Comparative study of CXC chemokines modulation in brown trout (Salmo trutta) following infection with a bacterial or viral pathogen

Acknowledgements We would like to acknowledge Richard Paley, Tom Hill and Georgina Rimmer for their collaboration during brown trout infection challenges in CEFAS-Weymouth biosecurity facilities. Bartolomeo Gorgoglione, Stephen W. Feist and Nick G. H. Taylor were supported by a DEFRA grant (F1198).Peer reviewedPostprin

Nanoplasmonic Lattices for Ultracold atoms

We propose to use sub-wavelength confinement of light associated with the near field of plasmonic systems to create nanoscale optical lattices for ultracold atoms. Our approach combines the unique coherence properties of isolated atoms with the sub-wavelength manipulation and strong light-matter interaction associated with nano-plasmonic systems. It allows one to considerably increase the energy scales in the realization of Hubbard models and to engineer effective long-range interactions in coherent and dissipative many-body dynamics. Realistic imperfections and potential applications are discussed.Comment: 5 pages, 3 figures, V2: minor changes, V3: minor changes, added supplemental materia

Impact of molecular spectroscopy on carbon monoxide abundances from tropomi

The impact of SEOM–IAS (Scientific Exploitation of Operational Missions–Improved Atmospheric Spectroscopy) spectroscopic information on CO columns from TROPOMI (Tropospheric Monitoring Instrument) shortwave infrared (SWIR) observations was examined. HITRAN 2016 (High Resolution Transmission) and GEISA 2015 (Gestion et Etude des Informations Spectroscopiques Atmosphériques 2015) were used as a reference upon which the spectral fitting residuals, retrieval errors and inferred quantities were assessed. It was found that SEOM–IAS significantly improves the quality of the CO retrieval by reducing the residuals to TROPOMI observations. The magnitude of the impact is dependent on the climatological region and spectroscopic reference used. The difference in the CO columns was found to be rather small, although discrepancies reveal, for selected scenes, in particular, for observations with elevated molecular concentrations. A brief comparison to Total Column Carbon Observing Network (TCCON) and Network for the Detection of Atmospheric Composition Change (NDACC) also demonstrated that both spectroscopies cause similar columns; however, the smaller retrieval errors in the SEOM with Speed-Dependent Rautian and line-Mixing (SDRM) inferred CO turned out to be beneficial in the comparison of post-processed mole fractions with ground-based references

The genetic basis for adaptation of model-designed syntrophic co-cultures.

Understanding the fundamental characteristics of microbial communities could have far reaching implications for human health and applied biotechnology. Despite this, much is still unknown regarding the genetic basis and evolutionary strategies underlying the formation of viable synthetic communities. By pairing auxotrophic mutants in co-culture, it has been demonstrated that viable nascent E. coli communities can be established where the mutant strains are metabolically coupled. A novel algorithm, OptAux, was constructed to design 61 unique multi-knockout E. coli auxotrophic strains that require significant metabolite uptake to grow. These predicted knockouts included a diverse set of novel non-specific auxotrophs that result from inhibition of major biosynthetic subsystems. Three OptAux predicted non-specific auxotrophic strains-with diverse metabolic deficiencies-were co-cultured with an L-histidine auxotroph and optimized via adaptive laboratory evolution (ALE). Time-course sequencing revealed the genetic changes employed by each strain to achieve higher community growth rates and provided insight into mechanisms for adapting to the syntrophic niche. A community model of metabolism and gene expression was utilized to predict the relative community composition and fundamental characteristics of the evolved communities. This work presents new insight into the genetic strategies underlying viable nascent community formation and a cutting-edge computational method to elucidate metabolic changes that empower the creation of cooperative communities

