Since late 2021, the variant landscape of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been dominated by the variant of concern (VoC) Omicron and its sublineages. We and ...others have shown that the detection of Omicron-BA.1 and -BA.2-positive respiratory specimens by rapid antigen tests (RATs) is impaired compared to Delta VoC-containing samples. Here, in a single-center retrospective laboratory study, we evaluated the performance of ten most commonly used RATs for the detection of Omicron-BA.4 and -BA.5 infections. We used 171 respiratory swab specimens from SARS-CoV-2 RNA-positive patients, of which 71 were classified as BA.4 and 100 as BA.5. All swabs were collected between July and September 2022. 50 SARS-CoV-2 PCR-negative samples from healthy individuals, collected in October 2022, showed high specificity in 9 out of 10 RATs. When assessing analytical sensitivity using clinical specimens, the 50% limit of detection (LoD50) ranged from 7.6 × 10
4
to 3.3 × 10
6
RNA copies subjected to the RATs for BA.4 compared to 6.8 × 10
4
to 3.0 × 10
6
for BA.5. Overall, intra-assay differences for the detection of these two Omicron subvariants were not significant for both respiratory swabs and tissue culture-expanded virus isolates. In contrast, marked heterogeneity was observed among the ten RATs: to be positive in these point-of-care tests, up to 443-fold (BA.4) and up to 56-fold (BA.5) higher viral loads were required for the worst performing RAT compared to the best performing RAT. True-positive rates for Omicron-BA.4- or -BA.5-containing specimens in the highest viral load category (
C
t
values < 25) ranged from 94.3 to 34.3%, dropping to 25.6 to 0% for samples with intermediate
C
t
values (25–30). We conclude that the high heterogeneity in the performance of commonly used RATs remains a challenge for the general public to obtain reliable results in the evolving Omicron subvariant-driven pandemic.
Human immunodeficiency virus type 1 (HIV-1) Nef enhances virus replication and contributes to immune evasion in vivo, but the underlying molecular mechanisms remain incompletely defined. Nef ...interferes with host cell actin dynamics to restrict T lymphocyte responses to chemokine stimulation and T cell receptor engagement. This relies on the assembly of a labile multiprotein complex including the host kinase PAK2 that Nef usurps to phosphorylate and inactivate the actin-severing factor cofilin. Components of the exocyst complex (EXOC), an octameric protein complex involved in vesicular transport and actin remodeling, were recently reported to interact with Nef via the same molecular surface that mediates PAK2 association. Exploring the functional relevance of EXOC in Nef-PAK2 complex assembly/function, we found Nef-EXOC interactions to be specifically mediated by the PAK2 interface of Nef, to occur in infected human T lymphocytes, and to be conserved among lentiviral Nef proteins. In turn, EXOC was dispensable for direct downstream effector functions of Nef-associated PAK2. Surprisingly, PAK2 was essential for Nef-EXOC association, which required a functional Rac1/Cdc42 binding site but not the catalytic activity of PAK2. EXOC was dispensable for Nef functions in vesicular transport but critical for inhibition of actin remodeling and proximal signaling upon T cell receptor engagement. Thus, Nef exploits PAK2 in a stepwise mechanism in which its kinase activity cooperates with an adaptor function for EXOC to inhibit host cell actin dynamics.
Human immunodeficiency virus type 1 (HIV-1) Nef contributes to AIDS pathogenesis, but the underlying molecular mechanisms remain incompletely understood. An important aspect of Nef function is to facilitate virus replication by disrupting T lymphocyte actin dynamics in response to stimulation via its association with the host cell kinase PAK2. We report here that the molecular surface of Nef for PAK2 association also mediates interaction of Nef with EXOC and establish that PAK2 provides an essential adaptor function for the subsequent formation of Nef-EXOC complexes. PAK2 and EXOC specifically cooperate in the inhibition of actin dynamics and proximal signaling induced by T cell receptor engagement by Nef. These results establish EXOC as a functionally relevant Nef interaction partner, emphasize the suitability of the PAK2 interaction surface for future therapeutic interference with Nef function, and show that such strategies need to target activity-independent PAK2 functions.
