Journal: Methods in Molecular Biology

Abbreviation

Methods Mol Biol

Publisher

Humana

Journal Volumes

ISSN

1064-3745
1940-6029

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Publications 1 - 10 of 42
  • Influenza Virus
    Item type: Edited Volume
    (2025)
    Methods in Molecular Biology
  • Understanding Influenza
    Item type: Book Chapter
    Hutchinson, Edward C.; Amorim, Maria João; Yamauchi, Yohei (2025)
    Methods in Molecular Biology ~ Influenza Virus: Methods and Protocols
    Influenza, a serious illness of humans and domesticated animals, has been studied intensively for many years. It therefore provides an example of how much we can learn from detailed studies of an infectious disease, and of how even the most intensive scientific research leaves further questions to answer. This introduction is written for researchers who have become interested in one of these unanswered questions, but who may not have previously worked on influenza. To investigate these questions, researchers must not only have a firm grasp of relevant methods and protocols; they must also be familiar with the basic details of our current understanding of influenza. This chapter briefly covers the burden of disease that has driven influenza research, summarizes how our thinking about influenza has evolved over time, and sets out key features of influenza viruses by discussing how we classify them and what we currently understand of their replication. It does not aim to be comprehensive, as any researcher will read deeply into the specific areas that have grasped their interest. Instead, it aims to provide a general summary of how we came to think about influenza in the way we do now, in the hope that the reader’s own research will help us to understand it better.
  • Correction to: Understanding Influenza
    Item type: Book Chapter
    Hutchinson, Edward C.; Amorim, Maria João; Yamauchi, Yohei (2025)
    Methods in Molecular Biology ~ Influenza Virus: Methods and Protocols
    Influenza, a serious illness of humans and domesticated animals, has been studied intensively for many years. It therefore provides an example of how much we can learn from detailed studies of an infectious disease, and of how even the most intensive scientific research leaves further questions to answer. This introduction is written for researchers who have become interested in one of these unanswered questions, but who may not have previously worked on influenza. To investigate these questions, researchers must not only have a firm grasp of relevant methods and protocols; they must also be familiar with the basic details of our current understanding of influenza. This chapter briefly covers the burden of disease that has driven influenza research, summarizes how our thinking about influenza has evolved over time, and sets out key features of influenza viruses by discussing how we classify them and what we currently understand of their replication. It does not aim to be comprehensive, as any researcher will read deeply into the specific areas that have grasped their interest. Instead, it aims to provide a general summary of how we came to think about influenza in the way we do now, in the hope that the reader's own research will help us to understand it better.
  • Microfluidics for single-cell study of antibiotic tolerance and persistence induced by nutrient limitation
    Item type: Book Chapter
    Moreno-Gámez, Stefany; Dal Co, Alma; van Vliet, Simon; et al. (2021)
    Methods in Molecular Biology ~ Bacterial Persistence
    Nutrient limitation is one of the most common triggers of antibiotic tolerance and persistence. Here, we present two microfluidic setups to study how spatial and temporal variation in nutrient availability lead to increased survival of bacteria to antibiotics. The first setup is designed to mimic the growth dynamics of bacteria in spatially structured populations (e.g., biofilms) and can be used to study how spatial gradients in nutrient availability, created by the collective metabolic activity of a population, increase antibiotic tolerance. The second setup captures the dynamics of feast-and-famine cycles that bacteria recurrently encounter in nature, and can be used to study how phenotypic heterogeneity in growth resumption after starvation increases survival of clonal bacterial populations. In both setups, the growth rates and metabolic activity of bacteria can be measured at the single-cell level. This is useful to build a mechanistic understanding of how spatiotemporal variation in nutrient availability triggers bacteria to enter phenotypic states that increase their tolerance to antibiotics.
  • Applications of MicroArrays for Mass Spectrometry (MAMS) in Single-Cell Metabolomics
    Item type: Book Chapter
    Ibáñez, Alfredo J.; Svatos, Ales (2020)
    Methods in Molecular Biology ~ Single Cell Metabolism
