Direct presentation of inflammation-associated self-antigens by thymic innate-like T cells induces elimination of autoreactive CD8+ thymocytes.

Upregulation of diverse self-antigens that constitute components of the inflammatory response overlaps spatially and temporally with the emergence of pathogen-derived foreign antigens. Therefore, discrimination between these inflammation-associated self-antigens and pathogen-derived molecules represents a unique challenge for the adaptive immune system. Here, we demonstrate that CD8+ T cell tolerance to T cell-derived inflammation-associated self-antigens is efficiently induced in the thymus and supported by redundancy in cell types expressing these molecules. In addition to thymic epithelial cells, this included thymic eosinophils and innate-like T cells, a population that expressed molecules characteristic for all major activated T cell subsets. We show that direct T cell-to-T cell antigen presentation by minute numbers of innate-like T cells was sufficient to eliminate autoreactive CD8+ thymocytes. Tolerance to such effector molecules was of critical importance, as its breach caused by decreased thymic abundance of a single model inflammation-associated self-antigen resulted in autoimmune elimination of an entire class of effector T cells.

Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains.

Many biochemical reactions require controlled recruitment of proteins to membranes. This is largely regulated by posttranslational modifications. A frequent one is S-acylation, which consists of the addition of acyl chains and can be reversed by poorly understood acyl protein thioesterases (APTs). Using a panel of computational and experimental approaches, we dissect the mode of action of the major cellular thioesterase APT2 (LYPLA2). We show that soluble APT2 is vulnerable to proteasomal degradation, from which membrane binding protects it. Interaction with membranes requires three consecutive steps: electrostatic attraction, insertion of a hydrophobic loop and S-acylation by the palmitoyltransferases ZDHHC3 or ZDHHC7. Once bound, APT2 is predicted to deform the lipid bilayer to extract the acyl chain bound to its substrate and capture it in a hydrophobic pocket to allow hydrolysis. This molecular understanding of APT2 paves the way to understand the dynamics of APT2-mediated deacylation of substrates throughout the endomembrane system.

Fast autofocusing using tiny transformer networks for digital holographic microscopy.

The numerical wavefront backpropagation principle of digital holography confers unique extended focus capabilities, without mechanical displacements along z-axis. However, the determination of the correct focusing distance is a non-trivial and time consuming issue. A deep learning (DL) solution is proposed to cast the autofocusing as a regression problem and tested over both experimental and simulated holograms. Single wavelength digital holograms were recorded by a Digital Holographic Microscope (DHM) with a 10x microscope objective from a patterned target moving in 3D over an axial range of 92 µm. Tiny DL models are proposed and compared such as a tiny Vision Transformer (TViT), tiny VGG16 (TVGG) and a tiny Swin-Transfomer (TSwinT). The proposed tiny networks are compared with their original versions (ViT/B16, VGG16 and Swin-Transformer Tiny) and the main neural networks used in digital holography such as LeNet and AlexNet. The experiments show that the predicted focusing distance ZRPred is accurately inferred with an accuracy of 1.2 µm in average in comparison with the DHM depth of field of 15 µm. Numerical simulations show that all tiny models give the ZRPred with an error below 0.3 µm. Such a prospect would significantly improve the current capabilities of computer vision position sensing in applications such as 3D microscopy for life sciences or micro-robotics. Moreover, all models reach an inference time on CPU, inferior to 25 ms per inference. In terms of occlusions, TViT based on its Transformer architecture is the most robust.

Image-based analysis of living mammalian cells using label-free 3D refractive index maps reveals new organelle dynamics and dry mass flux.

Holo-tomographic microscopy (HTM) is a label-free microscopy method reporting the fine changes of a cell's refractive indices (RIs) in three dimensions at high spatial and temporal resolution. By combining HTM with epifluorescence, we demonstrate that mammalian cellular organelles such as lipid droplets (LDs) and mitochondria show specific RI 3D patterns. To go further, we developed a computer-vision strategy using FIJI, CellProfiler3 (CP3), and custom code that allows us to use the fine images obtained by HTM in quantitative approaches. We could observe the shape and dry mass dynamics of LDs, endocytic structures, and entire cells' division that have so far, to the best of our knowledge, been out of reach. We finally took advantage of the capacity of HTM to capture the motion of many organelles at the same time to report a multiorganelle spinning phenomenon and study its dynamic properties using pattern matching and homography analysis. This work demonstrates that HTM gives access to an uncharted field of biological dynamics and describes a unique set of simple computer-vision strategies that can be broadly used to quantify HTM images.

