Methods in molecular medicine最新文献_第3页

Whole genome-wide association study using affymetrix SNP chip: a two-stage sequential selection method to identify genes that increase the risk of developing complex diseases. 利用 affymetrix SNP 芯片进行全基因组关联研究：采用两阶段顺序选择法识别增加患复杂疾病风险的基因。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-60327-148-6_2

Howard H Yang, Nan Hu, Philip R Taylor, Maxwell P Lee

{"title":"Whole genome-wide association study using affymetrix SNP chip: a two-stage sequential selection method to identify genes that increase the risk of developing complex diseases.","authors":"Howard H Yang, Nan Hu, Philip R Taylor, Maxwell P Lee","doi":"10.1007/978-1-60327-148-6_2","DOIUrl":"10.1007/978-1-60327-148-6_2","url":null,"abstract":"Whole-genome association studies of complex diseases hold great promise to identify systematically genetic loci that influence one's risk of developing these diseases. However, the polygenic nature of the complex diseases and genetic interactions among the genes pose significant challenge in both experimental design and data analysis. High-density genotype data make it possible to identify most of the genetic loci that may be involved in the etiology. On the other hand, utilizing large number of statistic tests could lead to false positives if the tests are not adequately adjusted. In this paper, we discuss a two-stage method that sequentially applies a generalized linear model (GLM) and principal components analysis (PCA) to identify genetic loci that jointly determine the likelihood of developing disease. The method was applied to a pilot case-control study of esophageal squamous cell carcinoma (ESCC) that included 50 ESCC patients and 50 neighborhood-matched controls. Genotype data were determined by using the Affymetrix 10K SNP chip. We will discuss some of the special considerations that are important to the proper interpretation of whole genome-wide association studies, which include multiple comparisons, epistatic interaction among multiple genetic loci, and generalization of predictive models.","PeriodicalId":18460,"journal":{"name":"Methods in molecular medicine","volume":"141 ","pages":"23-35"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10759808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27420098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microarrays--planning your experiment. 微阵列——规划你的实验。

Methods in molecular medicine Pub Date : 2008-01-01

Jean Yee Hwa Yang

引用次数: 0

Methods for assessing the structure and function of cationic antimicrobial peptides. 评价阳离子抗菌肽结构和功能的方法。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-246-5_13

Michelle Pate, Jack Blazyk

{"title":"Methods for assessing the structure and function of cationic antimicrobial peptides.","authors":"Michelle Pate, Jack Blazyk","doi":"10.1007/978-1-59745-246-5_13","DOIUrl":"https://doi.org/10.1007/978-1-59745-246-5_13","url":null,"abstract":"Widespread resistance to antibiotics in current clinical use is increasing at an alarming rate. Novel approaches in antimicrobial therapy will be required in the near future to maintain control of infectious diseases. An enormous array of small cationic peptides exists in nature as part of the innate defense systems of organisms ranging from bacteria to humans. For most naturally occurring linear peptides, such as magainins and cecropins, a common feature is their capacity to form an amphipathic alpha-helix (with polar and nonpolar groups on opposite faces of the helix), a structural feature believed to be important in their antimicrobial function as membrane-lytic agents. A massive effort over the past two decades has resulted in a better understanding of the molecular mechanism of antimicrobial peptides and the production of more potent analogues. To date, however, few of these peptides have been shown to have clinical efficacy, especially for systemic use, in large part due to insufficient selectivity between target and host cells. Recently, we developed a new strategy in the design of antimicrobial peptides. These linear cationic peptides, which form amphipathic beta-sheets rather than alpha-helices, demonstrated superior selectivity in binding to the lipids contained in bacterial vs. mammalian plasma membranes. Here we describe methods to evaluate the structure and function of cationic antimicrobial peptides.","PeriodicalId":18460,"journal":{"name":"Methods in molecular medicine","volume":"142 ","pages":"155-73"},"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_13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27404786","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: 9

Screening for compounds that affect the interaction between bacterial two-component signal transduction response regulator protein and cognate promoter DNA. 影响细菌双组分信号转导反应调节蛋白与同源启动子DNA相互作用的化合物筛选。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-246-5_17

Matthew G Erickson, Andrew T Ulijasz, Bernard Weisblum

引用次数: 1

Web-based resources for clinical bioinformatics. 临床生物信息学的网络资源。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-60327-148-6_17

Anthony M Joshua, Paul C Boutros

引用次数: 4

Experimental activation of mast cells and their pharmacological modulation. 肥大细胞的实验活化及其药理调节。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-366-0_26

Shaoheng He, Andrew F Walls

引用次数: 0

Short-term culture of CD8 cells and intracellular cytokine staining. CD8细胞短期培养及细胞内细胞因子染色。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-366-0_7

