微生物学

Cellular sensitivity is an approach to inhibit the growth of certain cells in response to any non-permissible conditions, as the presence of a cytotoxic agent or due to changes in growth parameters such as temperature, salt, or media components. Sensitivity tests are easy and informative assays to get insight into essential gene functions in various cellular processes. For example, cells having any functionally defective genes involved in DNA replication exhibit sensitivity to non-permissive temperatures and to chemical agents that block DNA replication fork movement. Here, we describe a sensitivity test for multiple strains of Saccharomyces cerevisiae and Candida albicans of diverged genetic backgrounds subjected to several genotoxic chemicals simultaneously. We demonstrate it by testing the sensitivity of DNA polymerase defective yeast mutants by using spot analysis combined with colony forming unit (CFU) efficiency estimation. The method is very simple and inexpensive, does not require any sophisticated equipment, can be completed in 2–3 days, and provides both qualitative and quantitative data. We also recommend the use of this reliable methodology for assaying the sensitivity of these and other fungal species to antifungal drugs and xenobiotic factors.

Oral mucositis is a common complication of cancer chemotherapy treatment. Because of the lack of relevant oral mucositis experimental models, it is not clear how chemotherapeutic agents injure the oral mucosa and if commensal microorganisms accelerate tissue damage. We developed an organotypic oral mucosa model that mimics cellular responses commonly associated with cytotoxic chemotherapy. The organotypic model consists of multilayer oral epithelial cells growing over a collagen type I matrix, with embedded fibroblasts. Treatment of organotypic constructs with the chemotherapeutic agent, 5-fluorouracil (5-FU), leads to major histopathologic changes resembling mucositis, such as DNA synthesis inhibition, increased apoptosis and cytoplasmic vacuolation. Candida albicans formed mucosal biofilms on these tissues and augmented the inflammatory responses to 5-FU. This model can be used in further mechanistic studies of oral mucositis and associated opportunistic infections.

In the presence of oxidative stress, cellular defense systems that can detoxify reactive oxygen species are activated through multiple signaling cascades and transcriptional reprogramming. The budding yeast Saccharomyces cerevisiae has served as an excellent model for genetically-identifying factors important for the response to oxidative stress. Here, we describe two assays for testing yeast gene deletion strains or strains overexpressing a gene of interest for viability following oxidative stress induced by hydrogen peroxide treatment. These include a plate-based spot assay for visualizing cell growth and a quantitative colony counting assay. As stress response assays can be highly variable depending on cell growth conditions, these protocols have been optimized for obtaining highly-reproducible results between experiments. We demonstrate the use of these protocols for genetic tests of a putative chromatin regulator implicated in regulating the transcriptional response to oxidative stress.

E. coli resides in the gastrointestinal tract of humans and other warm-blooded animals but recent studies have shown that E. coli can persist and grow in various external environments including soil. The general stress response regulator, RpoS, helps E. coli overcome various stresses, however its role in soil survival was unknown. This soil survival assay protocol was developed and used to determine the role of the general stress response regulator, RpoS, in the survival of E. coli in soil. Using this soil survival assay, we demonstrated that RpoS was important for the survival of E. coli in soil. This protocol describes the development of the soil survival assay especially the recovery of E. coli inoculated into soil and can be adapted to allow further investigations into the survival of other bacteria in soil.

Bdellovibrio bacteriovorus HD100 is an obligate predator that preys upon a wide variety of Gram negative bacteria. The biphasic growth cycle of Bdellovibrio includes a free-swimming attack phase and an intraperiplasmic growth phase, where the predator replicates its DNA and grows using the prey as a source of nutrients, finally dividing into individual cells (Sockett, 2009). Due to its obligatory predatory lifestyle, manipulation of Bdellovibrio requires two-member culturing techniques using selected prey microorganisms (Lambert et al., 2003). In this protocol, we describe a detailed workflow to grow and quantify B. bacteriovorus HD100 and its predatory ability, to easily carry out these laborious and time-consuming techniques.

