Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection

The Gram-positive bacterium Listeria monocytogenes occurs widespread in the environment and infects humans when ingested along with contaminated food. Such infections are particularly dangerous for risk group patients, for whom they represent a life-threatening disease. To invent novel strategies to control contamination and disease, it is important to identify those cellular processes that maintain pathogen growth inside and outside the host. Here, we have applied transposon insertion sequencing (Tn-Seq) to L. monocytogenes for the identification of such processes on a genome-wide scale. Our approach identified 394 open reading frames that are required for growth under standard laboratory conditions and 42 further genes, which become necessary during intracellular growth in macrophages. Most of these genes encode components of the translation machinery and act in chromosome-related processes, cell division, and biosynthesis of the cellular envelope. Several cofactor biosynthesis pathways and 29 genes with unknown functions are also required for growth, suggesting novel options for the development of antilisterial drugs. Among the genes specifically required during intracellular growth are known virulence factors, genes compensating intracellular auxotrophies, and several cell division genes. Our experiments also highlight the importance of PASTA kinase signaling for general viability and of glycine metabolism and chromosome segregation for efficient intracellular growth of L. monocytogenes.Peer Reviewe

Corrigendum: Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus

Peer Reviewe

Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus

Background: As next generation sequencing (NGS) technologies have experienced a rapid development over the last decade, the investigation of the bacterial genetic architecture reveals a high potential to dissect causal loci of antibiotic resistance phenotypes. Although genome-wide association studies (GWAS) have been successfully applied for investigating the basis of resistance traits, complex resistance phenotypes have been omitted so far. For S. aureus this especially refers to antibiotics of last resort like daptomycin and ceftaroline. Therefore, we aimed to perform GWAS for the identification of genetic variants associated with DAP and CPT resistance in clinical S. aureus isolates. Materials/methods: To conduct microbial GWAS, we selected cases and controls according to their clonal background, date of isolation, and geographical origin. Association testing was performed with PLINK and SEER analysis. By using in silico analysis, we also searched for rare genetic variants in candidate loci that have previously been described to be involved in the development of corresponding resistance phenotypes. Results: GWAS revealed MprF P314L and L826F to be significantly associated with DAP resistance. These mutations were found to be homogenously distributed among clonal lineages suggesting convergent evolution. Additionally, rare and yet undescribed single nucleotide polymorphisms could be identified within mprF and putative candidate genes. Finally, we could show that each DAP resistant isolate exhibited at least one amino acid substitution within the open reading frame of mprF. Due to the presence of strong population stratification, no genetic variants could be associated with CPT resistance. However, the investigation of the staphylococcal cassette chromosome mec (SCCmec) revealed various mecA SNPs to be putatively linked with CPT resistance. Additionally, some CPT resistant isolates revealed no mecA mutations, supporting the hypothesis that further and still unknown resistance determinants are crucial for the development of CPT resistance in S. aureus. Conclusion: We hereby confirmed the potential of GWAS to identify genetic variants that are associated with antibiotic resistance traits in S. aureus. However, precautions need to be taken to prevent the detection of spurious associations. In addition, the implementation of different approaches is still essential to detect multiple forms of variations and mutations that occur with a low frequency.Peer Reviewe

Design and characterization of a magnetic bottle electron spectrometer for time-resolved extreme UV and X-ray photoemission spectroscopy of liquid microjets

We describe a magnetic bottle time-of-flight electron spectrometer designed for time-resolved photoemission spectroscopy of a liquid microjet using extreme UV and X-ray radiation. The spectrometer can be easily reconfigured depending on experimental requirements and the energy range of interest. To improve the energy resolution at high electron kinetic energy, a retarding potential can be applied either via a stack of electrodes or retarding mesh grids, and a flight-tube extension can be attached to increase the flight time. A gated electron detector was developed to reject intense parasitic signal from light scattered off the surface of the cylindrically shaped liquid microjet. This detector features a two-stage multiplication with a microchannel plate plus a fast-response scintillator followed by an image-intensified photon detector. The performance of the spectrometer was tested at SPring-8 and SACLA, and time-resolved photoelectron spectra were measured for an ultrafast charge transfer to solvent reaction in an aqueous NaI solution with a 200 nm UV pump pulses from a table-top ultrafast laser and the 5.5 keV hard X-ray probe pulses from SACLA

Radiationless decay spectrum of O 1s double core holes in liquid water

We present a combined experimental and theoretical investigation of the radiationless decay spectrum of an O 1s double core hole in liquid water. Our experiments were carried out using liquid-jet electron spectroscopy from cylindrical microjets of normal and deuterated water. The signal of the double-core-hole spectral fingerprints (hypersatellites) of liquid water is clearly identified, with an intensity ratio to Auger decay of singly charged O 1s of 0.0014(5). We observe a significant isotope effect between liquid H2O and D2O. For theoretical modeling, the Auger electron spectrum of the central water molecule in a water pentamer was calculated using an electronic-structure toolkit combined with molecular-dynamics simulations to capture the influence of molecular rearrangement within the ultrashort lifetime of the double core hole. We obtained the static and dynamic Auger spectra for H2O, (H2O)5, D2O, and (D2O)5, instantaneous Auger spectra at selected times after core-level ionization, and the symmetrized oxygen-hydrogen distance as a function of time after double core ionization for all four prototypical systems. We consider this observation of liquid-water double core holes as a new tool to study ultrafast nuclear dynamics

