Conversion of monoclonal IgG to dimeric and secretory IgA restores neutralizing ability and prevents infection of Omicron lineages

The emergence of Omicron lineages and descendent subvariants continues to present a severe threat to the effectiveness of vaccines and therapeutic antibodies. We have previously suggested that an insufficient mucosal immunoglobulin A (IgA) response induced by the mRNA vaccines is associated with a surge in breakthrough infections. Here, we further show that the intramuscular mRNA and/or inactivated vaccines cannot sufficiently boost the mucosal secretory IgA response in uninfected individuals, particularly against the Omicron variant. We thus engineered and characterized recombinant monomeric, dimeric, and secretory IgA1 antibodies derived from four neutralizing IgG monoclonal antibodies (mAbs 01A05, rmAb23, DXP-604, and XG014) targeting the receptor-binding domain of the spike protein. Compared to their parental IgG antibodies, dimeric and secretory IgA1 antibodies showed a higher neutralizing activity against different variants of concern (VOCs), in part due to an increased avidity. Importantly, the dimeric or secretory IgA1 form of the DXP-604 antibody significantly outperformed its parental IgG antibody, and neutralized the Omicron lineages BA.1, BA.2, and BA.4/5 with a 25- to 75-fold increase in potency. In human angiotensin converting enzyme 2 (ACE2) transgenic mice, a single intranasal dose of the dimeric IgA DXP-604 conferred prophylactic and therapeutic protection against Omicron BA.5. Thus, dimeric or secretory IgA delivered by nasal administration may potentially be exploited for the treatment and prevention of Omicron infection, thereby providing an alternative tool for combating immune evasion by the current circulating subvariants and, potentially, future VOCs.

Analytical Ultracentrifugation Detects Quaternary Rearrangements and Antibody-Induced Conformational Selection of the SARS-CoV-2 Spike Trimer

Analytical ultracentrifugation (AUC) analysis shows that the SARS-CoV-2 trimeric Spike (S) protein adopts different quaternary conformations in solution. The relative abundance of the "open" and "close" conformations is temperature-dependent, and samples with different storage temperature history have different open/close distributions. Neutralizing antibodies (NAbs) targeting the S receptor binding domain (RBD) do not alter the conformer populations; by contrast, a NAb targeting a cryptic conformational epitope skews the Spike trimer toward an open conformation. The results highlight AUC, which is typically applied for molecular mass determination of biomolecules as a powerful tool for detecting functionally relevant quaternary protein conformations.

Adapting Neutralizing Antibodies to Viral Variants by Structure-Guided Affinity Maturation Using Phage Display Technology

Neutralizing monoclonal antibodies have achieved great efficacy and safety for the treatment of numerous infectious diseases. However, their neutralization potency is often rapidly lost when the target antigen mutates. Instead of isolating new antibodies each time a pathogen variant arises, it can be attractive to adapt existing antibodies, making them active against the new variant. Potential benefits of this approach include reduced development time, cost, and regulatory burden. Here a methodology is described to rapidly evolve neutralizing antibodies of proven activity, improving their function against new pathogen variants without losing efficacy against previous ones. The reported procedure is based on structure-guided affinity maturation using combinatorial mutagenesis and phage display technology. Its use against the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is demonstrated, but it is suitable for any other pathogen. As proof of concept, the method is applied to CoV-X2, a human bispecific antibody that binds with high affinity to the early SARS-CoV-2 variants but lost neutralization potency against Delta. Antibodies emerging from the affinity maturation selection exhibit significantly improved neutralization potency against Delta and no loss of efficacy against the other viral sequences tested. These results illustrate the potential application of structure-guided affinity maturation in facilitating the rapid adaptation of neutralizing antibodies to pathogen variants.

19n01, a broadly neutralizing antibody against Omicron BA.1, BA.2, BA.4/5, and other SARS-CoV-2 variants of concern

This study reports the isolation and characterization of a human monoclonal antibody (mAb) called 19n01. This mAb was isolated by using single-cell RNAseq of B cells from donors infected with the ancestral strain. This mAb possesses a potent and broad capacity to bind and neutralize all previously circulating variants of concern (VOCs), including Omicron sublineages BA.1, BA.2, and BA.4/5. The pseudovirus neutralization assay revealed robust neutralization capacity against the G614 strain, BA.1, BA.2, and BA.4/5, with inhibitory concentration (IC50) values ranging from 0.0035 to 0.0164 μg/mL. The microneutralization assay using the G614 strain and VOCs demonstrated IC50 values of 0.013-0.267 μg/mL. Biophysical and structural analysis showed that 19n01 cross-competes with ACE2 binding to the receptor-binding domain (RBD) and the kinetic parameters confirmed the high affinity against the Omicron sublineages (K_D of 61 and 30 nM for BA.2 and BA.4/5, respectively). These results suggest that the 19n01 is a remarkably potent and broadly reactive mAb.

Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein

Emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike glycoprotein that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera, including the nine human coronaviruses, through recognition of a conserved motif that includes the S2' site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization, and, similar to fp.006 and hr2.016, protects mice expressing human angiotensin-converting enzyme 2 against infection when present as a bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae, including SARS-CoV-2 variants.

