Deuterium isotope probing (DIP) on Listeria innocua: Optimisation of labelling and impact on viability state.

An innovative approach, Raman microspectroscopy coupled with deuterium isotope probing (Raman-DIP), can be used to evaluate the metabolism of deuterated carbon source in bacteria and also to presume different anabolic pathways. This method requires the treatment of cells with heavy water that could affect the bacterial viability state at higher concentration. In this study, we evaluated the effect of heavy water incorporation on the viability state of Listeria innocua cells. We exposed the L. innocua suspensions to different heavy water concentrations (0%, 25%, 50% and 75%) from 30 minutes to 72 h of incubation times at 37°C. The total, viable and viable culturable populations were quantified by qPCR, PMA-qPCR and plate count agar respectively. We analyzed heavy water incorporation by Raman-DIP. The exposure of L. innocua cells to different concentrations of heavy water did not alter their cell viability to 24 h incubation time. In addition, the maximum intensity for C-D band, specific for the incorporation of heavy water, was reached after 2 h of exposure in a media containing 75% v/v D2O but an early detection of the labelling was possible at t = 1 h 30 min. In conclusion, the use of D2O as a metabolic marker was validated and can be developed for the detection of L. innocua cell viability state.

3D time-lapse imaging of a mouse embryo using intensity diffraction tomography embedded inside a deep learning framework.

We present a compact 3D diffractive microscope that can be inserted directly in a cell incubator for long-term observation of developing organisms. Our setup is particularly simple and robust, since it does not include any moving parts and is compatible with commercial cell culture containers. It has been designed to image large specimens (>100×100×100µm3) with subcellular resolution. The sample's optical properties [refractive index (RI) and absorption] are reconstructed in 3D from intensity-only images recorded with different illumination angles produced by an LED array. The reconstruction is performed using the beam propagation method embedded inside a deep-learning network where the layers encode the optical properties of the object. This deep neural network is trained for a given multiangle intensity acquisition. After training, the weights of the neural network deliver the 3D distribution of the optical properties of the sample. The effect of spherical aberrations due to the sample holder/air interfaces are taken into account in the forward model. Using this approach, we performed time-lapse 3D imaging of preimplantation mouse embryos over six days. Images of embryos from a single cell (low-scattering regime) to the blastocyst stage (highly scattering regime) were successfully reconstructed. Due to its subcellular resolution, our system can provide quantitative information on the embryos' development and viability. Hence, this technology opens what we believe to be novel opportunities for 3D label-free live-cell imaging of whole embryos or organoids over long observation times.

Spatio-temporal based deep learning for rapid detection and identification of bacterial colonies through lens-free microscopy time-lapses.

Detection and identification of pathogenic bacteria isolated from biological samples (blood, urine, sputum, etc.) are crucial steps in accelerated clinical diagnosis. However, accurate and rapid identification remain difficult to achieve due to the challenge of having to analyse complex and large samples. Current solutions (mass spectrometry, automated biochemical testing, etc.) propose a trade-off between time and accuracy, achieving satisfactory results at the expense of time-consuming processes, which can also be intrusive, destructive and costly. Moreover, those techniques tend to require an overnight subculture on solid agar medium delaying bacteria identification by 12-48 hours, thus preventing rapid prescription of appropriate treatment as it hinders antibiotic susceptibility testing. In this study, lens-free imaging is presented as a possible solution to achieve a quick and accurate wide range, non-destructive, label-free pathogenic bacteria detection and identification in real-time using micro colonies (10-500 µm) kinetic growth pattern combined with a two-stage deep learning architecture. Bacterial colonies growth time-lapses were acquired thanks to a live-cell lens-free imaging system and a thin-layer agar media made of 20 µl BHI (Brain Heart Infusion) to train our deep learning networks. Our architecture proposal achieved interesting results on a dataset constituted of seven different pathogenic bacteria-Staphylococcus aureus (S. aureus), Enterococcus faecium (E. faecium), Enterococcus faecalis (E. faecalis), Staphylococcus epidermidis (S. epidermidis), Streptococcus pneumoniae R6 (S. pneumoniae), Streptococcus pyogenes (S. pyogenes), Lactococcus Lactis (L. Lactis). At T = 8h, our detection network reached an average 96.0% detection rate while our classification network precision and sensitivity averaged around 93.1% and 94.0% respectively, both were tested on 1908 colonies. Our classification network even obtained a perfect score for E. faecalis (60 colonies) and very high score for S. epidermidis at 99.7% (647 colonies). Our method achieved those results thanks to a novel technique coupling convolutional and recurrent neural networks together to extract spatio-temporal patterns from unreconstructed lens-free microscopy time-lapses.

Anticancer effects of the PLK4 inhibitors CFI-400945 and centrinone in Ewing's sarcoma cells.