How to measure work functions from aqueous solutions

The recent application of concepts from condensed-matter physics to photoelectron spectroscopy (PES) of volatile, liquid-phase systems has enabled the measurement of electronic energetics of liquids on an absolute scale. Particularly, vertical ionization energies, VIEs, of liquid water and aqueous solutions, both in the bulk and at associated interfaces, can now be routinely determined. These IEs are referenced to the local vacuum level, which is the appropriate quantity for condensed matter with associated surfaces, including liquids. Here, we connect this newly accessible energy level to another important surface property, namely, the solution work function, e$\Phi_{liq}$. We lay out the prerequisites for and unique challenges of determining e$\Phi$ of aqueous solutions and liquids in general. We demonstrate - for a model aqueous solution with a tetra-n-butylammonium iodide (TBAI) surfactant solute - that concentration-dependent work functions, associated with the surface dipoles generated by the segregated interfacial layer of TBA$^+$ and I$^-$ions, can be accurately measured under controlled conditions. We detail the nature of surface potentials, uniquely tied to the nature of the flowing-liquid sample, which must be eliminated or quantified to enable such measurements. This allows us to refer measured spectra of aqueous solutions to the Fermi level and quantitatively assign surfactant concentration-dependent spectral shifts to competing work function and electronic-structure effects, the latter determining, e.g., (electro)chemical reactivity. We describe the extension of liquid-jet PES to quantitatively access concentration-dependent surface descriptors that have so far been restricted to solid-phase measurements. These studies thus mark the beginning of a new era in the characterization of the interfacial electronic structure of aqueous solutions and liquids more generally.Comment: Main manuscript: 26 pages, 7 figures. Supporting information: 5 pages, 5 figure

Photoelectron spectra of alkali metal–ammonia microjets: From blue electrolyte to bronze metal

Experimental studies of the electronic structure of excess electrons in liquids—archetypal quantum solutes—have been largely restricted to very dilute electron concentrations. We overcame this limitation by applying soft x-ray photoelectron spectroscopy to characterize excess electrons originating from steadily increasing amounts of alkali metals dissolved in refrigerated liquid ammonia microjets. As concentration rises, a narrow peak at ~2 electron volts, corresponding to vertical photodetachment of localized solvated electrons and dielectrons, transforms continuously into a band with a sharp Fermi edge accompanied by a plasmon peak, characteristic of delocalized metallic electrons. Through our experimental approach combined with ab initio calculations of localized electrons and dielectrons, we obtain a clear picture of the energetics and density of states of the ammoniated electrons over the gradual transition from dilute blue electrolytes to concentrated bronze metallic solutions

Femtosecond time-resolved X-ray absorption spectroscopy of anatase TiO2 nanoparticles using XFEL

光触媒ナノ粒子における光照射後10兆分の1秒での電子の動きをX線自由電子レーザーで観測. 京都大学プレスリリース. 2017-07-06.The charge-carrier dynamics of anatase TiO2 nanoparticles in an aqueous solution were studied by femtosecond time-resolved X-ray absorption spectroscopy using an X-ray free electron laser in combination with a synchronized ultraviolet femtosecond laser (268 nm). Using an arrival time monitor for the X-ray pulses, we obtained a temporal resolution of 170 fs. The transient X-ray absorption spectra revealed an ultrafast Ti K-edge shift and a subsequent growth of a pre-edge structure. The edge shift occurred in ca. 100 fs and is ascribed to reduction of Ti by localization of generated conduction band electrons into shallow traps of self-trapped polarons or deep traps at penta-coordinate Ti sites. Growth of the pre-edge feature and reduction of the above-edge peak intensity occur with similar time constants of 300–400 fs, which we assign to the structural distortion dynamics near the surface

Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021

Background Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern led to an expansion of genomic sequencing activities in Germany. Methods At Robert Koch Institute (RKI), the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance at the national scale, SARS-CoV-2–positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. Results We report analyses of 3623 SARS-CoV-2 genomes collected between December 2020 and December 2021, of which 3282 were randomly sampled. All variants of concern were identified in the sequenced sample set, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modeled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave. Conclusions SARS-CoV-2 molecular and genomic surveillance may inform public health policies including vaccination strategies and enable a proactive approach to controlling coronavirus disease 2019 spread as the virus evolves.Peer Reviewe

Observation of electron transfer mediated decay in aqueous solution

Photoionization is at the heart of X ray photoelectron spectroscopy XPS , which gives access to important information on a sample s local chemical environment. Local and non local electronic decay after photoionization in which the refilling of core holes results in electron emission from either the initially ionized species or a neighbour, respectively have been well studied. However, electron transfer mediated decay ETMD , which involves the refilling of a core hole by an electron from a neighbouring species, has not yet been observed in condensed phase. Here we report the experimental observation of ETMD in an aqueous LiCl solution by detecting characteristic secondary low energy electrons using liquid microjet soft XPS. Experimental results are interpreted using molecular dynamics and high level ab initio calculations. We show that both solvent molecules and counterions participate in the ETMD processes, and different ion associations have distinctive spectral fingerprints. Furthermore, ETMD spectra are sensitive to coordination numbers, ion solvent distances and solvent arrangemen