Rapidly rising cases with Omicron in Senegal.

•Omicron variant continues to progress in Senegal with the appearance of new contaminations.•IRESSEF detected the first positive case of the Omicron variant on Friday, December 3, 2021.•Since this date, the number of Omicron variant infections has increased over the weeks.•Molecular surveillance of the Omicron variant is carried out in real time to inform the medical authorities.

Suppression of the vacuum space-charge effect in fs-photoemission by a retarding electrostatic front lens.

The performance of time-resolved photoemission experiments at fs-pulsed photon sources is ultimately limited by the e-e Coulomb interaction, downgrading energy and momentum resolution. Here, we present an approach to effectively suppress space-charge artifacts in momentum microscopes and photoemission microscopes. A retarding electrostatic field generated by a special objective lens repels slow electrons, retaining the k-image of the fast photoelectrons. The suppression of space-charge effects scales with the ratio of the photoelectron velocities of fast and slow electrons. Fields in the range from -20 to -1100 V/mm for Ekin = 100 eV to 4 keV direct secondaries and pump-induced slow electrons back to the sample surface. Ray tracing simulations reveal that this happens within the first 40 to 3 µm above the sample surface for Ekin = 100 eV to 4 keV. An optimized front-lens design allows switching between the conventional accelerating and the new retarding mode. Time-resolved experiments at Ekin = 107 eV using fs extreme ultraviolet probe pulses from the free-electron laser FLASH reveal that the width of the Fermi edge increases by just 30 meV at an incident pump fluence of 22 mJ/cm2 (retarding field -21 V/mm). For an accelerating field of +2 kV/mm and a pump fluence of only 5 mJ/cm2, it increases by 0.5 eV (pump wavelength 1030 nm). At the given conditions, the suppression mode permits increasing the slow-electron yield by three to four orders of magnitude. The feasibility of the method at high energies is demonstrated without a pump beam at Ekin = 3830 eV using hard x rays from the storage ring PETRA III. The approach opens up a previously inaccessible regime of pump fluences for photoemission experiments.

The TRIXS end-station for femtosecond time-resolved resonant inelastic x-ray scattering experiments at the soft x-ray free-electron laser FLASH.

We present the experimental end-station TRIXS dedicated to time-resolved soft x-ray resonant inelastic x-ray scattering (RIXS) experiments on solid samples at the free-electron laser FLASH. Using monochromatized ultrashort femtosecond XUV/soft x-ray photon pulses in combination with a synchronized optical laser in a pump-probe scheme, the TRIXS setup allows measuring sub-picosecond time-resolved high-resolution RIXS spectra in the energy range from 35 eV to 210 eV, thus spanning the M-edge (M1 and M2,3) absorption resonances of 3d transition metals and N4,5-edges of rare earth elements. A Kirkpatrick-Baez refocusing mirror system at the first branch of the plane grating monochromator beamline (PG1) provides a focus of (6 × 6) µm2 (FWHM) at the sample. The RIXS spectrometer reaches an energy resolution of 35-160 meV over the entire spectral range. The optical laser system based on a chirped pulse optical parametric amplifier provides approximately 100 fs (FWHM) long photon pulses at the fundamental wavelength of 800 nm and a fluence of 120 mJ/cm2 at a sample for optical pump-XUV probe measurements. Furthermore, optical frequency conversion enables experiments at 400 nm or 267 nm with a fluence of 80 and 30 mJ/cm2, respectively. Some of the first (pump-probe) RIXS spectra measured with this setup are shown. The measured time resolution for time-resolved RIXS measurements has been characterized as 287 fs (FWHM) for the used energy resolution.

Strain analysis from M-edge resonant inelastic X-ray scattering of nickel oxide films.

