Profiling experiments

As in the other -omics, analyses may be directed at a specific metabolite, at all metabolites in a given system in a shot-gun approach, or at accessible groups of molecules in profiling experiments. In that also the technology varies. In addition, the chemistry of different metabolites is very heterogeneous since it involves hydrophobic lipids, hydrophilic carbohydrates, ionic inorganic species, and other secondary natural products and already the choice of solvent in metabolite extraction dictates which types of molecules will be present (Fig. 10.8). Therefore, total metabolome profiling is not possible, because no analytical method will be able to accommodate all the different molecule classes at once. 

Examples of specialized molecular therapeutics that have been developed from discoveries made using expression profiling experiments include chimeric human/murine antibodies for the treatment of various cancers. Ritux-imab (Rituxan Genentech Inc. South San Francisco, CA), an anti-CD20 antibody in use since 1997, was the first chimeric monoclonal antibody to... 

DNA Microarray The advent of DNA microarray high-throughput profiling experiments has allowed us to explore a major subset or all genes of an organism under a variety of conditions such as alternative treatments (drug-influenced condition vs. condition influenced by... 

A typical gene expression profiling experiment takes place in five separate processes. They are (i) microarray fabrication, (ii) purification and labeling of the target material, (iii) hybridization, (iv) detection and (v) data analysis. The characteristics of each step were briefly discussed in the introduction. A closer look at each of these steps is the object of this section. Here we mainly refer to biochips where the probe is constituted by nucleic acids (DNA microarrays). 

Fig. 31. Plot of interfacial width w vs D for a blend of olefinic copolymers d75/h66 (cf.text) at T0=356 K, extracted from nuclear reaction depth profiling experiments, based on the reaction 3He+2H 4He+1H+18.35 MeV and backward angle detection of 1H. Note that the spatial resolution is optimal near the air surface (4 nm) but quickly deteriorates for large distances from the air surface. Therefore, the error bar on w/2 increases strongly with increasing D. Full and dotted curves represent the approximate asymptotic formula w2 = Wq + D / 4 (a factor 7tco/(l+co/2) in Eq. (127) being approximated as unity), choosing w0= b> and b=l 1 8 nm or b=10.6 nm, respectively. From Kerle et al. [84]...

The aim of a typical microarray-based transcriptional profiling experiment is to identify target genes for down-stream validation experiments, for example to identify genes that are expressed differentially after treatment with a certain componnd. Likewise, the array technology can be used to verify a hypothesis, for example to verify that a compound does induce a certain expected effect. Furthermore, microarrays are used widely in various classification studies in which an initial set of samples with known labels (e.g., type of leukaemia) are profiled, followed by a profiling of a different set of samples with nn-known labels (e.g., patient biopsies) and assigning these into the previously identified classes based on their expression profile. 

The conformational stabilities of HI and Pal-HI have been compared by studying the respective guanidine-HCl induced denaturation profiles. Experiments were conducted utilizing a concentration of 0.1 mg/mL protein in pH... 

The product nitrogen concentration (see fig. 3) in all experiments varies in the same manner as the PNA profiles. Experiments with the carrier at both temperatures and with the catalyst at 200°C show a gradual increase in N from 1000 ppm in the very first... 

Small Molecules as Versatile Tools for Activity-Based Protein Profiling Experiments... 

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