Methods in molecular biology (Clifton, N.J.) (Meth Mol Biol)

Publisher: Humana Press

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Current impact factor: 1.29

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Other titles Methods in molecular biology (Clifton, N.J.), Methods in molecular biology
ISSN 1940-6029
OCLC 24839341
Material type Series
Document type Journal / Magazine / Newspaper

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Humana Press

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Publications in this journal

  • Maria Jung, Barbara Uhl, Glen Kristiansen, Dimo Dietrich
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    ABSTRACT: Locus-specific analyses of DNA methylation patterns usually require a bisulfite conversion of the DNA, where cytosines are deaminated to uracils, while methylated and hydroxymethylated cytosines remain unaffected. The specific discrimination of hydroxymethylation and methylation can be achieved by introducing an oxidation of 5-hydroxymethylcytosines to 5-formylcytosines and subsequent bisulfite-mediated deamination of 5-formylcytosines.DNA methylation analysis of cell-free circulating DNA in liquid biopsies, i.e., blood samples (serum and plasma), urine, aspirates, bronchial lavages, pleural effusions, and ascites, is of great interest in clinical research. However, due to the generally low concentration of circulating cell-free DNA in body fluids, high volumes need to be analyzed. A reduction of this volume, e.g., by means of a polymer-mediated enrichment, is required in order to facilitate the bisulfite conversion. Further, these sample types usually contain a cellular fraction which is of additional interest and requires specific protocols for the sample preparation.Formalin-fixed, paraffin-embedded (FFPE) tissue is the most commonly used source for tissue-based clinical research. Due to degradation and covalent modifications of DNA in FFPE tissue samples, optimized protocols for the DNA preparation and bisulfite conversion are required.This chapter describes methods and protocols for the sample preparation and subsequent high-speed bisulfite conversion and DNA clean-up for several types of relevant samples, i.e., serum, plasma, urine, buffy coat, aspirates, sputum, lavages, effusions, ascites, swabs, fresh tissues, cell lines, FFPE tissues, and laser microdissected cells.Additionally, two real-time PCR assays for DNA quantification and quality control are described. The cytosine-free fragment (CFF) assay allows for the simultaneous quantification of bisulfite converted and total DNA and thus the determination of bisulfite conversion efficiency. The Mer9 real-time PCR assay amplifies the bisulfite converted sequence of the repetitive element Mer9 and enables the accurate quantification of minute DNA amounts, as present in microdissected cells and body fluids.
    Methods in molecular biology (Clifton, N.J.) 07/2015; DOI:10.1007/7651_2015_260
  • Lee M Butcher, Stephan Beck
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    ABSTRACT: DNA methylation is an epigenetic mark that is indispensable for mammalian development and occurs at cytosine residues throughout the genome (the "methylome"). Approximately 70 % of all CpG dinucleotides are affected by DNA methylation, which serve to "lock in" chromatin states and thus transcriptional programs. The systemic and pervasive occurrence of DNA methylation throughout the genome defines cellular identity and therefore requires genome-wide assays to fully appreciate and discern differential patterns of methylation that influence aspects of phenotypic plasticity including susceptibility to common complex disease.One method that permits methylome analysis is methylated DNA immunoprecipitation (MeDIP) combined with next-generation sequencing (MeDIP-seq). MeDIP uses an antibody raised against 5-methylcytosine to capture methylated fragments of DNA, which are subsequently sequenced to envisage the methylome landscape. The advantageous cost versus coverage balance of MeDIP-seq has made it the method of choice to replace or complement array-based methods for population epigenetic studies. Here we detail nano-MeDIP-seq, which allows methylome analysis using nanogram quantities of starting material.
    Methods in molecular biology (Clifton, N.J.) 07/2015; DOI:10.1007/7651_2015_259
  • Atsumasa Okada, Katsuhisa Tashiro, Tomoko Yamaguchi, Kenji Kawabata
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    ABSTRACT: Flk1-expressing (+) mesodermal cells are useful source for the generation of hematopoietic cells and cardiomyocytes from pluripotent stem cells (PSCs). However, they have been reported as a heterogenous population that includes hematopoietic and cardiac progenitors. Therefore, to provide a method for a highly efficient production of hematopoietic cells and cardiomyocytes, cell surface markers are often used for separating these progenitors in Flk1(+) cells. Our recent study has shown that the expression of coxsackievirus and adenovirus receptor (CAR), a tight junction component molecule, could divide mouse and human PSC- and mouse embryo-derived Flk1(+) cells into Flk1(+)CAR(-) and Flk1(+)CAR(+) cells. Flk1(+)CAR(-) and Flk1(+)CAR(+) cells efficiently differentiated into hematopoietic cells and cardiomyocytes, respectively. These results indicate that CAR is a novel cell surface marker for separating PSC-derived Flk1(+) mesodermal cells into hematopoietic and cardiac progenitors. We herein describe a differentiation method from PSCs into hematopoietic cells and cardiomyocytes based on CAR expression.