A Fluorescent Kinase Inhibitor that Exhibits Diagnostic Changes in Emission upon Binding.

The development of a fluorescent LCK inhibitor that exhibits favourable solvatochromic properties upon binding the kinase is described. Fluorescent properties were realised through the inclusion of a prodan-derived fluorophore into the pharmacophore of an ATP-competitive kinase inhibitor. Fluorescence titration experiments demonstrate the solvatochromic properties of the inhibitor, in which dramatic increase in emission intensity and hypsochromic shift in emission maxima are clearly observed upon binding LCK. Microscopy experiments in cellular contexts together with flow cytometry show that the fluorescence intensity of the inhibitor correlates with the LCK concentration. Furthermore, multiphoton microscopy experiments demonstrate both the rapid cellular uptake of the inhibitor and that the two-photon cross section of the inhibitor is amenable for excitation at 700 nm.

Digital Holography as Computer Vision Position Sensor with an Extended Range of Working Distances.

Standard computer vision methods are usually based on powerful contact-less measurement approaches but applications, especially at the micro-scale, are restricted by finite depth-of-field and fixed working distance of imaging devices. Digital holography is a lensless, indirect imaging method recording the optical wave diffracted by the object onto the image sensor. The object is reconstructed numerically by propagating the recorded wavefront backward. The object distance becomes a computation parameter that can be chosen arbitrarily and adjusted to match the object position. No refractive lens is used and usual depth-of-field and working distance limitations are replaced by less restrictive ones tied to the laser-source coherence-length and to the size and resolution of the camera sensor. This paper applies digital holography to artificial visual in-plane position sensing with an extra-large range-to-resolution ratio. The object is made of a pseudoperiodic pattern allowing a subpixel resolution as well as a supra field-of-observation displacement range. We demonstrate an in-plane resolution of 50 nm and 0.002deg. in X, Y and θ respectively, over a working distance range of more than 15 cm. The allowed workspace extends over 12×10×150mm3. Digital holography extends the field of application of computer vision by allowing an extra-large range of working distances inaccessible to refractive imaging systems.

Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin.

Cellular functions are largely regulated by reversible post-translational modifications of proteins which act as switches. Amongst these, S-palmitoylation is unique in that it confers hydrophobicity. Due to technical difficulties, the understanding of this modification has lagged behind. To investigate principles underlying dynamics and regulation of palmitoylation, we have here studied a key cellular protein, the ER chaperone calnexin, which requires dual palmitoylation for function. Apprehending the complex inter-conversion between single-, double- and non-palmitoylated species required combining experimental determination of kinetic parameters with extensive mathematical modelling. We found that calnexin, due to the presence of two cooperative sites, becomes stably acylated, which not only confers function but also a remarkable increase in stability. Unexpectedly, stochastic simulations revealed that palmitoylation does not occur soon after synthesis, but many hours later. This prediction guided us to find that phosphorylation actively delays calnexin palmitoylation in resting cells. Altogether this study reveals that cells synthesize 5 times more calnexin than needed under resting condition, most of which is degraded. This unused pool can be mobilized by preventing phosphorylation or increasing the activity of the palmitoyltransferase DHHC6.

Efferocytosis of apoptotic human papillomavirus-positive cervical cancer cells by human primary fibroblasts.

BACKGROUND INFORMATION: Efficient clearance of apoptotic cells, named efferocytosis, is a fundamental physiological process for tissue development and homeostasis. The contribution of non-professional phagocytes like fibroblasts to efferocytosis has been established, although the underlying mechanisms are not well understood. We recently demonstrated that horizontal DNA transfer can occur through the uptake of apoptotic human papillomavirus-positive cancer cells by human primary fibroblasts leading to their transformation. The aim of this present study was to analyse the cellular and molecular mechanisms that drive the phagocytic activity of human primary fibroblasts in the context of apoptotic cervical cancer cell removal. RESULTS: Here we provide evidence that human primary fibroblasts engulf late more efficiently than early apoptotic cells, but their phagocytic ability remains limited compared to professional phagocytes such as human monocyte-derived macrophages. The engulfment occurs in a time-, temperature- and calcium-dependent manner. Remodelling of actin-fibers contributes to the biogenesis of apoptotic cell containing macroendocytic vacuoles. Both morphological analyses and pharmacological approaches confirmed the involvement of actin-driven phagocytosis and likely macropinocytotic mechanisms in apoptotic target internalization. The uptake of apoptotic cells requires phosphatidylserine recognition, which is mainly mediated by phosphatidylserine-receptor brain-specific angiogenesis inhibitor 1. Confocal microscopy analyses with organelle-specific markers revealed that internalised apoptotic material traffics into late phagolysosomes and specific features of microtubule-associated protein 1 light chain 3-associated phagocytosis were observed. CONCLUSIONS: Our in vitro data show that fibroblasts contribute to apoptotic tumour cell removal by phagocytosis and likely macropinocytotic mechanisms. Efferocytosis by fibroblasts involves phosphatidylserine receptor brain-specific angiogenesis inhibitor 1, which participates in subsequent uptake orchestration via actin cytoskeleton remodelling. SIGNIFICANCE: Our results highlight the cellular and molecular mechanisms of fibroblast-mediated clearance of apoptotic tumour cells. Consequences regarding alternative mechanism of carcinogenesis or tumour progression should be addressed.

