as top down strategies the idea of what is to be achieved comes first only then do we attempt to find ways to arrive at the specified goal. Nature s approach is best described as bottom up - random variations are fixed in populations if they provide a selective advantage. Here the combinatorial complexity of context dependent variations is an advantage. It provides the raw material for evolution. 

Thus, our methodological approach builds on the theoretical developments of ethnographical and historical accounts of engineering cultures. Following Downey and Lucena (2004), we consider engineering educators not as passive agents that react to external social influences or to institutional top-down strategies. Instead,... 

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