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X-ray free-electron lasers (FELs) deliver ultrabright X-ray pulses, but not the sequences of phase-coherent pulses required for time-domain interferometry and control of quantum states. For conventional split-and-delay schemes to produce such sequences, the challenge stems from extreme stability requirements when splitting Ångstrom wavelength beams, where the tiniest pathlength differences introduce phase jitter. We describe an FEL mode based on selective electron-bunch degradation and transverse beam shaping in the accelerator, combined with a self-seeded photon emission scheme. Instead of splitting the photon pulses after their generation by the FEL,we split the electron bunch in the accelerator, prior to photon generation, to obtain phase-locked X-ray pulses with subfemtosecond duration. Time-domain interferometry becomes possible, enabling the concomitant program of classical and quantum optics experiments with X-rays. The scheme leads to scientific benefits of cutting-edge FELs with attosecond and/or high-repetition rate capabilities, ranging from the X-ray analog of Fourier transform infrared spectroscopy to damage-free measurements. [ABSTRACT FROM AUTHOR]

This article presents a demonstration of the improved performance of an X‐ray free‐electron laser (FEL) using the optical klystron mechanism and helical undulator configuration, in comparison with the common planar undulator configuration without optical klystron. The demonstration was carried out at Athos, the soft X‐ray beamline of SwissFEL. Athos has variable‐polarization undulators, and small magnetic chicanes placed between every two undulators to fully exploit the optical klystron. It was found that, for wavelengths of 1.24 nm and 3.10 nm, the required length to achieve FEL saturation is reduced by about 35% when using both the optical klystron and helical undulators, with each effect accounting for about half of the improvement. Moreover, it is shown that a helical undulator configuration provides a 20% to 50% higher pulse energy than planar undulators. This work represents an important step towards more compact and high‐power FELs, rendering this key technology more efficient, affordable and accessible to the scientific community. [ABSTRACT FROM AUTHOR]

A simple and compact scheme that enhances the brightness of self‐amplified spontaneous‐emission (SASE) free‐electron lasers is presented. The method combines the high‐brightness SASE scheme and the optical klystron concept to increase the temporal coherence of the produced radiation and to reduce the required length of the undulator beamline at the same time. The scheme is very simple and only requires compact chicanes between the modules of the undulator beamline. Simulations show that, in comparison with SASE, the brightness can be improved by up to a factor of ten and the required length to achieve saturation can be reduced by 20% or more. [ABSTRACT FROM AUTHOR]

X‐ray free‐electron lasers (FELs) are cutting‐edge scientific tools able to generate transversely coherent radiation with very high power and ultra‐short pulse durations. The self‐seeding mechanism has been proven to increase the longitudinal coherence of the FEL radiation but its efficiency could be significantly improved, especially for soft X‐rays. This paper proposes the enhancement of the performance of self‐seeding by combining it with the harmonic generation mechanism. In particular, by starting the process with a subharmonic of the wavelength of interest, the coherence of the produced radiation is improved, the undulator beamline becomes more compact, and the monochromator realization is simplified. Numerical simulations for SwissFEL are presented showing that the method can be employed, within a given space, to increase the spectral brightness by one order of magnitude or more with respect to standard self‐seeding. This coherence enhancement will be fundamental for many photon science applications and techniques such as resonant inelastic X‐ray scattering. [ABSTRACT FROM AUTHOR]

With the successful operation of free-electron lasers (FELs) as user facilities there has been a growing demand for experiments with two photon pulses with variable photon energy and time separation. A configuration of an undulator with variable-gap control and a delaying chicane in the middle of the beamline is proposed. An injected electron beam with a transverse tilt will only yield FEL radiation for the parts which are close to the undulator axis. This allows, after re-aligning and delaying the electron beam, a different part of the bunch to be used to produce a second FEL pulse. This method offers independent control in photon energy and delay. For the parameters of the soft X-ray beamline Athos at the SwissFEL facility the photon energy tuning range is a factor of five with an adjustable delay between the two pulses from −50 to 950 fs. [ABSTRACT FROM AUTHOR]