Electronic structure modifications due to strain are an effective method for tailoring nano-scale functional materials. Demonstrated on nickel oxide (NiO) thin films, Resonant Inelastic X-ray Scattering (RIXS) at the transition-metal M2,3-edge is shown to be a powerful tool for measuring the electronic structure modification due to strain in the near-surface region. Analyses from the M2,3-edge RIXS in comparison with dedicated crystal field multiplet calculations show distortions in 40 nm NiO grown on a magnesium oxide (MgO) substrate (NiO/MgO) similar to those caused by surface relaxation of bulk NiO. The films of 20 and 10 nm NiO/MgO show slightly larger differences from bulk NiO. Quantitatively, the NiO/MgO samples all are distorted from perfect octahedral (Oh) symmetry with a tetragonal parameter Ds of about -0.1 eV, very close to the Ds distortion from octahedral (Oh) symmetry parameter of -0.11 eV obtained for the surface-near region from a bulk NiO crystal. Comparing the spectra of a 20 nm film of NiO grown on a 20 nm magnetite (Fe3O4) film on a MgO substrate (NiO/Fe3O4/MgO) with the calculated multiplet analyses, the distortion parameter Ds appears to be closer to zero, showing that the surface-near region of this templated film is less distorted from Oh symmetry than the surface-near region in bulk NiO. Finally, the potential of M2,3-edge RIXS for other investigations of strain on electronic structure is discussed.

Non-linear soft x-ray methods on solids with MUSIX-the multi-dimensional spectroscopy and inelastic x-ray scattering endstation.

With the intense and coherent x-ray pulses available from free-electron lasers, the possibility to transfer non-linear spectroscopic methods from the laser lab to the x-ray world arises. Advantages especially regarding selectivity and thus information content as well as an improvement of signal levels are expected. The use of coherences is especially fruitful and the example of coherent x-ray/optical sum-frequency generation is discussed. However, many non-linear x-ray methods still await discovery, partially due to the necessity for extremely adaptable and versatile instrumentation that can be brought to free-electron lasers for the analysis of the spectral content emitted from the sample into a continuous range of emission angles. Such an instrument (called MUSIX) is being developed and employed at FLASH, the free-electron laser in Hamburg and is described in this contribution together with first results.

Improving genetic transformation rates in honeybees.

Functional genetic studies in honeybees have been limited by transformation tools that lead to a high rate of transposon integration into the germline of the queens. A high transformation rate is required to reduce screening efforts because each treated queen needs to be maintained in a separate honeybee colony. Here, we report on further improvement of the transformation rate in honeybees by using a combination of different procedures. We employed a hyperactive transposase protein (hyPBaseapis), we tripled the amount of injected transposase mRNAs and we injected embryos into the first third (anterior part) of the embryo. These three improvements together doubled the transformation rate from 19% to 44%. We propose that the hyperactive transposase (hyPBaseapis) and the other steps used may also help to improve the transformation rates in other species in which screening and crossing procedures are laborious.

Probing the non-equilibrium transient state in magnetite by a jitter-free two-color X-ray pump and X-ray probe experiment.

We present a general experimental concept for jitter-free pump and probe experiments at free electron lasers. By generating pump and probe pulse from one and the same X-ray pulse using an optical split-and-delay unit, we obtain a temporal resolution that is limited only by the X-ray pulse lengths. In a two-color X-ray pump and X-ray probe experiment with sub 70 fs temporal resolution, we selectively probe the response of orbital and charge degree of freedom in the prototypical functional oxide magnetite after photoexcitation. We find electronic order to be quenched on a time scale of (30 ± 30) fs and hence most likely faster than what is to be expected for any lattice dynamics. Our experimental result hints to the formation of a short lived transient state with decoupled electronic and lattice degree of freedom in magnetite. The excitation and relaxation mechanism for X-ray pumping is discussed within a simple model leading to the conclusion that within the first 10 fs the original photoexcitation decays into low-energy electronic excitations comparable to what is achieved by optical pump pulse excitation. Our findings show on which time scales dynamical decoupling of degrees of freedom in functional oxides can be expected and how to probe this selectively with soft X-ray pulses. Results can be expected to provide crucial information for theories for ultrafast behavior of materials and help to develop concepts for novel switching devices.

Ultrafast Self-Induced X-Ray Transparency and Loss of Magnetic Diffraction.

Using ultrafast ≃2.5 fs and ≃25 fs self-amplified spontaneous emission pulses of increasing intensity and a novel experimental scheme, we report the concurrent increase of stimulated emission in the forward direction and loss of out-of-beam diffraction contrast for a Co/Pd multilayer sample. The experimental results are quantitatively accounted for by a statistical description of the pulses in conjunction with the optical Bloch equations. The dependence of the stimulated sample response on the incident intensity, coherence time, and energy jitter of the employed pulses reveals the importance of increased control of x-ray free electron laser radiation.

