Fluorescence Microscopy of the HIV-1 Envelope

Human immunodeficiency virus (HIV) infection constitutes a major health and social issue worldwide. HIV infects cells by fusing its envelope with the target cell plasma membrane. This process is mediated by the viral Env glycoprotein and depends on the envelope lipid composition. Fluorescent microscopy has been employed to investigate the envelope properties, and the processes of viral assembly and fusion, but the application of this technique to the study of HIV is still limited by a number of factors, such as the small size of HIV virions or the difficulty to label the envelope components. Here, we review fluorescence imaging studies of the envelope lipids and proteins, focusing on labelling strategies and model systems

Blob-B-Gone: a lightweight framework for removing blob artifacts from 2D/3D MINFLUX single-particle tracking data

In this study, we introduce Blob-B-Gone, a lightweight framework to computationally differentiate and eventually remove dense isotropic localization accumulations (blobs) caused by artifactually immobilized particles in MINFLUX single-particle tracking (SPT) measurements. This approach uses purely geometrical features extracted from MINFLUX-detected single-particle trajectories, which are treated as point clouds of localizations. Employing k-means++ clustering, we perform single-shot separation of the feature space to rapidly extract blobs from the dataset without the need for training. We automatically annotate the resulting sub-sets and, finally, evaluate our results by means of principal component analysis (PCA), highlighting a clear separation in the feature space. We demonstrate our approach using two- and three-dimensional simulations of freely diffusing particles and blob artifacts based on parameters extracted from hand-labeled MINFLUX tracking data of fixed 23-nm bead samples and two-dimensional diffusing quantum dots on model lipid membranes. Applying Blob-B-Gone, we achieve a clear distinction between blob-like and other trajectories, represented in F1 scores of 0.998 (2D) and 1.0 (3D) as well as 0.995 (balanced) and 0.994 (imbalanced). This framework can be straightforwardly applied to similar situations, where discerning between blob and elongated time traces is desirable. Given a number of localizations sufficient to express geometric features, the method can operate on any generic point clouds presented to it, regardless of its origin

Biosynthesis of mycobacterial arabinogalactan: identification of a novel (13)arabinofuranosyltransferase

The cell wall mycolyl-arabinogalactan-peptidoglycan complex is essential in mycobacterial species, such as Mycobacterium tuberculosis and is the target of several anti-tubercular drugs. For instance, ethambutol targets arabinogalactan biosynthesis through inhibition of the arabinofuranosyltransferases Mt-EmbA and Mt-EmbB. A bioinformatics approach identified putative integral membrane proteins, MSMEG2785 in Mycobacterium smegmatis, Rv2673 in Mycobacterium tuberculosis and NCgl1822 in Corynebacterium glutamicum, with 10 predicted transmembrane domains and a glycosyltransferase motif (DDX), features that are common to the GT-C superfamily of glycosyltransferases. Deletion of M. smegmatis MSMEG2785 resulted in altered growth and glycosyl linkage analysis revealed the absence of AG (13)-linked arabinofuranosyl (Araf) residues. Complementation of the M. smegmatis deletion mutant was fully restored to a wild type phenotype by MSMEG2785 and Rv2673, and as a result, we have now termed this previously uncharacterized open reading frame, arabinofuranosyltransferase C (aftC). Enzyme assays using the sugar donor -D-arabinofuranosyl-1-monophosphoryldecaprenol (DPA) and a newly synthesized linear (15)-linked Ara5 neoglycolipid acceptor together with chemical identification of products formed, clearly identified AftC as a branching (13) arabinofuranosyltransferase. This newly discovered glycosyltransferase sheds further light on the complexities of Mycobacterium cell wall biosynthesis, such as in M. tuberculosis and related species and represents a potential new drug target

Symmetric coupling of four spin-1/2 systems

We address the non-binary coupling of identical angular momenta based upon the representation theory for the symmetric group. A correspondence is pointed out between the complete set of commuting operators and the reference-frame-free subsystems. We provide a detailed analysis of the coupling of three and four spin-1/2 systems and discuss a symmetric coupling of four spin-1/2 systems.Comment: 20 pages, no figure

Infection with a Brazilian isolate of Zika virus generates RIG‐I stimulatory RNA and the viral NS5 protein blocks type I IFN induction and signalling