    The metabolic network is the endpoint in the flow of information that begins with the "gene" and ends with "phenotype" (observable function) of the cell. Previously, due to the variety of metabolites analyzed inside cells, the metabolomic measurements were performed with samples including multiple cells. Unfortunately, this sampling process may mask important metabolic phenomena, such as cell-to-cell heterogeneity. For these studies, we must use analytical techniques that can robustly deliver reproducible results with single-cell sensitivity. In this chapter, we summarize laser-based methods for single-cell analysis and a novel approach of MicroArrays for Mass Spectrometry (or MAMS) is described in full detail. This particular type of microarrays was tailored for the study of cells grown in liquid medium using multiple-analytical readouts, such as optical and laser desorption/ionization (LDI) or MALDI mass spectrometry.
  • High-Throughput RPLC-MS/MS Quantification of Short- and Medium-Chain Fatty Acids
    Item type: Book Chapter
    Schauer, Stefan; Othman, Alaa (2025)
    Methods in Molecular Biology ~ Clinical Metabolomics
    Short- and medium-chain fatty acids (SMCFA) are monocarboxylic acids with a carbon chain length of 1–12 carbon atoms. They are mainly produced in humans by the gut microbiota, play crucial metabolic roles, are vital for intestinal health, and have multifaceted impact on immune and neurological functions. Accurate detection and quantification of SMCFA in different human biofluids is achieved using 3-nitro phenylhydrazine (3-NPH) derivatization of the free fatty acids followed by reverse phase liquid chromatography (RPLC) separation and detection by tandem mass spectrometry (MS/MS). Here, we describe the simultaneous measurement of 14 SMCFA and lactate in detail. All 3-NPH-SMCFA-hydrazones are separated in less than 5 min with an 8-min total run time (injection-to-injection). Linear dynamic range over 0.1–500 μM is achieved for most SCFAs, while it is 0.05–100 μM for MCFAs. Validation of the procedure depicts good linearity (R2 > 0.98) and repeatability (CV ≤ 20%). The lower limit of detection (LLOD) is 10–30 nM. The lower limit of quantification (LLOQ) is 50–100 nM for most analytes, while it is 0.5 μM for acetate. In conclusion, the method offers several benefits compared to alternative methods regarding throughput, selectivity, sensitivity, and robustness.
  • A MALDI-MS Methodology for Studying Metabolic Heterogeneity of Single Cells in a Population
    Item type: Book Chapter
    Krismer, Jasmin; Sobek, Jens; Steinhoff, Robert F.; et al. (2020)
    Methods in Molecular Biology ~ Single Cell Metabolism
    Mass spectrometry based metabolomics is the highly multiplexed, label-free analysis of small molecules such as metabolites or lipids in biological systems, and thus one of the most direct ways to characterize phenotypes. However, the phenotyping of populations with single-cell resolution is a great challenge due to the small number of molecules contained in an individual cell. Here we describe a microarray-based sample preparation workflow for MALDI mass spectrometry that has single-cell sensitivity and allows high-throughput analysis of lipids and pigments in single algae cells. The microarray targets receive individual cells in 1430 separate spots that allow the cells to be lysed individually without cross-contamination. Using positive ion mode and 2,5-dihydroxybenzoic acid as the MALDI matrix, the mass spectra unveil information about the relative composition of more than 20 different lipids/pigments in each individual cell within the population. Thus, the method allows the analysis of cellular phenotypes in a population on a completely new level.
  • Induced Formation of Plasma Membrane Protrusions with Porous Materials as Instructive Surfaces
    Item type: Book Chapter
    Aramesh, Morteza; Persson, Cecilia (2024)
    Methods in Molecular Biology ~ Imaging Cell Signaling
    The plasma membrane is a vital component in cellular processes, and its structure has a significant impact on cellular behavior. The physical characteristics of the extracellular environment, along with the presence of surface pores, can influence the formation of membrane protrusions. Nanoporous surfaces have demonstrated their capacity to induce membrane protrusions in both adherent and non-adherent cells. This chapter presents a methodology that utilizes a nanoporous substrate with nanotopographical constraints to effectively stimulate the formation of membrane protrusions in cells.
  • Selection on the Protein-Coding Genome
    Item type: Book Chapter
    Kosiol, Carolin; Anisimova, Maria (2012)
    Methods in Molecular Biology ~ Evolutionary Genomics. Statistical and Computational Methods. 2
  • Enrichment of Persister Cells Through Β-Lactam-Induced Filamentation and Size Separation
    Item type: Book Chapter
    Windels, Etthel; Van den Bergh, Bram; Michiels, Jan (2021)
    Methods in Molecular Biology ~ Bacterial Persistence
    Analyzing persisters at the single-cell level is crucial to properly define their phenotypic traits. However, single-cell analyses are challenging due to the rare and temporary nature of persister cells, thus requiring their rapid and efficient enrichment in a culture. Existing methods to isolate persisters from a bacterial population show important shortcomings, including contamination with susceptible cells and/or cell debris, which complicate subsequent microscopic analyses. We here describe a protocol to enrich persisters in a culture using β-lactam-induced filamentation followed by size separation. This protocol minimizes the amount of cell debris in the final sample, facilitating single-cell studies of persister cells.
Publications 1 - 10 of 42