Performance Characterization of an xy-Stage Applied to Micrometric Laser Direct Writing Lithography.

This article concerns the characterization of the stability and performance of a motorized stage used in laser direct writing lithography. The system was built from commercial components and commanded by G-code. Measurements use a pseudo-periodic-pattern (PPP) observed by a camera and image processing is based on Fourier transform and phase measurement methods. The results report that the built system has a stability against vibrations determined by peak-valley deviations of 65 nm and 26 nm in the x and y directions, respectively, with a standard deviation of 10 nm in both directions. When the xy-stage is in movement, it works with a resolution of 0.36 µm, which is an acceptable value for most of research and development (R and D) microtechnology developments in which the typical feature size used is in the micrometer range.

How many lives does CLIMP-63 have?

In 1995, in the Biochemical Society Transactions, Mundy published the first review on CLIMP-63 (cytoskeleton-linking membrane protein 63) or CKPA4 (cytoskeleton-associated protein 4), initially just p63 [1]. Here we review the following 20 years of research on this still mysterious protein. CLIMP-63 is a type II transmembrane protein, the cytosolic domain of which has the capacity to bind microtubules whereas the luminal domain can form homo-oligomeric complexes, not only with neighbouring molecules but also, in trans, with CLIMP-63 molecules on the other side of the endoplasmic reticulum (ER) lumen, thus promoting the formation of ER sheets. CLIMP-63 however also appears to have a life at the cell surface where it acts as a ligand-activated receptor. The still rudimentary information of how CLIMP-63 fulfills these different roles, what these are exactly and how post-translational modifications control them, will be discussed.

Sugar additives improve signal fidelity for implementing two-phase resorufin-based enzyme immunoassays.

Enzymatic signal amplification based on fluorogenic substrates is commonly used for immunoassays; however, when transitioning these assays to a digital format in water-in-mineral oil emulsions, such amplification methods have been limited by the leakage of small reporting fluorescent probes. In the present study, we used a microfluidic system to study leakage from aqueous droplets in a controlled manner and confirmed that the leakage of fluorescent resorufin derivatives is mostly due to the presence of the lipophilic surfactant Span80, which is commonly used to preserve emulsion stability. This leakage can be overcome by the addition of specific sugars that most strongly interfered with the surfactants ability to form micelles in water. The application of the microfluidic system to the quantitative analysis of droplets and the implementation of the described sugar additives would allow for alternatives to fluorinated surfactant-based platforms and improve the signal fidelity in enzyme immunoassays implemented through multiphase microfluidics.

Subpixelic measurement of large 1D displacements: principle, processing algorithms, performances and software.

This paper presents a visual measurement method able to sense 1D rigid body displacements with very high resolutions, large ranges and high processing rates. Sub-pixelic resolution is obtained thanks to a structured pattern placed on the target. The pattern is made of twin periodic grids with slightly different periods. The periodic frames are suited for Fourier-like phase calculations-leading to high resolution-while the period difference allows the removal of phase ambiguity and thus a high range-to-resolution ratio. The paper presents the measurement principle as well as the processing algorithms (source files are provided as supplementary materials). The theoretical and experimental performances are also discussed. The processing time is around 3 µs for a line of 780 pixels, which means that the measurement rate is mostly limited by the image acquisition frame rate. A 3-σ repeatability of 5 nm is experimentally demonstrated which has to be compared with the 168 µm measurement range.

Dynamics of CLIMP-63 S-acylation control ER morphology.