The bacterial flagellar type III export apparatus consists of a cytoplasmic ATPase complex and a transmembrane export gate complex, which are powered by ATP and proton motive force (PMF) across the cytoplasmic membrane, respectively, and transports flagellar component proteins from the cytoplasm to the distal end of the growing flagellar structure where their assembly occurs (Minamino, 2014). The export gate complex can utilize sodium motive force in addition to PMF when the cytoplasmic ATPase complex does not work properly. A transmembrane export gate protein FlhA acts as a dual ion channel to conduct both H⁺ and Na⁺ (Minamino et al., 2016). Here, we describe how to measure the intracellular Na⁺ concentrations in living Escherichia coli cells using a sodium-sensitive fluorescent dye, CoroNa Green (Minamino et al., 2016). Fluorescence intensity measurements of CoroNa Green by epi-fluorescence microscopy allows us to measure the intracellular Na⁺ concentration quantitatively.

Akinetes are spore-like resting (dormant) cells formed by strains of filamentous cyanobacteria for surviving long periods of unfavorable conditions. During deprivation for potassium, vegetative photosynthetic cells along the filaments of the cyanobacterium Aphanizomenon ovalisporum (A. ovalisporum) (strain ILC-164) differentiate into akinetes. Akinetes are larger than vegetative cell, have a thick wall, accumulate storage compounds (cyanophycine, glycogen, lipids) and excess of DNA (Sukenik et al., 2015; Sukenik et al., 2007; Maldener et al., 2014). Differences in structure and composition between akinetes and vegetative cells allow separation and isolation of akinetes. Akinetes isolated by the described protocol can be utilized for protein analysis, measurements of metabolic activities, fluorescence in situ hybridization (FISH) studies and more.

Cyanobacteria are prokaryotic organisms performing oxygenic photosynthesis. The cyanobacterium Synechocystis sp. PCC 6803 is a model organism for the study of photosynthesis, gene regulation and biotechnological applications because it is easy to manipulate genetically. Moreover, this cyanobacterium can grow photoautotrophically as well as chemoheterotrophically in the dark utilizing glucose. Microbiologists often use optical density measured with a spectrophotometer for the comparison of growth performance of different strains in liquid cultures. Because Synechocystis sp. PCC 6803 (especially motile strains) tend to form aggregates under stress conditions this method might be not suitable for evaluation of different strains under different growth conditions. In addition, many labs are not well equipped with standardized photobioreactors and illumination facilities to ensure reproducibility of growth curves. Here, we describe a highly reproducible spot assay for viability analysis of Cyanobacterial strains.

The ability to enter monocyte-derived macrophage (MDM) in vitro is commonly used to define macrophage-tropic HIV-1 despite the fact that viruses vary continuously in their ability to enter MDMs in vitro, and MDMs vary in their ability to support HIV-1 entry (Joseph et al., 2014; Peters et al., 2006). This makes it difficult to distinguish viruses that are adapted to replicating in macrophage from those that are adapted to replicating in T cells. We use the Affinofile cell line ( Johnston et al., 2009) to assay for macrophage tropism by capitalizing on the fact that macrophage-tropic HIV-1 has an enhanced ability to enter cells expressing low levels of CD4 (Joseph et al., 2014; Peters et al., 2006; Duenas-Decamp et al., 2009; Dunfee et al., 2006; Gorry et al., 2002; Martin-Garcia et al., 2006; Peters et al., 2004) and Affinofile cells can be induced to express a wide range of CD4 densities (Johnston et al., 2009). We induce Affinofile cells to express either high or low CD4, infect those cells with pseudotyped reporter virus, and quantify percent infectivity at low CD4 relative to infectivity at high CD4. Macrophage-tropic viruses have an enhanced ability to infect at low CD4. Using this approach we have found that macrophage-tropic strains of HIV-1 are relatively rare and that most HIV-1 variants require high levels of CD4 to enter cells, a phenotype we have referred to as R5 T cell-tropic.

Antimicrobial peptides are known to disrupt bacterial membranes allowing solutes to flow across the membrane in an unregulated manner resulting in death of the organism. Disrupting the bacterial membrane would thus perturb the cells osmotic balance resulting in an initial influx of the external aqueous buffer. We have designed an assay to investigate how antimicrobial peptide concentration affects the ability of fluorescently labelled dextran moieties of differing molecular weight and hydrodynamic radii to cross membranes of viable bacteria. This assay was used to show that diffusion of low and high molecular weight dextrans into bacteria was a function of antimicrobial peptide concentration (Sani et al., 2013).