Wavepackets obtained as solutions of the flow equations linearised around the mean flow have been shown in recent work to yield good agreement, in terms of amplitude and phase, with those educed from ...turbulent jets. Compelling agreement has been demonstrated, for the axisymmetric and first helical mode, up to Strouhal numbers close to unity. We here extend the range of validity of wavepacket models to Strouhal number
$St=4.0$
and azimuthal wavenumber
$m=4$
by comparing solutions of the parabolised stability equations with a well-validated large-eddy simulation of a Mach 0.9 turbulent jet. The results show that the near-nozzle dynamics can be correctly described by the homogeneous linear model, the initial growth rates being accurately predicted for the entire range of frequencies and azimuthal wavenumbers considered. Similarly to the lower-frequency wavepackets reported prior to this work, the high-frequency linear waves deviate from the data downstream of their stabilisation locations, which move progressively upstream as the frequency increases.
Immature dendritic cells (iDCs) migrate in microenvironments with distinct cell and extracellular matrix densities in vivo and contribute to HIV‐1 dissemination and mounting of antiviral immune ...responses. Here, we find that, compared to standard 2D suspension cultures, 3D collagen as tissue‐like environment alters iDC properties and their response to HIV‐1 infection. iDCs adopt an elongated morphology with increased deformability in 3D collagen at unaltered activation, differentiation, cytokine secretion, or responsiveness to LPS. While 3D collagen reduces HIV‐1 particle uptake by iDCs, fusion efficiency is increased to elevate productive infection rates due to elevated cell surface exposure of the HIV‐1‐binding receptor DC‐SIGN. In contrast, 3D collagen reduces HIV transfer to CD4 T cells from iDCs. iDC adaptations to 3D collagen include increased pro‐inflammatory cytokine production and reduced antiviral gene expression in response to HIV‐1 infection. Adhesion to a 2D collagen matrix is sufficient to increase iDC deformability, DC‐SIGN exposure, and permissivity to HIV‐1 infection. Thus, mechano‐physical cues of 2D and 3D tissue‐like collagen environments regulate iDC function and shape divergent roles during HIV‐1 infection.
Synopsis
Immature dendritic cells contribute to HIV immune recognition and spread in tissue but are typically only studied in 2D suspension cultures. This study shows that 2D and 3D tissue environments markedly change the response of iDCs to HIV‐1 infection.
Ex vivo 2D suspension cultures do not recapitulate functional in vivo interactions of iDCs with HIV‐1.
3D collagen alters iDC morphology and increases productive HIV infection and pro‐inflammatory cytokine production.
iDC interactions with and transfer of HIV‐1 to CD4‐T cells is reduced in 3D collagen.
Polarized interactions with 2D collagen are sufficient to increase iDC permissivity to HIV‐1 infection.
Immature dendritic cells contribute to HIV immune recognition and spread in tissue but are typically only studied in 2D suspension cultures. This study shows that 2D and 3D tissue environments markedly change the response of iDCs to HIV‐1 infection.
p21 regulates the HIV-1 restriction factor SAMHD1 Pauls, Eduardo; Ruiz, Alba; Riveira-Muñoz, Eva ...
Proceedings of the National Academy of Sciences - PNAS,
04/2014, Letnik:
111, Številka:
14
Journal Article
The spread of SARS-CoV-2 has caused a worldwide pandemic that has affected almost every aspect of human life. The development of an effective COVID-19 vaccine could limit the morbidity and mortality ...caused by infection and may enable the relaxation of social-distancing measures. Age is one of the most significant risk factors for poor health outcomes after SARS-CoV-2 infection; therefore, it is desirable that any new vaccine candidates elicit a robust immune response in older adults.
Here, we use in-depth immunophenotyping to characterize the innate and adaptive immune response induced upon intramuscular administration of the adenoviral vectored ChAdOx1 nCoV-19 (AZD-1222) COVID-19 vaccine candidate in mice.
A single vaccination generates spike-specific Th1 cells, Th1-like Foxp3+ regulatory T cells, polyfunctional spike-specific CD8+ T cells. and granzyme-B-producing CD8 effectors. Spike-specific IgG and IgM are generated from both the early extrafollicular antibody response and the T follicular helper cell-supported germinal center reaction, which is associated with the production of virus-neutralizing antibodies. A single dose of this vaccine generated a similar type of immune response in aged mice but of a reduced magnitude than in younger mice. We report that a second dose enhances the immune response to this vaccine in aged mice.
