Deciphering factors linked with reduced SARS-CoV-2 susceptibility in the Swiss HIV Cohort Study

BACKGROUND Factors influencing susceptibility to SARS-CoV-2 remain to be resolved. Using data of the Swiss HIV Cohort Study (SHCS) on 6,270 people with HIV (PWH) and serologic assessment for SARS-CoV-2 and circulating-human-coronavirus (HCoV) antibodies, we investigated the association of HIV-related and general parameters with SARS-CoV-2 infection. METHODS We analyzed SARS-CoV-2 PCR-tests, COVID-19 related hospitalizations, and deaths reported to the SHCS between January 1, 2020 and December 31, 2021. Antibodies to SARS-CoV-2 and HCoVs were determined in pre-pandemic (2019) and pandemic (2020) bio-banked plasma and compared to HIV-negative individuals. We applied logistic regression, conditional logistic regression, and Bayesian multivariate regression to identify determinants of SARS-CoV-2 infection and Ab responses to SARS-CoV-2 in PWH. RESULTS No HIV-1-related factors were associated with SARS-CoV-2 acquisition. High pre-pandemic HCoV antibodies were associated with a lower risk of subsequent SARS-CoV-2 infection and with higher SARS-CoV-2 antibody responses upon infection. We observed a robust protective effect of smoking on SARS-CoV-2-infection risk (aOR= 0.46 [0.38,0.56], p=2.6*10-14), which occurred even in previous smokers, and was highest for heavy smokers. CONCLUSIONS Our findings of two independent protective factors, smoking and HCoV antibodies, both affecting the respiratory environment, underscore the importance of the local immune milieu in regulating susceptibility to SARS-CoV-2

Characterization of catalysts in an aberration-corrected scanning transmission electron microscope

Aberration-corrected scanning transmission electron microscopes (STEM) with a sub-angström resolution and outstanding analytical capabilities provide a superior means for the characterization of heterogeneous catalysts. Images can be recorded with bright field, annular dark field, and secondary electron detectors using various signals. This is demonstrated here for different model catalysts, including metal particles on ZrO and CeO. While it is often difficult to detect metal nanoparticles with a diameter of 1 nm or below supported on strongly scattering crystalline oxides by conventional transmission electron microscopy, the combinations of information obtained with different detectors in a STEM may facilitate their visualization. Of particular importance is the combination of the images with the spectroscopic investigation of selected points and areas. Efficiently collected electron energy loss and X-ray spectra are often essential to identify the nanoparticles unambiguously

Height and width of adsorbed dendronized polymers: electron and atomic force microscopy of homologous series

The width, w, and height, h, of dendronized polymers (DPs) adsorbed onto mica and highly oriented pyrolitic graphite (HOPG) were characterized by atomic force microscopy (AFM) and electron microscopy (EM). The study utilized a homologous series of generations g = 1-5, hence enabling coadsorption and characterization under identical conditions and thus facilitating comparison. The w and h values, as acquired by AFM and EM on HOPG and mica are comparable and can be collapsed onto a single master curve by a constant horizontal shift of each set of points. This master curve exhibits the scaling behavior of a cylinder and supports the visual impression that DPs adsorb as weakly deformed cylinders. The h and w curves suggest a dendron density of ρ ≃ 1.35 to 1.45 g/cm. Density measurements of solutions of the "attached-to monomer" suggest ρ ≃ 1.10 g/cm. The corresponding estimates of the maximal generation of structurally perfect DP for this family is g = 6 to 7 and close to the currently explored range of g = 1-5

Freezing Continuous-Flow Self-Assembly in a Microfluidic Device: Toward Imaging of Liposome Formation

A new method is described that combines a microfluidic device for the controlled formation of liposomes with instantaneous immobilization by means of ultrarapid cooling. The microfluidic device is composed of capillaries to hydrodynamically focus a stream of lipids dissolved in 2-propanol by two adjacent aqueous buffer streams before rapidly cooling by propane jet-freezing. The capillary containing the frozen sheath-flow is subsequently separated from the flow-focusing unit and trimmed with cryo-ultramicrotomy for imaging with cryo-scanning electron microscopy (SEM). The emergence of liposomes could be visualized by cryo-SEM without the need for chemical fixation or labeling. We demonstrate that the method is capable of revealing in more detail the formation of nonequilibrium liposomes. Partially and completely formed liposomes were observed at the miscible alcohol–buffer interface. The number density of lipid vesicles varied along the focused interface, and we frequently found clusters of liposomes. Additionally, evidence for the formation of disclike transient intermediates is presented. The method is not limited to studying self-assembly processes only. It can be extended to other biochemical reactions, crystallization processes, and even systematic interfacial mixing studies between different solvents