The diversity of virus-specific antibodies and of B cells among different individuals is unknown. Using single-cell cloning of antibody genes, we generated recombinant human monoclonal antibodies from influenza nucleoprotein-specific memory B cells in four adult humans with and without preceding influenza vaccination. We examined the diversity of the antibody repertoires and found that NP-specific B cells used numerous immunoglobulin genes. The heavy chains (HCs) originated from 26 and the kappa light chains (LCs) from 19 different germ line genes. Matching HC and LC chains gave rise to 43 genetically distinct antibodies that bound influenza NP. The median lengths of the CDR3 of the HC, kappa and lambda LC were 14, 9 and 11 amino acids, respectively. We identified changes at 13.6% of the amino acid positions in the V gene of the antibody heavy chain, at 8.4 % in the kappa and at 10.6 % in the lambda V gene. We identified somatic insertions or deletions in 8.1% of the variable genes. We also found several small groups of clonal relatives that were highly diversified. Our findings demonstrate broadly diverse memory B cell repertoires for the influenza nucleoprotein. We found extensive variation within individuals with a high number of point mutations, insertions, and deletions, and extensive clonal diversification. Thus, structurally conserved proteins can elicit broadly diverse and highly mutated B-cell responses. [ABSTRACT FROM AUTHOR]

Abstract: A central, yet unresolved issue in the pathogenesis of HIV disease is the mechanism of antibody perturbation. In this study, HIV-specific memory B-cells were quantified in groups of infected subjects and compared with memory responses to other antigens and antibody titers. HIV-specific memory B-cell responses were vigorous in individuals with CD4+ T-cell counts >350/μl and weak or undetectable in subjects with CD4+ T-cell numbers <200/μl. Memory B-cell loss was permanent, because antiretroviral therapy failed to restore HIV-specific memory responses while influenza- and tetanus toxoid-specific memory B-cells remained unaffected or recovered. Antibody titers to Gag strongly correlated with memory B-cell frequencies. In contrast, Env-specific antibodies were maintained in advanced disease despite low or undetectable levels of memory B-cells. These results provide a potential mechanism by which destruction of HIV-specific CD4+ T-cells affects the humoral immune response against HIV and compromises the ability to maintain an effective antibody response. [Copyright &y& Elsevier]

The aim of this study was to analyse the hygienic suitability of wood often used in animal husbandry. To this end, the inactivation of viruses (Enterovirus E as a surrogate for non-enveloped viruses and Newcastle disease virus as a surrogate for enveloped viruses) on germ carriers consisting of various types of wood was studied over an extended period to assess the biosafety of wood as an agricultural building material. The study was designed to assess the intrinsic biocidal activity of the wood itself, without the use of a disinfectant. The laboratory tests were based on German test guidelines and current European standards. Five different types of wood germ carriers, i.e., spruce (Picea abies), pine (Pinus sylvestris), poplar (Populus sp.), beech (Fagus sylvatica) and Douglas fir (Pseudotsuga menziesii), as well as stainless-steel carriers, were inoculated with enveloped and non-enveloped viruses and stored for up to four months, and the remaining infectivity of the viruses was continuously assessed. The results showed that intact, finely sawn timber with a low depth of roughness had an inactivating effect on the viruses up to 7.5 decadal logarithmic levels. For the non-enveloped virus, inactivation was fastest on Douglas fir wood, with the target reduction for effective inactivation (reduction by factor 4.0 log10) being achieved after two weeks, and for the enveloped virus on pine wood, it was already achieved from the day of drying. The hygienic effects of the wood carriers may be due to their hygroscopic properties and wood constituents. These effects offer potential for further investigation, including tests with other wood species rich in extractives. [ABSTRACT FROM AUTHOR]

Background: Newcastle disease is a devastating disease in poultry caused by virulent Newcastle disease virus (NDV), a paramyxovirus endemic in many regions of the world despite intensive vaccination. Phylogenetic analyses reveal ongoing evolution of the predominant circulating genotype 2.VII, and the relevance of potential antigenic drift is under discussion. To investigate variation within neutralization-sensitive epitopes within the protein responsible for receptor binding, i.e. the Hemagglutinin-Neuraminidase (HN) spike protein, we were interested in establishing genotype-specific monoclonal antibodies (MAbs). Methods: An HN-enriched fraction of a gradient-purified NDV genotype 2.VII was prepared and successfully employed to induce antibodies in BalbC mice that recognize conformationally intact sites reactive by haemagglutination inhibition (HI). For subsequent screening of mouse hybridoma cultures, an NDV-ELISA was established that utilizes Concanavalin A (ConA-ELISA) coupled glycoproteins proven to present conformation-dependent epitopes. Results: Six out of nine selected MAbs were able to block receptor binding as demonstrated by HI activity. One MAb recognized an epitope only present in the homologue virus, while four other MAbs showed weak reactivity to selected other genotypes. On the other hand, one broadly cross-reacting MAb reacted with all genotypes tested and resembled the reactivity profile of genotype-specific polyclonal antibody preparations that point to minor antigenic differences between tested NDV genotpyes. Conclusions: These results point to the concurrent presence of variable and conserved epitopes within the HN molecule of NDV. The described protocol should help to generate MAbs against a variety of NDV strains and to enable in depth analysis of the antigenic profiles of different genotypes. [ABSTRACT FROM AUTHOR]