This study shows that ChAdOx1 nCoV-19 induces both cellular and humoral immunity in adult and aged mice and suggests a prime-boost strategy is a rational approach to enhance immunogenicity in older persons.
This study was supported by BBSRC, Lister institute of Preventative Medicine, EPSRC VaxHub, and Innovate UK.
Display omitted
ChAdOx1 nCoV-19 induces spike-specific polyfunctional CD8+ and CD4+ T cellsChAdOx1 nCoV-19 stimulates extrafollicular plasma cell and germinal center formationA single dose of ChAdOx1 nCoV-19 induces cellular and humoral immunity in aged miceA booster dose of ChAdOx1 nCoV-19 enhances immunogenicity in aged mice
Effective COVID-19 vaccines will play a central role in the exit strategy from the worldwide pandemic. However, older persons often do not generate protective immunity upon vaccination due to age-dependent changes in their immune system. Because older people are more likely to have poor clinical outcomes after SARS-CoV-2 infection, vaccine strategies that elicit an optimal immune response in older bodies are urgently required. Researchers from the Babraham Institute , the Jenner Institute, and the Pirbright Institute in the UK performed pre-clinical testing of the COVID-19 vaccine candidate ChAdOx1 nCoV-19 in aged mice to assess how aging influences the immune response to this vaccine. The results show that a “prime-boost” vaccine regime enhances immunogenicity in aged mice, indicating that this approach is a rational strategy for vaccinating older persons.
Older persons are more likely to have poor health outcomes after SARS-CoV-2 infection; therefore, they are most in need of effective COVID-19 vaccines. Silva-Cayetano et al. show that a prime-boost strategy of the COVID-19 vaccine ChAdOx1 nCoV-19 enhances immunogenicity in aged mice, suggesting this as a strategy for immunizing older people.
Global machine learning force fields, with the capacity to capture collective interactions in molecular systems, now scale up to a few dozen atoms due to considerable growth of model complexity with ...system size. For larger molecules, locality assumptions are introduced, with the consequence that nonlocal interactions are not described. Here, we develop an exact iterative approach to train global symmetric gradient domain machine learning (sGDML) force fields (FFs) for several hundred atoms, without resorting to any potentially uncontrolled approximations. All atomic degrees of freedom remain correlated in the global sGDML FF, allowing the accurate description of complex molecules and materials that present phenomena with far-reaching characteristic correlation lengths. We assess the accuracy and efficiency of sGDML on a newly developed MD22 benchmark dataset containing molecules from 42 to 370 atoms. The robustness of our approach is demonstrated in nanosecond path-integral molecular dynamics simulations for supramolecular complexes in the MD22 dataset.
Post-learning stress has been reported to enhance memory consolidation in humans. This effect was observed in studies using physical stressors or an anticipatory speech task. In the present study 58 ...participants (28 females and 30 males) were exposed to a psychosocial stressor (Trier Social Stress Test) or a control condition following the presentation of neutral and emotionally arousing positive and negative pictures, which were accompanied by a brief narrative. The stressor induced a significant neuroendocrine stress response in men and women. In a 24
h delayed free recall test the stress group showed an enhanced memory for neutral but not for emotionally arousing positive and negative items. Additionally, a significant correlation between the cortisol stress response and memory for neutral items was evident. Thus, in contrast to previous studies, post-learning stress primarily enhanced consolidation of neutral material. Several theoretical and methodological explanations for the observed effects are discussed.
For
imaging, the short-wavelength infrared region (SWIR; 1000-2000 nm) provides several advantages over the visible and near-infrared regions: general lack of autofluorescence, low light absorption ...by blood and tissue, and reduced scattering. However, the lack of versatile and functional SWIR emitters has prevented the general adoption of SWIR imaging by the biomedical research community. Here, we introduce a class of high-quality SWIR-emissive indium-arsenide-based quantum dots (QDs) that are readily modifiable for various functional imaging applications, and that exhibit narrow and size-tunable emission and a dramatically higher emission quantum yield than previously described SWIR probes. To demonstrate the unprecedented combination of deep penetration, high spatial resolution, multicolor imaging and fast-acquisition-speed afforded by the SWIR QDs, we quantified, in mice, the metabolic turnover rates of lipoproteins in several organs simultaneously and in real time as well as heartbeat and breathing rates in awake and unrestrained animals, and generated detailed three-dimensional quantitative flow maps of the mouse brain vasculature.
PDF