Temperature dependent local inhomogeneity and magnetic moments of (Li1-xFex)OHFeSe superconductors

We have combined the extended X-ray absorption fine structure (EXAFS) and X-ray emission spectroscopy (XES) to investigate the local structure and the local iron magnetic moments of (Li_1-xFe_x)OHFeSe (x∼0.2) superconductors. The local structure, studied by Fe K-edge EXAFS measurements, is found to be inhomogeneous that is characterized by different Fe-Se bond lengths. The inhomogeneous phase exhibits a peculiar temperature dependence with lattice anomalies in the local structural parameters at the critical temperature T_c (36 K) and at the spin density wave (SDW) transition temperature T_N (130 K). Fe Kβ XES shows iron to be in a low spin state with the local Fe magnetic moment evolving anomalously as a function of temperature. Apart from a quantitative measurement of the local structure of (Li_1-xFe_x)OHFeSe, providing direct evidence of nanoscale inhomogeneity, the results provide further evidence of the vital role that the coupled electronic, lattice and magnetic degrees of freedom play in the iron-based superconductors.

The CLEAR X-ray emission spectrometer available at the CLAESS beamline of ALBA synchrotron

The CLEAR X-ray emission spectrometer installed at the CLAESS beamline of the ALBA synchrotron is described. It is an energy-dispersive spectrometer based on Rowland circle geometry with 1 m-diameter circle. The energy dispersion is achieved by the combination of a diced analyzer crystal and a unidimensional detector. A single unconventional dynamically bent analyzer crystal (Si 111) permits a wide energy range to be covered, just by exploiting its different reflections (333, 444, 555, 777, 888): 6-22 keV, with a spectrometer efficiency that decreases above 11 keV because of the Si detector thickness (Mythen, 350 µm), while the relative scattering intensities for the Si 333, 444, 555, 777 and 888 reflections correspond to 36, 40, 21, 13 and 15, respectively. The provided energy resolution is typically below 1-2 eV and depends on the beam size, working Bragg angle and reflection exploited. In most cases the energy dispersion ranges from 10 to 20 eV and can be enlarged by working in the out-of-Rowland geometry up to 40 eV. The spectrometer works in full backscattering geometry with the beam passing through the two halves of the analyzer. The vacuum beam path and the particular geometry allow a typical average noise of only 0.5 counts per second per pixel. The spectrometer is mainly used for measuring emission lines and high-resolution absorption spectra, with a typical scanning time for highly concentrated systems of around half an hour, including several repeats. The intrinsic energy dispersion allows systematic collection of resonant X-ray emission maps by measuring high-resolution absorption spectra. Moreover, it allows spectra to be measured on a single-shot basis. Resonant inelastic X-ray scattering experiments to probe electronic excitations are feasible, although the spectrometer is not optimized for this purpose due to the limited energy resolution and scattering geometry provided. In that case, to minimize the quasi-elastic line, the spectrometer is able to rotate along the beam path. Advantages and disadvantages with respect to other existing spectrometers are highlighted.

Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2

Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera , including the nine human coronaviruses, through recognition of a conserved motif that includes the S2' site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization and, like fp.006 and hr2.016, protects mice when present as bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae , including SARS-CoV-2 variants.

One sentence summary

Broadly cross-reactive antibodies that protect from SARS-CoV-2 variants are revealed by virus coldspot-driven discovery.

Humoral and cell-mediated response against SARS-CoV-2 variants elicited by mRNA vaccine BNT162b2 in healthcare workers: a longitudinal observational study

OBJECTIVES

To assess the humoral and cell-mediated response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) elicited by the mRNA BNT162b2 vaccine in SARS-CoV-2-experienced and -naive subjects against a reference strain and SARS-CoV-2 variants.

METHODS

The humoral response (including neutralizing antibodies) and T-cell-mediated response elicited by BNT162b2 vaccine in 145 healthcare workers (both naive and positive for previous SARS-CoV-2 infection) were evaluated. In a subset of subjects, the effect of SARS-CoV-2 variants on antibody level and cell-mediated response was also investigated.

RESULTS

Overall, 125/127 naive subjects (98.4%) developed both neutralizing antibodies and specific T cells after the second dose of vaccine. Moreover, the antibody and T-cell responses were effective against viral variants since SARS-CoV-2 NT Abs were still detectable in 55/68 (80.9%) and 25/29 (86.2%) naive subjects when sera were challenged against β and δ variants, respectively. T-cell response was less affected, with no significant difference in the frequency of responders (p 0.369). Of note, two doses of vaccine were able to elicit sustained neutralizing antibody activity against all the SARS-CoV-2 variants tested in SARS-CoV-2-experienced subjects.

CONCLUSIONS

BNT162b2 vaccine elicited a sustained humoral and cell-mediated response in immunocompetent subjects after two-dose administration of the vaccine, and the response seemed to be less affected by SARS-CoV-2 variants, the only exceptions being the β and δ variants. Increased immunogenicity, also against SARS-CoV-2 variant strains, was observed in SARS-CoV-2-experienced subjects. These results suggest that triple exposure to SARS-CoV-2 antigens might be proposed as valuable strategy for vaccination campaigns.

Systematic Development of Peptide Inhibitors Targeting the CXCL12/HMGB1 Interaction

During inflammatory reactions, the production and release of chemotactic factors guide the recruitment of selective leukocyte subpopulations. The alarmin HMGB1 and the chemokine CXCL12, both released in the microenvironment, can form a heterocomplex, which exclusively acts on the chemokine receptor CXCR4, enhancing cell migration, and in some pathological conditions such as rheumatoid arthritis exacerbates the immune response. An excessive cell influx at the inflammatory site can be diminished by disrupting the heterocomplex. Here, we report the computationally driven identification of the first peptide (HBP08) binding HMGB1 and selectively inhibiting the activity of the CXCL12/HMGB1 heterocomplex. Furthermore, HBP08 binds HMGB1 with the highest affinity reported so far (K_d of 0.8 ± 0.4 μM). The identification of this peptide represents an important step toward the development of innovative pharmacological tools for the treatment of severe chronic inflammatory conditions characterized by an uncontrolled immune response.