Genome analysis and description of Xanthomonas massiliensis sp. nov., a new species isolated from human faeces.

Xanthomonas massiliensis strain SN6T is a Gram-negative bacterium which is aerobic, motile and nonsporulating. This new species isolated from human faeces exhibited the characteristic traits of members of this genus, such as yellow pigmentation and viscosity. Here we present the main phenotypic characteristics and the taxonogenomics description of this strain. The genome is 3 690 720 bp long with DNA G + C content of about 70.52%.

Time-resolved electron spectroscopy for chemical analysis of photodissociation: Photoelectron spectra of Fe(CO)5, Fe(CO)4, and Fe(CO)3.

The prototypical photoinduced dissociation of Fe(CO)5 in the gas phase is used to test time-resolved x-ray photoelectron spectroscopy for studying photochemical reactions. Upon one-photon excitation at 266 nm, Fe(CO)5 successively dissociates to Fe(CO)4 and Fe(CO)3 along a pathway where both fragments retain the singlet multiplicity of Fe(CO)5. The x-ray free-electron laser FLASH is used to probe the reaction intermediates Fe(CO)4 and Fe(CO)3 with time-resolved valence and core-level photoelectron spectroscopy, and experimental results are interpreted with ab initio quantum chemical calculations. Changes in the valence photoelectron spectra are shown to reflect changes in the valence-orbital interactions upon Fe-CO dissociation, thereby validating fundamental theoretical concepts in Fe-CO bonding. Chemical shifts of CO 3σ inner-valence and Fe 3p core-level binding energies are shown to correlate with changes in the coordination number of the Fe center. We interpret this with coordination-dependent charge localization and core-hole screening based on calculated changes in electron densities upon core-hole creation in the final ionic states. This extends the established capabilities of steady-state electron spectroscopy for chemical analysis to time-resolved investigations. It could also serve as a benchmark for how charge and spin density changes in molecular dissociation and excited-state dynamics are expressed in valence and core-level photoelectron spectroscopy.

Peptoniphilus lacydonensis sp. nov., a new human-associated species isolated from a patient with chronic refractory sinusitis.

Strain EL1T was isolated from a sinus sample of an 85-year-old man with chronic refractory sinusitis complicating ethmoidal adenocarcinoma. We studied its phenotypic and genomic characteristics. This is a Gram stain-positive, anaerobic and microaerophilic coccus. Cells are catalase negative, nonmotile and non-spore forming. The major fatty acids are saturated hexadecanoic acid (34%), unsaturated 9-octadecenoic acid (32%) and 9.12-octadecadienoic acid (21%). The 1.86 Mb long genome exhibits a 29.9% G+C content and contains 1750 protein-coding and 43 RNA genes. On the basis of these data, we propose the creation of the new human-associated bacterial species Peptoniphilus lacydonensis sp. nov.

'Cellulomonas timonensis' sp. nov., taxonogenomics description of a new bacterial species isolated from human gut.

'Cellulomonas timonensis' sp. nov. strain sn7T is a new species within the Cellulomonas genus. We present the main phenotypic characteristics and provide a complete annotation of its genome sequence. This facultative anaerobic bacterium, isolated from the stool of 38-year-old obese Frenchman, is Gram-positive, has motile rods and is sporulating. The genome is 4 057 828 bp long with 72.42% G + C content. Of the 3732 predicted genes, 3667 were protein-coding genes and 65 were RNAs.

Careful use of 16S rRNA gene sequence similarity values for the identification of Mycobacterium species.

In order to evaluate the suitability of 16S rRNA nucleotide sequence similarity for the classification of new Mycobacterium isolates at the species level, we systematically studied the pairwise identity values of this gene for 131 Mycobacterium species with standing in nomenclature. Only one of the studied species, M. poriferae (0.76%), strictly respected the 95% and 98.65% threshold values currently recommended to determine the affiliation of bacterial isolates to an existing or new genus or species, respectively. All other species exhibited at least an identity value >98.65% and/or <95% with another Mycobacterium species. Therefore, we suggest that interpretation of interspecies 16S rRNA identity values should be made cautiously when classifying a new mycobacterial isolate at the species level.

