Methods in molecular medicine最新文献_第6页

Microarrays--identifying molecular portraits for prostate tumors with different Gleason patterns. 微阵列-识别具有不同格里森模式的前列腺肿瘤的分子图谱。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-60327-148-6_8

Alexandre Mendes, Rodney J Scott, Pablo Moscato

{"title":"Microarrays--identifying molecular portraits for prostate tumors with different Gleason patterns.","authors":"Alexandre Mendes, Rodney J Scott, Pablo Moscato","doi":"10.1007/978-1-60327-148-6_8","DOIUrl":"https://doi.org/10.1007/978-1-60327-148-6_8","url":null,"abstract":"We present in this chapter the combined use of several recently introduced methodologies for the analysis of microarray datasets. These computational techniques are varied in type and very powerful when combined. We have selected a prostate cancer dataset which is available in the public domain to allow for further comparisons with existing methods. The task is to identify biomarkers that correlate with the clinical phenotype of interest, i.e., Gleason patterns 3, 4, and 5. A supervised method, based on the mathematical formalism of (alpha, beta)-k-feature sets (1), is used to select differentially expressed genes. After these \"molecular signatures\" are identified, we applied an unsupervised method (a memetic algorithm) to order the samples (2). The objective is to maximize a global measure of correlation in the two-dimensional display of gene expression profiles. With the resulting ordering and taxonomy we are able to identify samples that have been assigned a certain Gleason pattern, and have gene expression patterns different from most of the other samples in the group. We reiterate the approach to obtain molecular signatures that produce coherent patterns of gene expression in each of the three Gleason pattern groups, and we analyze the statistically significant patterns of gene expression that seem to be implicated in these different stages of disease.","PeriodicalId":18460,"journal":{"name":"Methods in molecular medicine","volume":"141 ","pages":"131-51"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-1-60327-148-6_8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27418338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 22

Utilizing HapMap and tagging SNPs. 利用HapMap和标记snp。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-60327-148-6_3

Christopher A Haiman, Daniel O Stram

引用次数: 18

Identification of mast cells and mast cell subpopulations. 肥大细胞和肥大细胞亚群的鉴定。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-366-0_24

Mark Buckley, Andrew F Walls

{"title":"Identification of mast cells and mast cell subpopulations.","authors":"Mark Buckley, Andrew F Walls","doi":"10.1007/978-1-59745-366-0_24","DOIUrl":"10.1007/978-1-59745-366-0_24","url":null,"abstract":"Mast cells generate mediators of inflammation which are stored in granules and secreted on activation either by allergen crosslinking of membrane-bound IgE or through other stimuli. Most methods for mast cell identification rely on the histochemical detection of constituents of the secretory granules. Although staining for mast cells with histochemical stains can be rapid and relatively inexpensive, it is not always possible to distinguish reliably between mast cells and basophils in tissues. A further problem with the staining of mast cells with commonly used basic dyes is that the reagents employed to fix the tissues can influence the results, leading to confusion regarding the numbers of mast cells present in various tissues. Recognition that there is considerable heterogeneity between mast cell populations in the degree to which staining properties are lost with formalin fixation has led to mast cell subsets being defined on this basis. The development and application of procedures for identifying mast cell proteases has led to important advances in our understanding of the role of mast cells and in the nature of heterogeneity in man. The techniques described here should allow the reliable detection of mast cells and mast cell subsets in a range of tissues and cell preparations. There will be a continuing need for validation, for consideration of potential sources of error, and for the development of new and more reliable techniques for mast cell identification.","PeriodicalId":18460,"journal":{"name":"Methods in molecular medicine","volume":"138 ","pages":"285-97"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27523995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Purification and characterization of mast cell tryptase and chymase from human tissues. 人组织肥大细胞胰蛋白酶和乳糜酶的纯化和特性研究。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-366-0_25

