Room temperature coherent control of defect spin qubits in silicon carbide

Electronic spins in semiconductors have been used extensively to explore the limits of external control over quantum mechanical phenomena. A long-standing goal of this research has been to identify or develop robust quantum systems that can be easily manipulated, for future use in advanced information and communication technologies. Recently, a point defect in diamond known as the nitrogen-vacancy centre has attracted a great deal of interest because it possesses an atomic-scale electronic spin state that can be used as an individually addressable, solid-state quantum bit (qubit), even at room temperature. These exceptional quantum properties have motivated efforts to identify similar defects in other semiconductors, as they may offer an expanded range of functionality not available to the diamond nitrogen-vacancy centre. Notably, several defects in silicon carbide (SiC) have been suggested as good candidates for exploration, owing to a combination of computational predictions and magnetic resonance data. Here we demonstrate that several defect spin states in the 4H polytype of SiC (4H-SiC) can be optically addressed and coherently controlled in the time domain at temperatures ranging from 20 to 300 kelvin. Using optical and microwave techniques similar to those used with diamond nitrogen-vacancy qubits, we study the spin-1 ground state of each of four inequivalent forms of the neutral carbon-silicon divacancy, as well as a pair of defect spin states of unidentified origin. These defects are optically active near telecommunication wavelengths, and are found in a host material for which there already exist industrial-scale crystal growth and advanced microfabrication techniques. In addition, they possess desirable spin coherence properties that are comparable to those of the diamond nitrogen-vacancy centre. This makes them promising candidates for various photonic, spintronic and quantum information applications that merge quantum degrees of freedom with classical electronic and optical technologies.     

In defence of inclusive fitness theory

Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. Arguably the defining characteristic of the scientific process is its capacity for self-criticism and correction. Nowak et al. challenge proposed connections between relatedness and the evolution of eusociality, suggest instead that defensible nests and "spring-loaded" traits are key, and present alternative modelling approaches. They then dismiss the utility of Hamilton's insight that relatedness has a profound evolutionary effect, formalized in his widely accepted inclusive fitness theory as Hamilton's rule ("Rise and fall of inclusive fitness theory"). However, we believe that Nowak et al. fail to make their case for logical, theoretical and empirical reasons.     

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

Recent advances in DNA synthesis technology have enabled the construction of novel genetic pathways and genomic elements, furthering our understanding of system-level phenomena. The ability to synthesize large segments of DNA allows the engineering of pathways and genomes according to arbitrary sets of design principles. Here we describe a synthetic yeast genome project, Sc2.0, and the first partially synthetic eukaryotic chromosomes, Saccharomyces cerevisiae chromosome synIXR, and semi-synVIL. We defined three design principles for a synthetic genome as follows: first, it should result in a (near) wild-type phenotype and fitness; second, it should lack destabilizing elements such as tRNA genes or transposons; and third, it should have genetic flexibility to facilitate future studies. The synthetic genome features several systemic modifications complying with the design principles, including an inducible evolution system, SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution). We show the utility of SCRaMbLE as a novel method of combinatorial mutagenesis, capable of generating complex genotypes and a broad variety of phenotypes. When complete, the fully synthetic genome will allow massive restructuring of the yeast genome, and may open the door to a new type of combinatorial genetics based entirely on variations in gene content and copy number.     

Activating mutations in ALK provide a therapeutic target in neuroblastoma

Neuroblastoma, an embryonal tumour of the peripheral sympathetic nervous system, accounts for approximately 15% of all deaths due to childhood cancer. High-risk neuroblastomas are rapidly progressive; even with intensive myeloablative chemotherapy, relapse is common and almost uniformly fatal. Here we report the detection of previously unknown mutations in the ALK gene, which encodes a receptor tyrosine kinase, in 8% of primary neuroblastomas. Five non-synonymous sequence variations were identified in the kinase domain of ALK, of which three were somatic and two were germ line. The most frequent mutation, F1174L, was also identified in three different neuroblastoma cell lines. ALK complementary DNAs encoding the F1174L and R1275Q variants, but not the wild-type ALK cDNA, transformed interleukin-3-dependent murine haematopoietic Ba/F3 cells to cytokine-independent growth. Ba/F3 cells expressing these mutations were sensitive to the small-molecule inhibitor of ALK, TAE684 (ref. 4). Furthermore, two human neuroblastoma cell lines harbouring the F1174L mutation were also sensitive to the inhibitor. Cytotoxicity was associated with increased amounts of apoptosis as measured by TdT-mediated dUTP nick end labelling (TUNEL). Short hairpin RNA (shRNA)-mediated knockdown of ALK expression in neuroblastoma cell lines with the F1174L mutation also resulted in apoptosis and impaired cell proliferation. Thus, activating alleles of the ALK receptor tyrosine kinase are present in primary neuroblastoma tumours and in established neuroblastoma cell lines, and confer sensitivity to ALK inhibition with small molecules, providing a molecular rationale for targeted therapy of this disease.     

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

Acute myeloid leukaemia is a highly malignant haematopoietic tumour that affects about 13,000 adults in the United States each year. The treatment of this disease has changed little in the past two decades, because most of the genetic events that initiate the disease remain undiscovered. Whole-genome sequencing is now possible at a reasonable cost and timeframe to use this approach for the unbiased discovery of tumour-specific somatic mutations that alter the protein-coding genes. Here we present the results obtained from sequencing a typical acute myeloid leukaemia genome, and its matched normal counterpart obtained from the same patient's skin. We discovered ten genes with acquired mutations; two were previously described mutations that are thought to contribute to tumour progression, and eight were new mutations present in virtually all tumour cells at presentation and relapse, the function of which is not yet known. Our study establishes whole-genome sequencing as an unbiased method for discovering cancer-initiating mutations in previously unidentified genes that may respond to targeted therapies.