References of "Methods in molecular biology (Clifton, N.J.)"
     in
Bookmark and Share    
See detailA Specialized Method to Resolve Fine 3D Features of Astrocytes in Nonhuman Primate (Marmoset, Callithrix jacchus) and Human Fixed Brain Samples.
Quesseveur, Gael; Fouquier d'Hérouël, Aymeric UL; Murai, Keith K. et al

in Methods in molecular biology (Clifton, N.J.) (2019), 1938

Astrocytes are among the most numerous cells in the brain and fulfill diverse functions in homeostasis and regulation of neuronal activity. Astrocytes also dramatically change their properties in response ... [more ▼]

Astrocytes are among the most numerous cells in the brain and fulfill diverse functions in homeostasis and regulation of neuronal activity. Astrocytes also dramatically change their properties in response to brain injury or disease, a process called reactive gliosis. Precisely how astrocytes contribute to healthy brain function and play differential roles in brain pathology and regeneration remain important areas of investigation. To better understand the properties of astrocytes, more sophisticated approaches for probing their rich and complex anatomical and molecular features are needed to fully determine their contribution to brain physiology. Here we present an efficient and straightforward immunolabeling protocol to obtain high-resolution fluorescence-based images from fixed nonhuman primate (common marmoset Callithrix jacchus) and human brain samples. Importantly, the protocol is useful for obtaining images from samples that have been stored in fixative solutions (such as formalin) for years. This approach is especially useful for three-dimensional, multichannel confocal microscopy and can be optimized for super-resolution techniques such as stimulated emission depletion (STED) microscopy. We also present a strategy for using specific combinations of markers to define the phenotypic variations and cellular/subcellular properties of astrocytes to better predict the function of these cells on their surrounding brain microenvironment. [less ▲]

Detailed reference viewed: 84 (4 UL)
Full Text
Peer Reviewed
See detailThe FASTCORE Family: For the Fast Reconstruction of Compact Context-Specific Metabolic Networks Models.
Pacheco, Maria UL; Sauter, Thomas UL

in Methods in Molecular Biology (Clifton, N.J.) (2018), (1716), 101-110

The FASTCORE family is a family of algorithms that are mainly used to build context-specific models but can also be applied to other tasks such as gapfilling and consistency testing. The FASTCORE family ... [more ▼]

The FASTCORE family is a family of algorithms that are mainly used to build context-specific models but can also be applied to other tasks such as gapfilling and consistency testing. The FASTCORE family has very low computational demands with running times that are several orders of magnitude lower than its main competitors. Furthermore, the models built by the FASTCORE family have a better resolution power (defined as the ability to capture metabolic variations between different tissues, cell types, or contexts) than models from other algorithms. [less ▲]

Detailed reference viewed: 148 (8 UL)
Full Text
Peer Reviewed
See detailResources for Systems Genetics.
Williams, Robert W.; Williams, Evan UL

in Methods in molecular biology (Clifton, N.J.) (2017), 1488

A key characteristic of systems genetics is its reliance on populations that vary to a greater or lesser degree in genetic complexity-from highly admixed populations such as the Collaborative Cross and ... [more ▼]

A key characteristic of systems genetics is its reliance on populations that vary to a greater or lesser degree in genetic complexity-from highly admixed populations such as the Collaborative Cross and Diversity Outcross to relatively simple crosses such as sets of consomic strains and reduced complexity crosses. This protocol is intended to help investigators make more informed decisions about choices of resources given different types of questions. We consider factors such as costs, availability, and ease of breeding for common scenarios. In general, we recommend using complementary resources and minimizing depth of resampling of any given genome or strain. [less ▲]

Detailed reference viewed: 8 (0 UL)
Full Text
Peer Reviewed
See detailNeurological Diseases from a Systems Medicine Point of View.
Ostaszewski, Marek UL; Skupin, Alexander UL; Balling, Rudi UL

in Methods in molecular biology (Clifton, N.J.) (2016), 1386

The difficulty to understand, diagnose, and treat neurological disorders stems from the great complexity of the central nervous system on different levels of physiological granularity. The individual ... [more ▼]

The difficulty to understand, diagnose, and treat neurological disorders stems from the great complexity of the central nervous system on different levels of physiological granularity. The individual components, their interactions, and dynamics involved in brain development and function can be represented as molecular, cellular, or functional networks, where diseases are perturbations of networks. These networks can become a useful research tool in investigating neurological disorders if they are properly tailored to reflect corresponding mechanisms. Here, we review approaches to construct networks specific for neurological disorders describing disease-related pathology on different scales: the molecular, cellular, and brain level. We also briefly discuss cross-scale network analysis as a necessary integrator of these scales. [less ▲]

Detailed reference viewed: 263 (8 UL)
Full Text
Peer Reviewed
See detailCo-immunoprecipitation protocol to investigate cytokine receptor-associated proteins, e.g., Janus kinases or other associated signaling proteins.
Haan, Claude UL; Haan, Serge UL

in Methods in Molecular Biology (Clifton, N.J.) (2013), 967

Jak binding to cytokine receptors has been shown to be a complex and tight interaction. When studying loss-of-function or gain-of-function mutants of the Jaks or cytokine receptors it is often necessary ... [more ▼]

