Abstract:
:Mechanistic modeling in biology allows to investigate, based on first principles, if putative hypotheses are compatible with observations and to drive further experimental works. Along this line, polymer modeling has been instrumental in 3D genomics to better understand the impact of key mechanisms on the spatial genome organization. Here, I describe how polymer-based models can be practically used to study the role of epigenome in chromosome folding. I illustrate this methodology in the context of Drosophila epigenome folding.
journal_name
Methods Mol Bioljournal_title
Methods in molecular biology (Clifton, N.J.)authors
Jost Ddoi
10.1007/978-1-0716-1390-0_15keywords:
["Chromosome organization","Coarse-graining","Drosophila","Epigenomics","Polymer physics","Simulations"]subject
Has Abstractpub_date
2022-01-01 00:00:00pages
293-305eissn
1064-3745issn
1940-6029journal_volume
2301pub_type
杂志文章相关文献
文献大全abstract::The chemical composition of Cannabis sativa L. has been extensively studied for tens of years, but little is known about its lipidome. This chapter describes an analytical workflow for polar lipid determination in hemp. After extraction, lipids are enriched and isolated by graphitized carbon black sorbent, and the iso...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1410-5_17
更新日期:2021-01-01 00:00:00
abstract::Charge-switch derivatization to convert long-chain fatty acids (LCFAs) to their N-(4-aminomethylphenyl) pyridinium (AMPP) derivatives (FA-AMPP derivative) drastically increases their sensitivity (>102) detected by electrospray ionization (ESI) or matrix assisted laser desorption ionization (MALDI). Lipidomic analyses ...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1410-5_7
更新日期:2021-01-01 00:00:00
abstract::Here, we describe a proteomic pipeline to use a human microglial cell line as a biological model to study schizophrenia. In order to maximize the proteome coverage, we apply two-dimensional liquid chromatography coupled with ultra-definition MSE mass spectrometry (LC-UDMSE) using a data-independent acquisition (DIA) a...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1024-4_24
更新日期:2021-01-01 00:00:00
abstract::Post-translational modifications (PTMs) are essential for the regulation of all cellular processes. The interplay of various PTMs on a single protein or different proteins comprises a complexity that we are far from understanding in its entirety. Reliable strategies for the enrichment and accurate quantification of PT...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1024-4_14
更新日期:2021-01-01 00:00:00
abstract::Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when multiple quantitative comparisons of samples must be made, and even for large samples ...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1024-4_4
更新日期:2021-01-01 00:00:00
abstract::Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several ...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1406-8_11
更新日期:2021-01-01 00:00:00
abstract::Protein Data Bank is the single worldwide archive of experimentally determined macromolecular structure data. Established in 1971 as the first open access data resource in biology, the PDB archive is managed by the worldwide Protein Data Bank (wwPDB) consortium which has four partners-the RCSB Protein Data Bank (RCSB ...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1406-8_1
更新日期:2021-01-01 00:00:00
abstract::Advances in induced pluripotent stem cell (iPSC) technology provide a renewable source of cells for tissue regeneration and therefore hold great promise for cell replacement therapy. However, immune rejection of allograft due to human leukocyte antigen (HLA) mismatching remains a major challenge. Considerable efforts ...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/7651_2021_352
更新日期:2021-05-05 00:00:00
abstract::The formation of electrostatic interactions between polyanionic siRNA and polycations gives an easy access to the formation of colloidal particles capable of delivering siRNA in vitro or in vivo. Among the polycations used for siRNA delivery, chitosan occupies a special place due to its unique physicochemical and biol...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1298-9_17
更新日期:2021-01-01 00:00:00
abstract::GalNAc oligonucleotide conjugates demonstrate improved potency in vivo due to selective and efficient delivery to hepatocytes in the liver via receptor-mediated endocytosis. GalNAc-siRNA and GalNAc-antisense oligonucleotides are at various stages of clinical trials, while the first two drugs were already approved by F...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1298-9_7
更新日期:2021-01-01 00:00:00
abstract::Metabolomics, lipidomics, and the study of cellular metabolism are gaining increasing interest particularly in the field of immunology, since the activation and effector functions of immune cells are profoundly controlled by changes in cellular metabolic asset. Among the different techniques that can be used for the e...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1311-5_24
更新日期:2021-01-01 00:00:00
abstract::Human T cells represent a heterogeneous population, including cells with different phenotypical and function properties. Despite, in the last years, several technologies were developed to investigate phenotypical properties of T cells at single cell level, in vitro T cell clone 's culture remains the only way to perfo...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1311-5_14
更新日期:2021-01-01 00:00:00
abstract::CD4+ T cells or helper T cells play various roles in the immune response to pathogens, tumors, as well as in asthma, allergy, and autoimmunity. Consequently, there is great interest in the comprehensive investigation of different T helper cell subsets. Here, we use mass cytometry (CyTOF), which is similar to flow cyto...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1311-5_4
更新日期:2021-01-01 00:00:00
abstract::The presence of sialic acids is one characteristic of glycosylated therapeutic proteins. The presence of these charged monosaccharides is critical for the immunogenicity properties and structural properties of the proteins. Profiling of the N-glycans and their charge state is a requisite for complete protein character...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1241-5_17
更新日期:2021-01-01 00:00:00