    Methods in molecular biology (Clifton, N.J.) 07/2015; DOI:10.1007/7651_2015_232
  • L Koumakis, G Potamias, M Tsiknakis, M Zervakis, V Moustakis
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    ABSTRACT: With the completion of the Human Genome Project and the emergence of high-throughput technologies, a vast amount of molecular and biological data are being produced. Two of the most important and significant data sources come from microarray gene-expression experiments and respective databanks (e,g., Gene Expression Omnibus-GEO ( http://www.ncbi.nlm.nih.gov/geo )), and from molecular pathways and Gene Regulatory Networks (GRNs) stored and curated in public (e.g., Kyoto Encyclopedia of Genes and Genomes-KEGG ( http://www.genome.jp/kegg/pathway.html ), Reactome ( http://www.reactome.org/ReactomeGWT/entrypoint.html )) as well as in commercial repositories (e.g., Ingenuity IPA ( http://www.ingenuity.com/products/ipa )). The association of these two sources aims to give new insight in disease understanding and reveal new molecular targets in the treatment of specific phenotypes.Three major research lines and respective efforts that try to utilize and combine data from both of these sources could be identified, namely: (1) de novo reconstruction of GRNs, (2) identification of Gene-signatures, and (3) identification of differentially expressed GRN functional paths (i.e., sub-GRN paths that distinguish between different phenotypes). In this chapter, we give an overview of the existing methods that support the different types of gene-expression and GRN integration with a focus on methodologies that aim to identify phenotype-discriminant GRNs or subnetworks, and we also present our methodology.
    Methods in molecular biology (Clifton, N.J.) 07/2015; DOI:10.1007/7651_2015_252
  • Yee Ki Lee, X Ran, K W H Lai, V Y M Lau, D C W Siu, H F Tse
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    ABSTRACT: Advances in differentiation of cardiomyocytes from human induced pluripotent stem cell (hiPSC) were emerged as a tool for modeling of cardiovascular disease that recapitulates the phenotype for the purpose of drug screening, biomarker discovery, and testing of single-nucleotide polymorphism (SNP) as a modifier for disease stratification. Here, we describe the (1) retroviral reprogramming strategies in the generation of human iPSC, (2) methodology in characterization of iPSC in order to identify the stem cell clones with the best quality, and (3) protocol of cardiac differentiation by modulation of Wnt signaling and β-catenin pathway.
    Methods in molecular biology (Clifton, N.J.) 07/2015; DOI:10.1007/7651_2015_273
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    ABSTRACT: Since its "re-discovery" in 2009, there has been significant interest in defining the genome-wide distribution of DNA marked by 5-hydroxymethylation at cytosine bases (5hmC). In recent years, technological advances have resulted in a multitude of unique strategies to map 5hmC across the human genome. Here we discuss the wide range of approaches available to map this modification and describe in detail the affinity based methods which result in the enrichment of 5hmC marked DNA for downstream analysis.
    Methods in molecular biology (Clifton, N.J.) 07/2015; DOI:10.1007/7651_2015_268
  • Talita Glaser, Ana Regina G Castillo, Ágatha Oliveira, Henning Ulrich
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    ABSTRACT: The central and peripheral nervous system is built by a network of many different neuronal phenotypes together with glial and other supporting cells. The repertoire of expressed receptors and secreted neurotransmitters and neuromodulators are unique for each single neuron leading to intracellular signaling cascades, many of them involving intracellular calcium signaling. Here we suggest the use of calcium signaling analysis upon specific agonist application to reliably identify neuronal phenotypes, being important not only for basic science, but also providing a reliable tool for functional characterization of cells prior to transplantation. Calcium imaging provides various cellular information including signaling amplitudes, cell localization, duration, and frequency. Microfluorimetry reveals a signal summarizing the entire population, and its use is indicated for high-throughput screening purposes.