Rational engineering of the lccβ T. versicolor laccase for the mediator-less oxidation of large polycyclic aromatic hydrocarbons

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Computational-assisted protein engineering of the binding pocket of laccases.

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Mutants have activity increased up to ~ 300% in a broader pH range compared to the WT.

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Enhanced activity towards bulky PAHs in comparison to the WT enzyme.

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Ability to oxidize harmful PAH model compounds (dyes) that the WT enzyme cannot modify.

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Higher oxidation levels without mediators compared to the WT laccase with mediators.

Laccases are among the most sought-after biocatalyst for many green applications, from biosensors to pollution remedial, because they simply need oxygen from the air to oxidize and degrade a broad range of substrates. However, natural laccases cannot process large and toxic polycyclic aromatic hydrocarbons (PAHs) except in the presence of small molecules, called mediators, which facilitate the reaction but are inconvenient for practical on-field applications. Here we exploited structure-based protein engineering to generate rationally modified fungal laccases with increased ability to process bulky PAHs even in a mediator-less reaction. Computational simulations were used to estimate the impact of mutations in the enzymatic binding pocket on the ability to bind and oxidize a selected set of organic compounds. The most promising mutants were produced and their activity was evaluated by biochemical assays with phenolic and non-phenolic substrates. Mutant laccases engineered with a larger binding pocket showed enhanced activity (up to ~ 300% at pH 3.0) in a wider range of pH values (3.0–8.0) in comparison to the wild type enzyme. In contrast to the natural laccase, these mutants efficiently degraded bulky and harmful triphenylmethane dyes such as Ethyl Green (up to 91.64% after 24 h), even in the absence of mediators, with positive implications for the use of such modified laccases in many green chemistry processes (e.g. wastewater treatment).

SARS-CoV-2 neutralizing human recombinant antibodies selected from pre-pandemic healthy donors binding at RBD-ACE2 interface

COVID-19 is a severe acute respiratory disease caused by SARS-CoV-2, a new recently emerged sarbecovirus. This virus uses the human ACE2 enzyme as receptor for cell entry, recognizing it with the receptor binding domain (RBD) of the S1 subunit of the viral spike protein. We present the use of phage display to select anti-SARS-CoV-2 spike antibodies from the human naïve antibody gene libraries HAL9/10 and subsequent identification of 309 unique fully human antibodies against S1. 17 antibodies are binding to the RBD, showing inhibition of spike binding to cells expressing ACE2 as scFv-Fc and neutralize active SARS-CoV-2 virus infection of VeroE6 cells. The antibody STE73-2E9 is showing neutralization of active SARS-CoV-2 as IgG and is binding to the ACE2-RBD interface. Thus, universal libraries from healthy human donors offer the advantage that antibodies can be generated quickly and independent from the availability of material from recovering patients in a pandemic situation.

Bispecific antibody neutralizes circulating SARS-CoV-2 variants, prevents escape and protects mice from disease

Neutralizing antibodies targeting the receptor binding domain (RBD) of the SARS-CoV-2 Spike (S) are among the most promising approaches against coronavirus disease 2019 (COVID-19) ^1,2 . We developed a bispecific, IgG1-like molecule (CoV-X2) based on two antibodies derived from COVID-19 convalescent donors, C121 and C135 ³ . CoV-X2 simultaneously binds two independent sites on the RBD and, unlike its parental antibodies, prevents detectable S binding to Angiotensin-Converting Enzyme 2 (ACE2), the virus cellular receptor. Furthermore, CoV-X2 neutralizes SARS-CoV-2 and its variants of concern, as well as the escape mutants generated by the parental monoclonals. In a novel animal model of SARS-CoV-2 infection with lung inflammation, CoV-X2 protects mice from disease and suppresses viral escape. Thus, simultaneous targeting of non-overlapping RBD epitopes by IgG-like bispecific antibodies is feasible and effective, combining into a single molecule the advantages of antibody cocktails.

Mn substitution effect on the local structure of La(Fe1-x Mn x )AsO studied by temperature dependent x-ray absorption measurements

The local structure of La(Fe1-x Mn x )AsO has been investigated using temperature dependent Fe K-edge extended x-ray absorption fine structure (EXAFS) measurements. The EXAFS data reveal distinct behavior of Fe-As and Fe-Fe atomic displacements with a clear boundary between x ⩽ 0.02 and x > 0.02. The Fe-As bondlength shows a gradual thermal expansion while the Fe-Fe bond manifests a temperature dependent anomaly at ∼180 K for x > 0.02. It is interesting to find characteristically different nature of Fe-As and Fe-Fe bondlengths shown by the temperature dependent mean square relative displacements. Indeed, the Fe-As bond, stiffer than that of the Fe-Fe, gets softer for x ⩽ 0.02 and hardly shows any change for x > 0.02. On the other hand, Fe-Fe bond tends to be stiffer for x ⩽ 0.02 followed by a substantial softening for x > 0.02. Such a distinction has been seen also in the As K-edge x-ray absorption near edge structure, probing local geometry around As atom together with the valence electronic structure. The results suggest that local atomic displacements by Mn substitution inducing increased iron local magnetic moment that should be the main reason for its dramatic effect in iron-based superconductors.

