Methods in molecular medicine最新文献

Peptide mass fingerprinting is a simple, quick, cheap, and relatively effective method of identifying proteins from mass spectrometry data. Proteins extracted from the complex mixture comprising the proteome of a sample are individually digested with a proteolytic enzyme into a series of peptide fragments. The set of masses of these peptides, determined by mass spectrometry, form a peptide mass fingerprint of the protein. Comparison of this experimental fingerprint with the theoretical fingerprints of all known protein sequences for this organism, derived computationally from a protein sequence database, allows the identification of the particular protein. In this chapter, I discuss the technique including preparation for the peptide mass fingerprinting analysis, the appropriate selection of computational search parameters, and the analysis and interpretation of search results in the context of identifying proteins from microbial samples.

There is a growing demand for tools to support clinicians utilize genomic results generated by molecular diagnostic and cytogenetic methods in support of their decision-making. This chapter reviews existing experience and methods for the design, implementation and evaluation of clinical bioinformatics electronic decision support systems (EDSS). It provides a roadmap for identifying decision tasks for automation and selecting optimal tools for building task-specific systems. Key success factors for EDSS implementation and evaluation are also outlined.

The ability, either innate or acquired, to produce beta-lactamases, enzymes capable of hydrolyzing the endocyclic peptide bond in beta-lactam antibiotics, would appear to be a primary contributor to the ever-increasing incidences of resistance to this class of antibiotics. To date, four distinct classes, A, B, C, and D, of beta-lactamases have been identified. Of these, enzymes in classes A, C, and D utilize a serine residue as a nucleophile in their catalytic mechanism while class B members are Zn2+-dependent for their function. Efforts have been and still continue to be made toward the development of potent inhibitors of these enzymes as a means to ensure the efficacy of beta-lactam antibiotics in clinical medicine. This chapter concerns procedures for the evaluation of the catalytic activity of beta-lactamases as a means to screen compounds for their inhibitory potency.

Treatment of Gram-negative bacterial infections is complicated by innate and acquired drug resistance resulting in a limited number of effective antibiotics. Several Gram-negative bacteria, for which current therapies are ineffective, have recently been identified as potential bioterror agents. These findings highlight the need for new antibiotics, specifically antibiotics that act on new drug targets to circumvent drug resistance. Potential targets in Gram-negative bacteria include enzymes involved in the biosynthesis of lipopolysaccharides (LPS) that form outer membranes of these organisms. UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) catalyzes the committed step in the biosynthesis of the lipid A portion of LPS. Therefore, inhibitors of this enzyme have the potential to serve as antibiotics, and efforts toward the development of LpxC inhibitors are currently underway. Here we describe methods for assaying LpxC inhibitors, including methods for measuring deacetylase activity and binding affinity for LpxC, which will be useful for the development of LpxC inhibitors.

The Halogen assay is a new technique for measuring airborne allergen. The assay is unique in that it is capable of analyzing allergens and particles together, combining the advantages of morphological approaches and immunoassay. The Halogen assay allows direct observation of the particles that carry the allergen as well as being capable of identifying all the allergen sources an individual is exposed and sensitized to. The assay is sensitive because the extracted allergen is bound to the membrane at a high local concentration within the minute area around each particle and so is easily detected by immunostaining. It is therefore easy to detect few pollen grains. The Halogen method supersedes other methods commonly used to identify allergens as it is capable of identifying airborne particles that are allergen sources.

Identification of pollen is like entering a world of great variation in size, shape, and structure. To obtain a correct result, a good microscope, basic information on pollen grain morphology and a reference sample of the plant to be identified are needed. Purity determination of pollen can be performed by particle count or by volumetric analysis. In our experience, particle counting is the better and most reproducible method and is not greatly influenced by interindividual variation. In this chapter, we have described the detailed procedure to obtain satisfactory results for identification and determination of pollen purity.

Immunoglobulins are a heterogeneous group of proteins. It naturally follows that the strategies for purifying them are diverse and numerous. A good knowledge of their respective physiochemical properties will obviously make the task easier. The choice between using polyclonal and/or monoclonal antibodies will govern the basic approach. Each approach will present its own advantages/disadvantages including cost, ability to produce a high yield, quality, and a need for standardization. The context in which the antibodies will be used is another important aspect to consider. When the demand is for establishing "ultrasensitive" assays, optimal purity and specificity is obviously required. This chapter will focus on the purification of mammalian IgG from polyclonal (i.e., rabbit) and monoclonal (i.e., mouse sources). IgG is the principal immunoglobulin constituent of mammalian sera. In older animals, it may well represent >80% of the total Ig concentration, because of its higher rate of synthesis and longer half-life.

Resistance to antibiotics that target the bacterial ribosome is often conferred by methylation at specific nucleotides in the rRNA. The nucleotides that become methylated are invariably key sites of antibiotic interaction. The addition of methyl groups to each of these nucleotides is catalyzed by a specific methyltransferase enzyme. The Erm methyltransferases are a clinically prevalent group of enzymes that confer resistance to the therapeutically important macrolide, lincosamide, and streptogramin B (MLS B) antibiotics. The target for Erm methyltransferases is at nucleotide A2058 in 23S rRNA, and methylation occurs before the rRNA has been assembled into 50S ribosomal particles. Erm methyltransferases occur in a phylogenetically wide range of bacteria and differ in whether they add one or two methyl groups to the A2058 target. The dimethylated rRNA confers a more extensive MLS B resistance phenotype. We describe here a method using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to determine the location and number of methyl groups added at any site in the rRNA. The method is particularly suited to studying in vitro methylation of RNA transcripts by resistance methyltransferases such as Erm.

Searching online resources can provide medical researchers with an efficient means of gathering existing knowledge on the molecular causes of disease. The researcher may choose to explore the following areas, e.g., genetic mutations associated with the disease, function and cellular sub-localization of the associated protein(s) and their protein interaction partners. Using a small case study, examining the disease retinoblastoma, this chapter guides the reader through the relevant information contained within relevant databases. It is shown that the integration of online biological knowledge with genomic and proteomic experimental data provides insights into the understanding of diseases in their molecular context.