Jak binding to cytokine receptors has been shown to be a complex and tight interaction. When studying loss-of-function or gain-of-function mutants of the Jaks or cytokine receptors it is often necessary to know if a certain mutant still associates correctly in the context of the signaling complex. The standard technique to show interaction of Jaks with cytokine receptors or other signalling molecules is Co-immunoprecipitation. Here we describe our protocol and discuss different pitfalls that can be encountered during the procedure. [less ▲]

Detailed reference viewed: 163 (2 UL)
Full Text
Peer Reviewed
See detailDetection of activated STAT species using electrophoretic mobility shift assay (EMSA) and potential pitfalls arising from the use of detergents.
Haan, Serge UL; Haan, Claude UL

in Methods in Molecular Biology (Clifton, N.J.) (2013), 967

Here we describe the preparation of nuclear extracts and the electrophoretic mobility shift assay (EMSA) for the detection of STAT species. We use the method for the investigation of STAT1 and STAT3 homo ... [more ▼]

Here we describe the preparation of nuclear extracts and the electrophoretic mobility shift assay (EMSA) for the detection of STAT species. We use the method for the investigation of STAT1 and STAT3 homo- and heterodimers and show how the preparation of the extracts can influence the distribution of the STAT species observed in the EMSA. We show that detergents can massively influence the STAT dimer distribution. Although it is unclear whether they primarily interfere with STAT DNA binding and/or whether they break up or further oligomerize STATs, the observation may also have an impact on the results of other techniques performed with detergent-containing cell lysates (e.g., coimmunoprecipitations of STATs with other proteins). [less ▲]

Detailed reference viewed: 133 (3 UL)
Full Text
Peer Reviewed
See detailHierarchical representation of supersecondary structures using a graph-theoretical approach.
Koch, Ina; Kreuchwig, Annika; May, Patrick UL

in Methods in Molecular Biology (Clifton, N.J.) (2013), 932

The unique representation of proteins becomes more and more important with the growing number of known protein structure data. Graph-theory provides many methods not only for the description but also for ... [more ▼]

The unique representation of proteins becomes more and more important with the growing number of known protein structure data. Graph-theory provides many methods not only for the description but also for comparison and classification of protein structures. Here, we describe a graph-theoretical modeling approach of the protein supersecondary structure. The resulting linear notations are intuitive and can be used to find common substructures very fast and easily. We illustrate the necessary definitions by biological examples and discuss the representation of various supersecondary structure motifs. [less ▲]

Detailed reference viewed: 123 (14 UL)
Full Text
Peer Reviewed
See detailIntegration of proteomic and metabolomic profiling as well as metabolic modeling for the functional analysis of metabolic networks.
May, Patrick UL; Christian, Nils UL; Ebenhoh, Oliver et al

in Methods in Molecular Biology (Clifton, N.J.) (2011), 694

The integrated analysis of different omics-level data sets is most naturally performed in the context of common process or pathway association. In this chapter, the two basic approaches for a metabolic ... [more ▼]

The integrated analysis of different omics-level data sets is most naturally performed in the context of common process or pathway association. In this chapter, the two basic approaches for a metabolic pathway-centric integration of proteomics and metabolomics data are described: the knowledge-based approach relying on existing metabolic pathway information, and a data-driven approach that aims to deduce functional (pathway) associations directly from the data. Relevant algorithmic approaches for the generation of metabolic networks of model organisms, their functional analysis, database resources, visualization and analysis tools will be described. The use of proteomics data in the process of metabolic network reconstruction will be discussed. [less ▲]

Detailed reference viewed: 87 (6 UL)
Full Text
Peer Reviewed
See detailMeasurement of plasma membrane calcium-calmodulin-dependent ATPase (PMCA) activity.
Mohamed, Tamer M. A.; Baudoin-Stanley, Florence M.; Abou-Leisa, Riham et al

in Methods in molecular biology (Clifton, N.J.) (2010), 637

The plasma membrane calcium-calmodulin-dependent ATPase (PMCA) is a calcium-extruding enzymatic pump that ejects calcium from the cytoplasm to the extracellular compartment. Although in excitable cells ... [more ▼]

The plasma membrane calcium-calmodulin-dependent ATPase (PMCA) is a calcium-extruding enzymatic pump that ejects calcium from the cytoplasm to the extracellular compartment. Although in excitable cells such as skeletal and cardiac muscle cells PMCA has been shown to play only a minor role in regulating global intracellular calcium concentration, increasing evidence points to an important role for PMCA in signal transduction, in particular in the nitric oxide signaling pathway. Moreover, recent evidence has shown the functional importance of PMCA in mediating cardiac contractility and vascular tone. Here we describe a method in determining PMCA activity in the microsomal membrane preparation from cultured cells that overexpress specific isoform of PMCA by using modified coupled enzyme assay. [less ▲]

Detailed reference viewed: 98 (0 UL)