Beejal Vyas, Alistair Noble

{"title":"Short-term culture of CD8 cells and intracellular cytokine staining.","authors":"Beejal Vyas, Alistair Noble","doi":"10.1007/978-1-59745-366-0_7","DOIUrl":"https://doi.org/10.1007/978-1-59745-366-0_7","url":null,"abstract":"CD8 T cells play an important role in the regulation of allergic disease. Human and murine CD8 T cells have been shown to be capable of differentiating into distinct subsets defined by cytokine profiles analogous to the Th1 and Th2 subsets and termed T cytotoxic 1 (Tc1, IFN-gamma producing) and 2 (Tc2, IL-4 producing). Effector cell phenotype can be analyzed in vitro on a single cell basis using intracellular cytokine staining and flow cytometry or analysis of other phenotypic markers. Human PBMC usually contain only very low percentages of effector cells which produce relatively high levels of cytokines required for this kind of analysis. It is therefore necessary to activate the T cells to induce rapid accumulation of cytoplasmic cytokines before analysis. This makes it difficult to analyze the antigen specificity of responding T cells but will indicate the type 1/type 2 bias of the population, reflecting previous exposures to antigen. In this chapter, we provide protocols for the generation of polarized populations of CD8 T effector cells using polyclonal stimulation and for their subsequent analysis by intracellular cytokine staining.","PeriodicalId":18460,"journal":{"name":"Methods in molecular medicine","volume":"138 ","pages":"73-83"},"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_7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27524493","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: 1

Monoclonal antibodies. 单克隆抗体。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-366-0_15

Helga Kahlert, Oliver Cromwell

{"title":"Monoclonal antibodies.","authors":"Helga Kahlert, Oliver Cromwell","doi":"10.1007/978-1-59745-366-0_15","DOIUrl":"https://doi.org/10.1007/978-1-59745-366-0_15","url":null,"abstract":"Monoclonal antibodies (mabs) are powerful tools for the quantification, detection, and targeting of specific molecules. Allergen-specific mabs are important for the quantification of major allergens in allergen preparations used for allergen-specific immunotherapy and allergy diagnosis. Indeed, progress in the understanding of the mechanisms of the immunological responses underlying allergic disease would not have been possible without the use of mabs. Quantification assays are also important in the assessment of environmental allergen exposure and monitoring of avoidance procedures.Mabs against human IgE provide the basis for various test systems for the detection of specific and nonspecific IgE. Mabs raised against IgE or defined cytokines or cytokine receptors have potential as neutralizing reagents in vivo for the treatment of allergic diseases.Allergen-specific mabs are also valuable tools for the localization of allergens within their source material and the characterization of allergens derived from natural sources and by recombinant technologies. Furthermore they are often used for the isolation of allergens from complex extracts by affinity chromatography. The procedure described in this chapter has been used successfully to produce mabs against numerous allergens from house dust mites, insect venoms, cat, hens egg white, tree-, grass-, and herb pollens, and fungi, with the ultimate aim of obtaining matched antibody pairs to establish two-site binding assays for the quantification of major allergens. The method has also been used successfully to generate mabs against human IgE.","PeriodicalId":18460,"journal":{"name":"Methods in molecular medicine","volume":"138 ","pages":"183-96"},"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_15","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27522386","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

Biopanning for the characterization of allergen mimotopes. 变态反应原模位特征的生物筛选。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-366-0_23

Isabella Pali-Schöll, Erika Jensen-Jarolim

{"title":"Biopanning for the characterization of allergen mimotopes.","authors":"Isabella Pali-Schöll, Erika Jensen-Jarolim","doi":"10.1007/978-1-59745-366-0_23","DOIUrl":"https://doi.org/10.1007/978-1-59745-366-0_23","url":null,"abstract":"Proper understanding of the pathogenesis of type I allergy relies on the identification of allergen epitopes. The phage display technique is a relatively new one to define peptide structures that mimic natural epitopes, including conformational B-cell epitopes. Peptides displayed on the phage recognized by an antiallergen antibody mimic the physicochemical properties of the amino acids and are, therefore, called mimotopes. The main advantage of the biopanning technique described in this chapter is that the structure of the antigen/allergen may be completely unknown; the only material needed is an antibody binding to it. The mimotopes generated by this technique display the features of the antigen/allergen but do not crosslink the mast cell-bound IgE-antibodies. Thus mimotopes could be used as a safe alternative to the commonly applied allergen extracts in immunotherapy of allergic patients and direct the immune response toward the desired allergen epitopes. In the selection procedure called biopanning, phages with the mimotopes best recognized by the selecting antibody are amplified. The titers of phages specifically binding to the selection antibody are checked. In this chapter we describe two alternative methods for colony screening: the immunoblot and ELISA.","PeriodicalId":18460,"journal":{"name":"Methods in molecular medicine","volume":"138 ","pages":"271-83"},"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_23","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27523994","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: 6

Methods to assay inhibitors of tRNA synthetase activity. 方法测定tRNA合成酶活性抑制剂。

Methods in molecular medicine Pub Date : 2008-01-01 DOI: 10.1007/978-1-59745-246-5_5

Dieter Beyer, Hein Peter Kroll, Heike Brötz-Oesterhelt

引用次数: 1