X-ray spectroscopy on the active ion in laser crystals.

The active ions in typical laser crystals were studied with Resonant Inelastic X-ray Scattering (RIXS) and Partial Fluorescence Yield X-ray Absorption (PFY-XAS) spectroscopies as solid state model systems for dilute active centers. We analyzed Ti3+ and Cr3+ in α-Al2O3:Ti3+ and LiCaAlF6:Cr3+, respectively. The comparison of experimental data with semi-empirical multiplet calculations provides insights into the electronic structure and shows how measured crystal field energies are related across different spectroscopies.

Real-Time Elucidation of Catalytic Pathways in CO Hydrogenation on Ru.

The direct elucidation of the reaction pathways in heterogeneous catalysis has been challenging due to the short-lived nature of reaction intermediates. Here, we directly measured on ultrafast time scales the initial hydrogenation steps of adsorbed CO on a Ru catalyst surface, which is known as the bottleneck reaction in syngas and CO2 reforming processes. We initiated the hydrogenation of CO with an ultrafast laser temperature jump and probed transient changes in the electronic structure using real-time X-ray spectroscopy. In combination with theoretical simulations, we verified the formation of CHO during CO hydrogenation.

Communication: Direct evidence for sequential dissociation of gas-phase Fe(CO)5 via a singlet pathway upon excitation at 266 nm.

We prove the hitherto hypothesized sequential dissociation of Fe(CO)5 in the gas phase upon photoexcitation at 266 nm via a singlet pathway with time-resolved valence and core-level photoelectron spectroscopy with an x-ray free-electron laser. Valence photoelectron spectra are used to identify free CO molecules and to determine the time constants of stepwise dissociation to Fe(CO)4 within the temporal resolution of the experiment and further to Fe(CO)3 within 3 ps. Fe 3p core-level photoelectron spectra directly reflect the singlet spin state of the Fe center in Fe(CO)5, Fe(CO)4, and Fe(CO)3 showing that the dissociation exclusively occurs along a singlet pathway without triplet-state contribution. Our results are important for assessing intra- and intermolecular relaxation processes in the photodissociation dynamics of the prototypical Fe(CO)5 complex in the gas phase and in solution, and they establish time-resolved core-level photoelectron spectroscopy as a powerful tool for determining the multiplicity of transition metals in photochemical reactions of coordination complexes.

Genomic analysis of a Streptococcus pyogenes strain causing endocarditis in a child.

We sequenced the genome of Streptococcus pyogenes strain G773 that caused an infective endocarditis in a 4-year-old boy suffering from acute endocarditis. The 1.9-Mb genome exhibited a specific combination of virulence factors including a complete integrative and conjugative element, sp2905, previously described as incomplete in S. pyogenes, and five bacteriocin-coding genes. However, strain G773 lacked a CRISPR-Cas system.

Tessaracoccus massiliensis sp. nov., a new bacterial species isolated from the human gut.

A new Actinobacterium, designated Tessaracoccus massiliensis type strain SIT-7(T) (= CSUR P1301 = DSM 29060), have been isolated from a Nigerian child with kwashiorkor. It is a facultative aerobic, Gram positive, rod shaped, non spore-forming, and non motile bacterium. Here, we describe the genomic and phenotypic characteristics of this isolate. Its 3,212,234 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 67.81% and contains 3,058 protein-coding genes and 49 RNA genes.

"Lascolabacillus massiliensis": a new species isolated from the human gut.

We report here the main characteristics of "Lascolabacillus massiliensis" strain SIT8 (CSUR P1560) that was isolated from the stool of a healthy 28-month-old boy.

Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov.

Strain FF10(T) (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of a lizard (Varanus niloticus) in Dakar, Senegal. Here we used a polyphasic study including phenotypic and genomic analyses to describe the strain FF10(T). Results support strain FF10(T) being a Gram-positive coccus, facultative anaerobic bacterium, catalase-negative, non-motile and non-spore forming. The sequenced genome counts 2.46 Mb with one chromosome but no plasmid. It exhibits a G+C content of 40.4% and contains 2471 protein-coding and 45 RNA genes. On the basis of these data, we propose the creation of Streptococcus varani sp. nov.