Fluorescence-based sensing of the bioenergetic and physicochemical status of the cell

Fluorescence-based sensors play a fundamental role in biological research. These sensors can be based on fluorescent proteins, fluorescent probes or they can be hybrid systems. The availability of a very large dataset of fluorescent molecules, both genetically encoded and synthetically produced, together with the structural insights on many sensing domains, allowed to rationally design a high variety of sensors, capable of monitoring both molecular and global changes in living cells or in in vitro systems. The advancements in the fluorescence-imaging field helped researchers to obtain a deeper understanding of how and where specific changes occur in a cell or in vitro by combining the readout of the fluorescent sensors with the spatial information provided by fluorescent microscopy techniques. In this review we give an overview of the state of the art in the field of fluorescent biosensors and fluorescence imaging techniques, and eventually guide the reader through the choice of the best combination of fluorescent tools and techniques to answer specific biological questions. We particularly focus on sensors for probing the bioenergetics and physicochemical status of the cell.

A sample-preparation-free, automated, sample-to-answer system for cell counting in human body fluids

While many clinical laboratory tests are now highly automated, body fluid cell counting, particularly in low-cellularity samples such as cerebral spinal fluid (CSF), is often performed manually. Here, we report a simple, cost-effective method to obtain white and red blood cell counts from human body fluids such as CSF. The method consists of a compact, automated, and low-cost fluorescence microscope system, coupled to a sample chamber containing all of the necessary reagents in dry form to stain and prepare the sample. Sample focus and scanning are handled automatically, and the acquired multimodal images are automatically analyzed to extract cell counts. Comparison with manual counting on over 200 clinical samples shows excellent agreement. As the system counts a substantially larger image region than a standard manual cell count, we find our sensitivity to extremely low cellularity samples to potentially be higher than the manual gold standard, evidenced by our system recording images of cells in samples whose cell count was registered as "0" by a trained user. Thus, our system holds promise for routine, automated, and sensitive analysis of body fluids whose cellularity extends across a wide dynamic range.

Migration arrest of chemoresistant leukemia cells mediated by MRTF-SRF pathway

Background

Dormant chemotherapy-resistant leukemia cells can survive for an extended period before relapse. Nevertheless, the mechanisms underlying the development of chemoresistance in vivo remain unclear.

Methods

Using intravital bone imaging, we characterized the behavior of murine acute myeloid leukemia (AML) cells (C1498) in the bone marrow before and after chemotherapy with cytarabine.

Results

Proliferative C1498 cells exhibited high motility in the bone marrow. Cytarabine treatment impaired the motility of residual C1498 cells. However, C1498 cells regained their migration potential after relapse. RNA sequencing revealed that cytarabine treatment promoted MRTF-SRF pathway activation. MRTF inhibition using CCG-203971 augmented the anti-tumor effects of chemotherapy in our AML mouse model, as well as suppressed the migration of chemoresistant C1498 cells.

Conclusions

These results provide novel insight into the role of cell migration arrest on the development of chemoresistance in AML, as well as provide a strong rationale for the modulation of cellular motility as a therapeutic target for refractory AML.

Assessing functional status of cardiac lymphatics: From macroscopic imaging to molecular profiling

Here we describe various techniques for visualization of the lymphatic vasculature, particularly in the heart. Addressing macro-, microscopic, and molecular levels of lymphatic organization, we give examples of how to explore the roles of specific antigens/markers expressed in lymphatic vessels and their extracellular matrix as structural and functional elements involved in various biological functions of lymphatics. Some obstacles and technical challenges related to lymphatic visualization are also discussed.

Evaluation of heavy metal-induced responses in Silene vulgaris ecotypes

Silene vulgaris is a pseudometallophyte that spontaneously occurs in various ecological niches. Therefore, three ecotypes of this species representing calamine (CAL), serpentine (SER), and non-metallicolous (NM) populations were investigated in this study. Owing to the presence of Pb or Ni ions in natural habitats from metallicolous populations originated, we used these metals as model stressors to determine the survival strategy of tested ecotypes and analyze metal distribution at various levels of organism organization. We focused on growth tolerance, non-enzymatic antioxidants, and photosynthetic apparatus efficiency as well as anatomical and ultrastructural changes occurred in contrasting ecotypes exposed in vitro to excess amounts of Pb2+ and Ni2+. Although Ni application contributed to shoot culture death, the study revealed that the mechanisms of Pb detoxification differed between ecotypes. The unspecific reaction of both metallicolous specimens relied on the formation of effective mechanical barrier against toxic ion penetration, while the Pb appearance in the protoplasts led to the activation of ecotype-specific intracellular defense mechanisms. Hence, the response of CAL and SER ecotypes was almost unchanged under Pb treatment, whereas the reaction of NM one resulted in growth disturbances and physiological alternations. Moreover, both metallicolous ecotypes exhibited increase generation of reactive oxygen species (ROS) in leaves, even before the harmful ions got into these parts of plants. It may implicate the potential role of ROS in CAL and SER adaptation to heavy metals and, for the first time, indicate on integral function of ROS as signaling molecules in metal-tolerant species.