Magnetosomes could be protective shields against metal stress in magnetotactic bacteria

Magnetotactic bacteria are aquatic microorganisms with the ability to biomineralise membrane-enclosed magnetic nanoparticles, called magnetosomes. These magnetosomes are arranged into a chain that behaves as a magnetic compass, allowing the bacteria to align in and navigate along the Earth’s magnetic field lines. According to the magneto-aerotactic hypothesis, the purpose of producing magnetosomes is to provide the bacteria with a more efficient movement within the stratified water column, in search of the optimal positions that satisfy their nutritional requirements. However, magnetosomes could have other physiological roles, as proposed in this work. Here we analyse the role of magnetosomes in the tolerance of Magnetospirillum gryphiswaldense MSR-1 to transition metals (Co, Mn, Ni, Zn, Cu). By exposing bacterial populations with and without magnetosomes to increasing concentrations of metals in the growth medium, we observe that the tolerance is significantly higher when bacteria have magnetosomes. The resistance mechanisms triggered in magnetosome-bearing bacteria under metal stress have been investigated by means of x-ray absorption near edge spectroscopy (XANES). XANES experiments were performed both on magnetosomes isolated from the bacteria and on the whole bacteria, aimed to assess whether bacteria use magnetosomes as metal storages, or whether they incorporate the excess metal in other cell compartments. Our findings reveal that the tolerance mechanisms are metal-specific: Mn, Zn and Cu are incorporated in both the magnetosomes and other cell compartments; Co is only incorporated in the magnetosomes, and Ni is incorporated in other cell compartments. In the case of Co, Zn and Mn, the metal is integrated in the magnetosome magnetite mineral core.

Temperature dependent local atomic displacements in NaSn2As2 system

NaSn₂As₂ is mechanically exfoliable layered van der Waals (vdW) Zintl phase that is getting interesting due to its low thermal conductivity and recently observed superconductivity. Here, we have investigated the temperature dependent local structure of NaSn₂As₂ by a combined analysis of As K-edge and Sn K-edge extended x-ray absorption fine structure measurements. The system is intrinsically disordered with the interatomic distances largely consistent to those estimated by average structure measurements. The stretching force constants of different bond distances have been determined using temperature dependent mean square relative displacements. The Sn-As distance is the strongest bond in this system, having covalent nature, unlike the weaker interlayer distances which are characterized by vdW type bonding. Among them, As-Na distance is slightly weaker than Sn-Sn(i) below  ∼200 K and tends to get stronger above this temperature. The anomalous behavior of As-Na bond suggests that the mechanical exfoliation in this system is likely to be temperature dependent. The anomaly in the interlayer atomic correlations may be due to a charge density wave-like instability around this temperature, indicated by earlier experiments. The local structure and disorder are discussed in relation to the physical properties of NaSn₂As₂.

A high-energy-resolution resonant inelastic X-ray scattering spectrometer at ID20 of the European Synchrotron Radiation Facility

An end-station for resonant inelastic X-ray scattering and (resonant) X-ray emission spectroscopy at beamline ID20 of ESRF - The European Synchrotron is presented. The spectrometer hosts five crystal analysers in Rowland geometry for large solid angle collection and is mounted on a rotatable arm for scattering in both the horizontal and vertical planes. The spectrometer is optimized for high-energy-resolution applications, including partial fluorescence yield or high-energy-resolution fluorescence detected X-ray absorption spectroscopy and the study of elementary electronic excitations in solids. In addition, it can be used for non-resonant inelastic X-ray scattering measurements of valence electron excitations.

Mapping Antibody Epitopes by Solution NMR Spectroscopy: Practical Considerations

Identifying an epitope, the region of the antigen in contact with an antibody, is useful in both basic and pharmaceutical research, as well as in vaccine design. Solution NMR spectroscopy is particularly well suited to the residue level characterization of intermolecular interfaces, including antibody-antigen interactions, and thus to epitope identification. Here, we describe the use of NMR for residue level characterization of protein epitopes, focusing on experimental protocols and practical considerations, highlighting advantages and drawbacks of the approach.

A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential

Zika virus (ZIKV), a mosquito-borne flavivirus, causes devastating congenital birth defects. We isolated a human monoclonal antibody (mAb), ZKA190, that potently cross-neutralizes multi-lineage ZIKV strains. ZKA190 is highly effective in vivo in preventing morbidity and mortality of ZIKV-infected mice. NMR and cryo-electron microscopy show its binding to an exposed epitope on DIII of the E protein. ZKA190 Fab binds all 180 E protein copies, altering the virus quaternary arrangement and surface curvature. However, ZIKV escape mutants emerged in vitro and in vivo in the presence of ZKA190, as well as of other neutralizing mAbs. To counter this problem, we developed a bispecific antibody (FIT-1) comprising ZKA190 and a second mAb specific for DII of E protein. In addition to retaining high in vitro and in vivo potencies, FIT-1 robustly prevented viral escape, warranting its development as a ZIKV immunotherapy.

Balance of Anti-CD123 Chimeric Antigen Receptor Binding Affinity and Density for the Targeting of Acute Myeloid Leukemia

Chimeric antigen receptor (CAR)-redirected T lymphocytes are a promising immunotherapeutic approach and object of pre-clinical evaluation for the treatment of acute myeloid leukemia (AML). We developed a CAR against CD123, overexpressed on AML blasts and leukemic stem cells. However, potential recognition of low CD123-positive healthy tissues, through the on-target, off-tumor effect, limits safe clinical employment of CAR-redirected T cells. Therefore, we evaluated the effect of context-dependent variables capable of modulating CAR T cell functional profiles, such as CAR binding affinity, CAR expression, and target antigen density. Computational structural biology tools allowed for the design of rational mutations in the anti-CD123 CAR antigen binding domain that altered CAR expression and CAR binding affinity without affecting the overall CAR design. We defined both lytic and activation antigen thresholds, with early cytotoxic activity unaffected by either CAR expression or CAR affinity tuning but later effector functions impaired by low CAR expression. Moreover, the anti-CD123 CAR safety profile was confirmed by lowering CAR binding affinity, corroborating CD123 is a good therapeutic target antigen. Overall, full dissection of these variables offers suitable anti-CD123 CAR design optimization for the treatment of AML.