Viral disinfection is important for medical facilities, the food industry, and the veterinary field, especially in terms of controlling virus outbreaks. Therefore, standardized methods and activity levels are available for these areas. Usually, disinfectants used in these areas are characterized by their activity against test organisms (i.e., viruses, bacteria, and/or yeasts). This activity is usually determined using a suspension test in which the test organism is incubated with the respective disinfectant in solution to assess its bactericidal, yeasticidal, or virucidal activity. In addition, carrier methods that more closely reflect real-world applications have been developed, in which microorganisms are applied to the surface of a carrier (e.g., stainless steel frosted glass, or polyvinyl chloride (PVC)) and then dried. However, to date, no standardized methods have become available for addressing genetically modified vectors or disinfection-resistant oncolytic viruses such as the H1-parvovirus. Particularly, such non-enveloped viruses, which are highly resistant to disinfectants, are not taken into account in European standards. This article proposes a new activity claim known as "virucidal activity PLUS", summarizes the available methods for evaluating the virucidal activity of chemical disinfectants against genetically modified organisms (GMOs) using current European standards, including the activity against highly resistant parvoviridae such as the adeno-associated virus (AAV), and provides guidance on the selection of disinfectants for pharmaceutical manufacturers, laboratories, and clinical users. [ABSTRACT FROM AUTHOR]

Objectives: To determine the seroprevalence of dengue in central and eastern Sudan and the breadth of neutralising antibody responses.Methods: Blood was drawn from 483 patients with fever who visited outpatient clinics in Port Sudan, Red Sea state, in three towns in Kassala state and in El Obeid, North Kordofan, in December 2012 and January 2013. Sera were tested for dengue virus IgG and IgM by ELISA (Panbio) and sera without serologic evidence of acute infection (IgM negative) were used for the analysis of the seroprevalence. DENV neutralisation tests were performed to determine the specificity of the ELISA and to examine the degree of cross-neutralisation of multiple DENV serotypes.Results: Sixty-seven per cent (302 of 448) of the sera were dengue virus IgG-positive. The seroprevalence in Port Sudan was 89% (106 of 119 sera), in Kassala 61% (128 of 209) and in North Kordofan 56.7% (68 of 120). Thirty-one of 32 ELISA-positive sera neutralised dengue viruses indicating that the ELISA was highly specific. The majority of the sera broadly neutralised all four dengue virus serotypes indicating multiple infections.Conclusions: The majority of the population in central and eastern Sudan has been infected with dengue viruses, many people repeatedly. The high seroprevalence underscores the need for extended dengue surveillance in Sudan, broad disease awareness in medical institutions and in the population and diagnostic capacity building for severe dengue infections. [ABSTRACT FROM AUTHOR]

Schmallenberg virus (SBV) induces fetal malformation, abortions and stillbirth in ruminants. While the non-structural protein NSs is a major virulence factor, the biological function of NSm, the second non-structural protein which consists of three hydrophobic transmembrane (I, III, V) and two non-hydrophobic regions (II, IV), is still unknown. Here, a series of NSm mutants displaying deletions of nearly the entire NSm or of the non-hydrophobic domains was generated and the intracellular distribution of NSm was assessed. SBV-NSm is dispensable for the generation of infectious virus and mutants lacking domains II – V showed growth properties similar to the wild-type virus. In addition, a comparable intracellular distribution of SBV-NSm was observed in mammalian cells infected with domain II mutants or wild-type virus. In both cases, NSm co-localized with the glycoprotein Gc in the Golgi compartment. However, domain IV-deletion mutants showed an altered distribution pattern and no co-localization of NSm and Gc. [ABSTRACT FROM AUTHOR]

The Paul Scherrer Institute is implementing laser-based seeding in the soft X-ray beamline (Athos) of its free-electron laser, SwissFEL, to enhance the temporal and spectral properties of the delivered photon pulses. This technique requires, among other components, two identical modulators for coupling the electron beam with an external laser with a wavelength range between 260 and 1600 nm. The design, magnetic measurements results, alignment, operation and also details of the novel and exotic magnetic configuration of the prototype are described. [ABSTRACT FROM AUTHOR]

