High-affinity chromodomains engineered for improved detection of histone methylation and enhanced CRISPR-based gene repression

Histone methylation is an important post-translational modification that plays a crucial role in regulating cellular functions, and its dysregulation is implicated in cancer and developmental defects. Therefore, systematic characterization of histone methylation is necessary to elucidate complex biological processes, identify biomarkers, and ultimately, enable drug discovery. Studying histone methylation relies on the use of antibodies, but these suffer from lot-to-lot variation, are costly, and cannot be used in live cells. Chromatin-modification reader domains are potential affinity reagents for methylated histones, but their application is limited by their modest affinities. We used phage display to identify key residues that greatly enhance the affinities of Cbx chromodomains for methylated histone marks and develop a general strategy for enhancing the affinity of chromodomains of the human Cbx protein family. Our strategy allows us to develop powerful probes for genome-wide binding analysis and live-cell imaging. Furthermore, we use optimized chromodomains to develop extremely potent CRISPR-based repressors for tailored gene silencing. Our results highlight the power of engineered chromodomains for analyzing protein interaction networks involving chromatin and represent a modular platform for efficient gene silencing.

Macropinocytosis of the PDGF β-receptor promotes fibroblast transformation by H-RasG12V

Fibroblast transformation by H-RasG12V induces internalization of PDGFRβ by macropinocytosis, enhancing its signaling activity and increasing anchorage-independent proliferation. It is proposed that H-Ras transformation promotes tumor progression by enhancing growth factor receptor signaling through increased receptor macropinocytosis.

Receptor tyrosine kinase (RTK) signaling is frequently increased in tumor cells, sometimes as a result of decreased receptor down-regulation. The extent to which the endocytic trafficking routes can contribute to such RTK hyperactivation is unclear. Here, we show for the first time that fibroblast transformation by H-RasG12V induces the internalization of platelet-derived growth factor β-receptor (PDGFRβ) by macropinocytosis, enhancing its signaling activity and increasing anchorage-independent proliferation. H-RasG12V transformation and PDGFRβ activation were synergistic in stimulating phosphatidylinositol (PI) 3-kinase activity, leading to receptor macropinocytosis. PDGFRβ macropinocytosis was both necessary and sufficient for enhanced receptor activation. Blocking macropinocytosis by inhibition of PI 3-kinase prevented the increase in receptor activity in transformed cells. Conversely, increasing macropinocytosis by Rabankyrin-5 overexpression was sufficient to enhance PDGFRβ activation in nontransformed cells. Simultaneous stimulation with PDGF-BB and epidermal growth factor promoted macropinocytosis of both receptors and increased their activation in nontransformed cells. We propose that H-Ras transformation promotes tumor progression by enhancing growth factor receptor signaling as a result of increased receptor macropinocytosis.

Toxicity of the crude oil water-soluble fraction and kaolin-adsorbed crude oil on Daphnia magna (Crustacea: Anomopoda)

Crude oil is a complex mixture of hydrocarbons entering aquatic environments from accidental or normal marine and transportation activities. Toxicologic crude oil analysis is usually performed on the basis of the water-soluble fraction. However, this yields only a partial estimate of the damage caused by these contaminants because a substantial hydrophobic amount can be adsorbed onto suspended solids (biotic and abiotic), which directly affects filter-feeding species and permits bioaccumulation through trophic relationships. This study determined the acute toxic damage sustained after 48 hours caused by seven types of crude oil from Tabasco, Mexico on the cladoceran Daphnia magna. Comparisons were documented based on the responses of D. magna from application of the water-soluble fraction and exposure to entire crude oil samples adsorbed on kaolin clay. Oil-sorbed kaolin was more toxic than the water-soluble fraction in acute exposure. This confirms that tests of the water-soluble fraction tend to underestimate the toxic damage that can be produced in natural environments. Furthermore, chronic toxicity (21 days) was evaluated for crude oil samples adsorbed on kaolin at sublethal concentrations as established from Application Factors (AF) criteria. Results showed that in most cases, it is impossible to predict safe concentrations on the basis of LC(50) values because samples with lower acute toxicity exercised a greater influence on D. magna reproduction and survival when subjected to chronic exposure.

Retrospective comparison of simultaneous and non-simultaneous bilateral radial keratotomy

PURPOSE

Many radial keratotomy surgeons advocate bilateral simultaneous surgery, in which there is an inherent, although rare, risk of bilateral sight-threatening complications such as microbial keratitis. This study was designed to evaluate the refractive outcomes of simultaneous and non-simultaneous radial keratotomy performed by a single surgeon.

METHODS

We retrospectively compared the results of radial keratotomy performed simultaneously (both eyes operated on the same day, 20 patients) versus non-simultaneously (right and left eyes operated on different days, 71 patients) by a single surgeon. Both eyes had the same surgical procedure, including clear zone diameter and number of incisions.

RESULTS

The refractive results of bilateral simultaneous and non-simultaneous surgery were largely equivalent for all parameters analyzed except one. The variability of the difference in postoperative refractive error between right and left eyes was less for those patients undergoing simultaneous surgery (p = .0008).

CONCLUSION

Our data suggest that performing radial keratotomy as a bilateral simultaneous procedure increases the symmetry of the refractive effect. In view of recent reports of sight-threatening risks such as bilateral microbial keratitis following bilateral keratotomy, however, the potential risks and benefits of bilateral surgery should be carefully considered before operating on both eyes on the same day.