    Methods in molecular biology (Clifton, N.J.) 07/2015; DOI:10.1007/7651_2015_271
  • Meaghan J Jones, Sumaiya A Islam, Rachel D Edgar, Michael S Kobor
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    ABSTRACT: Analysis of DNA methylation in a population context has the potential to uncover novel gene and environment interactions as well as markers of health and disease. In order to find such associations it is important to control for factors which may mask or alter DNA methylation signatures. Since tissue of origin and coinciding cell type composition are major contributors to DNA methylation patterns, and can easily confound important findings, it is vital to adjust DNA methylation data for such differences across individuals. Here we describe the use of a regression method to adjust for cell type composition in DNA methylation data. We specifically discuss what information is required to adjust for cell type composition and then provide detailed instructions on how to perform cell type adjustment on high dimensional DNA methylation data. This method has been applied mainly to Illumina 450K data, but can also be adapted to pyrosequencing or genome-wide bisulfite sequencing data.
    Methods in molecular biology (Clifton, N.J.) 07/2015; DOI:10.1007/7651_2015_262
  • Kerem Fidan, Ayyub Ebrahimi, Özlem H Çağlayan, Burcu Özçimen, Tamer T Önder
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    ABSTRACT: Induced pluripotent stem cells (iPSCs) offer great promise as tools for basic biomedical research, disease modeling, and drug screening. In this chapter, we describe the generation of patient-specific, transgene-free iPSCs from skin biopsies and peripheral blood mononuclear cells through electroporation of episomal vectors and growth under two different culture conditions. The resulting iPSC lines are characterized with respect to pluripotency marker expression through immunostaining, tested for transgene integration by PCR, and assayed for differentiation capacity via teratoma formation.
    Methods in molecular biology (Clifton, N.J.) 07/2015; DOI:10.1007/7651_2015_278
  • Knut Woltjen, Shin-Il Kim, Andras Nagy
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    ABSTRACT: Somatic cell reprogramming to induced pluripotent stem cells (iPSCs) is a revolutionary technology, with repercussions affecting modern functional genomics and regenerative medicine. Still, relatively little is known about the processes underlying this dramatic cellular and molecular metamorphosis. Reprogramming technology based on the implementation of piggyBac (PB) transposons has enabled studies of iPSC reprogramming mechanisms, shedding an increasing light on these processes. Unique characteristics of PB transposons such as efficient genomic integration, unlimited cargo capacity, robust gene expression, and even seamless excision highlight the importance of this transgenic tool in advancing stem cell biology. In this chapter, we provide a detailed overview of versatile primary iPSC generation from mouse somatic cells using PB transposons, and the subsequent establishment of robust secondary reprogramming systems. These protocols are highlighted with examples from recent studies as to how PB has been, and continues to be, conducive to the dissection of reprogramming processes at the cellular and molecular levels.
    Methods in molecular biology (Clifton, N.J.) 07/2015; DOI:10.1007/7651_2015_274
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    ABSTRACT: Microarray analysis in glioblastomas is done using either cell lines or patient samples as starting material. A survey of the current literature points to transcript-based microarrays and immunohistochemistry (IHC)-based tissue microarrays as being the preferred methods of choice in cancers of neurological origin. Microarray analysis may be carried out for various purposes including the following: i. To correlate gene expression signatures of glioblastoma cell lines or tumors with response to chemotherapy (DeLay et al., Clin Cancer Res 18(10):2930-2942, 2012) ii. To correlate gene expression patterns with biological features like proliferation or invasiveness of the glioblastoma cells (Jiang et al., PLoS One 8(6):e66008, 2013) iii. To discover new tumor classificatory systems based on gene expression signature, and to correlate therapeutic response and prognosis with these signatures (Huse et al., Annu Rev Med 64(1):59-70, 2013; Verhaak et al., Cancer Cell 17(1):98-110, 2010) While investigators can sometimes use archived tumor gene expression data available from repositories such as the NCBI Gene Expression Omnibus to answer their questions, new arrays must often be run to adequately answer specific questions. Here, we provide a detailed description of microarray methodologies, how to select the appropriate methodology for a given question, and analytical strategies that can be used. Experimental methodology for protein microarrays is outside the scope of this chapter, but basic sample preparation techniques for transcript-based microarrays are included here.
