Complex carbohydrates, protocol

We use the term programmable to describe the rational (and ideally, computer-aided and automated) approach to polysaccharide synthesis.20 To reduce the synthesis of complex carbohydrates to routine, we envision a four-step protocol (1) the sequence of interest is keyed into a computer, (2) the computer selects appropriate reagent combinations, (3) a laboratory worker (human or robotic) prepares the reagent... 

The tissue surrogates described here clearly represent a simplification of real FFPE tissues. However, they represent a useful and efficient construct for the evaluation and optimization of tissue extraction conditions for proteomic studies. More informative studies will likely be realized by using more complex tissue surrogates, which can be created by incorporating additional proteins into lysozyme solutions. Tissue surrogates comprised of up to five proteins have been successfully analyzed by MS (Fowler, unpublished data). Additionally, RNA, DNA, lipids, or carbohydrates can be added at nanomolar to millimolar concentrations to increase the complexity of the model system to better mimic whole tissue. The use of these more complex tissue surrogates should facilitate the development of protein recovery protocols optimal for proteomic investigation. 

Immunocytochemical methods have been widely applied to visualize proteins, carbohydrates, or lipids in sectioned material. The advantage of using immunocytochemistry is to be able to localize the molecules of interest within the tissue. Several procedures have been described. Basically, these procedures can be split into four main steps that are described in subheadings (1) tissue preparation, (2) the primary antibodies, (3) the visualization of the target, and (4) enhancement of signals with antibody complexes. In addition, a protocol for alkaline phosphatase will be presented in detail in Subheading 5. The terms primary and secondary antibodies refer to the order in which they are applied to the target. The immunocytochemical procedures are not limited to sectioned... 

The majority of the many methods used to study the composition of equilibrium solutions of carbohydrates examine the mixture without separating the individual components. With the discovery that the anomeric forms of sugars could be readily separated by gas chromatography of their tri-methylsilyl ethers, a new approach to the problem was found. A protocol was developed for the direct gas chromatographic analysis of the amount of each anomer present in an aqueous solution. The protocol can be used on the micro scale and can be used in enzyme assays such as that for mutarotase. The method has been made more effective by combining gas chromatography with mass spectrometry. It is shown how mass spectral intensity ratios can be used to discriminate anomers one from another. The application of these methods to the study of complex mutarotations is discussed. 

An important point which should be re-emphasised in relation to in vitro studies is the now substantial evidence that certain cestodes exist as a complex of intraspecific variants or strains (pp. 97-98). These strains may exhibit considerable quantitative and qualitative differences in carbohydrate metabolism, thereby complicating the interpretation of results. This particular aspect is elaborated on later. Furthermore, there is the additional problem of differing protocols used by independent research workers which can often make in vitro data comparisons difficult. 

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