Research Tools

J. Dcifrini . Com pulcr-aidcd Molecular Modelling RescatTh Slitdy or Research Tool 1 Computer Aided Mulerular Dcsicn 2 17U IS J, lUSS. 

The utilization of commercially available finite element packages in the simulation of routine operations in industrial polymer processing is well established. However, these packages cannot be usually used as general research tools. Thus flexible in-house -created programs are needed to carry out the analysis required in the investigation, design and development of novel equipment and operations. 

Bearing, A., Computer-aided Molecular Modelling Research Study or Research Tool... 

P-Endorphin. A peptide corresponding to the 31 C-terminal amino acids of P-LPH was first discovered in camel pituitary tissue (10). This substance is P-endorphin, which exerts a potent analgesic effect by binding to cell surface receptors in the central nervous system. The sequence of P-endorphin is well conserved across species for the first 25 N-terminal amino acids. Opiates derived from plant sources, eg, heroin, morphine, opium, etc, exert their actions by interacting with the P-endorphin receptor. On a molar basis, this peptide has approximately five times the potency of morphine. Both P-endorphin and ACTH ate cosecreted from the pituitary gland. Whereas the physiologic importance of P-endorphin release into the systemic circulation is not certain, this molecule clearly has been shown to be an important neurotransmitter within the central nervous system. Endorphin has been invaluable as a research tool, but has not been clinically useful due to the avadabihty of plant-derived opiates. 

Heat. Personal monitoring of the environmental conditions which impose a heat stress on a worker is impractical, so fixed station measurement of such parameters as wet bulb globe temperature are usually made (see Temperature measurements). These stations are carefully selected so that the results, plus worker location and workload data, can be combined to yield an overall heat stress estimate. Heat strain, the effect on the human, can be estimated from core body temperature, but this is usually only a research tool. 

Western European chemical companies were slower in adopting market and marketing research tools to assist in their operations and planning. A few large companies such as ICI, Bayer, Hoechst, and Solvay were using the techniques in the late 1950s, but not until the early 1970s did European chemical companies use these studies as frequendy as their U.S. counterparts. 

Databases may be viewed as a research tool for those in highly competitive fields such as science, engineering, and technology. This tool makes information available so that its user can make decisions based on comprehensive and timely data (7). A guide to commercially available databases relating to topics associated with science and technology follows. 

BioMolecular research tools—A collection of WWW links to information and services useful to molecular biologists http //www.public.iastate.edu/ pedro/research tools.html... 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Appendix F is a case study by Hjertager et al. illustrating the above method. Such numerical methods will become more widely used in the long term. These techniques will probably remain research tools, rather than routine evaluation methods, until such time as available computing power and algorithm efficiency greatly increase. 

Exact computability in this sense, however, is achieved only at the cost of being able to obtain approximate solutions. Perturbation analysis, for example, is rendered virt ially meaningless in this context. It is not s irprising that traditional investigatory methodologies are not very well suited to studies of complex systems. Since the behavior of such models can generally be obtained only through explicit simulation, the computer becomes the one absolutely indispensable research tool. 

We conclude this chapter with a few illustrative color plates. Simple B W graphics are sufficient for viewing CA only in the special case when sites take on one of two values. In all other cases, color is indispensable for visualizing the behavior of the system. The plates were produced using the freely available CA software packages MCell, Cellab and WinCA. See Appendix A CA Research Tools for a description of these programs and links to web sites from which they can be HnwnlnnHpH... 

Photoelectric-Colorimetric Method. Although the recording spectrophotometer is, for food work at least, a research tool, another instrument, the Hunter multipurpose reflectometer (4), is available and may prove to be applicable to industrial quality control. (The newer Hunter color and color difference meter which eliminates considerable calculation will probably be even more directly applicable. Another make of reflection meter has recently been made available commercially that uses filters similar to those developed by Hunter and can be used to obtain a similar type of data.) This instrument is not a spectrophotometer, for it does not primarily measure the variation of any property of samples with respect to wave length, but certain colorimetric indexes are calculated from separate readings with amber, blue, and green filters, designated A, B, and G, respectively. The most useful indexes in food color work obtainable with this type of instrument have been G, which gives a... 

