Whole genome analysis for 163 gRNAs in Cas9-edited mice reveals minimal off-target activity.

Genome editing with CRISPR-associated (Cas) proteins holds exceptional promise for correcting variants causing genetic disease. To realize this promise, off-target genomic changes cannot occur during the editing process. Here, we use whole genome sequencing to compare the genomes of 50 Cas9-edited founder mice to 28 untreated control mice to assess the occurrence of S. pyogenes Cas9-induced off-target mutagenesis. Computational analysis of whole-genome sequencing data detects 26 unique sequence variants at 23 predicted off-target sites for 18/163 guides used. While computationally detected variants are identified in 30% (15/50) of Cas9 gene-edited founder animals, only 38% (10/26) of the variants in 8/15 founders validate by Sanger sequencing. In vitro assays for Cas9 off-target activity identify only two unpredicted off-target sites present in genome sequencing data. In total, only 4.9% (8/163) of guides tested have detectable off-target activity, a rate of 0.2 Cas9 off-target mutations per founder analyzed. In comparison, we observe ~1,100 unique variants in each mouse regardless of genome exposure to Cas9 indicating off-target variants comprise a small fraction of genetic heterogeneity in Cas9-edited mice. These findings will inform future design and use of Cas9-edited animal models as well as provide context for evaluating off-target potential in genetically diverse patient populations

Decoherence, einselection, and the quantum origins of the classical

Decoherence is caused by the interaction with the environment. Environment monitors certain observables of the system, destroying interference between the pointer states corresponding to their eigenvalues. This leads to environment-induced superselection or einselection, a quantum process associated with selective loss of information. Einselected pointer states are stable. They can retain correlations with the rest of the Universe in spite of the environment. Einselection enforces classicality by imposing an effective ban on the vast majority of the Hilbert space, eliminating especially the flagrantly non-local "Schr\"odinger cat" states. Classical structure of phase space emerges from the quantum Hilbert space in the appropriate macroscopic limit: Combination of einselection with dynamics leads to the idealizations of a point and of a classical trajectory. In measurements, einselection replaces quantum entanglement between the apparatus and the measured system with the classical correlation.Comment: Final version of the review, with brutally compressed figures. Apart from the changes introduced in the editorial process the text is identical with that in the Rev. Mod. Phys. July issue. Also available from http://www.vjquantuminfo.or

Creatine Fails to Augment the Benefits from Resistance Training in Patients with HIV Infection: A Randomized, Double-Blind, Placebo-Controlled Study

Progressive resistance exercise training (PRT) improves physical functioning in patients with HIV infection. Creatine supplementation can augment the benefits derived from training in athletes and improve muscle function in patients with muscle wasting. The objective of this study was to determine whether creatine supplementation augments the effects of PRT on muscle strength, energetics, and body composition in HIV-infected patients.This is a randomized, double blind, placebo-controlled, clinical research center-based, outpatient study in San Francisco. 40 HIV-positive men (20 creatine, 20 placebo) enrolled in a 14-week study. Subjects were randomly assigned to receive creatine monohydrate or placebo for 14 weeks. Treatment began with a loading dose of 20 g/day or an equivalent number of placebo capsules for 5 days, followed by maintenance dosing of 4.8 g/day or placebo. Beginning at week 2 and continuing to week 14, all subjects underwent thrice-weekly supervised resistance exercise while continuing on the assigned study medication (with repeated 6-week cycles of loading and maintenance). The main outcome measurements included muscle strength (one repetition maximum), energetics ((31)P magnetic resonance spectroscopy), composition and size (magnetic resonance imaging), as well as total body composition (dual-energy X-ray absorptiometry). Thirty-three subjects completed the study (17 creatine, 16 placebo). Strength increased in all 8 muscle groups studied following PRT, but this increase was not augmented by creatine supplementation (average increase 44 vs. 42%, difference 2%, 95% CI -9.5% to 13.9%) in creatine and placebo, respectively). There were no differences between groups in changes in muscle energetics. Thigh muscle cross-sectional area increased following resistance exercise, with no additive effect of creatine. Lean body mass (LBM) increased to a significantly greater extent with creatine. CONCLUSIONS / SIGNIFICANCE: Resistance exercise improved muscle size, strength and function in HIV-infected men. While creatine supplementation produced a greater increase in LBM, it did not augment the robust increase in strength derived from PRT.ClinicalTrials.gov NCT00484627

Investigating the Andromeda Stream: I. Simple Analytic Bulge-Disk-Halo Model for M31

This paper is the first in a series which studies interactions between M31 and its satellites, including the origin of the giant southern stream. We construct accurate yet simple analytic models for the potential of the M31 galaxy to provide an easy basis for calculation of orbits in M31's halo. We use an NFW dark halo, an exponential disk, a Hernquist bulge, and a central black hole point mass to describe the galaxy potential. We constrain the parameters of these functions by comparing to existing surface brightness, velocity dispersion, and rotation curve measurements of M31. Our description provides a good fit to the observations, and agrees well with more sophisticated modeling of M31. While in many respects the parameter set is well constrained, there is substantial uncertainty in the outer halo potential and a near-degeneracy between the disk and halo components, producing a large, nearly two-dimensional allowed region in parameter space. We limit the allowed region using theoretical expectations for the halo concentration, baryonic content, and stellar $M/L$ ratio, finding a smaller region where the parameters are physically plausible. Our proposed mass model for M31 has M_{bulge} = 3.2 \times 10^{10} \Msun, M_{disk} = 7.2 \times 10^{10} \Msun, and M_{200} = 7.1\times 10^{11} \Msun, with uncorrected (for internal and foreground extinction) mass-to-light ratios of $M/L_R = 3.9$ and 3.3 for the bulge and disk, respectively. We present some illustrative test particle orbits for the progenitor of the stellar stream in our galaxy potential, highlighting the effects of the remaining uncertainty in the disk and halo masses.Comment: 17 pages, 8 color figures, 2 tables. Accepted by Monthly Notices; Models listed in tables modified, text reorganized and shortene

Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts.

[This corrects the article DOI: 10.1038/s42003-018-0226-0.]