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- Assessing Tolerance to Heavy-Metal Stress in Arabidopsis thaliana SeedlingsPublication . Remy, Estelle; Duque, PaulaHeavy-metal soil contamination is one of the major abiotic stress factors that, by negatively affecting plant growth and development, severely limit agricultural productivity worldwide. Plants have evolved various tolerance and detoxification strategies in order to cope with heavy-metal toxicity while ensuring adequate supply of essential micronutrients at the whole-plant as well as cellular levels. Genetic studies in the model plant Arabidopsis thaliana have been instrumental in elucidating such mechanisms. The root assay constitutes a very powerful and simple method to assess heavy-metal stress tolerance in Arabidopsis seedlings. It allows the simultaneous determination of all the standard growth parameters affected by heavy-metal stress (primary root elongation, lateral root development, shoot biomass, and chlorophyll content) in a single experiment. Additionally, this protocol emphasizes the tips and tricks that become particularly useful when quantifying subtle alterations in tolerance to a given heavy-metal stress, when simultaneously pursuing a large number of plant lines, or when testing sensitivity to a wide range of heavy metals for a single line.
- Methods for the Measurement of Early Events in Toxoplasma gondii Immunity in Mouse CellsPublication . Alvarez, Catalina; Campos, Ana Claudia; Howard, Jonathan C; Loureiro, Joana; Müller, Urs Benedikt; Rodrigues, Ana LinaCritical steps in resistance of mice against Toxoplasma gondii occur in the first 2 or 3 h after the pathogen has entered a cell that has been exposed to interferon γ (IFNγ). The newly formed parasitophorous vacuole is attacked by the IFNγ-inducible IRG proteins and disrupted, resulting in death of the parasite and necrotic death of the cell. Here we describe some techniques that we have used to describe and quantify these events in different combinations of the host and the parasite.
- Quantitative Microscopy Reveals Centromeric Chromatin Stability, Size, and Cell Cycle Mechanisms to Maintain Centromere HomeostasisPublication . Stankovic, Ana; Jansen, Lars E. T.Centromeres are chromatin domains specified by nucleosomes containing the histone H3 variant, CENP-A. This unique centromeric structure is at the heart of a strong self-templating epigenetic mechanism that renders centromeres heritable. We review how specific quantitative microscopy approaches have contributed to the determination of the copy number, architecture, size, and dynamics of centromeric chromatin and its associated centromere complex and kinetochore. These efforts revealed that the key to long-term centromere maintenance is the slow turnover of CENP-A nucleosomes, a critical size of the chromatin domain and its cell cycle-coupled replication. These features come together to maintain homeostasis of a chromatin locus that directs its own epigenetic inheritance and facilitates the assembly of the mitotic kinetochore.
- The scaling of genetic diversity in a changing and fragmented worldPublication . Arenas, M.; Mona, S.; Trochet, A.; Sramkova Hanulova, A.; Currat, M.; Ray, N.; Chikhi, L.; Rasteiro, R.; Schmeller, D.S.; Excoffier, L.Most species do not live in a constant environment over space or time. Their environment is often heterogeneous with a huge variability in resource availability and exposure to pathogens or predators, which may affect the local densities of the species. Moreover, the habitat might be fragmented, preventing free and isotropic migrations between local sub-populations (demes) of a species, making some demes more isolated than others. For example, during the last ice age populations of many species migrated towards refuge areas from which re-colonization originated when conditions improved. However, populations that could not move fast enough or could not adapt to the new environmental conditions faced extinctions. Populations living in these types of dynamic environments are often referred to as metapopulations and modeled as an array of subdivisions (or demes) that exchange migrants with their neighbors. Several studies have focused on the description of their demography, probability of extinction and expected patterns of diversity at different scales. Importantly, all these evolutionary processes may affect genetic diversity, which can affect the chance of populations to persist. In this chapter we provide an overview on the consequences of fragmentation, long-distance dispersal, range contractions and range shifts on genetic diversity. In addition, we describe new methods to detect and quantify underlying evolutionary processes from sampled genetic data.