Selection-dependent and Independent Generation of CRISPR/Cas9-mediated Gene Knockouts in Mammalian Cells.

The CRISPR/Cas9 genome engineering system has revolutionized biology by allowing for precise genome editing with little effort. Guided by a single guide RNA (sgRNA) that confers specificity, the Cas9 protein cleaves both DNA strands at the targeted locus. The DNA break can trigger either non-homologous end joining (NHEJ) or homology directed repair (HDR). NHEJ can introduce small deletions or insertions which lead to frame-shift mutations, while HDR allows for larger and more precise perturbations. Here, we present protocols for generating knockout cell lines by coupling established CRISPR/Cas9 methods with two options for downstream selection/screening. The NHEJ approach uses a single sgRNA cut site and selection-independent screening, where protein production is assessed by dot immunoblot in a high-throughput manner. The HDR approach uses two sgRNA cut sites that span the gene of interest. Together with a provided HDR template, this method can achieve deletion of tens of kb, aided by the inserted selectable resistance marker. The appropriate applications and advantages of each method are discussed.

Thirdhand smoke: Chemical dynamics, cytotoxicity, and genotoxicity in outdoor and indoor environments.

We tested the toxicity of thirdhand smoke (THS) using two controlled laboratory exposure scenarios and low levels of THS. One exposure modeled THS in a car parked outdoors, while the second modeled THS in a room without sunlight. The fabrics were exposed to cigarette smoke and then extracted in culture medium. Concentrations of nicotine, nicotine related alkaloids, and tobacco specific nitrosamines (TSNAs) were determined in fresh and aged extracts. The concentration of TSNAs increased with aging in the indoor experiment. THS extracts were used for cytotoxicity testing using mouse neural stem cells (mNSC), human dermal fibroblasts (hDF) and human palatal mesenchyme cells (hPM). Extracts from the car experiment inhibited mNSC proliferation in a live cell imaging assay and induced single strand DNA breaks in mNSC and hDF. In the indoor experiment, THS extracts made with medium containing serum proteins were significantly more toxic than extracts made with basal medium, and mNSC and hPM were more sensitive than hDF. These data indicate that: (1) aging of THS chemical differs on different fabrics and differs with and without sunlight; (2) very few cigarettes are sufficient to produce a toxic THS residue; and (3) protein enhances the efficiency of extraction of cytotoxic chemicals.

BMP signaling and the maintenance of primordial germ cell identity in Drosophila embryos.

The specification of primordial germ cells (PGCs) and subsequent maintenance of germ-line identity in Drosophila embryos has long been thought to occur solely under the control of cell-autonomous factors deposited in the posterior pole plasm during oogenesis. However, here we document a novel role for somatic BMP signaling in the maintenance of PGC fate during the period leading up to embryonic gonad coalescence. We find that PGCs fail to maintain their germline identity when BMP signaling is compromised. They initiate but are unable to properly assemble the germline stem cell-specific organelle, the spectrosome, and they lose expression of the germline-specific gene Vasa. BMP signaling must, however, be finely tuned as there are deleterious consequences to PGCs when the pathway is excessively active. We show that one mechanism used to calibrate the effects of BMP signals is dependent on the Ubc9 homolog Lesswright (Lwr).