Methods in molecular biology最新文献

Hypothyroidism, characterized by inadequate production of thyroid hormones, and malaria, a mosquito-borne infectious disease caused by Plasmodium parasites, are significant health concerns worldwide. Understanding the interplay between these two conditions could offer insights into their complex relationship and potential therapeutic strategies. To induce hypothyroidism, pharmacological inhibition of thyroid hormone synthesis was employed. Subsequently, mice were infected with Plasmodium berghei ANKA to simulate cerebral malaria infection. It needs to monitor the progression of the disease in male mice before it can identify infiltrating immune system populations of interest in the brain by multiparametric techniques such as flow cytometry.

Electrophoretic Mobility Shift Assay (EMSA) is a powerful technique for studying nucleic acid and protein interactions. This technique is based on the principle that nucleic acid-protein complex and nucleic acid migrate at different rates due to differences in size and charge. Nucleic acid and protein interactions are fundamental to various biological processes, such as gene regulation, replication, transcription, and recombination. Transcription factors and DNA interaction regulate gene expression. Homeobox (Hox) genes encode a family of transcription factors and are essential during embryonic development. Understanding the specific interactions between Hox proteins and their DNA targets is critical for elucidating the mechanisms underlying their regulatory functions.This chapter explains the principles and methodologies of EMSA in the context of Hox genes. This chapter includes detailed experimental design, including the formulation of reagents, labeling DNA probes, preparation of nuclear extracts/recombinant proteins, and binding conditions. The step-by-step protocol has been provided as an initial reference point to help a researcher conduct EMSA.

A key goal of biology is to understand the origin of the many cell types that can be observed during diverse processes such as development, regeneration, and disease. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the origins of cell states and relationships between cells remains challenging. Here we present LINNAEUS (Spanjaard et al, Nat Biotechnol 36:469-473. https://doi.org/10.1038/nbt.4124 , 2018; Hu et al, Nat Genet 54:1227-1237. https://doi.org/10.1038/s41588-022-01129-5 , 2022) (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, LINNAEUS can be used to reconstruct organism-wide single-cell lineage trees. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.

Measurements of cell phylogeny based on natural or induced mutations, known as lineage barcodes, in conjunction with molecular phenotype have become increasingly feasible for a large number of single cells. In this chapter, we delve into Quantitative Fate Mapping (QFM) and its computational pipeline, which enables the interrogation of the dynamics of progenitor cells and their fate restriction during development. The methods described here include inferring cell phylogeny with the Phylotime model, and reconstructing progenitor state hierarchy, commitment time, population size, and commitment bias with the ICE-FASE algorithm. Evaluation of adequate sampling based on progenitor state coverage statistics is emphasized for interpreting the QFM results. Overall, this chapter describes a general framework for characterizing the dynamics of cell fate changes using lineage barcoding data.

The human genome is composed of distinct genomic regions that are susceptible to various types of somatic mutations. Among these, Short Tandem Repeats (STRs) stand out as the most mutable genetic elements. STRs are short repetitive polymorphic sequences, predominantly situated within noncoding sectors of the genome. The intrinsic repetition characterizing these sequences makes them highly mutable in vivo. Consequently, this characteristic provides the chance to unravel the natural developmental history of human viable cells retrospectively. However, STRs also introduce stutter noise in vitro amplification, which makes their analysis challenging. Here we describe our integrated biochemical-computational platform for single-cell lineage analysis. It consists of a pipeline whose inputs are single cells and whose output is a lineage tree of input cells.

Metabolic profiling performed using untargeted metabolomics of different, complex biological samples aims to apply agnostic/holistic, hypothesis-free, analysis of the small molecules that are present in the analyzed sample. This approach has been the center of major investments and dedicated efforts from the research community for many years. However, limitations and challenges remain, particularly with regard to the validation and the quality of the obtained results. This has led to increasing community engagement, with the formation of think tanks, the establishment of working groups, and the many seminars on quality control (QC) in metabolomics. Here we describe a quality control (QC) protocol used to monitor LC-MS-based metabolomics analysis. A key target is the monitoring of analytical precision. This methodology is described for the analysis of urine but can be applied to different biological matrices, such as various biofluids, cell, and tissue extracts.

Lipidomics has attracted attention in the discovery of unknown biomolecules and for capturing the changes in metabolism caused by genetic and environmental factors in an unbiased manner. However, obtaining reliable lipidomics data, including structural diversity and quantification data, is still challenging. Supercritical fluid chromatography (SFC) is a suitable technique for separating lipid molecules with high throughput and separation efficiency. Here, we describe a quantitative lipidomics method using SFC coupled with mass spectrometry. This technique is suitable for characterizing the structural diversity of lipids (e.g., phospholipids, sphingolipids, glycolipids, and glycerolipids) with high quantitative accuracy to understand their biological functions.

The role of shear stress in regulating aqueous humor (AH) outflow and intraocular pressure (IOP) in the trabecular meshwork (TM) and Schlemm's canal (SC) of the eye is an emerging field. Shear stress has been shown to activate mechanosensitive ion channels in TM cells and induce nitric oxide production in SC cells, which can affect outflow resistance and lower IOP. Live-cell imaging using fluorescent protein sensors has provided real-time data to investigate the physiological relationship between fluid flow and shear stress in the outflow pathway cells. The successful application of time-lapse live-cell imaging in primary cultured cells has led to the identification of key cellular and molecular mechanisms involved in regulating AH outflow and IOP, including the role of autophagy and primary cilia as mechanosensors. This chapter presents a detailed protocol for conducting time-lapse live-cell imaging under fluid flow conditions in the outflow pathway cells.

Mitochondrial morphology and membrane potential (Δψ) are important readouts of mitochondrial function. Integrated analysis of these parameters in living cells can be performed using fluorescent lipophilic cations, which enter cells and accumulate in the mitochondrial matrix in a Δψ-dependent manner. Here, we describe the use of tetramethylrhodamine methyl ester (TMRM) and Mitotracker Green FM (MG) for mitochondrial morphology and semiquantitative Δψ analysis in living primary human skin fibroblasts (PHSFs). Practically, we present an integrated protocol to quantify mitochondrial morphology parameters and signal intensity using epifluorescence microscopy of PHSFs co-stained with TMRM and MG. This approach performs best using large flat cells like PHSFs, which display a high mitochondria-specific fluorescence signal and are imaged at a relatively high (x40) magnification.

Measuring respiration rate can be a powerful way to assess energetic function in isolated mitochondria and intact cells. Current plate-based methods have several advantages over older suspension-based systems, including greater throughput and the requirement of only microgram quantities of material. In this chapter, we provide an update to our previously published methods for plate-based measurement of oxygen consumption in isolated adherent mitochondria in a 96-well format plate. We also describe methods for performing the same measurements on intact cells in a 96-well format.