Microscopic imaging quality improvement through L0 gradient constraint model based on multi-fields of view analysis

The degradation of optical microscopic imaging is space-variant, and how to fast restore optical degraded image remains a special problem. Based on point spread function (PSF) estimation under each field of view (FOV), a L0 gradient-constrained image restoration method is proposed to solve optical degradation in microscopic imaging. Firstly, the whole scene is segmented into several different regions according to different FOV. The PSFs for each region are estimated from modulation transfer function (MTF) measured in advance. Secondly, a penalty function is designed using L0 gradient constraint to deblur the degraded images of each sub-FOV. Finally, a weighted stitching approach is used to stitch the restored images of multiple FOV (m-FOV). Experimental results indicate that the m-FOV analysis could well solve the problem of space-variant degradation. Compared with the other methods, both subjective and objective evaluation results prove that the L0 norm idea could rapidly and effectively restore the degraded image. The approach could be well applied to a real product.

Spectral phasor analysis of LAURDAN fluorescence in live A549 lung cells to study the hydration and time evolution of intracellular lamellar body-like structures

Using LAURDAN spectral imaging and spectral phasor analysis we concurrently studied the growth and hydration state of subcellular organelles (lamellar body-like, LB-like) from live A549 lung cancer cells at different post-confluence days. Our results reveal a time dependent two-step process governing the size and hydration of these intracellular LB-like structures. Specifically, a first step (days 1 to 7) is characterized by an increase in their size, followed by a second one (days 7 to 14) where the organelles display a decrease in their global hydration properties. Interestingly, our results also show that their hydration properties significantly differ from those observed in well-characterized artificial lamellar model membranes, challenging the notion that a pure lamellar membrane organization is present in these organelles at intracellular conditions. Finally, these LB-like structures show a significant increase in their hydration state upon secretion, suggesting a relevant role of entropy during this process.

In Vivo study of naturally deformed Escherichia coli bacteria

A combination of light-microscopy and image processing has been applied to study naturally deformed Escherichia coli under in vivo condition and at the order of sub-pixel high-resolution accuracy. To classify deflagellated non-dividing E. coli cells to the rod-shape and bent-shape, a geometrical approach has been applied. From the analysis of the geometrical data which were obtained of image processing, we estimated the required effective energy for shaping a rod-shape to a bent-shape with the same size. We evaluated the energy of deformation in the naturally deformed bacteria with minimum cell manipulation, under in vivo condition, and with minimum influence of any external force, torque and pressure. Finally, we have also elaborated on the possible scenario to explain how naturally deformed bacteria are formed from initial to final-stage.

Rapid drug susceptibility test of Mycobacterium tuberculosis using microscopic time-lapse imaging in an agarose matrix

Tuberculosis (TB) is a major global health problem, and multi-drug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) are spreading throughout the world. However, conventional drug susceptibility test (DST) methods, which rely on the detection of the colony formation on a solid medium, require 1-2 months to the result. A rapid and accurate DST is necessary to identify patients with drug-resistant TB and treat them with appropriate drugs. Here, we used microscopic imaging of Mycobacterium tuberculosis (MTB) immobilized in an agarose matrix for a rapid DST. The agarose matrix, which was molded in a microfluidic chip, was inoculated with MTB, and TB drugs in liquid culture medium diffused throughout the agarose to reach the MTB immobilized in the agarose matrix. After the responses of MTB to drugs were tracked with an automated microscopic system, an image-processing program automatically determined the susceptibility and resistance of MTB to specific doses of TB drugs. The automatic DST system was able to assess the drug susceptibility of various drug-resistant clinical TB strains within 9 days with an accuracy comparable to that of conventional method. Our rapid DST method based on microscopic time-lapse imaging greatly reduces the time required for a DST and can be used to rapidly and accurately treat TB patients.

Non-rigid Registration for Large Sets of Microscopic Images on Graphics Processors

Microscopic imaging is an important tool for characterizing tissue morphology and pathology. 3D reconstruction and visualization of large sample tissue structure requires registration of large sets of high-resolution images. However, the scale of this problem presents a challenge for automatic registration methods. In this paper we present a novel method for efficient automatic registration using graphics processing units (GPUs) and parallel programming. Comparing a C++ CPU implementation with Compute Unified Device Architecture (CUDA) libraries and pthreads running on GPU we achieve a speed-up factor of up to 4.11× with a single GPU and 6.68× with a GPU pair. We present execution times for a benchmark composed of two sets of large-scale images: mouse placenta (16K × 16K pixels) and breast cancer tumors (23K × 62K pixels). It takes more than 12 hours for the genetic case in C++ to register a typical sample composed of 500 consecutive slides, which was reduced to less than 2 hours using two GPUs, in addition to a very promising scalability for extending those gains easily on a large number of GPUs in a distributed system.