A new and simple method to generate X-ray free-electron-laser radiation with unprecedented spectral bandwidth above the 10% level is presented. The broad bandwidth is achieved by sending a transversely tilted beam through a transverse-gradient undulator. The extent of the bandwidth can easily be controlled by variation of the beam tilt or the undulator gradient. Numerical simulations confirm the validity and feasibility of this method. [ABSTRACT FROM AUTHOR]

Airborne disinfection of high-containment facilities before maintenance or between animal studies is crucial. Commercial spore carriers (CSC) coated with 106 spores of Geobacillus stearothermophilus are often used to assess the efficacy of disinfection. We used quantitative carrier testing (QCT) procedures to compare the sensitivity of CSC with that of surrogates for nonenveloped and enveloped viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mycobacteria, and spores, to an aerosolized mixture of peroxyacetic acid and hydrogen peroxide (aPAA-HP). We then used the QCT methodology to determine relevant process parameters to develop and validate effective disinfection protocols (≥4-log10 reduction) in various large and complex facilities. Our results demonstrate that aPAA-HP is a highly efficient procedure for airborne room disinfection. Relevant process parameters such as temperature and relative humidity can be wirelessly monitored. Furthermore, we found striking differences in inactivation efficacies against some of the tested microorganisms. Overall, we conclude that dry fogging a mixture of aPAA-HP is highly effective against a broad range of microorganisms as well as material compatible with relevant concentrations. Furthermore, CSC are artificial bioindicators with lower resistance and thus should not be used for validating airborne disinfection when microorganisms other than viruses have to be inactivated. [ABSTRACT FROM AUTHOR]

Background: Technical protection measures for laboratory activities involving biological agents include biological safety cabinets (BSC) that may be contaminated. In the case of diagnostic activities with SARS-CoV-2, this may also affect BSC that are operated at protection level 2; therefore, decontamination of all contaminated surfaces of the BSC may be required. In addition to fumigation with hydrogen peroxide (H 2 O 2), dry fogging of H 2 O 2 -stabilized peroxyacetic acid (PAA) represents another alternative to fumigation with formalin. However, to prove their efficacy, these alternatives need to be validated for each model of BSC. Methods: The validation study was performed on 4 different BSCs of Class II A2 using the "Mini Dry Fog" system. Results: An aerosol concentration of 0.03% PAA and 0.15% H 2 O 2 during a 30 min exposure was sufficient to inactivate SARS-CoV-2. Effective concentrations of 1.0% PAA and 5% H 2 O 2 were required to decontaminate the custom-prepared biological indicators loaded with spores of G. stearothermophilus and deployed at 9 different positions in the BSC. Commercial spore carriers were easier to inactivate by a factor of 4, which corresponded to a reduction of 106 in all localizations. Conclusions: Dry fogging with PAA is an inexpensive, robust, and highly effective decontamination method for BSCs for enveloped viruses such as SARS-CoV-2. The good material compatibility, lack of a requirement for neutralization, low pH – which increases the range of efficacy compared to H 2 O 2 fumigation – the significantly shorter processing time, and the lower costs argue in favor of this method. [ABSTRACT FROM AUTHOR]

Rift Valley fever virus (RVFV) is a zoonotic arbovirus that causes severe disease in humans and ruminants. The infection is characterized by abortions in pregnant animals, high mortality in neonates as well as febrile illness in humans that develop in 1% of cases encephalitis or hemorrhagic fever. There is presently no specific antiviral treatment for RVFV infection available. In this study, two monoclonal antibodies (mAbs), raised against glycoprotein Gn, were applied in a therapeutic study. Treatment of RVFV infected mice with neutralizing mAb Gn3 alone at two different time points (30 minutes before or 30 minutes after virus challenge) showed only moderate efficacy of about 58.3% survival in both applications. However, a combination therapy together with non-neutralizing mAb Gn32 demonstrated complete protection (100% survival) when applied 30 minutes after the lethal challenge dose. The increase of mAb efficacy is probably based on cooperative neutralization effects. These data suggest that a combination therapy with mAbs Gn3 and Gn32 could be an effective treatment option against RVFV infection. Author summary: Rift Valley fever virus represents an acute viral disease affecting animals especially livestock and humans and is responsible for widespread outbreaks throughout Africa and on the Arabian Peninsula. The virus causes abortions and high mortality especially in young animals, whereas the symptoms in humans range from mild flu-like illness to severe hemorrhagic manifestations that can be lethal. So far, no antiviral therapeutics for animals nor humans were available yet. Therefore, we evaluated two monoclonal antibodies—one neutralizing and one non-neutralizing—in a mouse model for therapeutic treatment against Rift Valley fever. We selected these antibodies since they exhibited cooperative effects in vitro. During Rift Valley fever virus infection in mice, the applied neutralizing antibody alone showed only partial protection. In contrast, a combined application with both antibodies, lead to a complete protection in one treatment group (100% survival). A detailed pathological and molecular analysis clearly indicated a strong reduction of virus replication in target tissues of treated mice. Taken together, these results identified two monoclonal antibodies with strong antiviral effects against Rift Valley fever infection, which are promising candidates for therapeutic interventions against RVFV. [ABSTRACT FROM AUTHOR]