Alan R McEuen, Andrew F Walls

{"title":"Purification and characterization of mast cell tryptase and chymase from human tissues.","authors":"Alan R McEuen, Andrew F Walls","doi":"10.1007/978-1-59745-366-0_25","DOIUrl":"10.1007/978-1-59745-366-0_25","url":null,"abstract":"Mast cells are key effector cells of the allergic response. When stimulated by specific allergen through the high-affinity IgE receptors or through other stimuli, these cells release a number of potent mediators of inflammation. Amongst these are the serine proteases tryptase and chymase. In humans, tryptase is the most abundant mediator stored in mast cells. Chymase is present in more moderate amounts in a subpopulation of mast cells (MC(TC)). This subtype of mast cells predominates in connective tissue, whereas the other major subtype, the MC(T), predominates in mucosal tissue. Both proteases have been shown to act on specific extracellular proteins and peptides, as well as to alter the behavior of various cell types. Inhibitors of tryptase have been found to be efficacious in animal and human models of asthma, and both proteases are currently being investigated as potential targets for therapeutic intervention. Such pharmacological, physiological, and biochemical studies require the availability of purified tryptase and chymase. In this chapter, we shall describe procedures for the purification of tryptase and chymase from human tissues and provide protocols for monitoring purification and characterization of the final product. The preparation of recombinant proteases will not be covered, though some of the procedures described may be readily adapted for their purification from recombinant expression systems. The procedures described here have been developed for the purification of the human proteases and will require some modification if applied to purify mast cell proteases from the tissues of other species.","PeriodicalId":18460,"journal":{"name":"Methods in molecular medicine","volume":"138 ","pages":"299-317"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27523996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Immunoelectrophoresis for the characterization of allergen extracts. 过敏原提取物的免疫电泳鉴定。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-366-0_13

Gitte Nordskov Hansen, Jørgen Nedergaard Larsen

{"title":"Immunoelectrophoresis for the characterization of allergen extracts.","authors":"Gitte Nordskov Hansen, Jørgen Nedergaard Larsen","doi":"10.1007/978-1-59745-366-0_13","DOIUrl":"https://doi.org/10.1007/978-1-59745-366-0_13","url":null,"abstract":"Immunoelectrophoresis can be used for analysis of individual proteins in complex mixtures. The conditions involved in immunoelectrophoresis are mild, avoiding the risk of denaturation, and it is possible to perform relative quantification of individual components. The principle disadvantage is the dependence on rabbit antisera as reagents. The usefulness of immunoelectrophoresis in allergy research is greatly enhanced by the possibility of identification of allergens to which the individual in question has IgE. The common principle is characterized by two independent electrophoreses having direction of current perpendicular to each other, i.e., crossed immunoelectrophoresis (CIE). This ultimately results in the formation of characteristic bell-shaped precipitates, each precipitate representing one antigen. There is a linear relationship between the amount of antigen and size of precipitate for a given antibody concentration for each precipitate and so relative quantification can be performed. The sensitivity and resolution power of CIE is very high and there are multiple variations of the technique, some of which will be illustrated in this chapter.","PeriodicalId":18460,"journal":{"name":"Methods in molecular medicine","volume":"138 ","pages":"147-65"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-1-59745-366-0_13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27522384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Measurement of specific IgG anti-Fel d 1 antibodies. 特异性IgG抗fel d1抗体测定。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-366-0_20

Meinir G Jones

引用次数: 2

SPARK: a new peptidyl transferase activity assay. SPARK:一种新的肽基转移酶活性测定方法。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-246-5_9

Alexander S Mankin, Norbert Polacek

{"title":"SPARK: a new peptidyl transferase activity assay.","authors":"Alexander S Mankin, Norbert Polacek","doi":"10.1007/978-1-59745-246-5_9","DOIUrl":"https://doi.org/10.1007/978-1-59745-246-5_9","url":null,"abstract":"The formation of peptide bonds is the central chemical reaction during protein synthesis and is catalyzed by the peptidyl transferase center residing in the large ribosomal subunit. This active site is composed of universally conserved rRNA nucleosides. The peptidyl transferase center is by far the most frequently used target site of natural antibiotics in the cell. Here we describe a novel, simple, and convenient method to assess peptide bond formation which we named SPARK. The basic principle of SPARK is the use of two reaction substrates that closely resemble the natural tRNA substrates (one is biotinylated and the other carries a tritium label) that become covalently connected during transpeptidation. Formation of this peptide bond then allows capture and direct quantification of the radiolabled product, now joined to the biotin group, using the scintillation proximity assay technology. Binding of the tritiated radioligand to streptavidin-coated beads causes the excitation of the bead-embedded scintillant, thus resulting in the detection of radioactivity. Since no product purification step is required, SPARK is amenable to simple automation, which makes it useful in high-throughput screens of natural or synthetic compound libraries in the search for novel antibiotics.","PeriodicalId":18460,"journal":{"name":"Methods in molecular medicine","volume":"142 ","pages":"107-16"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-1-59745-246-5_9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27404318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Methods to assay inhibitors of DNA gyrase and topoisomerase IV activities. 方法测定DNA旋切酶和拓扑异构酶抑制剂的活性。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-246-5_2

L Mark Fisher, Xiao-Su Pan

引用次数: 0

Clinical uses of microarrays in cancer research. 微阵列在癌症研究中的临床应用。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-60327-148-6_6

Carl Virtanen, James Woodgett

引用次数: 0

T cell - primary culture from peripheral blood. 外周血T细胞原代培养。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-366-0_2

Monika Raulf-Heimsoth

引用次数: 16