High resolution x-ray absorption and emission spectroscopy of Li x CoO2 single crystals as a function delithiation

The effect of delithiation in Li _x CoO₂ is studied by high resolution Co K-edge x-ray absorption and x-ray emission spectroscopy. Polarization dependence of the x-ray absorption spectra on single crystal samples is exploited to reveal information on the anisotropic electronic structure. We find that the electronic structure of Li _x CoO₂ is significantly affected by delithiation in which the Co ions oxidation state tending to change from 3+  to 4+. The Co intersite (intrasite) 4p-3d hybridization suffers a decrease (increase) by delithiation. The unoccupied 3d t _2g orbitals with a _1g symmetry, containing substantial O 2p character, hybridize isotropically with Co 4p orbitals and likely to have itinerant character unlike anisotropically hybridized 3d e _g orbitals. Such a peculiar electronic structure could have significant effect on the mobility of Li in Li _x CoO₂ cathode and hence the battery characteristics.

A large-solid-angle X-ray Raman scattering spectrometer at ID20 of the European Synchrotron Radiation Facility

An end-station for X-ray Raman scattering spectroscopy at beamline ID20 of the European Synchrotron Radiation Facility is described. This end-station is dedicated to the study of shallow core electronic excitations using non-resonant inelastic X-ray scattering. The spectrometer has 72 spherically bent analyzer crystals arranged in six modular groups of 12 analyzer crystals each for a combined maximum flexibility and large solid angle of detection. Each of the six analyzer modules houses one pixelated area detector allowing for X-ray Raman scattering based imaging and efficient separation of the desired signal from the sample and spurious scattering from the often used complicated sample environments. This new end-station provides an unprecedented instrument for X-ray Raman scattering, which is a spectroscopic tool of great interest for the study of low-energy X-ray absorption spectra in materials under in situ conditions, such as in operando batteries and fuel cells, in situ catalytic reactions, and extreme pressure and temperature conditions.

Temperature dependent EXAFS study on transition metal dichalcogenides MoX2 (X = S, Se, Te)

The local structure of molybdenum dichalcogenide MoX2 (X  =  S, Se, Te) single crystal has been studied by means of multi-edge (Mo, Se, and Te K-edges) extended x-ray absorption fine-structure spectroscopy as function of temperature. The temperature dependences of the interatomic distances Mo-X, Mo-Mo and X-X (X  =  S, Se, and Te) and of the corresponding Debye-Waller factors have been extracted over the 70-500 K temperature range. Exploiting the correlated Einstein model, we found that the Einstein frequencies of Mo-X and X-X bonds obtained by present data are in close agreement with the frequencies of the optical (Raman and infrared) stretching modes for both MoS2 and MoSe2, whereas a significant deviation has been found for MoTe2. A similar anomaly has been found for the force constants related to the Mo-X bonds in the MoTe2 case. Our findings, accordingly with the results reported in a recent theoretical paper, support the idea that the optical vibrational modes have a dominant role in MoS2 and MoSe2, whereas the effects of acoustic vibrational modes cannot be neglected in the case of MoTe2.

Specificity, cross-reactivity, and function of antibodies elicited by Zika virus infection

Zika virus (ZIKV), a mosquito-borne flavivirus with homology to Dengue virus (DENV), has become a public health emergency. By characterizing memory lymphocytes from ZIKV-infected patients, we dissected ZIKV-specific and DENV-cross-reactive immune responses. Antibodies to nonstructural protein 1 (NS1) were largely ZIKV-specific and were used to develop a serological diagnostic tool. In contrast, antibodies against E protein domain I/II (EDI/II) were cross-reactive and, although poorly neutralizing, potently enhanced ZIKV and DENV infection in vitro and lethally enhanced DENV disease in mice. Memory T cells against NS1 or E proteins were poorly cross-reactive, even in donors preexposed to DENV. The most potent neutralizing antibodies were ZIKV-specific and targeted EDIII or quaternary epitopes on infectious virus. An EDIII-specific antibody protected mice from lethal ZIKV infection, illustrating the potential for antibody-based therapy.

A study of temperature dependent local atomic displacements in a Ba(Fe(1-x)Co(x))2As2 superconductor

We have studied the local structure of a Ba(Fe(1-x)Co(x))2As2 superconductor using temperature dependent extended X-ray absorption fine structure (EXAFS) measurements. Polarized EXAFS at the Fe K-edge on an optimally doped (x = 0.06) single crystal has permitted us to determine atomic displacements across the superconducting transition temperature (T(c)). The Fe-As bondlength hardly shows any change with temperature; however, the Fe-Fe sublattice reveals a sharp anomaly across T(c), indicated by a significant drop in mean square relative displacements, similar to the one known for cuprates and A15-type superconductors. We have also found a large atomic disorder around the substituted Co, revealed by polarized Co K-edge EXAFS measurements. The Co-Fe/Co bonds are more flexible than the Fe-Fe bonds with the As-height in Co-containing tetrahedra being larger than the one in FeAs4. The results suggest that the local Fe-Fe bondlength fluctuations and the atomic disorder in this sub-lattice should have some important role in the superconductivity of Ba(Fe(1-x)Co(x))2As2 pnictides.