    Methods in molecular biology (Clifton, N.J.) 06/2015; DOI:10.1007/7651_2015_245
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    ABSTRACT: Regulation of gene expression is essential to enable embryonic stem cells (ESCs) to either self-renew or to differentiate. Translational regulation of mRNA plays a major role in regulating gene expression and has been shown to be important for ESC differentiation. Sucrose gradients can be used to separate mRNAs based on the number of associated ribosomes and this can be used as a readout of the rate of translation. Following centrifugation through a sucrose gradient, mRNAs can be recovered, purified, and analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) to determine their ribosomal load in different cell states. Here, we describe how to differentiate mouse ESCs to Neural Precursor Cells (NPCs) and analyze the rate of translation of individual mRNAs by qRT-PCR following polysome fractionation.
    Methods in molecular biology (Clifton, N.J.) 06/2015; DOI:10.1007/7651_2015_233
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    ABSTRACT: Protocols available for the cryopreservation of human embryonic stem (ES) and induced pluripotent stem (iPS) cells are very inefficient and laborious compared to those for the cryopreservation of murine ES/iPS cells or other general cell lines. While the vitrification method may be adequate when working with small numbers of human ES/iPS cells, it requires special skills and is unsuitable when working with large cell numbers. Here, we describe a simple and efficient method for the cryopreservation of hES/hiPS cells that is based on a conventional slow freezing method that uses a combination of Pronase/EDTA for Stem™ and CP-5E™ [final concentrations: 6 % hydroxyethyl starch, 5 % DMSO, and 5 % ethylene glycol in saline]. CP-5E™ is highly effective for the cryopreservation of small cell clumps produced by hES/hiPS colony detachment in the presence of Pronase and EDTA (Pronase/EDTA for Stem™, a formulation containing multiple digestive enzymes from Streptomyces griseus). This novel method would be quite useful for large-scale hES/iPS cell banking for use in clinical applications.
    Methods in molecular biology (Clifton, N.J.) 06/2015; DOI:10.1007/7651_2015_211
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    ABSTRACT: Genomic data analysis consists of techniques to analyze and extract information from genes. In particular, genome sequencing technologies allow to characterize genomic profiles and identify biomarkers and mutations that can be relevant for diagnosis and designing of clinical therapies. Studies often regard identification of genes related to inherited disorders, but recently mutations and phenotypes are considered both in diseases studies and drug designing as well as for biomarkers identification for early detection.Gene mutations are studied by comparing fold changes in a redundancy version of numeric and string representation of analyzed genes starting from macromolecules. This consists of studying often thousands of repetitions of gene representation and signatures identified by biological available instruments that starting from biological samples generate arrays of data representing nucleotides sequences representing known genes in an often not well-known sequence.High-performance platforms and optimized algorithms are required to manipulate gigabytes of raw data that are generated by the so far mentioned biological instruments, such as NGS (standing for Next-Generation Sequencing) as well as for microarray. Also, data analysis requires the use of several tools and databases that store gene targets as well as gene ontologies and gene-disease association.In this chapter we present an overview of available software platforms for genomic data analysis, as well as available databases with their query engines.
    Methods in molecular biology (Clifton, N.J.) 06/2015; DOI:10.1007/7651_2015_238
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    ABSTRACT: Antibodies able to bind and modify the function of cell surface signaling components in vivo are increasingly being used as therapeutic drugs. The identification of such "functional" antibodies from within large antibody pools is, therefore, the subject of intense research. Here we describe a novel cell-based expression and reporting system for the identification of functional antibodies from antigen-binding populations preselected with phage display. The system involves inducible expression of the antibody gene population from the Rosa-26 locus of embryonic stem (ES) cells, followed by secretion of the antibodies during ES cell differentiation. Target antigens are cell-surface signaling components (receptors or ligands) with a known effect on the direction of cell differentiation (FGFR1 mediating ES cell exit from self renewal in this particular protocol). Therefore, inhibition or activation of these components by functional antibodies in a few elite clones causes a shift in the differentiation outcomes of these clones, leading to their phenotypic selection. Functional antibody genes are then recovered from positive clones and used to produce the purified antibodies, which can be tested for their ability to affect cell fates exogenously. Identified functional antibody genes can be further introduced in different stem cell types. Inducible expression of functional antibodies has a temporally controlled protein-knockdown capability, which can be used to study the unknown role of the signaling pathway in different developmental contexts. Moreover, it provides a means for control of stem cell differentiation with potential in vivo applications.