Integrated photonics enables continuous-beam electron phase modulation

Integrated photonics facilitates extensive control over fundamental light–matter interactions in manifold quantum systems including atoms1, trapped ions2,3, quantum dots4 and defect centres5. Ultrafast electron microscopy has recently made free-electron beams the subject of laser-based quantum manipulation and characterization6,7,8,9,10,11, enabling the observation of free-electron quantum walks12,13,14, attosecond electron pulses10,15,16,17 and holographic electromagnetic imaging18. Chip-based photonics19,20 promises unique applications in nanoscale quantum control and sensing but remains to be realized in electron microscopy. Here we merge integrated photonics with electron microscopy, demonstrating coherent phase modulation of a continuous electron beam using a silicon nitride microresonator. The high-finesse (Q0 ≈ 106) cavity enhancement and a waveguide designed for phase matching lead to efficient electron–light scattering at extremely low, continuous-wave optical powers. Specifically, we fully deplete the initial electron state at a cavity-coupled power of only 5.35 microwatts and generate >500 electron energy sidebands for several milliwatts. Moreover, we probe unidirectional intracavity fields with microelectronvolt resolution in electron-energy-gain spectroscopy21. The fibre-coupled photonic structures feature single-optical-mode electron–light interaction with full control over the input and output light. This approach establishes a versatile and highly efficient framework for enhanced electron beam control in the context of laser phase plates22, beam modulators and continuous-wave attosecond pulse trains23, resonantly enhanced spectroscopy24,25,26 and dielectric laser acceleration19,20,27. Our work introduces a universal platform for exploring free-electron quantum optics28,29,30,31, with potential future developments in strong coupling, local quantum probing and electron–photon entanglement

Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis

Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for the study of extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction for the microorganism. The reconstruction itself represents a knowledge base of the haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, we experimentally determined several parameters relevant to growth, including a characterization of the biomass composition and a quantification of carbon and oxygen consumption. Using the metabolic reconstruction and the experimental data, we formulated a constraints-based model which we used to analyze the behavior of the archaeon when grown on a single carbon source. Results of the analysis include the finding that Natronomonas pharaonis, when grown aerobically on acetate, uses a carbon to oxygen consumption ratio that is theoretically near-optimal with respect to growth and energy production. This supports the hypothesis that, under simple conditions, the microorganism optimizes its metabolism with respect to the two objectives. We also found that the archaeon has a very low carbon efficiency of only about 35%. This inefficiency is probably due to a very low P/O ratio as well as to the other difficulties posed by its extreme environment

Spectroscopy and Biosensing with Optically Resonant Dielectric Nanostructures

Resonant dielectric nanoparticles (RDNs) made of materials with large positive dielectric permittivity, such as Si, GaP, GaAs, have become a powerful platform for modern light science, enabling various fascinating applications in nanophotonics and quantum optics. In addition to light localization at the nanoscale, dielectric nanostructures provide electric and magnetic resonant responses throughout the visible and infrared spectrum, low dissipative losses and optical heating, low doping effect and absence of quenching, which are interesting for spectroscopy and biosensing applications. In this review, we present state-of-the-art applications of optically resonant high-index dielectric nanostructures as a multifunctional platform for light-matter interactions. Nanoscale control of quantum emitters and applications for enhanced spectroscopy including fluorescence spectroscopy, surface-enhanced Raman scattering (SERS), biosensing, and lab-on-a-chip technology are surveyed. We describe the theoretical background underlying these effects, overview realizations of specific resonant dielectric nanostructures and hybrid excitonic systems, and outlook the challenges in this field, which remain open to future research

Cavity-mediated electron-photon pairs

Quantum information, communication, and sensing rely on the generation and control of quantum correlations in complementary degrees of freedom. Free electrons coupled to photonics promise novel hybrid quantum technologies, although single-particle correlations and entanglement have yet to be shown. In this work, we demonstrate the preparation of electron-photon pair states using the phase-matched interaction of free electrons with the evanescent vacuum field of a photonic chip–based optical microresonator. Spontaneous inelastic scattering produces intracavity photons coincident with energy-shifted electrons, which we employ for noise-suppressed optical mode imaging. This parametric pair-state preparation will underpin the future development of free-electron quantum optics, providing a route to quantum-enhanced imaging, electron-photon entanglement, and heralded single-electron and Fock-state photon sources