Zika virus (ZIKV) is a major public health concern in the Americas. We report that ZIKV infection and RNA extracted from ZIKV infected cells potently activated the induction of type I interferons (IFNs). This effect was fully dependent on the mitochondrial antiviral signalling protein (MAVS), implicating RIG‐I‐like receptors (RLRs) as upstream sensors of viral RNA. Indeed, RIG‐I and the related RNA sensor MDA5 contributed to type I IFN induction in response to RNA from infected cells. We found that ZIKV NS5 from a recent Brazilian isolate blocked type I IFN induction downstream of RLRs and also inhibited type I IFN receptor (IFNAR) signalling. We defined the ZIKV NS5 nuclear localization signal and report that NS5 nuclear localization was not required for inhibition of signalling downstream of IFNAR. Mechanistically, NS5 blocked IFNAR signalling by both leading to reduced levels of STAT2 and by blocking phosphorylation of STAT1, two transcription factors activated by type I IFNs. Taken together, our observations suggest that ZIKV infection induces a type I IFN response via RLRs and that ZIKV interferes with this response by blocking signalling downstream of RLRs and IFNAR

Управління трудовим потенціалом при створенні інноваційної продукції

Super-resolution microscopy (SRM) bypasses the diffraction limit, a physical barrier that restricts the optical resolution to roughly 250 nm and was previously thought to be impenetrable. SRM techniques allow the visualization of subcellular organization with unprecedented detail, but also confront biologists with the challenge of selecting the best-suited approach for their particular research question. Here, we provide guidance on how to use SRM techniques advantageously for investigating cellular structures and dynamics to promote new discoveries

Immune mobilising T cell receptors redirect polyclonal CD8+ T cells in chronic HIV infection to form immunological synapses

T cell exhaustion develops in human immunodeficiency virus (HIV) infection due to chronic viral antigenic stimulation. This adaptive response primarily affects virus-specific CD8+ T cells, which may remain dysfunctional despite viral load-reducing antiretroviral therapy; however, abnormalities may also be evident in non-HIV-specific populations. Both could limit the efficacy of cell therapies against viral reservoirs. Here, we show that bulk (polyclonal) CD8+ T cells from people living with HIV (PLWH) express proposed markers of dysfunctional HIV-specific T cells at high levels yet form lytic immunological synapses (IS) and eliminate primary resting infected (HIV Gaglo) CD4+ T cells, when redirected by potent bispecific T cell-retargeting molecules, Immune mobilising monoclonal T cell receptors (TCR) Against Virus (ImmTAV). While PLWH CD8+ T cells are functionally impaired when compared to CD8+ T cells from HIV-naïve donors, ImmTAV redirection enables them to eliminate Gaglo CD4+ T cells that are insensitive to autologous HIV-specific cytolytic T cells. ImmTAV molecules may therefore be able to target HIV reservoirs, which represent a major barrier to a cure

Transforming quantum operations: quantum supermaps

We introduce the concept of quantum supermap, describing the most general transformation that maps an input quantum operation into an output quantum operation. Since quantum operations include as special cases quantum states, effects, and measurements, quantum supermaps describe all possible transformations between elementary quantum objects (quantum systems as well as quantum devices). After giving the axiomatic definition of supermap, we prove a realization theorem, which shows that any supermap can be physically implemented as a simple quantum circuit. Applications to quantum programming, cloning, discrimination, estimation, information-disturbance trade-off, and tomography of channels are outlined.Comment: 6 pages, 1 figure, published versio

Better detection of Multipartite Bound Entanglement with Three-Setting Bell Inequalities

It was shown in Phys. Rev. Lett., 87, 230402 (2001) that N (N >= 4) qubits described by a certain one parameter family F of bound entangled states violate Mermin-Klyshko inequality for N >= 8. In this paper we prove that the states from the family F violate Bell inequalities derived in Phys. Rev. A, 56, R1682 (1997), in which each observer measures three non-commuting sets of orthogonal projectors, for N >=7. We also derive a simple one parameter family of entanglement witnesses that detect entanglement for all the states belonging to F. It is possible that these new entanglement witnesses could be generated by some Bell inequalities.Comment: Revtex4, 1 figur