Simulation-based inference of differentiation trajectories from RNA velocity fields.

We report Cytopath, a method for trajectory inference that takes advantage of transcriptional activity information from the RNA velocity of single cells to perform trajectory inference. Cytopath performs this task by defining a Markov chain model, simulating an ensemble of possible differentiation trajectories, and constructing a consensus trajectory. We show that Cytopath can recapitulate the topological and molecular characteristics of the differentiation process under study. In our analysis, we include differentiation trajectories with varying bifurcated, circular, convergent, and mixed topologies studied in single-snapshot as well as time-series single-cell RNA sequencing experiments. We demonstrate the capability to reconstruct differentiation trajectories, assess the association of RNA velocity-based pseudotime with actually elapsed process time, and identify drawbacks in current state-of-the art trajectory inference approaches.

Assessment of legionella-specific immunity in mice.

Legionella pneumophila is the causative agent of the potentially fatal Legionnaires' disease in humans. Mice have proved to be valuable model organisms to study the pathogenesis of this intracellular bacterium, as well as immune responses against it. In this chapter we describe a selection of mouse infection protocols to study the innate and adaptive immune responses raised after an infection with Legionella. Included are protocols for systemic and pulmonary infections, surgical collection of organs as well as determination of cell composition, cytokines, and antibody titers therein. Furthermore, we describe an immunohistology protocol to analyze lung tissue sections by fluorescence microscopy.