Temperature dependent nanoscale atomic correlations in Ir1-xPtxTe2 (x = 0.0, 0.03 and 0.04) system

X-ray absorption near-edge structure (XANES) spectroscopy has been used to investigate the unoccupied electronic states and local geometry of Ir1-xPtxTe2(x = 0.0, 0.03 and 0.04) as a function of temperature. The Ir L3-edge absorption white line, as well as high energy XANES features due to the photoelectron multiple scatterings with near neighbours, reveal clear changes in the unoccupied 5d-electronic states and the local geometry with Pt substitution. We find an anomalous spectral weight transfer across the known first-order structural phase transition from the trigonal to monoclinic phase in IrTe2, which characterizes the reduced atomic structure symmetry below the transition temperature. No such changes with temperature are seen in the Pt substituted superconducting samples. In addition, a gradual increase of the spectral weight transfer is observed in IrTe2 with a further decrease in temperature below the transition, indicating that the low temperature phase is likely to have a symmetry lower than the monoclinic one. The results suggest that the interplay between inter-layer and intra-layer atomic correlations should have a significant role in the properties of an Ir1-xPtxTe2 system.

Is HE4 serum level a valid screening test in women candidates for kidney transplant? A case report and a review of literature

While studying a candidate for kidney transplant it is essential to exclude active malignant diseases. Serum biomarkers help to exclude specific cancers. Tumor markers are proteins secreted by neoplastic cells that can mark their activities. HE4 is a new tumor marker used in ovarian cancer. It is an epithelium protein that appears overexpressed in ovarian cancer, but it is also present in other normal human tissues. Often in patients with kidney failure serum biomarkers are increased compared to healthy people. We report a case of a Caucasian woman suffering from kidney failure examined by our team to be included on the kidney transplantation list. Patient had a known pelvic mass. Determination of serum biomarkers, CA125 and HE4, was performed to exclude pelvic tumor, and we found high levels of HE4 with normal levels of CA125. A new transvaginal ultrasound was performed on the patient and it showed a pelvic mass near the left ovary. This mass resulted bigger than in the previous ultrasound, performed about a month before. We decided to perform a pelvic CT for improved diagnostic accuracy. The reports of this exam showed that the mass was a hematoma correlated with a previous knee prosthetic surgery. Even tough many serum biomarkers are higher in patients with renal failure, there is no study to demonstrate that HE4 blood levels are modified in these patients. This case report shows how HE4 can be elevated in people in hemodialysis in a benign situation, also in a pelvic mass not from the genital tract. There is no similar case described in literature.

Temperature dependence of crystal field excitations in CuO

We report a study on the temperature dependence of charge-neutral crystal field (dd) excitations in cupric oxide, using nonresonant inelastic x-ray scattering spectroscopy. Thanks to a very high-energy resolution (ΔE = 60 meV), we observe thermal effects on the dd excitation spectrum fine structure between temperatures of 10-320 K. The spectra broaden considerably with increasing temperature, consistently with an enhancement of the coupling between crystal field excitations and the temperature-dependent continuum of states above the band gap. We discuss this and other mechanisms that may explain this temperature dependence.

Study of the electronic and magnetic properties as a function of isoelectronic substitution in SmFe(1-x)RuxAsO0.85F0.15

We have studied the electronic and magnetic properties of SmFe(1-x)RuxAsO0.85F0.15 (x = 0, 0.05, 0.25, 0.33, 0.5) by high-resolution x-ray absorption and x-ray emission spectroscopy. The local Fe magnetic moment (μ) tends to decrease for a small Ru substitution, but it shows a clear increase with further substitution. It appears that impurity scattering prevails in reducing the μ with small Ru substitution due to an extended Ru d-band. A nanoscale phase separation, that decouples the FeAs layers from the spacer layers, drives the increase of μ at higher Ru substitution. The results provide important information on nanoscale phase separation due to isoelectronic substitution in the active layers of iron-based 1111-superconductors and its effect on the local magnetic properties.

Abdominal emergency in elderly: a case of small bowel obstruction and ischemia caused by bulky IA ovarian cancer

Bowel obstruction resulting from colorectal and ovarian cancer is a serious and distressing complication of these malignancies. This may be caused by diffuse peritoneal carcinomatosis, bulky masses filling the pelvis and abdomen or postoperative adhesions, and should be carefully worked out by pre-operative imaging. We report the case of a small bowel obstruction and intestinal ischemia caused by a bulky (20x40 cm in diameter) cystic ovarian neoplasm that was found to be a stage IA G2 cystadenocarcinoma, successfully managed by uterus-sparing surgery.

Dispersive x-ray absorption studies at the Fe K-edge on the iron chalcogenide superconductor FeSe under pressure

The local structure and the electronic properties of FeSe under hydrostatic pressure were studied by means of dispersive x-ray absorption measurements at the Fe K-edge. The pressure dependence of the x-ray absorption near edge structure features seems to follow the behavior of the superconducting transition temperature Tc. The local structure, that has an important impact on the superconducting properties, appears to fall into two regimes: the pressure dependence of the Fe-Fe bond distance shows a clear change in the compressibility at p ∼ 5 GPa; in contrast, the Fe-Se bond distance decreases continuously with increasing pressure with a lower compressibility than the Fe-Fe bond. The results suggest that the pressure dependent changes in Tc of FeSe are closely related to the changes in local structure.

Rational engineering of a human anti-dengue antibody through experimentally validated computational docking

Antibodies play an increasing pivotal role in both basic research and the biopharmaceutical sector, therefore technology for characterizing and improving their properties through rational engineering is desirable. This is a difficult task thought to require high-resolution x-ray structures, which are not always available. We, instead, use a combination of solution NMR epitope mapping and computational docking to investigate the structure of a human antibody in complex with the four Dengue virus serotypes. Analysis of the resulting models allows us to design several antibody mutants altering its properties in a predictable manner, changing its binding selectivity and ultimately improving its ability to neutralize the virus by up to 40 fold. The successful rational design of antibody mutants is a testament to the accuracy achievable by combining experimental NMR epitope mapping with computational docking and to the possibility of applying it to study antibody/pathogen interactions.