PURPOSE: Polo-like kinase 4 (PLK4) inhibitors, such as CFI-400945 and centrinone, are emerging as promising antineoplastic agents. However, their effectiveness against Ewing's sarcoma, a highly aggressive childhood cancer, remains to be established. METHODS: CFI-400945 and centrinone were tested in three Ewing's sarcoma cell lines with different TP53 status. Effects were assessed by flow-cytometric analyses of cell death, dissipation of the mitochondrial transmembrane potential and cell cycle distribution, by cell viability assay as well as by caspase 3/7 activity measurement, by immunoblotting and by immunofluorescence microscopy. RESULTS: CFI-400945 and centrinone elicited cell death in p53 wild-type and mutant Ewing's sarcoma cells. Both agents induced mitochondrial membrane depolarisation, caspase 3/7 activation, PARP1 cleavage and DNA fragmentation, indicating an apoptotic form of cell death. In addition, the PLK4 inhibitors induced a G2/M cell cycle arrest, particularly when cell killing was attenuated by the pan-caspase inhibitor z-VAD-fmk. Moreover, CFI-400945 treatment produced polyploidy. CONCLUSION: Our findings show that PLK4 inhibitors were effective against Ewing's sarcoma cells in vitro and thus provide a rationale for their evaluation in vivo.

Phase and fluorescence imaging with a surprisingly simple microscope based on chromatic aberration.

We propose a simple and compact microscope combining phase imaging with multi-color fluorescence using a standard bright-field objective. The phase image of the sample is reconstructed from a single, approximately 100 µm out-of-focus image taken under semi-coherent illumination, while fluorescence is recorded in-focus in epi-fluorescence geometry. The reproducible changes of the focus are achieved with specifically introduced chromatic aberration in the imaging system. This allows us to move the focal plane simply by changing the imaging wavelength. No mechanical movement of neither sample nor objective or any other part of the setup is therefore required to alternate between the imaging modality. Due to its small size and the absence of motorized components the microscope can easily be used inside a standard biological incubator and allows long-term imaging of cell culture in physiological conditions. A field-of-view of 1.2 mm2 allows simultaneous observation of thousands of cells with micro-meter spatial resolution in phase and multi-channel fluorescence mode. In this manuscript we characterize the system and show a time-lapse of cell culture in phase and multi-channel fluorescence recorded inside an incubator. We believe that the small dimensions, easy usage and low cost of the system make it a useful tool for biological research.

Large field-of-view phase and fluorescence mesoscope with microscopic resolution.

Phase and fluorescence are complementary contrasts that are commonly used in biology. However, the coupling of these two modalities is traditionally limited to high magnification and complex imaging systems. For statistical studies of biological populations, a large field-of-view is required. We describe a 30 mm2 field-of-view dual-modality mesoscope with a 4-µm resolution. The potential of the system to address biological questions is illustrated on white blood cell numeration in whole blood and multiwavelength imaging of the human osteosarcoma (U2-OS) cells.

Magnetoencephalography With Optically Pumped 4He Magnetometers at Ambient Temperature.

In this paper, we present the first proof of concept confirming the possibility to record magnetoencephalographic (MEG) signals with optically pumped magnetometers (OPMs) based on the parametric resonance of 4He atoms. The main advantage of this kind of OPM is the possibility to provide a tri-axis vector measurement of the magnetic field at room-temperature (the 4He vapor is neither cooled nor heated). The sensor achieves a sensitivity of 210 fT/ √ Hz in the bandwidth [2-300 Hz]. MEG simulation studies with a brain phantom were cross-validated with real MEG measurements on a healthy subject. For both studies, MEG signal was recorded consecutively with OPMs and superconducting quantum interference devices (SQUIDs) used as reference sensors. For healthy subject MEG recordings, three MEG proofs of concept were carried out: auditory evoked fields, visual evoked fields, and spontaneous activity. M100 peaks have been detected on evoked responses recorded by both OPMs and SQUIDs with no significant difference in latency. Concerning spontaneous activity, an attenuation of the signal power between 8-12 Hz (alpha band) related to eyes opening has been observed with OPM similarly to SQUID. All these results confirm that the room temperature vector 4He OPMs can record MEG signals and provide reliable information on brain activity.

Lens-free microscopy for 3D + time acquisitions of 3D cell culture.

Thanks to a novel three-dimensional imaging platform based on lens-free microscopy, it is possible to perform multi-angle acquisitions and holographic reconstructions of 3D cell cultures directly into the incubator. Being able of reconstructing volumes as large as ~5 mm3 over a period of time covering several days, allows us to observe a broad range of migration strategies only present in 3D environment, whether it is single cell migration, collective migrations of cells and dispersal of cells. In addition we are able to distinguish new interesting phenomena, e.g. large-scale cell-to-matrix interactions (>1 mm), fusion of cell clusters into large aggregate (~10,000 µm2) and conversely, total dissociation of cell clusters into clumps of migrating cells. This work on a novel 3D + time lens-free microscopy technique thus expands the repertoire of phenomena that can be studied within 3D cell cultures.

Lens-free Video Microscopy for the Dynamic and Quantitative Analysis of Adherent Cell Culture.

Here, we demonstrate that lens-free video microscopy enables us to simultaneously capture the kinetics of thousands of cells directly inside the incubator and that it is possible to monitor and quantify single cells along several cell cycles. We describe the full protocol used to monitor and quantify a HeLa cell culture for 2.7 days. First, cell culture acquisition is performed with a lens-free video microscope, and then the data is analyzed following a four-step process: multi-wavelength holographic reconstruction, cell-tracking, cell segmentation and cell division detection algorithms. As a result, we show that it is possible to gather a dataset featuring more than 10,000 cell cycle tracks and more than 2 x 106 cell morphological measurements.