Robust workflow and instrumentation for cryo-focused ion beam milling of samples for electron cryotomography

Electron cryotomography is able to visualize macromolecular complexes in their cellular context, in a frozen-hydrated state, and in three dimensions. The method, however, is limited to relatively thin samples. Cryo-focused ion beam (FIB) milling is emerging as a powerful technique for sample thinning prior to cryotomography imaging. Previous cryo-FIB milling reports utilized custom-built non-standard equipment. Here we present a workflow and the required commercially available instrumentation to either implement the method de novo, or as an upgrade of pre-existing dual beam milling instruments. We introduce two alternative protocols and the respective sample holders for milling. The “bare grid holder” allows for milling on plain grids, having the advantage of enabling relatively shallow milling angles for wedge geometries. The “Autogrid holder” is designed for milling grids clamped into a mechanical support ring (Autogrid), resulting in increased stability for lamella geometries. We applied the workflow to prepare samples and record high-quality tomograms of diverse model organisms, including infected and uninfected HeLa cells, amoebae, yeast, multicellular cyanobacteria, Pseudomonas aeruginosa and Escherichia coli cells. The workflow will contribute to the dissemination of electron cryotomography of cryo-FIB milled samples in the biological sciences

Phase tomography from x-ray coherent diffractive imaging projections

Coherent diffractive imaging provides accurate phase projections that can be tomographically combined to yield detailed quantitative 3D reconstructions with a resolution that is not limited by imaging optics. We present robust algorithms for post-processing and alignment of these tomographic phase projections. A simple method to remove undesired constant and linear phase terms on the reconstructions is given. Also, we provide an algorithm for automatic alignment of projections that has good performance even for samples with no fiducial markers. Currently applied to phase projections, this alignment algorithm has proven to be robust and should also be useful for lens-based tomography techniques that pursue nanoscale 3D imaging. Lastly, we provide a method for tomographic reconstruction that works on phase projections that are known modulo 2π, such that the phase unwrapping step is avoided. We demonstrate the performance of these algorithms by 3D imaging of bacteria population in legume root-nodule cells

Deciphering factors linked with reduced SARS-CoV-2 susceptibility in the Swiss HIV Cohort Study.

BACKGROUND Factors influencing susceptibility to SARS-CoV-2 remain to be resolved. Using data of the Swiss HIV Cohort Study (SHCS) on 6,270 people with HIV (PWH) and serologic assessment for SARS-CoV-2 and circulating-human-coronavirus (HCoV) antibodies, we investigated the association of HIV-related and general parameters with SARS-CoV-2 infection. METHODS We analyzed SARS-CoV-2 PCR-tests, COVID-19 related hospitalizations, and deaths reported to the SHCS between January 1, 2020 and December 31, 2021. Antibodies to SARS-CoV-2 and HCoVs were determined in pre-pandemic (2019) and pandemic (2020) bio-banked plasma and compared to HIV-negative individuals. We applied logistic regression, conditional logistic regression, and Bayesian multivariate regression to identify determinants of SARS-CoV-2 infection and Ab responses to SARS-CoV-2 in PWH. RESULTS No HIV-1-related factors were associated with SARS-CoV-2 acquisition. High pre-pandemic HCoV antibodies were associated with a lower risk of subsequent SARS-CoV-2 infection and with higher SARS-CoV-2 antibody responses upon infection. We observed a robust protective effect of smoking on SARS-CoV-2-infection risk (aOR= 0.46 [0.38,0.56], p=2.6*10-14), which occurred even in previous smokers, and was highest for heavy smokers. CONCLUSIONS Our findings of two independent protective factors, smoking and HCoV antibodies, both affecting the respiratory environment, underscore the importance of the local immune milieu in regulating susceptibility to SARS-CoV-2

SCLEM on FM and EM stained tissue sections.

<p>(a) FM image of human skin tissue stained with DiIC18 fluorescence and uranyl acetate and osmium tetroxide for EM contrast. Scalebar 5 µm (b) BSE image of a selected region from (a), showing a cell nucleus not discernible in (a) (marked with a red arrow), and bundles of longitudinally and transversally cut collagen fibers. Scalebar is 5 µm (c, d) High-magnification images of the areas marked with (c) a red star, scalebar 1 µm, and (d) a yellow star, scalebar 2 µm.</p

Simultaneous Correlative Light and Electron Microscopy.

<p>(a) schematic lay-out for SCLEM, BSE: backscattered electrons, SE: secondary electrons, ETD: Everhard-Thornley detector, LED: light emitting diode, CCD: charge coupled device camera. (b) inside view of the integrated microscope for SCLEM showing optical objective lens in epi-configuration underneath sample holder and electron lens.</p