abstract::Glycosylation is a crucial posttranslational modification (PTM) that might affect the safety and efficacy of monoclonal antibodies (mAbs). Capillary electrophoresis-mass spectrometry (CE-MS) enables the characterization of the primary structure of mAbs. A bottom-up proteomic workflow is designed to provide detailed in...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1241-5_7
更新日期:2021-01-01 00:00:00
abstract::Transposable elements (TEs) are powerful generators of major-effect mutations, most of which are deleterious at the species level and maintained at very low frequencies within populations. As reference genomes can only capture a minor fraction of such variants, methods were developed to detect TE insertion polymorphis...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1134-0_15
更新日期:2021-01-01 00:00:00
abstract::Miniature form transposable elements (mTEs) are ubiquitous in plant genomes and directly linked to gene regulation and evolution. With the advantage of completely sequenced genomes of Brassica rapa and Brassica oleracea, an open-source web portal called, BrassicaTED was developed. This database provides a user-friendl...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1134-0_5
更新日期:2021-01-01 00:00:00
abstract::Current computer architectures, coupled with state-of-the-art molecular dynamics simulation software, facilitate the in-depth study of large biomolecular systems at high levels of detail. However, biological phenomena take place at various time and length scales and as a result a multiscale approach must be adopted. O...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1394-8_14
更新日期:2021-01-01 00:00:00
abstract::Ion channels play crucial roles in cell physiology, and are a major class of targets for clinically relevant pharmaceuticals. Because they carry ionic current, the function and pharmacology of ion channels can be studied using electrophysiological approaches that range in resolution from the single molecule to many mi...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1394-8_4
更新日期:2021-01-01 00:00:00
abstract::Linear dichroism (LD) is the differential absorbance of light polarized parallel and perpendicular to an orientation direction. Any oriented sample will show a signal in its electronic as well as vibrational transitions. Model membrane small unilamellar vesicles or liposomes provide an oriented system when they are su...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1197-5_21
更新日期:2021-01-01 00:00:00
abstract::This chapter describes the use of NMR to screen a fragment library as part of a fragment-based lead discovery (FBLD) campaign. The emphasis is on the practicalities involved in fragment screening by NMR, with particular attention to the use of 1D ligand-observed 1H NMR experiments. An overview of the theoretical consi...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1197-5_11
更新日期:2021-01-01 00:00:00
abstract::One essential prerequisite of any experiment involving a purified protein, such as interaction studies or structural and biophysical characterization, is to work with a "good-quality" sample in order to ensure reproducibility and reliability of the data. Here, we define a "good-quality" sample as a protein preparation...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1197-5_1
更新日期:2021-01-01 00:00:00
abstract::There is a growing expectation that research will be used to inform decision-making. It is important for researchers to understand how health policy is developed and the different ways they can influence the development of policy.Public policy is developed to resolve identified problems. Health policy is a subset of p...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1138-8_28
更新日期:2021-01-01 00:00:00
abstract::As technology advances, diagnostic tests continue to improve and each year, we are presented with new alternatives to standard procedures. Given the plethora of diagnostic alternatives, diagnostic tests must be evaluated to determine their place in the diagnostic armamentarium. The first step involves determining the ...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1138-8_18
更新日期:2021-01-01 00:00:00
abstract::In longitudinal studies, the relationship between exposure and disease can be measured once or multiple times while participants are monitored over time. Traditional regression techniques are used to model outcome data when each epidemiological unit is observed once. These models include generalized linear models for ...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1138-8_8
更新日期:2021-01-01 00:00:00
abstract::Yarrowia lipolytica has emerged as an attractive solution for screening enzyme activities thanks to the numerous tools available for heterologous protein production and its strong secretory ability. Nowadays, activity screening for improved enzymes mostly relies on the evaluation of independent clones in microtiter pl...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1414-3_14
更新日期:2021-01-01 00:00:00
abstract::Metabolic engineering frequently requires both gene knockouts and gene integration. CRISPR-Cas9 has been extensively used to create double-stranded DNA breaks that result in indel mutations; however, such mutations can revert or create toxic product. Gene integration can also be accomplished by CRISPR-Cas9 introduced ...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1414-3_4
更新日期:2021-01-01 00:00:00
abstract::Single-stranded DNA-binding proteins (SSBs) are essential to all living organisms as protectors and guardians of the genome. Apart from the well-characterized RPA, humans have also evolved two further SSBs, termed hSSB1 and hSSB2. Over the last few years, we have used NMR spectroscopy to determine the molecular and st...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1290-3_14
更新日期:2021-01-01 00:00:00
abstract::Single-stranded DNA (ssDNA)-binding protein (SSB) is essential for DNA metabolic processes. SSB also binds to many DNA-binding proteins that constitute the SSB interactome. The mechanism through which PriA helicase, an initiator protein in the DNA replication restart process, is stimulated by SSB in Escherichia coli (...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1290-3_4
更新日期:2021-01-01 00:00:00
abstract::Immunofluorescence staining of tissues has become a reliable and informative technique used in a diverse set of applications, ranging from simple detection of an antigen of interest in a specific location to the semiquantitative analysis of spatial relationships between multiple antigens and/or cell types. During comp...
journal_title:Methods in molecular biology (Clifton, N.J.)
pub_type: 杂志文章
doi:10.1007/978-1-0716-1016-9_17
更新日期:2021-01-01 00:00:00