Single Atom Imaging with an sCMOS camera

Single atom imaging requires discrimination of weak photon count events above background and has typically been performed using either EMCCD cameras, photomultiplier tubes or single photon counting modules. sCMOS provides a cost effective and highly scalable alternative to other single atom imaging technologies, offering fast readout and larger sensor dimensions. We demonstrate single atom resolved imaging of two site-addressable single atom traps separated by 10~$\mu$m using an sCMOS camera, offering a competitive signal-to-noise ratio at intermediate count rates to allow high fidelity readout discrimination (error $<10^{-6}$) and sub-$\mu$m spatial resolution for applications in quantum technologies.Comment: 4 pages, 4 figure

Entanglement of neutral-atom qubits with long ground-Rydberg coherence times

We report results of a ground-state entanglement protocol for a pair of Cs atoms separated by 6~μm, combining the Rydberg blockade mechanism with a two-photon Raman transitions to prepare the |Ψ+⟩=(|10⟩+|01⟩)/2‾√ Bell state with a loss-corrected fidelity of 0.81(5), equal to the best demonstrated fidelity for atoms trapped in optical tweezers but without the requirement for dynamically adjustable interatomic spacing. Qubit state coherence is also critical for quantum information applications, and we characterise both ground-state and ground-Rydberg dephasing rates using Ramsey spectroscopy. We demonstrate transverse dephasing times T∗2=10(1)~ms and T′2=0.14(1)~s for the qubit levels and achieve long ground-Rydberg coherence times of T∗2=17(2) μs as required for implementing high-fidelity multi-qubit gate sequences where a control atom remains in the Rydberg state while applying local operations on neighbouring target qubits

Coherent control of addressable Rydberg atoms for hybrid quantum information processing

Neutral atoms provide an excellent resource for quantum information processing, combining the long atomic coherence times of the hyperfine ground-state with strong dipole-dipole interactions of highly excited Rydberg states for generating deterministic entanglement between qubits separated by < 10 µm [1]. Scalable long-range interactions can be obtained by coupling the atomic array to a superconducting microwave cavity enabling hybrid quantum information processing where the cavity-mediated entanglement allows atoms to be coupled over cm length scales. We present the first steps towards such an experiment incorporating high fidelity readout using an sCMOS camera [2] and the ability to drive fast, optically addressable rotations of the hyperfine-encoded qubits to the Rydberg state. Using our sub-kHz cavitystabilised laser system [3] we demonstrate coherent control of single Rydberg atoms, performing Ramsey spectroscopy to determine coherence time and to generate entanglement between a pair of atoms separated by 6 µm. Combining this excitation scheme with our ground-state Raman lasers we show progress towards the implementation of a mesoscopic Rydberg gate based on electromagnetically induced transparency (EIT) offering robust entanglement of multi-atom ensembles [4]

Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture

[EN] Bacteria in the genus Streptomyces are soil-dwelling oligotrophs and important producers of secondary metabolites. Previously, we showed that global messenger RNA expression was subject to a series of metabolic and regulatory switches during the lifetime of a fermentor batch culture of Streptomyces coelicolor M145. Here we analyze the proteome from eight time points from the same fermentor culture and, because phosphate availability is an important regulator of secondary metabolite production, compare this to the proteome of a similar time course from an S. coelicolor mutant, INB201 (ΔphoP), defective in the control of phosphate utilization. The proteomes provide a detailed view of enzymes involved in central carbon and nitrogen metabolism. Trends in protein expression over the time courses were deduced from a protein abundance index, which also revealed the importance of stress pathway proteins in both cultures. As expected, the ΔphoP mutant was deficient in expression of PhoP-dependent genes, and several putatively compensatory metabolic and regulatory pathways for phosphate scavenging were detected. Notably there is a succession of switches that coordinately induce the production of enzymes for five different secondary metabolite biosynthesis pathways over the course of the batch culturesSIThis work was funded by Biotechnology and Biological Sciences Research Council Grant BB/F003439/1, ERA-NET SysMO Project GEN2006-27745-E/SYS Grant P-UK-01-11-3i, and Research Council of Norway Project 181840/I30. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact

The dynamic architecture of the metabolic switch in Streptomyces coelicolor

[EN] Background: During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix genechip and a high-resolution time-series of fermenter-grown samples.Results: Surprisingly, we find that the metabolic switch actually consists of multiple finely orchestrated switching events. Strongly coherent clusters of genes show drastic changes in gene expression already many hours before the classically defined transition phase where the switch from primary to secondary metabolism was expected. The main switch in gene expression takes only 2 hours, and changes in antibiotic biosynthesis genes are delayed relative to the metabolic rearrangements. Furthermore, global variation in morphogenesis genes indicates an involvement of cell differentiation pathways in the decision phase leading up to the commitment to antibiotic biosynthesis.Conclusions: Our study provides the first detailed insights into the complex sequence of early regulatory events during and preceding the major metabolic switch in S. coelicolor, which will form the starting point for future attempts at engineering antibiotic production in a biotechnological settingSIWe are very grateful to Mervyn Bibb for his generous support with the Affymetrix custom microarray design. We acknowledge the excellent technical help of K. Klein, S. Poths, M. Walter, A. Øverby and E. Hansen. This project was supported by grants of the ERA-NET SySMO Project [GEN2006-27745-E/SYS]: (P-UK-01-11-3i) and the Research Council of Norway [project no. 181840/I30

Single atom imaging with an sCMOS camera

Single atom imaging requires discrimination of weak photon count events above background and has typically been performed using either EMCCD cameras, photomultiplier tubes or single photon counting modules. sCMOS provides a cost effective and highly scalable alternative to other single atom imaging technologies, offering fast readout and larger sensor dimensions. We demonstrate the first single atom resolved imaging of two site-addressable single atom traps separated by 10 μm using an sCMOS camera, offering a competitive signal-to-noise ratio at intermediate count rates to allow high fidelity readout discrimination (error < 10−6) and sub-μm spatial resolution for applications in quantum technologies

The dynamic architecture of the metabolic switch in Streptomyces coelicolor

Background: During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix genechip and a high-resolution time-series of fermenter-grown samples. Results: Surprisingly, we find that the metabolic switch actually consists of multiple finely orchestrated switching events. Strongly coherent clusters of genes show drastic changes in gene expression already many hours before the classically defined transition phase where the switch from primary to secondary metabolism was expected. The main switch in gene expression takes only 2 hours, and changes in antibiotic biosynthesis genes are delayed relative to the metabolic rearrangements. Furthermore, global variation in morphogenesis genes indicates an involvement of cell differentiation pathways in the decision phase leading up to the commitment to antibiotic biosynthesis. Conclusions: Our study provides the first detailed insights into the complex sequence of early regulatory events during and preceding the major metabolic switch in S. coelicolor, which will form the starting point for future attempts at engineering antibiotic production in a biotechnological setting

De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

Spiny mice of the genus Acomys display several unique physiological traits, including menstruation and scar-free wound healing; characteristics that are exceedingly rare in mammals, and of considerable interest to the scientific community. These unique attributes, and the potential for spiny mice to accurately model human diseases, are driving increased use of this genus in biomedical research, however little genetic information is accessible for this species. This project aimed to generate a draft transcriptome for the Common spiny mouse (Acomys cahirinus). Illumina sequencing of RNA from 15 organ types (male and female) produced 451 million, 150 bp paired-end reads (92.4Gbp). An extensive survey of de novo transcriptome assembly approaches using Trinity, SOAPdenovo-Trans, and Oases at multiple kmer lengths was conducted, producing 50 single-kmer assemblies from this dataset. Non-redundant transcripts from all assemblies were merged into a meta-assembly using the EvidentialGene tr2aacds pipeline, producing the largest gene catalogue to date for Acomys cahirinus. This study provides the first detailed characterization of the spiny mouse transcriptome. It validates use of the EvidentialGene tr2aacds pipeline in mammals to augment conventional de novo assembly approaches, and provides a valuable scientific resource for further investigation into the unique physiological characteristics inherent in the genus Acomys

De novo transcriptome assemblies for the spiny mouse (Acomys cahirinus)

Transcriptome assemblies generated per https://dx.doi.org/10.1101/076067 (preprint) / https://dx.doi.org/10.17504/protocols.io.ghebt3e (protocol). Manuscript available at Scientific Reports