Ebola virus (EBOV) causes severe outbreaks of viral hemorrhagic fever in humans. While virus-host interactions are promising targets for antivirals, there is only limited knowledge regarding the interactions of EBOV with cellular host factors. Recently, we performed a genome-wide siRNA screen that identified the nuclear RNA export factor 1 (NXF1) as an important host factor for the EBOV life cycle. NXF1 is a major component of the nuclear mRNA export pathway that is usurped by many viruses whose life cycles include nuclear stages. However, the role of NXF1 in the life cycle of EBOV, a virus replicating in cytoplasmic inclusion bodies, remains unknown. In order to better understand the role of NXF1 in the EBOV life cycle, we performed a combination of co-immunoprecipitation and double immunofluorescence assays to characterize the interactions of NXF1 with viral proteins and RNAs. Additionally, using siRNA-mediated knockdown of NXF1 together with functional assays, we analyzed the role of NXF1 in individual aspects of the virus life cycle. With this approach we identified the EBOV nucleoprotein (NP) as a viral interaction partner of NXF1. Further studies revealed that NP interacts with the RNA-binding domain of NXF1 and competes with RNA for this interaction. Co-localization studies showed that RNA binding-deficient, but not wildtype NXF1, accumulates in NP-derived inclusion bodies, and knockdown experiments demonstrated that NXF1 is necessary for viral protein expression, but not for viral RNA synthesis. Finally, our results showed that NXF1 interacts with viral mRNAs, but not with viral genomic RNAs. Based on these results we suggest a model whereby NXF1 is recruited into inclusion bodies to promote the export of viral mRNA:NXF1 complexes from these sites. This would represent a novel function for NXF1 in the life cycle of cytoplasmically replicating viruses, and may provide a basis for new therapeutic approaches against EBOV, and possibly other emerging viruses. [ABSTRACT FROM AUTHOR]

Hendra virus (HeV) and Nipah virus (NiV) belong to the genus Henipavirus in the family Paramyxoviridae. Henipavirus infections were first reported in the 1990’s causing severe and often fatal outbreaks in domestic animals and humans in Southeast Asia and Australia. NiV infections were observed in humans in Bangladesh, India and in the first outbreak in Malaysia, where pigs were also infected. HeV infections occurred in horses in the North-Eastern regions of Australia, with singular transmission events to humans. Bats of the genus Pteropus have been identified as the reservoir hosts for henipaviruses. Molecular and serological indications for the presence of henipa-like viruses in African fruit bats, pigs and humans have been published recently. In our study, truncated forms of HeV and NiV attachment (G) proteins as well as the full-length NiV nucleocapsid (N) protein were expressed using different expression systems. Based on these recombinant proteins, Enzyme-linked Immunosorbent Assays (ELISA) were developed for the detection of HeV or NiV specific antibodies in porcine serum samples. We used the NiV N ELISA for initial serum screening considering the general reactivity against henipaviruses. The G protein based ELISAs enabled the differentiation between HeV and NiV infections, since as expected, the sera displayed higher reactivity with the respective homologous antigens. In the future, these assays will present valuable tools for serosurveillance of swine and possibly other livestock or wildlife species in affected areas. Such studies will help assessing the potential risk for human and animal health worldwide by elucidating the distribution of henipaviruses. [ABSTRACT FROM AUTHOR]

An optimization of the undulator layout of X-ray free-electron-laser (FEL) facilities based on placing small chicanes between the undulator modules is presented. The installation of magnetic chicanes offers the following benefits with respect to state-of-the-art FEL facilities: reduction of the required undulator length to achieve FEL saturation, improvement of the longitudinal coherence of the FEL pulses, and the ability to produce shorter FEL pulses with higher power levels. Numerical simulations performed for the soft X-ray beamline of the SwissFEL facility show that optimizing the advantages of the layout requires shorter undulator modules than the standard ones. This proposal allows a very compact undulator beamline that produces fully coherent FEL pulses and it makes possible new kinds of experiments that require very short and high-power FEL pulses. [ABSTRACT FROM AUTHOR]