    Methods in molecular biology (Clifton, N.J.) 06/2015; DOI:10.1007/7651_2015_270
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    ABSTRACT: Since the development of inhibitor-based defined culture conditions (known as "2i"), multiple clonal embryonic stem cell (ESC) lines can be readily derived from single cells isolated directly from mouse embryos. In addition to providing an efficient means to generate ES cells from compound transgenic or murine disease models on any genetic background, this technology can be used to investigate the process of ESC derivation at both a functional and molecular level. Here, we provide details of the procedure for both maximizing the number of cells in the donor tissue and subsequent effective derivation of multiple clonal ES cell lines.
    Methods in molecular biology (Clifton, N.J.) 05/2015; DOI:10.1007/7651_2015_253
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    ABSTRACT: Human Embryonic Stem Cells (hESC) offer an important resource as a limitless supply of any differentiated cell type of the human body. Keratocytes, cells from the corneal stroma, may have the potential for restoration of vision in cell therapy and biomedical engineering applications, but these specialized cells are not readily expanded in vitro. Here we describe a two-part method to produce keratocytes from the H1 hESC cell line. The hESC cells, maintained and expanded in feeder-free culture medium are first differentiated to neural crest cells using the stromal-derived inducing activity (SDIA) of the PA6 mouse embryonic fibroblast cell line. The resulting neural crest cells are selected by their expression of cell-surface CD271 and subsequently cultured as 3D pellets in a defined differentiation medium to induce a keratocyte phenotype.
    Methods in molecular biology (Clifton, N.J.) 05/2015; DOI:10.1007/7651_2015_231
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    ABSTRACT: Embryonic stem cell (ESC) culture comprises a mixture of cells that are primed to differentiate into different lineages. In conditions where ESCs self-renew, these primed populations continuously interconvert and consequently show highly dynamic coordinated changes in their expression of different sets of pluripotency and differentiation markers. It has become increasingly apparent that this transcriptional heterogeneity is an important characteristic of ESC culture. By sorting for specific populations of ESCs it is possible to enrich for cells with a capacity to colonize the embryo proper or the extra-embryonic lineages such as the descendents of the primitive endoderm or trophoblast. Here, we describe a method of isolating specific sub-sets of ESCs from the pluripotent cells present in in vitro ESC culture using SSEA1 antibody staining in combination with reporter lines and fluorescence activated cell sorting (FACS).
    Methods in molecular biology (Clifton, N.J.) 05/2015; DOI:10.1007/7651_2015_254
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    ABSTRACT: Mobile genetic elements are discrete DNA elements that can move around and copy themselves in a genome. As a ubiquitous component of the genome, mobile elements contribute to both genetic and epigenetic variation. Therefore, it is important to determine the genome-wide distribution of mobile elements. Here we present a targeted high-throughput sequencing protocol called Mobile Element Scanning (ME-Scan) for genome-wide mobile element detection. We will describe oligonucleotides design, sequencing library construction, and computational analysis for the ME-Scan protocol.
    Methods in molecular biology (Clifton, N.J.) 05/2015; DOI:10.1007/7651_2015_265
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    ABSTRACT: There can now be little doubt that the cis-regulatory genome represents the largest information source within the human genome essential for health. In addition to containing up to five times more information than the coding genome, the cis-regulatory genome also acts as a major reservoir of disease-associated polymorphic variation. The cis-regulatory genome, which is comprised of enhancers, silencers, promoters, and insulators, also acts as a major functional target for epigenetic modification including DNA methylation and chromatin modifications. These epigenetic modifications impact the ability of cis-regulatory sequences to maintain tissue-specific and inducible expression of genes that preserve health. There has been limited ability to identify and characterize the functional components of this huge and largely misunderstood part of the human genome that, for decades, was ignored as "Junk" DNA. In an attempt to address this deficit, the current chapter will first describe methods of identifying and characterizing functional elements of the cis-regulatory genome at a genome-wide level using databases such as ENCODE, the UCSC browser, and NCBI. We will then explore the databases on the UCSC genome browser, which provides access to DNA methylation and chromatin modification datasets. Finally, we will describe how we can superimpose the huge volume of study data contained in the NCBI archives onto that contained within the UCSC browser in order to glean relevant in vivo study data for any locus within the genome. An ability to access and utilize these information sources will become essential to informing the future design of experiments and subsequent determination of the role of epigenetics in health and disease and will form a critical step in our development of personalized medicine.
    Methods in molecular biology (Clifton, N.J.) 05/2015; DOI:10.1007/7651_2015_263