系统生物学

Memory systems can hold previously presented information for several seconds, bridging gaps between discontinuous events. It has been previously demonstrated that the hippocampus and the medial entorhinal cortex (mEC) are necessary for memory retention over delay intervals in alternation tasks. Here we describe the delayed alternation task, a spatial working memory (WM) task in which animals need to alternate between left and right sides of a figure-8 maze on a trial-by-trial basis to receive a reward. On each trial of this task, the rat has to remember the last episode and turn in the opposite direction compared to the previous trial. We manipulated the WM load by introducing delays of various lengths (10 s and 60 s) between trials. While other alternation task protocols use short delay intervals between trials, our protocol introduces a longer delay condition that requires animals to use long-term memory resources that are not necessarily supported by sequential neuronal firing patterns (i.e., time cells) as are seen with shorter delay intervals.

Genome modification in budding yeast has been extremely successful largely due to its highly efficient homology-directed DNA repair machinery. Several methods for modifying the yeast genome have previously been described, many of them involving at least two-steps: insertion of a selectable marker and substitution of that marker for the intended modification. Here, we describe a CRISPR-Cas9 mediated genome editing protocol for modifying any yeast gene of interest (either essential or nonessential) in a single-step transformation without any selectable marker. In this system, the Cas9 nuclease creates a double-stranded break at the locus of choice, which is typically lethal in yeast cells regardless of the essentiality of the targeted locus due to inefficient non-homologous end-joining repair. This lethality results in efficient repair via homologous recombination using a repair template derived from PCR. In cases involving essential genes, the necessity of editing the genomic lesion with a functional allele serves as an additional layer of selection. As a motivating example, we describe the use of this strategy in the replacement of HEM2, an essential yeast gene, with its corresponding human ortholog ALAD.

Genomic sequencing efforts can implicate large numbers of genes and de novo mutations as potential disease risk factors. A high throughput in vivo model system to validate candidate gene association with pathology is therefore useful. We present such a system employing Drosophila to validate candidate congenital heart disease (CHD) genes. The protocols exploit comprehensive libraries of UAS-GeneX-RNAi fly strains that when crossed into a 4XHand-Gal4 genetic background afford highly efficient cardiac-specific knockdown of endogenous fly orthologs of human genes. A panel of quantitative assays evaluates phenotypic severity across multiple cardiac parameters. These include developmental lethality, larva and adult heart morphology, and adult longevity. These protocols were recently used to evaluate more than 100 candidate CHD genes implicated by patient whole-exome sequencing (Zhu et al., 2017).

Relative chromosome dosage, i.e., increases or decreases in the number of copies of specific chromosome regions in one sample versus another, can be determined using aligned read-counts from Illumina sequencing (Henry et al., 2010). The following protocol was used to identify the different classes of aneuploids that result from uniparental genome elimination in Arabidopsis thaliana, including chromosomes that have undergone chromothripsis (Tan et al., 2015). Uniparental genome elimination results in the production of haploid progeny from crosses to specific strains called “haploid inducers” (Ravi et al., 2014). On the other hand, chromothripsis, which was first discovered in cancer genomes, is a phenomenon that results in clustered, highly rearranged chromosomes. In plants, chromothripsis has been observed as a result of genome elimination (Tan et al., 2015). Detecting variation in chromosome dosage has multiple applications beside those linked to genome elimination. For example, a dosage variant population of poplar hybrids was created by gamma-irradiation of pollen grains. Hundreds of dosage lesions, insertions and deletions, were identified using this technique and provide a way to associate loci with the phenotypic consequences observed in this population (Henry et al., 2015).

This method has been successfully used to detect changes in chromosome dosage in many different species, including Arabidopsis thaliana (Tan et al., 2015), Arabidopsis suecica (Ravi et al., 2014), rice (Henry et al., 2010) and poplar (Henry et al., 2015). It is important to note that dosage plots always indicate dosage variation relative to the control sample used (Note 1). Therefore, this approach is not suitable to detect ploidy variants (diploid vs triploid, for example). Similarly, this technique does not allow the detection of balanced chromosomal rearrangements such as reciprocal translocations.

Here, we describe a method enabling the phenotypic profiling of genome-scale deletion collections of fungal mutants to detect phenotypes for various stress conditions. These stress conditions include among many others antifungal drug susceptibility, temperature-induced and osmotic as well as heavy metal or oxidative stress. The protocol was extensively used to phenotype a collection of gene deletion mutants in the human fungal pathogen Candida glabrata (C. glabrata) (Schwarzmüller et al., 2014).