Electronic properties of FeSe(1-x)Te(x) probed by x-ray emission and absorption spectroscopy

The electronic structure of FeSe(1-x)Te(x) chalcogenide superconductors has been studied by x-ray emission (XES) and x-ray absorption (XAS) as a function of Te substitution. The Fe Kβ XES spectra reveal a relatively low spin state for Fe in FeSe(1-x)Te(x) superconductors, persisting in the whole range of Te substitution. The Fe K-edge high-resolution XAS shows systematic spectral changes due to the evolving hybridization between the Fe 3d (4p) and chalcogen p (d) orbitals. The resonant inelastic x-ray scattering (RIXS) spectra hardly show any feature except the one due to charge transfer from occupied to unoccupied bands, that changes substantially from FeSe to FeTe. The results provide important information on the electronic states and their evolution in the FeSe(1-x)Te(x) chalcogenides.

Local structure of LiCoO2 nanoparticles studied by Co K-edge x-ray absorption spectroscopy

We have studied the local structure of LiCoO(2) nanoparticles by Co K-edge x-ray absorption spectroscopy as a function of particle size. Extended x-ray absorption fine structure data reveal substantial changes in the near neighbor distances and the associated mean square relative displacements with decreasing particle size. X-ray absorption near edge structure spectra show clear local geometrical changes with decreasing particle size, similar to those that appear in the charging (delithiation) process. The results suggest that the LiCoO(2) nanoparticles are characterized by a large atomic disorder confined to the Co-O octahedra, similar to the distortions generated during the delithiation, and this disorder should be the primary limiting factor for a reversible diffusion of Li ions when nanoparticles of LiCoO(2) are used as cathode material in rechargeable Li ion batteries.

Large local disorder in superconducting K(0.8)Fe(1.6)Se2 studied by extended x-ray absorption fine structure

We have measured the local structure of superconducting K(0.8)Fe(1.6)Se(2) chalcogenide (T(c) = 31.8 K) by temperature dependent polarized extended x-ray absorption fine structure (EXAFS) at the Fe and Se K-edges. We find that the system is characterized by a large local disorder. The Fe-Se and Fe-Fe distances are found to be shorter than the distances measured by diffraction, while the corresponding mean square relative displacements reveal large Fe-site disorder and relatively large c-axis disorder. The local force constant for the Fe-Se bondlength (k ~ 5.8 eV Å(-2)) is similar to the one found in the binary FeSe superconductor, however, the Fe-Fe bondlength appears to be flexible (k ~ 2.1 eV Å(-2)) in comparison to the binary FeSe (k ~ 3.5 eV Å(-2)), an indication of partly relaxed Fe-Fe networks in K(0.8)Fe(1.6)Se(2). The results suggest a glassy nature for the title system, with the superconductivity being similar to that in the granular materials.

Isolated pancreatic tuberculosis: a diagnostic challenge

Abdominal tuberculosis is quite commonly found in miliary tuberculosis, especially in countries where TB is endemic, however the abdominal localization of tuberculosis in absence of disseminated disease is a rare condition and the involvement of the pancreas alone is extremely rare. Epidemiology of TB is changing in the latest years, often this illness is found in non-endemic regions and physicians are asked to interpret what happen when an old disease meets new diagnostic technologies. We describe the case of a young male admitted in our hospital for abdominal pain. Echotomography, CT scan and MRI showed a pancreatic mass suspected to be cancer and susceptible to surgical treatment, Endoscopic Ultrasound guided fine needle aspiration (FNA) showed isolated pancreatic tuberculosis.

Random alloy-like local structure of Fe(Se, S)(1-x)Te(x) superconductors revealed by extended x-ray absorption fine structure

The local structure of Fe(Se, S)(1-x)Te(x) ternary (11-type) chalcogenides has been studied by temperature dependent Fe K-edge extended x-ray absorption fine structure measurements. We find that the Fe-Se and Fe-Te distances in ternary FeSe(1-x)Te(x) are closer to the respective distances in the binary systems, revealing significant divergence of the local structure from the average one. The mean square relative displacements show a systematic change with Te content, consistent with bond relaxation in the inhomogeneous ternary phases. Also, the Fe-Te and Fe-S distances in the FeS(0.2)Te(0.8) ternary system are found to be different in the crystallographically homogeneous structure. The observed features are characteristic of ternary random alloys, suggesting that a proper consideration should be given to the atomic distribution for describing the complex electronic structure of these multi-band Fe-based chalcogenides.

The human immune response to Dengue virus is dominated by highly cross-reactive antibodies endowed with neutralizing and enhancing activity

Antibodies protect against homologous Dengue virus (DENV) infection but can precipitate severe dengue by promoting heterotypic virus entry via Fcγ receptors (FcγR). We immortalized memory B cells from individuals after primary or secondary infection and analyzed anti-DENV monoclonal antibodies (mAbs) thus generated. MAbs to envelope (E) protein domain III (DIII) were either serotype specific or cross-reactive and potently neutralized DENV infection. DI/DII- or viral membrane protein prM-reactive mAbs neutralized poorly and showed broad cross-reactivity with the four DENV serotypes. All mAbs enhanced infection at subneutralizing concentrations. Three mAbs targeting distinct epitopes on the four DENV serotypes and engineered to prevent FcγR binding did not enhance infection and neutralized DENV in vitro and in vivo as postexposure therapy in a mouse model of lethal DENV infection. Our findings reveal an unexpected degree of cross-reactivity in human antibodies against DENV and illustrate the potential for an antibody-based therapy to control severe dengue.