Table 3). For example, arabinose and xylose differ from ribose only in the orientation of the 2 - and 3 -OH groups yet exhibit markedly different potencies. Whereas 9-(tetrahydrofuryl)-Ade ( SQ 22,536) and 9-(cyclopentyl)-Ade are without hydroxyl groups and are less potent, they offer metabolic and biochemical stability useful for many types of studies. It is, however, the removal of two of the hydroxyl groups, that elicits the largest improvement in inhibitory potency, in particular the 2, 5 -dideoxy- modification (Table 3). With these improvements in potency, these cell permeable compounds, in particular 2, 5 -dd-Ado, have become useful research tools and have been used to inhibit adenylyl cyclases and to lower cAMP levels and alter function in numerous studies in isolated cells or intact tissues. 

Similar residues in the cores of protein structures especially hydrophobic residues at the same positions, are responsible for common folds of homologous proteins. Certain sequence profiles of conserved residue successions have been identified which give rise to a common fold of protein domains. They are organized in the smart database (simple modular architecture research tool) http //smait.embl-heidelberg.de. 

Probability Theory.—To pursue our study of methods of operations research, a brief, although incomplete, and somewhat abstract, presentation of ideas from probability theory will be given. In part it shows that mathematical abstraction and rigor are also in the nature of operations research. Illustrations of this topic will be given in later sections. We then give a longer discussion of maximization and minimization methods and in turn illustrate the ideas in subsequent sections. Probability and statistics and optimization methods are two major sources of operations research tools. 

Explore our innovative research tools - try the Research Dashboard now ... 

An historical outline has been presented of some of the important developments in the study of luminescence, which reveals that most of the theory and practise used today were already in place by 1930. This is followed by a selection of recent developments in applications of luminescence intended to suggest to the reader possible uses of this versatile research tool in his own research. 

Inhibitors of the catalytic activities of enzymes provide both pharmacologic agents and research tools for study of the mechanism of enzyme action. Inhibitors can be classified based upon their site of action on the enzyme, on whether or not they chemically modify the enzyme, or on the kinetic parameters they influence. KineticaUy, we distinguish two classes of inhibitors based upon whether raising the substrate concentration does or does not overcome the inhibition. 

Nonhydrolyzable Nucleoside Triphosphate Analogs Serve as Research Tools... 

One peptide toxin from the mushroom Amanita phalhides, a-amanitin, is a specific differential inhibitor of the eukaryotic nuclear DNA-dependent RNA polymerases and as such has proved to be a powerful research tool (Table 37-2). a-Amanitin blocks the translocation of RNA polymerase during transcription. 

Anatoxin-a has already proven its usefulness as a research tool in our laboratories. It is facilitating the understanding of the biophysical properties of the AChR and of the localization of the AChR in the CNS. The toxin or derivatives of it could be useful therapeutically in diseases of nicotinic receptor pathology (myasthenia gravis or Alzheimer s disease), because as a secondary amine (+)-anatoxin-a can penetrate into the CNS. 

So much for the advantages. Virtual organs clearly have one major drawback they are models only. While this very nature of in silico technology is the core foundation for the benefits listed above, it also calls for a word of caution. It is imperative for in silico tools to be seen in the context of a whole range of scientific and research tools, and to never neglect that theoretical considerations will continue to need experimental validation. 

Chemists, biochemists, biotechnologists, and physicists now routinely use NMR spectroscopy as a powerful research tool. The effective application of ID and 2D NMR expteriments depends largely on the skill and innovation of the user. This book is intended to provide practical knowledge to research workers in the use of NMR spectroscopic techniques to elucidate the structure of organic molecules. Every attempt has been made to prevent the book from becoming too technical, and the underlying principles behind many of the experiments have been described nonmathematically. 

Du, H. et al., Photochem CAD a computer-aided design and research tool in photochemistry, Photochem. PhotobioL, 68, 141, 1998. 

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