Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.

Type II CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA–induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation.

This paper describes the conclusions that can be drawn from the data taken thus far with the PHOBOS detector at RHIC. In the most central Au+Au collisions at the highest beam energy, evidence is found for the formation of a very high energy density system whose description in terms of simple hadronic degrees of freedom is inappropriate. Furthermore, the constituents of this novel system are found to undergo a significant level of interaction. The properties of particle production at RHIC energies are shown to follow a number of simple scaling behaviors, some of which continue trends found at lower energies or in simpler systems. As a function of centrality, the total number of charged particles scales with the number of participating nucleons. When comparing Au+Au at different centralities, the dependence of the yield on the number of participants at higher p T (∼4 GeV/c) is very similar to that at low transverse momentum. The measured values of charged particle pseudorapidity density and elliptic flow were found to be independent of energy over a broad range of pseudorapidities when effectively viewed in the rest frame of one of the colliding nuclei, a property we describe as "extended longitudinal scaling". Finally, the centrality and energy dependences of several observables were found to factorize to a surprising degree.

THERMUS is a package of C++ classes and functions allowing statistical-thermal model analyses of particle production in relativistic heavy-ion collisions to be performed within the ROOT framework of analysis. Calculations are possible within three statistical ensembles; a grand-canonical treatment of the conserved charges B, S and Q, a fully canonical treatment of the conserved charges, and a mixedcanonical ensemble combining a canonical treatment of strangeness with a grandcanonical treatment of baryon number and electric charge. THERMUS allows for the assignment of decay chains and detector efficiencies specific to each particle yield, which enables sensible fitting of model parameters to experimental data. Nature of problem:Statistical-thermal model analyses of heavy-ion collision data require the calculation of both primordial particle densities and contributions from resonance decay. A set of thermal parameters (the number depending on the particular model imposed) and a set of thermalised particles, with their decays specified, is required as input to these models. The output is then a complete set of primordial thermal quantities for each particle, together with the contributions to the final particle yields from resonance decay.In many applications of statistical-thermal models it is required to fit experimental particle multiplicities or particle ratios. In such analyses, the input is a set of experimental yields and ratios, a set of particles comprising the assumed hadron resonance gas formed in the collision and the constraints to be placed on the system. The thermal model parameters consistent with the specified constraints leading to the best-fit to the experimental data are then output. Solution method:THERMUS is a package designed for incorporation into the ROOT [2] framework, used extensively by the heavy-ion community. As such, it utilises a great deal of ROOT's functionality in its operation. ROOT features used in THERMUS include its containers, the wrapper TMinuit implementing the MINUIT fitting package, and the TMath class of mathematical functions and routines. Arguably the most useful feature is the utilisation of CINT as the control language, which allows interactive 2 access to the THERMUS objects. Three distinct statistical ensembles are included in THERMUS, while additional options to include quantum statistics, resonance width and excluded volume corrections are also available. THERMUS provides a default particle list including all mesons (up to the K * 4 (2045)) and baryons (up to the Ω − ) listed in the July 2002 Particle Physics Booklet [3]. For each typically unstable particle in this list, THERMUS includes a text-file listing its decays. With thermal parameters specified, THERMUS calculates primordial thermal densities either by performing numerical integrations or else, in the case of the Boltzmann approximation without resonance width in the grand-canonical ensemble, by evaluating Bessel functions. Particle decay chains are then used to evaluate experimental observables...