A study of the electronic structure of FeSe(1-x)Te(x) chalcogenides by Fe and Se K-edge x-ray absorption near edge structure measurements

Fe K-edge and Se K-edge x-ray absorption near edge structure (XANES) measurements are used to study the FeSe(1 - x)Te(x) electronic structure of chalcogenides. An intense Fe K-edge pre-edge peak due to Fe 1s --> 3d (and admixed Se/Te p states) is observed, showing substantial change with Te substitution and x-ray polarization. The main white line peak in the Se K-edge XANES due to Se 1s --> 4p transition appears similar to the one expected for Se(2-) systems and changes with Te substitution. Polarization dependence reveals that unoccupied Se orbitals near the Fermi level have predominant p(x, y) character. The results provide key information on the hybridization of Fe 3d and chalcogen p states in the Fe-based chalcogenide superconductors.

Traumatic complex wounds, multidisciplinary approach: our experience in a case series

"Limb-salvage" is a social problem that is rapidly increasing, both in Italy and in the rest of world. Today, as in earlier times, the main causes of open wounds are traumas and such injuries are mainly of II and III stage of Gustilo's classification. Nowadays, the use of modern techniques determined a further dramatic reduction in the infection rates and, above all, in the risk of limb amputation. The most important techniques include: V.A.C. therapy (vacuum assisted closure); PRP gel (platelet-rich plasma gel); hyperbaric oxygen therapy. We treated 4 patients with high energy acute trauma through the combined and innovative use of advanced dressings. The authors report their experience and a brief review of the literature as contribution in regards to treatment of complex wounds of the limbs.

Altered cellular distribution and sub-cellular sorting of doppel (Dpl) protein in human astrocytoma cell lines

Doppel, a prion-like protein, is a GPI-membrane anchored protein generally not expressed in the Central Nervous System (CNS) of different mammalian species, including human. Nevertheless, in astrocytomas, a particular kind of glial tumors, the doppel encoding gene (PRND) is over-expressed and the corresponding protein product (Dpl) is ectopically localized in the cytoplasm of the tumor cells. In this study we have analysed the sub-cellular localization of Dpl using double-immunofluorescence staining and confocal microscopy examinations in two astrocytoma-derived human cell lines (IPDDC-A2 and D384-MG). Our results confirmed that Dpl is localized in the cytoplasm of the astrocytoma cells and indicated that it is mostly associated with Lamp-1 and Limp-2 positive lysosomal vesicles and, marginally, to the Golgi apparatus and other cellular organelles. Noticeably, none of the examined tumor cells showed a membrane-Dpl localization. The membrane-associated Dpl expression was restored after the transfection of the astrocytoma cells with mutated Dpl-expression vectors in its glycosylation sites. Additionally, Dpl showed altered expression and traffic using the acidotropic agent ammonium chloride, leading to the accumulation of Dpl in nascent exocytic vesicles. Altogether, these results indicated that in the astrocytic tumor cells Dpl has an altered biosynthetic trafficking, likely derived from abnormal post-translational processes: these modifications do not permit the localization of Dpl in correspondence of the plasma membrane and lead to its intracellular accumulation in the lysosomes. In these proteolytic compartments, the astrocytic tumor cells might provide to the degradation of the excess of a potentially cytotoxic Dpl product.

Primary psoas abscess in a patient affected by acquired immunodeficiency syndrome: a rare case according to the reviewed literature

Abscesses of the psoas muscle can be divided into primary and secondary. In the primary ones, it is not possible to identify any further infected site. The localization to this muscle is due to its rich vascularization and Staphylococcus aureus is the most frequent aetiological agent of the infection. Treatment requires the use of appropriate antibiotics, as well as surgical or percutaneous drainage of the abscess. The percutaneous drainage is much less invasive and a low risk in the patients with acquired immunodeficiency syndrome, and is effective for draining even multiloculated abscess. The authors present a rare case of primary psoas abscess in patient affected by acquired human immunodeficiency syndrome, showing a mass in the inferior lumbar region through the lumbar triangle of Petit and fever. Treatment consisting in percutaneous drainage combined with systemic antibiotic administration was successful.

ERCP in total situs viscerum inversus

A 69-year-old cholecystectomized female with known total situs viscerum inversus presented recurrent colicky pain in the left upper abdominal quadrant and jaundice. Laboratory parameters showed increased neutrophils and coniugated bilirubin of 5.53 mg/dl. US and MRCP confirmed total situs viscerum inversus and a dilatation of the intra- and extrahepatic ducts with a peripapillary 13 mm stone. ERCP, sphincterotomy and successful common bile duct stone extraction were performed in the conventional way. ERCP was carried out successfully despite situs inversus maintaining the patient in the prone position with the endoscopist on the right side of the table. Some authors have reported similar cases in whom ERCP was performed in other positions, while this report shows that an experienced endoscopist can achieve the same results in the conventional way as it is possible when anatomical changes, Billroth II or Roux-en-Y, or different positions of the patient, supine or on the left side, are present.

Gastrointestinal bleeding in emergency setting: two cases of intestinal angiodysplasia and unusual conservative surgical treatment

The authors report two cases of gastrointestinal bleeding in an emergency setting caused by angiodysplasia of colon and small bowel. They stress the rarity of the lesion and consider the difficulties involved in obtaining a preoperative diagnosis. The optimal management is uncertain and depends on the severity and rate of bleeding. A conservative medical approach is indicated for many patients, while surgery constitutes definitive treatment in case of massive hemorrhage or recurrent bleeding. In the cases reported the diagnosis was performed only via intra-operative enteroscopy. An unusual conservative surgical treatment was performed based on ligation of the vascular elements of the angiodysplasia. This method makes it possible to avoid an intestinal resection and yelds good results.