The complex architecture of the endoplasmic reticulum (ER) comprises distinct dynamic features, many at the nanoscale, that enable the coexistence of the nuclear envelope, regions of dense sheets and a branched tubular network that spans the cytoplasm. A key player in the formation of ER sheets is cytoskeleton-linking membrane protein 63 (CLIMP-63). The mechanisms by which CLIMP-63 coordinates ER structure remain elusive. Here, we address the impact of S-acylation, a reversible post-translational lipid modification, on CLIMP-63 cellular distribution and function. Combining native mass-spectrometry, with kinetic analysis of acylation and deacylation, and data-driven mathematical modelling, we obtain in-depth understanding of the CLIMP-63 life cycle. In the ER, it assembles into trimeric units. These occasionally exit the ER to reach the plasma membrane. However, the majority undergoes S-acylation by ZDHHC6 in the ER where they further assemble into highly stable super-complexes. Using super-resolution microscopy and focused ion beam electron microscopy, we show that CLIMP-63 acylation-deacylation controls the abundance and fenestration of ER sheets. Overall, this study uncovers a dynamic lipid post-translational regulation of ER architecture.

Modulation of lytic molecules restrain serial killing in γδ T lymphocytes.

γδ T cells play a pivotal role in protection against various types of infections and tumours, from early childhood on and throughout life. They consist of several subsets characterised by adaptive and innate-like functions, with Vγ9Vδ2 being the largest subset in human peripheral blood. Although these cells show signs of cytotoxicity, their modus operandi remains poorly understood. Here we explore, using live single-cell imaging, the cytotoxic functions of γδ T cells upon interactions with tumour target cells with high temporal and spatial resolution. While γδ T cell killing is dominated by degranulation, the availability of lytic molecules appears tightly regulated in time and space. In particular, the limited co-occurrence of granzyme B and perforin restrains serial killing of tumour cells by γδ T cells. Thus, our data provide new insights into the cytotoxic arsenal and functions of γδ T cells, which may guide the development of more efficient γδ T cell based adoptive immunotherapies.

Toward stereovisual monitoring of three-dimensional translations with submicrometer resolution.

We reported on stereovisual localization of a labeled target versus three-dimensional (3D) position and orientation with a resolution of a few micrometers [Opt. Express 18, 24152 (2010)]. A pseudo-periodic pattern (PPP) is fixed on the target, whose center is identified with subpixel accuracy in both stereo images. This subpixel position definition is fed into the geometrical model of the stereovision system and, thus, leads to subvoxel resolution in the 3D target positioning. This paper reports on improvements and specialization of the method for addressing the measurement of 3D translations: (a) The use of an encrypted PPP wider than the field of observation of the cameras has two beneficial effects. First, the allowed lateral target displacements are wider than the field of view of each camera, thus extending the workspace volume. Second, the 3D position is always derived from the same zone located at the center of the camera sensor chip. A simplified geometrical model is thus sufficient, and the effects of the lens distortions lead to a different kind of calibration issues. (b) By considering only translations, the pattern directions remain stationary in the recorded images. Two-dimensional Fourier transforms are then replaced by single dimension ones, thus reducing the computation time. (c) The choice of a higher magnification lens allows the achievement of submicrometer resolution in target position determination. This level of performance makes the method attractive in various automated applications requiring microstage position control and sensing. This approach may, for instance, fulfill the requirements for the coarse positioning of specimens in front of nanotechnology instruments that are equipped with their own high-accuracy but short-excursion-range translation stages.

Live single cell imaging assays in glass microwells produced by laser-induced deep etching.

Miniaturization of cell culture substrates enables controlled analysis of living cells in confined micro-scale environments. This is particularly suitable for imaging individual cells over time, as they can be monitored without escaping the imaging field-of-view (FoV). Glass materials are ideal for most microscopy applications. However, with current methods used in life sciences, glass microfabrication is limited in terms of either freedom of design, quality, or throughput. In this work, we introduce laser-induced deep etching (LIDE) as a method for producing glass microwell arrays for live single cell imaging assays. We demonstrate novel microwell arrays with deep, high-aspect ratio wells that have rounded, dimpled or flat bottom profiles in either single-layer or double-layer glass chips. The microwells are evaluated for microscopy-based analysis of long-term cell culture, clonal expansion, laterally organized cell seeding, subcellular mechanics during migration and immune cell cytotoxicity assays of both adherent and suspension cells. It is shown that all types of microwells can support viable cell cultures and imaging with single cell resolution, and we highlight specific benefits of each microwell design for different applications. We believe that high-quality glass microwell arrays enabled by LIDE provide a great option for high-content and high-resolution imaging-based live cell assays with a broad range of potential applications within life sciences.

