Cell Biology

Weeds compete with crops for growth resources, causing tremendous yield losses. Paraquat is one of the three most common non-selective herbicides. To study the mechanisms of paraquat resistance, we need to trace the movement of paraquat in plants and within the cell. ¹⁴C is a radioactive carbon isotope widely used to trace substances of interest in various biological studies, especially in transport analyses. Here, we describe a detailed protocol using ¹⁴C-paraquat to demonstrate paraquat efflux in Arabidopsis protoplasts.

The brown alga Ectocarpus has a haploid-diploid life cycle that involves alternation between two multicellular generations, the sporophyte and the gametophyte. Life cycle generation is not determined by ploidy but by a genetic system that includes two different three amino acid loop extension homeodomain transcription factors called OUROBOROS and SAMSARA. In addition, sporophytes have been shown to secrete a diffusible factor into the medium that can induce gametophyte initial cells to switch from the gametophyte to the sporophyte developmental program. The protocol presented here describes how to produce sporophyte-conditioned medium containing the diffusible sporophyte-inducing factor and how to assay for activity of the factor using a meio-spore-based bioassay. The protocol, which describes how several steps of these procedures can be optimised, will represent a useful tool for future work aimed at characterising the diffusible factor and investigating its mode of action.

Organotypic slice culture is a powerful technique for exploring the embryonic development of the mammalian brain. In this protocol we describe a basic slice culture technique we have used for two sets of experiments: axon guidance transplant assays and bead culture assays.

Noncanonical Wnt signaling functions independently of the β-catenin pathway to control diverse developmental processes, and dysfunction of the pathway contributes to a number of human pathological conditions, including birth defects and metastatic cancer. Progress in the field, however, has been hampered by the scarcity of functional assays for measuring noncanonical Wnt signaling activity. We recently described the Wnt5a-Ror-Kif26b (WRK) reporter assay, which directly monitors a post-transcriptional regulatory event in noncanonical Wnt signaling. In this protocol, we describe the generation of the stable GFP-Kif26b reporter cell line and a quantitative reporter assay for detecting and measuring Wnt5a signaling activities in live cells via flow cytometry.

1-MCP (1-methylcyclopropene) is a simple synthetic hydrocarbon molecule that interacts with the ethylene receptor and inhibits the response of fruit or plant to ethylene. 1-MCP has opened new opportunities in handling harvested crops and serves as a powerful tool to learn about plant response to ethylene (Watkins and Miller, 2006). 1-MCP is manufactured by Agrofresh and known by its commercial name Smartfresh^SM.

This protocol describes the procedure of visualizing secreted Wnt5 protein in serum free media via western blotting. This procedure can also be used to visualize other secreted proteins larger than 10,000 daltons. The work presented in this paper visualizes Wnt5 secreted by mouse embryonic fibroblast (MEF), but can be adapted to other cell lines including those transiently transfected by plasmids.

TGFβ is a potent cytokine modulating various processes including proliferation, differentiation, ECM synthesis and apoptosis (Siegel and Massague, 2003). Thus in many tissues availability of TGFβ is tightly regulated. TGFβ is secreted as an inactive complex where it is encapsulated by the latency associated protein (LAP), a ligand trap protein, which inhibits TGFβ binding to its receptor and retains TGFβ in the extracellular matrix (ten Dijke and Arthur, 2007). TGFβ can be released from the matrix and converted into its biological active form by huge number of processes including heat, high and low pH, release of reactive oxygen species (ROS) or various proteases (e.g. plasmin, elastase, matrix metalloproteinase-2 and -9) (Barcellos-Hoff and Dix, 1996; Lyons et al., 1988; Taipale et al., 1994; Yu and Stamenkovic, 2000). However, under physiological conditions the interaction of αv-class integrins with the RGD tripeptide motif in the LAP protein represents the key factor for TGFβ release in vivo. The relevance of integrin mediated TGFβ release for in vivo development and homeostasis is further underlined by the observation that mice with the integrin-binding deficient LAP proteins (RGD motif mutated to RGE) recapitulate all major phenotypes of TGFβ1 null mice, including multi-organ inflammation and defects in vasculogenesis (Shull et al., 1992; Yang et al., 2007). This striking phenotype overlap with TGFβ deficient mice and phenotypes of mice lacking αv-class integrins (Aluwihare et al., 2009; Bader et al., 1998) demonstrates an essential interconnection of integrins with TGFβ signaling in vivo, while the role of non-integrin mediated release mechanisms (ROS, pH, proteolytic cleavage etc.) during development remains less clear.

The TGFβ release assay measures the ability of cells to release TGFβ from a matrix. The assay was developed by (Annes et al., 2004) and we further optimized the protocol for keratinocytes. For other cell types the cell culture medium and culturing conditions would need to be adapted accordingly.

In keratinocytes TGFβ release is mainly mediated by αvβ6 integrin but also integrin αvβ3, αvβ5 and αvβ8 have been shown to liberate TGFβ, while other RGD binding integrins, such as α5β1 or α8β1 cannot release TGFβ (Asano et al., 2005a, 2005b; Mu et al., 2002; Munger et al., 1999). Mechanistically, the interaction with αvβ3, αvβ5 or αvβ6 integrin induces a conformational change in the LAP-TGFβ by generating an actin cytoskeleton dependent pulling force, allowing TGFβ to access its receptors. For αvβ8 integrin mediated TGFβ release it was shown that proteolytic cleavage is involved [see (Mu et al., 2002) for blocking conditions of TGFβ release by proteolytic cleavage and αvβ8 integrin].

The following protocol is optimized for the study of αvβ6-integrin mediated TGFβ release in keratinocytes.

Mitochondria are organelles that have important functions in oxidative phosphorylation, fatty acid oxidation and apoptosis signaling. They have two distinct membranes, outer membrane (OM) and inner membrane (IM). IM contains respiratory chain complexes that produce ATP. IM is rich in cardiolipin, a specific phospholipid reportedly having a critical role for organizing super-complex formation of respiratory chain complexes. IM abundant in cardiolipin exhibits resistance to extraction by digitonin (a non-ionic detergent), whereas the detergent easily lyses OM. Therefore, digitonin is useful to separate mitoplast (IM plus matrix) and OM from mitochondria. Here, we describe a method to isolate mitochondria from HeLa cells, and a method to isolate mitochondrial outer membrane proteins and inner membrane proteins by using digitonin. This method is applicable also to other types of cultured cells such as COS-7.

This protocol is for testing responses of a candidate cell line/cell lines to Wnt ligands or Wnt pathway agonists stimulation. This protocol can also be adapted to screen small molecule libraries or biologics that contain activities to either increase or decrease Wnt pathway responses. Canonical Wnt signaling activity transcriptionally induces Wnt target genes that contain concensus TCF/LEF binding element. Wnt pathway activity responsive cells transiently or stably expressing luciferase proteins under the TCF/LEF promoter element can be used to report stimulus-dependent Wnt-pathway activity. We acquired the TopFlash (TCL/LEF-Firefly luciferase) construct from Addgene.

This protocol is for testing responses of a candidate cell line/cell lines to Hh ligands or Hh pathway agonists stimulation. This protocol can also be adapted to screen small molecule libraries or biologics that contain activities to either increase or decrease Hh pathway responses. Canonical Hh signaling activity transcriptionally induces Hh target genes that contain consensus Gli binding element. Hh-responsive cells transiently or stably expressing luciferase protein under the regulation of the Gli promoter element can be used to report stimulus-dependent Hh-pathway activity.