CAS9 is a genome mutator by directly disrupting DNA-PK dependent DNA repair pathway.

With its high efficiency for site-specific genome editing and easy manipulation, the clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR associated protein 9 (CAS9) system has become the most widely used gene editing technology in biomedical research. In addition, significant progress has been made for the clinical development of CRISPR/CAS9 based gene therapies of human diseases, several of which are entering clinical trials. Here we report that CAS9 protein can function as a genome mutator independent of any exogenous guide RNA (gRNA) in human cells, promoting genomic DNA double-stranded break (DSB) damage and genomic instability. CAS9 interacts with the KU86 subunit of the DNA-dependent protein kinase (DNA-PK) complex and disrupts the interaction between KU86 and its kinase subunit, leading to defective DNA-PK-dependent repair of DNA DSB damage via non-homologous end-joining (NHEJ) pathway. XCAS9 is a CAS9 variant with potentially higher fidelity and broader compatibility, and dCAS9 is a CAS9 variant without nuclease activity. We show that XCAS9 and dCAS9 also interact with KU86 and disrupt DNA DSB repair. Considering the critical roles of DNA-PK in maintaining genomic stability and the pleiotropic impact of DNA DSB damage responses on cellular proliferation and survival, our findings caution the interpretation of data involving CRISPR/CAS9-based gene editing and raise serious safety concerns of CRISPR/CAS9 system in clinical application

Signal Transduction Pathways in the Pentameric Ligand-Gated Ion Channels

The mechanisms of allosteric action within pentameric ligand-gated ion channels (pLGICs) remain to be determined. Using crystallography, site-directed mutagenesis, and two-electrode voltage clamp measurements, we identified two functionally relevant sites in the extracellular (EC) domain of the bacterial pLGIC from Gloeobacter violaceus (GLIC). One site is at the C-loop region, where the NQN mutation (D91N, E177Q, and D178N) eliminated inter-subunit salt bridges in the open-channel GLIC structure and thereby shifted the channel activation to a higher agonist concentration. The other site is below the C-loop, where binding of the anesthetic ketamine inhibited GLIC currents in a concentration dependent manner. To understand how a perturbation signal in the EC domain, either resulting from the NQN mutation or ketamine binding, is transduced to the channel gate, we have used the Perturbation-based Markovian Transmission (PMT) model to determine dynamic responses of the GLIC channel and signaling pathways upon initial perturbations in the EC domain of GLIC. Despite the existence of many possible routes for the initial perturbation signal to reach the channel gate, the PMT model in combination with Yen's algorithm revealed that perturbation signals with the highest probability flow travel either via the β1-β2 loop or through pre-TM1. The β1-β2 loop occurs in either intra- or inter-subunit pathways, while pre-TM1 occurs exclusively in inter-subunit pathways. Residues involved in both types of pathways are well supported by previous experimental data on nAChR. The direct coupling between pre-TM1 and TM2 of the adjacent subunit adds new insight into the allosteric signaling mechanism in pLGICs. © 2013 Mowrey et al

Anti-Hyperon polarization in high energy pp collisions with polarized beams

We study the longitudinal polarization of the Sigma_bar and Xi_bar anti-hyperons in polarized high energy pp collisions at large transverse momenta, extending a recent study for the Lambda_bar anti-hyperon. We make predictions by using different parametrizations of the polarized parton densities and models for the polarized fragmentation functions. Similar to the Lambda_bar polarization, the Xi_bar0 and Xi_bar+ polarizations are found to be sensitive to the polarized anti-strange sea in the nucleon. The Sigma_bar- and Sigma_bar+ polarizations show sensitivity to the light sea quark polarizations, \Delta \bar u(x) and \Delta \bar d(x), and their asymmetry.Comment: 17 pages, 9 figures,version to appear in PR

Molecular Lines of 13 Galactic Infrared Bubble Regions

We investigated the physical properties of molecular clouds and star formation processes around infrared bubbles which are essentially expanding HII regions. We performed observations of 13 galactic infrared bubble fields containing 18 bubbles. Five molecular lines, 12CO (J=1-0), 13CO (J=1-0), C18O(J=1-0), HCN (J=1-0), and HCO+ (J=1-0), were observed, and several publicly available surveys, GLIMPSE, MIPSGAL, ATLASGAL, BGPS, VGPS, MAGPIS, and NVSS, were used for comparison. We find that these bubbles are generally connected with molecular clouds, most of which are giant. Several bubble regions display velocity gradients and broad shifted profiles, which could be due to the expansion of bubbles. The masses of molecular clouds within bubbles range from 100 to 19,000 solar mass, and their dynamic ages are about 0.3-3.7 Myr, which takes into account the internal turbulence pressure of surrounding molecular clouds. Clumps are found in the vicinity of all 18 bubbles, and molecular clouds near four of these bubbles with larger angular sizes show shell-like morphologies, indicating that either collect-and-collapse or radiation-driven implosion processes may have occurred. Due to the contamination of adjacent molecular clouds, only six bubble regions are appropriate to search for outflows, and we find that four of them have outflow activities. Three bubbles display ultra-compact HII regions at their borders, and one of them is probably responsible for its outflow. In total, only six bubbles show star formation activities in the vicinity, and we suggest that star formation processes might have been triggered.Comment: 55 Pages, 32 figures. Accepted for publication in A

Attribute-Guided Sketch Generation

Facial attributes are important since they provide a detailed description and determine the visual appearance of human faces. In this paper, we aim at converting a face image to a sketch while simultaneously generating facial attributes. To this end, we propose a novel Attribute-Guided Sketch Generative Adversarial Network (ASGAN) which is an end-to-end framework and contains two pairs of generators and discriminators, one of which is used to generate faces with attributes while the other one is employed for image-to-sketch translation. The two generators form a W-shaped network (W-net) and they are trained jointly with a weight-sharing constraint. Additionally, we also propose two novel discriminators, the residual one focusing on attribute generation and the triplex one helping to generate realistic looking sketches. To validate our model, we have created a new large dataset with 8,804 images, named the Attribute Face Photo & Sketch (AFPS) dataset which is the first dataset containing attributes associated to face sketch images. The experimental results demonstrate that the proposed network (i) generates more photo-realistic faces with sharper facial attributes than baselines and (ii) has good generalization capability on different generative tasks.Comment: 7 pages, 6 figures, accepted to FG 201