Miniaturized and multiplexed high-content screening of drug and immune sensitivity in a multichambered microwell chip.

Here, we present a methodology based on multiplexed fluorescence screening of two- or three-dimensional cell cultures in a newly designed multichambered microwell chip, allowing direct assessment of drug or immune cell cytotoxic efficacy. We establish a framework for cell culture, formation of tumor spheroids, fluorescence labeling, and imaging of fixed or live cells at various magnifications directly in the chip together with data analysis and interpretation. The methodology is demonstrated by drug cytotoxicity screening using ovarian and non-small cell lung cancer cells and by cellular cytotoxicity screening targeting tumor spheroids of renal carcinoma and ovarian carcinoma with natural killer cells from healthy donors. The miniaturized format allowing long-term cell culture, efficient screening, and high-quality imaging of small sample volumes makes this methodology promising for individualized cytotoxicity tests for precision medicine.

Lensless vision system for in-plane positioning of a patterned plate with subpixel resolution.

Whereas vision is an efficient way for noncontact sensing of many physical quantities, it assumes a cumbersome imaging system that may be very problematic in confined environments. In such contexts, the design of a compact vision probe can be based on digital holography that is a lensless imaging principle. In this interferometric method, object scenes are reconstructed numerically through wave propagation computations applied to a diffracted optical field recorded as an interferogram. We applied this approach to the visual positioning of a micropatterned glass plate. The pseudoperiodic pattern deposited on the surface is suited for absolute in-plane position determination as well as for fine object-feature interpolation leading to subpixel resolution. Results obtained demonstrate a lateral resolution of 0.1 µm, corresponding to 1/20th of a pixel, from a 150 µm period of the pseudoperiodic pattern and with a demonstrated excursion range of 1.6 cm. In the future, such position encoding could be applied to the backside of standardized sample holders for the easy localization of regions of interest when specimens are transferred from an instrument to another one, for instance in nanotechnology processes.

3D localization of a labeled target by means of a stereo vision configuration with subvoxel resolution.

We present a method for the visual measurement of the 3D position and orientation of a moving target. Three dimensional sensing is based on stereo vision while high resolution results from a pseudo-periodic pattern (PPP) fixed onto the target. The PPP is suited for optimizing image processing that is based on phase computations. We describe experimental setup, image processing and system calibration. Resolutions reported are in the micrometer range for target position (x,y,z) and of 5:3x10(-4) rad: for target orientation (θx,θy,θz). These performances have to be appreciated with respect to the vision system used. The latter makes that every image pixel corresponds to an actual distance of 0:3x0:3 mm2 on the target while the PPP is made of elementary dots of 1 mm with a period of 2 mm. Target tilts as large as π=4 are allowed with respect to the Z axis of the system.

Recognition of synthetic polyanionic ligands underlies "spontaneous" reactivity of Vγ1 γδTCRs.

Although γδTCRs were discovered more than 30 yr ago, principles of antigen recognition by these receptors remain unclear and the nature of these antigens is largely elusive. Numerous studies reported that T cell hybridomas expressing several Vγ1-containing TCRs, including the Vγ1Vδ6 TCR of γδNKT cells, spontaneously secrete cytokines. This property was interpreted as recognition of a self-ligand expressed on the hybridoma cells themselves. Here, we revisited this finding using a recently developed reporter system and live single cell imaging. We confirmed strong spontaneous signaling by Vγ1Vδ6 and related TCRs, but not by TCRs from several other γδ or innate-like αß T cells, and demonstrated that both γ and δ chains contributed to this reactivity. Unexpectedly, live single cell imaging showed that activation of this signaling did not require any interaction between cells. Further investigation revealed that the signaling is instead activated by interaction with negatively charged surfaces abundantly present under regular cell culture conditions and was abrogated when noncharged cell culture vessels were used. This mode of TCR signaling activation was not restricted to the reporter cell lines, as interaction with negatively charged surfaces also triggered TCR signaling in ex vivo Vγ1 γδ T cells. Taken together, these results explain long-standing observations on the spontaneous reactivity of Vγ1Vδ6 TCR and demonstrate an unexpected antigen presentation-independent mode of TCR activation by a spectrum of chemically unrelated polyanionic ligands.